[cig-commits] [commit] devel: Update PBS scripts and examples. (409219b)

[cig_noreply at geodynamics.org]

Repository : ssh://geoshell/specfem3d

On branch  : devel
Link       : https://github.com/geodynamics/specfem3d/compare/6405469307ca0a824c4e85db0233642c7e4f9037...a668bacb1ee6d977dbb736f361fd6a1c87643cf0

>---------------------------------------------------------------

commit 409219b4621b2a46caa091d7d13024b1c5ad6046
Author: Carl Tape <carltape at gi.alaska.edu>
Date:   Mon Apr 21 21:53:55 2014 -0400

    Update PBS scripts and examples.


>---------------------------------------------------------------

409219b4621b2a46caa091d7d13024b1c5ad6046
 examples                                                 |  2 +-
 ..._decomposer_pbs.bash => go_combine_vol_data_pbs.bash} | 16 +++++-----------
 utils/Cluster/pbs/go_decomposer_pbs.bash                 |  5 ++---
 utils/Cluster/pbs/go_generate_databases_pbs.bash         | 14 +-------------
 utils/Cluster/pbs/go_solver_pbs.bash                     |  5 ++---
 5 files changed, 11 insertions(+), 31 deletions(-)

diff --git a/examples b/examples
index 3342a03..1e6f3ac 160000
--- a/examples
+++ b/examples
@@ -1 +1 @@
-Subproject commit 3342a03b2a09d8c8566ce2c655f2440260062a5b
+Subproject commit 1e6f3acb1db67d72da8d3a7dbbe8487777286250
diff --git a/utils/Cluster/pbs/go_decomposer_pbs.bash b/utils/Cluster/pbs/go_combine_vol_data_pbs.bash
similarity index 72%
copy from utils/Cluster/pbs/go_decomposer_pbs.bash
copy to utils/Cluster/pbs/go_combine_vol_data_pbs.bash
index b1ed069..9d8bf7d 100755
--- a/utils/Cluster/pbs/go_decomposer_pbs.bash
+++ b/utils/Cluster/pbs/go_combine_vol_data_pbs.bash
@@ -29,19 +29,13 @@ 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`
 
-echo starting decomposer for $NPROC partitions
-echo " "
+nmax=$(($NPROC-1))
 
-mkdir -p OUTPUT_FILES/
+make xcombine_vol_data
 
-# save a copy
-cp go_decomposer_pbs.bash OUTPUT_FILES/
+# model variable is vs; output file will be vs.vtk
+./bin/xcombine_vol_data 0 $nmax vs $LOCALPATH/ $LOCALPATH 0
 
-# USER CHANGE MESH DIRECTORY
-MESHDIR=examples/homogeneous_halfspace/MESH
-
-cd bin/
-mkdir -p $LOCALPATH
-./xdecompose_mesh $NPROC ../$MESHDIR/ $LOCALPATH/
+cp go_combine_vol_data_pbs.bash OUTPUT_FILES/
 
 echo "done "
diff --git a/utils/Cluster/pbs/go_decomposer_pbs.bash b/utils/Cluster/pbs/go_decomposer_pbs.bash
index b1ed069..5b52cc3 100755
--- a/utils/Cluster/pbs/go_decomposer_pbs.bash
+++ b/utils/Cluster/pbs/go_decomposer_pbs.bash
@@ -38,10 +38,9 @@ mkdir -p OUTPUT_FILES/
 cp go_decomposer_pbs.bash OUTPUT_FILES/
 
 # USER CHANGE MESH DIRECTORY
-MESHDIR=examples/homogeneous_halfspace/MESH
+MESHDIR=./examples/homogeneous_halfspace/MESH
 
-cd bin/
 mkdir -p $LOCALPATH
-./xdecompose_mesh $NPROC ../$MESHDIR/ $LOCALPATH/
+./bin/xdecompose_mesh $NPROC $MESHDIR/ $LOCALPATH/
 
 echo "done "
diff --git a/utils/Cluster/pbs/go_generate_databases_pbs.bash b/utils/Cluster/pbs/go_generate_databases_pbs.bash
index 4f49ccf..296640c 100755
--- a/utils/Cluster/pbs/go_generate_databases_pbs.bash
+++ b/utils/Cluster/pbs/go_generate_databases_pbs.bash
@@ -44,18 +44,6 @@ echo starting MPI mesher on $NPROC processors
 echo " "
 
 sleep 2
-cd bin/
-mpiexec -np $NPROC ./xgenerate_databases
+mpiexec -np $NPROC ./bin/xgenerate_databases
 
 echo "done "
-
-# per instructions in manual, view low-res mesh with these commands
-# [there are other options for viewing the high-res mesh of any partitions]
-# > 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/
-# > ./xcombine_vol_data 0 $nmax vs $LOCALPATH/ $LOCALPATH 0
-# > cd $LOCALPATH
-# > paraview &
\ No newline at end of file
diff --git a/utils/Cluster/pbs/go_solver_pbs.bash b/utils/Cluster/pbs/go_solver_pbs.bash
index c505a8e..b64ea04 100755
--- a/utils/Cluster/pbs/go_solver_pbs.bash
+++ b/utils/Cluster/pbs/go_solver_pbs.bash
@@ -47,10 +47,9 @@ echo starting run in current directory $PWD
 echo " "
 
 sleep 2
-cd bin/
-mpiexec -np $NPROC ./xspecfem3D
+mpiexec -np $NPROC ./bin/xspecfem3D
 
-cp ../DATA/STATIONS_FILTERED ../OUTPUT_FILES/
+cp DATA/STATIONS_FILTERED OUTPUT_FILES/
 
 echo "finished successfully"