Changeset 3164

Timestamp:

Jun 15, 2006, 5:31:57 PM (18 years ago)

Author:

jack

Message:

Added code samples for batch scripts. Need to update results.tex to make it less confusing

Location:

inundation/parallel/documentation

Files:

• code.tex (modified) (1 diff)
• code/pbs-run-parallel-merimbula-metis-4-apac (added)
• code/pbs-run-parallel-merimbula-metis-4-bogong (added)
• parallel.tex (modified) (5 diffs)

inundation/parallel/documentation/code.tex

@@ -1 +1 @@
 
 \chapter{Code Listing}\label{chap:code}
-\section{run_parallel_advection.py}\label{sec:codeRPA}
+\section{Python Programs}\label{sec:codePP}
+\subsection{run_parallel_advection.py}\label{subsec:codeRPA}
 \verbatiminput{code/RunParallelAdvection.py}
 \newpage
-\section{run_parallel_merimbula_metis.py}\label{sec:codeRPMM}
+\subsection{run_parallel_merimbula_metis.py}\label{subsec:codeRPMM}
 \verbatiminput{code/RunParallelMerimbulaMetis.py}
 \newpage
-\section{run_parallel_sw_merimbula_metis.py}\label{sec:codeRPSMM}
+\subsection{run_parallel_sw_merimbula_metis.py}\label{subsec:codeRPSMM}
 \verbatiminput{code/RunParallelSwMerimbulaMetis.py}
+\newpage
+\section{Sample Jobscripts}\label{sec:codeSJ}
+\subsection{4 Processor run_parallel_sw_merimbula_metis.py (APAC Linux Cluster)}\label{subsec:code4RPSMMAPAC}
+The APAC cluster charges computing time spent on jobs to project
+accounts. This creates extra directives at the start of the
+jobscript. Further, there is a bug in the environment module system used on
+this cluster. For jobs to run correctly, there must be no ``module load''
+statements in the files .bashrc, .cshrc, .profile or .login.
+\verbatiminput{code/pbs-run-parallel-merimbula-metis-4-apac}
+\newpage
+\subsection{4 Processor run_parallel_sw_merimbula_metis.py (``Bogong'' Linux Cluster)}\label{subsec:code4RPSMMBogong}
+\verbatiminput{code/pbs-run-parallel-merimbula-metis-4-bogong}

inundation/parallel/documentation/parallel.tex

@@ -143 +143 @@
 Chapter \ref{chap:code} gives full listings of some example codes. 
 
-The first example in Section \ref{sec:codeRPA} solves the advection equation on a
+The first example in Section \ref{subsec:codeRPA} solves the advection equation on a
 rectangular mesh. A rectangular mesh is highly structured so a coordinate based decomposition can be use and the partitioning is simply done by calling the
 routine \code{parallel_rectangle} as shown below. 
@@ -161 +161 @@
 
 
-A more \lq real life\rq\ mesh is the Merimbula mesh used in the code shown in Section \ref{sec:codeRPMM}. This example also solves the advection equation. In this case the techniques described in Section \ref{sec:part} must be used to partition the mesh. Figure \ref{fig:code} shows the part of the code that is responsible for spreading the mesh over the processors. We now look at the code in detail.
+A more \lq real life\rq\ mesh is the Merimbula mesh used in the code shown in Section \ref{subsec:codeRPMM}. This example also solves the advection equation. In this case the techniques described in Section \ref{sec:part} must be used to partition the mesh. Figure \ref{fig:code} shows the part of the code that is responsible for spreading the mesh over the processors. We now look at the code in detail.
 
 \begin{figure}[htbp]
@@ -203 +203 @@
              rec_submesh(0)
 \end{verbatim}
-  \caption{A section of code taken from {\tt run_parallel_merimbula_metis.py} (Section \protect \ref{sec:codeRPMM}) showing how to subdivide the mesh.}
+  \caption{A section of code taken from {\tt run_parallel_merimbula_metis.py} (Section \protect \ref{subsec:codeRPMM}) showing how to subdivide the mesh.}
  \label{fig:code}
 \end{figure}
@@ -209 +209 @@
 \begin{itemize}
 \item 
-These first few lines of code read in and define the (global) mesh. The \code{Set_Stage} function sets the initial conditions. See the code in \ref{sec:codeRPMM} for the definition of \code{Set_Stage}.
+These first few lines of code read in and define the (global) mesh. The \code{Set_Stage} function sets the initial conditions. See the code in \ref{subsec:codeRPMM} for the definition of \code{Set_Stage}.
 \begin{verbatim}
     filename = 'merimbula_10785.tsh'
@@ -252 +252 @@
 \section{Running the Code}
 \subsection{Compiling Pymetis and Metis}
-Building the Pymetis wrapper is done using Make, but there are variations
-depening on the host system type. Under most types of Linux, simply running
-\verb|make| will work. Under x86\_64 versions of Linux, the command is
-\verb|make COPTIONS="-fPIC"|. Finally, under windows, the command is
-\verb|make for_win32|. For a sanity check, a simple PyUnit test is provided,
-called test\_metis.py . A metis 4.0 source tree is expected to exist in the
-metis-4.0 subdirectory and is automatically built by the makefile.
+Currently, Metis and its Python wrapper Pymetis are not built by the
+\verb|compile_all.py| script. A makefile is provided to automate the build
+process. Change directory to the \verb|ga/inundation/pymetis/| directory and
+ensure that the subdirectory \verb|metis-4.0| exists and contains an
+unmodified Metis 4.0 source tree. Under most varieties of Linux, build the
+module by running \verb|make|. Under x86\_64 versions of Linux, build the
+module by running \verb|make COPTIONS="-fPIC"|. Under Windows, build the
+module by running \verb|make for_win32|. After the build completes, verify
+that the module works by running the supplied PyUnit test case with
+\verb|python test_metis.py|.