[cig-commits] [commit] devel,master: updated instructions for homogeneous_halfspace example; tested process.sh with gfortran (f41bc89)
cig_noreply at geodynamics.org
cig_noreply at geodynamics.org
Wed Jun 18 16:54:28 PDT 2014
Repository : https://github.com/geodynamics/specfem3d
On branches: devel,master
Link : https://github.com/geodynamics/specfem3d/compare/6026e367984905ab133865f62fa6293b343759b9...47f703851338234f96397e7da9fbff63d8178b8a
>---------------------------------------------------------------
commit f41bc898bd79f330c0b5406fd554f084f1da5f5f
Author: Carl Tape <carltape at gi.alaska.edu>
Date: Sat Oct 5 05:56:22 2013 +0000
updated instructions for homogeneous_halfspace example; tested process.sh with gfortran
>---------------------------------------------------------------
f41bc898bd79f330c0b5406fd554f084f1da5f5f
.../HOWTO_run_this_example.txt | 11 -----
.../README | 52 +++++++++++++---------
.../process.sh | 21 ++-------
3 files changed, 35 insertions(+), 49 deletions(-)
diff --git a/homogeneous_halfspace_HEX8_elastic_absorbing_Stacey_5sides/HOWTO_run_this_example.txt b/homogeneous_halfspace_HEX8_elastic_absorbing_Stacey_5sides/HOWTO_run_this_example.txt
deleted file mode 100644
index b213498..0000000
--- a/homogeneous_halfspace_HEX8_elastic_absorbing_Stacey_5sides/HOWTO_run_this_example.txt
+++ /dev/null
@@ -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
-
diff --git a/homogeneous_halfspace_HEX8_elastic_absorbing_Stacey_5sides/README b/homogeneous_halfspace_HEX8_elastic_absorbing_Stacey_5sides/README
index 53e16e1..58cc18e 100644
--- a/homogeneous_halfspace_HEX8_elastic_absorbing_Stacey_5sides/README
+++ b/homogeneous_halfspace_HEX8_elastic_absorbing_Stacey_5sides/README
@@ -7,9 +7,29 @@ constant elastic material property, using CUBIT, and runs a forward simulation.
----------------------------------------------------------------------
-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
@@ -18,21 +38,13 @@ step-by-step tutorial (short version):
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
-
-----------------------------------------------------------------------
-
-step-by-step tutorial (long version):
-
-0. perform steps 0. and 1. above
-
-1. configure package:
+3. configure package:
- determine the path for your compiled version of SCOTCH
@@ -57,19 +69,17 @@ step-by-step tutorial (long version):
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
absorbing_surface_file_xmax
@@ -93,7 +103,7 @@ step-by-step tutorial (long version):
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 @@ step-by-step tutorial (long version):
> ./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 @@ step-by-step tutorial (long version):
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 @@ step-by-step tutorial (long version):
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):
diff --git a/homogeneous_halfspace_HEX8_elastic_absorbing_Stacey_5sides/process.sh b/homogeneous_halfspace_HEX8_elastic_absorbing_Stacey_5sides/process.sh
index 1dc2a3e..ec47524 100755
--- a/homogeneous_halfspace_HEX8_elastic_absorbing_Stacey_5sides/process.sh
+++ b/homogeneous_halfspace_HEX8_elastic_absorbing_Stacey_5sides/process.sh
@@ -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 @@ cp -fr DATA/* ../../DATA/.
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 @@ cp DATA/STATIONS OUTPUT_FILES/
# 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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