Révision 55
| submit/crystal/sub_crystal17.sh (revision 55) | ||
|---|---|---|
| 1 |
#!/bin/bash |
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| 2 |
#$ -S /bin/bash |
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| 3 |
#$ -N sp-LaTaS6-HSE06 |
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| 4 |
#$ -q M6*,E5-2667*,E5-2670* |
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| 5 |
#$ -pe mpi16_debian 16 |
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| 6 |
#$ -V |
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| 7 |
#$ -cwd |
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| 8 |
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| 9 |
module use /home/tjiang/modules/lmod |
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| 10 |
module load crystal/17 |
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| 11 |
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| 12 |
export HOMEDIR=$SGE_O_WORKDIR |
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| 13 |
cd $HOMEDIR |
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| 14 |
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| 15 |
INPUT=LaTaS6 |
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| 16 |
export CRY17_SCRDIR=/scratch/$USER/$JOB_ID |
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| 17 |
/bin/mkdir -p $CRY17_SCRDIR |
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| 18 |
export CRY17P_MACH=$HOMEDIR |
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| 19 |
|
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| 20 |
export MPIRUN=mpirun |
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| 21 |
export HOSTFILE=$TMPDIR/machines |
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| 22 |
#export hosts=$HOMEDIR/hosts_`basename $INPUT .d12` |
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| 23 |
cp $HOSTFILE $HOMEDIR/machines.LINUX |
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| 24 |
cp $HOSTFILE $HOMEDIR/nodes.par |
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| 25 |
#Too lazy to do a test, but the file needs to be refreshed! |
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| 26 |
#rm -f $hosts |
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| 27 |
#/bin/cat $TMPDIR/machines > $hosts |
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| 28 |
export OMP_NUM_THREADS=1 |
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| 29 |
export MKL_NUM_THREADS=1 |
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| 30 |
$CRYSTALROOT/utils/runmpi17 $NSLOTS $INPUT |
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| 31 |
rm -fr $CRY17_SCRDIR |
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| 32 |
#rm $HOMEDIR/hosts_`basename $INPUT .d12` |
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| submit/crystal/sub_properties17.sh (revision 55) | ||
|---|---|---|
| 1 |
#!/bin/bash |
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| 2 |
#$ -S /bin/bash |
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| 3 |
#$ -N LTS6-eff-mass |
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| 4 |
#$ -q monointeldeb48,monointeldeb128,r820deb768 |
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| 5 |
#$ -V |
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| 6 |
#$ -cwd |
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| 7 |
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| 8 |
module use /home/tjiang/modules/lmod |
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| 9 |
module load crystal/17 |
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| 10 |
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| 11 |
export HOMEDIR=$SGE_O_WORKDIR |
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| 12 |
cd $HOMEDIR |
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| 13 |
export CRY17_INP=$HOMEDIR |
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| 14 |
export CRY17_SCRDIR=/scratch/$USER/$JOB_ID |
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| 15 |
/bin/mkdir -p $CRY17_SCRDIR |
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| 16 |
export EXEC=$CRYSTALROOT/utils/runprop17 |
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| 17 |
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| 18 |
# Running crystal properties |
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| 19 |
# You should provide the name of .d3 and .f9 files, excluding the extension |
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| 20 |
# i.e., if there exist tmp1.d3 and tmp2.f9, then the command for running |
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| 21 |
# crystal properties should look like |
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| 22 |
# $EXEC tmp1 tmp2 |
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| 23 |
$EXEC LaTaS6 LaTaS6 |
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| 24 |
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| 25 |
# Cleaning up scratch directory |
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| 26 |
rm -fr $CRY17_SCRDIR |
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| submit/dalton/sub_dalton_bash (revision 55) | ||
|---|---|---|
| 1 |
#!/bin/bash |
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| 2 |
#$ -S /bin/bash |
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| 3 |
#$ -N test |
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| 4 |
#$ -q E5-2670deb64A,E5-2670deb64B,E5-2670deb64C |
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| 5 |
#$ -pe mpi16_debian 16 |
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| 6 |
#$ -V |
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| 7 |
#$ -cwd |
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| 8 |
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| 9 |
## Environement (SGE, VASP, MPI) |
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| 10 |
source /usr/share/modules/init/bash |
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| 11 |
module use /home/tjiang/modules/lmod |
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| 12 |
module load dalton/2016-ompi |
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| 13 |
#module load dalton/2016-ompi-with_yttrium |
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| 14 |
#module load dalton/2016-omp |
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| 15 |
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| 16 |
DALTON_TMPDIR=/scratch/$USER/$JOB_ID/ |
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| 17 |
dalton -t $DALTON_TMPDIR -noappend -omp 16 -mb 16000 dalinp.dal moinp.mol |
|
| submit/amber/sub_amber17.sh (revision 55) | ||
|---|---|---|
| 1 |
#!/bin/bash |
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| 2 |
#$ -S /bin/bash |
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| 3 |
#$ -N amber17 |
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| 4 |
#$ -cwd |
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| 5 |
#$ -V |
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| 6 |
#$ -o npt4.out |
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| 7 |
#$ -j y |
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| 8 |
##===================== |
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| 9 |
##Choose between cpu queues and gpu queues, default gpu queues |
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| 10 |
##cpu queues |
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| 11 |
##$ -q M6*,E5-2667*,E5-2697*,E5-2670deb* |
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| 12 |
##$ -pe mpi16_debian 16 |
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| 13 |
##gpu queues |
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| 14 |
#$ -q E5-2670gpu* |
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| 15 |
#$ -pe mpi_debian 1 |
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| 16 |
##===================== |
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| 17 |
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| 18 |
# PSMN: $Id$ |
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| 19 |
# |
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| 20 |
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| 21 |
export MODULEPATH=/home/tjiang/modules/lmod/:${MODULEPATH}
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| 22 |
module use ${MODULEPATH}
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| 23 |
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| 24 |
#module file for gpu version of amber |
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module load amber/17_gcc5.4.0_cuda8.0ga2_openmpi1.6.4 |
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| 26 |
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| 27 |
#module file for cpu only version of amber |
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| 28 |
#module load amber/17_intel15.0.2_openmpi1.6.4 |
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| 29 |
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| 30 |
ambermod=$(basename $AMBERHOME) |
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| 31 |
echo $ambermod |
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| 32 |
if [ $ambermod = "gcc5.4.0_cuda8.0ga2_openmpi1.6.4" ]; then |
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| 33 |
amberexe="pmemd.cuda" |
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| 34 |
else |
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| 35 |
amberexe="pmemd" |
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| 36 |
fi |
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| 37 |
echo $amberexe |
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| 38 |
|
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| 39 |
ulimit -v unlimited |
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| 40 |
ulimit -s unlimited |
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| 41 |
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| 42 |
######################" |
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| 43 |
HOMEDIR=$SGE_O_WORKDIR |
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| 44 |
HOSTFILE=$TMPDIR/machines |
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| 45 |
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| 46 |
cd $SGE_O_WORKDIR |
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| 47 |
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| 48 |
echo NSLOTS=$NSLOTS |
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| 49 |
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| 50 |
SCRATCHDIR=/scratch/$USER/$JOB_ID/ |
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| 51 |
echo $SCRATCHDIR |
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| 52 |
/bin/mkdir -p $SCRATCHDIR |
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| 53 |
################### |
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| 54 |
Mac=`hostname | awk '{print substr($1,1,2)}' `
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| 55 |
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| 56 |
NbMac=`wc $PE_HOSTFILE | awk '{print $1}' `
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|
| 57 |
rm ./machines |
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| 58 |
for i in `seq 1 $NbMac` |
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| 59 |
do |
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| 60 |
Mac=` head -n $i $PE_HOSTFILE | tail -1 | awk '{print $1}' `
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| 61 |
Nb=` head -n $i $PE_HOSTFILE | tail -1 | awk '{print $2}' `
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| 62 |
for j in `seq 1 $Nb` |
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| 63 |
do |
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| 64 |
echo $Mac >> ./machines |
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| 65 |
done |
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| 66 |
done |
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| 67 |
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| 68 |
cp $PE_HOSTFILE ./PE_HOSTFILE |
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| 69 |
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| 70 |
cd $SCRATCHDIR |
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| 71 |
|
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| 72 |
echo "start at" |
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| 73 |
date |
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| 74 |
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| 75 |
echo -n "Starting Script at: " |
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| 76 |
date |
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| 77 |
$amberexe -O -i $HOMEDIR/min.in \ |
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| 78 |
-o $HOMEDIR/min.out \ |
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| 79 |
-p $HOMEDIR/dna_TT.prmtop \ |
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| 80 |
-c $HOMEDIR/dna3_TT.inpcrd \ |
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| 81 |
-r $HOMEDIR/dna_TT_min.rst \ |
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| 82 |
-x $HOMEDIR/dna_TT_min.mdcrd |
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| 83 |
|
|
| 84 |
echo "done at" |
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| 85 |
date |
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| 86 |
cp -rf * $HOMEDIR |
|
| 87 |
|
|
| 88 |
|
|
| submit/gaussian/sub_gaussian09.sh (revision 55) | ||
|---|---|---|
| 1 |
#!/bin/bash |
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| 2 |
#$ -S /bin/bash |
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| 3 |
#$ -N test |
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| 4 |
#$ -o $JOB_NAME.batch-log |
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| 5 |
#$ -j y |
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| 6 |
#$ -cwd |
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| 7 |
#$ -V |
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| 8 |
#$ -q E5* |
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| 9 |
##$ -pe gaussian8 8 |
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| 10 |
#$ -pe openmp8 8 |
|
| 11 |
|
|
| 12 |
# Version: $Id$ |
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| 13 |
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|
| 14 |
# trace script (debug purpose, not mandatory) |
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| 15 |
set -x |
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| 16 |
# set globals |
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| 17 |
job=structure11 |
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| 18 |
ExtIn=com |
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| 19 |
ExtOut=log |
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| 20 |
|
|
| 21 |
# Environment setting for gaussian |
|
| 22 |
g09root=/home/tjiang/softs/gaussian/g09d01 |
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| 23 |
source $g09root/g09/bsd/g09.profile |
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| 24 |
export Gaussian=$g09root/g09/g09 |
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| 25 |
|
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| 26 |
export RSHCOMMAND=ssh |
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| 27 |
export P4_RSHCOMMAND=ssh |
|
| 28 |
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| 29 |
#export LD_LIBRARY_PATH=/softs/acml/acml2.7.0/pathscale64/lib:/softs/fftw/2.1.5/ps-ib/lib:$LD_LIBRARY_PATH:/usr/lib |
|
| 30 |
|
|
| 31 |
cd ${SGE_O_WORKDIR}
|
|
| 32 |
|
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| 33 |
echo "########## debut env##################" |
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| 34 |
env |
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| 35 |
echo "########## fin env ##################" |
|
| 36 |
|
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| 37 |
echo "########## Hostname ##################" |
|
| 38 |
hostname |
|
| 39 |
|
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| 40 |
HOMEDIR=${SGE_O_WORKDIR}
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| 41 |
cd ${HOMEDIR}
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|
| 42 |
|
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| 43 |
# Replace 'home' by 'scratch', from SGE_O_WORKDIR, store to SCRATCHDIR |
|
| 44 |
SCRATCHDIR=/scratch/$USER/$JOB_ID/ |
|
| 45 |
# check if scratch exist, create or complain |
|
| 46 |
if [[ -d "/scratch" ]] |
|
| 47 |
then |
|
| 48 |
mkdir -p ${SCRATCHDIR}
|
|
| 49 |
else |
|
| 50 |
echo "/scratch not found, cannot create ${SCRATCHDIR}"
|
|
| 51 |
fi |
|
| 52 |
|
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| 53 |
# check if scratchdir is OK |
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| 54 |
echo "ok" > ${SCRATCHDIR}/toto
|
|
| 55 |
Ok=$(cat ${SCRATCHDIR}/toto)
|
|
| 56 |
if [[ "${Ok}" != "ok" ]]
|
|
| 57 |
then |
|
| 58 |
# if scratch is unavailable, fallback to home |
|
| 59 |
CalcDir="${SGE_O_WORKDIR}/scratch"_${job}
|
|
| 60 |
mkdir -p ${CalcDir}
|
|
| 61 |
else |
|
| 62 |
CalcDir=${SCRATCHDIR}
|
|
| 63 |
fi |
|
| 64 |
mkdir -p ${CalcDir}
|
|
| 65 |
|
|
| 66 |
# Gaussian specific ScratchDir |
|
| 67 |
#export GAUSS_SCRDIR=${CalcDir}
|
|
| 68 |
|
|
| 69 |
Machine=$(hostname) |
|
| 70 |
|
|
| 71 |
# check if there is a chk or chk.gz |
|
| 72 |
# TODO/FIXME there's a problem here, watching the trace: if no chk, it create a .chk.chk |
|
| 73 |
NChk=` grep -i "chk" ${job}.${ExtIn} | head -1 | sed 's/=/ /g' | awk '{print $2}'`
|
|
| 74 |
if [ "$NChk" != "" ] |
|
| 75 |
then |
|
| 76 |
NChk=` basename $NChk .chk`.chk |
|
| 77 |
fi |
|
| 78 |
if [[ -s ${HOMEDIR}/${NChk} ]]
|
|
| 79 |
then |
|
| 80 |
cp ${HOMEDIR}/${NChk} ${CalcDir}/${NChk}
|
|
| 81 |
fi |
|
| 82 |
if [[ -s ${HOMEDIR}/${NChk}.gz ]]
|
|
| 83 |
then |
|
| 84 |
cp ${HOMEDIR}/${NChk}.gz ${CalcDir}/${NChk}.gz
|
|
| 85 |
gunzip ${CalcDir}/${NChk}.gz
|
|
| 86 |
fi |
|
| 87 |
|
|
| 88 |
cp ${HOMEDIR}/${job}.${ExtIn} ${CalcDir}/
|
|
| 89 |
|
|
| 90 |
# prepare postprocess script |
|
| 91 |
# TODO/FIXME is this still usefull ? |
|
| 92 |
# - compress .chk |
|
| 93 |
# - copy chk from $SCRATCHDIR to $HOMEDIR |
|
| 94 |
# - cleanup $SCRATCHDIR |
|
| 95 |
# add exec mode on script |
|
| 96 |
#echo "ssh ${SGE_O_LOGNAME}@${Machine} gzip ${CalcDir}/*.chk " > ${HOMEDIR}/${job}_${Machine}_CLEAN.${ExtOut}
|
|
| 97 |
#echo "scp ${SGE_O_LOGNAME}@${Machine}:${CalcDir}/* ." > ${HOMEDIR}/${job}_${Machine}_CLEAN.${ExtOut}
|
|
| 98 |
#echo "ssh ${SGE_O_LOGNAME}@${Machine} rm -fr ${CalcDir}" >> ${HOMEDIR}/${job}_${Machine}_CLEAN.${ExtOut}
|
|
| 99 |
#echo "rm ${job}_${Machine}_CLEAN.${ExtOut}" >> ${HOMEDIR}/${job}_${Machine}_CLEAN.${ExtOut}
|
|
| 100 |
#chmod u+x ${HOMEDIR}/${job}_${Machine}_CLEAN.${ExtOut}
|
|
| 101 |
|
|
| 102 |
# logrotate old logs |
|
| 103 |
if [[ -s ${HOMEDIR}/${job}.${ExtOut} ]]
|
|
| 104 |
then |
|
| 105 |
Ext=1 |
|
| 106 |
while [[ -s ${HOMEDIR}/${job}.${ExtOut}_${Ext} ]]
|
|
| 107 |
do |
|
| 108 |
let Ext=Ext+1 |
|
| 109 |
done |
|
| 110 |
mv ${HOMEDIR}/${job}.${ExtOut} ${HOMEDIR}/${job}.${ExtOut}_${Ext}
|
|
| 111 |
fi |
|
| 112 |
|
|
| 113 |
cd ${CalcDir}
|
|
| 114 |
echo ${CalcDir}
|
|
| 115 |
ls -al |
|
| 116 |
|
|
| 117 |
echo "time ${Gaussian} < ${job}.${ExtIn} > ${HOMEDIR}/${job}.${ExtOut}"
|
|
| 118 |
|
|
| 119 |
#/usr/bin/time ${Gaussian} < ${job}.${ExtIn} > ${HOMEDIR}/${job}.${ExtOut}
|
|
| 120 |
${Gaussian} < ${job}.${ExtIn} > ${HOMEDIR}/${job}.${ExtOut}
|
|
| 121 |
|
|
| 122 |
cp * ${HOMEDIR}/
|
|
| 123 |
|
|
| 124 |
if [[ -s ${NChk} ]]
|
|
| 125 |
then |
|
| 126 |
gzip -9 ${NChk}
|
|
| 127 |
cp ${NChk}.gz ${HOMEDIR}/
|
|
| 128 |
fi |
|
| 129 |
|
|
| 130 |
# final cleanup (commented during debug) |
|
| 131 |
#rm -r ${GAUSS_SCRDIR}
|
|
| 132 |
#rm -r ${CalcDir}
|
|
| submit/gaussian/sub_gaussian16.sh (revision 55) | ||
|---|---|---|
| 1 |
#!/bin/bash |
|
| 2 |
#$ -S /bin/bash |
|
| 3 |
#$ -N test |
|
| 4 |
#$ -o $JOB_NAME.batch-log |
|
| 5 |
#$ -j y |
|
| 6 |
#$ -cwd |
|
| 7 |
#$ -V |
|
| 8 |
#$ -q E5* |
|
| 9 |
##$ -pe gaussian8 8 |
|
| 10 |
#$ -pe openmp8 8 |
|
| 11 |
|
|
| 12 |
# Version: $Id$ |
|
| 13 |
|
|
| 14 |
# trace script (debug purpose, not mandatory) |
|
| 15 |
set -x |
|
| 16 |
# set globals |
|
| 17 |
job=structure11 |
|
| 18 |
ExtIn=com |
|
| 19 |
ExtOut=log |
|
| 20 |
|
|
| 21 |
# Environment setting for gaussian |
|
| 22 |
module use /home/tjiang/modules/lmod |
|
| 23 |
module load gaussian/g16-avx |
|
| 24 |
#module load gaussian/g16-avx2 |
|
| 25 |
source $g16root/g16/bsd/g16.profile |
|
| 26 |
export Gaussian=$g16root/g16/g16 |
|
| 27 |
#export LD_LIBRARY_PATH=/softs/acml/acml2.7.0/pathscale64/lib:/softs/fftw/2.1.5/ps-ib/lib:$LD_LIBRARY_PATH:/usr/lib |
|
| 28 |
|
|
| 29 |
cd ${SGE_O_WORKDIR}
|
|
| 30 |
|
|
| 31 |
echo "########## debut env##################" |
|
| 32 |
env |
|
| 33 |
echo "########## fin env ##################" |
|
| 34 |
|
|
| 35 |
echo "########## Hostname ##################" |
|
| 36 |
hostname |
|
| 37 |
|
|
| 38 |
HOMEDIR=${SGE_O_WORKDIR}
|
|
| 39 |
cd ${HOMEDIR}
|
|
| 40 |
|
|
| 41 |
# Replace 'home' by 'scratch', from SGE_O_WORKDIR, store to SCRATCHDIR |
|
| 42 |
SCRATCHDIR=/scratch/$USER/$JOB_ID/ |
|
| 43 |
# check if scratch exist, create or complain |
|
| 44 |
if [[ -d "/scratch" ]] |
|
| 45 |
then |
|
| 46 |
mkdir -p ${SCRATCHDIR}
|
|
| 47 |
else |
|
| 48 |
echo "/scratch not found, cannot create ${SCRATCHDIR}"
|
|
| 49 |
fi |
|
| 50 |
|
|
| 51 |
# check if scratchdir is OK |
|
| 52 |
echo "ok" > ${SCRATCHDIR}/toto
|
|
| 53 |
Ok=$(cat ${SCRATCHDIR}/toto)
|
|
| 54 |
if [[ "${Ok}" != "ok" ]]
|
|
| 55 |
then |
|
| 56 |
# if scratch is unavailable, fallback to home |
|
| 57 |
CalcDir="${SGE_O_WORKDIR}/scratch"_${job}
|
|
| 58 |
mkdir -p ${CalcDir}
|
|
| 59 |
else |
|
| 60 |
CalcDir=${SCRATCHDIR}
|
|
| 61 |
fi |
|
| 62 |
#mkdir -p ${CalcDir}
|
|
| 63 |
|
|
| 64 |
# Gaussian specific ScratchDir |
|
| 65 |
export GAUSS_SCRDIR=${CalcDir}
|
|
| 66 |
|
|
| 67 |
Machine=$(hostname) |
|
| 68 |
|
|
| 69 |
# check if there is a chk or chk.gz |
|
| 70 |
# TODO/FIXME there's a problem here, watching the trace: if no chk, it create a .chk.chk |
|
| 71 |
NChk=` grep -i "chk" ${job}.${ExtIn} | head -1 | sed 's/=/ /g' | awk '{print $2}'`
|
|
| 72 |
if [ "$NChk" != "" ] |
|
| 73 |
then |
|
| 74 |
NChk=` basename $NChk .chk`.chk |
|
| 75 |
fi |
|
| 76 |
if [[ -s ${HOMEDIR}/${NChk} ]]
|
|
| 77 |
then |
|
| 78 |
cp ${HOMEDIR}/${NChk} ${CalcDir}/${NChk}
|
|
| 79 |
fi |
|
| 80 |
if [[ -s ${HOMEDIR}/${NChk}.gz ]]
|
|
| 81 |
then |
|
| 82 |
cp ${HOMEDIR}/${NChk}.gz ${CalcDir}/${NChk}.gz
|
|
| 83 |
gunzip ${CalcDir}/${NChk}.gz
|
|
| 84 |
fi |
|
| 85 |
|
|
| 86 |
cp ${HOMEDIR}/${job}.${ExtIn} ${CalcDir}/
|
|
| 87 |
|
|
| 88 |
# prepare postprocess script |
|
| 89 |
# TODO/FIXME is this still usefull ? |
|
| 90 |
# - compress .chk |
|
| 91 |
# - copy chk from $SCRATCHDIR to $HOMEDIR |
|
| 92 |
# - cleanup $SCRATCHDIR |
|
| 93 |
# add exec mode on script |
|
| 94 |
#echo "ssh ${SGE_O_LOGNAME}@${Machine} gzip ${CalcDir}/*.chk " > ${HOMEDIR}/${job}_${Machine}_CLEAN.${ExtOut}
|
|
| 95 |
#echo "scp ${SGE_O_LOGNAME}@${Machine}:${CalcDir}/* ." > ${HOMEDIR}/${job}_${Machine}_CLEAN.${ExtOut}
|
|
| 96 |
#echo "ssh ${SGE_O_LOGNAME}@${Machine} rm -fr ${CalcDir}" >> ${HOMEDIR}/${job}_${Machine}_CLEAN.${ExtOut}
|
|
| 97 |
#echo "rm ${job}_${Machine}_CLEAN.${ExtOut}" >> ${HOMEDIR}/${job}_${Machine}_CLEAN.${ExtOut}
|
|
| 98 |
#chmod u+x ${HOMEDIR}/${job}_${Machine}_CLEAN.${ExtOut}
|
|
| 99 |
|
|
| 100 |
# logrotate old logs |
|
| 101 |
if [[ -s ${HOMEDIR}/${job}.${ExtOut} ]]
|
|
| 102 |
then |
|
| 103 |
Ext=1 |
|
| 104 |
while [[ -s ${HOMEDIR}/${job}.${ExtOut}_${Ext} ]]
|
|
| 105 |
do |
|
| 106 |
let Ext=Ext+1 |
|
| 107 |
done |
|
| 108 |
mv ${HOMEDIR}/${job}.${ExtOut} ${HOMEDIR}/${job}.${ExtOut}_${Ext}
|
|
| 109 |
fi |
|
| 110 |
|
|
| 111 |
cd ${CalcDir}
|
|
| 112 |
echo ${CalcDir}
|
|
| 113 |
ls -al |
|
| 114 |
|
|
| 115 |
echo "time ${Gaussian} < ${job}.${ExtIn} > ${HOMEDIR}/${job}.${ExtOut}"
|
|
| 116 |
|
|
| 117 |
#/usr/bin/time ${Gaussian} < ${job}.${ExtIn} > ${HOMEDIR}/${job}.${ExtOut}
|
|
| 118 |
${Gaussian} < ${job}.${ExtIn} > ${HOMEDIR}/${job}.${ExtOut}
|
|
| 119 |
|
|
| 120 |
cp * ${HOMEDIR}/
|
|
| 121 |
|
|
| 122 |
if [[ -s ${NChk} ]]
|
|
| 123 |
then |
|
| 124 |
gzip -9 ${NChk}
|
|
| 125 |
cp ${NChk}.gz ${HOMEDIR}/
|
|
| 126 |
fi |
|
| 127 |
|
|
| 128 |
# final cleanup (commented during debug) |
|
| 129 |
#rm -r ${GAUSS_SCRDIR}
|
|
| 130 |
#rm -r ${CalcDir}
|
|
| submit/namd/sub_namd_gpu_bash (revision 55) | ||
|---|---|---|
| 1 |
#!/bin/bash |
|
| 2 |
#$ -S /bin/bash |
|
| 3 |
#$ -N mutm_ap-oxog |
|
| 4 |
#$ -q E5-2670gpuK20deb128 |
|
| 5 |
#$ -l h=!c82gpgpu33 |
|
| 6 |
#$ -pe mpi_debian 16 |
|
| 7 |
#$ -cwd |
|
| 8 |
#$ -V |
|
| 9 |
|
|
| 10 |
# Loading modules to set up environment |
|
| 11 |
export MODULEPATH=/home/tjiang/modules/lmod/:${MODULEPATH}
|
|
| 12 |
module use ${MODULEPATH}
|
|
| 13 |
module load NAMD/multicore+CUDA/2.12 |
|
| 14 |
|
|
| 15 |
# Setting up home and scratch directories |
|
| 16 |
HOMEDIR=$SGE_O_WORKDIR |
|
| 17 |
cd $HOMEDIR |
|
| 18 |
SCRATCHDIR=/scratch/$USER/$JOB_ID |
|
| 19 |
/bin/mkdir -p $SCRATCHDIR |
|
| 20 |
HOSTFILE=$TMPDIR/machines |
|
| 21 |
cp $HOSTFILE . |
|
| 22 |
sed -i -e 's/^/host\ /' machines |
|
| 23 |
|
|
| 24 |
# Please provide the following files for namd |
|
| 25 |
CONFIGFILE=run2.namd |
|
| 26 |
TOPFILE=DDB2_CT_hmr.prmtop |
|
| 27 |
PDBFILE=DDB2_CT_run1_0.coor |
|
| 28 |
FIXFILE=DDB2_CT_new.fix |
|
| 29 |
COLVARSFILE=dihedral_run1.in |
|
| 30 |
LOGFILE=run2.out |
|
| 31 |
#CONFIGFILE=run1.namd |
|
| 32 |
#TOPFILE=ap-oxog3go8.prmtop |
|
| 33 |
#PDBFILE=mutm_ap-oxog.coor |
|
| 34 |
#COLVARSFILE=dihedral_run1.in |
|
| 35 |
#LOGFILE=run1.out |
|
| 36 |
|
|
| 37 |
# Copying files to scratchdir |
|
| 38 |
rsync -c $CONFIGFILE $TOPFILE $PDBFILE $FIXFILE $COLVARSFILE machines runscript $SCRATCHDIR |
|
| 39 |
|
|
| 40 |
# The executables for mpirun and namd2 |
|
| 41 |
MPIRUN=mpirun |
|
| 42 |
COMMAND=`which namd2` |
|
| 43 |
|
|
| 44 |
# Go to scratch directory and run calculation there |
|
| 45 |
cd $SCRATCHDIR |
|
| 46 |
echo 'group main ++shell ssh' > nodelist |
|
| 47 |
cat machines>>nodelist |
|
| 48 |
|
|
| 49 |
#/applis/PSMN/generic/NAMD/2.12/NAMD_2.12_Linux-x86_64-ibverbs-smp-CUDA/charmrun ++p $NSLOTS ++ppn 8 ++nodelist nodelist ++remote-shell ssh /applis/PSMN/generic/NAMD/2.12/NAMD_2.12_Linux-x86_64-ibverbs-smp-CUDA/namd2 +setcpuaffinity +idlepoll $CONFIGFILE> ${LOGFILE}_2nodes
|
|
| 50 |
#/applis/PSMN/generic/NAMD/2.12/NAMD_2.12_Linux-x86_64-ibverbs-smp-CUDA/charmrun +p${NSLOTS} ++ppn 8 ++nodelist nodelist ++remote-shell ssh /applis/PSMN/generic/NAMD/2.12/NAMD_2.12_Linux-x86_64-ibverbs-smp-CUDA/namd2 +setcpuaffinity +idlepoll $CONFIGFILE> ${LOGFILE}_2nodes
|
|
| 51 |
#charmrun +p$NSLOTS $MPIRUN $COMMAND $CONFIGFILE> $LOGFILE |
|
| 52 |
#namd2 +p 16 $CONFIGFILE> $LOGFILE |
|
| 53 |
namd2 +idlepoll +p $NSLOTS +devices 0,1 $CONFIGFILE> ${LOGFILE}_${NSLOTS}cpu_2gpu_node31
|
|
| 54 |
|
|
| 55 |
# Copy back data |
|
| 56 |
rsync -c --exclude '$CONFIGFILE $TOPFILE $PDBFILE $COLVARSFILE' * $HOMEDIR |
|
| 57 |
cd $HOMEDIR |
|
| 58 |
|
|
| 59 |
# Cleaning up scratch directory and hostfile |
|
| 60 |
rm -fr $SCRATCHDIR |
|
Formats disponibles : Unified diff