ticket summary _milestone component type severity priority owner status created changetime _description _reporter 1 migrate old svn Migrate SVN Management and planning defect normal normal ole closed 2005-08-02T19:48:34+10:00 2005-10-19T18:50:55+10:00 Ole to work with Kat (ANU MSI IT) and work out methodology for migration. ole 2 Finish ferret2sww (converting MOST output to SWW format) AnuGA ready for release Functionality and features defect normal low duncan closed 2005-08-31T20:40:01+10:00 2012-02-13T13:49:01+11:00 "The bulk is written. All that remains is to check changeset:1113 where prow added bathymetric info and make sure that the code is tested. https://datamining.anu.edu.au/anuga/changeset/1113 changeset:1113" ole 3 Conversion from sww to ERMapper FESA - Karratha Scenario Functionality and features defect normal normal tdhu closed 2005-08-31T20:49:54+10:00 2005-10-19T18:49:42+10:00 "Convert selected timesteps from sww to gridded ERMapper format * 1: SWW Reader (Ole) * 2: Map from irregular mesh to grid (see sww2asc and refactor out) * 3: Store selected timesteps to ERMap (tdhu)" ole 4 improve efficency of least_squares algorithm for speed increase least_squares module finished Efficiency and optimisation enhancement normal normal duncan closed 2005-08-31T21:00:01+10:00 2006-05-05T13:36:49+10:00 "Arrange quad tree algorithm so that all datapoints contribute to interpolation matrix A, without having to set the expand search flag to true. Currently this is fixed by expand search but that can be very slow. Need e.g. algorithm for searching neighbouring treenodes. " ole 5 test Migrate SVN Other defect normal normal ole closed 2005-08-31T21:02:23+10:00 2005-10-19T19:02:09+10:00 test ole 6 test 2 Migrate SVN Other defect normal normal ole closed 2005-08-31T21:05:33+10:00 2005-10-19T19:01:41+10:00 kk ole 7 get 100m bathymetric data FESA - Karratha Scenario Other defect normal normal ole closed 2005-08-31T21:17:11+10:00 2005-10-19T18:50:09+10:00 ole 8 Least squares memory issue (A vs AtA) least_squares module finished Efficiency and optimisation enhancement normal high duncan closed 2005-09-13T07:18:16+10:00 2006-05-26T14:12:49+10:00 "memory issue: ! If LS is used for fitting compute self.Atz and self AtA directly and avoid self.A. need alpha If LS is to be used for interpolation compute self.A no alpha needed Rethink design and API so that this is addressed without duplicating code. " ole 9 Feedback on errors least_squares module finished Functionality and features enhancement normal low duncan closed 2005-09-13T07:19:17+10:00 2006-05-30T15:10:42+10:00 "I've shortened the points that this ticket raises to: Give feedback when; points outside mesh. (Done) mesh outside points boundary. I'm assuming this is when using least_squares fit_to_mesh and least_squares interpolate (or any wrapper of these functions). other points are now in tickets 23 and 24. " ole 10 Use CSR format consistently least_squares module finished Architecture and API defect normal normal duncan closed 2005-09-13T07:20:33+10:00 2005-10-19T18:52:56+10:00 "use sparse matrix (CSR) format in ""build_interpolation_matrix_A""" ole 11 Geo referencing least_squares module finished Functionality and features enhancement normal normal duncan closed 2005-09-13T07:21:49+10:00 2005-10-19T18:51:52+10:00 "simplify geo-referencing (make sure that coordinate changes 'change_points' are used everywhere in the code) This affects other modules than least squares as well" ole 12 set_quantity API ANUGA maintenance Architecture and API defect normal normal ole closed 2005-09-13T07:28:21+10:00 2006-02-02T18:47:07+11:00 "Suggestion for set_quantity set_quantity(name, X, location, region) where name: Name of quantity X: -Compatible list, -compatible list or numeric array, -constant -list of points or array with attribute values (use LS) (How to distinguish this from a numeric array? - perhaps use keyword arguments for everything) -callable object (f: x, y -> z) where x,y,z are arrays - inline - file functions - polygon functions -another quantity Q or an expression of the form a*Q+b*R+c, where a,b,c are scalars, arrays or quantities Q,R are quantities (or 1?) - pts filename (use LS and caching) (how to select attribute?) - general expression to be parsed location: Where values are to be stored. Permissible options are: vertices, edges, centroid, unique_vertices region: Identify subset of triangles. Permissible values are - tag name (refers to tagged region) - indices (refers to specific triangles) - polygon (identifies region) (incorporate uniqueness/non-uniqueness) IDEA for set_quantity: Use keywords and call underlying specific method, e.g. if filename is not None: vertex_values = caching( fitfunc, filename, dependencies = ...) set_quantity(..., ..., vertex_values) elif: Largely done. Should create class Point_set representing points and attribute(s) Include filename too? Yep (and selected attributes) This could also facilitate use of multiple point sources (e.g. at different resolutions) " ole 13 Cancel button on alpha shape window doesn't work Mesh generation maintenance Architecture and API defect normal low duncan closed 2005-09-20T09:57:55+10:00 2012-02-13T13:48:17+11:00 Cancel button on alpha shape window doesn't work. If you cancel an alpha shape is still generated. duncan 14 Bypass arguments for caching AnuGA ready for release Functionality and features defect minor low ole closed 2005-09-20T17:35:55+10:00 2012-02-13T13:54:36+11:00 Caching needs optional arguments: bypass_args and bypass_kwargs. These should be passed onto the function when it is evaluated but not participate in the hashing. Rationale: Some arguments such as classes change their signature at every run and thus cause the functin to be evaluated every time, defeating the purpose of caching. ole 15 Search for appropriate procedure for OSS release AnuGA ready for release Management and planning defect normal normal ole closed 2005-09-20T17:51:19+10:00 2006-08-14T11:58:51+10:00 "Ole is onto that with AGIMO The PUG gruop to define a QA procedure to be required for an OSS release" ole 17 refactor interpolate_sww in terms of Interpolation_function least_squares module finished Architecture and API enhancement normal lowest duncan closed 2005-09-20T18:05:23+10:00 2007-02-27T14:37:46+11:00 "The Interpolation function is a general way of mapping from values on a mesh to arbitrary data points and arbitrary times. interpolate_sww.py could be refactored using this function." ole 18 checkpointing AnuGA ready for release Efficiency and optimisation enhancement normal normal nariman closed 2005-09-20T18:06:25+10:00 2010-06-16T13:52:32+10:00 Checkpointing (largely done in inundation/pyvolution/data_manager.py but needs to be revisited and properly tested) ole 19 Incorporate code like 'create_mesh' into pmesh Mesh generation finished Architecture and API enhancement normal low duncan closed 2005-09-23T13:37:36+10:00 2006-02-02T16:00:56+11:00 "We have a prototype a code called create_mesh_from_regions which creates a mesh from polygons. It simplifies the scripted mesh generation greatly and could be evolved to be part of pmesh. It is used by the Karratha study. See https://datamining.anu.edu.au/anuga/browser/inundation/pmesh/create_mesh.py and https://datamining.anu.edu.au/anuga/browser/production/karratha_2005 Please have a think about what could be done along those lines" ole 20 C extensions not used if called as a package AnuGA ready for release Architecture and API defect normal normal ole closed 2005-09-28T13:34:08+10:00 2005-09-29T12:38:24+10:00 "In particular util_ext.c was not used when used within the karratha study. Why not? The reason was that pmesh was trying to get to util_ext directly rather than just importing util.py. This has been addressed in changeset:1856" ole 21 Introduce Point_set class AnuGA ready for release Functionality and features enhancement normal normal ole closed 2005-09-29T14:50:16+10:00 2006-03-09T10:06:57+11:00 "It may be desirable to have a class Point_set which contains collections of points with possible attribute values. This would be very useful for set_quantity but also for allowing points to have methods for georeferencing and mappings between latitude/longitudes and UTM as in create_mesh.py in the Karratha study. Point_set would point to geo_ref object and know whether values are relative to that or absolute. Points can also be geographic (lat/lon) " ole 22 test_fit_to_mesh_errorsIII least_squares module finished Functionality and features defect minor normal duncan closed 2005-10-06T14:44:26+10:00 2005-10-19T18:52:34+10:00 "I noticed that this test failed on some windows machines. Then I changed the sys.exit() actions to raise IOError. This seams to be cleaner \ and provides more info than sys.exit() However. the test nom fails on the Linux platforms probably due to the underlying function not detecting the 'bad fliename' properly. " ole 23 bad mesh generated. Mesh generation maintenance Functionality and features defect normal normal duncan closed 2005-10-11T15:05:40+10:00 2006-05-30T14:26:57+10:00 "This is from ticket #9, which was overloaded. here's an error from least-squares.py {{{ v 6 self.mesh.vertexlist[v] None Traceback (most recent call last): File ""I:\inundation\debug\mesh_error_reporting\show_mesh_bug.py"", li ne 123, in ? verbose=True) File ""I:\inundation\pyvolution\least_squares.py"", line 211, in fit_t o_mesh precrop = precrop) File ""I:\inundation\pyvolution\least_squares.py"", line 360, in __ini t__ precrop = precrop) File ""I:\inundation\pyvolution\least_squares.py"", line 545, in build _interpolation_matrix_A element_found, sigma0, sigma1, sigma2, k = \ File ""I:\inundation\pyvolution\least_squares.py"", line 608, in searc h_triangles_of_vertices for k, _ in self.mesh.vertexlist[v]: TypeError: iteration over non-sequence }}} It's caused since vertex 6 is not part of any triangle. I:\inundation\debug\mesh_error_reporting\show_bad_mesh.py (changeset:1954) produces a different mesh that shows the same error. Vertex 10 is not associated with any triangle. This is evident in the .tsh file. See show_mesh_bug.py (changeset:1878) for 1st report of bug. Currently least squares assumes a mesh is ok. Should this be changed? probably. I just had a look at the mesh.py, at the triang.genMesh call. The error seems to be coming from triangle." duncan 24 give feedback if segments are repeated Mesh generation maintenance Architecture and API defect normal lowest duncan closed 2005-10-11T15:09:20+10:00 2009-09-07T15:08:41+10:00 "This is a ticket based on ticket #9, which was overloaded. I think its referering to the pmesh.mesh engine." duncan 25 duplication of util_ext.h files AnuGA ready for release Architecture and API enhancement normal normal ole closed 2005-10-17T10:44:08+10:00 2006-03-09T10:12:38+11:00 It seems that all the packages that rely on utilities need the util_ext.h file in their directory. It would be good if this duplication was not necesary duncan 26 Loading module inside a package can't find C-extension AnuGA ready for release Architecture and API defect normal normal ole closed 2005-10-17T11:02:36+10:00 2005-10-19T18:58:46+10:00 "When loading a module inside a package Python can't find it's C-extension. Example import pyvolution.util then util can't find its C-extension even though it exists within the pyvolution directory. It could be solved by adding pyvolution to the PYTHONPATH, but it seems silly." ole 27 zeroDivisionError using cg_solve least_squares module finished Functionality and features defect normal low steve closed 2005-10-18T17:27:01+10:00 2009-09-04T12:36:45+10:00 "here's the error {{{ ERROR: test_expand_search3 (__main__.Test_Least_Squares) ---------------------------------------------------------------------- Traceback (most recent call last): File ""I:\inundation\fit_interpolate\benchmark_least_squares.py"", lin e 147, in test_expand_search3 calc = interp.fit_points(point_atts ) File ""I:\inundation\pyvolution\least_squares.py"", line 881, in fit_p oints return self.fit(z) File ""I:\inundation\pyvolution\least_squares.py"", line 869, in fit return conjugate_gradient(self.B, Atz, Atz, imax=2*len(Atz) ) File ""I:\inundation\pyvolution\cg_solve.py"", line 55, in conjugate_g radient alpha = rTr/dot(d,q) ZeroDivisionError: float division }}} see show_cg_bug.py (changeset:1959) " duncan 28 Possible issues with compiling pmesh under Linux Mesh generation finished Compilation and installation defect normal normal ole closed 2005-10-19T11:46:50+10:00 2005-12-15T11:46:43+11:00 "Even though we moved the triangle c-extensions down one level we are still experiencing problems. On nautilus (Linux): ole@nautilus:~/anuga/inundation/pmesh$ python test_mesh.py Traceback (most recent call last): File ""test_mesh.py"", line 5, in ? from mesh import * File ""/home/ole/anuga/inundation/pmesh/mesh.py"", line 20, in ? import triang ImportError: /home/ole/anuga/inundation/pmesh/triangmodule.so: undefined symbol: triangulate " ole 29 Come up with new 'components' - that cut across milestones AnuGA ready for release Management and planning defect normal normal ole closed 2005-10-19T13:17:17+10:00 2005-10-19T18:42:42+10:00 "Curruntly components are very similar to Milestones. They should rather reflect another dimension. Examples: * Functionality and features * Efficiency and optimisation * Appearance and visualisation * Architecture and compilation * Testing and validation * Interface(API) * Documentation * Management * Other " ole 30 pmesh test_mesh failing on cyclone Mesh generation finished Architecture and API defect normal normal duncan closed 2005-10-24T14:26:16+10:00 2005-11-15T11:44:28+11:00 run it and see. tests segtag, exportpointsfile regionalmaxarea fail/ are broken. duncan 31 Move util.py and its extension out from pyvolution to utilities/numerical_tools AnuGA ready for release Compilation and installation defect normal normal ole closed 2005-10-26T05:33:30+10:00 2006-03-09T19:37:39+11:00 "This relates to the issues raised in ticket:20 and changeset:1856 about c-extensions. Background: * util.py provides general functionality such as gradient computations * util.py relies on its C-extension and the associated header file for speed * However, other C extensions (such as shallow_water) relies directly on util_ext.h We need an elegant solution that 1. Avoids code duplication 2. Allows common libraries to appear in directories separate from e.g. pyvolution 3. Minimises any extra setup requirements One idea would be to move the functionality from util and its extensions to utilities/numerical_tools and then have shallow_water_ext.c do {{{ #include }}} This could be accomplihed by adding the root dir (currently also in PYTHONPATH) to the -I option when compiling. If this could be done automatically, this solution will work nicely. However, it would be undesirable to introduce another environmant variable specifying the root dir for compilation purposes. A clean solution is required. Ideas Look at how is Numeric/arrayobject.h is found and mimic that! (This assumes that Numeric is already in Python/include) The cleanest for our installation would be to add the anuga root dir to include_dirs in distutils, but for running out of the sandpit I suggest we add directories from sys.path to -I in compile.py " ole 32 Move test_all.py (and building of C-extensions) up one level AnuGA ready for release Testing and validation defect normal normal ole closed 2005-10-26T05:40:01+10:00 2006-02-01T13:43:13+11:00 "Rationale Currently most tests and build are controlled from within pyvolution. As more common functionality is being migrated out into separate packages, it would be desirable to have test_all and the build steps at pyvolutions parent directory, /svn/anuga/inundation This should wait until we have sorted out the buildbot platform since that may set requirements on our testing strategy " ole 33 Get buildbot configured and ready to run AnuGA ready for release Testing and validation defect normal normal ole closed 2005-10-26T05:41:32+10:00 2006-03-09T07:53:26+11:00 "It works now calling compile Need to redo test_all.py to be cealled from root dir. Done and launched at GA 8 March 2005. Link is available on TRAC front page " ole 34 triangle behaves differently, depending on the OS Mesh generation maintenance Functionality and features defect trivial lowest rwilson closed 2005-11-15T11:48:26+11:00 2012-02-13T13:55:00+11:00 "triangle, used by pmesh, behaves differently, depending on the OS. The meshes it produces are different. test_mesh shows this, in the code. {{{ if sys.platform == 'win32': }}} is used to test the different results." duncan 35 Introduce large file support for NetCDF to allow larger than 2 GByte files AnuGA ready for release Efficiency and optimisation defect normal normal rwilson closed 2005-11-18T12:35:46+11:00 2009-09-10T16:00:13+10:00 "The barrier of 2GB can be removed by moving 2 v3.6 and 64bit storage (even on 32 bit platforms). See http://www.unidata.ucar.edu/software/netcdf/docs/faq.html#Large%20File%20Support4" ole 36 have trac generate an email to the person a ticket is assigned to AnuGA ready for release Management and planning defect normal normal duncan closed 2005-11-18T16:22:45+11:00 2006-02-02T17:21:54+11:00 test duncan 37 simplify generateMesh Mesh generation finished Architecture and API enhancement normal normal duncan closed 2005-11-22T11:02:25+11:00 2006-02-02T15:58:52+11:00 "In pmesh.mesh.generateMesh remove the need to pass a command string. Done. Use pmesh.mesh.generate_mesh " duncan 38 pmesh2Domain should have its own directory Mesh generation maintenance Architecture and API defect minor lowest duncan closed 2005-11-24T09:39:16+11:00 2006-08-14T11:56:53+10:00 "pmesh2Domain depends on pmesh and pyvolution. Therefore take it out of pyvolution, to reduce pyvolutions' dependencies. " duncan 39 testing autogenerated email Appearance and visualisation defect normal normal ole closed 2005-12-06T11:20:23+11:00 2006-02-02T17:21:08+11:00 duncan 40 cache exiting from a simulation AnuGA ready for release Functionality and features defect normal low ole closed 2005-12-16T09:20:49+11:00 2006-08-18T17:33:50+10:00 "While running run_gippsland2.py (changeset:2150) I got the following error; {{{ Traceback (most recent call last): File ""I:\production\gippsland_2005\run_gippsland2.py"", line 97, in ? ,verbose = False File ""I:\inundation\caching\caching.py"", line 359, in cache funcname, dependencies, compression) File ""I:\inundation\caching\caching.py"", line 1072, in save_results_ to_cache mysave(T,datafile,compression) # Save data to cache File ""I:\inundation\caching\caching.py"", line 1268, in mysave raise MemoryError, msg MemoryError: ****WARNING (caching.py): Could not pickle data for compr ession. Try using compression = False }}} This should continue, without caching, rather than exiting. (But still give the warning) " duncan 41 tests are 'leaking files' Appearance and visualisation defect minor normal ole closed 2006-01-25T17:15:03+11:00 2006-01-31T13:27:57+11:00 "It would be great if, when executing inundation\test_all, it didn't create files in the inundation directory. Currently it does, since some tests create files and then don't delete these files. Here's a list of files it creates; bedslope.sww datatest_elevation datatest_elevation.ers most_small_ua.nc most_small_va.nc most_small_ha.nc most_small_e.nc test_windstress_from_file.tms test_windstress_from_file.txt " duncan 42 Tests are 'leaking' files. AnuGA ready for release Testing and validation defect normal normal ole closed 2006-01-25T17:16:39+11:00 2006-01-31T12:34:53+11:00 "It would be great if, when executing test_all, it didn't create files in the inundation directory. Currently it does, since some tests create files and then don't delete these files. Here's a list of files it creates; bedslope.sww datatest_elevation datatest_elevation.ers most_small_ua.nc most_small_va.nc most_small_ha.nc most_small_e.nc test_windstress_from_file.tms test_windstress_from_file.txt See changeset:2305" duncan 43 Duplicate points in interior regions cause spurious mesh Mesh generation maintenance Functionality and features defect normal normal duncan closed 2006-01-27T10:11:19+11:00 2006-05-30T14:32:23+10:00 "Created interior region polygon which had duplicate points. Called create_mesh_from_regions, with resulting mesh could not even be seen, as viewed through swollen. In addition, saw diagnostic output of ""Vertex 23 does not belong to a triangle"". No exceptions were thrown." sexton 44 Duplicate points in interior regions cause spurious mesh AnuGA ready for release Functionality and features defect minor normal ole closed 2006-01-27T10:14:29+11:00 2006-01-27T10:16:29+11:00 "Created interior region polygon which had duplicate points. Called create_mesh_from_regions, with resulting mesh could not even be seen, as viewed through swollen. In addition, saw diagnostic output of ""Vertex 23 does not belong to a triangle"". No exceptions were thrown." sexton 46 test_all at ANUGA level fails for me Testing and validation defect normal normal duncan closed 2006-02-02T15:54:31+11:00 2006-02-03T11:14:38+11:00 "test_all at the root level fails. This is in Windows. It doesn't do this for Ole ; {{{ Testing path ...I:\inundation: test_interpolate.py test_quad.py test_mesh.py test_quantity.py test_cg_solve.py test_sparse.py test_generic_boundary_conditions.py test_advection.py test_region.py test_general_mesh.py test_combine_pts.py test_data_manager.py test_least_squares.py test_shallow_water.py test_domain.py test_all.py test_ermapper.py test_util.py test_most2nc.py test_smf.py test_interpolate_sww.py test_pmesh2domain.py test_metis.py test_caching.py test_version.py test_triangmodule.py test_alpha_shape.py test_numerical_tools.py test_polygon.py test_mesh.py test_mesh_interface.py test_all.py test_loadASCII.py test_all.py test_geo_reference.py test_point.py test_redfearn.py test_geospatial_data.py WARNING: File test_metis.py excluded from testing WARNING: File test_version.py excluded from testing WARNING: File test_interpolate.py excluded from testing WARNING: File test_all.py excluded from testing buildroot I:\inundation Traceback (most recent call last): File ""I:\test_all.py"", line 8, in ? execfile('test_all.py') File ""test_all.py"", line 90, in ? unittest.main(defaultTest='regressionTest') File ""C:\Software\Python23\lib\unittest.py"", line 720, in __init__ self.parseArgs(argv) File ""C:\Software\Python23\lib\unittest.py"", line 747, in parseArgs self.createTests() File ""C:\Software\Python23\lib\unittest.py"", line 753, in createTest s self.module) File ""C:\Software\Python23\lib\unittest.py"", line 519, in loadTestsF romNames suites.append(self.loadTestsFromName(name, module)) File ""C:\Software\Python23\lib\unittest.py"", line 504, in loadTestsF romName test = obj() File ""test_all.py"", line 85, in regressionTest modules = map(__import__, moduleNames) File ""I:\test_all.py"", line 5, in ? os.chdir('inundation') OSError: [Errno 2] No such file or directory: 'inundation' }}} " duncan 47 Trac internal error Management and planning defect minor low ole closed 2006-02-03T11:20:40+11:00 2006-03-09T10:03:04+11:00 "this is a cut and paste from my browser, after changing a ticket. This is not the first one I've got. The ticket change did occur. I didn't recieve an email about it though. Did Ole get an email saying ticket #46 had been resolved? {{{ Oops... Trac detected an internal error: (451, '4.3.2 Please try again later', 'ole.nielsen@anu.edu.au')If you think this really should work and you can reproduce it. Then you should consider to report this problem to the Trac team. Go to http://trac.edgewall.com/ and create a new ticket where you describe the problem, how to reproduce it. Don't forget to include the python traceback found below. TracGuide — The Trac User and Administration Guide Python traceback Traceback (most recent call last): File ""/usr/lib/python2.3/site-packages/trac/core.py"", line 531, in cgi_start real_cgi_start() File ""/usr/lib/python2.3/site-packages/trac/core.py"", line 526, in real_cgi_start dispatch_request(path_info, args, req, env) File ""/usr/lib/python2.3/site-packages/trac/core.py"", line 441, in dispatch_request module.run() File ""/usr/lib/python2.3/site-packages/trac/Module.py"", line 44, in run self.render() File ""/usr/lib/python2.3/site-packages/trac/Ticket.py"", line 449, in render self.save_changes (id) File ""/usr/lib/python2.3/site-packages/trac/Ticket.py"", line 378, in save_changes tn.notify(ticket, newticket=0, modtime=now) File ""/usr/lib/python2.3/site-packages/trac/Notify.py"", line 228, in notify NotifyEmail.notify(self, ticket['id'], subject) File ""/usr/lib/python2.3/site-packages/trac/Notify.py"", line 131, in notify Notify.notify(self, resid) File ""/usr/lib/python2.3/site-packages/trac/Notify.py"", line 81, in notify self.send(to) File ""/usr/lib/python2.3/site-packages/trac/Notify.py"", line 346, in send NotifyEmail.send(self, rcpt, hdrs) File ""/usr/lib/python2.3/site-packages/trac/Notify.py"", line 160, in send self.server.sendmail(self.from_email, rcpt, msg.as_string()) File ""/usr/lib/python2.3/smtplib.py"", line 676, in sendmail raise SMTPSenderRefused(code, resp, from_addr) SMTPSenderRefused: (451, '4.3.2 Please try again later', 'ole.nielsen@anu.edu.au') }}} " duncan 48 Separate ghost boundary from physical boundary Efficiency and optimisation defect major lowest ole closed 2006-02-07T11:32:27+11:00 2006-09-20T11:15:13+10:00 "Currently, update_boundary goes through all boundary elements even though they may only appear as ghosts in the parallel version. This affects speedup adversely. Update_boundary must be able to distinguish, e.g. by having access to a separate list containing only physical elements" ole 49 Address missing logger in cg_solve when tested at the anuga level Appearance and visualisation defect minor low steve closed 2006-02-07T13:26:43+11:00 2006-03-31T17:31:29+11:00 "When test_all.py is run at the anuga level, cg_solve can't find its logger. This works OK when test_all is run at the pyvolution level. One solution might be to disable logger in tests..." ole 50 Write module for timeseries plotting and report generation Appearance and visualisation enhancement normal normal jane or nick closed 2006-02-15T10:53:00+11:00 2006-08-14T10:45:34+10:00 "Currently we are generatieng timeseries plots of conserved and derived quantities using a 'throw away' script like get_timeseries: https://datamining.anu.edu.au/anuga/file/production/sydney_2006/get_timeseries.py It would make sense to write a generic module that given a set of locations produces this kind of information and generates a pdf file of it. Using LaTeX for this might be a good idea. First step towards this would be a short requirements and design spec." ole 51 Integrated damage modelling Functionality and features enhancement normal normal nick and duncan closed 2006-02-15T10:54:29+11:00 2006-08-14T10:44:59+10:00 Write a module that given an sww file, a list of locations and a damage curve computes damage levels. ole 52 Investigate reproducibility of model runs Management and planning defect normal normal nick closed 2006-02-21T11:37:54+11:00 2006-08-14T10:47:08+10:00 "One idea would be to store the model script itself inside the sww file. Also store the ANUGA revision number Also data revision if available." ole 53 Investigate discretisation error presumably due to steep bedslopes combined with coarse triangles ANUGA maintenance Functionality and features defect minor lowest someone closed 2006-02-21T16:48:08+11:00 2009-09-04T12:43:32+10:00 "In the vicinity of steep slopes and shallow depths we observe triangles 'sticking' out of the water. This is due to the combined constraints * conservation of volume * gradient limiters * h >= 0 In addition it may be that storing the output with unique vertex values averaged exacerbates this problem by affecting neighbouring triangles. The remedies so far have been to refine areas affected. We need a test that will reproduce the problem and then compare the two storage schemes. Alternatively, a comprehensive solution at the level of the numerical solver, but that has not yet been discovered by the team. " ole 54 if the sww files are large the tools used to interigate them crash. Functionality and features defect normal low duncan closed 2006-02-22T11:55:58+11:00 2012-02-13T13:53:17+11:00 "Here's where file_function fails; {{{ Reading O:/2/cit/inundation/Gippsland Lakes/120106/lakes_100_628759.sww Get variables File_function data obtained from: O:/2/cit/inundation/Gippsland Lakes/120106/lak es_100_628759.sww References: Lower left corner: [555000.000000, 5793000.000000] Start time: 0.000000 Traceback (most recent call last): File ""I:\production\gippsland_2005\get_timeseries.py"", line 50, in ? use_cache = True) File ""I:\inundation\pyvolution\util.py"", line 225, in file_function verbose = verbose) File ""I:\inundation\caching\caching.py"", line 349, in cache T = apply(func,args,kwargs) File ""I:\inundation\pyvolution\util.py"", line 285, in _file_function verbose = verbose) File ""I:\inundation\pyvolution\util.py"", line 453, in get_netcdf_file_function quantities[name] = fid.variables[name][:] MemoryError: can't allocate memory for array }}} Here's where interpolate_sww fails {{{ :\production\gippsland_2005>python get_point_info.py Traceback (most recent call last): File ""get_point_info.py"", line 18, in ? point_file_out, display_errors = True) File ""I:\inundation\pyvolution\interpolate_sww.py"", line 35, in interpolate_sw w2xya interp = Interpolate_sww(sww_file, quantity_name) File ""I:\inundation\pyvolution\interpolate_sww.py"", line 62, in __init__ x, y, volumes, time, quantity = self.read_sww(file_name, quantity_name) File ""I:\inundation\pyvolution\interpolate_sww.py"", line 164, in read_sww quantity = stage - z # 2D, using broadcasting MemoryError: can't allocate memory for array }}} " duncan 55 Negative stage values have been observed in e.g. the Sydney study. Functionality and features defect normal lowest jane closed 2006-02-24T11:51:57+11:00 2006-08-14T11:39:28+10:00 Find out what happens in the vicinity of gauges where negative stages are observed. Is this a discretisation problem? ole 56 Replace pmesh_to_domain_instance with new interface AnuGA ready for release Architecture and API defect minor normal duncan closed 2006-03-10T12:15:08+11:00 2006-03-27T13:54:48+11:00 "Suggestion: Build functionality into the Domain constructor domain = Domain(mesh_filename) " ole 57 Move general_mesh, mesh and mesh_factory from pyvolution into separate dir AnuGA ready for release Architecture and API defect minor normal duncan or ole closed 2006-03-12T22:01:49+11:00 2006-08-14T11:19:32+10:00 Firs make their tests independent of shallow_water.py. See FIXME's in tests. ole 58 Consider migrating ANUGA to use numpy (from scipy) rather than Numeric Architecture and API defect normal highest rwilson closed 2006-03-13T11:01:16+11:00 2009-09-04T09:30:51+10:00 "Numpy is more mature and in particular supports Nan and Inf See http://numeric.scipy.org/ and http://projects.scipy.org/scipy/numpy/browser/trunk/numpy/lib/convertcode.py" ole 59 remove dependency on points dicts from export pts to file Efficiency and optimisation defect normal normal Nick closed 2006-03-23T10:23:10+11:00 2006-04-20T11:14:52+10:00 "inside geospatial_data.py, “export_points_file"" should not need a points dict to write file. should get values from ""self"". maybe replace with a ""save"" or ""save as file"" method " Nick 60 Add Crop method to geospatial_data Functionality and features defect normal lowest Nick closed 2006-03-23T11:50:02+11:00 2006-11-27T14:24:21+11:00 "write a crop method for geospatial_data. maybe included in the ""_read_???_file"" part.... therefore go through file only once" Nick 61 Get boundary of a Geospatial_data object, to allow addition of high res accurate data and low res region data Functionality and features defect normal low ole closed 2006-03-27T13:46:53+11:00 2009-09-04T12:35:06+10:00 "Need to find the boundary of a set of data points... Question: should the boundary be rectanglar?... gut says No I suggest we use the alpha-shape code to produce tightly hugging polygon's containing the dataset and return them using a method such as G.get_boundary() with an optional argument for alpha. (Ole) ---------------------- Use a clip function eg Pa= G1.boundary() [need to do!] G2.clip(Pa, inside =true) [DONE] G = G1 + G2 [Done] look inside utilities/polygon.py for clip function" Nick 62 Clean up Load ASCII Efficiency and optimisation defect normal low Duncan closed 2006-03-28T11:26:07+11:00 2007-01-10T16:55:38+11:00 alot of the importing and exporting of files is now in Geospatial_data and can be removed from LoadASCII. This goes for the tests as well Nick 63 Match elevation at 'deep' water grids with 'shallow water' meshes Functionality and features defect normal low someone closed 2006-03-31T13:16:18+11:00 2009-09-10T16:20:02+10:00 "MOST and URS work on grids derived from deep water bathymetries. When used as boundary conditions for ANUGA, depths seen by the two models must be consistent. A test would consist of a comparison of grid with mesh data in an overlapping region." ole 64 cg_solve error least_squares module maintenance Functionality and features defect normal normal Steve closed 2006-04-05T15:00:50+10:00 2006-08-14T11:44:32+10:00 "Jane got this error. She's working on a simulation where it seems that least squares gives incorrect fitted values. [There isn't enough info here to reproduce the bug sorry.] {{{ Traceback (most recent call last): File ""Z:\inundation\sandpits\jsexton\ANUGA\production\sydney_2006\run_sydney_smf_polyingo.py"", line 223, in ? ,verbose = False File ""z:\inundation\sandpits\jsexton\ANUGA\inundation\caching\caching.py"", line 349, in cache T = apply(func,args,kwargs) File ""z:\inundation\sandpits\jsexton\ANUGA\inundation\pyvolution\least_squares.py"", line 124, in fit_to_mesh_file precrop = precrop) File ""z:\inundation\sandpits\jsexton\ANUGA\inundation\pyvolution\least_squares.py"", line 215, in fit_to_mesh vertex_attributes = interp.fit_points(point_attributes, verbose = verbose) File ""z:\inundation\sandpits\jsexton\ANUGA\inundation\pyvolution\least_squares.py"", line 942, in fit_points f[:,i] = self.fit(z[:,i]) File ""z:\inundation\sandpits\jsexton\ANUGA\inundation\pyvolution\least_squares.py"", line 916, in fit return conjugate_gradient(self.B, Atz, Atz, imax=2*len(Atz) ) File ""z:\inundation\sandpits\jsexton\ANUGA\inundation\utilities\cg_solve.py"", line 65, in conjugate_gradient d = r + bt*d OverflowError: math range error }}} " duncan 65 mesh.get_boundary_polygon does not work as expected if triangles are discontinuous least_squares module finished Functionality and features defect major high ole closed 2006-04-10T11:43:46+10:00 2006-04-12T14:41:09+10:00 "Hi Ole, Would you be able to change get_boundary_polygon so it works with discontinuous triangles? Not having this means that the new interpolate.py can't be used when creating a boundary from an sww file. Thanks Duncan" duncan 66 Problem with large meshes and cache Functionality and features defect normal normal nick closed 2006-04-10T13:25:27+10:00 2006-08-14T11:06:41+10:00 "it was noticed that if model has more than about 400,000 triangles a problem with Cache occurs when the elevation data is applied to the mesh. this was solved by turning cache to False. however there might be an other better solution domain.set_quantity('elevation', filename = project.combined_dem_name + '.pts', use_cache = True, verbose = True, alpha = 0.05 ) " Nick 67 "possible error in ""create_mesh_from_regions" Functionality and features defect normal normal ole closed 2006-04-12T14:10:14+10:00 2006-04-13T09:59:19+10:00 "using the below... eg no interior region defined produces an error from caching import cache _ = cache(create_mesh_from_regions, project.polyAll, {'boundary_tags': {'top': [0], 'topleft': [1], 'topleft1': [2], 'bottomleft': [3], 'bottom': [4], 'bottomright': [5], 'topright':[6]}, 'maximum_triangle_area': 500, 'filename': meshname}, verbose = True) following is the error message Traceback (most recent call last): File ""run_onslow.py"", line 138, in ? 'filename': meshname},verbose = True) File ""/export/home/nbartzis/anuga/inundation/caching/caching.py"", line 349, in cache File ""pmesh/mesh_interface.py"", line 86, in create_mesh_from_regions File ""/home/nbartzis/anuga/inundation/pmesh/mesh.py"", line 660, in add_region_from_polygon region=create_region) File ""/home/nbartzis/anuga/inundation/pmesh/mesh.py"", line 719, in _add_area_from_polygon segment_tags[i] = key IndexError: list assignment index out of range" Nick 68 "possible error in ""create_mesh_from_regions" Functionality and features defect normal normal ole closed 2006-04-12T14:10:44+10:00 2006-04-13T09:58:42+10:00 "using the below... eg no interior region defined produces an error from caching import cache _ = cache(create_mesh_from_regions, project.polyAll, {'boundary_tags': {'top': [0], 'topleft': [1], 'topleft1': [2], 'bottomleft': [3], 'bottom': [4], 'bottomright': [5], 'topright':[6]}, 'maximum_triangle_area': 500, 'filename': meshname}, verbose = True) following is the error message Traceback (most recent call last): File ""run_onslow.py"", line 138, in ? 'filename': meshname},verbose = True) File ""/export/home/nbartzis/anuga/inundation/caching/caching.py"", line 349, in cache File ""pmesh/mesh_interface.py"", line 86, in create_mesh_from_regions File ""/home/nbartzis/anuga/inundation/pmesh/mesh.py"", line 660, in add_region_from_polygon region=create_region) File ""/home/nbartzis/anuga/inundation/pmesh/mesh.py"", line 719, in _add_area_from_polygon segment_tags[i] = key IndexError: list assignment index out of range" Nick 69 "possible error in ""create_mesh_from_regions" Functionality and features defect normal normal ole closed 2006-04-12T14:12:18+10:00 2006-04-13T09:57:00+10:00 "using the below... eg no interior region defined produces an error from caching import cache _ = cache(create_mesh_from_regions, project.polyAll, {'boundary_tags': {'top': [0], 'topleft': [1], 'topleft1': [2], 'bottomleft': [3], 'bottom': [4], 'bottomright': [5], 'topright':[6]}, 'maximum_triangle_area': 500, 'filename': meshname}, verbose = True) following is the error message Traceback (most recent call last): File ""run_onslow.py"", line 138, in ? 'filename': meshname},verbose = True) File ""/export/home/nbartzis/anuga/inundation/caching/caching.py"", line 349, in cache File ""pmesh/mesh_interface.py"", line 86, in create_mesh_from_regions File ""/home/nbartzis/anuga/inundation/pmesh/mesh.py"", line 660, in add_region_from_polygon region=create_region) File ""/home/nbartzis/anuga/inundation/pmesh/mesh.py"", line 719, in _add_area_from_polygon segment_tags[i] = key IndexError: list assignment index out of range" Nick 70 Memory useage of Create_mesh_from_regions Efficiency and optimisation defect normal low nick closed 2006-04-13T11:15:04+10:00 2008-01-15T16:04:06+11:00 "create_mesh_from_regions, starts uses alot of swap mem when the mesh is over about 600,000 triangles. it will work for jobs around 1,200,000 triangles however starts using alot of swap memory with mesh over 1,500,000 and tested at 3,500,000. In this case python uses about 1% (or less) of the CPU and the rest is in manageing the swap memory. these tests were on Cyclone, each node has 2 G RAM... with more RAM it could be assumed that more triangles can be possible. Is it possible to optimises this part to handle more triangles? " Nick 71 Automatically obtain head revision number from subversion Appearance and visualisation enhancement normal low ole closed 2006-04-19T16:38:41+10:00 2006-05-17T12:12:59+10:00 "Need code to get current revision of ANUGA. A beginning (working only on Win32) is available in get_version.py (https://datamining.anu.edu.au/anuga/file/inundation/get_version.py) See comments in that file." ole 72 test_all fails, but the tests, when run in their local directory work. Testing and validation defect minor low Ole closed 2006-04-24T16:09:12+10:00 2006-04-26T15:44:39+10:00 "This could be caused by multiple files with the same name, import statements that don't give the directory structure and that test_all add's directories to sys.path. A solution is to stop test all adding directories to sys.path." duncan 73 test_advection fails on nautilus. It's to do with weave.. AnuGA ready for release Compilation and installation defect minor low Steve closed 2006-04-26T10:31:12+10:00 2012-02-13T13:54:07+11:00 "Here's some of the error messges printed. It prints more than this though. Cyclone doesn't have this problem. On Nautilus Duncan and Jane have this problem. It works fine for Ole on Nautilus. No one has had this on cyclone or windows snadpits. {{{ file changed unix cc1plus: warning: command line option ""-Wstrict-prototypes"" is valid for Ada/C/ObjC but not for C++ In file included from /usr/include/python2.3/Python.h:8, from /home/duncan/.python23_compiled/sc_13328 EEEEE. ====================================================================== ERROR: test_advection_example (__main__.Test_Advection) ---------------------------------------------------------------------- Traceback (most recent call last): File ""test_advection.py"", line 167, in test_advection_example for t in domain.evolve(yieldstep = 0.05, finaltime = 10): File ""pyvolution/advection.py"", line 366, in evolve skip_initial_step=skip_initial_step): File ""pyvolution/domain.py"", line 608, in evolve self.compute_fluxes() File ""pyvolution/advection.py"", line 122, in compute_fluxes self.compute_fluxes_weave() File ""pyvolution/advection.py"", line 336, in compute_fluxes_weave type_converters = converters.blitz, compiler='gcc'); File ""/usr/lib/python2.3/site-packages/weave/inline_tools.py"", line 335, in inline auto_downcast = auto_downcast, File ""/usr/lib/python2.3/site-packages/weave/inline_tools.py"", line 439, in compile_function verbose=verbose, **kw) File ""/usr/lib/python2.3/site-packages/weave/ext_tools.py"", line 340, in compile verbose = verbose, **kw) File ""/usr/lib/python2.3/site-packages/weave/build_tools.py"", line 274, in build_extension setup(name = module_name, ext_modules = [ext],verbose=verb) File ""/usr/lib/python2.3/site-packages/scipy_distutils/core.py"", line 73, in setup return old_setup(**new_attr) File ""/usr/lib/python2.3/distutils/core.py"", line 166, in setup raise SystemExit, ""error: "" + str(msg) CompileError: error: Command ""g++ -pthread -fno-strict-aliasing -DNDEBUG -g -O3 -Wstrict-prototypes -fPIC -I/usr/lib/python2.3/site-packages/weave -I/usr/lib/python2.3/site-packages/weave/scxx -I/usr/lib/python2.3/site-packages/weave/blitz-20001213 -I/usr/include/python2.3 -c /home/duncan/.python23_compiled/sc_1332884f49c5046962e6d04fdb903c7d20.cpp -o /tmp/duncan/python23_intermediate/compiler_b4affb8230daad99a1fb80c00d7ddd42/home/duncan/.python23_compiled/sc_1332884f49c5046962e6d04fdb903c7d20.o"" failed with exit status 1 }}} " duncan 74 Compute values at centroids from sww file AnuGA ready for release Appearance and visualisation defect normal normal Ole closed 2006-05-05T17:42:24+10:00 2006-05-17T12:14:39+10:00 This is perceived to be better than interpolating to regular grids. ole 75 Build in okushiri validation as an automatic validation test AnuGA ready for release Testing and validation defect normal low ole closed 2006-05-16T11:29:16+10:00 2006-11-15T06:02:53+11:00 "The Okushiri validation checks that the model is capturing essential physical features of waterflow. It must be turned into an automatic test that guarantees that Anuga remains intact. However, it is a timeconsuming computation and should not be part of the test_all suite. Options are: Make special suite that captures validation results: validate_all.py Make it part of the buildbot" ole 76 Allow job recovery after a node crash Efficiency and optimisation defect normal normal Ole closed 2006-05-18T10:52:29+10:00 2006-08-14T11:13:03+10:00 "Store all values of all varibles every 12-24 hours to disk and develop some code to run from this point. This will prevent having to rerun the whole model if the node crashes " Nick 77 test_all is segmentation faulting, some of the time Appearance and visualisation defect normal normal duncan closed 2006-05-30T15:15:13+10:00 2006-05-31T14:59:48+10:00 "In windows. I can't reproduce it. It's coming from test_triangmodule. test_lone_verts" duncan 78 triangle seg faulting Mesh generation maintenance Appearance and visualisation defect major lowest duncan closed 2006-05-31T14:41:29+10:00 2008-01-09T15:19:17+11:00 running the tests in test_triangmodule and test_triangmoduleII in the same file cause triangle to seg fault. Also, the first test in test_triangmoduleII seg faults in windows. It happens before triangles are removed (Make sure you are not in Q mode to see info from triangle). Fix if it effects real mesh generation. Noticed the error around version 3013. It happens to the ealier version of triang.c though. duncan 79 Create mesh should check that interior regions are contained in bounding polygon AnuGA ready for release Functionality and features defect minor normal duncan closed 2006-06-01T12:17:00+10:00 2006-06-02T15:05:34+10:00 "Jane's test has been added to the beginning but because georeferencing is resolved further down in the code it won't work yet. Perhaps, the interface needs to assume absolute UTM coordinates ? See changeset:3038 for details" ole 80 Enable caching and verbose in create_mesh_from_regions AnuGA ready for release Functionality and features defect minor normal ole closed 2006-06-01T16:32:22+10:00 2006-10-09T16:47:42+10:00 It would be nice if create_mesh_from_regions behaved like most other computationally intensive public functions by taking boolean arguments use_cache and verbose. ole 81 mesh doesn't know it has a geo_reference ANUGA maintenance Functionality and features defect normal normal Ole closed 2006-06-02T15:24:42+10:00 2006-06-05T12:05:42+10:00 When using pyvolution.mesh.get_boundary_polygon with georeferencing it doesn't know it has a geo_reference. See test test_mesh.FIXME_test_mesh_get_boundary_polygon_with_georeferencing. duncan 82 do not let mesh interface accept duplicate tags Mesh generation maintenance Architecture and API defect normal low duncan closed 2006-06-09T12:10:00+10:00 2009-09-04T12:33:50+10:00 "Do not let mesh interface accept duplicate tags. See revision 3133 for a great test Ole made to show this feature additionally, catch bad indexes of segments. this is what currently happens; {{{ Traceback (most recent call last): File ""run_sydney_smf.py"", line 146, in ? verbose = True) File ""Z:\inundation\sandpits\jsexton\ANUGA\inundation\caching\caching.py"", lin e 349, in cache T = apply(func,args,kwargs) File ""Z:\inundation\sandpits\jsexton\ANUGA\inundation\pmesh\mesh_interface.py"" , line 86, in create_mesh_from_regions geo_reference=poly_geo_reference) File ""Z:\inundation\sandpits\jsexton\ANUGA\inundation\pmesh\mesh.py"", line 660 , in add_region_from_polygon region=create_region) File ""Z:\inundation\sandpits\jsexton\ANUGA\inundation\pmesh\mesh.py"", line 719 , in _add_area_from_polygon segment_tags[i] = key IndexError: list assignment index out of range }}} " duncan 83 Duplicate edge indices in create_mesh_from_regions should cause an exception to be raised. Mesh generation finished Appearance and visualisation defect normal normal duncan closed 2006-06-09T13:34:46+10:00 2006-06-09T13:36:32+10:00 "Currently the user may inadvertently specify two different tags for one edge. This should raise an Exception. Unit test in test_mesh_interface reveals this. Duncan already made a ticket for this (ticket:82)" anonymous 84 find out module/class dependencies in ANUGA Architecture and API task normal lowest ole closed 2006-06-21T16:52:11+10:00 2009-01-06T04:47:35+11:00 It would be good to know what code depends on what other code in ANUGA. Find a tool to automatically generate this information. duncan 85 Problem with boundary conditions being interpolated incorrectly to some meshes Functionality and features defect normal normal ole closed 2006-06-28T11:34:11+10:00 2006-08-14T11:16:05+10:00 "The stage values from the same cached results are interpolated on to different meshes with very different stage properties such as max and min values. for example the difference between the follow results is large \\inundation\pt_hedland_tsunami_scenario_2006\output\20060620_022643 and \\inundation\pt_hedland_tsunami_scenario_2006\output\20060627_071417 this has occurs serveral times generally when mesh is changed " Nick 86 tests in data_manager are being skipped. ANUGA maintenance Appearance and visualisation defect minor low Ole closed 2006-07-04T15:32:07+10:00 2006-10-11T17:46:52+10:00 "Testsin data_manager were being skipped, due to the __main__ code being before some tests. I've made it more obvious that test are being skipped by adding NOT_ before tests. Should these tests be running though, or are they testing obsolete code?" duncan 87 Refactor dem2pts AnuGA ready for release Efficiency and optimisation defect minor low hudson closed 2006-07-10T15:57:47+10:00 2010-06-09T15:34:40+10:00 "To save space and to simplify the API refactor the two functions asc2dem and dem2pts as follows: Rename dem2pts to netcdf_dem2pts and create new function something like {{{ def dem2pts(filename, ....): basename, ext = os.path.splitext(filename) if ext == '': ext = 'asc' #Default if ext == 'asc': asc2dem(filename, ...) netcdf_dem2pts(filename, ...) os.remove(basename + '.dem' elif ext == 'dem': netcdf_dem2pts(filename, ...) }}} " ole 88 test Appearance and visualisation defect normal normal ole closed 2006-08-02T15:04:00+10:00 2006-08-02T15:04:59+10:00 Duncan 89 Have Minimum Water depth accessable when executing run script AnuGA ready for release Functionality and features defect normal normal Duncan closed 2006-08-14T12:19:16+10:00 2006-08-25T11:46:29+10:00 "currently the min water depth is hard wired in the code... somewhere (dunc knows where) this should change and have the default value come from /anuga/inundation/config minimum_water_depth " Nick 90 How about having boundary conditions take keyword arguments ANUGA maintenance Architecture and API enhancement normal lowest ole closed 2006-08-17T16:28:52+10:00 2012-02-13T13:56:02+11:00 "Currently Dirichlet and Time Boundaries take triplets (in case of the shallow water eq) as in Bd = Dirichlet_boundary([0.,0.,0.]) or Bw = Time_boundary(domain=domain, f=lambda t: [sin(t), 0.0, 0.0]) These triplets represent conserved quantities in a specific order (eg stage, xmomentum, ymomentum). It would be better to have something like Bd = Dirichlet_boundary({'stage': 0, 'xmomentum': 0, 'ymomentum': 0}) with default values of 0 if anything is omitted. Similarly for the time boundary Bw = Time_boundary(domain=domain, {'stage': lambda t: sin(t)}) again with constant 0 as default. This will also fit the new Transmissive_Momentum_Set_Stage_boundary make more sense as it only need on quantity, namely stage. What do the other developers think? " ole 91 User manual Sydney example crashes Other defect normal normal Ole closed 2006-08-29T10:45:21+10:00 2006-10-16T13:33:22+10:00 "When trying to run the Sydney example I got a crash. Does this work for anyone else? Is there a known reason why it doesn't work? The crash; {{{ Using attribute elevation from file m:\inundation\sydney_tsunami_examp le_2006\topographies\sydneytopo.pts Available attributes: ['elevation'] Caching: looking for cached files c:\.python_cache\fit_to_mesh[-132031 2002]_{Result,Args,Admin}.z +---------------------------------------------------------- | Tue Aug 29 10:38:42 2006. Evaluating function fit_to_mesh +---------------------------------------------------------- | Arguments: (Array: (14961, 2), Array: (29311, 3), Array: (989056, 2), Array: (989056,)) | Keyword Args: {'alpha': None, 'mesh_origin': (-1, 316000.0, 6238000. 0), 'verbose': True, 'data_origin': (56, 332090, 6246250)} | Reason: No cached result +---------------------------------------------------------- Traceback (most recent call last): File ""I:\documentation\user_manual\examples\runsydney.py"", line 119, in ? verbose = True) File ""i:\anuga_core\source\anuga\pyvolution\domain.py"", line 301, in set_quantity self.quantities[name].set_values(*args, **kwargs) File ""i:\anuga_core\source\anuga\pyvolution\quantity.py"", line 352, in set_values use_cache = use_cache) File ""i:\anuga_core\source\anuga\pyvolution\quantity.py"", line 745, in set_values_from_file use_cache = use_cache) File ""i:\anuga_core\source\anuga\pyvolution\quantity.py"", line 606, in set_values_from_geospatial_data use_cache = use_cache) File ""i:\anuga_core\source\anuga\pyvolution\quantity.py"", line 672, in set_values_from_points compression=False) File ""I:\anuga_core\source\anuga\caching\caching.py"", line 349, in c ache T = apply(func,args,kwargs) File ""I:\anuga_core\source\anuga\fit_interpolate\fit.py"", line 438, in fit_to_mesh alpha=alpha) File ""I:\anuga_core\source\anuga\fit_interpolate\fit.py"", line 93, i n __init__ max_vertices_per_cell) File ""i:\anuga_core\source\anuga\fit_interpolate\general_fit_interpo late.py"", line 83, in __init__ self.mesh.check_integrity() File ""I:\anuga_core\source\anuga\pyvolution\neighbour_mesh.py"", line 601, in check_integrity a0 = anglediff(v1, v0) File ""i:\anuga_core\source\anuga\utilities\numerical_tools.py"", line 73, in anglediff a1 = angle(v1) File ""i:\anuga_core\source\anuga\utilities\numerical_tools.py"", line 49, in angle theta = acos(p) ValueError: math domain error }}} " duncan 92 spam spam Appearance and visualisation defect normal normal anonymous 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Axes would allow better interpretation of simulation outputs. This could either be implemented in the swollen viewer or the new VTK viewer. Being able to overlay polygons in the visualisation will allow easy reference to e.g. coastline." ole 94 sww2dem - math domain error Appearance and visualisation defect normal normal ole closed 2006-10-03T13:32:50+10:00 2006-10-09T16:50:10+10:00 "During production runs, we have an export_results.py script which takes a given sww file and outputs an asc grid of a desired quantity (eg elevation, depth) at a desired grid size. A recent example from the hobart_2006 scenario returns a math domain error (in finding the angle). The same result is found for different cell sizes and different alphas (0.01, 0.1 and 1) and whether a grid or points are used to create the elevation. The script in the hobart_2006 directory lists a series of examples which will generate the error, but importantly show an example which does work. The difference between them is whether the 50m asc grid is used as the elevation function, or whether a series of data sets are used (time_dir = 20060926_064750). However, having said that, timedir = 20060929_075009 uses points rather than grid and the error persists. BUT - having talked over lunch, the one that worked had a simple bounding polygon and the one that didn't work had a more complicated bounding polygon! The 50m asc grid has a number of NODATA values embedded in it (but presumably dem2pts removes them?). Another example has been run where the NODATA values have been removed from the 50m asc grid, and the same result is found (time_dir = 20060929_075954). Out of interest, I changed the bounding polygon to be defined anti-clockwise rather than clockwise, and the error persists. Again, this example is listed in the script." sexton 95 adding two clipped data sets fails Appearance and visualisation defect normal normal ole closed 2006-10-09T17:31:14+10:00 2006-10-10T12:10:59+10:00 "New functionality to clip a data set on an arbitrary polygon (either keep data in the polygon or outside of it). Get an error message when attempt to add two clipped data sets together (see no_test_clip1_inside_outside in test_geospatial_data.py) ---------------------------------------------------------------------- Traceback (most recent call last): File ""test_geospatial_data.py"", line 496, in test_clip1_inside_outside assert allclose((G1+G2).get_data_points(),points) File ""T:\sandpits\jsexton\ANUGA\anuga_core\source\anuga\geospatial_data\geospa tial_data.py"", line 408, in __add__ for x in self.attributes.keys(): AttributeError: 'NoneType' object has no attribute 'keys' ----------------------------------------------------------------------" sexton 96 exporting points file from clipped datasets Functionality and features defect normal normal ole closed 2006-10-10T16:10:50+10:00 2006-10-11T17:54:10+10:00 "New functionality to clip data by arbitrary polygon then add up works. Now we need to be able to export the added data set to a pts file. Error log below. Test name is no_test_clip1_inside_outside in test_geospatial_data.py ====================================================================== ERROR: test_clip1_inside_outside(self): ---------------------------------------------------------------------- Traceback (most recent call last): File ""test_geospatial_data.py"", line 510, in test_clip1_inside_outside G.export_points_file(FN) File ""T:\sandpits\jsexton\ANUGA\anuga_core\source\anuga\geospatial_data\geospa tial_data.py"", line 523, in export_points_file self.get_all_attributes()) File ""T:\sandpits\jsexton\ANUGA\anuga_core\source\anuga\geospatial_data\geospa tial_data.py"", line 675, in _write_pts_file for key in write_attributes.keys(): AttributeError: 'NoneType' object has no attribute 'keys' ----------------------------------------------------------------------" sexton 97 Diagnostics about which triangle causes the smallest timestep AnuGA ready for release Functionality and features defect normal normal ole closed 2006-10-16T14:18:23+10:00 2007-03-28T14:46:59+10:00 "It would be useful to get information about which triangle causes the smallest timesteps (and the largest speed). The id and the location could help track down where mesh should be coarsened to speed up overall computation. " ole 98 A test that failed the first time test_all is run, after an anuga install, but not the 2nd time Testing and validation defect normal low anybody closed 2006-10-17T08:33:53+10:00 2009-09-04T12:32:40+10:00 "Some tests only seem to fail once, after an install. Here's an example; {{{ ====================================================================== ERROR: Test that stage is conserved globally ---------------------------------------------------------------------- Traceback (most recent call last): File ""shallow_water\test_shallow_water_domain.py"", line 2191, in tes t_conservation_4 for t in domain.evolve(yieldstep = 0.05, finaltime = 10.0): File ""shallow_water\shallow_water_domain.py"", line 398, in evolve self.initialise_storage() File ""shallow_water\shallow_water_domain.py"", line 437, in initialis e_storage self.writer = get_dataobject(self, mode = 'w') File ""source\anuga\shallow_water\data_manager.py"", line 1197, in get _dataobject return cls(domain, mode) File ""source\anuga\shallow_water\data_manager.py"", line 266, in __in it__ fid = NetCDFFile(self.filename, mode) File ""C:\Software\Python23\lib\site-packages\Scientific\IO\NetCDF.py "", line 143, in NetCDFFile return apply(_NetCDFFile, args) IOError: No error ---------------------------------------------------------------------- }}} " duncan 99 test_inundation_damage2 fails intermitently Testing and validation defect normal low Duncan closed 2006-10-17T10:00:17+10:00 2006-10-17T11:54:10+10:00 "this is what happens when it fails; {{{ ====================================================================== ERROR: test_inundation_damage2 (test_inundation_damage.Test_inundation _damage) ---------------------------------------------------------------------- Traceback (most recent call last): File ""damage_modelling\test_inundation_damage.py"", line 146, in tear Down os.remove(self.sww.filename) OSError: [Errno 2] No such file or directory: '.\\datatest1161043015.2 .sww' ---------------------------------------------------------------------- Ran 576 tests in 21.532s FAILED (errors=1) }}} " Duncan 100 test_shallow water_domain failing Testing and validation defect normal low Duncan and Ole closed 2006-10-17T10:18:11+10:00 2009-09-04T12:31:16+10:00 "I get this error when installing ANUGA, not precompiled on win2000, python 2.3. #The problem is the gauge_values[X] are 52 long, not 51. I've added a hack to the code so the test doesn't fail, since the test is not there to test the length of the gauge_values, but it would be good to know what is causing the problem and removing the hack. {{{ ERROR: test_another_runup_example ---------------------------------------------------------------------- Traceback (most recent call last): File ""test_shallow_water_domain.py"", line 1043, in test_another_runu p_example assert allclose(gauge_values[1], G1) File ""C:\Software\Python23\lib\site-packages\Numeric\Numeric.py"", li ne 707, in allclose d = less(absolute(x-y), atol + rtol * absolute(y)) ValueError: frames are not aligned ---------------------------------------------------------------------- }}} " Duncan 101 urs2mux needs more tests Appearance and visualisation defect normal normal Duncan closed 2006-10-18T12:29:15+10:00 2006-11-24T10:02:23+11:00 test that more quantities are correct duncan 103 Get Sydney example to work as a user guide example Documentation defect normal normal someone closed 2006-10-24T11:41:16+10:00 2006-11-15T06:04:33+11:00 "Set up run_sydney.py in user_guide/example such that The script is short and sharp It runs from that directory with no other dependencies Data used is OK to release (check this with Neil Corby)." ole 104 more tests needed for urs2sww or urs2nc Testing and validation defect normal normal ole closed 2006-10-24T16:19:01+10:00 2006-11-13T17:51:08+11:00 "suggestions 1) create a simple elevation as a MUX file and then compare after convert to SWW 2) test that lats are varying faster than longs (maybe already done?) 3)??? " nick.bartzis@… 105 new unit test for create_mesh_from_regions Testing and validation defect normal normal Nick closed 2006-10-25T17:59:30+10:00 2007-04-17T15:40:25+10:00 "Just noticed if a bounding polygon doesn't have a bounding tag it will simply pass the test even if it should fail... this is associated to complicated polygons... see def test_create_mesh_from_regions_interior_regions1(self): also there is a test for interior polygons that are outside of the bounding polygon but i'm not sure if that is new (implemented after Jane noticed a problem) or old... as i cannot get it to fail with any new more complex meshes ... but i don't really understand the test... Nick" anonymous 106 Realtime Visualiser hangs on pause AnuGA ready for release Appearance and visualisation defect normal high jack closed 2006-10-27T12:33:22+10:00 2006-11-03T19:47:48+11:00 "Report from Steve: I tried the visualise_rectangle, but for me it hangs when I use the pause button." jack 107 add tests to urs2sww to check minlat and minlon are correct Testing and validation defect normal normal duncan closed 2006-10-30T16:31:56+11:00 2006-12-04T18:28:20+11:00 check minlat is smaller than maxlat and the same with minlon and maxlon... also at the moment i think east longs are assumed to be the minimum??? which may not be logical anonymous 108 Interpolation function (and file_function) need to accept geospatial data Architecture and API defect normal normal duncan closed 2006-10-31T11:25:29+11:00 2006-11-08T16:31:08+11:00 "Currently, Interpolation_function (in interpolate.py) only accepts point coordinates as Numeric arrays. This is unfortunate if the points aren't absolute and have different georeferences. It would be more in line with the rest of the code to have these functions accept geospatial data objects." ole 109 rounding problems with ferret2sww and (urs2sww) Functionality and features defect normal normal duncan closed 2006-10-31T12:14:27+11:00 2006-11-21T16:52:00+11:00 "when a minlat = -21, 0 ,0 and maxlat = -19, 0, 0 the statistics for the extent is (and file created has) -21.00000, -19.500000 even though there is data for -19,0,0 i think this should not happen " anonymous 111 anuga_user_manual.pdf can not be accessed via trac Documentation defect normal normal Ole closed 2006-11-13T09:44:34+11:00 2006-11-29T16:11:53+11:00 "clicking on; http://datamining.anu.edu.au/~ole/anuga/user_manual/anuga_user_manual.pdf Gives the error; the file is damaged and cound not be repaired." duncan 112 runcairns Documentation defect normal normal ole closed 2006-11-16T18:13:50+11:00 2006-11-17T10:27:25+11:00 "Just tried to run demo program runcairn.py The data files are not available in the directory. " steve 113 Output data for the centroid of the triangle NOT just the interpolated results ANUGA enhancements Functionality and features enhancement normal high hudson closed 2006-11-20T14:08:12+11:00 2010-04-14T18:46:05+10:00 "Currently if exporting gauges the resolution of the mesh and orientation of the triangles will effect the results, this is not always desired. Having the values at the centroid will increase speed in trouble shooting model errors or problems It would be great to provide the gauge location and recieve either the interpolated results or the values at the triangle's centroid and the position of the centroid. look in sww2dem " Nick 114 Join together output sww files from parallel ANUGA code Appearance and visualisation defect normal normal steve closed 2006-11-20T15:05:54+11:00 2010-06-15T09:23:37+10:00 "Currently when anuga is run in parallel there is one sww file for each node used. this results in many small sww files and makes it difficult to trouble shoots issues, view results, export results and make visualations it would be very useful to have all the final sww files joined together into one complete sww file." Nick 115 Problem with file_boundary using a boundary sww file with no origin Functionality and features defect normal high ole closed 2006-11-20T15:25:47+11:00 2007-02-05T15:42:52+11:00 "There seems to be a problem loading a file boundary using File_boundary if the origin of the boundary has not been set. For example using the below urs2sww (in build_dampier.py) ----------------------- from anuga.shallow_water.data_manager import urs2sww from caching import cache cache(urs2sww, (boundaries_in_dir_name, project.boundaries_dir_name1), {'verbose': True, 'minlat': project.south_boundary, 'maxlat': project.north_boundary, 'minlon': project.west_boundary, 'maxlon': project.east_boundary, 'mint': 0, 'maxt': 35000, # 'origin': domain.geo_reference.get_origin(), 'mean_stage': project.tide, 'fail_on_NaN': False}, verbose = True, ) -------------------- *** a sww file is created, here is the call to load and interpolate ---------------- Bf = File_boundary(project.boundaries_dir_name1 + '.sww', domain, time_thinning=5, use_cache=True, verbose=True) -------------------- *** here are the results... note the 'inf' in the interpolated results ------------------- Caching: looking for cached files /d/cit/1/cit/unixhome/nbartzis/.python_cache/_file_function[5361887147248772811]_{Result,Args,Admin}.z +------------------------------------------------------------- | Tue Nov 21 01:33:32 2006. Evaluating function _file_function +------------------------------------------------------------- | Argument: '/d/xrd/gem/2/ramp/risk_assessment_methods_project/inundation/data/western_australia/dampier_tsunami_scenario_2006/anuga/boundaries/... | Keyword Args: {'quantities': None, 'domain': Mesh: 102684 vertices, 204683 triangles, 683 boundary segments, 'interpolation_points': Array: (683, ... | Reason: No cached result +------------------------------------------------------------- Reading /d/xrd/gem/2/ramp/risk_assessment_methods_project/inundation/data/western_australia/dampier_tsunami_scenario_2006/anuga/boundaries/dampiertest.sww File_function data obtained from: /d/xrd/gem/2/ramp/risk_assessment_methods_project/inundation/data/western_australia/dampier_tsunami_scenario_2006/anuga/boundaries/dampiertest.sww References: Lower left corner: [412922.456514, 7677626.654401] Start time: 0.000000 Building interpolation matrix from source mesh (780 vertices, 1450 triangles) FitInterpolate: Building mesh FitInterpolate: Building quad tree Interpolating (683 interpolation points, 1400 timesteps). Timesteps were thinned by a factor of 5 time step 0 of 1400 time step 141 of 1400 time step 282 of 1400 time step 423 of 1400 time step 564 of 1400 time step 705 of 1400 time step 846 of 1400 time step 987 of 1400 time step 1128 of 1400 time step 1269 of 1400 ------------------------------------------------ Interpolation_function (spatio-temporal) statistics: Extent: x in [0.000000, 101006.776851], len(x) == 780 y in [0.000000, 92448.178132], len(y) == 780 t in [0.000000, 34975.000000], len(t) == 1400 Quantities: stage in [-4.912385, 8.462469] xmomentum in [-92.791469, 84.464149] ymomentum in [-100.180145, 107.720670] Interpolation points (xi, eta): number of points == 683 xi in [12293.138000, 104455.822670] eta in [9282.735912, 83226.491136] Interpolated quantities (over all timesteps): stage at interpolation points in [-0.033441, inf] xmomentum at interpolation points in [-28.994856, inf] ymomentum at interpolation points in [-53.002702, inf] ------------------------------------------------ +------------------------------------------------------- | Tue Nov 21 04:30:21 2006. Caching statistics (storing) +------------------------------------------------------- | Function: _file_function | Argument: '/d/xrd/gem/2/ramp/risk_assessment_methods_project/inundation/data/western_australia/dampier_tsunami_scenario_2006/anuga/boundaries/... | Keyword Args: {'quantities': None, 'domain': Mesh: 102684 vertices, 204683 triangles, 683 boundary segments, 'interpolation_points': Array: (683, ... | Reason: No cached result | CPU time: 10580.57 seconds | Loading time: 3.06 seconds (estimated) | | Caching dir: /d/cit/1/cit/unixhome/nbartzis/.python_cache/ | Result file: _file_function[5361887147248772811]_Result (22983934 bytes) | Args file: _file_function[5361887147248772811]_Args (138438149 bytes) | Admin file: _file_function[5361887147248772811]_Admin (684 bytes) | | Dependencies: | /d/xrd/gem/2/ramp/risk_assessment_methods_project/inundation/data/western_australia/dampier_tsunami_scenario_2006/anuga/boundaries/dampiertest.sww: Tue Nov 21 00:44:32 2006 131139736 bytes +------------------------------------------------------- finished reading boundary file set_boundary finish set boundary Time = 0.0000, steps=0 (0) Boundary values at time 0.0000: ocean: stage in [ 2.40000000, inf] xmomentum in [ 0.00000000, inf] ymomentum in [ 0.00000000, inf] ---------------- *** no error is thrown until 'evolve' -------------------- Traceback (most recent call last): File ""run_dampier.py"", line 244, in ? for t in domain.evolve(yieldstep = 120, finaltime = 9000): File ""/d/cit/1/cit/unixhome/nbartzis/anuga/anuga_core/source/anuga/shallow_water/shallow_water_domain.py"", line 461, in evolve skip_initial_step=skip_initial_step): File ""/d/cit/1/cit/unixhome/nbartzis/anuga/anuga_core/source/anuga/abstract_2d_finite_volumes/domain.py"", line 792, in evolve self.distribute_to_vertices_and_edges() File ""/d/cit/1/cit/unixhome/nbartzis/anuga/anuga_core/source/anuga/shallow_water/shallow_water_domain.py"", line 374, in distribute_to_vertices_and_edges distribute_to_vertices_and_edges(self) File ""/d/cit/1/cit/unixhome/nbartzis/anuga/anuga_core/source/anuga/shallow_water/shallow_water_domain.py"", line 953, in distribute_to_vertices_and_edges balance_deep_and_shallow(domain) File ""/d/cit/1/cit/unixhome/nbartzis/anuga/anuga_core/source/anuga/shallow_water/shallow_water_domain.py"", line 1205, in balance_deep_and_shallow_c hc = wc - zc OverflowError: math range error ------------------------------------ *** NOW if you use this urs2sww the interpolated results are correct and the evolvtion works perfectly Furthermore here are the directories that contain the actual code used T:\data\western_australia\dampier_tsunami_scenario_2006\anuga\outputs\20061121_001525_build T:\data\western_australia\dampier_tsunami_scenario_2006\anuga\outputs\20061121_012318_run" Nick 116 Change the 'xya' file type in anuga to 'txt' Functionality and features defect normal normal duncan closed 2006-11-20T16:17:25+11:00 2007-01-10T10:48:18+11:00 "the 'xya' file format should be changed to a 'txt' extension and have a header that contains all column info not just the 'attribute'... this would make the ascii file format for anuga and geospatial_data object more usable" Nick 117 test_asc_csiro2sww, test_asc_csiro2sww3, test_asc_csiro2sww4 are failing Testing and validation defect normal normal ole closed 2006-11-21T20:27:32+11:00 2006-11-24T14:30:00+11:00 "Observed at revision 4025. I have no experience with the data manager, so someone who does should look at this and email me if there's more information needed. The unit test messages are below: ====================================================================== FAIL: test_asc_csiro2sww (test_data_manager.Test_Data_Manager) ---------------------------------------------------------------------- Traceback (most recent call last): File ""shallow_water/test_data_manager.py"", line 3476, in test_asc_csiro2sww asc_csiro2sww(bath_dir,elevation_dir, ucur_dir, vcur_dir, sww_file) File ""shallow_water/data_manager.py"", line 3654, in asc_csiro2sww assert elevation_files[0] == 'el' + base_start AssertionError ====================================================================== FAIL: test_asc_csiro2sww3 (test_data_manager.Test_Data_Manager) ---------------------------------------------------------------------- Traceback (most recent call last): File ""shallow_water/test_data_manager.py"", line 3784, in test_asc_csiro2sww3 mean_stage = 100) File ""shallow_water/data_manager.py"", line 3654, in asc_csiro2sww assert elevation_files[0] == 'el' + base_start AssertionError ====================================================================== FAIL: test_asc_csiro2sww4 (test_data_manager.Test_Data_Manager) ---------------------------------------------------------------------- Traceback (most recent call last): File ""shallow_water/test_data_manager.py"", line 3975, in test_asc_csiro2sww4 minlon = 148.3, maxlon = 148.3 File ""shallow_water/data_manager.py"", line 3654, in asc_csiro2sww assert elevation_files[0] == 'el' + base_start AssertionError ---------------------------------------------------------------------- " jack 118 overflow error in geospatial data - on cyclone compute nodes Functionality and features defect normal low nick closed 2006-11-22T11:13:24+11:00 2006-11-27T13:36:03+11:00 "doing a test all on cyclone nodes (node 20 and 15), I get the following error; {{{ WARNING: File test_advection.py to be excluded from testing ..............................................................E................. ................................................................................ ................................................................................ ................................................................................ ................................................................................ ............................................................sh: line 1: svn: com mand not found ................................................................................ .................................................. ====================================================================== ERROR: test if the results from spilt are disjoin sets ---------------------------------------------------------------------- Traceback (most recent call last): File ""geospatial_data/test_geospatial_data.py"", line 1647, in test_split G1, G2 = G.split(factor) #will return G1 with 10% for points and G2 with 90 % File ""/d/cit/1/dgray/sandpit/anuga/anuga_core/source/anuga/geospatial_data/geo spatial_data.py"", line 643, in split remainder_list.pop(i) OverflowError: long int too large to convert to int ---------------------------------------------------------------------- Ran 590 tests in 55.476s }}} I don't get the error on the head node though (or anywhere else). " duncan 119 unhashable type error on runcairns Testing and validation defect normal normal ole closed 2006-12-13T11:36:24+11:00 2009-09-10T16:01:34+10:00 "I tried to run runcairns.py from the demos. I get the following error: Traceback (most recent call last): File ""runcairns.py"", line 93, in ? domain = Domain(meshname, use_cache = True, verbose = True) File ""/home/steve/ga/anuga_core/source/anuga/shallow_water/shallow_water_domain.py"", line 146, in __init__ number_of_full_triangles=number_of_full_triangles) File ""/home/steve/ga/anuga_core/source/anuga/abstract_2d_finite_volumes/domain.py"", line 86, in __init__ verbose=verbose) File ""/home/steve/ga/anuga_core/source/anuga/abstract_2d_finite_volumes/pmesh2domain.py"", line 146, in pmesh_to_domain verbose = verbose) File ""/home/steve/ga/anuga_core/source/anuga/caching/caching.py"", line 349, in cache T = apply(func,args,kwargs) File ""/home/steve/ga/anuga_core/source/anuga/abstract_2d_finite_volumes/pmesh2domain.py"", line 179, in _pmesh_to_domain tag_dict = pmesh_dict_to_tag_dict(mesh_dict) File ""/home/steve/ga/anuga_core/source/anuga/abstract_2d_finite_volumes/pmesh2domain.py"", line 204, in pmesh_dict_to_tag_dict sides = calc_sides(triangles) File ""/home/steve/ga/anuga_core/source/anuga/abstract_2d_finite_volumes/pmesh2domain.py"", line 228, in calc_sides sides[a,b] = (id, 2) #(id, face) TypeError: unhashable type " steve 120 "Make ""set_quantity"" read in blocks of file into memory and not the entire file. " Efficiency and optimisation defect normal normal duncan closed 2006-12-14T16:53:04+11:00 2007-01-15T15:19:29+11:00 "Currently domain.set_quantity is very slow... especial as we are getting bigger and more detail elevation files. When a large file (greater 200 Meg) is loaded with set_quantity the CPU with start using swap very quickly and the CPU drops to less that 10% :( And loading a 700M file is taking ages.... 10hours? especially bad as everytime the mesh changes this is recalculated Also can this style of loading a file be applied to the file_boundary " nick 121 changeset:4107 broke validation test Appearance and visualisation defect major highest duncan closed 2006-12-21T12:08:46+11:00 2006-12-28T18:35:39+11:00 Reference to names was removed in changeset:4107 and the Qkushiri island validation does not run anymore. ole 122 problem unit testing using enthon-python2.4-1.0.0.exe Testing and validation defect minor low ole closed 2007-01-03T11:58:58+11:00 2009-09-04T12:30:01+10:00 "When unit testing using enthon-python2.4-1.0.0.exe the following error is thrown; Ran 594 tests in 48.720s OK Error in atexit._run_exitfuncs: Traceback (most recent call last): File ""C:\Python24\lib\atexit.py"", line 24, in _run_exitfuncs func(*targs, **kargs) File ""C:\Python24\lib\logging\__init__.py"", line 1333, in shutdown h.close() File ""C:\Python24\lib\logging\__init__.py"", line 674, in close del _handlers[self] KeyError: Error in sys.exitfunc: Traceback (most recent call last): File ""C:\Python24\lib\atexit.py"", line 24, in _run_exitfuncs func(*targs, **kargs) File ""C:\Python24\lib\logging\__init__.py"", line 1333, in shutdown h.close() File ""C:\Python24\lib\logging\__init__.py"", line 674, in close del _handlers[self] KeyError: __________________________________________________________ It's not really an ANUGA error, but it's good to keep track of." duncan 123 python24.dll not installed with enthought Compilation and installation defect normal low ole closed 2007-01-08T16:06:49+11:00 2007-10-29T14:47:45+11:00 "i followed the instructions to the letter in the installation instructions and when i compiled it had an error ""python24.dll file not found"". I'm installing it on a freshy built dell laptop D810 with Win2000 i copied ""python24.dll"" from my desktop and then it was fine" nick 124 swallow_water.util.get_version_info doesn't work in Linux Functionality and features defect minor low ole closed 2007-01-09T10:37:17+11:00 2007-01-10T14:26:25+11:00 "I have put an ""if"" statement to stop the error msg when running the tests on Linux def test_get_version_info(self): if sys.platform == 'win32': info = get_version_info() assert info.startswith('Revision') this should be fixed in the future" nick 125 Get version info Compilation and installation defect normal normal ole closed 2007-01-10T18:08:00+11:00 2007-01-11T14:44:33+11:00 "Change get_version info to use values stored in a file failing 'svn info' Also change create_version info so that such a file is created as well as using currently checked out version for release. See FIXME's in util.py and create_release.py " ole 126 Validate_okushiri unit test fails Functionality and features defect major highest ole closed 2007-01-11T10:17:19+11:00 2007-03-29T17:57:37+10:00 "Auto validation fails with the following error message (in revision 4168). It worked yesterday 10th of January. cd ./okushiri_tank_validation; python validate_okushiri.py test_that_output_is_as_expected (__main__.Test_Okushiri) ... Traceback (most recent call last): File ""run_okushiri.py"", line 50, in ? use_cache=True) File ""/home/ole/inundation/anuga_core/source/anuga/abstract_2d_finite_volumes/domain.py"", line 330, in set_quantity self.quantities[name].set_values(*args, **kwargs) File ""/home/ole/inundation/anuga_core/source/anuga/abstract_2d_finite_volumes/quantity.py"", line 361, in set_values use_cache = use_cache) File ""/home/ole/inundation/anuga_core/source/anuga/abstract_2d_finite_volumes/quantity.py"", line 747, in set_values_from_file verbose=verbose) File ""/home/ole/inundation/anuga_core/source/anuga/fit_interpolate/fit.py"", line 490, in fit_to_mesh verbose=verbose) File ""/home/ole/inundation/anuga_core/source/anuga/fit_interpolate/fit.py"", line 329, in fit load_file_now=False)): File ""/home/ole/inundation/anuga_core/source/anuga/geospatial_data/geospatial_data.py"", line 720, in next max_read_lines=self.max_read_lines) File ""/home/ole/inundation/anuga_core/source/anuga/geospatial_data/geospatial_data.py"", line 834, in _read_csv_file_blocking header.pop(0) IndexError: pop from empty list ERROR ====================================================================== ERROR: test_that_output_is_as_expected (__main__.Test_Okushiri) ---------------------------------------------------------------------- Traceback (most recent call last): File ""validate_okushiri.py"", line 29, in setUp assert res == 0 AssertionError ---------------------------------------------------------------------- Ran 1 test in 61.172s FAILED (errors=1) " ole 127 Some codes in the Examples directory don't work Functionality and features defect minor normal Ole closed 2007-01-11T11:30:06+11:00 2007-06-08T16:09:00+10:00 "User's downloading ANUGA complain that some examples (such as rungong.py, twolevels.py, etc) don't work. Maybe we should move them to anuga_work?" ole 128 okushiri validation fails Testing and validation defect normal normal Ole closed 2007-01-12T12:06:55+11:00 2007-02-07T10:11:12+11:00 "This is more about system setup. {{{ dgray@cyclone:~/sandpit/anuga/anuga_validation/automated_validation_tests$ python validate_all.py Skipping . Searching dir ./okushiri_tank_validation Found validate_okushiri.py in ./okushiri_tank_validation cd ./okushiri_tank_validation; python validate_okushiri.py test_that_output_is_as_expected (__main__.Test_Okushiri) ... Traceback (most recent call last): File ""run_okushiri.py"", line 29, in ? from anuga_parallel.parallel_api import myid, numprocs, distribute File ""/d/cit/1/dgray/sandpit/anuga/anuga_core/source/anuga_parallel/parallel_api.py"", line 23, in ? from anuga_parallel.pmesh_divide import pmesh_divide_metis File ""/d/cit/1/dgray/sandpit/anuga/anuga_core/source/anuga_parallel/pmesh_divide.py"", line 88, in ? from pymetis.metis import partMeshNodal ImportError: No module named metis ERROR ====================================================================== ERROR: test_that_output_is_as_expected (__main__.Test_Okushiri) ---------------------------------------------------------------------- Traceback (most recent call last): File ""validate_okushiri.py"", line 29, in setUp assert res == 0 AssertionError ---------------------------------------------------------------------- Ran 1 test in 5.783s }}} " duncan 129 Developer installation guide. Documentation defect normal normal Ole closed 2007-01-12T12:10:50+11:00 2009-09-11T09:44:07+10:00 A new guide or a section in the current installation guide would be useful for documenting things that are needed to get the development version of ANUGA working. For example, how to get the svn_version stuff to work, as well as parallisation and the new visualiser. duncan 130 Okushiri auto validation unit test broken on cyclone Testing and validation defect normal normal ole closed 2007-01-17T17:40:53+11:00 2007-03-29T17:58:46+10:00 "This unit test fails at present (17th January). When I tried revision 3929 it worked. We need to bisect to find out when it stopped working" ole 131 Fit to mesh take a lot longer than it used to Efficiency and optimisation defect normal high duncan closed 2007-02-02T15:21:37+11:00 2007-02-09T18:05:55+11:00 "I have run Okushiri using the versions 4106 and the more recent Setting the elevation data takes a lot longer than it used to - even when caching is used. Running version 4106 without caching is still lots faster than the new version . Output from version 4106 looks like this: =========================================== {{{ Mesh: Building neigbour structure Mesh: Building surrogate neigbour structure Mesh: Building boundary dictionary Mesh: Building tagged elements dictionary Mesh: Done Initialising Domain Domain: Set up communication buffers (parallel) Domain: Initialising quantity values Domain: Done ------------------------------------------------ Mesh statistics: Number of triangles = 56479 Extent [m]: x in [0.000000, 5.448000] y in [0.000000, 3.402000] Areas [m^2]: A in [0.000004, 0.096541] number of distinct areas: 56479 Histogram: [0.000004, 0.009657[: 56246 [0.009657, 0.019311[: 55 [0.019311, 0.028965[: 23 [0.028965, 0.038619[: 9 [0.038619, 0.048272[: 26 [0.048272, 0.057926[: 32 [0.057926, 0.067580[: 24 [0.067580, 0.077234[: 32 [0.077234, 0.086887[: 16 [0.086887, 0.096541]: 16 Percentiles (10%): 5647 triangles in [0.000004, 0.000010] 5647 triangles in [0.000010, 0.000012] 5647 triangles in [0.000012, 0.000014] 5647 triangles in [0.000014, 0.000016] 5647 triangles in [0.000016, 0.000080] 5647 triangles in [0.000080, 0.000112] 5647 triangles in [0.000112, 0.000141] 5647 triangles in [0.000141, 0.000190] 5647 triangles in [0.000190, 0.000320] 5647 triangles in [0.000320, 0.089484] 9 triangles in [0.089484, 0.096541] Boundary: Number of boundary segments == 99 Boundary tags == ['wall', 'wave'] ------------------------------------------------ Using attribute attribute from file Benchmark_2_Bathymetry.pts Available attributes: ['attribute'] Caching: looking for cached files /home/ole/.python_cache/fit_to_mesh[-47538529]_{Result,Args,Admin}.z +---------------------------------------------------------- | Fri Feb 2 22:25:59 2007. Caching statistics (retrieving) +---------------------------------------------------------- | Function: fit_to_mesh | Arguments: (Array: (28290, 2), Array: (56479, 3), Array: (95892, 2), Array: (95892,)) | Keyword Args: {'alpha': 0.02, 'mesh_origin': (-1, 0.0, 0.0), 'verbose': True, 'data_origin': (-1, 0.0, 0.0)} | CPU time: 656.89 seconds | Loading time: 0.0 seconds | Time saved: 656.89 seconds | | Caching dir: /home/ole/.python_cache/ | Result file: fit_to_mesh[-47538529]_Result (226372 bytes) | Args file: fit_to_mesh[-47538529]_Args (3432060 bytes) | Admin file: fit_to_mesh[-47538529]_Admin (1564 bytes) | | No dependencies +---------------------------------------------------------- Reading Benchmark_2_input.tms File_function data obtained from: Benchmark_2_input.tms References: Start time: 0.000000 }}} ==================================================== Where's the new version with blocking takes forever and looks like this =================================================== {{{ Mesh: Building neigbour structure Mesh: Building surrogate neigbour structure Mesh: Building boundary dictionary Mesh: Building tagged elements dictionary Mesh: Done Initialising Domain Domain: Set up communication buffers (parallel) Domain: Initialising quantity values Domain: Done ------------------------------------------------ Mesh statistics: Number of triangles = 56541 Extent [m]: x in [0.000000, 5.448000] y in [0.000000, 3.402000] Areas [m^2]: A in [0.000007, 0.099799] number of distinct areas: 56541 Histogram: [0.000007, 0.009986[: 56321 [0.009986, 0.019965[: 46 [0.019965, 0.029945[: 21 [0.029945, 0.039924[: 7 [0.039924, 0.049903[: 25 [0.049903, 0.059882[: 38 [0.059882, 0.069861[: 32 [0.069861, 0.079841[: 27 [0.079841, 0.089820[: 16 [0.089820, 0.099799]: 8 Percentiles (10%): 5654 triangles in [0.000007, 0.000010] 5654 triangles in [0.000010, 0.000012] 5654 triangles in [0.000012, 0.000014] 5654 triangles in [0.000014, 0.000016] 5654 triangles in [0.000016, 0.000080] 5654 triangles in [0.000080, 0.000112] 5654 triangles in [0.000112, 0.000142] 5654 triangles in [0.000142, 0.000191] 5654 triangles in [0.000191, 0.000319] 5654 triangles in [0.000319, 0.099799] 1 triangles in [0.099799, 0.099799] Boundary: Number of boundary segments == 95 Boundary tags == ['wall', 'wave'] ------------------------------------------------ Caching: looking for cached files c:\.python_cache\_fit[-2051356540]_{Result,Args,Admin}.z +---------------------------------------------------------- | Fri Feb 02 14:45:01 2007. Caching statistics (retrieving) +---------------------------------------------------------- | Function: _fit | Arguments: (Array: (28319, 2), Array: (56541, 3)) | Keyword Args: {'alpha': 0.02, 'mesh_origin': None, 'verbose': True} | CPU time: 137.47 seconds | Loading time: 1.64 seconds | Time saved: 135.83 seconds | | Caching dir: c:\.python_cache\ | Result file: _fit[-2051356540]_Result.z (11208238 bytes, compressed) | Args file: _fit[-2051356540]_Args.z (712707 bytes, compressed) | Admin file: _fit[-2051356540]_Admin.z (167 bytes, compressed) | | No dependencies +---------------------------------------------------------- Got 1 variables: ['attribute'] Doing 0 of 95902 Block 0 Reading Benchmark_2_input.tms File_function data obtained from: Benchmark_2_input.tms References: Start time: 0.000000 Time = 0.0000, steps=0 (0) }}} =================================================== At this point 'Block 0' is was hanging for more than 30 minutes while I was able to run version 4106 twice both with and without caching. " ole 132 set mean_stage after the sww boundary file is created. Efficiency and optimisation enhancement normal normal ole closed 2007-03-05T16:32:41+11:00 2007-03-22T12:18:11+11:00 "If mean_stage could be set after the sww boundary file is created it would mean we mouldn't have to create a new sww file for each tide level. These sww files are big. " Duncan 133 automatic validation only works on Nautilus Testing and validation defect normal low Ole closed 2007-03-14T14:17:55+11:00 2007-03-30T12:35:51+10:00 "Hi, Automatic validation works on Nautilus for version 4262. It does not work on my windows box or tornado. This is sorta ok with me, but I know if it's documented." duncan 134 Problem with URS data?, momentum or conversion problem Functionality and features defect normal high duncan closed 2007-03-21T11:26:59+11:00 2007-04-16T10:08:48+10:00 "Looking at this point (469000.00,7759900.00,0) which is located 100m from the ANUGA model boundary in 40m of water and it is not near any land, plus the water depth in both the URS and ANUGA models are every similar. The stage height and momentum at this point were compare from the boundary sww file created by URS data (\\Gneiss\gem5nhi\inundation\data\western_australia\dampier_tsunami_scenario_2006\anuga\boundaries\o_test_8500_12000.sww) and a very simple ANUGA model (\\Gneiss\gem5nhi\inundation\data\western_australia\dampier_tsunami_scenario_2006\anuga\outputs\20070311_225041_run\dampier.sww) that has only the URS data as boundary conditions and they are very similar. However it seems that the momentum (in particular the y momentum) from the URS data and therefore the ANUGA model is travelling towards the north instead of towards the south. In another simple ANUGA model (\\Gneiss\gem5nhi\inundation\data\western_australia\dampier_tsunami_scenario_2006\anuga\outputs\20070312_005351_run\dampier.sww), this time with a URS boundary on the north edge and on the southern edges there is no time varying input wave just Dirichlet condition at the tide height. This simple ANUGA model represents the basic model used for tsunami inundation in this region where the source is towards the north and travels to the coast towards in the south. The comparison shows that the stage height to be significantly different between models at this point. The time series plot from the URS boundary file has a 2 meter wave on top of the tide height and where the ANUGA model has only a 0.3m wave on top on the tide. The momentum is also significantly reduced. I believe this shows that the input wave from the URS data is not correct. After many tests of different parts of ANUGA i'm pretty certain that the problem is not the reading of the boundary sww file, or the interpolation to the model boundary or how the model is tagged with certain boundaries or the evolution of the ANUGA model. What also confirm is the momentum is definite going to the north where other MOST boundary condition for a similar event has the momentum heading south. " nick 135 Optimise compute_fluxes when quantities are equal on either side Efficiency and optimisation defect normal normal ole closed 2007-03-29T17:54:06+10:00 2007-10-30T16:23:42+11:00 "I think we could get ANUGA to run faster if we only compute fluxes where there is a non-zero gradient in one or more quantities." ole 136 Allow max inundation level to apply to polygons only Architecture and API defect normal high ole closed 2007-04-02T11:23:28+10:00 2009-09-04T12:17:53+10:00 Rosh Ranasinghe needs this for his convergence study. ole 137 test_caching crashes Testing and validation defect normal lowest ole closed 2007-04-16T14:40:56+10:00 2012-02-13T13:57:48+11:00 "I got this error when running anuga_core\source\anuga\test_all.py in Windows. (Note, not the standard test_all.py) {{{ Traceback (most recent call last): File ""test_all.py"", line 100, in ? suite = regressionTest() File ""test_all.py"", line 88, in regressionTest modules = map(__import__, moduleNames) File ""caching\test_caching.py"", line 419, in ? clear_and_create_cache(Dummy_memorytest, verbose=False) File ""caching\test_caching.py"", line 36, in clear_and_create_cache verbose=verbose) File ""I:\inundation\anuga_core\source\anuga\caching\caching.py"", line 360, in cache funcname, dependencies, compression) File ""I:\inundation\anuga_core\source\anuga\caching\caching.py"", line 1074, in save_results_to_cache mysave(T,datafile,compression) # Save data to cache File ""I:\inundation\anuga_core\source\anuga\caching\caching.py"", line 1266, in mysave Ts = pickler.dumps(T, bin) cPickle.PicklingError: Can't pickle test_caching.Dummy_memorytest: import of mod ule test_caching failed }}} " duncan 138 one problem with caching Efficiency and optimisation defect major normal rwilson closed 2007-04-17T10:53:54+10:00 2009-09-10T16:03:53+10:00 "this problem is hard to track as it seems to disappear when you simplify the problem. I will explain the situation Model 1 (low res mesh, res_factor=2) see \inundation\data\western_australia\dampier_tsunami_scenario_2006\anuga\outputs\20070416_231316_run the interesting part is the number of triangle in the mesh see ""screen_output_0_2.txt"" for details, there is 254859 triangles Model 2(high res mesh, res_factor=1) see J:\inundation\data\western_australia\dampier_tsunami_scenario_2006\anuga\outputs\20070417_000545_run there is 499366 triangles only difference between the 2 models is the ""res_factor"" in the project.py file Now running Model 1 again using the exactly same files as before. see J:\inundation\data\western_australia\dampier_tsunami_scenario_2006\anuga\outputs\20070417_102354_run The model retrieves cached results of the wrong mesh resolution, producing 499366 triangles I have tried to simplify the problem but it seems to change. This is not the first time this has occurred and is very frustrating. Can someone please try and replicate this." nick 139 Model seems to die with dampier runs on cyclone, using 8 processors Functionality and features defect critical low duncan closed 2007-04-18T12:33:46+10:00 2009-09-04T12:28:43+10:00 "I have this model J:\inundation\data\western_australia\dampier_tsunami_scenario_2006\anuga\outputs\20070418_014035_run and the run dies in FitInterpolate, no error is caught by the python code but the screen output is in ""screen_output_0_8.txt"" It was run in parallel on cyclone and here is the error message from the commandline --------------------- One of the processes started by mpirun has exited with a nonzero exit code. This typically indicates that the process finished in error. If your process did not finish in error, be sure to include a ""return 0"" or ""exit(0)"" in your C code before exiting the application. PID 23136 failed on node n11 (192.168.255.242) due to signal 9. ------------------------ I have run the same model again in J:\inundation\data\western_australia\dampier_tsunami_scenario_2006\anuga\outputs\20070418_020329_run and it fails in the same spot Please Help " nick 140 I can't remember how to compile metis Appearance and visualisation defect normal normal anonymous closed 2007-04-18T16:29:27+10:00 2007-04-20T15:32:09+10:00 if the .so for metis isn't in X:\anuga_core\source\pymetis parallel codes crash. I always forget how to compile this guy. Catch the import error and give directions on when the README file to compile this is. Duncan 141 Problem with parallel code in Field_boundary (Interpolation_function) Functionality and features defect major high duncan closed 2007-04-20T15:28:55+10:00 2007-04-20T15:47:29+10:00 "I have run similar code in parallel on both Tornado and cyclone and they die at the same place. J:\inundation\data\western_australia\dampier_tsunami_scenario_2006\anuga\outputs\20070419_161713_run This is the tornado run on 8 cpus, using ""mpirun c40-47 python run_dampier.py"" All cpus fail at the same point. ------------------------------------- starting to create boundary conditions Setup initial conditions Start Set quantity Caching: looking for cached files /d/cit/1/cit/unixhome/nbartzis/.python_cache/_fit_to_mesh[4973251167741820141]_{Result,Args,Admin}.z +---------------------------------------------------------- | Thu Apr 19 16:22:11 2007. Caching statistics (retrieving) +---------------------------------------------------------- | Function: _fit_to_mesh | Arguments: (Array: (171482, 2), Array: (342366, 3), '/d/xrd/gem/5/nhi/inundation/data/western_australia/dampier_tsunami_scenario_2006/anuga/topographies/dampier_combined_elevation.txt') | Keyword Args: {'point_attributes': None, 'use_cache': True, 'attribute_name': None, 'verbose': True, 'max_read_lines': 500, 'acceptable_overshoot': 1.01, 'mesh_origin': None, 'alpha': 0.1, 'data_origin': None} | CPU time: 66649.26 seconds | Loading time: 0.1 seconds | Time saved: 66649.16 seconds | | Caching dir: /d/cit/1/cit/unixhome/nbartzis/.python_cache/ | Result file: _fit_to_mesh[4973251167741820141]_Result (1371910 bytes) | Args file: _fit_to_mesh[4973251167741820141]_Args (10960903 bytes) | Admin file: _fit_to_mesh[4973251167741820141]_Admin (1620 bytes) | | No dependencies +---------------------------------------------------------- Finished Set quantity Subdivide mesh Build submeshes There are 323 ghost nodes and 630 ghost triangles on proc 0 There are 201 ghost nodes and 394 ghost triangles on proc 1 There are 179 ghost nodes and 358 ghost triangles on proc 2 There are 312 ghost nodes and 636 ghost triangles on proc 3 There are 141 ghost nodes and 271 ghost triangles on proc 4 There are 271 ghost nodes and 562 ghost triangles on proc 5 There are 269 ghost nodes and 546 ghost triangles on proc 6 There are 277 ghost nodes and 545 ghost triangles on proc 7 Distribute submeshes process 0 sending submesh to process 1 process 0 sending submesh to process 2 process 0 sending submesh to process 3 process 0 sending submesh to process 4 process 0 sending submesh to process 5 process 0 sending submesh to process 6 process 0 sending submesh to process 7 domain id 183276205480 domain id 183276205480 Available boundary tags ['ghost'] domain id 183276205480 Find midpoint coordinates of entire boundary Initialise file_function Caching: looking for cached files /d/cit/1/cit/unixhome/nbartzis/.python_cache/_file_function[-4478828065918996396]_{Result,Args,Admin}.z +------------------------------------------------------------- | Thu Apr 19 16:26:23 2007. Evaluating function _file_function +------------------------------------------------------------- | Argument: '/d/xrd/gem/5/nhi/inundation/data/western_australia/dampier_tsunami_scenario_2006/anuga/boundaries/o_5000_35000.sww' | Keyword Args: {'quantities': ['stage', 'xmomentum', 'ymomentum'], 'interpolation_points': Array: (518, 2), 'time_thinning': 1, 'domain_starttime': 0, 'verbose': True} | Reason: No cached result +------------------------------------------------------------- Reading /d/xrd/gem/5/nhi/inundation/data/western_australia/dampier_tsunami_scenario_2006/anuga/boundaries/o_5000_35000.sww File_function data obtained from: /d/xrd/gem/5/nhi/inundation/data/western_australia/dampier_tsunami_scenario_2006/anuga/boundaries/o_5000_35000.sww References: Lower left corner: [419902.228863, 7683195.214508] Start time: 5000.000000 --------------------------------------- J:\inundation\data\western_australia\dampier_tsunami_scenario_2006\anuga\outputs\20070417_021606_run This is the cyclone run on 8 cpus, using ""mpirun c20-27 python run_dampier.py"". There was a print statement in the code that has been removed that wrote that the last ""before interpolation function1"" (i think there was two more print line before interpolation function, but don't quote me on that) One funny thing is that 4 of the processes in this model actucally pass this part of the code. ----------------------- +------------------------------------------------------- | Tue Apr 17 20:52:53 2007. Caching statistics (storing) +------------------------------------------------------- | Function: _fit_to_mesh | Arguments: (Array: (171482, 2), Array: (342366, 3), '/d/xrd/gem/5/nhi/inundation/data/western_australia/dampier_tsunami_scenario_2006/anuga/topographies/dampier_combined_elevation.txt') | Keyword Args: {'point_attributes': None, 'use_cache': True, 'attribute_name': None, 'verbose': True, 'max_read_lines': 500, 'acceptable_overshoot': 1.01, 'mesh_origin': None, 'alpha': 0.1, 'data_origin': None} | Reason: No cached result | CPU time: 66649.26 seconds | Loading time: 0.18 seconds (estimated) | | Caching dir: /d/cit/1/cit/unixhome/nbartzis/.python_cache/ | Result file: _fit_to_mesh[4973251167741820141]_Result (1371910 bytes) | Args file: _fit_to_mesh[4973251167741820141]_Args (10960903 bytes) | Admin file: _fit_to_mesh[4973251167741820141]_Admin (1620 bytes) | | No dependencies +------------------------------------------------------- Finished Set quantity Subdivide mesh Build submeshes There are 323 ghost nodes and 630 ghost triangles on proc 0 There are 201 ghost nodes and 394 ghost triangles on proc 1 There are 179 ghost nodes and 358 ghost triangles on proc 2 There are 312 ghost nodes and 636 ghost triangles on proc 3 There are 141 ghost nodes and 271 ghost triangles on proc 4 There are 271 ghost nodes and 562 ghost triangles on proc 5 There are 269 ghost nodes and 546 ghost triangles on proc 6 There are 277 ghost nodes and 545 ghost triangles on proc 7 Distribute submeshes process 0 sending submesh to process 1 process 0 sending submesh to process 2 process 0 sending submesh to process 3 process 0 sending submesh to process 4 process 0 sending submesh to process 5 process 0 sending submesh to process 6 process 0 sending submesh to process 7 domain id 183904840592 domain id 183904840592 Available boundary tags ['ghost'] domain id 183904840592 Find midpoint coordinates of entire boundary Initialise file_function Caching: looking for cached files /d/cit/1/cit/unixhome/nbartzis/.python_cache/_file_function[-4478816493114003663]_{Result,Args,Admin}.z +------------------------------------------------------------- | Tue Apr 17 20:58:43 2007. Evaluating function _file_function +------------------------------------------------------------- | Argument: '/d/xrd/gem/5/nhi/inundation/data/western_australia/dampier_tsunami_scenario_2006/anuga/boundaries/o_5000_35000.sww' | Keyword Args: {'quantities': ['stage', 'xmomentum', 'ymomentum'], 'interpolation_points': Array: (518, 2), 'time_thinning': 12, 'domain_starttime': 0, 'verbose': True} | Reason: No cached result +------------------------------------------------------------ Reading /d/xrd/gem/5/nhi/inundation/data/western_australia/dampier_tsunami_scenario_2006/anuga/boundaries/o_5000_35000.sww File_function data obtained from: /d/xrd/gem/5/nhi/inundation/data/western_australia/dampier_tsunami_scenario_2006/anuga/boundaries/o_5000_35000.sww References: Lower left corner: [419902.228863, 7683195.214508] Start time: 5000.000000 before interpolation function1 --------------------- i will attach the script files to this ticket" nick 142 small change in Data_manager that needs to be checked Functionality and features defect minor normal Duncan closed 2007-04-23T09:08:42+10:00 2007-04-23T16:33:41+10:00 "Hi Dunc This is tiny... But for some reason I was getting this error ---------------- nbartzis@cyclone:~/anuga/anuga_validation/automated_validation_tests/urs_mux_files_validation$ python validate_Bf.py test_compare_URSsww_vs_EvolveANUGAsww (__main__.Test_Bf) ... Traceback (most recent call last): File ""run_Bf.py"", line 99, in ? fail_on_NaN= False) File ""/d/cit/1/cit/unixhome/nbartzis/anuga/anuga_core/source/anuga/shallow_water/data_manager.py"", line 3891, in urs2sww verbose=verbose) File ""/d/cit/1/cit/unixhome/nbartzis/anuga/anuga_core/source/anuga/shallow_water/data_manager.py"", line 2754, in ferret2sww print ' Start time: %f' %starttime NameError: global name 'starttime' is not defined ------------------------ when i ran this code ------------------------ urs2sww(boundaries_dir_name,boundaries_dir_name, mint=9200, maxt= 11200, fail_on_NaN= False, verbose=True) -------------------- I changed data_manager.py line 2754 from print ' Start time: %f' %starttime to print ' Start time: %f' %mint # print ' Start time: %f' %starttime i did have a look in the log for 'data_manager.py' to see if there were any changes and why but couldn't find anything Question: Is this change Ok (all the tests still pass)? and do you know why this problem occured? Can you review this asap? Cheers Nick " nick 143 setting initial conditions using Polygon_function FESA - Karratha Scenario Functionality and features defect major highest duncan closed 2007-04-29T15:16:13+10:00 2007-05-01T13:45:32+10:00 "When setting high tide initial conditions, we want to ensure that onshore areas under the high tide value are not filled with water. The idea is to allow the high tide to be applied in the ocean only and set stage to zero on the land. The following lines in run_dampier.py show how this is done: from polygon import * IC = Polygon_function( [(project.poly_mainland, 0.)], default = tide) domain.set_quantity('stage', IC) However, it doesn't appear to be working - see \\gneiss\gem5nhi\data\western_australia\dampier_tsunami_scenario_2006\anuga\outputs\20070419_065050_run\testIC.ppt I have included the polygon into a test which has been checked in to test_polygon.py. It appears to pass this test. Nick ran another example with default = 200 - see dampier.sww in 20070424_043504_run. " jane.sexton@… 144 Investigate small timesteps induced by 'new' slope limiters AnuGA ready for release Functionality and features defect normal high ole closed 2007-04-30T18:51:49+10:00 2009-09-04T12:16:24+10:00 "Make new slope limiters default. A few unprepared tests remaini and one example in test_data_manager reveal that small timesteps are generated. See changeset:4376 The way forward is to improve the timestepping diagnostics to accumulate min and max values between yieldsteps." ole 145 Forcing function implementing Culverts Functionality and features enhancement normal high ole closed 2007-04-30T18:54:34+10:00 2009-09-04T12:13:42+10:00 "A forcing function that can add and remove water at arbitrary locations may be used to model culvert or pipe flows. This was suggested by Ruby Van Drie and would allow ANUGA to be incorporated in Hydrological modelling, e.g. with the WBNM model. Rudy will visit on 9th of May, so it would be good to have a prototype ready by then." ole 146 unable to browse source via trac Management and planning defect critical highest steve closed 2007-05-01T05:11:39+10:00 2007-05-15T16:17:55+10:00 "{{{ Traceback (most recent call last): File ""/usr/lib/python2.3/site-packages/trac/core.py"", line 531, in cgi_start real_cgi_start() File ""/usr/lib/python2.3/site-packages/trac/core.py"", line 526, in real_cgi_start dispatch_request(path_info, args, req, env) File ""/usr/lib/python2.3/site-packages/trac/core.py"", line 439, in dispatch_request module = module_factory(args, env, database, req) File ""/usr/lib/python2.3/site-packages/trac/core.py"", line 175, in module_factory pool, rep, fs_ptr = open_svn_repos(repos_dir) File ""/usr/lib/python2.3/site-packages/trac/core.py"", line 458, in open_svn_repos rep = repos.svn_repos_open(repos_dir, pool) SubversionException: (""Berkeley DB error while opening 'nodes' table for filesystem /home/svn/ga/db:\nCannot allocate memory"", 160029) }}}" darran 147 Store min and max values of all quantities in sww file Functionality and features enhancement normal normal duncan closed 2007-05-01T10:58:43+10:00 2007-09-19T15:28:57+10:00 "A viewer that colour-codes surfaces based on values of quantities will need the range of each quantities. Otherwise the viewer would have to read the entire sww file everytime it is launched. To alleviate that, I propose that we introduce an array of lenght 2 for each quantity in the sww file which will store the minimal vertex value and the maximal vertex value encountered for all triangles and all timesteps. These should be updated every time a new timestep is stored into the sww file. Example stage_range = [3.1, 10.7] means that vertex values in stage have never been smaller than 3.1 or larger than 10.7 anywhere or anytime so far. The arrays could be named: stage_range xmomentum_range ymomentum_range elevation_range (just in case) friction_range " ole 148 problem with loading .pts file in Sri lanka Functionality and features defect normal normal duncan closed 2007-05-03T16:54:42+10:00 2007-05-16T16:06:51+10:00 "run on cyclone on one cpu G2 = Geospatial_data(file_name = project.hikka_name + '.pts') error below it seems that the verison of Anuga Samam is running doesn't have this assertion and therefore passes ---------------------- self.false_northing 0.0 DEFAULT_FALSE_NORTHING 10000000 Traceback (most recent call last): File ""build_gal5.py"", line 70, in ? G2 = Geospatial_data(file_name = project.hikka_name + '.pts') File ""/d/cit/1/cit/unixhome/nbartzis/anuga/anuga_core/source/anuga/geospatial_data/geospatial_data.py"", line 162, in __init__ self.import_points_file(file_name, delimiter, verbose) File ""/d/cit/1/cit/unixhome/nbartzis/anuga/anuga_core/source/anuga/geospatial_data/geospatial_data.py"", line 532, in import_points_file data_points, attributes, geo_reference =\ File ""/d/cit/1/cit/unixhome/nbartzis/anuga/anuga_core/source/anuga/geospatial_data/geospatial_data.py"", line 895, in _read_pts_file geo_reference = Geo_reference(NetCDFObject=fid) File ""/d/cit/1/cit/unixhome/nbartzis/anuga/anuga_core/source/anuga/coordinate_transforms/geo_reference.py"", line 65, in __init__ self.read_NetCDF(NetCDFObject) File ""/d/cit/1/cit/unixhome/nbartzis/anuga/anuga_core/source/anuga/coordinate_transforms/geo_reference.py"", line 123, in read_NetCDF assert (self.false_northing == DEFAULT_FALSE_NORTHING) AssertionError ------------------------ it is late in the day, i can more info if needed " nick 150 incorporate the Export_data.py script into anuga source Efficiency and optimisation enhancement minor normal anonymous closed 2007-05-08T16:57:33+10:00 2007-05-21T10:24:27+10:00 "I feel that importing export_data.py into the anuga source would reduce confusion and increase the usefuliness of it. 1)And the same time it can be slightly refactored to so it uses a dictionary to define the grids it will export. 2) add the ability to automatically determine if it was run in parallel and on how many nodes from the output sww files 3) change name to export_grid have a look in dampier I:\unixhome\nbartzis\anuga\anuga_work\production\dampier_2006\export_results.py -------------------- import project, os import sys from anuga.shallow_water.data_manager import sww2dem from os import sep time_dir = '20070418_035124_run' # cellsize = 25 timestep = None directory = project.output_dir #name = directory + time_dir + sep + project.scenario_name name = directory+time_dir+sep+project.scenario_name is_parallel = False if is_parallel == True: nodes = 4 print 'output dir:', name which_var = 2 if which_var == 0: # Stage outname = name + '_stage' quantityname = 'stage' if which_var == 1: # Absolute Momentum outname = name + '_momentum_i1' quantityname = '(xmomentum**2 + ymomentum**2)**0.5' if which_var == 2: # Depth outname = name + '_depth' quantityname = 'stage-elevation' if which_var == 3: # Speed outname = name + '_speed_i0' quantityname = '(xmomentum**2 + ymomentum**2)**0.5/(stage-elevation+1.e-6/(stage-elevation))' #Speed if which_var == 4: # Elevation outname = name + '_elevation' quantityname = 'elevation' #Elevation if is_parallel == True: # print 'is_parallel',is_parallel for i in range(0,nodes): namei = name + '_P%d_%d' %(i,nodes) outnamei = outname + '_P%d_%d' %(i,nodes) print 'start sww2dem for sww file %d' %(i) sww2dem(namei, basename_out = outnamei, quantity = quantityname, timestep = timestep, cellsize = cellsize, easting_min = project.e_min_area, easting_max = project.e_max_area, northing_min = project.n_min_area, northing_max = project.n_max_area, reduction = max, verbose = True, format = 'asc') else: print 'start sww2dem' sww2dem(name, basename_out = outname, quantity = quantityname, timestep = timestep, cellsize = cellsize, easting_min = project.e_min_area, easting_max = project.e_max_area, northing_min = project.n_min_area, northing_max = project.n_max_area, reduction = max, verbose = True, format = 'asc') ------------------------" nick 151 incorporate the get_timeseries.py script into anuga source Efficiency and optimisation enhancement minor low nick and jane closed 2007-05-08T17:14:25+10:00 2008-03-06T17:00:45+11:00 "This is similar to ticket 150, I believe this can plot multiple timeseries from different swws in one png file. I found this a bit tricky to understand, ask me and i will tell you what i know. it could also do with a bit of cleaning up and refactoring and maybe renaming -------------------- """""" Generate images of ""gauges"" for production run Inputs: production dirs: dictionary of production directories with a association to that simulation run, eg high tide, low tide and MSL. Outputs: * figures used for report stored in the report_figure directory """""" from os import getcwd, sep, altsep, mkdir, access, F_OK import project from anuga.abstract_2d_finite_volumes.util import sww2timeseries # Create report directory reportdir = getcwd()+sep+'report'+sep if access(reportdir,F_OK) == 0: mkdir (reportdir) # sww file created from URS boundary production_dirs = {#'boundaries': '10000 yr wave height' '20070418_035124_run': 'URS boundary normal' } is_parallel = False if is_parallel == True: nodes = 8 # Generate figures swwfiles = {} #J:\inundation\data\western_australia\onslow_tsunami_scenario_2006\anuga\boundaries SU-AU_high_res1.sww #boundary_dir_filename= os.path.join(home,data,state,'onslow_tsunami_scenario_2006',an,bo,'SU-AU_high_res1.sww') #gauges_dir_name_simple = if is_parallel is True: print 'bugger' for i in range(nodes): print 'Sending node %d of %d' %(i,nodes) swwfiles = {} #reportname = report_name + '_%s' %(i) for label_id in production_dirs.keys(): if label_id == 'boundaries': # file_loc = project.boundaries_in_dir swwfile = best_boundary_sww print 'hi' else: file_loc = project.output_dir + label_id + sep sww_extra = '_P%s_%s' %(i,nodes) swwfile = file_loc + project.scenario_name + sww_extra + '.sww' print 'swwfile',swwfile swwfiles[swwfile] = label_id texname, elev_output = sww2timeseries(swwfiles, project.gauges_dir_name_simple, production_dirs, report = False, #reportname = reportname, plot_quantity = ['stage', 'momentum'], generate_fig = False, surface = False, time_min = None, time_max = None, title_on = False, verbose = True) #latex_output.append(texname) else: for label_id in production_dirs.keys(): if label_id == 'boundaries': print 'boundaries' file_loc = project.boundaries_in_dir swwfile = project.boundaries_dir_name3 + '.sww' # swwfile = boundary_dir_filename else: file_loc = project.output_dir + label_id + sep swwfile = file_loc + project.scenario_name + '.sww' swwfiles[swwfile] = label_id texname, elev_output = sww2timeseries(swwfiles, project.gauges_dir_name, # project.gauges_dir_name_simple, production_dirs, report = False, #reportname = report_name, # plot_quantity = ['stage', 'momentum'], plot_quantity = ['stage', 'xmomentum', 'ymomentum'], surface = False, time_min = None, time_max = None, title_on = False, verbose = True) ---------------------" nick 152 Add version info to sww files. Architecture and API defect normal normal nariman closed 2007-05-14T14:48:51+10:00 2009-09-29T16:51:05+10:00 "Add the ANUGA version number info to sww files. The function, get_revision_number can be used for this." ole 153 get_revision_number doesn't get revision # if executed with IDLE or emacs Functionality and features defect normal normal ole closed 2007-05-17T11:34:49+10:00 2009-09-10T16:05:05+10:00 "Running script through IDLE resulted in sww file with revision_number = ""None"". Running from the DOS prompt was OK. The example was dam_sample.py in \\Gneiss\gem5nhi\inundation\sandpits\onielsen\anuga_work\development\dam_test_from_brad_2007 " ole 154 quantity.get_vertex_values is slow Efficiency and optimisation defect major normal ole closed 2007-05-18T15:41:03+10:00 2007-05-23T12:14:11+10:00 "Profiling of okushiri (yieldstep=0.05, finaltime=2) gave the following runtimes: store_vertex_values_uniquely(True): 138.3s store_vertex_values_uniquely(False): 505.6s No storing: 28.2s Profiling revealed that quantity.get_vertex_values is the culprit. I suggest rewriting some of it in C and perhaps always use mean as the reduction operator. We don't really need any other. This problem is worst in simulations with frequents storing. " anonymous 155 Error msg on Geospatial_data input Functionality and features defect minor normal duncan closed 2007-05-21T11:16:09+10:00 2007-05-21T16:40:47+10:00 "Geospatial expects a comma separated file (with header). This needs to be communicated in case the format is wrong. Here's what happens if a space separated file is passed: {{{ X:\inundation\sandpits\onielsen\anuga_work\development\Rudy_vandrie_2007\blackbutt>python run_blackbutt.py Traceback (most recent call last): File ""run_blackbutt.py"", line 63, in ? G = Geospatial_data(elevation_file+'.txt') File ""X:\inundation\sandpits\onielsen\anuga_core\source\anuga\geospatial_data\geospatial_data.py"", line 164, in __init__ self.import_points_file(file_name, delimiter, verbose) File ""X:\inundation\sandpits\onielsen\anuga_core\source\anuga\geospatial_data\geospatial_data.py"", line 548, in import_points_file data_points, attributes, geo_reference =\ File ""X:\inundation\sandpits\onielsen\anuga_core\source\anuga\geospatial_data\geospatial_data.py"", line 937, in _read_csv_file max_read_lines=1e30) #If the file is bigger that this, block.. File ""X:\inundation\sandpits\onielsen\anuga_core\source\anuga\geospatial_data\geospatial_data.py"", line 973, in _read_csv_file_blocking y_header = header.pop(0) IndexError: pop from empty list }}}" anonymous 156 Could we remove shallow_water_kinetic ? ANUGA enhancements Management and planning task minor low steve closed 2007-05-21T14:54:32+10:00 2012-02-13T13:59:22+11:00 "This file causes compile to take longer and is essentially just a copy of the normal shallow water module which already has a kinetic flux calculation. I suggest removing shallow_water_kinetic_ext.c shallow_water_domain_kinetic.py " ole 157 Export grid may fail if old sww files are around?? Appearance and visualisation defect minor lowest duncan closed 2007-05-21T15:11:38+10:00 2007-05-25T12:16:57+10:00 "In the presence for old sww files, test_all (verbose) gave the following error {{{ ====================================================================== ERROR: Test that sww information can be converted correctly to asc/prj ---------------------------------------------------------------------- Traceback (most recent call last): File ""shallow_water\test_data_manager.py"", line 1345, in test_export_grid format = 'asc') File ""X:\inundation\sandpits\onielsen\anuga_core\source\anuga\shallow_water\data_manager.py"", line 1673, in export_grid format) File ""X:\inundation\sandpits\onielsen\anuga_core\source\anuga\shallow_water\data_manager.py"", line 1824, in sww2dem print ' t [s] in [%f, %f], len(t) == %d'\ ValueError: min() arg is an empty sequence ====================================================================== ERROR: Test that sww information can be converted correctly to asc/prj ---------------------------------------------------------------------- Traceback (most recent call last): File ""shallow_water\test_data_manager.py"", line 1421, in test_export_gridII format = 'asc') File ""X:\inundation\sandpits\onielsen\anuga_core\source\anuga\shallow_water\data_manager.py"", line 1673, in export_grid format) File ""X:\inundation\sandpits\onielsen\anuga_core\source\anuga\shallow_water\data_manager.py"", line 1824, in sww2dem print ' t [s] in [%f, %f], len(t) == %d'\ ValueError: min() arg is an empty sequence ====================================================================== ERROR: Test that sww information can be converted correctly to asc/prj ---------------------------------------------------------------------- Traceback (most recent call last): File ""shallow_water\test_data_manager.py"", line 1546, in test_export_gridIII format = 'asc') File ""X:\inundation\sandpits\onielsen\anuga_core\source\anuga\shallow_water\data_manager.py"", line 1673, in export_grid format) File ""X:\inundation\sandpits\onielsen\anuga_core\source\anuga\shallow_water\data_manager.py"", line 1824, in sww2dem print ' t [s] in [%f, %f], len(t) == %d'\ ValueError: min() arg is an empty sequence ---------------------------------------------------------------------- Ran 617 tests in 53.203s }}}" ole 159 Variable forcing functions Appearance and visualisation enhancement minor low ole closed 2007-05-22T10:08:17+10:00 2012-02-13T14:04:22+11:00 "There is a need to apply a forcing function such as 'rainfall' based on data from a few gauges. This should be doable using our least squares module in the same way it is done for set_quantity. We will act on this once a crude rainfall forcing term and some data is available from Rudy van Drie." ole 160 """could not find triangle"" crash when exporting a grid from parallel results" Functionality and features enhancement normal normal duncan closed 2007-05-22T13:48:08+10:00 2007-05-30T15:18:54+10:00 "When running \anuga_work\production\onslow_2006/test_export_results.py there is the following error; {{{ USER: dgray bound /d/xrd/gem/5/nhi/inundation/data/western_australia/onslow_tsunami_scenario_2006/anuga/boundaries/ meshname /d/xrd/gem/5/nhi/inundation/data/western_australia/onslow_tsunTraceback (most recent call last): File ""test_export_results.py"", line 45, in ? format = 'asc') File ""/d/cit/1/dgray/inundation/anuga_core/source/anuga/shallow_water/data_manager.py"", line 1945, in sww2dem grid_values = interp.interpolate(q, grid_points).flat File ""/d/cit/1/dgray/inundation/anuga_core/source/anuga/fit_interpolate/interpolate.py"", line 176, in interpolate verbose=verbose) File ""/d/cit/1/dgray/inundation/anuga_core/source/anuga/fit_interpolate/interpolate.py"", line 202, in interpolate_block verbose=verbose) File ""/d/cit/1/dgray/inundation/anuga_core/source/anuga/fit_interpolate/interpolate.py"", line 295, in _build_interpolation_matrix_A raise Exception(msg) Exception: ('Could not find triangle for point', array([ 16375., 0.])) }}} " ole 161 "Group directory and file permissions not working correctly when using ""mpirun""" Management and planning defect minor normal nick closed 2007-05-23T13:26:05+10:00 2007-05-23T13:29:31+10:00 When running anuga models using 'mpirun' command the permissions of the directory and files created does NOT reflect the permissions set by umask in my .bashrc. nick 162 Move test file used by test polygon into same directory as the test Appearance and visualisation task trivial low jane closed 2007-05-24T05:08:29+10:00 2007-06-03T16:45:22+10:00 "The test test_polygon_function_csvfile currently relies on a test file 'mainland_only.csv' which resides outside the anuga code repository. Consequently, the test will fail on most installations (see output below). I suggest making a local copy of the test file in the same directory as test_polygon.py. ===================================================================== ERROR: test_polygon_function_csvfile (test_polygon.Test_Polygon) ---------------------------------------------------------------------- Traceback (most recent call last): File ""utilities\test_polygon.py"", line 64, in test_polygon_function_csvfile p1 = read_polygon(home+sep+'data'+sep+'western_australia'+sep+'dampier_tsunami_scenario_2006'+sep+'anuga'+sep+'polygons' +sep+'2007polys'+sep+'mainland_only.csv') TypeError: unsupported operand type(s) for +: 'NoneType' and 'str' " ole 163 Problem with export grid on tornado Appearance and visualisation defect normal normal duncan closed 2007-05-24T16:57:06+10:00 2007-05-25T12:17:16+10:00 "Starting in changeset:4463 there is an error that only shows up on the 64 bit tornado cluster (see below). The error is not there in changeset:4461 and there is something else going on in changeset:4462 which may be masking error. ====================================================================== FAIL: Test that sww information can be converted correctly to asc/prj ---------------------------------------------------------------------- Traceback (most recent call last): File ""shallow_water/test_data_manager.py"", line 1345, in test_export_grid format = 'asc') File ""/d/cit/1/cit/unixhome/onielsen/inundation/anuga_core/source/anuga/shallow_water/data_manager.py"", line 1673, in export_grid format) File ""/d/cit/1/cit/unixhome/onielsen/inundation/anuga_core/source/anuga/shallow_water/data_manager.py"", line 1932, in sww2dem interp = Interpolate(vertex_points, volumes, verbose = verbose) File ""fit_interpolate/interpolate.py"", line 91, in __init__ max_vertices_per_cell) File ""/d/cit/1/cit/unixhome/onielsen/inundation/anuga_core/source/anuga/fit_interpolate/general_fit_interpolate.py"", line 84, in __init__ self.mesh = Mesh(vertex_coordinates, triangles) File ""/d/cit/1/cit/unixhome/onielsen/inundation/anuga_core/source/anuga/abstract_2d_finite_volumes/neighbour_mesh.py"", line 89, in __init__ verbose=verbose) File ""/d/cit/1/cit/unixhome/onielsen/inundation/anuga_core/source/anuga/abstract_2d_finite_volumes/general_mesh.py"", line 176, in __init__ assert self.areas[i] > 0.0, msg AssertionError: Triangle (0.000000,0.000000), (0.000000,0.000000), (0.000000, 0.000000) is degenerate: area == 0.000000 ====================================================================== FAIL: Test that sww information can be converted correctly to asc/prj ---------------------------------------------------------------------- Traceback (most recent call last): File ""shallow_water/test_data_manager.py"", line 1421, in test_export_gridII format = 'asc') File ""/d/cit/1/cit/unixhome/onielsen/inundation/anuga_core/source/anuga/shallow_water/data_manager.py"", line 1673, in export_grid format) File ""/d/cit/1/cit/unixhome/onielsen/inundation/anuga_core/source/anuga/shallow_water/data_manager.py"", line 1932, in sww2dem interp = Interpolate(vertex_points, volumes, verbose = verbose) File ""fit_interpolate/interpolate.py"", line 91, in __init__ max_vertices_per_cell) File ""/d/cit/1/cit/unixhome/onielsen/inundation/anuga_core/source/anuga/fit_interpolate/general_fit_interpolate.py"", line 84, in __init__ self.mesh = Mesh(vertex_coordinates, triangles) File ""/d/cit/1/cit/unixhome/onielsen/inundation/anuga_core/source/anuga/abstract_2d_finite_volumes/neighbour_mesh.py"", line 89, in __init__ verbose=verbose) File ""/d/cit/1/cit/unixhome/onielsen/inundation/anuga_core/source/anuga/abstract_2d_finite_volumes/general_mesh.py"", line 176, in __init__ assert self.areas[i] > 0.0, msg AssertionError: Triangle (0.000000,0.000000), (0.000000,0.000000), (0.000000, 0.000000) is degenerate: area == 0.000000 ====================================================================== FAIL: Test that sww information can be converted correctly to asc/prj ---------------------------------------------------------------------- Traceback (most recent call last): File ""shallow_water/test_data_manager.py"", line 1546, in test_export_gridIII format = 'asc') File ""/d/cit/1/cit/unixhome/onielsen/inundation/anuga_core/source/anuga/shallow_water/data_manager.py"", line 1673, in export_grid format) File ""/d/cit/1/cit/unixhome/onielsen/inundation/anuga_core/source/anuga/shallow_water/data_manager.py"", line 1932, in sww2dem interp = Interpolate(vertex_points, volumes, verbose = verbose) File ""fit_interpolate/interpolate.py"", line 91, in __init__ max_vertices_per_cell) File ""/d/cit/1/cit/unixhome/onielsen/inundation/anuga_core/source/anuga/fit_interpolate/general_fit_interpolate.py"", line 84, in __init__ self.mesh = Mesh(vertex_coordinates, triangles) File ""/d/cit/1/cit/unixhome/onielsen/inundation/anuga_core/source/anuga/abstract_2d_finite_volumes/neighbour_mesh.py"", line 89, in __init__ verbose=verbose) File ""/d/cit/1/cit/unixhome/onielsen/inundation/anuga_core/source/anuga/abstract_2d_finite_volumes/general_mesh.py"", line 176, in __init__ assert self.areas[i] > 0.0, msg AssertionError: Triangle (0.000000,0.000000), (0.000000,0.000000), (0.000000, 0.000000) is degenerate: area == 0.000000 ---------------------------------------------------------------------- Ran 617 tests in 39.309s FAILED (failures=3, errors=1) " ole 164 allow inundation_damage to work with multiple sww files Functionality and features enhancement normal high duncan closed 2007-05-25T11:40:13+10:00 2007-05-28T16:42:50+10:00 " The current inundation_damage functionality has a single sww file as input (example; see production/dampier/run_building_inundation.py It would be desirable that all sww files created through a parallel run would be sent as input with the combined results available in one output csv file (a csv file has been generated from the NEXIS database and a modified csv file is generated which lists the structural and contents losses for each building location) this would be similar to the new export_grid functionality" jane.sexton@… 165 """glibc detected"" error in exmouth when ran in parallal" Functionality and features defect normal high ole closed 2007-05-28T10:14:43+10:00 2007-06-06T17:52:40+10:00 "Can you provide any information about this error, it is the third time it has occurred with this code {{{ ----------------------- *** glibc detected *** double free or corruption (!prev): 0x000000000162fc10 *** One of the processes started by mpirun has exited with a nonzero exit code. This typically indicates that the process finished in error. If your process did not finish in error, be sure to include a ""return 0"" or ""exit(0)"" in your C code before exiting the application. PID 8578 failed on node n10 (192.168.0.241) due to signal 6. ----------------------------------------------------------------------------- }}} It occurs when running an exmouth model in parallel, (the sequential run works this is the directory of the parallel run J:\inundation\data\western_australia\exmouth_tsunami_scenario\anuga\outputs\20070525_034301_run_basic_1.4_nbartzis this is the directory of the last serial run J:\inundation\data\western_australia\exmouth_tsunami_scenario\anuga\outputs\20070525_033245_run_basic_1.4_nbartzis {{{ +------------------------------------------------------------- | Fri May 25 15:02:22 2007. Evaluating function _file_function +------------------------------------------------------------- | Argument: '/d/xrd/gem/5/nhi/inundation/data/western_australia/exmouth_tsunami_scenario/anuga/boundaries/urs/dampier/1_10000/exmouth_3854_17042007.sww' | Keyword Args: {'quantities': ['stage', 'xmomentum', 'ymomentum'], 'interpolation_points': Array: (187, 2), 'time_thinning': 12, 'domain_starttime': 0, 'verbose': True} | Reason: No cached result +------------------------------------------------------------- Reading /d/xrd/gem/5/nhi/inundation/data/western_australia/exmouth_tsunami_scenario/anuga/boundaries/urs/dampier/1_10000/exmouth_3854_17042007.sww File_function data obtained from: /d/xrd/gem/5/nhi/inundation/data/western_australia/exmouth_tsunami_scenario/anuga/boundaries/urs/dampier/1_10000/exmouth_3854_17042007.sww References: Lower left corner: [189945.759564, 7488724.335279] Start time: 4000.000000 Building interpolation matrix from source mesh (648 vertices, 1086 triangles) FitInterpolate: Building mesh FitInterpolate: Building quad tree Interpolating (187 interpolation points, 1034 timesteps). Timesteps were thinned by a factor of 12 time step 0 of 1034 time step 104 of 1034 time step 208 of 1034 time step 312 of 1034 }}} here is an example of the same problem with code that runs quicker \inundation\data\western_australia\exmouth_tsunami_scenario\anuga\outputs\20070530_062210_run_store_0_nbartzis you should be able to execute ""run_exmouth.py"" from this directory and it will create another directory with the output results there is one difference i can see the code fails at a slightly different spot {{{ Find midpoint coordinates of entire boundary Initialise file_function Caching: looking for cached files /d/cit/1/cit/unixhome/nbartzis/.python_cache/_file_function[-1913934578119235209]_{Result,Args,Admin}.z Caching: Dependencies are ['/d/xrd/gem/5/nhi/inundation/data/western_australia/exmouth_tsunami_scenario/anuga/boundaries/urs/dampier/1_10000/exmouth_3854_17042007.sww'] +------------------------------------------------------------- | Tue Jun 5 08:49:22 2007. Evaluating function _file_function +------------------------------------------------------------- | Argument: '/d/xrd/gem/5/nhi/inundation/data/western_australia/exmouth_tsunami_scenario/anuga/boundaries/urs/dampier/1_10000/exmouth_3854_17042007.sww' | Keyword Args: {'quantities': ['stage', 'xmomentum', 'ymomentum'], 'interpolation_points': [[ 192783.96757945 7566067.52060781] [ 192597.7735207 7576851.25925281] [ 192621.04777805 7575503.29192219] [ 192807.2418368 7564719.55327719] [ 192644.32203539 7574155.32459156] [ 192714.14480742 7570111.... | Reason: No cached result +------------------------------------------------------------- Reading /d/xrd/gem/5/nhi/inundation/data/western_australia/exmouth_tsunami_scenario/anuga/boundaries/urs/dampier/1_10000/exmouth_3854_17042007.sww File_function data obtained from: /d/xrd/gem/5/nhi/inundation/data/western_australia/exmouth_tsunami_scenario/anuga/boundaries/urs/dampier/1_10000/exmouth_3854_17042007.sww References: Lower left corner: [189945.759564, 7488724.335279] Start time: 4000.000000 }}} Processes 1,2,3 fail at this point and processor 0 continues on until it creates a .sww file. All the results are in the directory noted above. Here's how processor 0 fails; {{{ +------------------------------------------------------------- | Wed May 30 16:23:08 2007. Evaluating function _file_function +------------------------------------------------------------- | Argument: '/d/xrd/gem/5/nhi/inundation/data/western_australia/exmouth_tsunami_scenario/anuga/boundaries/urs/dampier/1_10000/exmouth_3854_17042007.sww' | Keyword Args: {'quantities': ['stage', 'xmomentum', 'ymomentum'], 'interpolation_points': Array: (305, 2), 'time_thinning': 48, 'domain_starttime': 0, 'verbose': True} | Reason: No cached result +------------------------------------------------------------- Reading /d/xrd/gem/5/nhi/inundation/data/western_australia/exmouth_tsunami_scenario/anuga/boundaries/urs/dampier/1_10000/exmouth_3854_17042007.sww File_function data obtained from: /d/xrd/gem/5/nhi/inundation/data/western_australia/exmouth_tsunami_scenario/anuga/boundaries/urs/dampier/1_10000/exmouth_3854_17042007.sww References: Lower left corner: [189945.759564, 7488724.335279] Start time: 4000.000000 }}} " nick 166 both of the tests in source/anuga_parallel fail ANUGA enhancements Testing and validation defect normal normal steve closed 2007-05-29T16:11:36+10:00 2009-09-10T16:06:20+10:00 both tests in X:\anuga_core\source\anuga_parallel fail. Having more robust parallel tests might help in reducing/understanding problems such as ticket:160. duncan 167 Trac is not sending duncan emails Management and planning defect normal normal Ole closed 2007-05-29T16:14:18+10:00 2007-05-29T16:44:44+10:00 I used to get emails from trac all the time. But I don't get any these days, even when I submit a ticket. duncan 168 """could not find triangle"" crash when exporting a grid from SERIAL results" Functionality and features defect major high ole closed 2007-05-30T15:23:31+10:00 2009-03-18T17:09:28+11:00 "from ticket#160; running \production\onslow_2006\export_results.py for sww file stored in output directory 20060704_063005 produces a similar error - could not find triangle for point. What is important in this example, is that the sww file here was created in sequential mode. The example I ran was to export the grid for the entire model area. It was successful when the cell size was 250, but failed when it was 150. The sww file is large 750Mb. Based on this, Ole suggested reassigning the ticket to you to do the same troubleshooting for this sequential case. running \production\onslow_2006\test_export_results.py revision 4521 should exibit this ticket " duncan 169 export_grid doesn't throw an error if swwfile doesn't exist Functionality and features defect minor normal duncan closed 2007-06-01T13:54:35+10:00 2007-06-01T16:43:51+10:00 "data_mananger.export_grid doesn't throw an error if swwfile doesn't exist. It would be useful if it did.... it is tricky to troubleshoot without an error. " nick 170 Investigate further improvements on code management Management and planning task minor low ole closed 2007-06-01T15:56:54+10:00 2009-09-04T12:27:11+10:00 "Look at Python Eggs Cruise Control Maven (if a Python version exists) All should integrate with Subversion and Track" ole 171 test all on cyclone is creating large files and not finishing. Testing and validation defect major high Duncan closed 2007-06-12T15:06:08+10:00 2007-06-12T17:18:22+10:00 "test all on cyclone is creating large files and not finishing. just updating anuga-core\source\anuga 4535 is bad. 4490 is bad 4470 is bad 4456 is bad 4455 is bad 4454 is good (other errors though, as noted in log) 4452 is good 4450 is good 4418 hassels compiling triangle stuff So the refactoring of writing sww files is causing problems on cyclone." duncan 172 Compute Maximal Runup height from sww files. Functionality and features defect normal normal ole closed 2007-06-19T11:13:11+10:00 2007-06-25T17:37:21+10:00 "Create a function that will read an sww file and produce the maximal runup height within a given polygon. The algorithm should mimick the method get_maximum_inundation_elevation which was introduced into shallow_water_domain in changeset:3689. The algorithm would be along the lines {{{ Get triangles with depth>0 within given polygon Find maximum elevation amoung those triangles }}} This relates to ticket:136 except that this one will work on sww files. " ole 173 Time series plots have incorrect starttimes Functionality and features enhancement minor high nick closed 2007-06-20T10:57:21+10:00 2008-01-15T12:21:06+11:00 "In some of the scenarios to increase speed on the model, i have remove X seconds from begining of the boundary sww file when it was created in ""urs_ungridded2sww"" using ""mint"" and ""maxt"". Generally because the wave would arrive after 4 hours therefore removing 1-1.5 hours speeds up the program. It would be great if ""mint"" eg 4000 secs was recorded as the first time step in the resulting sww file. In the model script the boundary file is loaded using ""Field_boundary"" This carrying of ""mint"" info through to the final evolved sww is mainly important in the generation of the time_series plots which currently require to manually input the correct ""mint"" into the function.... which has lead to errors and wasted time." nick 174 urs_mux_files_validation fails Functionality and features defect normal high duncan closed 2007-06-21T09:43:11+10:00 2007-06-25T14:02:04+10:00 "{{{ ole@nautilus:~/inundation/anuga_validation/automated_validation_tests$ python validate_all.py Skipping . Searching dir ./urs_mux_files_validation Found validate_Bf.py in ./urs_mux_files_validation Searching dir ./okushiri_tank_validation Found validate_okushiri.py in ./okushiri_tank_validation filename path ./urs_mux_files_validation validate_Bf.py test_compare_URSsww_vs_EvolveANUGAsww (__main__.Test_Bf) ... Traceback (most recent call last): File ""run_Bf.py"", line 93, in ? domain, mean_stage=tide, use_cache=True, verbose=False) File ""/home/ole/inundation/anuga_core/source/anuga/shallow_water/shallow_water_domain.py"", line 1429, in __init__ verbose=verbose) File ""/home/ole/inundation/anuga_core/source/anuga/abstract_2d_finite_volumes/generic_boundary_conditions.py"", line 253, in __ini t__ q = self.F(0, point_id=0) File ""/home/ole/inundation/anuga_core/source/anuga/fit_interpolate/interpolate.py"", line 606, in __call__ if t < self.time[0]: raise Exception(msg) Exception: Time interval [9240.0000000000000000:11160.0000000000000000] does not match model time: 0.0000000000000000 FAIL ====================================================================== FAIL: test_compare_URSsww_vs_EvolveANUGAsww (__main__.Test_Bf) ---------------------------------------------------------------------- Traceback (most recent call last): File ""validate_Bf.py"", line 33, in test_compare_URSsww_vs_EvolveANUGAsww assert res == 0 AssertionError ---------------------------------------------------------------------- Ran 1 test in 19.937s FAILED (failures=1) }}}" ole 175 Compute flow through a cross section Functionality and features enhancement normal highest ole closed 2007-06-21T11:52:23+10:00 2008-05-07T16:03:19+10:00 "For ANUGA to be used with flood modelling it will need a way to compute flow through an arbitrary cross section. The output, Q, would be a vector of flows for each stored timesteps. This was initially suggested by Rudy van Drie. The function could be called as follows: {{{ Q = flow_at_cross_section(‘model.sww’, polyline, verbose=True) Where polyline has the form [p_1, p_2, p_3, …..] and p_i = [x,y] Q is a vector of flows with units [m^3/s] }}} The algorithm would be as follows: {{{ 1: Obtain all intersections between polyline and triangle edges 2: From these, derive for each triangle: length of intersecting segment and its midpoint. 3: Obtain from file_function (or Interpolation_function) interpolated values for xmomentum and ymomentum at each segment midpoint. The units are [m^2/s]. 4: Compute the momentum along the normal vector of the segment at its midpoint. 5: Multiply the normal momentum with the segment length to obtain flow for that triangle. The unit is now [m^3/s]. 6: Sum up normal flows for all participating triangles and enter into Q. }}} A simple unit test would consist of a channel flow on a flat bed with a known inflow and the same outflow. Flow across a cross section in the channel should equal the inflow. Issues include: What if the polyline has a corner inside a triangle? Maybe, we only do this for straight lines to begin with. " ole 176 export_grid in data_manager sometimes has memory allocation error Functionality and features defect minor high duncan closed 2007-06-22T14:59:44+10:00 2009-09-04T12:09:52+10:00 "When using export_grid to export multiple quantities from one sww file, often a memory allocation error is thrown. This seems more common with big sww files. {{{ Traceback (most recent call last): File ""run_broome_urs.py"", line 268, in ? File ""run_broome_urs.py"", line 252, in run_model buildings_filename_out = project_urs.buildings_filename_out File ""/d/cit/1/cit/unixhome/nbartzis/anuga/anuga_core/source/anuga/shallow_water/data_manager.py"", line 1687, in export_grid format) File ""/d/cit/1/cit/unixhome/nbartzis/anuga/anuga_core/source/anuga/shallow_water/data_manager.py"", line 1859, in sww2dem quantity_dict[name] = fid.variables[name][:] MemoryError: can't allocate memory for array }}} Looking at the code the memory should not be increasing each time it outputs a different quantities' grid but thats what seems to happen. As the error always occurs after at least one grid has been written. J:\inundation\data\western_australia\broome_tsunami_scenario_2006\anuga\outputs\20070615_063022_run_final_4.9_exmouth_nbartzis So we need to look in to where the memory is being allocated and minimise it. " anonymous 177 test for 'zscale' in ferret2sww in data_manager Functionality and features enhancement minor normal ole closed 2007-06-22T16:16:37+10:00 2007-06-25T17:34:07+10:00 "There is no test for the zscale parameter used by the ferret2sww in test_data_mananger. Please fix this :)" nick 178 Time to load and fit mesh file (domain.set_quantity) is the slowest part for large parallel model runs Efficiency and optimisation enhancement normal normal steve closed 2007-06-27T13:55:38+10:00 2010-06-15T09:29:17+10:00 "Here are the some stats and times for different parts of ANUGA for 3 similar models scenarios except for the number of triangles {{{ J:\inundation\data\western_australia\broome_tsunami_scenario_2006\anuga\outputs\20070518_060438_run_final_0_dampier_nbartzis 380000 triangles, on Tornado bathy file load 58000 sec (15hrs) load and fit boundary condition 35000 (10hrs) evolution 25000 (7hrs) J:\inundation\data\western_australia\broome_tsunami_scenario_2006\anuga\outputs\20070621_235838_run_final_0_onslow_nbartzis 430000 triangles, on cyclone bathy file load 160000 sec (44hrs) load and fit boundary condition 56000 (15hrs) evolution 80000 (22hrs) PARALLEL using 4 cpus J:\inundation\data\western_australia\broome_tsunami_scenario_2006\anuga\outputs\20070615_062002_run_final_0_onslow_nbartzis 590000 triangles, on cyclone bathy file load 250000 sec (70hrs) load and fit boundary condition 25000 (7hrs) evolution 270000 (75hrs) NOT parallel, so can expect around 25 hours with parallel }}} I think the next effort to increase speed in anuga should be focused on loading and fiting the bathy file to the mesh (domain.set_quantity). Even if this process cached more regularly so when it is half way through and there is a failure it doesn't need to run the whole thing again. Also the length of time a model needs to run is not the biggest issue really, but greatly increases the risk of the following things we can't control. Such as network issue, file access problems, node failures, custer node reboots, gniess and perlite system reboots and rifts in the space-time continuum." nick 179 Add the number of points read by domain.set_quantity(elevation) to the output stats Functionality and features enhancement minor normal nick closed 2007-06-27T14:20:02+10:00 2007-07-04T16:16:20+10:00 "I think this would be helpful and if it is written at the end of that function it will get recorded in the model output file THANKS OLE" nick 180 Things to do when we get it support for GA's clusters Management and planning defect minor normal isb closed 2007-07-02T13:36:08+10:00 2009-09-10T16:10:10+10:00 update pypar and svn. When svn is updated fix test_util.test_get_revision_number anonymous 181 Write unit tests for search_functions in fit_interpolate Testing and validation defect normal high ole closed 2007-07-03T08:49:21+10:00 2007-07-13T01:42:12+10:00 The module search_functions has no unit tests. A proper test suite will be critical when addressing ticket:178 and would be good to have anyway. ole 183 "Modify ""get_maximum_inundation_data"" to use ""get_all_swwfiles""" Appearance and visualisation enhancement minor normal nick closed 2007-07-04T17:06:02+10:00 2007-07-06T11:52:35+10:00 "data_manager.get_all_swwfiles finds all the sww files in a directory which contains a ""base_name"" string. This is very useful with parallel modlel runs. If ""get_maximum_inundation_data"" could use this and report only the maximum result from a series of sww files it would be more useful. Similar to data_manager.export_grids " nick 184 Mesh instance has no attribute 'number_of_triangles_per_node' Functionality and features defect major high duncan closed 2007-07-04T17:46:23+10:00 2007-07-06T11:57:35+10:00 "I'm modelling pt hedland, i have sucessfully run a model with 118000 triangle, see inundation\data\western_australia\pt_hedland_tsunami_scenario_2006\anuga\outputs\20070704_010800_run_basic_3.6_onslow_nbartzis however now i'm trying to run the ""final"" triangle resolutions for the model and there is an error. {{{ Traceback (most recent call last): File ""run_pt_hedland_urs.py"", line 259, in ? dir_comment=project_urs.dir_comment) File ""run_pt_hedland_urs.py"", line 140, in run_model alpha = kwargs['alpha']) File ""/d/cit/1/cit/unixhome/nbartzis/anuga/anuga_core/source/anuga/abstract_2d_finite_volumes/domain.py"", line 334, in set_quantity self.quantities[name].set_values(*args, **kwargs) File ""/d/cit/1/cit/unixhome/nbartzis/anuga/anuga_core/source/anuga/abstract_2d_finite_volumes/quantity.py"", line 419, in set_values use_cache = use_cache) File ""/d/cit/1/cit/unixhome/nbartzis/anuga/anuga_core/source/anuga/abstract_2d_finite_volumes/quantity.py"", line 813, in set_values_from_file max_read_lines=max_read_lines) File ""/d/cit/1/cit/unixhome/nbartzis/anuga/anuga_core/source/anuga/fit_interpolate/fit.py"", line 476, in fit_to_mesh dependencies=dep) File ""/d/cit/1/cit/unixhome/nbartzis/anuga/anuga_core/source/anuga/caching/caching.py"", line 351, in cache T = apply(func,args,kwargs) File ""/d/cit/1/cit/unixhome/nbartzis/anuga/anuga_core/source/anuga/fit_interpolate/fit.py"", line 552, in _fit_to_mesh verbose=verbose) File ""/d/cit/1/cit/unixhome/nbartzis/anuga/anuga_core/source/anuga/fit_interpolate/fit.py"", line 349, in fit self.build_fit_subset(points, z) File ""/d/cit/1/cit/unixhome/nbartzis/anuga/anuga_core/source/anuga/fit_interpolate/fit.py"", line 430, in build_fit_subset self._build_matrix_AtA_Atz(point_coordinates, z, verbose) File ""/d/cit/1/cit/unixhome/nbartzis/anuga/anuga_core/source/anuga/fit_interpolate/fit.py"", line 278, in _build_matrix_AtA_Atz element_found, sigma0, sigma1, sigma2, k = \ File ""/d/cit/1/cit/unixhome/nbartzis/anuga/anuga_core/source/anuga/fit_interpolate/search_functions.py"", line 35, in search_tree_of_vertices candidate_vertices, x) File ""/d/cit/1/cit/unixhome/nbartzis/anuga/anuga_core/source/anuga/fit_interpolate/search_functions.py"", line 68, in _search_triangles_of_vertices if mesh.number_of_triangles_per_node[v] == 0: AttributeError: Mesh instance has no attribute 'number_of_triangles_per_node' }}} all the files used in this run are in this directory \inundation\data\western_australia\pt_hedland_tsunami_scenario_2006\anuga\outputs\20070704_060636_run_final_3.6_onslow_nbartzis There is very little difference between these two model, I simply changed the parameter ""setup"" in project_urs.py from ""basic"" to ""final"" which changes res_factor from 4 to 1 increasing the number of triangles in the mesh. the final screen output is below {{{ Caching: looking for cached files /d/cit/1/cit/unixhome/nbartzis/.python_cache/_fit[-2139543826238746427]_{Result,Args,Admin}.z Caching: Dependencies are [] +---------------------------------------------------------- | Wed Jul 4 06:20:10 2007. Caching statistics (retrieving) +---------------------------------------------------------- | Function: _fit | Arguments: (Array: (233097, 2), Array: (465557, 3)) | Keyword Args: {'alpha': 0.1, 'mesh_origin': None, 'verbose': True} | CPU time: 822.88 seconds | Loading time: 252.75 seconds | Time saved: 570.13 seconds | | Caching dir: /d/cit/1/cit/unixhome/nbartzis/.python_cache/ | Result file: _fit[-2139543826238746427]_Result.z (95238084 bytes, compressed) | Args file: _fit[-2139543826238746427]_Args.z (5862211 bytes, compressed) | Admin file: _fit[-2139543826238746427]_Admin.z (174 bytes, compressed) | | No dependencies +---------------------------------------------------------- Geospatial data created from file: /d/xrd/gem/5/nhi/inundation/data/western_australia/pt_hedland_tsunami_scenario_2006/anuga/topographies/pt_hedland_combined_elevation.pts Data will be loaded blockwise on demand Got 1 variables: ['elevation'] Reading 2217250 points (in ~4434 blocks) from file /d/xrd/gem/5/nhi/inundation/data/western_australia/pt_hedland_tsunami_scenario_2006/anuga/topographies/pt_hedland_combined_elevation.pts. Each block consists of 500 data points Reading block 0 (points 0 to 500) out of 4434 Processing Block 0 }}} " nick 185 Deprecate xya format Functionality and features defect normal normal duncan closed 2007-07-23T15:10:02+10:00 2007-08-07T10:47:20+10:00 "Make sure all references to the xya format trigger a Deprecation Warning. User's who inadvertently use the xya format for large data files will currently get a memory error because blocking isn't used. Better to inform them about the reason. Also check that the user guide reflects the use of csv/txt files. " ole 187 Problem with 400,000+ triangles and Parallel ANUGA Functionality and features defect normal high ole closed 2007-07-27T14:12:53+10:00 2009-09-04T12:07:03+10:00 "Can someone please confirm that this is a problem, by running the following on either cyclone or tornado ""mpirun c0-3 python run_pt_hedland_urs.py"" from this directory. \\Gneiss\gem5nhi\inundation\data\western_australia\pt_hedland_tsunami_scenario_2006\anuga\outputs\20070711_014308_run_final_3.6_onslow_nbartzis This script runs pt hedland with 465000 triangles, The problems is that the script gets to {{{ +------------------------------------------------------------- | Wed Jul 11 11:57:11 2007. Evaluating function _file_function +------------------------------------------------------------- | Argument: '/d/xrd/gem/5/nhi/inundation/data/western_australia/pt_hedland_tsunami_scenario_2006/anuga/boundaries/urs/onslow_hedland_broome/1_10000/pt_hedland_3859_16052007.sww' | Keyword Args: {'quantities': ['stage', 'xmomentum', 'ymomentum'], 'interpolation_points': Array: (1523, 2), 'time_thinning': 1, 'domain_starttime': 0, 'verbose': True} | Reason: No cached result +------------------------------------------------------------- Reading /d/xrd/gem/5/nhi/inundation/data/western_australia/pt_hedland_tsunami_scenario_2006/anuga/boundaries/urs/onslow_hedland_broome/1_10000/pt_hedland_3859_16052007.sww File_function data obtained from: /d/xrd/gem/5/nhi/inundation/data/western_australia/pt_hedland_tsunami_scenario_2006/anuga/boundaries/urs/onslow_hedland_broome/1_10000/pt_hedland_3859_16052007.sww References: Lower left corner: [576824.153048, 7736310.061742] Start time: 5000.000000 }}} and then hangs... forever.... (2weeks) or stops and throws no python error but prints the following. {{{ ----------------------------------------------------------------------------- One of the processes started by mpirun has exited with a nonzero exit code. This typically indicates that the process finished in error. If your process did not finish in error, be sure to include a ""return 0"" or ""exit(0)"" in your C code before exiting the application. PID 18209 failed on node n6 (192.168.255.247) due to signal 9. ----------------------------------------------------------------------------- }}} I have run very similar code however with less triangles around 200,000 and it is fine. This can be found here \\Gneiss\gem5nhi\inundation\data\western_australia\pt_hedland_tsunami_scenario_2006\anuga\outputs\20070704_010800_run_basic_3.6_onslow_nbartzis I have tried to run other scenarios like onslow in parallel with over 400000 triangles, and they have failed too. please help " nick 188 test_make_plots_from_csv_files fails on Tornado Testing and validation defect normal normal duncan closed 2007-07-31T11:08:12+10:00 2008-03-07T16:58:48+11:00 "test_make_plots_from_csv_files fails on Tornado with the following error; {{{ dgray@tornado:~/inundation/anuga_core/source/anuga/abstract_2d_finite_volumes$ p test_util.py X Error of failed request: BadAtom (invalid Atom parameter) Major opcode of failed request: 18 (X_ChangeProperty) Atom id in failed request: 0x151 Serial number of failed request: 12 Current serial number in output stream: 15 dgray@tornado:~/inundation/anuga_core/source/anuga/abstract_2d_finite_volumes$ }}} I've removed the test since it was stopping test all from completing." duncan 189 pmesh.mesh is leaking Efficiency and optimisation defect normal normal duncan closed 2007-08-08T14:27:45+10:00 2007-12-21T12:46:12+11:00 " pmesh.mesh is leaking. The data structure returned from the c code is not released. X:\anuga_core\source\anuga\shallow_water\benchmark_sww2dem.py shows this." duncan 190 Convert UQ validation into automatic unit test Testing and validation task normal normal duncan closed 2007-08-29T09:43:20+10:00 2007-10-29T12:12:56+11:00 "Code from Matt at UQ was installed in changeset:4680 It needs to be elevated a unit test and added to the suite of automatic validations. " ole 191 time varying bathymetry Functionality and features enhancement normal low ole closed 2007-08-30T13:48:40+10:00 2009-09-04T12:25:46+10:00 "time varying bathymetry - could be used for sediment transport, coastal erosion, storm surge etc (see ticket:281) Tom has a PhD student looking at aspects of this using 2flow (Ted identified some issues with 2flow for this sort of problem) For hydraulic jumps, can you get a measure of turbulence? Video evidence" ole 192 Obtain maximal and minimal values for conserved quantities Functionality and features enhancement normal low ole closed 2007-09-03T10:17:13+10:00 2012-02-13T14:09:33+11:00 "Will Power suggested at the August Tsunami Risk Modelling Workshop that a simple feature reporting maxima and minima (and the times they occurred) of all conserved quantities would be very useful. Tom Baldock further suggested that the location of reported extrema should be specified (e.g. as an (x,y) coordinate). I'd suggest we implement this feature to have an optional polygon (and time interval) restricting the domain in which extrema are sought. This would be very similar to the maximal runup height defined in ticket:172 and implemented in changeset:4551 and changeset:4554. A decision whether this function should work on sww files or during computation must be made. I leand towards the former as it allows the feature to be recomputed without having to rerun the model. " ole 193 Mesh generation (and consequently, timestepping) differs between Linux and Windows. Functionality and features defect normal normal Nick closed 2007-09-11T12:10:40+10:00 2007-10-16T10:57:04+10:00 "The same script and same ANUGA version generates slightly different meshes on different platforms. The example anuga_work/development/demos/island.py shows this. I have checked in the generated meshes using the names island_linux.msh and island_windows.msh. On either platform the timestepping is dramatically different depending on which mesh is being used. Here's some output: Using the Linux mesh {{{ Mesh statistics: Number of triangles = 7208 Extent [m]: x in [0.000000, 100.000000] y in [0.000000, 100.000000] Areas [m^2]: A in [0.644829, 9.596606] number of distinct areas: 7208 Histogram: [0.644829, 1.540006[: 5421 [1.540006, 2.435184[: 1610 [2.435184, 3.330362[: 37 [3.330362, 4.225539[: 35 [4.225539, 5.120717[: 37 [5.120717, 6.015895[: 21 [6.015895, 6.911073[: 18 [6.911073, 7.806250[: 11 [7.806250, 8.701428[: 8 [8.701428, 9.596606]: 10 Percentiles (10%): 720 triangles in [0.644829, 0.931708] 720 triangles in [0.931708, 1.017388] 720 triangles in [1.017388, 1.096717] 720 triangles in [1.096717, 1.173627] 720 triangles in [1.173627, 1.265768] 720 triangles in [1.265768, 1.367499] 720 triangles in [1.367499, 1.473311] 720 triangles in [1.473311, 1.605096] 720 triangles in [1.605096, 1.788979] 720 triangles in [1.788979, 9.002288] 8 triangles in [9.002288, 9.596606] Boundary: Number of boundary segments == 230 Boundary tags == ['top', 'right', 'bottom', 'left'] ------------------------------------------------ Time = 0.0000, steps=0 (0) Time = 1.0000, delta t in [0.00490999, 0.02104604], steps=120 (0) Time = 2.0000, delta t in [0.00488622, 0.00548481], steps=194 (0) }}} Using the Windows mesh {{{ Mesh statistics: Number of triangles = 7210 Extent [m]: x in [0.000000, 100.000000] y in [0.000000, 100.000000] Areas [m^2]: A in [0.629728, 9.479879] number of distinct areas: 7210 Histogram: [0.629728, 1.514743[: 5259 [1.514743, 2.399758[: 1773 [2.399758, 3.284773[: 40 [3.284773, 4.169788[: 38 [4.169788, 5.054803[: 37 [5.054803, 5.939819[: 16 [5.939819, 6.824834[: 21 [6.824834, 7.709849[: 9 [7.709849, 8.594864[: 10 [8.594864, 9.479879]: 7 Percentiles (10%): 721 triangles in [0.629728, 0.938614] 721 triangles in [0.938614, 1.023260] 721 triangles in [1.023260, 1.099714] 721 triangles in [1.099714, 1.180817] 721 triangles in [1.180817, 1.270424] 721 triangles in [1.270424, 1.373040] 721 triangles in [1.373040, 1.479134] 721 triangles in [1.479134, 1.602771] 721 triangles in [1.602771, 1.780142] 721 triangles in [1.780142, 9.479879] Boundary: Number of boundary segments == 232 Boundary tags == ['top', 'right', 'bottom', 'left'] ------------------------------------------------ Time = 0.0000, steps=0 (0) Time = 1.0000, delta t in [0.00046156, 0.02104604], steps=947 (0) Time = 2.0000, delta t in [0.00040646, 0.00047853], steps=2306 (0) }}} Can you investigate 1: Why this is? 2: If there is a way of avoiding the mesh condition that creates the degenerate timestepping (194 steps/s to 2306 steps/s)? This problem was produced in changeset:4725 Ta Ole " ole 194 Retire the separate h-limiter Functionality and features defect normal normal stephen closed 2007-09-11T12:19:23+10:00 2008-06-26T13:22:20+10:00 "A separete limiter on depth (h-limiter) was introduced in changeset:907 to address problem with triangles sticking out near steep bedslopes and perhaps also the condition known as 'creep'. This never really address the problems, and I believe, at least, the first was better addressed with the 'tight slope limiters'. If we can retire the h-limiter, there is scope to simplify the number of parameters and also optimise the function _balance_deep_and_shallow. However, I won't do this until Stephen has agreed to it. When and if you do, please reassign this ticket to me. " ole 195 Convergence problem Functionality and features defect major high stephen closed 2007-09-17T13:48:27+10:00 2009-09-04T12:04:31+10:00 "A pure sine wave gets attenuated when propagated over a long distance. Will Power identified this problem at the August 2007 workshop at GA (see https://datamining.anu.edu.au/anuga/wiki/FirstAnugaMeeting). A code that will reveal this fact is available in https://datamining.anu.edu.au/anuga/browser/anuga_validation/convergence_study Attached graphs show that the sine wave gets attenuated unless mesh is very refined. Initially, Stephen suggested that this may be a timestepping issue. However, refining timesteps or trying high order timestepping (see changeset:4721 and changeset:4722) did not change the attenuation. The current plan is for Stephen to look at the 2nd order gradient limiters. If they are essentially behaving as first order limiters, this could explain what is now believed to be diffusive effects. " ole 196 damage modelling with more than one exposure input file Functionality and features enhancement minor low duncan closed 2007-09-18T18:10:10+10:00 2007-09-28T17:17:02+10:00 "inundation_damage function allows for one exposure input file. For large cities such as Perth, more than one csv file has been required to store all the data. It would be great if the function could grab the relevant csv files from the directory (/scenario/anuga/gauges ) A final summation would still be required over all the csv files to calculate damage anyway. " jane.sexton@… 197 interpolate can't handle a grid where one vertex is connected to 14 triangles Functionality and features defect normal lowest hudson closed 2007-09-26T16:27:06+10:00 2010-05-13T09:48:06+10:00 "Interpolate can't handle a grid where one vertex is connected to 14 triangles. Quad.py will crash with a runtimeError. it gets into a recursion loop trying to split a quadtree cell up with 14 verts in the same position, so it can't split the cell. The standard way we run ANUGA will not produce a vert connected to more than 13 triangles though. 14 triangles connected to one vert is a high ratio. If you have 13 triangles the average angle for the triangle corners is 27.7 deg. Meshes with min angles less than 28 deg cause problems with triangle. The default min angle is 28 deg." duncan 198 restricting csv file for damage modelling Efficiency and optimisation defect normal lowest duncan closed 2007-10-02T13:23:25+10:00 2009-09-04T12:42:10+10:00 " Some input csv files for damage modelling will be very large (especially for Aus. capital cities) and it would be advantageous for ANUGA to ""trim"" the input csv file for a given distance from the coastline (the input csv file has a SHORE_DIST column). The damage modelling funciton would then need an input describing the distance from coast required, for example, 2000m, then the damage function would only use the data which satisfied the distance <= the desired distance. The user would still be required to check the results against the actual inundation extent to ensure the desired distance was appropriate." anonymous 199 tracking the coastline Functionality and features enhancement normal low nariman closed 2007-10-04T17:12:20+10:00 2012-02-13T14:10:19+11:00 " It would be beneficial to be able to dynamically track the location of the waterline (i.e. stage = elevation) for analysis purposes. Discussed at the 30-31 August workshop (cannot remember who identified this, but it has been noted in previous work with Rosh where he has investigated the runup value for a solitary wave on a planar beach)." anonymous 200 Finish Earthquake generated tsunami source function Functionality and features task trivial low jane closed 2007-10-05T17:10:34+10:00 2009-09-04T12:24:34+10:00 "This has been worked on to some extent and is close to finished. See shallow_water eqf_v2.py there is a small error still in the code, something with a negative maybe. Need to check formula with Phil. Another thought is ""what is GNS do to model their Tsunami?"" and can we work that into ANUGA? there is a bit of cleaning up of old files to be done to like eq_test.py and eqf.py" Nick 201 Memory errors in latest version (1.0beta_4733) - and possible speed problems Efficiency and optimisation defect normal normal Duncan closed 2007-10-16T09:56:33+10:00 2007-11-21T11:22:09+11:00 "Hi, I've encountered memory errors when applying ANUGA to large (~1,000,000 triangle) meshes, that I didn't have in previous versions. I'll attach a typical error message below. Any ideas about how I can prevent this? Cheers, William GNS Science, NZ Traceback (most recent call last): File ""run_subduction_splay_1200yr.py"", line 207, in ? alpha = 0.1) File ""/seis/tsunami/ANUGA/exported_anuga/anuga_core/source/anuga/abstract_2d_f inite_volumes/quantity.py"", line 421, in set_values use_cache = use_cache) File ""/seis/tsunami/ANUGA/exported_anuga/anuga_core/source/anuga/abstract_2d_f inite_volumes/quantity.py"", line 796, in set_values_from_file max_read_lines=max_read_lines) File ""/seis/tsunami/ANUGA/exported_anuga/anuga_core/source/anuga/fit_interpola te/fit.py"", line 477, in fit_to_mesh dependencies=dep) File ""/seis/tsunami/ANUGA/exported_anuga/anuga_core/source/anuga/caching/cachi ng.py"", line 351, in cache T = apply(func,args,kwargs) File ""/seis/tsunami/ANUGA/exported_anuga/anuga_core/source/anuga/fit_interpola te/fit.py"", line 544, in _fit_to_mesh verbose=verbose) File ""/seis/tsunami/ANUGA/exported_anuga/anuga_core/source/anuga/fit_interpola te/fit.py"", line 377, in fit self._build_coefficient_matrix_B(verbose) File ""/seis/tsunami/ANUGA/exported_anuga/anuga_core/source/anuga/fit_interpola te/fit.py"", line 127, in _build_coefficient_matrix_B self.B = self.AtA + self.alpha*self.D File ""/seis/tsunami/ANUGA/exported_anuga/anuga_core/source/anuga/utilities/spa rse.py"", line 162, in __add__ new = other.copy() File ""/seis/tsunami/ANUGA/exported_anuga/anuga_core/source/anuga/utilities/spa rse.py"", line 86, in copy new[i,j] = self.Data[i,j] File ""/seis/tsunami/ANUGA/exported_anuga/anuga_core/source/anuga/utilities/spa rse.py"", line 63, in __setitem__ self.Data[key] = float(x) MemoryError " duncan 202 value error in shallow_water_domain, gravity Architecture and API defect normal high ole closed 2007-10-26T11:03:04+10:00 2007-10-26T14:53:59+10:00 "from Matt; I'm encountering an error ""need more than two values to unpack"" (see attached screen shot) when attempting to run ANUGA release 4733. I've since uninstalled the latest release (including Python and associated pre-requisites) re-installed everything and ANUGA release 4669 (which has been running without error for the past couple of months) and I continue to encounter the same problem. Has anyone else had this issue?" anonymous 203 current release has no mesh_engine_c_layer module Appearance and visualisation defect normal normal ole closed 2007-10-26T11:08:10+10:00 2007-10-29T11:02:58+11:00 "From Matt; when attempting to run the current release I initially encounter an error regarding a missing mesh_engine_c_layer module. I have been overcoming this by simply copying the required module from another machine running release 4669." duncan 204 okushiri validation failing on remotely accessing linux Testing and validation defect normal normal Ole closed 2007-10-26T14:50:55+10:00 2007-11-21T15:15:34+11:00 "From Linux (tornado) I get the error (ANUGA 4756); {{{ test_that_output_is_as_expected (__main__.Test_Okushiri) ... X Error of failed request: BadAtom (invalid Atom parameter) Major opcode of failed request: 18 (X_ChangeProperty) Atom id in failed request: 0x152 Serial number of failed request: 12 Current serial number in output stream: 15 FAIL ====================================================================== FAIL: test_that_output_is_as_expected (__main__.Test_Okushiri) ---------------------------------------------------------------------- Traceback (most recent call last): File ""validate_okushiri.py"", line 48, in test_that_output_is_as_expected assert res == 0 AssertionError ---------------------------------------------------------------------- Ran 1 test in 1429.687s }}} It passes in windows. Unit tests pass on both platforms. Got the same error on Nautilus, logging into it from my Windows Box, using exceed. Note the error is an X error, so maybe you can only see if when logging in remotely. Ole ran the test on the Nautilus terminal and it worked fine." duncan 205 test_all failing on windows for current release - due to test_advection.py Functionality and features defect normal lowest Stephen closed 2007-10-29T11:12:03+11:00 2009-09-04T12:41:01+10:00 "I installed ANUGA from anuga-1.0beta_4733.tgz onto a windows box and got the following error; {{{ __________________________________________________________ .....................................................WARNING: Too small timestep 0.0000000000000000 reached even after 50 steps of 1 order scheme E............................................................................... ................................................................................ ................................................................................ ................................................................................ ................................................................................ ................................................................................ ........................................ ====================================================================== ERROR: test_advection_example (test_advection.Test_Advection) ---------------------------------------------------------------------- Traceback (most recent call last): File ""advection\test_advection.py"", line 166, in test_advection_example for t in domain.evolve(yieldstep = 0.05, finaltime = 10): File ""C:\Python24\lib\site-packages\anuga\advection\advection.py"", line 362, i n evolve skip_initial_step=skip_initial_step): File ""abstract_2d_finite_volumes\domain.py"", line 1117, in evolve self.evolve_one_euler_step(yieldstep,finaltime) File ""abstract_2d_finite_volumes\domain.py"", line 1176, in evolve_one_euler_st ep self.update_timestep(yieldstep, finaltime) File ""abstract_2d_finite_volumes\domain.py"", line 1483, in update_timestep raise Exception, msg Exception: WARNING: Too small timestep 0.0000000000000000 reached even after 50 steps of 1 order scheme ---------------------------------------------------------------------- Ran 653 tests in 107.307s FAILED (errors=1) }}} " duncan 206 Discharge across tagged boundary Functionality and features enhancement normal low ole closed 2007-10-29T11:41:20+11:00 2007-10-30T16:25:05+11:00 "It would be useful to be able to report flow (km^3/s) across a tagged boundary. This is a suggestion from Rudi van Drie. E.g domain.flow_across_boundary('outflow_tag') " ole 207 Include auto validations in distribution Compilation and installation defect minor normal ole closed 2007-11-05T18:06:18+11:00 2007-11-08T17:33:53+11:00 "Include the automatic validations in the sourceforge distribution. Also, consolidate the number of distributions files to 3 anuga (including demos and validation files) installation_guide user_guide" ole 208 Run Cairns Example again and update the manual. Documentation defect normal normal jane closed 2007-11-08T10:38:55+11:00 2008-02-22T16:01:36+11:00 "Discrepancies between the results reported in the manual and actual runs with recent versions of ANUGA have been found (see http://sourceforge.net/mailarchive/forum.php?thread_name=d7c6ed480710292319t535cf214ne771d74c6d143e58%40mail.gmail.com&forum_name=anuga-user and http://sourceforge.net/forum/forum.php?thread_id=1861165&forum_id=593114 as well as attachments mailed directly to us by Rajaraman). One thing we could do is to rerun the Cairns example and verify the outputs are consistent with the manual. " ole 209 "update ""find_optimal_smoothing_parameter"" to read a mesh file" Functionality and features enhancement minor normal nick closed 2007-11-09T09:08:39+11:00 2007-11-27T10:32:57+11:00 "find_optimal_smoothing_parameter in geospatial_data currently defines a uniform mesh resolution for a domain inside the function. However it would be appropriate to read a predined mesh file or pass a domain with a defined mesh and elevation to it. This is important as the best smoothing value of a mesh depends on the different mesh resolution that have been defined. " nick 212 Have proper installers written Compilation and installation enhancement minor high nariman closed 2007-11-13T12:38:55+11:00 2010-07-19T15:33:30+10:00 "It'd be good to distribute ANUGA using * a Win32 installer * a Debian Linux package * an Red Hat Package (RPM) In regard to Windows, this guy wrote an installer for EDM studio at a cost of a few hundred dollars: Contact: C.ZI [czi@gmx.net] Original message ------------------------------------------------------------ Hey Darran! As a response to your request in the NSIS Forums: http://forums.winamp.com/showthread.php?s=&threadid=268455 If you don't have it finished already, i may try. Just give me some details about what exactly the installer has to look like, and has to do. I'm into NSIS for about 4 or 5 years now and know most aspects of it :) Regarding payment, I'd like to hear your offer. From what you wrote in the forums, I guess it'l take about half an hour to code plus testing/bugfixing and maybe enhancing, if you need something else. Greetings, C.ZI (@users.sourceforge.net) aka Comm@nder21 (@forums.winamp.com) " ole 216 Add documentation of optimal_smoothing_parameter in user manual Documentation defect normal normal nick closed 2007-11-16T12:14:52+11:00 2008-03-10T11:53:41+11:00 The function needs to be documented in the user manual when it is ready to be tried out by users. ole 218 Try to replace momentum limiters with constant speed versions Efficiency and optimisation defect normal normal ole closed 2007-11-17T08:29:34+11:00 2009-09-10T16:24:55+10:00 Use idea from changeset:4825 and changeset:4826 to see if we can retire the momentum limiters altogether. It would be faster and potentially more stable. ole 219 A fitting algorithm to investigate. Efficiency and optimisation enhancement normal low Duncan or steve closed 2007-11-19T16:29:42+11:00 2007-11-26T10:23:10+11:00 "Currently when building the quad tree each cell stores the triangle vertices. This means that occasionally when searching for the triangle a point is in you have to go up the tree. Consider using a binary tree and checking if triangles are in a cell, even if the triangles vertices are not in the cell, when building the tree. This may speed things up. " duncan 221 Unit tests on latest sourceforge version and svn version will not complete on ubuntu Compilation and installation defect normal normal ole closed 2007-11-20T11:03:11+11:00 2007-11-22T14:47:20+11:00 I cannot install the latest svn version of ANUGA onto my ubuntu 7.04 system (64-bit Intel core 2). The system compiles without error. However when I run test_all.py several errors are returned before a floating point exception is raised and the core is dumped. Because of the core dump I am unable to tell which tests are failing and where. John Jakeman 222 Decide on a process for guaranteeing that datasets bundled with ANUGA are free of licenses Management and planning task normal highest duncan closed 2007-11-20T16:20:49+11:00 2008-03-04T14:57:04+11:00 "Here's an idea: First step is to identify all datasets distributed with ANUGA prior to releases I suggest modifying the script create_distribution.py such that all data files (based on agreed filename extensions) in the release are listed in a text file and on the screen. This would form the basis for a document that the release manager needs to get signed off in regard to datasets being unencumbered by licensing. To avoid repetition, we could look for special files accompanying each data file, with a description of its origin and if it has been vetted and approved for release. This is a start" ole 224 SWW aren't using single precision anymore? Functionality and features defect normal low duncan closed 2007-11-21T14:18:13+11:00 2007-11-30T08:11:53+11:00 "Joaquim Luis pointed this out on Sourceforge on 14th November 2007. We used to create all variables in SWW as single precision by setting self.precision = Float32. However, it seems that the new method store_header() is using a variable named 'precision' which isn't defined in the method and as such must come from the context. We need to check and test that sww files are using single precision. " ole 225 Add functionality to Screen_catcher to print to screen and save Functionality and features enhancement trivial low nick closed 2007-11-23T10:57:48+11:00 2008-03-04T16:48:43+11:00 "I think this should be fairly simply Here is the class Screen catcher, And all i think is needed is a way to exit the writ e method without having the sys.stdout write something. {{{ class Screen_Catcher: """"""this simply catches the screen output and stores it to file defined by start_screen_catcher (above) """""" def __init__(self, filename, old_stuff=''): self.filename = filename if exists(self.filename)is True: print'Old existing file ""%s"" has been deleted' %(self.filename) remove(self.filename) def write(self, stuff): fid = open(self.filename, 'a') fid.write(stuff) print_to_screen = True if print_to_screen: if old_stuff==stuff: return #somehow exit write without printing anything else: print stuff print 'old_stuff',old_stuff,'stuff',stuff old_stuff=stuff print 'old_stuff1',old_stuff,'stuff1',stuff }}} I have tried to implement the following case: If the print_to_screen is True, print the statement but stop sys.stdout printing out the results again which leads to an infinite loop. I tried using a test with old_stuff==stuff but i think the solution lies in exitting Screen_catcher Write() without printing anything... ""return"" doesn't work but is there something like return but works at a different level... if that makes any sense... Or explore a new way to pipe the print out away for sys.stdout to some other screen output" nick 226 Problem with sww2timeseries output file location is not consistent Functionality and features defect normal normal ole closed 2007-11-23T13:14:57+11:00 2009-09-10T16:21:30+10:00 "Matt Pittard installed anuga on C drive on a windows xp PC. He noticed that when running the gettimeseries.py in the cairns scenario in the anuga_demo. The graphs were outputted to the right directory but the csv files were outputed to the root directory. Both the csv files and the graphs are produced in ""generate_figures"" in util.py. The file id ""file_out"" used for the csv file is never closed... maybe this is a problem... Look at line 1058 {{{ thisfile = file_loc[j]+sep+'gauges_time_series'+'_'+gaugeloc+'.csv' fid_out = open(thisfile, 'w') }}} and around line 1087 {{{ s = '%.2f, %.2f, %.2f, %.2f, %.2f, %.2f, %.2f\n' %(t, w, m, vel, z, uh, vh) fid_out.write(s) }}} Also to note is that this function is over lapped with the ""make_plots_from_csv_file"" function in util.py. It could be useful to use parts of generate_figures to make a function say ""sww_gauges2csv"" or edit sww2timeseries to output the timeseries data into files..." nick 227 Add more printed out information about progress create_mesh_from_regions Functionality and features enhancement minor low nick closed 2007-11-23T17:18:52+11:00 2008-03-06T16:56:59+11:00 "It would be great to add some more printed out information in ""create_mesh_from_regions"". I'm running a model that has 1200000 triangles and there has been no output for about 2 hours... I think it is still running properly. The last information printed out is {{{ Recovering segments in Delaunay triangulation. Removing unwanted triangles. Spreading regional attributes and area constraints. Adding Steiner points to enforce quality. Writing vertices. Writing triangles. Writing segments. Writing neighbors. Statistics: Input vertices: 16 Input segments: 16 Input holes: 0 Mesh vertices: 599308 Mesh triangles: 1197392 Mesh edges: 1796699 Mesh exterior boundary edges: 1222 Mesh interior boundary edges: 3716 Mesh subsegments (constrained edges): 4938 }}} I'm not sure where this process is stuck but it is somewhere in ""mesh_interface.py""... I think. " nick 228 test_all failing Appearance and visualisation defect normal normal Duncan closed 2007-11-26T12:16:15+11:00 2007-11-26T12:16:23+11:00 " test_all fails with this error; {{{ execfile('test_all.py') File ""test_all.py"", line 158, in ? suite = regressionTest(test_verbose) File ""test_all.py"", line 110, in regressionTest modules = map(__import__, moduleNames) File ""damage_modelling/test_inundation_damage.py"", line 11, in ? from inundation_damage import * File ""damage_modelling/inundation_damage.py"", line 35, in ? from anuga_config import epsilon ImportError: No module named anuga_config }}} " duncan 229 Problem with Randint from Numeric when use by split in geospatial_data on cyclone however not tornado Other defect major low ole closed 2007-11-28T12:42:36+11:00 2007-11-28T12:50:36+11:00 "Here is a small piece of code that highlights the problem, it runs in seconds. Note the data file attached {{{ from anuga.geospatial_data.geospatial_data import * from os import sep, environ, getenv, getcwd,umask from anuga.pmesh.mesh_interface import create_mesh_from_regions from anuga.shallow_water import Domain from anuga.shallow_water import Reflective_boundary from anuga.shallow_water.data_manager import export_grid from anuga.shallow_water.data_manager import start_screen_catcher, copy_code_files from math import sqrt from time import localtime, strftime, gmtime home = getenv('INUNDATIONHOME') + sep +'data'+sep #output_dir = home + 'anuga_validation'+sep+'cocos'+sep+'anuga'+sep+'outputs'+sep+time+sep data_dir='/d/ehn/4/ehn/tsunami/data/bathymetry/Cocos/bathymetry/' data_dir_name = data_dir + 'new_edited_cocos_final' data_dir_name_small_clip=data_dir_name+'_small_clip' mesh_file=data_dir+'cocos.msh' sww_file='test_final' a_points = randint(0,99999,(80,2)) points = a_points.tolist() # print points Ga = Geospatial_data(points) G1, G2 = Ga.split(0.01,verbose=True) print 'finish test1 of split' G = Geospatial_data(file_name=data_dir_name_small_clip + '.txt') G1, G2 = G.split(0.01,verbose=True) }}} the data file is attached. When I run this code on cyclone two different problem occur. One of the problems is with randint() here is the error {{{ Traceback (most recent call last): File ""grid_test.py"", line 26, in ? a_points = randint(0,99999,(80,2)) File ""/opt/lib64/python2.3/site-packages/Numeric/RandomArray.py"", line 73, in randint a = ((maximum-minimum)* random(shape)) OverflowError: math range error }}} The other is here {{{ Traceback (most recent call last): File ""grid_test.py"", line 36, in ? G1, G2 = G.split(0.01,verbose=True) File ""/d/cit/1/cit/unixhome/nbartzis/anuga/anuga_core/source/anuga/geospatial_data/geospatial_data.py"", line 695, in split random_list.append(remainder_list.pop(i)) OverflowError: signed integer is greater than maximum }}} The interesting thing is that the unit tests for split in geospatial_data, force it to use randint and it is successful when run on cyclone It is not high on the list of things to do, but it does need to be recorded " nick 230 Problem with Randint from Numeric when use by split in geospatial_data on cyclone however not tornado Other defect normal low ole closed 2007-11-28T12:49:30+11:00 2009-09-04T12:23:13+10:00 "Here is a small piece of code that highlights the problem, it runs in seconds. Note the data file is here \\Gneiss\gem\5\nhi\inundation\data\anuga_validation\cocos\elevation_final\new_edited_cocos_final_small_clip.txt {{{ from anuga.geospatial_data.geospatial_data import * from os import sep, environ, getenv, getcwd,umask from anuga.pmesh.mesh_interface import create_mesh_from_regions from anuga.shallow_water import Domain from anuga.shallow_water import Reflective_boundary from anuga.shallow_water.data_manager import export_grid from anuga.shallow_water.data_manager import start_screen_catcher, copy_code_files from math import sqrt from time import localtime, strftime, gmtime home = getenv('INUNDATIONHOME') + sep +'data'+sep #output_dir = home + 'anuga_validation'+sep+'cocos'+sep+'anuga'+sep+'outputs'+sep+time+sep data_dir='/d/ehn/4/ehn/tsunami/data/bathymetry/Cocos/bathymetry/' data_dir_name = data_dir + 'new_edited_cocos_final' data_dir_name_small_clip=data_dir_name+'_small_clip' mesh_file=data_dir+'cocos.msh' sww_file='test_final' a_points = randint(0,99999,(80,2)) points = a_points.tolist() # print points Ga = Geospatial_data(points) G1, G2 = Ga.split(0.01,verbose=True) print 'finish test1 of split' G = Geospatial_data(file_name=data_dir_name_small_clip + '.txt') G1, G2 = G.split(0.01,verbose=True) }}} When I run this code on cyclone two different problem occur. One of the problems is with randint() here is the error {{{ Traceback (most recent call last): File ""grid_test.py"", line 26, in ? a_points = randint(0,99999,(80,2)) File ""/opt/lib64/python2.3/site-packages/Numeric/RandomArray.py"", line 73, in randint a = ((maximum-minimum)* random(shape)) OverflowError: math range error }}} The other is here {{{ Traceback (most recent call last): File ""grid_test.py"", line 36, in ? G1, G2 = G.split(0.01,verbose=True) File ""/d/cit/1/cit/unixhome/nbartzis/anuga/anuga_core/source/anuga/geospatial_data/geospatial_data.py"", line 695, in split random_list.append(remainder_list.pop(i)) OverflowError: signed integer is greater than maximum }}} The interesting thing is that the unit tests for split in geospatial_data, force it to use randint and it is successful when run on cyclone It is not high on the list of things to do, but it does need to be recorded " nick 231 validate_all fails on tornado node Testing and validation defect major low ole closed 2007-11-28T13:14:11+11:00 2007-11-30T16:15:54+11:00 "validate_all fails on tornado node since pylab could not be installed " duncan 232 maximum_inundation_from_sww test failing in windows Architecture and API defect normal normal Ole closed 2007-11-28T16:55:37+11:00 2007-11-29T18:13:25+11:00 "maximum_inundation_from_sww test failing in windows. I think the changeset:4862 broke this. Could you fix this one Ole? The values of runup & maximal_runup are both None. {{{ ERROR: test_get_maximum_inundation_from_sww(self) ---------------------------------------------------------------------- Traceback (most recent call last): File ""shallow_water\test_shallow_water_domain.py"", line 1286, in test_get_maxi mum_inundation_from_sww q = get_maximum_inundation_elevation('runup_test.sww') File ""X:\anuga_core\source\anuga\shallow_water\data_manager.py"", line 5512, in get_maximum_inundation_elevation verbose=verbose) File ""X:\anuga_core\source\anuga\shallow_water\data_manager.py"", line 5724, in get_maximum_inundation_data if runup > maximal_runup: TypeError: function not supported for these types, and can't coerce to supported types }}} " duncan 233 test_fit_time_and_mem fails on Nautilus Appearance and visualisation defect normal normal duncan closed 2007-11-29T18:56:57+11:00 2007-11-30T11:37:46+11:00 "---------------------------------------------------------------------- Ran 1 test in 1978.414s OK test_fit_time_and_mem (__main__.Test_uq) ... FAIL ====================================================================== FAIL: test_fit_time_and_mem (__main__.Test_uq) ---------------------------------------------------------------------- Traceback (most recent call last): File ""validate_benchmark_fit.py"", line 58, in test_fit_time_and_mem self.assert_(time>>>> ""Noe"" == Noe writes: Noe> thanks for your answer, but I already have a problem while Noe> launching the script : Noe> Fatal Python error: PyEval_RestoreThread: NULL tstate Noe> abnormal program termination This kind of error is almost always caused by an incompatibility in the GUI environment you are using and the backend you have chosen. The default backend is set in the configuration file - see http://matplotlib.sf.net/.matplotlibrc. See also http://matplotlib.sourceforge.net/faq.html#FREEZE and http://matplotlib.sourceforge.net/backends.html for general information on this problem. If you are running matplotlib from an IDE such as IDLE and you want to use the tkagg backend (a typical configuration for win32 users), it is recommended that you launch idle with -n. Unfortunately, there was an error in matplotlib/backends/backend_tkagg.py in the 'show' function in the 0.60.2 release. If this indeed is your configuration, try editing this file and commenting out the line Tk.mainloop() in the show function and relaunching idle with -n. The safest way to test/play/experiment with matplotlib is to launch your script from the command shell, choosing the backend with the -d flag, as in C:> python myscript.py -dTkAgg as described on http://matplotlib.sourceforge.net/backends.html. Once you have matplotlib configured to your satisfaction from the shell, you can refine your backend and IDE choice following the guidelines in the links above. Hope this helps, John Hunter" ole 236 update Cairns example with new plotting functions Documentation task normal normal nick closed 2007-12-03T18:04:38+11:00 2008-01-17T11:01:46+11:00 "When the new functions are ready, please update the Cairns demo to use these functions. Hopefully the outputs will look the same as those that are currently there. The last question in the FAQ should then refer back to this example (who knows how a user will use the manual?)" jane.sexton@… 237 test_all failing on cyclone nodes - test_find_optimal_smoothing_parameter failing Appearance and visualisation defect minor low Nick closed 2007-12-10T17:38:11+11:00 2008-03-05T08:03:11+11:00 " This may be related to ticket#230 What I'm getting; {{{ ====================================================================== ERROR: test_find_optimal_smoothing_parameter (test_geospatial_data.Test_Geospatial_data) ---------------------------------------------------------------------- Traceback (most recent call last): File ""geospatial_data/test_geospatial_data.py"", line 1855, in test_find_optimal_smoothing_parameter verbose=False) File ""/d/cit/1/dgray/inundation/anuga_core/source/anuga/geospatial_data/geospatial_data.py"", line 1480, in find_optimal_smoothing_parameter G_small, G_other = G.split(split_factor,seed_num, verbose=verbose) File ""/d/cit/1/dgray/inundation/anuga_core/source/anuga/geospatial_data/geospatial_data.py"", line 695, in split random_list.append(remainder_list.pop(i)) IndexError: pop index out of range ====================================================================== ERROR: test_find_optimal_smoothing_parameter1 (test_geospatial_data.Test_Geospatial_data) ---------------------------------------------------------------------- Traceback (most recent call last): File ""geospatial_data/test_geospatial_data.py"", line 1904, in test_find_optimal_smoothing_parameter1 verbose=False) File ""/d/cit/1/dgray/inundation/anuga_core/source/anuga/geospatial_data/geospatial_data.py"", line 1480, in find_optimal_smoothing_parameter G_small, G_other = G.split(split_factor,seed_num, verbose=verbose) File ""/d/cit/1/dgray/inundation/anuga_core/source/anuga/geospatial_data/geospatial_data.py"", line 695, in split random_list.append(remainder_list.pop(i)) IndexError: pop index out of range ====================================================================== ERROR: test if the results from spilt are disjoin sets ---------------------------------------------------------------------- Traceback (most recent call last): File ""geospatial_data/test_geospatial_data.py"", line 1812, in test_split G1, G2 = G.split(factor,100) File ""/d/cit/1/dgray/inundation/anuga_core/source/anuga/geospatial_data/geospatial_data.py"", line 695, in split random_list.append(remainder_list.pop(i)) IndexError: pop index out of range ---------------------------------------------------------------------- }}} " duncan 238 Too much output to screen in fitting algorithm Functionality and features enhancement normal normal ole closed 2007-12-11T15:26:54+11:00 2007-12-12T15:26:05+11:00 "Running real life simulations are now generating a lot of data that obscures the real progress i.e. how far the fitting has progressed. Here's an example from the Shark_bay 2007 scenario: It says that it is reading block 1262 out of 3155 which is great, but then it proceeds for hundreds of lines with repetitive information which I (at least) don't find helpful at all. This was much better and terser last time I ran this on the 30th of August 2007. Someone please find out what and why this has happened? {{{ Reading block 1262 (points 631000 to 631500) out of 3155 Getting indices inside mesh boundary Checking input to outside_polygon Checking input to separate_points_by_polygon Allocating array for indices Found 379 points (out of 500) inside polygon Building fitting matrix from 379 points Doing 0 of 379 Doing 38 of 379 Doing 76 of 379 Doing 114 of 379 Doing 152 of 379 Doing 190 of 379 Doing 228 of 379 Doing 266 of 379 Doing 304 of 379 Doing 342 of 379 Getting indices inside mesh boundary Checking input to outside_polygon Checking input to separate_points_by_polygon Allocating array for indices Found 373 points (out of 500) inside polygon Building fitting matrix from 373 points Doing 0 of 373 Doing 38 of 373 Doing 76 of 373 Doing 114 of 373 Doing 152 of 373 Doing 190 of 373 Doing 228 of 373 Doing 266 of 373 Doing 304 of 373 Doing 342 of 373 Getting indices inside mesh boundary Checking input to outside_polygon Checking input to separate_points_by_polygon Allocating array for indices Found 334 points (out of 500) inside polygon Building fitting matrix from 334 points Doing 0 of 334 Doing 34 of 334 Doing 68 of 334 Doing 102 of 334 Doing 136 of 334 Doing 170 of 334 Doing 204 of 334 Doing 238 of 334 Doing 272 of 334 Doing 306 of 334 Getting indices inside mesh boundary Checking input to outside_polygon Checking input to separate_points_by_polygon Allocating array for indices Found 393 points (out of 500) inside polygon Building fitting matrix from 393 points Doing 0 of 393 Doing 40 of 393 Doing 80 of 393 Doing 120 of 393 Doing 160 of 393 Doing 200 of 393 Doing 240 of 393 Doing 280 of 393 Doing 320 of 393 Doing 360 of 393 Getting indices inside mesh boundary Checking input to outside_polygon Checking input to separate_points_by_polygon Allocating array for indices Found 358 points (out of 500) inside polygon Building fitting matrix from 358 points Doing 0 of 358 Doing 36 of 358 Doing 72 of 358 Doing 108 of 358 Doing 144 of 358 Doing 180 of 358 Doing 216 of 358 Doing 252 of 358 Doing 288 of 358 Doing 324 of 358 Getting indices inside mesh boundary Checking input to outside_polygon Checking input to separate_points_by_polygon Allocating array for indices Found 334 points (out of 500) inside polygon Building fitting matrix from 334 points Doing 0 of 334 Doing 34 of 334 Doing 68 of 334 Doing 102 of 334 Doing 136 of 334 Doing 170 of 334 Doing 204 of 334 Doing 238 of 334 Doing 272 of 334 Doing 306 of 334 Getting indices inside mesh boundary Checking input to outside_polygon Checking input to separate_points_by_polygon Allocating array for indices Found 369 points (out of 500) inside polygon Building fitting matrix from 369 points Doing 0 of 369 Doing 37 of 369 Doing 74 of 369 Doing 111 of 369 Doing 148 of 369 Doing 185 of 369 Doing 222 of 369 Doing 259 of 369 Doing 296 of 369 Doing 333 of 369 Getting indices inside mesh boundary Checking input to outside_polygon Checking input to separate_points_by_polygon Allocating array for indices Found 380 points (out of 500) inside polygon Building fitting matrix from 380 points Doing 0 of 380 Doing 39 of 380 Doing 78 of 380 Doing 117 of 380 Doing 156 of 380 Doing 195 of 380 Doing 234 of 380 Doing 273 of 380 Doing 312 of 380 Doing 351 of 380 Getting indices inside mesh boundary Checking input to outside_polygon Checking input to separate_points_by_polygon Allocating array for indices Found 332 points (out of 500) inside polygon Building fitting matrix from 332 points Doing 0 of 332 Doing 34 of 332 Doing 68 of 332 Doing 102 of 332 Doing 136 of 332 Doing 170 of 332 Doing 204 of 332 Doing 238 of 332 Doing 272 of 332 Doing 306 of 332 Getting indices inside mesh boundary Checking input to outside_polygon Checking input to separate_points_by_polygon Allocating array for indices Found 332 points (out of 500) inside polygon Building fitting matrix from 332 points Doing 0 of 332 Doing 34 of 332 Doing 68 of 332 Doing 102 of 332 Doing 136 of 332 Doing 170 of 332 Doing 204 of 332 Doing 238 of 332 Doing 272 of 332 Doing 306 of 332 Getting indices inside mesh boundary Checking input to outside_polygon Checking input to separate_points_by_polygon Allocating array for indices Found 391 points (out of 500) inside polygon Building fitting matrix from 391 points Doing 0 of 391 Doing 40 of 391 Doing 80 of 391 Doing 120 of 391 Doing 160 of 391 Doing 200 of 391 Doing 240 of 391 Doing 280 of 391 Doing 320 of 391 Doing 360 of 391 Getting indices inside mesh boundary Checking input to outside_polygon Checking input to separate_points_by_polygon Allocating array for indices Found 357 points (out of 500) inside polygon Building fitting matrix from 357 points Doing 0 of 357 Doing 36 of 357 Doing 72 of 357 Doing 108 of 357 Doing 144 of 357 Doing 180 of 357 Doing 216 of 357 Doing 252 of 357 Doing 288 of 357 Doing 324 of 357 Getting indices inside mesh boundary Checking input to outside_polygon Checking input to separate_points_by_polygon Allocating array for indices Found 332 points (out of 500) inside polygon Building fitting matrix from 332 points Doing 0 of 332 Doing 34 of 332 Doing 68 of 332 Doing 102 of 332 Doing 136 of 332 Doing 170 of 332 Doing 204 of 332 Doing 238 of 332 Doing 272 of 332 Doing 306 of 332 Getting indices inside mesh boundary Checking input to outside_polygon Checking input to separate_points_by_polygon Allocating array for indices Found 355 points (out of 500) inside polygon Building fitting matrix from 355 points Doing 0 of 355 Doing 36 of 355 Doing 72 of 355 Doing 108 of 355 Doing 144 of 355 Doing 180 of 355 Doing 216 of 355 Doing 252 of 355 Doing 288 of 355 Doing 324 of 355 Getting indices inside mesh boundary Checking input to outside_polygon Checking input to separate_points_by_polygon Allocating array for indices Found 392 points (out of 500) inside polygon Building fitting matrix from 392 points Doing 0 of 392 Doing 40 of 392 Doing 80 of 392 Doing 120 of 392 Doing 160 of 392 Doing 200 of 392 Doing 240 of 392 Doing 280 of 392 Doing 320 of 392 Doing 360 of 392 Getting indices inside mesh boundary Checking input to outside_polygon Checking input to separate_points_by_polygon Allocating array for indices Found 330 points (out of 500) inside polygon Building fitting matrix from 330 points Doing 0 of 330 Doing 34 of 330 Doing 68 of 330 Doing 102 of 330 Doing 136 of 330 Doing 170 of 330 Doing 204 of 330 Doing 238 of 330 Doing 272 of 330 Doing 306 of 330 Getting indices inside mesh boundary Checking input to outside_polygon Checking input to separate_points_by_polygon Allocating array for indices Found 328 points (out of 500) inside polygon Building fitting matrix from 328 points Doing 0 of 328 Doing 33 of 328 Doing 66 of 328 Doing 99 of 328 Doing 132 of 328 Doing 165 of 328 Doing 198 of 328 Doing 231 of 328 Doing 264 of 328 Doing 297 of 328 Getting indices inside mesh boundary Checking input to outside_polygon Checking input to separate_points_by_polygon Allocating array for indices Found 413 points (out of 500) inside polygon Building fitting matrix from 413 points Doing 0 of 413 Doing 42 of 413 Doing 84 of 413 Doing 126 of 413 Doing 168 of 413 Doing 210 of 413 Doing 252 of 413 Doing 294 of 413 Doing 336 of 413 Doing 378 of 413 Getting indices inside mesh boundary Checking input to outside_polygon Checking input to separate_points_by_polygon Allocating array for indices Found 327 points (out of 500) inside polygon Building fitting matrix from 327 points Doing 0 of 327 Doing 33 of 327 Doing 66 of 327 Doing 99 of 327 Doing 132 of 327 Doing 165 of 327 Doing 198 of 327 Doing 231 of 327 Doing 264 of 327 Doing 297 of 327 Getting indices inside mesh boundary Checking input to outside_polygon Checking input to separate_points_by_polygon Allocating array for indices Found 326 points (out of 500) inside polygon Building fitting matrix from 326 points Doing 0 of 326 Doing 33 of 326 Doing 66 of 326 Doing 99 of 326 Doing 132 of 326 Doing 165 of 326 Doing 198 of 326 Doing 231 of 326 Doing 264 of 326 Doing 297 of 326 Getting indices inside mesh boundary Checking input to outside_polygon Checking input to separate_points_by_polygon Allocating array for indices Found 380 points (out of 500) inside polygon Building fitting matrix from 380 points Doing 0 of 380 Doing 39 of 380 Doing 78 of 380 Doing 117 of 380 Doing 156 of 380 Doing 195 of 380 Doing 234 of 380 Doing 273 of 380 Doing 312 of 380 Doing 351 of 380 Getting indices inside mesh boundary Checking input to outside_polygon Checking input to separate_points_by_polygon Allocating array for indices Found 356 points (out of 500) inside polygon Building fitting matrix from 356 points Doing 0 of 356 Doing 36 of 356 Doing 72 of 356 Doing 108 of 356 Doing 144 of 356 Doing 180 of 356 Doing 216 of 356 Doing 252 of 356 Doing 288 of 356 Doing 324 of 356 Getting indices inside mesh boundary Checking input to outside_polygon Checking input to separate_points_by_polygon Allocating array for indices Found 324 points (out of 500) inside polygon Building fitting matrix from 324 points Doing 0 of 324 Doing 33 of 324 Doing 66 of 324 Doing 99 of 324 Doing 132 of 324 Doing 165 of 324 Doing 198 of 324 Doing 231 of 324 Doing 264 of 324 Doing 297 of 324 Getting indices inside mesh boundary Checking input to outside_polygon Checking input to separate_points_by_polygon Allocating array for indices Found 373 points (out of 500) inside polygon Building fitting matrix from 373 points Doing 0 of 373 Doing 38 of 373 Doing 76 of 373 Doing 114 of 373 Doing 152 of 373 Doing 190 of 373 Doing 228 of 373 Doing 266 of 373 Doing 304 of 373 Doing 342 of 373 Getting indices inside mesh boundary Checking input to outside_polygon Checking input to separate_points_by_polygon Allocating array for indices ...... ...... }}}" ole 240 assignment warning in triang_genMesh Compilation and installation defect minor low duncan closed 2008-01-07T16:44:49+11:00 2008-01-09T13:28:24+11:00 "When running ""compile_all.py"" the following warnings are incountered. {{{ mesh_engine_c_layer.c: In function `triang_genMesh': mesh_engine_c_layer.c:254: warning: assignment from incompatible pointer type mesh_engine_c_layer.c:268: warning: assignment from incompatible pointer type mesh_engine_c_layer.c:275: warning: assignment from incompatible pointer type mesh_engine_c_layer.c:283: warning: assignment from incompatible pointer type mesh_engine_c_layer.c:293: warning: assignment from incompatible pointer type mesh_engine_c_layer.c:301: warning: assignment from incompatible pointer type mesh_engine_c_layer.c:309: warning: assignment from incompatible pointer type mesh_engine_c_layer.c:317: warning: assignment from incompatible pointer type }}} These warnings are created when run on both Linux and windows OS Furthermore Nick is experiencing a run-time error on his older Win 2000 PC and is hoping it is linked to this error. " nick 241 Nick is experiencing a run-time error on his older Win 2000 PC Appearance and visualisation defect critical highest Duncan closed 2008-01-08T09:56:09+11:00 2008-01-09T13:27:28+11:00 test all fails in test generate mesh. anonymous 242 auto validate, test fit and mem failing. Architecture and API defect normal normal ole closed 2008-01-08T10:01:32+11:00 2009-01-19T09:16:56+11:00 the fit is using more memory than previously. Could be related to ticket#241. Indicates a memory leak. duncan 244 Is fit_to_mesh caching properly? Architecture and API defect normal normal ole closed 2008-01-12T06:10:33+11:00 2009-01-18T13:16:58+11:00 "In Joaquim Luis' example it seems that caching doesn't work. It keeps saying (on my home computer) that arguments or bytecode have changed. The arguments hash to the same number. See https://datamining.anu.edu.au/anuga/browser/anuga_work/development/joaqium_luis/run.py " ole 245 Updating of mesh breaks on 64 bit machines Architecture and API defect critical highest duncan closed 2008-01-17T16:28:04+11:00 2008-01-18T11:48:10+11:00 "There has been some recent updates to mesh, which has broken anuga on 64 bit machines, using pyrhon 2.4. Probably the usual problem of something which should be an integer being a list containing one integer? For instance running test_all.py in the damage_modelling directory produces errors of the form: Testing: test_inundation_damage.py EEEEEEEEE ====================================================================== ERROR: test_calc_collapse_probability (test_inundation_damage.Test_inundation_damage) ---------------------------------------------------------------------- Traceback (most recent call last): File ""damage_modelling/test_inundation_damage.py"", line 62, in setUp m.auto_segment() File ""/home/steve/ga/anuga_core/source/anuga/pmesh/mesh.py"", line 1540, in auto_segment self._createBoundary(alpha=alpha) File ""/home/steve/ga/anuga_core/source/anuga/pmesh/mesh.py"", line 1553, in _createBoundary alpha=alpha) File ""/home/steve/ga/anuga_core/source/anuga/alpha_shape/alpha_shape.py"", line 66, in __init__ self._alpha_shape_algorithm(alpha) File ""/home/steve/ga/anuga_core/source/anuga/alpha_shape/alpha_shape.py"", line 213, in _alpha_shape_algorithm self._vertex_intervals() File ""/home/steve/ga/anuga_core/source/anuga/alpha_shape/alpha_shape.py"", line 364, in _vertex_intervals vertexnbrs[j].append(t) TypeError: list indices must be integers " anonymous 246 Errors in test_geospatial_data when run on node of cyclone. Functionality and features defect minor low nick closed 2008-02-05T17:00:21+11:00 2008-02-06T09:23:38+11:00 "4 tests fail when running test_geospatial_data.py on a node using mpirun. {{{ ====================================================================== ERROR: test_find_optimal_smoothing_parameter (__main__.Test_Geospatial_data) ---------------------------------------------------------------------- Traceback (most recent call last): File ""test_geospatial_data.py"", line 1878, in test_find_optimal_smoothing_parameter verbose=False) File ""/d/cit/1/cit/unixhome/nbartzis/anuga/anuga_core/source/anuga/geospatial_data/geospatial_data.py"", line 1485, in find_optimal_smoothing_parameter G_small, G_other = G.split(split_factor,seed_num, verbose=verbose) File ""/d/cit/1/cit/unixhome/nbartzis/anuga/anuga_core/source/anuga/geospatial_data/geospatial_data.py"", line 697, in split random_list.append(remainder_list.pop(i)) IndexError: pop index out of range ====================================================================== ERROR: test_find_optimal_smoothing_parameter1 (__main__.Test_Geospatial_data) ---------------------------------------------------------------------- Traceback (most recent call last): File ""test_geospatial_data.py"", line 1927, in test_find_optimal_smoothing_parameter1 verbose=False) File ""/d/cit/1/cit/unixhome/nbartzis/anuga/anuga_core/source/anuga/geospatial_data/geospatial_data.py"", line 1485, in find_optimal_smoothing_parameter G_small, G_other = G.split(split_factor,seed_num, verbose=verbose) File ""/d/cit/1/cit/unixhome/nbartzis/anuga/anuga_core/source/anuga/geospatial_data/geospatial_data.py"", line 697, in split random_list.append(remainder_list.pop(i)) IndexError: pop index out of range ====================================================================== ERROR: test if the results from spilt are disjoin sets ---------------------------------------------------------------------- Traceback (most recent call last): File ""test_geospatial_data.py"", line 1812, in test_split G1, G2 = G.split(factor,100) File ""/d/cit/1/cit/unixhome/nbartzis/anuga/anuga_core/source/anuga/geospatial_data/geospatial_data.py"", line 697, in split random_list.append(remainder_list.pop(i)) IndexError: pop index out of range ====================================================================== ERROR: test if the results from spilt are disjoin sets ---------------------------------------------------------------------- Traceback (most recent call last): File ""test_geospatial_data.py"", line 1836, in test_split1 G1, G2 = G.split(factor,100) File ""/d/cit/1/cit/unixhome/nbartzis/anuga/anuga_core/source/anuga/geospatial_data/geospatial_data.py"", line 697, in split random_list.append(remainder_list.pop(i)) IndexError: pop index out of range }}} This does not occur when test_all is run on the head node." nick 247 mesh_engine.c not compiling, since it shouldn't be there anyhow. Compilation and installation defect normal normal ole closed 2008-02-08T09:40:30+11:00 2008-02-08T09:43:43+11:00 " {{{ Trying to compile c-extension mesh_engine.c in C:\\Python25\\Lib\\site-packages\\anu\par ga\\mesh_engine\par Compiler: gcc.exe, version 3.4.5\par \par gcc.exe -c mesh_engine.c -I""C:\\Python25\\include"" -I""C:\\Python25\\Lib\\site-package\par s\\anuga\\utilities"" -o ""mesh_engine.o"" -Wall -O3\par mesh_engine.c: In function `triang_genMesh':\par mesh_engine.c:156: warning: implicit declaration of function `malloc'\par mesh_engine.c:545: warning: implicit declaration of function `free'\par mesh_engine.c:87: warning: 'n' might be used uninitialized in this function\par mesh_engine.c: At top level:\par C:/Python25/include/Numeric/arrayobject.h:287: warning: 'PyArray_API' defined bu\par t not used\par gcc.exe -shared mesh_engine.o -o mesh_engine.dll ""C:\\Python25\\python25.dll"" -lm\par \par mesh_engine.o:mesh_engine.c:(.text+0x806): undefined reference to `triangulate'\par collect2: ld returned 1 exit status\par compile_all.py:302: DeprecationWarning: raising a string exception is deprecated\par \par compile_all.py:304: DeprecationWarning: raising a string exception is deprecated\par \par }}} " anonymous 248 test all failing on tornado Management and planning defect normal normal ole closed 2008-02-11T10:45:50+11:00 2009-03-18T17:14:38+11:00 " {{{ ====================================================================== ERROR: Basic test using an invalid XML file. This one ---------------------------------------------------------------------- Traceback (most recent call last): File ""/d/xrd/gem/5/nhi/inundation/sandpits/dgray/inundation/anuga_core/source/anuga/utilities/test_data_audit.py"", line 150, in test_license_file_is_not_valid2 license_file_is_valid(licfid) File ""/d/xrd/gem/5/nhi/inundation/sandpits/dgray/inundation/anuga_core/source/anuga/utilities/data_audit.py"", line 214, in license_file_is_valid raise CRCMismatch, msg CRCMismatch: Bad checksum (CRC). The CRC reported in license file ""./tmp1WD6_0.lic"" is ""-1484449438"" The CRC computed from file ""././tmp1WD6_0.asc"" is ""2810517858"" ====================================================================== ERROR: Basic test using an valid XML file ---------------------------------------------------------------------- Traceback (most recent call last): File ""/d/xrd/gem/5/nhi/inundation/sandpits/dgray/inundation/anuga_core/source/anuga/utilities/test_data_audit.py"", line 292, in test_license_file_is_valid license_file_is_valid(licfid)#, verbose=True) File ""/d/xrd/gem/5/nhi/inundation/sandpits/dgray/inundation/anuga_core/source/anuga/utilities/data_audit.py"", line 214, in license_file_is_valid raise CRCMismatch, msg CRCMismatch: Bad checksum (CRC). The CRC reported in license file ""./tmp0jElRZ.lic"" is ""-1484449438"" The CRC computed from file ""./tmp0jElRZ.asc"" is ""2810517858"" ====================================================================== ERROR: Test of XML file with more than one datafile element. ---------------------------------------------------------------------- Traceback (most recent call last): File ""/d/xrd/gem/5/nhi/inundation/sandpits/dgray/inundation/anuga_core/source/anuga/utilities/test_data_audit.py"", line 366, in test_valid_license_file_with_multiple_files license_file_is_valid(licfid)#, verbose=True) File ""/d/xrd/gem/5/nhi/inundation/sandpits/dgray/inundation/anuga_core/source/anuga/utilities/data_audit.py"", line 214, in license_file_is_valid raise CRCMismatch, msg CRCMismatch: Bad checksum (CRC). The CRC reported in license file ""./tmpaRnKC6.lic"" is ""-1484449438"" The CRC computed from file ""././tmpaRnKC6.asc"" is ""2810517858"" ---------------------------------------------------------------------- Ran 688 tests in 36.076s FAILED (errors=3) }}} " duncan 249 problem with domain.set_time()... NO writer? Functionality and features defect normal low ole closed 2008-02-18T13:35:47+11:00 2009-09-04T12:22:03+10:00 "In the model to validate ANUGA to the circular island wavetank experiment. I have tried to start a model at 20 seconds using the following code. However I get an error about a 'writer'. I have checked in the code, look in anuga_validation circular_island, the 'domain.set_time(20.0)' line is commented out. {{{ domain.set_boundary({'wave': Bts, 'wall': Br, 'buffer':Bd}) domain.set_time(20.0) #------------------------- # Evolve through time #------------------------- import time t0 = time.time() for t in domain.evolve(yieldstep = 1, finaltime = 30): domain.write_time() }}} Here is the error {{{ File_function data obtained from: ts2cnew1_input.tms References: Start time: 0.000000 Traceback (most recent call last): File ""run_circular.py"", line 249, in ? for t in domain.evolve(yieldstep = 1, finaltime = 30): File ""/d/cit/1/cit/unixhome/nbartzis/anuga/anuga_core/source/anuga/shallow_water/shallow_water_domain.py"", line 432, in evolve self.store_timestep(self.quantities_to_be_stored) File ""/d/cit/1/cit/unixhome/nbartzis/anuga/anuga_core/source/anuga/shallow_water/shallow_water_domain.py"", line 461, in store_timestep self.writer.store_timestep(name) AttributeError: Domain instance has no attribute 'writer' }}} " nick 250 Extend set_quantity to allow addition of values Architecture and API enhancement normal normal ole closed 2008-02-20T06:20:18+11:00 2009-01-09T15:29:28+11:00 "Sometimes, there is a need for adding values to a quantity - e.g. to put buildings on top of a landscape. Polygon_function is often used for defining the buildings, but there is currently no mechanism for adding them. I suggest allowing a new boolean keyword, addition, in set_quantity so that one can say: {{{ set_quantity('elevation', elevation_data set_quantity('elevation', building_data, addition=True) }}} It would be easy to implement using the overloading of '+' already present in class Quantity. I suggest something like this if addition is True: {{{ def set_quantity(quantity_name, x, addition=False): ... if addition is True: Q1 = domain.get_quantity(quantity_name) Q2 = Quantity(domain) # Create new temporary quantity Q2.set_values(x) domain.set_quantity(quantity_name, Q1+Q2, addition=False) or domain.quantities[quantity_name] += Q2 }}} Alternatively, we could make this behaviour the default as quantities are initialised as zero, and have a keyword 'replace'. On the other hand, this could be confusing whenever a code needs to change a quantity. " ole 251 can't find ScientificPython 2.4.9 for use with the installation guide Compilation and installation defect normal high duncan closed 2008-02-22T12:40:11+11:00 2008-04-09T10:23:05+10:00 "The current link goes to an empty page The following link provides Scientific Python back to version 2.5.10 http://sourcesup.cru.fr/search/?type_of_search=full&group_id=180&words=scientificpython+2.4.9&Search=Search" jane.sexton@… 253 Can geospatial_data use caching? Efficiency and optimisation enhancement minor normal ole closed 2008-03-04T09:55:10+11:00 2009-03-18T17:17:11+11:00 "Currently geospatial_data object doesn't use caching. It would be beneficial for it to have caching especially when loading large datasets from 'pts' or 'txt' file. What might be a good idea is to allow for a 'blocking' read-write. This would e.g. be useful for converting large csv files to pts files in case where the data won't fit in memory." nick 255 ANUGA dies mysteriously in clip of geospatial_data dies with no error message! Functionality and features defect minor low ole closed 2008-03-07T16:02:30+11:00 2009-09-04T12:20:47+10:00 "The error should be replicated if you run the build_geraldton.py script in this directory: J:\inundation\data\western_australia\geraldton_tsunami_scenario\anuga\outputs\Keep_for_trac_ticket_20080305_020727_build_trial_0.75_other_nbartzis I did explore the problem with many print statements (but time was against me) It might be something to do with ensure_numeric or get_absolute... ??? good luck :)" nick 256 Is parallel anuga working? ANUGA enhancements Functionality and features defect minor normal hudson closed 2008-03-10T12:14:39+11:00 2010-05-14T10:58:43+10:00 "I have run a couple of test with parallel anuga and none have worked completely lately. Most recently i have ran this broome scenaria on 8 nodes and it stalled in the evolution J:\inundation\data\western_australia\broome_tsunami_scenario_2006\anuga\outputs\20080308_002224_run_trial_4.9_dampier_nbartzis Can someone please run this model and see if it works and it is not just a simple mistake i have made... Note, could it have anything to do with having 'bypass = True' commented out on 180 in pypar_broadcast and pypar.reduce inside of parallel_shallow_water Cheers Nick" nick 257 Catch error if polygons are warped Functionality and features defect normal normal hudson closed 2008-03-12T10:55:38+11:00 2010-04-21T14:24:20+10:00 "Petar Milevsky of Wollongong created a mesh with a warped polygon (see attached). A mesh was created, but excessive values for stage and momentum occurred. ANUGA should catch this condition and raise a meaningful exception. See code in https://datamining.anu.edu.au/anuga/browser/anuga_work/debug Turn it into a unit test and implement a proper exception." ole 258 Modelling the observed effects of the 1953 tsunami on Suva, Fiji Submarine mass failure capability Project proposals task normal lowest jane closed 2008-03-17T16:51:09+11:00 2012-02-13T14:39:40+11:00 "This is a graduate proposal: See source:/anuga_core/documentation/planning/graduate_proposal_suva1953.doc " ole 259 The role of the Great Barrier Reef in tsunami events Validation of GA tsunami modelling methodology Project proposals task normal lowest jane closed 2008-03-17T17:20:45+11:00 2012-02-13T14:40:03+11:00 "Graduate proposal aiming to study the effect of the GBR on tsunamis. See source:/anuga_core/documentation/planning/graduate_proposal_GBR.doc " ole 260 Validation of the tsunami modelling methodology against the 2004 tsunami Validation of GA tsunami modelling methodology Project proposals task normal normal jakeman closed 2008-03-17T17:23:43+11:00 2009-09-10T16:17:57+10:00 Conduct Validation of the Tsunami Modelling Methodology using impact data from Patong Beach in Phuket, Thailand. This is a contract with the ANU and carried out by John Jakeman. Link to document to appear here later. ole 261 Modelling the observed effects of the Nias March 2005 tsunami on Western Australian tide gauges Validation of GA tsunami modelling methodology Project proposals task normal lowest ole closed 2008-03-17T17:26:02+11:00 2012-02-13T14:40:34+11:00 Graduate proposal aiming at validationg the tsunami modelling methodology using WA tide gauges for the March 2005 event. See source:/anuga_core/documentation/planning/graduate_proposal_tsunami2005.doc ole 262 Implement option to calculate momentum using centroid speeds Efficiency and optimisation enhancement normal normal ole closed 2008-03-20T04:45:43+11:00 2009-09-10T16:16:41+10:00 "This calculation is currently part of the code balance_deep_and_shallow invoked by domain.tight_slope_limiters = True (see source:/anuga_core/source/anuga/shallow_water/shallow_water_domain.py). However, if pulled out as an independent option, we can disable the gradient-limiter for momentum altogether and thus improve the overall speed of ANUGA when this option is switched on. I understand that we may develop velocity limiters at a later point and use those to reconstruct momentum. However, this a step in that direction and will provide a further gain in computation speed. " ole 263 Build boundary object for URS point output Validation of GA tsunami modelling methodology Functionality and features enhancement normal normal jakeman closed 2008-03-26T14:43:53+11:00 2009-09-10T16:15:07+10:00 ole 264 John to provide Richard with coordinates tracing the existing ANUGA boundary and Richard to do the runs Validation of GA tsunami modelling methodology Other task normal normal richard closed 2008-03-26T15:42:01+11:00 2008-05-12T09:45:03+10:00 So that Richard may provide coarse URS output at the nearest 2min points. ole 265 Model to continue beyond end of time in forcing terms such as rainfall Functionality and features enhancement normal normal ole closed 2008-03-31T13:48:40+11:00 2008-10-28T17:21:28+11:00 "Currently, ANUGA will stop once a rainfall timeseries ends. It would be good to allow ANUGA to run even if forcing terms can't be called. Perhaps a warning should be issued first time this is encountered just in case it is symptomatic of another problem. This could be implemented by using a try-except construct where forcing terms are being evaluated. " ole 266 Tsunami Online Delivery Framework Project proposals task normal normal ole closed 2008-04-01T14:47:43+11:00 2009-09-10T16:14:09+10:00 "This is an IM project: See source:/anuga_core/documentation/planning/proposal_tsunami_database_2008.doc " ole 267 ANUGA maintenance and development ANUGA maintenance Project proposals task normal normal rwilson closed 2008-04-01T14:51:09+11:00 2009-09-10T16:11:23+10:00 This is an IM project: See source:/anuga_core/documentation/planning/proposal_anuga_maintenance_2008.doc ole 268 Update installation guide Compilation and installation task normal normal rwilson closed 2008-04-09T08:48:38+10:00 2009-09-11T09:07:19+10:00 Suggestions by Craig Palmer ole 269 How to extract elevation and other quantitites from sww files Validation of GA tsunami modelling methodology Documentation task normal normal ole closed 2008-04-11T10:19:11+10:00 2008-04-28T18:22:24+10:00 "Implement if necessary and add to FAQ in user manual (https://datamining.anu.edu.au/anuga/browser/anuga_core/documentation/user_manual/anuga_user_manual.tex) " ole 270 Obtain data underpinning 1964 tsunami simulation Validation of GA tsunami modelling methodology Testing and validation task normal lowest leharne closed 2008-04-11T10:58:18+10:00 2012-02-13T14:41:10+11:00 Uslu et al has reported on a tsunami simulation of the 1964 great Alaskan earthquake and tsunami. If we can get hold of the elevation data, the source model and the impact, this would form another good validation data set. ole 271 SWW header modification Documentation enhancement normal normal ole closed 2008-04-11T11:17:45+10:00 2009-09-10T16:13:13+10:00 "Tony Hunter has requested the following to be added to the sww file headers to enable more automated harvesting of metadata from the bathymetry files used in modelling runs. * the geographic bounding box co-ordinates to be output as 4 tuplets in an ascii format (priority highest) * as a secondary request the existing header information and the geographic bounding box to be output in XML format. (priority middle) First request is the highest priority as it will lead to testing of harvesting capabilities for Inundation Impact model runs, into MITS. " ole 274 Improved CFL condition Efficiency and optimisation enhancement normal high ole closed 2008-04-17T14:07:45+10:00 2008-04-30T13:17:23+10:00 "Ted suggested using the distance between centers of inscribed circles (or r1 + r2) for the CFL criterion instead of just the radius r1. r1 is the radius of the inscribed circle of the triangle in question and r2 the radius of the neighbouring triangle. This approach should be sufficient to maintain stability and make the code about twice as fast." ole 276 Allow ANUGA to work with python2.5 Compilation and installation task normal normal Duncan closed 2008-04-23T17:19:57+10:00 2008-06-12T21:40:43+10:00 " Jack added this, describing how to install python 2.5 \anuga_core\documentation\install_win32_python25.txt, So ANUGA can work with python 2.5. Can python 2.5 be easily installed for ANUGA? I have an admin install of python2.5 on my PC. " duncan 277 URS_points_needed_to_file - issue Validation of GA tsunami modelling methodology Functionality and features defect normal low duncan closed 2008-04-28T10:15:20+10:00 2008-04-30T11:46:36+10:00 " unit test has been written (in test_data_manager.py). First test uses the boundary from broome and it passes. The second test uses the boundary from boxing day scenario and it doesn't pass. I'm wondering whether it's a hemisphere problem, but I don't know. Duncan - with the development of the new boundary object to align with the hazard polyline output, this ticket will probably become moot. I'll change the priority to low and see how we go over the next month or so and whether this needs to be resolved or not." sexton 278 Implement Inflow Boundary Condition Functionality and features enhancement normal normal ole closed 2008-04-30T13:32:44+10:00 2012-02-13T14:46:12+11:00 "Create boundary object that can apply a hydrograph to a boundary segment. The units are cubic meters per second and it should be time varying. The challenge is to estimate the depth along the boundary segment based on Manning's formula and the slope into the domain. {{{ Q = V*A V = R^{2/3} * S^{1/2}/n Where Q is the inflow [m^3/s] A is the area of the boundary cross section V is the estimated velocity R is the perimeter width ~ estimated depth S is the slope of the energy line ~ inward bedslope }}} the estimated quantities may be the result of an iterative process. Please comment on this everyone. " ole 279 Concentrated ANUGA development Functionality and features task normal highest ole closed 2008-04-30T13:33:37+10:00 2009-09-04T09:29:32+10:00 "From Monday 5 May to Friday 9th May Ole will work at the ANU on the following issues: * Assist John Jakeman with Validation work, ticket:260 * Engage with reviving the parallel ANUGA capability, ticket:256 * Address other tickets by priority 1. Integrate new edge limiter which addresses Will Power's convergence observation and test it against our benchmarks. See ticket:195, ticket:262 and ticket:213 2. Flow through a cross section, ticket:175 3. Implement general polygons and refactor set_values, ticket:275 4. Look at kinematic viscosity, ticket:273 5. Blocking csv2pts script, ticket:272 6. Culvert flows: ticket:145 7. and more as appropriate, e.g. ticket:194, ticket:257, ticket:239, ticket:278 " ole 282 The unix home directories are getting a quota of 500 MB, this isn't enough for caching Appearance and visualisation defect normal normal Duncan closed 2008-05-23T13:58:42+10:00 2008-05-26T09:54:22+10:00 "The Unix home directories at GA are getting a quota of 500 MB, this isn't enough for caching, and ANUGA has crashed on people due to caching not being able to write to the unix home. Action: Move .python_cache to the nhip_models/inundation dir. " duncan 283 Work on Patong Beach validation Validation of GA tsunami modelling methodology Testing and validation task normal high john closed 2008-06-04T11:01:17+10:00 2009-09-04T11:59:38+10:00 " * Use 400 sqm resolution on beach instead of 100 sqm. Verify smoothing artefacts gone. * Decrease yieldsteps to 5s on a coarse grid to compare timeseries * Verify URS (mux2) and ANUGA time series from boundary into beach at identical points. They should be almost identical near boundary. Check also timing of wave arrivals. * Most and URS sources appear to be different. Check source parameters from Diana Greenslade's paper (John) and communicate with Richard and David (Ole) * If we see attenuation due to resolution, try running Edge_limiter + RK2 option. " ole 284 Compiler warning in urs_ext.c Compilation and installation defect normal lowest jakeman closed 2008-06-16T15:21:36+10:00 2009-09-04T12:38:16+10:00 "The C-code urs_ext.c is used to read mux files generated by URS. When compiled it warns of a possible uninitialised pointer in line 184: Memory for the variable mytgs is only allocated when numSrc > 1 and may thus be NIL otherwise. Here's an email trail that captures the discussion. --------------- Email trail ---------- That's the spirit Chris! Have no mercy. A slightly less brutal error message could be achieved by checking that numSrc is positive when it is first read in and failing with a more helpful error message is numSrc is <1. Neither of the subroutines make sense if numSrc is <1. In the calling routine which I assume one of you wrote (the PyObject) the same problem occurs since numSrc is used in a couple of malloc statements there as well. Therefore the sanity check needs to be in the PyObject ""*read_mux2"" if you want to add it in. I also note that numSrc isn't used in the statement which calls ""_read_mux2"" (line 117). Something called ""pyweights->nd"" is used instead. An earlier check (line 77) appears to require this to be 1, which means the ""numSrc"" variable in ""_read_mux2"" is always 1 which is not always true (but does ensure it is never zero at least). Am I reading your code correctly? David -----Original Message----- From: Thomas Chris Sent: Thursday, 29 May 2008 8:43 AM To: Nielsen Ole; Burbidge David; 'John Jakeman' Subject: RE: Possible uninitialised pointer in urs_ext.c [SEC=UNCLASSIFIED] Yes, if anyone tries to demultiplex a quantity of zero mux2 files then they deserve a segmentation violation. -----Original Message----- From: Nielsen Ole Sent: Wednesday, 28 May 2008 6:12 PM To: Thomas Chris; Burbidge David; 'John Jakeman' Subject: RE: Possible uninitialised pointer in urs_ext.c [SEC=UNCLASSIFIED] ... and John, Chris assures me that numSrc will be greater than zero when we aggregate events from the hazard map. Cheers Ole ----------------------------------------------------------------------------- Dr. Ole Nielsen | Senior Computational Scientist Natural Hazard Impacts Project | Tsunami Risk Modelling team leader Risk & Impact Analysis Group | E: Ole.Nielsen@ga.gov.au Geospatial and Earth Monitoring Division | P: +61 2 6249 9048 Geoscience Australia | F: +61 2 6249 9986 ----------------------------------------------------------------------------- -----Original Message----- From: Thomas Chris Sent: Wednesday, 28 May 2008 5:44 To: Nielsen Ole; Burbidge David; 'John Jakeman' Cc: Sexton Jane; Gray Duncan; Dhu Trevor Subject: RE: Possible uninitialised pointer in urs_ext.c [SEC=UNCLASSIFIED] Whew! I wish a software engineer wasn't looking at code I wrote. The original demuxing code allowed for the possibility of demuxing one or more mux2 files, weighting them and adding the results. This might be used for example if you have 10 unit sources, all comprising the one simulated earthquake. The mux files associated with the propagation from each unit source can be weighted (by the amount of slip on each unit source) and added to produce the time series for the combined event. The variable numSrc is the number of mux files that one is demuxing, weighting and adding together. Therefore it makes no sense whatsoever for the code to continue if numSrc == 0. The structure tgsrwg holds some information about the data in the mux file, including the time step and the total length of the time series. If numSrc == 1 then we only need allocated space for one variable of type tgsrwg to hold this information. If numSrc > 1 then the code works by reading and processing the first mux file (in which process mytgs0 will be used), and then by looping over the other mux files and one by one reading, demuxing, weighting and adding, each time using the variable mytgs. Thus only if numSrc > 1 do we need to allocate space for mytgs. Cheers Chris -----Original Message----- From: Nielsen Ole Sent: Wednesday, 28 May 2008 4:38 PM To: Burbidge David; Thomas Chris; 'John Jakeman' Cc: Sexton Jane; Gray Duncan; Dhu Trevor Subject: Possible uninitialised pointer in urs_ext.c [SEC=UNCLASSIFIED] Hi guys This is the C-code John Jakeman is using for reading mux files. When we compile it I noticed a possible uninitialised pointer in line 184: Memory for the variable mytgs is only allocated when numSrc > 1 and may thus be NIL otherwise. The question is whether it makes sense for the code to continue if numSrc == 0 but when I tried that tests were failing. I'd like to get a sense from you what the implications might be in this case. I can see that there are other if statements further down that ensure that things are done when numSrc>1 but it is not clear to me 1: Why it makes sense to continue when numSrc == 0 2: If there is a risk of using mytgs uninitialised. Can you help us? Cheers and thanks Ole " ole 285 Generate coastline Functionality and features enhancement normal low ole closed 2008-06-18T13:52:20+10:00 2012-02-13T14:50:00+11:00 "If ANUGA could output its coastline (0 < stage <= epsilon) as a polyline, it could be used to define buffered polygons for use with mesh refinement. This was requested by Rudy van Drie and Petar Milevski 16 June 2008 and would make for a very useful feature. ---- Original email ----- By the way... both Petar & I are convinced that when it comes to flood modelling ANUGA could be incredibly productive if we can some how get the extent of flow depth plotted and use that to initiate a refined mesh.. So the concept is ( I have spoken to you before about this...) 1. Just run rainfall over a catchment with any arbitrary mesh size. 2. ANUGA will provide a very rough extent of flooding 3. Create a function that will plot the extent of inundation to a defined depth say 300mm for now and create a polygon 4. This polygon is then used to refine the mesh, 5. Rerun ANUGA 6. Iterate Steps 2 - 5 to continue to refine the mesh !!! This will eliminate a very tedious and time consuming procedure every has to use to refine the model around a watercourse !!! This will really provide a big push in terms of productivity and accuracy !!! It is also apparently very do-able... The alpha-shape function could be manipulated to wrap a polygon around where depth exceeds 0.3m for instance.... Note this will reduce the need to have a terrain tool to identify the watercourse.... NOTE: would still be very useful to have terrain tools that can identify both RIDGE LINES (Locus of High Points) and WATERCOURSE LINES (locus of low points) Just food for thought.... Where we need to go to get ANUGA truly productive.... Regards Rudy " ole 286 Reduce culvert output to occur only at 'yieldsteps' ANUGA Flood Modelling Capability Functionality and features enhancement minor low ole closed 2008-07-03T10:21:09+10:00 2009-09-04T12:19:22+10:00 "This will require domain to store yieldsteps so that the forcing term can decide whether a particular call is at a yieldstep or not. Output to log files can then be restricted to yieldsteps." ole 287 Compute extrema occurring in culverts ANUGA Flood Modelling Capability Functionality and features enhancement minor low ole closed 2008-07-03T10:28:25+10:00 2012-02-13T14:50:31+11:00 "Petar Milevski suggests tracking for each Culvert Peak flow in the culvert, peak velocity, peak momentum and peak energy gradient were summarised, along with the time they occured at. Investigate if this should be generalised for all forcing terms somehow." ole 288 "Create ""What's New"" guide" Documentation task minor normal ole closed 2008-07-03T10:42:12+10:00 2008-08-11T16:45:32+10:00 "This was suggested by Craig Palmer. Take information from the Subversion log and compile the main ones into a What's New guide for every release. Currently this is captured in release_notes but it'd be much better to have a formal pdf document for each major release. " ole 289 Make 1D interpolation function ANUGA Flood Modelling Capability Functionality and features enhancement normal normal ole closed 2008-07-09T03:57:43+10:00 2012-02-13T14:51:40+11:00 "Create new callable object Interpolation_function_1D for general use. The constructor will take vectors x, y When called with an arbitrary value xi it will return the linear interpolation f(xi) based on the values x, y. This should be used whenever the user needs to create a function based on a timeseries - e.g. from a hydrograph. However, this fundamental object should also replace internal functionality in the 2D Interpolation function, file_function, file_boundary or where appropriate. " ole 291 Update ANUGA user manual to include Excel plotting Documentation task normal normal Leharne closed 2008-07-25T15:27:11+10:00 2010-06-17T17:17:48+10:00 Updating the manual to include instructions on plotting timeseries using Excel Leharne 292 sww2csv_gauges needs to ignore gauges that are not in the domain Functionality and features defect normal normal hudson closed 2008-08-12T09:17:41+10:00 2010-04-27T14:04:09+10:00 sww2timeseries had that functionality and this needs to be restored especially to cope with parrallel sexton 293 File_boundary and Field_boundary to be able to continue past their time interval Functionality and features enhancement normal highest ole closed 2008-08-12T11:41:05+10:00 2008-08-21T16:34:04+10:00 "Equip File_boundary and Field_boundary with a default keyword argument which can be either None or an object which should be a subclass of Generic_boundary. The functionality should be such that when the boundary object attemps to evaluate then a try-except construct will catch the condition when model time exceeds time interval in the boundary and pass on control to the default boundary object if specified. If default is None - reraise the Exception. " ole 294 Better format for input to Polygon_function Functionality and features enhancement normal low nariman closed 2008-08-14T13:15:22+10:00 2012-02-13T14:57:19+11:00 "The curren format is confusing: A list of tuples of the form (P, v) where P is a polygon which in turn is a list of points and v is a value or a function. We need some sort of object model. class Functional_region: # This contains a Polygon and a value (constant, function, dataset, ....) and then the Polygon function takes a list of these instances as input. " ole 295 Compute energy through a cross section Functionality and features enhancement normal high ole closed 2008-08-15T13:01:46+10:00 2008-09-08T17:02:19+10:00 "As suggested by Rudy van Drie, there would be a case to calculate the average energy through a line. This could be used for Culverts instead of the current enquiry polygon and would have the advantage that the mesh doesn't need to be refined. The formula for specific energy is Es = h + v**2 /(2g) where h and v are average depth and velocity along the line segment. and the similar formula for total energy is Et = w + v**2 /(2g) where w is average stage (w = z + h) This should be implemented reusing code developed for ticket:175 " ole 296 Compile ANUGA viewer for Linux Appearance and visualisation task normal normal nariman closed 2008-09-03T15:56:02+10:00 2010-04-23T21:05:39+10:00 "We know that the dependency !OpenSceneGraph works for Linux, so it should be possible to compile and run the ANUGA viewer under Linux. The source code is in the repository under ..\anuga_core\source\anuga_viewer Pending the succes of this, there is also the opportunity to fiddle with the code for the viewer as well - but that would the topic of other tickets." ole 297 Kristy doesn't have the ability to create a New Ticket! Other defect normal normal ole closed 2008-09-05T16:07:57+10:00 2008-09-08T10:52:07+10:00 sexton 298 sts file needs to record index number from hazard map Functionality and features enhancement normal normal Ole closed 2008-09-05T16:15:17+10:00 2008-09-08T16:54:19+10:00 "(on behalf of kristy) urs2sts takes a list of points (index, lon, lat) when using get_gauges.py that generates timeseries of the points contained in the sts file, easting and northing is returned, but the index can't be retrieved. This would be useful in order to compare with hazard map outputs directly (rather than matching easting and northing to lat and lon from DB). " kristy 299 Create ANUGA distribution CD with all dependencies ANUGA maintenance Compilation and installation task normal normal nhabili closed 2008-09-12T14:36:38+10:00 2009-09-10T16:12:18+10:00 "As an intermediate step towards a full installer (ticket:212) it would be handy to generate an image of ANUGA with all its dependencies for distribution on a CD or thumbdrive. This alleviate issues with finding and downloading dependencies. We may limit the scope of this to Windows machines since (Debian) Linux provides an easier installation procedure already." ole 300 Create ANUGA page on Wikipedia Appearance and visualisation task normal normal ole closed 2008-09-22T13:37:07+10:00 2010-04-23T21:07:24+10:00 "Use the page for MIKE 21 as a template. http://en.wikipedia.org/wiki/User:Uniomni " ole 301 Export_results - momentum - segmentation fault Functionality and features defect major low Nielson Ole closed 2008-10-07T08:41:40+11:00 2012-02-13T14:58:18+11:00 "The nodes are falling over when I am trying to export 'momentum' (let alone 'speed'). I have not yet been able to export a single speed ascii grid. The error is always segmentation fault, which I think has something to do with memory??? This will become a high priority once we need the information for the emergency managers, say start to mid Nov. " kristy 302 caching problem with _fit_to_mesh Functionality and features defect normal normal Ole closed 2008-10-19T12:29:45+11:00 2008-10-22T15:08:03+11:00 " I have been running run_okushiri.py (from the anuga_validation directory) on bogong (our 64bit amd machine). The caching doesn't seem to work for the command domain.set_quantity('elevation', filename=project.bathymetry_filename, alpha=0.02, verbose=True, use_cache=True) It produces files in my .python_cache directory, with the names such as _fit_to_mesh[-2966466518982282974]_Admin _fit_to_mesh[-2966466518982282974]_Args _fit_to_mesh[-2966466518982282974]_Result On the next run the code states that it is looking for _fit_to_mesh[-2966466518982282974]_Admin.z _fit_to_mesh[-2966466518982282974]_Args.z _fit_to_mesh[-2966466518982282974]_Result.z and then creates files _fit_to_mesh[-2966466518982282974]x_Admin _fit_to_mesh[-2966466518982282974]x_Args _fit_to_mesh[-2966466518982282974]x_Result This goes on in subsequent calls to produce _fit_to_mesh[-2966466518982282974]xx_Admin _fit_to_mesh[-2966466518982282974]xx_Args _fit_to_mesh[-2966466518982282974]xx_Result _fit_to_mesh[-2966466518982282974]xxx_Admin _fit_to_mesh[-2966466518982282974]xxx_Args _fit_to_mesh[-2966466518982282974]xxx_Result _fit_to_mesh[-2966466518982282974]xxxx_Admin _fit_to_mesh[-2966466518982282974]xxxx_Args _fit_to_mesh[-2966466518982282974]xxxx_Result _fit_to_mesh[-2966466518982282974]x_Admin _fit_to_mesh[-2966466518982282974]x_Args _fit_to_mesh[-2966466518982282974]x_Result _fit_to_mesh[-2966466518982282974]xx_Admin _fit_to_mesh[-2966466518982282974]xx_Args _fit_to_mesh[-2966466518982282974]xx_Result _fit_to_mesh[-2966466518982282974]xxx_Admin _fit_to_mesh[-2966466518982282974]xxx_Args _fit_to_mesh[-2966466518982282974]xxx_Result _fit_to_mesh[-2966466518982282974]xxxx_Admin _fit_to_mesh[-2966466518982282974]xxxx_Args _fit_to_mesh[-2966466518982282974]xxxx_Result I have attached a test program and its output Cheers Steve" steve 303 sww2dem read in numerous sww to produce one dem Efficiency and optimisation enhancement major high Ross Wilson closed 2008-10-31T11:32:29+11:00 2009-09-04T12:47:57+10:00 "As an sww file is unable to exceed 2GB, there are multiple sww files and hence in the export results script (sww2dem) you obtain multiple asc grids. I would appreciate if we could just have one asc grid produced for the entire time series. " kristy 304 Platform problem with urs_ext.c Architecture and API defect minor low ole closed 2008-11-18T20:00:49+11:00 2009-04-07T16:04:07+10:00 "The datamanager current has two tests failing on Windows platforms only due to some issue with urs_ext.c. John, Ole and Nariman have put in a significant amount of effort to track down this issue, but it has not been possible to determine the cause. See changesets: changeset:5968, changeset:5967, changeset:5964, changeset:5963, changeset:5962, changeset:5961, changeset:5960 changeset:5938, changeset:5937, changeset:5936, changeset:5935 changeset:5882, changeset:5880 " ole 305 Add breaklines to high level mesh interface ANUGA Flood Modelling Capability Functionality and features enhancement normal normal hudson closed 2008-11-19T11:41:48+11:00 2010-05-12T15:29:47+10:00 "Augment create_mesh_from_regions to include keyword argument: breaklines= Issues: * Does polyline have to connect to other lines * What if polyline is tiny * What happens if polyline goes outside bounding polygon?" ole 307 sww2csv, overwriting first sww with second. Functionality and features defect major high ole closed 2008-12-03T14:36:16+11:00 2009-09-04T12:46:18+10:00 "inside the sww2csv funtion (util.py line 2074) it calls all sww files, then runs the funtion for each titling the outcome callable_sww (line 2204). It then goes out of the loop and uses callable_sww to print the results, therefore overwriting the previous sww files, and printing only the last sww result. " kristy 308 ANUGA high level API Architecture and API enhancement normal normal hudson closed 2008-12-09T14:32:30+11:00 2010-06-15T09:22:09+10:00 "The functionality of ANUGA is increasing and some structures need to appear in different locations of the typical script and in a particular order. Examples are STS boundary data which must appear both in the mesh generation and the boundary setting. Culvert routines are heading in the same direction with openings needing to be refined in the mesh generator. Finally, parallelism still imposes a bit of ordering. Consequently I propose writing a high level ANUGA interface where data can be specified in any order to setup ANUGA models easily. At the same time, low level functionality should be exposed if required. Here's a beginning for this idea: {{{ from anuga.interface import model # Define mesh boundary and initial internal regions model.set_boundary_segment( segment1, tag1 ) model.set_boundary_segment( segment2, tag2 ) model.set_internal_region( polygon1, resolution1 ) model.set_internal_region( polygon2, resolution2 ) # Initial conditions model.set_quantity('elevation', pts_file) # Register, don't run it yet # Forcing terms model.add_forcing( Culvert(...) ) model.add_forcing( Rain(...) ) # Boundary conditions model.add_boundary_condition( sts_file, tag ) # Affect both the mesh boundary and set_boundary. model.add_boundary_condition( Dirichlet_boundary(), tag ) # Build internal structures and check model.build(...) # Run baby run model.run(...) }}} " ole 309 Consider replacing print statements by logging Other enhancement normal low rwilson closed 2008-12-17T05:01:21+11:00 2009-09-04T11:08:00+10:00 "A good idea suggested by several people. See e.g. http://72.14.235.132/search?q=cache:NlCkPdW3rHwJ:blog.tplus1.com/index.php/2007/09/28/the-python-logging-module-is-much-better-than-print-statements/+logging+Python&hl=en&ct=clnk&cd=6&gl=au " ole 310 Change culvert polygons Functionality and features enhancement minor normal ole closed 2008-12-23T13:58:49+11:00 2012-02-13T14:59:38+11:00 "Change culvert polygons so that they only compute the exchange polygon and one inquiry point on either side. The latter should be optionally specified by the user. Also, currently, the algorithm may place the point inside the exchange area. This should be changed to guarantee that it falls outside." ole 311 Arrange for regular releases of ANUGA Management and planning task minor low nariman closed 2009-01-05T14:25:08+11:00 2012-02-13T15:00:25+11:00 "Currently ANUGA is being release on an ad hoc basis whenever ""enough"" features and bug fixes have been entered. A predictable and regular release schedule will ensure that ANUGA users get access to updates relatively quickly. A 2-3 month interval would seem reasonable. In addition, we could arrange for nightly builds so that users can get access to the latest releases if they need to. See http://www.linuxfoundation.org/publications/linuxkerneldevelopment.php for details on the Linux kernel development model." ole 312 Jonathan doesn't have the ability to create a New Ticket! Management and planning defect normal normal Ole closed 2009-01-19T10:56:54+11:00 2009-01-19T13:19:44+11:00 kristy 313 Ordering CSV files for nearest neighbour ANUGA maintenance Efficiency and optimisation defect critical low Ross closed 2009-01-19T10:59:40+11:00 2012-02-13T15:01:42+11:00 This function will be used on the thinned_boundary_points, so that they are a straight line without manual labour. kristy 314 set_quantity crashes Functionality and features defect normal normal ole closed 2009-01-29T02:54:14+11:00 2009-03-18T15:33:36+11:00 "After reusing the mesh object with fitting, I observed examples where set_quantity crashed with a message about 'Could not find triangle for point' However, if mesh is being recreated from nodes and triangles no exception is thrown. I am investigating. " ole 315 Move test_caching_of_set_quantity.py to validation test suite Testing and validation task normal normal ole closed 2009-01-29T02:57:42+11:00 2009-03-18T17:06:26+11:00 "Do this when ticket:314 has been resolved. Also retire acceptable_overshoot in fitting as it was never implemented and update test script accordingly." ole 316 Reporting differences between different OS/CPU Functionality and features defect normal high rwilson closed 2009-01-30T11:09:48+11:00 2009-01-30T16:05:31+11:00 Rajaraman has a small test case that highlights differences in reported data when the test case is run on different OSes (WinXP, Ubuntu) and 32/64 bit versions of the same OS. rwilson 317 Event selection and build_boundary integration Architecture and API enhancement normal high rwilson closed 2009-01-30T16:48:03+11:00 2009-09-04T11:11:13+10:00 "Currently the !EventSelection tool generates a python fragment containing MUX filenames and the global weight, in the hope that the generated module would be used in build_boundary.py. A better approach would be to modify build_boundary.py to get urs2sts() to take the older generated event_.list file which already contains the MUX filenames and weight. The approach would be to remove the existing 'urs_filenames' and 'weight' parameters and replace them with a full path to the *.list file plus the 'base' path to the MUX files. Changes to build_boundary.py should be made with a view to eventually including the code into ANUGA proper, which means removing any reference to project-specific values and passing them in as a parameter. Note that any code existing outside ANUGA may have references to Numeric that must be changed when ANUGA goes to numpy." rwilson 318 error running get_timeseries.py Functionality and features defect major high rwilson closed 2009-02-11T15:46:22+11:00 2009-09-04T12:44:35+10:00 "When running python get_timeseries.py and get_all_swwfiles() return the sww files in the wrong order (ie not creation order), the csv data is written incorrectly. It *looks* like the last file has rewritten over the previous, however the time is just wrong??? A possible work-around is to sort the list of SWW filenames received from get_all_swwfiles(). This is currently being tested in get_timeseries.py. Maybe the sort should be in get_all_swwfiles()? But the problem of why the output is wrong when the SWW files are processed in the wrong order still remains." kristy 319 Add tide function to ANUGA Functionality and features defect normal normal Ole closed 2009-03-02T10:35:52+11:00 2009-09-04T13:10:52+10:00 "Using mean_stage is it possible to have a time series (csv file) that defines mean_stage at each time step. This would be instead of mean_stage being a constant. Superseded by 326." nick2009 321 Myall to gain access to making a new ticket Other defect normal normal Ole closed 2009-03-18T09:30:33+11:00 2009-03-18T09:44:11+11:00 "Hey Ole, can you please grant access to Myall so that he is able to put New tickets in and browse the source locations. Thanks!" kristy 322 Error in unit test using python 2.4 Compilation and installation defect normal normal Ole closed 2009-03-20T12:14:54+11:00 2009-03-23T08:36:53+11:00 "I am getting the following error from the unittest ====================================================================== ERROR: Test that sww information can be converted correctly to asc/prj ---------------------------------------------------------------------- Traceback (most recent call last): File ""/home/steve/ga/anuga_core/source/anuga/shallow_water/test_data_manager.py"", line 2604, in test_sww2dem_asc_missing_points format = 'asc') File ""/home/steve/ga/anuga_core/source/anuga/shallow_water/data_manager.py"", line 2267, in sww2dem var_list = get_vars_in_expression(quantity) File ""/home/steve/ga/anuga_core/source/anuga/utilities/system_tools.py"", line 277, in get_vars_in_expression return get_vars_body(compiler.parse(source)) File ""/home/steve/ga/anuga_core/source/anuga/utilities/system_tools.py"", line 271, in get_vars_body if any(isinstance(child, Node) for child in node.getChildren()): NameError: global name 'any' is not defined I assume this is because I am still using python 2.4, which I need to do until we move to numpy. " steve 324 Flow conservation error Functionality and features defect critical highest steve closed 2009-03-27T14:55:34+11:00 2009-04-19T13:41:45+10:00 "There is a problem with conservation of flow and match between domain depth and depth derived from Manning's equation. A test for this was added in changeset:6643. It is unclear as yet, but flow conservation seems to be sensitive to surface slope and Manning's n, raising concern as to the way friction is handled in the model. Additionally, it is noted that there is currently no mass balance check on the model. This is an important check in all hydrodynamic models and should be added to ANUGA. Such a check could shed further light on the flow conservation problem noted above. " ted 327 Export of results needs to be faster Efficiency and optimisation enhancement normal normal hudson closed 2009-05-18T11:34:52+10:00 2010-06-15T17:02:45+10:00 "The function sww2dem is being used extensively to produced inundation maps. It is fairly slow since it has never been profiled and optimised. Ideas for optimising it include: Specify polygon rather than rectangle and assign a value like -9999 to points outside of the polygon. Whether this will speed it up is unclear. Another option would be to profile the function and optimise the bottleneck if there is one. The function needs some TLC in any case, as it has been evolving over the years without much attention. Unfortunately, it may be that the slow performance comes from the interpolation code which is known to fairly slow." ole 328 Reinstate momentum jet in culverts Functionality and features enhancement minor low ole closed 2009-05-27T16:27:28+10:00 2009-11-02T12:23:48+11:00 "Now that the Boyd culvert has been tested, we should reinstate the momentum jet. A keyword argument should decide whether to apply it or not. The code for this is in culvert_class under the obsolete code. " ole 329 Default blockage for culverts Functionality and features enhancement minor low ole closed 2009-05-27T16:28:36+10:00 2012-02-13T15:08:19+11:00 "Introduce a default value for blockage used by culverts in config.py If no value is specified in the Culvert constructor, use this default." ole 330 Mailing archives do not show up in Google searches Management and planning defect normal low nhabili closed 2009-06-09T16:48:23+10:00 2012-02-13T15:08:40+11:00 "The mailing list hosted at sourceforge does not show up in Google searches. This may be because they are dynamically generated. I have tried everything I can such as submitting the link to Google, adding meta information to our TRAC link to the archives. It still doesn't work. It is possible to search the archives from with SourceForge, but it is not quite the same as using Google. Can someone help?" ole 331 Create ANUGA logo Management and planning task minor low ole closed 2009-06-13T04:21:35+10:00 2010-01-06T21:34:59+11:00 "It is time ANUGA gets a graphical face. It should appear on sourceforge and also replace the trac logo on our ANUGA TRAC pages. Logos can be generated automatically, but if someone could create an original one, it'd be great. The logo should be a simple and esthetic reference to either the name ANUGA or fluid flows. Automatic sites include: http://cooltext.com/ http://www.logoblog.org/logo-maker.php http://www.logoyes.com/logocreator.php One idea is to have a 3D representation of the letters ""ANUGA"" (with perspective effects) which are brown (earth) at the top but shade into a grid at the foot of the letters. The letters stand in flowing water." ole 333 Introduce __slots__ Functionality and features enhancement minor low ole closed 2009-06-25T14:11:57+10:00 2012-02-13T15:11:38+11:00 "With the new class idioms (inheritance form object) in Python we have the opportunity of restricting attributes using __slots__. That will allow users to directly manipulate and assign values to attributes without fear of misspellings being silently accepted to the detriment of all humankind." ole 335 incorporate revision number into screen capture for both windows and linux Other defect major normal nariman closed 2009-07-22T18:34:16+10:00 2010-01-27T16:46:45+11:00 "for auditing and reporting purposes, the version of ANUGA should be included in the ouput file - currently generated using screen_capture get_revision_number() from the module abstract_2d_finite_volumes.util is available, but works for Linux only get_version.get_version_sandpit_windows() from EQRM could be used for Windows " sexton 336 Using ungenerate format to add e.g. buildings Functionality and features enhancement minor low hudson closed 2009-08-26T16:07:07+10:00 2010-06-25T11:12:37+10:00 "Petar Milevsky suggested this and provided an example file (attached). Look at existing code for using ungenerate (e.g. in mesh generation and search through changesets referencing ungenerate) and reuse if applicable. " ole 337 sww2dem can't do one timestep at a time and also can't do very fine grids Functionality and features defect normal normal sexton closed 2009-08-26T16:15:08+10:00 2012-02-13T15:14:11+11:00 "Nils Goseberg reports that sww2dem no longer can export grid at one timestep. See ANUGA mailing list in August 2009. Kristy Van Putten reports that sww2dem produces very small files with missing numbers when grid size is something like 2m or 5m. Is this something to do with numpy and the way it converts one array row to a string?" ole 339 culvert flow not conserving flow ANUGA maintenance Testing and validation defect normal normal Ole closed 2009-09-07T15:17:14+10:00 2010-09-05T23:09:33+10:00 " Just noticed that one of the unit tests in test_culvert_class was actually failing (but the allclose test was passing as the relative error was 1.0e-5). The test is checking for conservation of water, and so we really want this to be essentially close to zero. I have now changed the relative tolerance on the tests checking for conservation to rtol = 1.0e-10" steve 341 Better project/setup_model interface for users Architecture and API enhancement minor normal hudson closed 2009-09-16T14:09:21+10:00 2010-06-09T12:32:13+10:00 "We need to think about refactoring the code users change to run ANUGA. This is files like project.py, setup_model.py, etc. Currently the code to put ASC elevations into ANUGA looks like:[[BR]] '''convert_dem_from_ascii2netcdf(project.demname, ...)[[BR]] dem2pts(project.demname, ...)[[BR]] domain = create_domain_...(...)[[BR]] domain.set_quantity('elevation', project.demname+'.pts', ...)''' Hidden away under all that is the assumption that the filename passed to dem2pts() is just a root and '.dem' is *assumed* as the extension. This leads to confusion as:[[BR]] 1. project.demname is used all over as a root filename, no real names used,[[BR]] 2. sometimes extensions are supplied to a function with the filename, sometimes not. We should always pass full filenames into functions. If there is an output file, the name for that should be supplied also. This will remove some confusion for beginners as to what is happening. Additionally, it may now be possible to get ANUGA code to *automatically* convert files. If we say that a file is an ""input elevation"" file, then ANUGA can convert an ASC file to a PTS file just by looking at the extension (not a real good idea, but simple) or by some 'file'-like magic (do 'man file'). Similarly, a consistent function naming convention would be nice. In runcairns.py we see this to convert an ASC file to a DEM file:[[BR]] '''convert_dem_from_ascii2netcdf(project.demname, ...)[[BR]] dem2pts(project.demname, ...)''' This could look like:[[BR]] '''asc2dem(project.demname, ...)[[BR]] dem2pts(project.demname, ...)''' or[[BR]] '''convert_asc_to_dem(project.demname, ...)[[BR]] convert_dem_to_pts(project.demname, ...)''' I general, a rethink on the 'user' code more from the aspect of 'a user just trying to run ANUGA' instead of an 'ANUGA developer' is called for." rwilson 342 Remove variable 'z' from sww format. Architecture and API enhancement normal normal ole closed 2009-11-27T02:55:25+11:00 2010-01-06T21:23:46+11:00 "The quantity use is 'elevation' and the only reason 'z' is still there is due to the old viewer. With the new viewer due to replace the old soon, 'z' can be safely phased out. The ticket in the viewer project is http://www.ausposdevelop.com.au/trac/anuga_viewer/index.cgi/ticket/3 " ole 343 Turn Patong validation into a proper unit test Testing and validation enhancement major normal ole closed 2009-12-02T16:46:18+11:00 2010-04-28T13:54:36+10:00 "Currently the Patong examples are part of the autovalidation suite, but they compare generated sww files number for number to the reference model. This is not desirable and , indeed, the tests fail. Instead, we need to follow the methodology used for the Okushiri autovalidation where time series are compared in terms of specific features such as maxima, minima. Look at the way Okushiri has been done and apply it to the Patong tests." ole 344 produce asc when there is a hole in the model ANUGA Flood Modelling Capability Functionality and features defect normal high hudson closed 2010-01-26T17:31:56+11:00 2010-04-19T13:56:12+10:00 "From Peter Wells to anuga user list 12 November 2009: I'm trying to produce an ASC file showing peak stage of a simulation. Unfortunately sww2dem does not dela very well with the hole in the middle of the model: Traceback (most recent call last): File ""makeASC.py"", line 52, in format = 'asc') File ""C:\Python25\lib\site-packages\anuga\shallow_water\data_manager.py"", line 2415, in sww2dem grid_values = interp.interpolate(result, grid_points).flatten() File ""C:\Python25\lib\site-packages\anuga\fit_interpolate\interpolate.py"", line 290, in interpolate verbose=verbose) File ""C:\Python25\lib\site-packages\anuga\fit_interpolate\interpolate.py"", line 378, in interpolate_block verbose=verbose) File ""C:\Python25\lib\site-packages\anuga\fit_interpolate\interpolate.py"", line 505, in _build_interpolation_matrix_A raise Exception(msg) Exception: ('Could not find triangle for point', array([ 13.8, 9.8])) " sexton 346 How to check the coastline polygon is ordered correctly Functionality and features defect normal normal hudson closed 2010-03-24T13:57:07+11:00 2010-04-21T14:26:08+10:00 "Setting up ANUGA tsunami models, eg: a coastline polygon is defined that consists of coastline dataset stitched to the outer domain. We need to ensure that the ordering of points is correct. The attached file shows an example of where points are out of order and the resultant polygon is not ordered propetly, and we are seeing crossovers in the polygon. We need a check for this to ensure it's correct. " sexton 347 Culverts: the ability to identify a single triangle instead of multiple triangles encompassed by the exchange polygon ANUGA enhancements Functionality and features enhancement normal normal ole closed 2010-04-10T17:33:34+10:00 2012-02-13T15:16:45+11:00 "From Rudy: ALso..... another pressing issue I have with regard to testing the CULVERT routine, is the ability to identify a single triangle instead of multiple triangles encompassed by the exchange polygon When the domain grid size is not fine enough the current routine, fails However it would be far better to identify a single triangle and use that triangle as the exchange area if the cell resolution is not high enough as in the above. Making the cells as small as a sub metre diameter pipe..... slows the entire run down" hudson 348 Verify that psyco is being used to optimal advantage in ANUGA Efficiency and optimisation enhancement normal normal hudson closed 2010-05-17T12:22:18+10:00 2010-06-08T14:41:19+10:00 It appears that psyco optimisation has been used selectively within ANUGA, and it would be worthwhile to check that it is being used in the right places, with the right settings. hudson 349 add hole_tags to add_hole_from_polygon ANUGA enhancements Architecture and API defect normal normal hudson closed 2010-06-02T09:49:32+10:00 2010-06-07T13:10:26+10:00 "Look at this code in mesh_interface.py, in the function add_hole_from_polygon: # Do interior holes if interior_holes is not None: for polygon in interior_holes: m.add_hole_from_polygon(polygon, geo_reference=poly_geo_reference) You would need to add this parameter # Do interior holes if interior_holes is not None: for polygon in interior_holes: m.add_hole_from_polygon(polygon, segment_tags=hole_tags, geo_reference=poly_geo_reference) and then pass hole_tags into add_hole_from_polygon. This has the same form as the boundary_tags. It's a 2-line fix" hudson 350 Error with log.critical in runcairns.py Testing and validation defect normal normal ole closed 2010-06-11T13:53:50+10:00 2010-06-21T10:47:47+10:00 "After installing the current version of ANUGA on a colleagues windows machine we tried to run the cairns scenario. After creating the mesh we got an error: no module named critical in log.py In the IDLE interface I was able to import log.critical but it fell over in the runcarins.py I hacked it by changing to verbose=False" horspool 351 New tool: csv2sts Functionality and features enhancement normal highest ole closed 2010-06-11T14:04:22+10:00 2010-06-17T14:03:22+10:00 "It would be great to have a tool that converted a time series in csv format into sts (NetCDF) format. This would enhance the functionality of tsunami models in ANUGA by allowing any deep water model (with csv output) to be coupled with ANUGA. This should be able to be run on windows and linux - command line only. I would imagine having a text file with a list of 'offshore gauges' files. With an associated lat lon for each gauge. eg. of gauge_list.txt {{{ gauge_1.csv gauge_2.csv ...... }}} eg. gauge_1.csv {{{