[cig-commits] r16757 - in short/3D/PyLith/trunk/doc/install: . Cluster_CIT-garuda
brad at geodynamics.org
brad at geodynamics.org
Thu May 20 17:36:43 PDT 2010
Author: brad
Date: 2010-05-20 17:36:43 -0700 (Thu, 20 May 2010)
New Revision: 16757
Added:
short/3D/PyLith/trunk/doc/install/Cluster_CIT-garuda.txt
short/3D/PyLith/trunk/doc/install/Cluster_CIT-garuda/
short/3D/PyLith/trunk/doc/install/Cluster_CIT-garuda/PyLith.README
short/3D/PyLith/trunk/doc/install/Cluster_CIT-garuda/sample.bash.tools
short/3D/PyLith/trunk/doc/install/Cluster_CIT-garuda/sample.bashrc
short/3D/PyLith/trunk/doc/install/Cluster_CIT-garuda/sample.pylithapp.cfg
Modified:
short/3D/PyLith/trunk/doc/install/Cluster_CIT-pangu.txt
Log:
Added garuda stuff.
Added: short/3D/PyLith/trunk/doc/install/Cluster_CIT-garuda/PyLith.README
===================================================================
--- short/3D/PyLith/trunk/doc/install/Cluster_CIT-garuda/PyLith.README (rev 0)
+++ short/3D/PyLith/trunk/doc/install/Cluster_CIT-garuda/PyLith.README 2010-05-21 00:36:43 UTC (rev 16757)
@@ -0,0 +1,36 @@
+How to setup your environment to use PyLith installed here.
+
+Currently, only the development version of PyLith is installed. In the near future
+both the development version and a stable (current release) version will be installed.
+
+1. Remove any PyLith related stuff (PETSc, MPI, etc) set in your .bashrc or .bash.tools.
+
+2. Edit your $HOME/.bashrc file to include the .bash.tools files as shown in sample.bashrc.
+
+3. Edit (create if necessary) $HOME/.bash.tools to match the sample.bash.tools file.
+ Place any of your own .bash.tools stuff AFTER the info in sample.bash.tools
+ and make sure your APPEND to any environment variables.
+
+4. Edit your $HOME/.pyre/pylithapp/pylithapp.cfg file to match the sample.pylithapp.cfg file.
+
+5. Try running examples/3d/tet4 dislocation.cfg.
+ a. Create a directory for the files.
+ cd $HOME
+ mkdir tmp_pylith
+ cd tmp_pylith
+ b. Copy all of the input files to the directory.
+ cp /home/baagaard/src/pylith-dev/examples/3d/tet4/* .
+ c. Run PyLith
+ pylith --pbs.ppn=1 --nodes=1 --job.name=tet4_dislocation --job.walltime=5*minute dislocation.cfg --job.stdout=myjob.out --job.stderr=myjob.err
+
+ (i) --pbs.ppn=N (N processes per node)
+ (ii) --nodes=M (M nodes) [total processes = M, number of compute nodes = M/N]
+ (iii) --job.walltime=5*minute [limit runtime to 5 minutes]
+ (iv) To see the PBS submission script use the command line argument --scheduler.dry
+ [job will not be submitted to the queue]
+ (v) Screen output will be in stdout.txt and stderr.txt in the directory where the
+ the job was submitted.
+
+NOTE: It is generally a bad idea to write output to any directory on /home because this
+ is a remote filesystem on the compute nodes. The preferred place for output is a
+ directory on the compute node or on a parallel filesystem (if one exists).
Added: short/3D/PyLith/trunk/doc/install/Cluster_CIT-garuda/sample.bash.tools
===================================================================
--- short/3D/PyLith/trunk/doc/install/Cluster_CIT-garuda/sample.bash.tools (rev 0)
+++ short/3D/PyLith/trunk/doc/install/Cluster_CIT-garuda/sample.bash.tools 2010-05-21 00:36:43 UTC (rev 16757)
@@ -0,0 +1,50 @@
+#! /bin/bash
+
+#
+if [ "$TOOLS_FORMAT" == "" ]; then
+ export TOOLS_FORMAT=intel-10.1
+fi
+
+# Store pre-tools info so we can reread this file after changing settings
+if (($READTOOLS)); then
+ PATH=${path_notools}
+ export LD_LIBRARY_PATH=${ld_library_path_notools}
+ export MANPATH=${manpath_notools}
+ export PYTHONPATH=${pythonpath_notools}
+else
+ export path_notools=${PATH}
+ export ld_library_path_notools=${LD_LIBRARY_PATH}
+ export manpath_notools=${MANPATH}
+ export pythonpath=${PYTHONPATH}
+ export READTOOLS=1
+fi
+
+PYTHON_VERSION=2.6
+
+export TOOLS_DIR=/home/baagaard/tools/${TOOLS_FORMAT}
+if [ "$LD_LIBRARY_PATH" == "" ]; then
+ export LD_LIBRARY_PATH=${TOOLS_DIR}/lib
+else
+ export LD_LIBRARY_PATH=${TOOLS_DIR}/lib:${LD_LIBRARY_PATH}
+fi
+if [ "${PYTHON_PATH}" == "" ]; then
+ export PYTHONPATH=${TOOLS_DIR}/lib/python${PYTHON_VERSION}/site-packages
+else
+ export PYTHONPATH=${TOOLS_DIR}/lib/python${PYTHON_VERSION}/site-packages:${PYTHONPATH}
+fi
+PATH=${TOOLS_DIR}/bin:${PATH}
+
+# MPI
+export MPI_DIR=/opt/mpich/infiniband/intel
+PATH=${MPI_DIR}/bin:${PATH}
+LD_LIBRARY_PATH=${MPI_DIR}/lib64:${MPI_DIR}/lib64/shared:${LD_LIBRARY_PATH}
+
+# PETSC
+export PETSC_DIR=/home/baagaard/src/petsc-dev
+export PETSC_ARCH=${TOOLS_FORMAT}_opt
+
+# PyLith development version
+export PYLITHDEV_DIR=/home/baagaard/pylith-dev/${TOOLS_FORMAT}
+export LD_LIBRARY_PATH=${PYLITHDEV_DIR}/lib:${LD_LIBRARY_PATH}
+export PYTHONPATH=${PYLITHDEV_DIR}/lib/python${PYTHON_VERSION}/site-packages:${PYTHONPATH}
+PATH=${PYLITHDEV_DIR}/bin:${PATH}
Added: short/3D/PyLith/trunk/doc/install/Cluster_CIT-garuda/sample.bashrc
===================================================================
--- short/3D/PyLith/trunk/doc/install/Cluster_CIT-garuda/sample.bashrc (rev 0)
+++ short/3D/PyLith/trunk/doc/install/Cluster_CIT-garuda/sample.bashrc 2010-05-21 00:36:43 UTC (rev 16757)
@@ -0,0 +1,12 @@
+# .bashrc
+
+# User specific aliases and functions
+
+# Source global definitions
+if [ -f /etc/bashrc ]; then
+ . /etc/bashrc
+fi
+
+if [ -f .bash.tools ]; then
+ . .bash.tools
+fi
Added: short/3D/PyLith/trunk/doc/install/Cluster_CIT-garuda/sample.pylithapp.cfg
===================================================================
--- short/3D/PyLith/trunk/doc/install/Cluster_CIT-garuda/sample.pylithapp.cfg (rev 0)
+++ short/3D/PyLith/trunk/doc/install/Cluster_CIT-garuda/sample.pylithapp.cfg 2010-05-21 00:36:43 UTC (rev 16757)
@@ -0,0 +1,9 @@
+[pylithapp]
+scheduler = pbs
+
+[pylithapp.pbs]
+shell = /bin/bash
+
+[pylithapp.launcher]
+command = mpirun -np ${nodes} -machinefile ${PBS_NODEFILE}
+
Added: short/3D/PyLith/trunk/doc/install/Cluster_CIT-garuda.txt
===================================================================
--- short/3D/PyLith/trunk/doc/install/Cluster_CIT-garuda.txt (rev 0)
+++ short/3D/PyLith/trunk/doc/install/Cluster_CIT-garuda.txt 2010-05-21 00:36:43 UTC (rev 16757)
@@ -0,0 +1,29 @@
+Python
+ http://www.python.org/ftp/python/2.6.5/Python-2.6.5.tgz
+
+cppunit
+
+proj.4
+
+FIAT
+
+swig
+
+pythia
+
+netcdf
+
+numpy
+
+spatialdata
+
+mercurial
+
+PETSc
+
+nemesis
+
+PyLith
+
+
+
Modified: short/3D/PyLith/trunk/doc/install/Cluster_CIT-pangu.txt
===================================================================
--- short/3D/PyLith/trunk/doc/install/Cluster_CIT-pangu.txt 2010-05-20 00:14:51 UTC (rev 16756)
+++ short/3D/PyLith/trunk/doc/install/Cluster_CIT-pangu.txt 2010-05-21 00:36:43 UTC (rev 16757)
@@ -2,6 +2,34 @@
INSTRUCTIONS FOR INSTALLING PYLITH ON THE CALTECH LINUX CLUSTER PANGU
======================================================================
+Python
+ http://www.python.org/ftp/python/2.6.5/Python-2.6.5.tgz
+
+cppunit
+
+proj.4
+
+FIAT
+
+swig
+
+pythia
+
+netcdf
+
+numpy
+
+spatialdata
+
+mercurial
+
+PETSc
+
+nemesis
+
+PyLith
+
+
I place applications that are rarely updated in $HOME/tools. For CIG
source code, I separate the source code, build directories, and
installed code. The source code sits in $HOME/src/cig, I build the
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