[cig-commits] r18124 - in seismo/3D/SPECFEM3D_GLOBE/trunk: EXAMPLES/noise_examples EXAMPLES/noise_examples/global_long EXAMPLES/noise_examples/global_short EXAMPLES/noise_examples/regional src/specfem3D
yangl at geodynamics.org
yangl at geodynamics.org
Tue Mar 22 14:52:39 PDT 2011
Author: yangl
Date: 2011-03-22 14:52:38 -0700 (Tue, 22 Mar 2011)
New Revision: 18124
Modified:
seismo/3D/SPECFEM3D_GLOBE/trunk/EXAMPLES/noise_examples/global_long/NOISE123.submit_atten
seismo/3D/SPECFEM3D_GLOBE/trunk/EXAMPLES/noise_examples/global_long/NOISE_clean_create
seismo/3D/SPECFEM3D_GLOBE/trunk/EXAMPLES/noise_examples/global_long/NOISE_collect
seismo/3D/SPECFEM3D_GLOBE/trunk/EXAMPLES/noise_examples/global_short/NOISE123.submit_atten
seismo/3D/SPECFEM3D_GLOBE/trunk/EXAMPLES/noise_examples/global_short/NOISE_clean_create
seismo/3D/SPECFEM3D_GLOBE/trunk/EXAMPLES/noise_examples/global_short/NOISE_collect
seismo/3D/SPECFEM3D_GLOBE/trunk/EXAMPLES/noise_examples/pre-processing
seismo/3D/SPECFEM3D_GLOBE/trunk/EXAMPLES/noise_examples/regional/NOISE123.submit_atten
seismo/3D/SPECFEM3D_GLOBE/trunk/EXAMPLES/noise_examples/regional/NOISE_clean_create
seismo/3D/SPECFEM3D_GLOBE/trunk/EXAMPLES/noise_examples/regional/NOISE_collect
seismo/3D/SPECFEM3D_GLOBE/trunk/src/specfem3D/specfem3D.f90
Log:
NOISE minor changes
Modified: seismo/3D/SPECFEM3D_GLOBE/trunk/EXAMPLES/noise_examples/global_long/NOISE123.submit_atten
===================================================================
--- seismo/3D/SPECFEM3D_GLOBE/trunk/EXAMPLES/noise_examples/global_long/NOISE123.submit_atten 2011-03-22 20:44:44 UTC (rev 18123)
+++ seismo/3D/SPECFEM3D_GLOBE/trunk/EXAMPLES/noise_examples/global_long/NOISE123.submit_atten 2011-03-22 21:52:38 UTC (rev 18124)
@@ -24,26 +24,13 @@
d=`date`
LOCAL_PATH_ALL=`grep LOCAL_PATH DATA/Par_file | cut -d = -f 2 | sed 's/ //g'`
echo "Start cleaning local disk on nodes, $d"
-for (( ievent=1;ievent<=$numnodes;ievent=ievent+1 ))
-do
- let line=$ievent
- machine_all=$(awk 'NR=='$line'{print}' zzz_job_info/compute_nodes_all)
- mpiexec -np 1 -host $machine_all ./NOISE_clean_create $LOCAL_PATH_ALL < /dev/null &
-done
-wait
-for (( ievent=1;ievent<=$numnodes;ievent=ievent+8 ))
-do
- let line=$ievent
- machine_all=$(awk 'NR=='$line'{print}' zzz_job_info/compute_nodes_all)
- mpiexec -np 1 -host $machine_all ./NOISE_clean_create $LOCAL_PATH_ALL < /dev/null &
-done
-wait
+pbsdsh $PBS_O_WORKDIR/NOISE_clean_create $LOCAL_PATH_ALL
d=`date`
echo "Finish cleaning local disk on nodes, $d"
## clean OUTPUT_FILES
-rm -rf OUTPUT_FILES
-mkdir OUTPUT_FILES
+rm -rf OUTPUT_FILES
+mkdir -p OUTPUT_FILES
#### backup Fortran source files
##rm -rf ZZZ_src
@@ -120,14 +107,7 @@
## collect outputs (e.g., kernels, meshes) from local nodes to global disk
d=`date`
echo "Start collecting outputs from nodes, $d"
-for (( ievent=1;ievent<=$numnodes;ievent++ ))
-do
- let line=$ievent
- machine_all=$(awk 'NR=='$line'{print}' zzz_job_info/compute_nodes_all)
- let myrank="$ievent-1"
- mpiexec -np 1 -host $machine_all ./NOISE_collect $machine_all $machine_all $LOCAL_PATH_ALL $LOCAL_PATH_ALL $myrank < /dev/null &
-done
-wait
+pbsdsh $PBS_O_WORKDIR/NOISE_collect $LOCAL_PATH_ALL OUTPUT_FILES/
d=`date`
echo "Finish collecting outputs from nodes, $d"
@@ -140,12 +120,6 @@
cp DATA/STATIONS ZZZ_3/
-for (( ievent=1;ievent<=$numnodes;ievent=ievent+1 ))
-do
- let line=$ievent
- machine_all=$(awk 'NR=='$line'{print}' zzz_job_info/compute_nodes_all)
- mpiexec -np 1 -host $machine_all ./NOISE_clean_create $LOCAL_PATH_ALL < /dev/null &
-done
-wait
+pbsdsh $PBS_O_WORKDIR/NOISE_clean_create $LOCAL_PATH_ALL
d=`date`
echo "Finish cleaning local disk on nodes, $d"
Modified: seismo/3D/SPECFEM3D_GLOBE/trunk/EXAMPLES/noise_examples/global_long/NOISE_clean_create
===================================================================
--- seismo/3D/SPECFEM3D_GLOBE/trunk/EXAMPLES/noise_examples/global_long/NOISE_clean_create 2011-03-22 20:44:44 UTC (rev 18123)
+++ seismo/3D/SPECFEM3D_GLOBE/trunk/EXAMPLES/noise_examples/global_long/NOISE_clean_create 2011-03-22 21:52:38 UTC (rev 18124)
@@ -1,7 +1,11 @@
-#!/bin/bash
-ulimit -s unlimited
+#!/bin/bash -eu
-LOCAL_PATH=$1
+DIR_LOCAL=$1
+iproc=$PBS_VNODENUM
-rm -rf $LOCAL_PATH
-mkdir -p $LOCAL_PATH
+##### other files can be collected in the same way
+if [ $(($iproc % 8)) = 0 ]; then
+ rm -rf $DIR_LOCAL
+ mkdir -p $DIR_LOCAL
+fi
+
Modified: seismo/3D/SPECFEM3D_GLOBE/trunk/EXAMPLES/noise_examples/global_long/NOISE_collect
===================================================================
--- seismo/3D/SPECFEM3D_GLOBE/trunk/EXAMPLES/noise_examples/global_long/NOISE_collect 2011-03-22 20:44:44 UTC (rev 18123)
+++ seismo/3D/SPECFEM3D_GLOBE/trunk/EXAMPLES/noise_examples/global_long/NOISE_collect 2011-03-22 21:52:38 UTC (rev 18124)
@@ -1,13 +1,11 @@
-#!/bin/bash
+#!/bin/bash -eu
-machine_new=$1
-machine_old=$2
-LOCAL_PATH_NEW=$3
-LOCAL_PATH_OLD=$4
-let myrank=$5
-myrank_new=`printf "%06d" $myrank`
+DIR_LOCAL=$1
+DIR_GLOBAL=$2
+iproc=`printf "%06d" $PBS_VNODENUM`
-##echo "cp $LOCAL_PATH_NEW/proc$myrank_new*kernel* OUTPUT_FILES/"
-mv $LOCAL_PATH_NEW/proc$myrank_new*reg1*kernel*.bin OUTPUT_FILES/
-mv $LOCAL_PATH_NEW/proc$myrank_new*reg1_*array_dims.txt OUTPUT_FILES/
-mv $LOCAL_PATH_NEW/proc$myrank_new*reg1_solver_data*.bin OUTPUT_FILES/
+##### other files can be collected in the same way
+mv $DIR_LOCAL/*$iproc*reg1*kernel*.bin $DIR_GLOBAL/
+mv $DIR_LOCAL/*$iproc*reg1_*array_dims.txt $DIR_GLOBAL/
+mv $DIR_LOCAL/*$iproc*reg1_solver_data*.bin $DIR_GLOBAL/
+
Modified: seismo/3D/SPECFEM3D_GLOBE/trunk/EXAMPLES/noise_examples/global_short/NOISE123.submit_atten
===================================================================
--- seismo/3D/SPECFEM3D_GLOBE/trunk/EXAMPLES/noise_examples/global_short/NOISE123.submit_atten 2011-03-22 20:44:44 UTC (rev 18123)
+++ seismo/3D/SPECFEM3D_GLOBE/trunk/EXAMPLES/noise_examples/global_short/NOISE123.submit_atten 2011-03-22 21:52:38 UTC (rev 18124)
@@ -24,26 +24,13 @@
d=`date`
LOCAL_PATH_ALL=`grep LOCAL_PATH DATA/Par_file | cut -d = -f 2 | sed 's/ //g'`
echo "Start cleaning local disk on nodes, $d"
-for (( ievent=1;ievent<=$numnodes;ievent=ievent+1 ))
-do
- let line=$ievent
- machine_all=$(awk 'NR=='$line'{print}' zzz_job_info/compute_nodes_all)
- mpiexec -np 1 -host $machine_all ./NOISE_clean_create $LOCAL_PATH_ALL < /dev/null &
-done
-wait
-for (( ievent=1;ievent<=$numnodes;ievent=ievent+8 ))
-do
- let line=$ievent
- machine_all=$(awk 'NR=='$line'{print}' zzz_job_info/compute_nodes_all)
- mpiexec -np 1 -host $machine_all ./NOISE_clean_create $LOCAL_PATH_ALL < /dev/null &
-done
-wait
+pbsdsh $PBS_O_WORKDIR/NOISE_clean_create $LOCAL_PATH_ALL
d=`date`
echo "Finish cleaning local disk on nodes, $d"
## clean OUTPUT_FILES
-rm -rf OUTPUT_FILES
-mkdir OUTPUT_FILES
+rm -rf OUTPUT_FILES
+mkdir -p OUTPUT_FILES
#### backup Fortran source files
##rm -rf ZZZ_src
@@ -120,14 +107,7 @@
## collect outputs (e.g., kernels, meshes) from local nodes to global disk
d=`date`
echo "Start collecting outputs from nodes, $d"
-for (( ievent=1;ievent<=$numnodes;ievent++ ))
-do
- let line=$ievent
- machine_all=$(awk 'NR=='$line'{print}' zzz_job_info/compute_nodes_all)
- let myrank="$ievent-1"
- mpiexec -np 1 -host $machine_all ./NOISE_collect $machine_all $machine_all $LOCAL_PATH_ALL $LOCAL_PATH_ALL $myrank < /dev/null &
-done
-wait
+pbsdsh $PBS_O_WORKDIR/NOISE_collect $LOCAL_PATH_ALL OUTPUT_FILES/
d=`date`
echo "Finish collecting outputs from nodes, $d"
@@ -140,12 +120,6 @@
cp DATA/STATIONS ZZZ_3/
-for (( ievent=1;ievent<=$numnodes;ievent=ievent+1 ))
-do
- let line=$ievent
- machine_all=$(awk 'NR=='$line'{print}' zzz_job_info/compute_nodes_all)
- mpiexec -np 1 -host $machine_all ./NOISE_clean_create $LOCAL_PATH_ALL < /dev/null &
-done
-wait
+pbsdsh $PBS_O_WORKDIR/NOISE_clean_create $LOCAL_PATH_ALL
d=`date`
echo "Finish cleaning local disk on nodes, $d"
Modified: seismo/3D/SPECFEM3D_GLOBE/trunk/EXAMPLES/noise_examples/global_short/NOISE_clean_create
===================================================================
--- seismo/3D/SPECFEM3D_GLOBE/trunk/EXAMPLES/noise_examples/global_short/NOISE_clean_create 2011-03-22 20:44:44 UTC (rev 18123)
+++ seismo/3D/SPECFEM3D_GLOBE/trunk/EXAMPLES/noise_examples/global_short/NOISE_clean_create 2011-03-22 21:52:38 UTC (rev 18124)
@@ -1,7 +1,11 @@
-#!/bin/bash
-ulimit -s unlimited
+#!/bin/bash -eu
-LOCAL_PATH=$1
+DIR_LOCAL=$1
+iproc=$PBS_VNODENUM
-rm -rf $LOCAL_PATH
-mkdir -p $LOCAL_PATH
+##### other files can be collected in the same way
+if [ $(($iproc % 8)) = 0 ]; then
+ rm -rf $DIR_LOCAL
+ mkdir -p $DIR_LOCAL
+fi
+
Modified: seismo/3D/SPECFEM3D_GLOBE/trunk/EXAMPLES/noise_examples/global_short/NOISE_collect
===================================================================
--- seismo/3D/SPECFEM3D_GLOBE/trunk/EXAMPLES/noise_examples/global_short/NOISE_collect 2011-03-22 20:44:44 UTC (rev 18123)
+++ seismo/3D/SPECFEM3D_GLOBE/trunk/EXAMPLES/noise_examples/global_short/NOISE_collect 2011-03-22 21:52:38 UTC (rev 18124)
@@ -1,13 +1,11 @@
-#!/bin/bash
+#!/bin/bash -eu
-machine_new=$1
-machine_old=$2
-LOCAL_PATH_NEW=$3
-LOCAL_PATH_OLD=$4
-let myrank=$5
-myrank_new=`printf "%06d" $myrank`
+DIR_LOCAL=$1
+DIR_GLOBAL=$2
+iproc=`printf "%06d" $PBS_VNODENUM`
-##echo "cp $LOCAL_PATH_NEW/proc$myrank_new*kernel* OUTPUT_FILES/"
-mv $LOCAL_PATH_NEW/proc$myrank_new*reg1*kernel*.bin OUTPUT_FILES/
-mv $LOCAL_PATH_NEW/proc$myrank_new*reg1_*array_dims.txt OUTPUT_FILES/
-mv $LOCAL_PATH_NEW/proc$myrank_new*reg1_solver_data*.bin OUTPUT_FILES/
+##### other files can be collected in the same way
+mv $DIR_LOCAL/*$iproc*reg1*kernel*.bin $DIR_GLOBAL/
+mv $DIR_LOCAL/*$iproc*reg1_*array_dims.txt $DIR_GLOBAL/
+mv $DIR_LOCAL/*$iproc*reg1_solver_data*.bin $DIR_GLOBAL/
+
Modified: seismo/3D/SPECFEM3D_GLOBE/trunk/EXAMPLES/noise_examples/pre-processing
===================================================================
--- seismo/3D/SPECFEM3D_GLOBE/trunk/EXAMPLES/noise_examples/pre-processing 2011-03-22 20:44:44 UTC (rev 18123)
+++ seismo/3D/SPECFEM3D_GLOBE/trunk/EXAMPLES/noise_examples/pre-processing 2011-03-22 21:52:38 UTC (rev 18124)
@@ -11,27 +11,21 @@
mkdir -p SEM zzz_job_info NOISE_TOMOGRAPHY
-#cp $dir/A0.II.LHZ.adj ./SEM/
-#cp $dir/cp_adj_sources ./SEM/
-
cp $dir/adj_traveltime_filter.f90 ./
cp $dir/NOISE123.submit_atten ./
cp $dir/NOISE_clean_create ./
cp $dir/NOISE_collect ./
cp $dir/NOISE_transfer ./
-cp $dir/S_squared ./NOISE_TOMOGRAPHY
+cp $dir/S_squared ./NOISE_TOMOGRAPHY/
cp $dir/irec_master_noise ./NOISE_TOMOGRAPHY/
cp $dir/nu_master ./NOISE_TOMOGRAPHY/
cp $dir/Par_file_NOISE_* ./DATA/
-cp $dir/CMTSOLUTION_NOISE ./DATA/
-cp $dir/STATIONS_NOISE ./DATA/
+cp $dir/CMTSOLUTION_NOISE ./DATA/CMTSOLUTION
+cp $dir/STATIONS_NOISE ./DATA/STATIONS
+cp $dir/STATIONS_NOISE_ADJOINT ./DATA/STATIONS_ADJOINT
-#cd SEM
-#./cp_adj_sources
-#cd ..
-
ifort -o NOISE_adj adj_traveltime_filter.f90
cp DATA/Par_file_NOISE_1_attenuation DATA/Par_file
Modified: seismo/3D/SPECFEM3D_GLOBE/trunk/EXAMPLES/noise_examples/regional/NOISE123.submit_atten
===================================================================
--- seismo/3D/SPECFEM3D_GLOBE/trunk/EXAMPLES/noise_examples/regional/NOISE123.submit_atten 2011-03-22 20:44:44 UTC (rev 18123)
+++ seismo/3D/SPECFEM3D_GLOBE/trunk/EXAMPLES/noise_examples/regional/NOISE123.submit_atten 2011-03-22 21:52:38 UTC (rev 18124)
@@ -24,26 +24,13 @@
d=`date`
LOCAL_PATH_ALL=`grep LOCAL_PATH DATA/Par_file | cut -d = -f 2 | sed 's/ //g'`
echo "Start cleaning local disk on nodes, $d"
-for (( ievent=1;ievent<=$numnodes;ievent=ievent+1 ))
-do
- let line=$ievent
- machine_all=$(awk 'NR=='$line'{print}' zzz_job_info/compute_nodes_all)
- mpiexec -np 1 -host $machine_all ./NOISE_clean_create $LOCAL_PATH_ALL < /dev/null &
-done
-wait
-for (( ievent=1;ievent<=$numnodes;ievent=ievent+8 ))
-do
- let line=$ievent
- machine_all=$(awk 'NR=='$line'{print}' zzz_job_info/compute_nodes_all)
- mpiexec -np 1 -host $machine_all ./NOISE_clean_create $LOCAL_PATH_ALL < /dev/null &
-done
-wait
+pbsdsh $PBS_O_WORKDIR/NOISE_clean_create $LOCAL_PATH_ALL
d=`date`
echo "Finish cleaning local disk on nodes, $d"
## clean OUTPUT_FILES
-rm -rf OUTPUT_FILES
-mkdir OUTPUT_FILES
+rm -rf OUTPUT_FILES
+mkdir -p OUTPUT_FILES
#### backup Fortran source files
##rm -rf ZZZ_src
@@ -120,14 +107,7 @@
## collect outputs (e.g., kernels, meshes) from local nodes to global disk
d=`date`
echo "Start collecting outputs from nodes, $d"
-for (( ievent=1;ievent<=$numnodes;ievent++ ))
-do
- let line=$ievent
- machine_all=$(awk 'NR=='$line'{print}' zzz_job_info/compute_nodes_all)
- let myrank="$ievent-1"
- mpiexec -np 1 -host $machine_all ./NOISE_collect $machine_all $machine_all $LOCAL_PATH_ALL $LOCAL_PATH_ALL $myrank < /dev/null &
-done
-wait
+pbsdsh $PBS_O_WORKDIR/NOISE_collect $LOCAL_PATH_ALL OUTPUT_FILES/
d=`date`
echo "Finish collecting outputs from nodes, $d"
@@ -140,12 +120,6 @@
cp DATA/STATIONS ZZZ_3/
-for (( ievent=1;ievent<=$numnodes;ievent=ievent+1 ))
-do
- let line=$ievent
- machine_all=$(awk 'NR=='$line'{print}' zzz_job_info/compute_nodes_all)
- mpiexec -np 1 -host $machine_all ./NOISE_clean_create $LOCAL_PATH_ALL < /dev/null &
-done
-wait
+pbsdsh $PBS_O_WORKDIR/NOISE_clean_create $LOCAL_PATH_ALL
d=`date`
echo "Finish cleaning local disk on nodes, $d"
Modified: seismo/3D/SPECFEM3D_GLOBE/trunk/EXAMPLES/noise_examples/regional/NOISE_clean_create
===================================================================
--- seismo/3D/SPECFEM3D_GLOBE/trunk/EXAMPLES/noise_examples/regional/NOISE_clean_create 2011-03-22 20:44:44 UTC (rev 18123)
+++ seismo/3D/SPECFEM3D_GLOBE/trunk/EXAMPLES/noise_examples/regional/NOISE_clean_create 2011-03-22 21:52:38 UTC (rev 18124)
@@ -1,7 +1,11 @@
-#!/bin/bash
-ulimit -s unlimited
+#!/bin/bash -eu
-LOCAL_PATH=$1
+DIR_LOCAL=$1
+iproc=$PBS_VNODENUM
-rm -rf $LOCAL_PATH
-mkdir -p $LOCAL_PATH
+##### other files can be collected in the same way
+if [ $(($iproc % 8)) = 0 ]; then
+ rm -rf $DIR_LOCAL
+ mkdir -p $DIR_LOCAL
+fi
+
Modified: seismo/3D/SPECFEM3D_GLOBE/trunk/EXAMPLES/noise_examples/regional/NOISE_collect
===================================================================
--- seismo/3D/SPECFEM3D_GLOBE/trunk/EXAMPLES/noise_examples/regional/NOISE_collect 2011-03-22 20:44:44 UTC (rev 18123)
+++ seismo/3D/SPECFEM3D_GLOBE/trunk/EXAMPLES/noise_examples/regional/NOISE_collect 2011-03-22 21:52:38 UTC (rev 18124)
@@ -1,13 +1,11 @@
-#!/bin/bash
+#!/bin/bash -eu
-machine_new=$1
-machine_old=$2
-LOCAL_PATH_NEW=$3
-LOCAL_PATH_OLD=$4
-let myrank=$5
-myrank_new=`printf "%06d" $myrank`
+DIR_LOCAL=$1
+DIR_GLOBAL=$2
+iproc=`printf "%06d" $PBS_VNODENUM`
-##echo "cp $LOCAL_PATH_NEW/proc$myrank_new*kernel* OUTPUT_FILES/"
-mv $LOCAL_PATH_NEW/proc$myrank_new*reg1*kernel*.bin OUTPUT_FILES/
-mv $LOCAL_PATH_NEW/proc$myrank_new*reg1_*array_dims.txt OUTPUT_FILES/
-mv $LOCAL_PATH_NEW/proc$myrank_new*reg1_solver_data*.bin OUTPUT_FILES/
+##### other files can be collected in the same way
+mv $DIR_LOCAL/*$iproc*reg1*kernel*.bin $DIR_GLOBAL/
+mv $DIR_LOCAL/*$iproc*reg1_*array_dims.txt $DIR_GLOBAL/
+mv $DIR_LOCAL/*$iproc*reg1_solver_data*.bin $DIR_GLOBAL/
+
Modified: seismo/3D/SPECFEM3D_GLOBE/trunk/src/specfem3D/specfem3D.f90
===================================================================
--- seismo/3D/SPECFEM3D_GLOBE/trunk/src/specfem3D/specfem3D.f90 2011-03-22 20:44:44 UTC (rev 18123)
+++ seismo/3D/SPECFEM3D_GLOBE/trunk/src/specfem3D/specfem3D.f90 2011-03-22 21:52:38 UTC (rev 18124)
@@ -4307,7 +4307,7 @@
endif
! save/read the surface movie using the same c routine as we do for absorbing boundaries (file ID is 21)
- if (NOISE_TOMOGRAPHY\=0) call close_file_abs(21)
+ if (NOISE_TOMOGRAPHY/=0) call close_file_abs(21)
! synchronize all processes
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