[cig-commits] r18081 - in seismo/3D/SPECFEM3D/trunk: examples/meshfem3D_examples/many_interfaces examples/meshfem3D_examples/simple_model utils/Cluster/pbs

carltape at geodynamics.org carltape at geodynamics.org
Tue Mar 8 15:41:38 PST 2011 

Author: carltape
Date: 2011-03-08 15:41:38 -0800 (Tue, 08 Mar 2011)
New Revision: 18081

Added:
   seismo/3D/SPECFEM3D/trunk/examples/meshfem3D_examples/simple_model/simple_model.png
   seismo/3D/SPECFEM3D/trunk/utils/Cluster/pbs/go_mesher_pbs.bash
Modified:
   seismo/3D/SPECFEM3D/trunk/examples/meshfem3D_examples/many_interfaces/README
   seismo/3D/SPECFEM3D/trunk/examples/meshfem3D_examples/simple_model/README
Log:
updated README for meshfem3D examples


Modified: seismo/3D/SPECFEM3D/trunk/examples/meshfem3D_examples/many_interfaces/README
===================================================================
--- seismo/3D/SPECFEM3D/trunk/examples/meshfem3D_examples/many_interfaces/README	2011-03-08 23:16:58 UTC (rev 18080)
+++ seismo/3D/SPECFEM3D/trunk/examples/meshfem3D_examples/many_interfaces/README	2011-03-08 23:41:38 UTC (rev 18081)
@@ -1,8 +1,69 @@
 ----------------------------------------------------------------------
 README
+(/SPECFEM3D/examples/meshfem3D_examples/many_interfaces/README)
 ----------------------------------------------------------------------
 
-To try this example, copy all the files within this folder to 'in_data_files/meshfem3D_files/'
-in the SPECFEM3D root directory.
+This is a more complicated example to explain the use of the internal mesher meshfem3D.
 
-Then you can compile and run xmeshfem3D.
+Option 1: run process.sh from local directory (must have access to mpi)
+Option 2: follow instructions below for submitting separate jobs with qsub (or bsub)
+
+----------------------------------------------------------------------
+
+0. Run the simple example under examples/meshfem3D_examples/simple_model
+
+1. Set up input files.
+
+   > cd SPECFEM3D
+   > rsync -av examples/meshfem3D_examples/many_interfaces/ in_data_files/meshfem3D_files/
+
+   > cd in_data_files/meshfem3D_files/
+   > cp Par_file CMTSOLUTION STATIONS ..
+   > cd SPECFEM3D
+
+   - adapt the submission scripts for the appropriate queues and number of cores:
+     go_mesher_pbs.bash, go_generate_databases_pbs.bash, go_solver_pbs.bash
+
+   - note: go_decomposer_pbs.bash is not used with the internal mesher
+
+2. compile and run internal mesher 
+
+   > make xmeshfem3D
+
+   > qsub go_mesher_pbs.bash
+
+   - this should generate "proc000***_Database" files in in_out_files/DATABASES_MPI/.
+
+   - save output file
+   > cp in_out_files/OUTPUT_FILES/output_mesher.txt in_out_files/OUTPUT_FILES/output_meshfem3D.txt
+
+3. generate databases:
+
+   - compile generate_databases in directory SPECFEM3D/:
+     > make xgenerate_databases
+
+   - submit job script:
+     > qsub go_generate_databases_pbs.bash
+
+     this job will take about XX minutes and will create binary mesh files, 
+     e.g. "proc000***_external_mesh.bin", in directory in_out_files/DATABASES_MPI/.
+
+     Optional: If you have paraview, load the .vtk files (see simple_model.png).
+
+4. run simulation:
+
+   - compile specfem3D:
+     > make xspecfem3D
+
+   - submit job script:
+     > qsub go_solver_pbs.bash
+
+   - the job should take about 70 minutes
+   - when the job is complete, you should have 3 sets (semd,semv,sema)
+     of XX (ls -1 *semd | wc) seismogram files in the directory in_out_files/OUTPUT_FILES,
+     as well as XX timestamp****** files
+
+   - view seismograms, for example, using xmgrace:
+   - xmgrace XXX &
+
+----------------------------------------------------------------------

Modified: seismo/3D/SPECFEM3D/trunk/examples/meshfem3D_examples/simple_model/README
===================================================================
--- seismo/3D/SPECFEM3D/trunk/examples/meshfem3D_examples/simple_model/README	2011-03-08 23:16:58 UTC (rev 18080)
+++ seismo/3D/SPECFEM3D/trunk/examples/meshfem3D_examples/simple_model/README	2011-03-08 23:41:38 UTC (rev 18081)
@@ -1,10 +1,85 @@
 ----------------------------------------------------------------------
 README
+(/SPECFEM3D/examples/meshfem3D_examples/simple_model/README)
 ----------------------------------------------------------------------
 
-This is a very simple example to explain the use of meshfem3D.
+This is a very simple example to explain the use of the internal mesher meshfem3D.
 
-To try this example, copy all the files within this folder to 'in_data_files/meshfem3D_files/'
-in the SPECFEM3D root directory.
+Option 1: run process.sh from local directory (must have access to mpi)
+Option 2: follow instructions below for submitting separate jobs with qsub (or bsub)
 
-Then you can compile and run xmeshfem3D.
+----------------------------------------------------------------------
+
+0. Run the default homogeneous halfspace example (external mesh).
+
+1. Set up input files.
+
+   > cd SPECFEM3D
+   > rsync -av examples/meshfem3D_examples/simple_model/ in_data_files/meshfem3D_files/
+
+   > cd in_data_files/meshfem3D_files/
+   > cp Par_file CMTSOLUTION STATIONS ..
+   > cd SPECFEM3D
+
+   - adapt the submission scripts for the appropriate queues and number of cores:
+     go_mesher_pbs.bash, go_generate_databases_pbs.bash, go_solver_pbs.bash
+
+   - note: go_decomposer_pbs.bash is not used with the internal mesher
+
+2. compile and run internal mesher 
+
+   > make xmeshfem3D
+
+   > qsub go_mesher_pbs.bash
+
+   This should generate these files in in_out_files/DATABASES_MPI/:
+
+   proc000000_Database
+   proc000000_.dx
+   proc000000_.INP
+   proc000001_Database
+   proc000001_.dx
+   proc000001_.INP
+   proc000002_Database
+   proc000002_.dx
+   proc000002_.INP
+   proc000003_Database
+   proc000003_.dx
+   proc000003_.INP
+
+   - save output file
+   > cp in_out_files/OUTPUT_FILES/output_mesher.txt in_out_files/OUTPUT_FILES/output_meshfem3D.txt
+
+3. generate databases:
+
+   - compile generate_databases in directory SPECFEM3D/:
+     > make xgenerate_databases
+
+   - submit job script:
+     > qsub go_generate_databases_pbs.bash
+
+     this will create binary mesh files, e.g. "proc000***_external_mesh.bin"
+     in directory in_out_files/DATABASES_MPI/.
+
+     Optional: If you have paraview, load the .vtk files (see simple_model.png).
+
+4. run simulation:
+
+   - compile specfem3D:
+     > make xspecfem3D
+
+   - submit job script:
+     > qsub go_solver_pbs.bash
+
+   - the job should take about 10 minutes
+   - when the job is complete, you should have 3 sets (semd,semv,sema)
+     of 27 (ls -1 *semd | wc) seismogram files in the directory in_out_files/OUTPUT_FILES,
+     as well as 5 timestamp****** files
+
+   - view seismograms, for example, using xmgrace:
+   - xmgrace K400.CE.BXZ.semd K851.CE.BXZ.semd K853.CE.BXZ.semd &
+
+   - compare with reference seismograms in
+     examples/meshfem3D_examples/simple_model/REF_SEIS/
+
+----------------------------------------------------------------------

Added: seismo/3D/SPECFEM3D/trunk/examples/meshfem3D_examples/simple_model/simple_model.png
===================================================================
(Binary files differ)


Property changes on: seismo/3D/SPECFEM3D/trunk/examples/meshfem3D_examples/simple_model/simple_model.png
___________________________________________________________________
Name: svn:mime-type
   + application/octet-stream

Added: seismo/3D/SPECFEM3D/trunk/utils/Cluster/pbs/go_mesher_pbs.bash
===================================================================
--- seismo/3D/SPECFEM3D/trunk/utils/Cluster/pbs/go_mesher_pbs.bash	                        (rev 0)
+++ seismo/3D/SPECFEM3D/trunk/utils/Cluster/pbs/go_mesher_pbs.bash	2011-03-08 23:41:38 UTC (rev 18081)
@@ -0,0 +1,44 @@
+#!/bin/bash
+#PBS -S /bin/bash
+
+## job name and output file
+#PBS -N go_mesher
+#PBS -j oe
+#PBS -o in_out_files/OUTPUT_FILES/$PBS_JOBID.o
+
+###########################################################
+# USER PARAMETERS
+
+## 4 CPUs ( 4  ), walltime 1 hour
+#PBS -l nodes=1:ppn=4,walltime=1:00:00
+##PBS -q debug
+
+###########################################################
+
+cd $PBS_O_WORKDIR
+
+# number of cores for the job
+NPROC=`grep NPROC in_data_files/Par_file | cut -d = -f 2 `
+numnodes=$NPROC
+
+mkdir -p in_out_files/OUTPUT_FILES
+
+# backup files used for this simulation
+cp in_data_files/Par_file in_out_files/OUTPUT_FILES/
+
+# save a complete copy of source files
+#rm -rf in_out_files/OUTPUT_FILES/src
+#cp -rp ./src in_out_files/OUTPUT_FILES/
+
+# obtain lsf job information
+cat $PBS_NODEFILE > in_out_files/OUTPUT_FILES/compute_nodes
+echo "$PBS_JOBID" > in_out_files/OUTPUT_FILES/jobid
+
+echo starting MPI internal mesher on $numnodes processors
+echo " "
+
+sleep 2
+cd bin/
+mpiexec -np $numnodes ./xmeshfem3D
+
+echo "done "


Property changes on: seismo/3D/SPECFEM3D/trunk/utils/Cluster/pbs/go_mesher_pbs.bash
___________________________________________________________________
Name: svn:executable
   + *

More information about the CIG-COMMITS mailing list