[cig-commits] [commit] devel,master: updates configure file to bundle with new scotch_5.1.11 version; updates in-house mesher examples meshfem3D_examples/; updates post-processing scripts process_data.pl and process_syn.pl (e38ab2b)
cig_noreply at geodynamics.org
cig_noreply at geodynamics.org
Wed Jun 18 16:48:22 PDT 2014
Repository : https://github.com/geodynamics/specfem3d
On branches: devel,master
Link : https://github.com/geodynamics/specfem3d/compare/6026e367984905ab133865f62fa6293b343759b9...47f703851338234f96397e7da9fbff63d8178b8a
>---------------------------------------------------------------
commit e38ab2bab2e82ed23dbb572f7ef85b6b3861f7f8
Author: Daniel Peter <peterda at ethz.ch>
Date: Thu Feb 3 20:16:10 2011 +0000
updates configure file to bundle with new scotch_5.1.11 version; updates in-house mesher examples meshfem3D_examples/; updates post-processing scripts process_data.pl and process_syn.pl
>---------------------------------------------------------------
e38ab2bab2e82ed23dbb572f7ef85b6b3861f7f8
.../{simple_model => many_interfaces}/CMTSOLUTION | 4 +-
meshfem3D_examples/many_interfaces/Mesh_Par_file | 6 +--
.../many_interfaces}/Par_file | 8 ++--
meshfem3D_examples/many_interfaces/STATIONS | 3 ++
.../go_process_pbs.bash} | 52 ++++++++++++++--------
.../{simple_model => many_interfaces}/process.sh | 7 +--
meshfem3D_examples/simple_model/Mesh_Par_file | 4 +-
meshfem3D_examples/simple_model/Par_file | 5 ++-
meshfem3D_examples/simple_model/process.sh | 1 +
9 files changed, 56 insertions(+), 34 deletions(-)
diff --git a/meshfem3D_examples/simple_model/CMTSOLUTION b/meshfem3D_examples/many_interfaces/CMTSOLUTION
similarity index 86%
copy from meshfem3D_examples/simple_model/CMTSOLUTION
copy to meshfem3D_examples/many_interfaces/CMTSOLUTION
index e252010..5b5ae65 100644
--- a/meshfem3D_examples/simple_model/CMTSOLUTION
+++ b/meshfem3D_examples/many_interfaces/CMTSOLUTION
@@ -2,8 +2,8 @@ PDE 1999 01 01 00 00 00.00 67000 67000 -25000 4.2 4.2 hom_explosion
event name: hom_explosion
time shift: 0.0000
half duration: 5.0
-latitude: 33.6
-longitude: -118.4
+latitude: 15150.0
+longitude: 14925.0
depth: 10.0
Mrr: 1.000000e+23
Mtt: 1.000000e+23
diff --git a/meshfem3D_examples/many_interfaces/Mesh_Par_file b/meshfem3D_examples/many_interfaces/Mesh_Par_file
index e724eb0..22c35db 100644
--- a/meshfem3D_examples/many_interfaces/Mesh_Par_file
+++ b/meshfem3D_examples/many_interfaces/Mesh_Par_file
@@ -14,8 +14,8 @@ INTERFACES_FILE = example_interfaces.dat
# number of elements at the surface along edges of the mesh at the surface
# (must be 8 * multiple of NPROC below if mesh is not regular and contains mesh doublings)
# (must be multiple of NPROC below if mesh is regular)
-NEX_XI = 648
-NEX_ETA = 720
+NEX_XI = 648 # 648
+NEX_ETA = 720 # 720
# number of MPI processors along xi and eta (can be different)
NPROC_XI = 9
@@ -30,7 +30,7 @@ NZ_DOUGLING_1 = 147
NZ_DOUGLING_2 = 145
# create mesh files for visualisation or further checking
-CREATE_ABAQUS_FILES = .false.
+CREATE_ABAQUS_FILES = .true.
CREATE_DX_FILES = .true.
# path to store the databases files
diff --git a/tomographic_model/in_data_files/Par_file b/meshfem3D_examples/many_interfaces/Par_file
similarity index 91%
copy from tomographic_model/in_data_files/Par_file
copy to meshfem3D_examples/many_interfaces/Par_file
index 44c4041..c4b17ea 100644
--- a/tomographic_model/in_data_files/Par_file
+++ b/meshfem3D_examples/many_interfaces/Par_file
@@ -9,11 +9,11 @@ UTM_PROJECTION_ZONE = 11
SUPPRESS_UTM_PROJECTION = .true.
# number of MPI processors
-NPROC = 4
+NPROC = 81
# time step parameters
-NSTEP = 4000
-DT = 0.01
+NSTEP = 2000
+DT = 0.03
# parameters describing the model
OCEANS = .false.
@@ -26,7 +26,7 @@ ANISOTROPY = .false.
ABSORBING_CONDITIONS = .true.
# save AVS or OpenDX movies
-MOVIE_SURFACE = .false.
+MOVIE_SURFACE = .true.
MOVIE_VOLUME = .false.
NTSTEP_BETWEEN_FRAMES = 200
CREATE_SHAKEMAP = .false.
diff --git a/meshfem3D_examples/many_interfaces/STATIONS b/meshfem3D_examples/many_interfaces/STATIONS
new file mode 100644
index 0000000..478e1bc
--- /dev/null
+++ b/meshfem3D_examples/many_interfaces/STATIONS
@@ -0,0 +1,3 @@
+K1 DB 1000. 15150.0 0.0 0.0
+K2 DB 10000. 15150.0 0.0 0.0
+K3 DB 20000. 15150.0 0.0 0.0
diff --git a/meshfem3D_examples/simple_model/process.sh b/meshfem3D_examples/many_interfaces/go_process_pbs.bash
similarity index 50%
copy from meshfem3D_examples/simple_model/process.sh
copy to meshfem3D_examples/many_interfaces/go_process_pbs.bash
index 4c66233..f6be768 100755
--- a/meshfem3D_examples/simple_model/process.sh
+++ b/meshfem3D_examples/many_interfaces/go_process_pbs.bash
@@ -1,21 +1,32 @@
#!/bin/bash
#
-# script runs mesher,database generation and solver
-# using this example setup
+# usage: submit this script in the current example directory like
+# > qsub go_process_pbs.bash
#
+#PBS -S /bin/bash
-###################################################
+## job name and output file
+#PBS -N go_process
+#PBS -j oe
+#PBS -o in_out_files/OUTPUT_FILES/$PBS_JOBID.o
+## PBS -q test
-# number of processes
-NPROC=4
+###########################################################
+# USER PARAMETERS
-##################################################
+## number of processes
+## 81 CPUs ( 10*8 + 1 ), walltime 4 hour
+#PBS -l nodes=10:ppn=8+1:ppn=1,walltime=4:00:00
+
+###########################################################
+
+cd $PBS_O_WORKDIR
echo "running example: `date`"
currentdir=`pwd`
echo
-echo "(will take about 15 minutes)"
+echo "(will take about 1 h 15 minutes)"
echo
# sets up directory structure in current example directoy
@@ -23,6 +34,7 @@ echo
echo " setting up example..."
echo
+# setup
mkdir -p bin
mkdir -p in_out_files/OUTPUT_FILES
mkdir -p in_out_files/DATABASES_MPI
@@ -34,18 +46,13 @@ mkdir -p in_data_files
mkdir -p in_data_files/meshfem3D_files/
cp Mesh_Par_file in_data_files/meshfem3D_files/
-cp interface*.dat in_data_files/meshfem3D_files/
+cp example_*.dat in_data_files/meshfem3D_files/
cp Par_file in_data_files/
cp CMTSOLUTION in_data_files/
cp STATIONS in_data_files/
-
-# compiles executables in root directory
-cd ../../../
-make > tmp.log
-cd $currentdir
-
+# compilation of executables must have been done prior on front node
# links executables
cd bin/
ln -s ../../../../bin/xmeshfem3D
@@ -53,13 +60,22 @@ ln -s ../../../../bin/xgenerate_databases
ln -s ../../../../bin/xspecfem3D
cd ../
+# script to run the mesher and the solver
+# read Par_file to get information about the run
+# compute total number of nodes needed
+NPROC=`grep NPROC in_data_files/Par_file | cut -d = -f 2 `
+
+# total number of nodes is the product of the values read
+numnodes=$NPROC
+
# decomposes mesh
echo
echo " meshing..."
echo
cd bin/
-mpirun -np $NPROC ./xmeshfem3D
+mpiexec -np $numnodes ./xmeshfem3D
cd ../
+mv in_out_files/OUTPUT_FILES/output_mesher.txt in_out_files/OUTPUT_FILES/output_meshfem3D.txt
# stores setup
cp in_data_files/Par_file in_out_files/OUTPUT_FILES/
@@ -71,7 +87,7 @@ echo
echo " running database generation..."
echo
cd bin/
-mpirun -np $NPROC ./xgenerate_databases
+mpiexec -np $numnodes ./xgenerate_databases
cd ../
# runs simulation
@@ -79,7 +95,7 @@ echo
echo " running solver..."
echo
cd bin/
-mpirun -np $NPROC ./xspecfem3D
+mpiexec -np $numnodes ./xspecfem3D
cd ../
echo
@@ -87,5 +103,3 @@ echo "see results in directory: in_out_files/OUTPUT_FILES/"
echo
echo "done"
echo `date`
-
-
diff --git a/meshfem3D_examples/simple_model/process.sh b/meshfem3D_examples/many_interfaces/process.sh
similarity index 89%
copy from meshfem3D_examples/simple_model/process.sh
copy to meshfem3D_examples/many_interfaces/process.sh
index 4c66233..0586c4d 100755
--- a/meshfem3D_examples/simple_model/process.sh
+++ b/meshfem3D_examples/many_interfaces/process.sh
@@ -7,7 +7,7 @@
###################################################
# number of processes
-NPROC=4
+NPROC=81
##################################################
@@ -15,7 +15,7 @@ echo "running example: `date`"
currentdir=`pwd`
echo
-echo "(will take about 15 minutes)"
+echo "(will take about 1 h 15 minutes)"
echo
# sets up directory structure in current example directoy
@@ -34,7 +34,7 @@ mkdir -p in_data_files
mkdir -p in_data_files/meshfem3D_files/
cp Mesh_Par_file in_data_files/meshfem3D_files/
-cp interface*.dat in_data_files/meshfem3D_files/
+cp example_*.dat in_data_files/meshfem3D_files/
cp Par_file in_data_files/
cp CMTSOLUTION in_data_files/
@@ -60,6 +60,7 @@ echo
cd bin/
mpirun -np $NPROC ./xmeshfem3D
cd ../
+mv in_out_files/OUTPUT_FILES/output_mesher.txt in_out_files/OUTPUT_FILES/output_meshfem3D.txt
# stores setup
cp in_data_files/Par_file in_out_files/OUTPUT_FILES/
diff --git a/meshfem3D_examples/simple_model/Mesh_Par_file b/meshfem3D_examples/simple_model/Mesh_Par_file
index 31e051b..32a4e33 100644
--- a/meshfem3D_examples/simple_model/Mesh_Par_file
+++ b/meshfem3D_examples/simple_model/Mesh_Par_file
@@ -30,8 +30,8 @@ NZ_DOUGLING_1 = 11
NZ_DOUGLING_2 = 0
# create mesh files for visualisation or further checking
-CREATE_ABAQUS_FILES = .false.
-CREATE_DX_FILES = .false.
+CREATE_ABAQUS_FILES = .true.
+CREATE_DX_FILES = .true.
# path to store the databases files
LOCAL_PATH = ../in_out_files/DATABASES_MPI
diff --git a/meshfem3D_examples/simple_model/Par_file b/meshfem3D_examples/simple_model/Par_file
index b620eb7..c97b11c 100644
--- a/meshfem3D_examples/simple_model/Par_file
+++ b/meshfem3D_examples/simple_model/Par_file
@@ -14,10 +14,10 @@ NPROC = 4
# time step parameters
NSTEP = 2000
DT = 0.03
-NTSTEP_BETWEEN_READ_ADJSRC = 0 # 0 = read the whole adjoint sources at the same time
# parameters describing the model
OCEANS = .false.
+TOPOGRAPHY = .false.
ATTENUATION = .false.
USE_OLSEN_ATTENUATION = .false.
ANISOTROPY = .false.
@@ -46,6 +46,9 @@ NTSTEP_BETWEEN_OUTPUT_INFO = 500
# interval in time steps for writing of seismograms
NTSTEP_BETWEEN_OUTPUT_SEISMOS = 10000
+# interval in time steps for reading adjoint traces
+NTSTEP_BETWEEN_READ_ADJSRC = 0 # 0 = read the whole adjoint sources at the same time
+
# print source time function
PRINT_SOURCE_TIME_FUNCTION = .false.
diff --git a/meshfem3D_examples/simple_model/process.sh b/meshfem3D_examples/simple_model/process.sh
index 4c66233..14ffa32 100755
--- a/meshfem3D_examples/simple_model/process.sh
+++ b/meshfem3D_examples/simple_model/process.sh
@@ -60,6 +60,7 @@ echo
cd bin/
mpirun -np $NPROC ./xmeshfem3D
cd ../
+mv in_out_files/OUTPUT_FILES/output_mesher.txt in_out_files/OUTPUT_FILES/output_meshfem3D.txt
# stores setup
cp in_data_files/Par_file in_out_files/OUTPUT_FILES/
More information about the CIG-COMMITS
mailing list