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開始行:
#menu(LABO/MenuBar)
* LABO/RockyOHPC/スクリプト例 [#se1cf7dd]
#contents
** 一行メモ [#yed96e8c]
#comment
//-------------------------------------------------------...
* gromacs [#me2ebaa4]
#!/bin/bash --norc
# ver 2.4c gromacs sample (for v2020.4 gromacs)
### SGE
#$-S /bin/bash # interpreting shell
#$-q pan.q
#$-cwd # execute for the current working directory
#$-j y # y/n: merge stderr into stdout
#$-pe mpi 4 # total num slots. NSLOTS is set to this ;...
### SLURM
#SBATCH -p all.p -w c10[1-5] #queue(partition) [-w hosts...
#SBATCH -N 3 #num of node; SLURM_NNODES
#SBATCH -n 12 #num of process(task); SLURM_NTASKS ...
#SBATCH -c 1 #num of thread in process; SLURM_CPUS_PE...
#SBATCH -o %x.o%j # output stdout and stderr into .oNNN
#SBATCH -e %x.o%j
OMP_NUM_THREADS=1 # 1 thread per process
export OMP_NUM_THREADS
# for SGE queues
if [ ${SGE_O_LOGNAME:-x} != x ]; then
if [ ${QUEUE:-x} = potp.q ]; then #taskset for Pcor...
echo "taskset 0-7 cores, and set OMPI_MCA_hwloc_bas...
taskset -p -c 0-7 $$
export OMPI_MCA_hwloc_base_cpu_set=0-7 #for OpenMPI...
elif [ ${QUEUE:-x} = pote.q ]; then #taskset for Ecor...
echo "taskset 8-23 cores, and set OMPI_MCA_hwloc_bas...
taskset -p -c 8-23 $$
export OMPI_MCA_hwloc_base_cpu_set=8-23 #for OpenMP...
else
echo "taskset not specified"
fi
fi
. ./RUN.LIB
#---- プロダクションラン -------------------------------...
#taken from Turorial Lysozyme in water, Justin A.Lemkul,...
# change constraints = all-bonds -> h-bonds
# remove title for v2020.4
# remove ns_type = grid for v2020.4
startMarker "GROMPP" > OUT.md01
cat > inpmd01.mdp << INPUT_EOF
; Run parameters
integrator = md ; leap-frog integrator
...
INPUT_EOF
$GMX_MPI_D grompp -f inpmd01.mdp \
-c npt.gro -t npt.cpt \
-p genion.top -o md01.tpr -po md01.mdp >>...
[ $? -ne 0 ] && errorStop "ERROR: grompp"; echo "OUT.md0...
rm inpmd01.mdp ###
# - - - - - - - - - -
startMarker "MD01" >> OUT.md01
$PMPIRUN $GMX_MPI_D mdrun -ntomp $OMP_NUM_THREADS \
-s md01.tpr \
-e md01.edr -g md01.log -o md01.trr -x md0...
-cpt 360 \
-v \
>> OUT.md01 2>&1
[ $? -ne 0 ] && errorStop "ERROR: md01"; echo "OUT.md01"
rm -f md01_prev.cpt ###
# - - - - - - - - - -
trjconv_grotpr2-protein_UC md01 >> OUT.md01 2>&1
[ $? -ne 0 ] && errorStop "ERROR: trjconv_grotpr2-protei...
closeMarker >> OUT.md01
# end of file
//-------------------------------------------------------...
* gaussian [#xb936ec8]
#!/bin/bash --norc
# ver 2.0 for SGE, SLURM and command line (gaussian16)
### SGE
#$-S /bin/bash # interpreting shell
#$-q pan.q@compute-0-1,pan.q@compute-0-2,pan.q@compute-0-3
#$-cwd # execute for the current working directory
#$-j y # y/n: merge stderr into stdout
#$-pe smp 4 # total num slots. NSLOTS is set to N of P...
### SLURM
#SBATCH -p all.p -w c172 #queue(partition) [-w hosts(nod...
#SBATCH -N 1 #num of node; SLURM_NNODES
#SBATCH -n 1 #num of process(task); SLURM_NTASKS ...
#SBATCH -c 4 #num of thread in process; SLURM_CPUS_PE...
#SBATCH -o %x.o%j # output stdout and stderr into .oNNN
#SBATCH -e %x.o%j
# -- jobs ------------------------------
sysName=`basename $0 ".inp"`
s_s_host=UNKNOWN
export OMP_NUM_THREADS=1
if [ ${SGE_O_LOGNAME:-x} != x ]; then
[ -z ${sysName//[0-9]/} ] && sysName=`basename ${...
s_s_host=${SGE_O_HOST:-C}
OMP_NUM_THREADS=${NSLOTS:-1}
elif [ ${SLURM_JOB_USER:-x} != x ]; then
[ $sysName = "slurm_script" ] && sysName=`basename ${...
s_s_host=${SLURM_SUBMIT_HOST:-C}
OMP_NUM_THREADS=${SLURM_CPUS_PER_TASK:-1}
fi
export nslots=$OMP_NUM_THREADS
### SGE
if [ ${SGE_O_LOGNAME:-x} != x ]; then
if [ ${QUEUE:-x} = potp.q ]; then #taskset for Pcor...
echo "taskset 0-7 cores" >> ${sysName}.out 2>&1
taskset -p -c 0-7 $$ >> ${sysName}.out 2>&1
elif [ ${QUEUE:-x} = pote.q ]; then #taskset for Ecor...
echo "taskset 8-23 cores" >> ${sysName}.out 2>&1
taskset -p -c 8-23 $$ >> ${sysName}.out 2>&1
else
echo "taskset not specified" >> ${sysName}.out 2>&1
fi
fi
#export g16root=/share/apps/gaussian16
#export g16root=/share/apps/gaussian16.binary
export g16root=/share/apps/gaussian16.source-sandybridge
#export g16root=/opt/apps/gaussian16.source-sandybridge
export GAUSS_SCRDIR=$HOME/.gauss_scratch
[ -d $HOME/.gauss_scratch ] || mkdir $HOME/.gauss_scratch
source $g16root/g16/bsd/g16.profile
echo ${s_s_host%%.*} ${HOSTNAME%%.*} using nslots=$nslot...
sed 's/\!\!.*//g' << end_of_input | g16 >> ${sysName}.ou...
%NProcShared=$nslots
#P TEST STO-3G COMPLEX pop=full scf=tight
Gaussian Test Job 01
SINGLET DELTA STO-3G//STO-3G DIOXYGEN
0 1
O
O 1 R
R 1.220
end_of_input
# end of file #
//-------------------------------------------------------...
終了行:
#menu(LABO/MenuBar)
* LABO/RockyOHPC/スクリプト例 [#se1cf7dd]
#contents
** 一行メモ [#yed96e8c]
#comment
//-------------------------------------------------------...
* gromacs [#me2ebaa4]
#!/bin/bash --norc
# ver 2.4c gromacs sample (for v2020.4 gromacs)
### SGE
#$-S /bin/bash # interpreting shell
#$-q pan.q
#$-cwd # execute for the current working directory
#$-j y # y/n: merge stderr into stdout
#$-pe mpi 4 # total num slots. NSLOTS is set to this ;...
### SLURM
#SBATCH -p all.p -w c10[1-5] #queue(partition) [-w hosts...
#SBATCH -N 3 #num of node; SLURM_NNODES
#SBATCH -n 12 #num of process(task); SLURM_NTASKS ...
#SBATCH -c 1 #num of thread in process; SLURM_CPUS_PE...
#SBATCH -o %x.o%j # output stdout and stderr into .oNNN
#SBATCH -e %x.o%j
OMP_NUM_THREADS=1 # 1 thread per process
export OMP_NUM_THREADS
# for SGE queues
if [ ${SGE_O_LOGNAME:-x} != x ]; then
if [ ${QUEUE:-x} = potp.q ]; then #taskset for Pcor...
echo "taskset 0-7 cores, and set OMPI_MCA_hwloc_bas...
taskset -p -c 0-7 $$
export OMPI_MCA_hwloc_base_cpu_set=0-7 #for OpenMPI...
elif [ ${QUEUE:-x} = pote.q ]; then #taskset for Ecor...
echo "taskset 8-23 cores, and set OMPI_MCA_hwloc_bas...
taskset -p -c 8-23 $$
export OMPI_MCA_hwloc_base_cpu_set=8-23 #for OpenMP...
else
echo "taskset not specified"
fi
fi
. ./RUN.LIB
#---- プロダクションラン -------------------------------...
#taken from Turorial Lysozyme in water, Justin A.Lemkul,...
# change constraints = all-bonds -> h-bonds
# remove title for v2020.4
# remove ns_type = grid for v2020.4
startMarker "GROMPP" > OUT.md01
cat > inpmd01.mdp << INPUT_EOF
; Run parameters
integrator = md ; leap-frog integrator
...
INPUT_EOF
$GMX_MPI_D grompp -f inpmd01.mdp \
-c npt.gro -t npt.cpt \
-p genion.top -o md01.tpr -po md01.mdp >>...
[ $? -ne 0 ] && errorStop "ERROR: grompp"; echo "OUT.md0...
rm inpmd01.mdp ###
# - - - - - - - - - -
startMarker "MD01" >> OUT.md01
$PMPIRUN $GMX_MPI_D mdrun -ntomp $OMP_NUM_THREADS \
-s md01.tpr \
-e md01.edr -g md01.log -o md01.trr -x md0...
-cpt 360 \
-v \
>> OUT.md01 2>&1
[ $? -ne 0 ] && errorStop "ERROR: md01"; echo "OUT.md01"
rm -f md01_prev.cpt ###
# - - - - - - - - - -
trjconv_grotpr2-protein_UC md01 >> OUT.md01 2>&1
[ $? -ne 0 ] && errorStop "ERROR: trjconv_grotpr2-protei...
closeMarker >> OUT.md01
# end of file
//-------------------------------------------------------...
* gaussian [#xb936ec8]
#!/bin/bash --norc
# ver 2.0 for SGE, SLURM and command line (gaussian16)
### SGE
#$-S /bin/bash # interpreting shell
#$-q pan.q@compute-0-1,pan.q@compute-0-2,pan.q@compute-0-3
#$-cwd # execute for the current working directory
#$-j y # y/n: merge stderr into stdout
#$-pe smp 4 # total num slots. NSLOTS is set to N of P...
### SLURM
#SBATCH -p all.p -w c172 #queue(partition) [-w hosts(nod...
#SBATCH -N 1 #num of node; SLURM_NNODES
#SBATCH -n 1 #num of process(task); SLURM_NTASKS ...
#SBATCH -c 4 #num of thread in process; SLURM_CPUS_PE...
#SBATCH -o %x.o%j # output stdout and stderr into .oNNN
#SBATCH -e %x.o%j
# -- jobs ------------------------------
sysName=`basename $0 ".inp"`
s_s_host=UNKNOWN
export OMP_NUM_THREADS=1
if [ ${SGE_O_LOGNAME:-x} != x ]; then
[ -z ${sysName//[0-9]/} ] && sysName=`basename ${...
s_s_host=${SGE_O_HOST:-C}
OMP_NUM_THREADS=${NSLOTS:-1}
elif [ ${SLURM_JOB_USER:-x} != x ]; then
[ $sysName = "slurm_script" ] && sysName=`basename ${...
s_s_host=${SLURM_SUBMIT_HOST:-C}
OMP_NUM_THREADS=${SLURM_CPUS_PER_TASK:-1}
fi
export nslots=$OMP_NUM_THREADS
### SGE
if [ ${SGE_O_LOGNAME:-x} != x ]; then
if [ ${QUEUE:-x} = potp.q ]; then #taskset for Pcor...
echo "taskset 0-7 cores" >> ${sysName}.out 2>&1
taskset -p -c 0-7 $$ >> ${sysName}.out 2>&1
elif [ ${QUEUE:-x} = pote.q ]; then #taskset for Ecor...
echo "taskset 8-23 cores" >> ${sysName}.out 2>&1
taskset -p -c 8-23 $$ >> ${sysName}.out 2>&1
else
echo "taskset not specified" >> ${sysName}.out 2>&1
fi
fi
#export g16root=/share/apps/gaussian16
#export g16root=/share/apps/gaussian16.binary
export g16root=/share/apps/gaussian16.source-sandybridge
#export g16root=/opt/apps/gaussian16.source-sandybridge
export GAUSS_SCRDIR=$HOME/.gauss_scratch
[ -d $HOME/.gauss_scratch ] || mkdir $HOME/.gauss_scratch
source $g16root/g16/bsd/g16.profile
echo ${s_s_host%%.*} ${HOSTNAME%%.*} using nslots=$nslot...
sed 's/\!\!.*//g' << end_of_input | g16 >> ${sysName}.ou...
%NProcShared=$nslots
#P TEST STO-3G COMPLEX pop=full scf=tight
Gaussian Test Job 01
SINGLET DELTA STO-3G//STO-3G DIOXYGEN
0 1
O
O 1 R
R 1.220
end_of_input
# end of file #
//-------------------------------------------------------...
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