[cig-commits] r21193 - seismo/3D/SPECFEM3D/trunk/utils/Cluster/pbs

[carltape at geodynamics.org]

Author: carltape
Date: 2012-12-24 12:45:29 -0800 (Mon, 24 Dec 2012)
New Revision: 21193

Modified:
   seismo/3D/SPECFEM3D/trunk/utils/Cluster/pbs/go_decomposer_pbs.bash
   seismo/3D/SPECFEM3D/trunk/utils/Cluster/pbs/go_generate_databases_pbs.bash
   seismo/3D/SPECFEM3D/trunk/utils/Cluster/pbs/go_mesher_pbs.bash
   seismo/3D/SPECFEM3D/trunk/utils/Cluster/pbs/go_solver_pbs.bash
   seismo/3D/SPECFEM3D/trunk/utils/Cluster/pbs/valgrind_go_solver_pbs.bash
Log:
run scripts: minor fixes and clean-up; tested default example from scratch


Modified: seismo/3D/SPECFEM3D/trunk/utils/Cluster/pbs/go_decomposer_pbs.bash
===================================================================
--- seismo/3D/SPECFEM3D/trunk/utils/Cluster/pbs/go_decomposer_pbs.bash	2012-12-24 20:18:38 UTC (rev 21192)
+++ seismo/3D/SPECFEM3D/trunk/utils/Cluster/pbs/go_decomposer_pbs.bash	2012-12-24 20:45:29 UTC (rev 21193)
@@ -23,14 +23,12 @@
 # script to run the mesher and the solver
 # read Par_file to get information about the run
 # compute total number of nodes needed
-NPROC=`grep NPROC DATA/Par_file | cut -d = -f 2 `
+NPROC=`grep NPROC DATA/Par_file | cut -d = -f 2`
 
 # path to database files for mesh (relative to bin/)
-LOCALPATH=`grep LOCAL_PATH DATA/Par_file | cut -d = -f 2 `
+LOCALPATH=`grep LOCAL_PATH DATA/Par_file | cut -d = -f 2`
 
-mkdir -p $LOCALPATH
-
-echo starting decomposer for $numnodes partitions
+echo starting decomposer for $NPROC partitions
 echo " "
 
 mkdir -p OUTPUT_FILES/
@@ -42,6 +40,7 @@
 MESHDIR=examples/homogeneous_halfspace_HEX8/MESH
 
 cd bin/
-./xdecompose_mesh $numnodes ../$MESHDIR/ $LOCALPATH/
+mkdir -p $LOCALPATH
+./xdecompose_mesh $NPROC ../$MESHDIR/ $LOCALPATH/
 
 echo "done "

Modified: seismo/3D/SPECFEM3D/trunk/utils/Cluster/pbs/go_generate_databases_pbs.bash
===================================================================
--- seismo/3D/SPECFEM3D/trunk/utils/Cluster/pbs/go_generate_databases_pbs.bash	2012-12-24 20:18:38 UTC (rev 21192)
+++ seismo/3D/SPECFEM3D/trunk/utils/Cluster/pbs/go_generate_databases_pbs.bash	2012-12-24 20:45:29 UTC (rev 21193)
@@ -23,7 +23,7 @@
 # script to run the mesher and the solver
 # read Par_file to get information about the run
 # compute total number of nodes needed
-NPROC=`grep NPROC DATA/Par_file | cut -d = -f 2 `
+NPROC=`grep NPROC DATA/Par_file | cut -d = -f 2`
 
 mkdir -p OUTPUT_FILES
 
@@ -39,7 +39,7 @@
 cat $PBS_NODEFILE > OUTPUT_FILES/compute_nodes
 echo "$PBS_JOBID" > OUTPUT_FILES/jobid
 
-echo starting MPI mesher on $numnodes processors
+echo starting MPI mesher on $NPROC processors
 echo " "
 
 sleep 2
@@ -49,8 +49,8 @@
 echo "done "
 
 # per instructions in manual, view low-res mesh with these commands
-# > NPROC=`grep NPROC DATA/Par_file | cut -d = -f 2 `
-# > LOCALPATH=`grep LOCAL_PATH DATA/Par_file | cut -d = -f 2 `
+# > NPROC=`grep NPROC DATA/Par_file | cut -d = -f 2`
+# > LOCALPATH=`grep LOCAL_PATH DATA/Par_file | cut -d = -f 2`
 # > nmax=$(($NPROC-1))
 # > make xcombine_vol_data
 # > cd bin/

Modified: seismo/3D/SPECFEM3D/trunk/utils/Cluster/pbs/go_mesher_pbs.bash
===================================================================
--- seismo/3D/SPECFEM3D/trunk/utils/Cluster/pbs/go_mesher_pbs.bash	2012-12-24 20:18:38 UTC (rev 21192)
+++ seismo/3D/SPECFEM3D/trunk/utils/Cluster/pbs/go_mesher_pbs.bash	2012-12-24 20:45:29 UTC (rev 21193)
@@ -21,8 +21,7 @@
 cd $PBS_O_WORKDIR
 
 # number of cores for the job
-NPROC=`grep NPROC DATA/Par_file | cut -d = -f 2 `
-numnodes=$NPROC
+NPROC=`grep NPROC DATA/Par_file | cut -d = -f 2`
 
 mkdir -p OUTPUT_FILES
 mkdir -p OUTPUT_FILES/DATABASES_MPI
@@ -40,11 +39,11 @@
 cat $PBS_NODEFILE > OUTPUT_FILES/compute_nodes
 echo "$PBS_JOBID" > OUTPUT_FILES/jobid
 
-echo starting MPI internal mesher on $numnodes processors
+echo starting MPI internal mesher on $NPROC processors
 echo " "
 
 sleep 2
 cd bin/
-mpiexec -np $numnodes ./xmeshfem3D
+mpiexec -np $NPROC ./xmeshfem3D
 
 echo "done "

Modified: seismo/3D/SPECFEM3D/trunk/utils/Cluster/pbs/go_solver_pbs.bash
===================================================================
--- seismo/3D/SPECFEM3D/trunk/utils/Cluster/pbs/go_solver_pbs.bash	2012-12-24 20:18:38 UTC (rev 21192)
+++ seismo/3D/SPECFEM3D/trunk/utils/Cluster/pbs/go_solver_pbs.bash	2012-12-24 20:45:29 UTC (rev 21193)
@@ -23,7 +23,7 @@
 # script to run the mesher and the solver
 # read Par_file to get information about the run
 # compute total number of nodes needed
-NPROC=`grep NPROC DATA/Par_file | cut -d = -f 2 `
+NPROC=`grep NPROC DATA/Par_file | cut -d = -f 2`
 
 mkdir -p OUTPUT_FILES
 

Modified: seismo/3D/SPECFEM3D/trunk/utils/Cluster/pbs/valgrind_go_solver_pbs.bash
===================================================================
--- seismo/3D/SPECFEM3D/trunk/utils/Cluster/pbs/valgrind_go_solver_pbs.bash	2012-12-24 20:18:38 UTC (rev 21192)
+++ seismo/3D/SPECFEM3D/trunk/utils/Cluster/pbs/valgrind_go_solver_pbs.bash	2012-12-24 20:45:29 UTC (rev 21193)
@@ -38,11 +38,8 @@
 # script to run the mesher and the solver
 # read Par_file to get information about the run
 # compute total number of nodes needed
-NPROC=`grep NPROC DATA/Par_file | cut -d = -f 2 `
+NPROC=`grep NPROC DATA/Par_file | cut -d = -f 2`
 
-# total number of nodes is the product of the values read
-numnodes=$NPROC
-
 mkdir -p OUTPUT_FILES
 
 # backup files used for this simulation
@@ -63,7 +60,7 @@
 sleep 2
 
 # memory leaks
-LD_PRELOAD=$PRELOAD_LIB mpiexec -np $numnodes valgrind --leak-check=full ./xspecfem3D >& ../OUTPUT_FILES/output.memory-leaks.log
+LD_PRELOAD=$PRELOAD_LIB mpiexec -np $NPROC valgrind --leak-check=full ./xspecfem3D >& ../OUTPUT_FILES/output.memory-leaks.log
 
 sleep 2
 echo " "
@@ -71,7 +68,7 @@
 echo " "
 
 # cache misses
-LD_PRELOAD=$PRELOAD_LIB mpiexec -np $numnodes valgrind --tool=cachegrind ./xspecfem3D >& ../OUTPUT_FILES/output.cache-misses.log
+LD_PRELOAD=$PRELOAD_LIB mpiexec -np $NPROC valgrind --tool=cachegrind ./xspecfem3D >& ../OUTPUT_FILES/output.cache-misses.log
 
 cp cachegrind.out.* ../OUTPUT_FILES/