[cig-commits] r22924 - seismo/3D/SPECFEM3D/trunk/examples/homogeneous_halfspace_HEX8_elastic_absorbing_Stacey_5sides
carltape at geodynamics.org
carltape at geodynamics.org
Fri Oct 4 22:56:22 PDT 2013
Author: carltape
Date: 2013-10-04 22:56:22 -0700 (Fri, 04 Oct 2013)
New Revision: 22924
Removed:
seismo/3D/SPECFEM3D/trunk/examples/homogeneous_halfspace_HEX8_elastic_absorbing_Stacey_5sides/HOWTO_run_this_example.txt
Modified:
seismo/3D/SPECFEM3D/trunk/examples/homogeneous_halfspace_HEX8_elastic_absorbing_Stacey_5sides/README
seismo/3D/SPECFEM3D/trunk/examples/homogeneous_halfspace_HEX8_elastic_absorbing_Stacey_5sides/process.sh
Log:
updated instructions for homogeneous_halfspace example; tested process.sh with gfortran
Deleted: seismo/3D/SPECFEM3D/trunk/examples/homogeneous_halfspace_HEX8_elastic_absorbing_Stacey_5sides/HOWTO_run_this_example.txt
===================================================================
--- seismo/3D/SPECFEM3D/trunk/examples/homogeneous_halfspace_HEX8_elastic_absorbing_Stacey_5sides/HOWTO_run_this_example.txt 2013-10-04 22:43:25 UTC (rev 22923)
+++ seismo/3D/SPECFEM3D/trunk/examples/homogeneous_halfspace_HEX8_elastic_absorbing_Stacey_5sides/HOWTO_run_this_example.txt 2013-10-05 05:56:22 UTC (rev 22924)
@@ -1,11 +0,0 @@
-
-To run this example on 4 processor cores for instance, type this (replace "4" with another value in the three lines below if you want to use more processor cores, and do the same modification in file DATA/Par_file):
-
-cd bin/
-
-./xdecompose_mesh 4 ../DATA/MESH-default/ ../OUTPUT_FILES/DATABASES_MPI/
-
-mpirun -np 4 ./xgenerate_databases
-
-mpirun -np 4 ./xspecfem3D
-
Modified: seismo/3D/SPECFEM3D/trunk/examples/homogeneous_halfspace_HEX8_elastic_absorbing_Stacey_5sides/README
===================================================================
--- seismo/3D/SPECFEM3D/trunk/examples/homogeneous_halfspace_HEX8_elastic_absorbing_Stacey_5sides/README 2013-10-04 22:43:25 UTC (rev 22923)
+++ seismo/3D/SPECFEM3D/trunk/examples/homogeneous_halfspace_HEX8_elastic_absorbing_Stacey_5sides/README 2013-10-05 05:56:22 UTC (rev 22924)
@@ -7,10 +7,30 @@
----------------------------------------------------------------------
-step-by-step tutorial (short version):
+step-by-step tutorial (short version -- use pre-saved mesh files):
-0. check that all software is available (or that modules are loaded):
+1. check that all software is available (or that modules are loaded):
openmpi: > which mpirun
+ scotch: > which gout
+
+2. from the directory SPECFEM3D/examples/homogeneous_halfspace/
+
+ > ./process.sh >& process.sh.log
+
+ note: by default, the command ./configure in process.sh will use gfortran;
+ you need to change this if you want something else (see 3. below)
+
+ This will configure, compile, then run the decomposer, database generation,
+ and solver in the local directory. The simulation takes about 15 minutes.
+
+3. see step 9. below to compare seismograms in REF_SEIS/ with those in OUTPUT_FILES/
+
+----------------------------------------------------------------------
+
+step-by-step tutorial (long version -- generate MESH with GEOCUBIT):
+
+1. check that all software is available (or that modules are loaded):
+ openmpi: > which mpirun
cubit: > which cubit
scotch: > which gout
python: > which python
@@ -18,22 +38,14 @@
gnuplot: > which gnuplot
xmgrace: > which xmgrace
-1. check paths and set paths for meshing with GEOCUBIT
+2. check paths and set paths for meshing with GEOCUBIT
- From the SPECFEM3D 'base' directory SPECFEM3D/
> cd CUBIT_GEOCUBIT
> source setpaths.sh
-2. run process.sh
+3. configure package:
-----------------------------------------------------------------------
-
-step-by-step tutorial (long version):
-
-0. perform steps 0. and 1. above
-
-1. configure package:
-
- determine the path for your compiled version of SCOTCH
- From the SPECFEM3D root directory SPECFEM3D/
@@ -57,18 +69,16 @@
note: you may need to adjust the commands (e.g., -q or -l)
note: in this example you do not need go_mesher_pbs.bash and valgrind_go_solver_pbs.bash
-2. copy three input files from examples directory into SPECFEM3D/DATA/
+4. copy three input files from examples directory into SPECFEM3D/DATA/
> cd examples/homogeneous_halfspace/DATA/
> cp * ../../../DATA/
-3. create mesh:
+5. create mesh:
- check path, then make mesh
> which GEOCUBIT.py
> make_mesh.sh
-
- - see instructions in make_mesh.sh
if everything goes fine, this creates the ten mesh files in subdirectory MESH/:
absorbing_surface_file_bottom
@@ -93,7 +103,7 @@
then open TOTALMESH_MERGED.e
(click "Apply", then select "Surface With Edges" in the toolbar)
-4. decompose mesh files:
+6. decompose mesh files:
- compile decomposer in directory SPECFEM3D/:
> make xdecompose_mesh
@@ -114,7 +124,7 @@
> ./bin/xdecompose_mesh 4 examples/homogeneous_halfspace/MESH/ OUTPUT_FILES/DATABASES_MPI/
-5. generate databases:
+7. generate databases:
- compile generate_databases in directory SPECFEM3D/:
> make xgenerate_databases
@@ -130,7 +140,7 @@
optional: load vtk files (e.g., vs) into paraview and check them out
-6. run simulation:
+8. run simulation:
- compile specfem3D:
> make xspecfem3D
@@ -144,13 +154,13 @@
and you can track the progress with the timestamp files
generated in OUTPUT_FILES/
- - the job should take about 30 minutes
+ - the job should take about 15 minutes
- when the job is complete, you should have 3 sets (semd,semv,sema)
of 18 (ls -1 *semd | wc) seismogram files in the directory OUTPUT_FILES,
as well as 3 timestamp****** files
-7. check with 6 reference seismograms in
+9. check with 6 reference seismograms in
SPECFEM3D/examples/homogeneous_halfspace/REF_SEIS/
- option 1: from SPECFEM3D/, quick viewing using xmgrace (if available):
Modified: seismo/3D/SPECFEM3D/trunk/examples/homogeneous_halfspace_HEX8_elastic_absorbing_Stacey_5sides/process.sh
===================================================================
--- seismo/3D/SPECFEM3D/trunk/examples/homogeneous_halfspace_HEX8_elastic_absorbing_Stacey_5sides/process.sh 2013-10-04 22:43:25 UTC (rev 22923)
+++ seismo/3D/SPECFEM3D/trunk/examples/homogeneous_halfspace_HEX8_elastic_absorbing_Stacey_5sides/process.sh 2013-10-05 05:56:22 UTC (rev 22924)
@@ -1,25 +1,10 @@
#!/bin/bash
-#
-# script runs decomposition,database generation and solver
-# using this example setup
-#
-# prior to running this script, you must create the mesh files
-# in directory MESH/
-# (see section 3.1 "Meshing with CUBIT" in user guide)
-#
-###################################################
-
-# number of processes
-NPROC=4
-
-##################################################
-
echo "running example: `date`"
currentdir=`pwd`
echo
-echo "(will take about 5 minutes)"
+echo "(will take about 15 minutes)"
echo
# sets up directory structure in current example directoy
@@ -42,6 +27,8 @@
cd ../../
+# note: ./configure will default to gfortran configuration
+# ./configure FC=ifort MPIFC=mpif90
./configure
make clean
make all > $currentdir/tmp.log
@@ -63,7 +50,7 @@
# get the number of processors
NPROC=`grep NPROC DATA/Par_file | cut -d = -f 2`
-# decomposes mesh
+# decomposes mesh using the pre-saved mesh files in MESH-default
echo
echo " decomposing mesh..."
echo
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