├── GridEngine ├── adf-mpi.sub ├── amber-11-ompi-iqtc04.sub ├── amber10-mpi.sub ├── crystal-09-mpi-iqtc01.sub ├── crystal-09-mpi-iqtc02.sub ├── crystal-09-mpi-iqtc03.sub ├── crystal-09-mpi-iqtc04.sub ├── gamess-2010r2-ompi-iqtc01.sub ├── gamess-2010r2-ompi-iqtc02.sub ├── gamess-2010r2-ompi-iqtc03.sub ├── gamess-2010r2-ompi-iqtc04.sub ├── gamess-2010r2-smp-iqtc01.sub ├── gamess-2010r2-smp-iqtc02.sub ├── gamess-2010r2-smp-iqtc03.sub ├── gamess-2010r2-smp-iqtc04.sub ├── gamess-smp.sub ├── gamess_uk-7.0-ompi-iqtc01.sub ├── gamess_uk-7.0-ompi-iqtc02.sub ├── gamess_uk-7.0-ompi-iqtc03.sub ├── gamess_uk-7.0-ompi-iqtc04.sub ├── gamess_uk-7.0-smp-iqtc01.sub ├── gamess_uk-7.0-smp-iqtc02.sub ├── gamess_uk-7.0-smp-iqtc03.sub ├── gamess_uk-7.0-smp-iqtc04.sub ├── gaussian-03-linda-iqtc01.sub ├── gaussian-03-smp-iqtc01.sub ├── gaussian-03-smp-iqtc02.sub ├── gaussian-03-smp-iqtc03.sub ├── gaussian-03-smp-iqtc04.sub ├── gaussian-09-linda-iqtc01.sub ├── gaussian-09-linda-iqtc02.sub ├── gaussian-09-linda-iqtc03.sub ├── gaussian-09-linda-iqtc04.sub ├── gaussian-09-smp-iqtc01.sub ├── gaussian-09-smp-iqtc02.sub ├── gaussian-09-smp-iqtc03.sub ├── gaussian-09-smp-iqtc04.sub ├── gaussian-linda.sub ├── gaussian-serial.sub ├── gaussian-smp.sub ├── gromacs-3.3.1-ompi-iqtc04.sub ├── gromacs-mpi.sub ├── gromacs-ompi-iqtc02.sub ├── gromacs-ompi-iqtc04.sub ├── lammps-mpi.sub ├── molcas.sub ├── molcas_7.4-ompi-iqtc04.sub ├── molcas_7.4-serial-iqtc01.sub ├── molcas_7.4-serial-iqtc02.sub ├── molcas_7.4-serial-iqtc03.sub ├── molcas_7.4-serial-iqtc04.sub ├── nwchem-ompi-iqtc04.sub ├── orca-ompi-iqtc04.sub ├── orca_ompi_scratch.sub ├── orca_ompi_work.sub ├── siesta-3.0-ompi-iqtc02.sub ├── siesta-3.0-ompi-iqtc02_tcsh.sub ├── siesta-3.0-ompi-iqtc04.sub ├── siesta-mpi.sub ├── stress_x86-64.sub ├── stress_x86.sub ├── vasp-4.6-ompi-iqtc01.sub ├── vasp-4.6-ompi-iqtc02.sub ├── vasp-4.6-ompi-iqtc03.sub ├── vasp-4.6-ompi-iqtc04.sub ├── vasp-5.2-ompi-iqtc01.sub ├── vasp-5.2-ompi-iqtc02.sub ├── vasp-5.2-ompi-iqtc03.sub ├── vasp-5.2-ompi-iqtc04.sub └── vasp-mpi.sub ├── LSF ├── ior.lsf ├── iozone.lsf └── mdtest.lsf ├── README.md └── Slurm ├── GATK_multithreads.sl ├── Intel-Trace-Analyser-and-Collector-instrumented.sl ├── Intel-Trace-Analyser-and-Collector.sl ├── OpenFOAM-parallel.sl ├── OpenFOAM-serial.sl ├── OpenSees.sl ├── QuantumESPRESSO-hybrid.sl ├── QuantumESPRESSO-mpi.sl ├── R-parallel-mpi.r ├── R-parallel-mpi.sl ├── R-template.sl ├── VASP-iomkl.sl ├── VTune-MPI.sl ├── VTune-OpenMP.sl ├── VTune-serial.sl ├── abaqus.sl ├── ansys-cfx.sl ├── ansys-fluent-requeue.sl ├── ansys-fluent.sl ├── array-io.sl ├── array-mpi.sl ├── array.sl ├── array_builder.sh ├── array_multi_parameters.sl ├── blast+_array.sl ├── blast+_array_multithreads.sl ├── checkpoint-blcr.sl ├── cuda-mpi.sl ├── cuda.sl ├── easybuild.sl ├── flexpart.sl ├── gaussian.sl ├── gromacs-cuda-mpi.sl ├── gromacs-mpi.sl ├── gromacs-openmp.sl ├── hello_world-array.sl ├── hello_world.sl ├── helloworld_multi ├── hybrid.sl ├── intel-mpi.sl ├── intel-mpitune.sl ├── lammps-hybrid.sl ├── launcher.sl ├── matlab.sl ├── mb.sl ├── migrate-benchmark-serial.sl ├── migrate-benchmark-tuned.sl ├── migrate-benchmark.sl ├── migrate-mpi.sl ├── migrate-profile.sl ├── migrate-traces.sl ├── mpi-all.sl ├── mpi.sl ├── multi-mpi.conf ├── multi-prog-mpi.sl ├── multi-prog.sl ├── multi.conf ├── multistage.sl ├── namd-cuda.sl ├── namd-mpi.sl ├── nextflow.config ├── node_stress.sl ├── octave.sl ├── open-mpi.sl ├── openmp.sl ├── orca-mpi.sl ├── orca-smp.sl ├── params.dat ├── platform-mpi.sl ├── post-processing.sl ├── pre-processing.sl ├── profile.sl ├── serial.sl ├── slurm_setup_abaqus-env.sh ├── slurm_setup_cfx-env.sh ├── slurm_setup_cfx-env2.sh ├── slurm_setup_cfx-env3.sh ├── slurm_setup_fluent.sh ├── star-ccm+-platform.sl ├── stress.sl ├── supermagic.sl └── trace.conf /GridEngine/adf-mpi.sub: -------------------------------------------------------------------------------- 1 | #!/bin/bash 2 | # Script per enviar calculs de ADF amb MPI 3 | #$ -o jobfile.out 4 | #$ -e jobfile.err 5 | #$ -N adf-test 6 | 7 | #$ -S /bin/bash 8 | #$ -V 9 | #$ -cwd 10 | #$ -m e 11 | #$ -notify 12 | #$ -M jblasco@fbg.ub.es 13 | #$ -l h_rt=10:00:00 14 | #$ -l h_vmem=1G 15 | #$ -pe mpi 4 16 | #$ -R y 17 | 18 | module load adf 19 | 20 | SDIR=$(pwd) 21 | export P4_RSHCOMMAND=ssh 22 | 23 | export SCM_MACHINEFILE=$SDIR/scm.machines 24 | export SCM_TMPDIR=$TMPDIR 25 | export SCM_USETMPDIR=yes 26 | export NSCM=$NSLOTS 27 | 28 | rm -f $SCM_MACHINEFILE 29 | for line in `cat $TMPDIR/machines`; do 30 | node=`echo $line | cut -f1 -d ":"` 31 | slots=`echo $line | cut -s -f2 -d ":"` 32 | ssh $node mkdir -p $SCM_TMPDIR 33 | if [[ $slots -le 0 ]]; then 34 | slots=1 35 | fi 36 | j=0 37 | while [ $j -lt $slots ]; do 38 | echo $node >> $SCM_MACHINEFILE 39 | j=$(($j + 1)) 40 | done 41 | done 42 | 43 | # Run your executable: 44 | $ADFBIN/adf -n $NSLOTS << EOR 45 | Title WATER Geometry Optimization with Delocalized Coordinates 46 | 47 | Atoms 48 | O 0.000000 0.000000 0.000000 49 | H 0.000000-0.689440-0.578509 50 | H 0.000000 0.689440-0.578509 51 | End 52 | 53 | Basis 54 | Type TZ2P 55 | Core Small 56 | End 57 | 58 | Geometry 59 | Optim Deloc 60 | End 61 | 62 | End Input 63 | EOR -------------------------------------------------------------------------------- /GridEngine/amber-11-ompi-iqtc04.sub: -------------------------------------------------------------------------------- 1 | #!/bin/bash 2 | ########################################## 3 | # SGE options and parameters 4 | ########################################## 5 | # (1) Name of the job 6 | #$ -N TEST-ncores 7 | # (2) Resources requested 8 | #$ -pe omp* ncores 9 | # Queue 10 | #$ -q iqtc04.q 11 | # (3) Output files 12 | #$ -cwd 13 | #$ -o amber-TEST-ncores_BINAMBER.out 14 | #$ -e amber-TEST-ncores_BINAMBER.err 15 | # (4) Remove the first '#' of the following 2 lines if you want to receive an email when the job ends. 16 | ##$ -m e 17 | ##$ -M yourmail@ub.edu 18 | #$ -S /bin/bash 19 | ########################################### 20 | ## User environment. 21 | ########################################### 22 | ## Load the modules needed 23 | #. /etc/profile.d/modules.sh 24 | module load amber/11_OpenMPI_1.4.2_intel_11.1.072 25 | ########################################## 26 | # Copying files needed 27 | ########################################## 28 | # We copy the inputs to the directory where the jobs will run 29 | cd $TMPDIR 30 | #mkdir -p /work/jblasco/TEST-ncores-BINAMBER 31 | #cd /work/jblasco/TEST-ncores-BINAMBER 32 | cp -r $HOME/bench/AMBER/TEST/input/* . 33 | ########################################## 34 | # Run the job 35 | ########################################## 36 | export OMP_NUM_THREADS=1 37 | ulimit -l unlimited 38 | 39 | 40 | A1=ispfv_trxm1_04_din 41 | A2=ispfv_trxm1 42 | A3=ispfv_trxm1_03_din 43 | A4=rst 44 | 45 | mpirun -np $NSLOTS pmemd \ 46 | -i $SGE_O_WORKDIR/$A1.in \ 47 | -o $TMPDIR/$A1.out \ 48 | -p $SGE_O_WORKDIR/$A2.top \ 49 | -c $SGE_O_WORKDIR/$A3.$A4 \ 50 | -ref $SGE_O_WORKDIR/$A3.$A4 \ 51 | -r $TMPDIR/$A1.rst \ 52 | -e $TMPDIR/$A1.mden \ 53 | -x $TMPDIR/$A1.mdcrd \ 54 | -v $TMPDIR/$A1.mdvel \ 55 | -l $TMPDIR/$A1.logfile \ 56 | -inf $TMPDIR/$A1.inf 57 | 58 | ########################################## 59 | # Copy the results to our home directory 60 | ########################################## 61 | mkdir -p $HOME/bench/AMBER/TEST/OUT/amber 62 | cp -r $TMPDIR $HOME/bench/AMBER/TEST/OUT/amber/ 63 | #cp -r /work/jblasco/TEST-ncores-BINAMBER $HOME/bench/AMBER/TEST/OUT/amber/ 64 | ########################################## 65 | # Temps dels resultats 66 | ########################################## 67 | TEMPS=$(cat $A1.out | grep "Master Total wall time" | awk '{print $6}') 68 | echo "$NSLOTS $TEMPS" >> $HOME/bench2/AMBER/benchmark-Nehalem-DP-TEST-BINAMBER.dat 69 | #cd 70 | #rm -fr /work/jblasco/TEST-ncores-BINAMBER 71 | 72 | -------------------------------------------------------------------------------- /GridEngine/amber10-mpi.sub: -------------------------------------------------------------------------------- 1 | #!/bin/bash 2 | ########################################## 3 | # Opcions i parametres de l'SGE 4 | ########################################## 5 | # (1) Nom del treball (per identificar) 6 | #$ -N AMBER-10-prova01 7 | # (2) Recursos sol.licitats 8 | #$ -l h_rt=0:50:0 9 | #$ -l mem_free=4.0G 10 | #$ -pe mpi 16 11 | # (3) Fitxers de sortida 12 | #$ -cwd 13 | #$ -o amber01.out 14 | #$ -e amber01.err 15 | #$ (4) Envia un mail quan acava el treball. 16 | #$ -m e 17 | #$ -M jblasco@fbg.ub.es 18 | ########################################## 19 | # Entorn d.usuari 20 | ########################################## 21 | # Es carreguen els moduls a utilitzar 22 | . /etc/profile 23 | module load amber 24 | module load openmpi 25 | ########################################## 26 | # transferencia de dades 27 | ########################################## 28 | # Es copien les dades al directori on es llenc,aran els calculs. 29 | cd $TMPDIR 30 | export Project=amber_mpi_16 31 | export Input=$Project 32 | cp -pr $HOME/path/amb/els/inputs/ $Input 33 | ########################################## 34 | # calcul 35 | ########################################## 36 | # Es crea un directori de sortida pels resultats. 37 | export OMP_NUM_THREADS=1 38 | #mpirun -np $NSLOTS $pe_machines sander.MPI -O -i in.md -c crd.md.23 -o cytosine.out 39 | mpirun -np $NSLOTS sander_mpi -O -i in.md -c crd.md.23 -o cytosine.out 40 | ########################################## 41 | # Transferencia dels resultats 42 | ########################################## 43 | cp -pr $Input $HOME/path/a/on/guardar/els/outputs/ 44 | -------------------------------------------------------------------------------- /GridEngine/crystal-09-mpi-iqtc01.sub: -------------------------------------------------------------------------------- 1 | #!/bin/bash 2 | ########################################## 3 | # SGE options and parameters 4 | ########################################## 5 | # (1) Name of the job 6 | #$ -N crystal09-MPI 7 | # (2) Requested resources 8 | # Parallel Environment and number of cores 9 | #$ -pe mpi 16 10 | # Queue 11 | #$ -q iqtc01.q 12 | # Shell 13 | #$ -S /bin/bash 14 | # (3) Output files 15 | #$ -cwd 16 | #$ -o crystal09-mpi.out 17 | #$ -e crystal09-mpi.err 18 | # (4) Remove the first '#' of the following 2 lines if you want to receive an email when the job ends. 19 | ##$ -m e 20 | ##$ -M yourmail@ub.edu 21 | ########################################## 22 | # User environment. 23 | ########################################## 24 | # Load the modules needed 25 | . /etc/profile.d/modules.sh 26 | module load crystal/09 27 | ########################################## 28 | # Run the job 29 | ######################################### 30 | runmpi.iqtc INPUT $NSLOTS 31 | 32 | ########################################## 33 | # Copy the results to our home directory 34 | ########################################## 35 | mkdir -p $HOME/TESTS/crystal09/tests/out 36 | cp -r $TMPDIR/* $HOME/TESTS/crystal09/tests/out/ 37 | 38 | 39 | 40 | -------------------------------------------------------------------------------- /GridEngine/crystal-09-mpi-iqtc02.sub: -------------------------------------------------------------------------------- 1 | #!/bin/bash 2 | ########################################## 3 | # SGE options and parameters 4 | ########################################## 5 | # (1) Name of the job 6 | #$ -N crystal09-MPI 7 | # (2) Requested resources 8 | # Parallel Environment and number of cores 9 | #$ -pe mpi 16 10 | # Queue 11 | #$ -q iqtc02.q 12 | # Shell 13 | #$ -S /bin/bash 14 | # (3) Output files 15 | #$ -cwd 16 | #$ -o crystal09-mpi.out 17 | #$ -e crystal09-mpi.err 18 | # (4) Remove the first '#' of the following 2 lines if you want to receive an email when the job ends. 19 | ##$ -m e 20 | ##$ -M yourmail@ub.edu 21 | ########################################## 22 | # User environment. 23 | ########################################## 24 | # Load the modules needed 25 | . /etc/profile.d/modules.sh 26 | module load crystal/09 27 | ########################################## 28 | # Run the job 29 | ######################################### 30 | runmpi.iqtc INPUT $NSLOTS 31 | 32 | ########################################## 33 | # Copy the results to our home directory 34 | ########################################## 35 | mkdir -p $HOME/TESTS/crystal09/tests/out 36 | cp -r $TMPDIR/* $HOME/TESTS/crystal09/tests/out/ 37 | 38 | 39 | 40 | -------------------------------------------------------------------------------- /GridEngine/crystal-09-mpi-iqtc03.sub: -------------------------------------------------------------------------------- 1 | #!/bin/bash 2 | ########################################## 3 | # SGE options and parameters 4 | ########################################## 5 | # (1) Name of the job 6 | #$ -N crystal09-MPI 7 | # (2) Requested resources 8 | # Parallel Environment and number of cores 9 | #$ -pe mpi 16 10 | # Queue 11 | #$ -q iqtc03.q 12 | # Shell 13 | #$ -S /bin/bash 14 | # (3) Output files 15 | #$ -cwd 16 | #$ -o crystal09-mpi.out 17 | #$ -e crystal09-mpi.err 18 | # (4) Remove the first '#' of the following 2 lines if you want to receive an email when the job ends. 19 | ##$ -m e 20 | ##$ -M yourmail@ub.edu 21 | ########################################## 22 | # User environment. 23 | ########################################## 24 | # Load the modules needed 25 | . /etc/profile.d/modules.sh 26 | module load crystal/09 27 | ########################################## 28 | # Run the job 29 | ######################################### 30 | runmpi.iqtc INPUT $NSLOTS 31 | 32 | ########################################## 33 | # Copy the results to our home directory 34 | ########################################## 35 | mkdir -p $HOME/TESTS/crystal09/tests/out 36 | cp -r $TMPDIR/* $HOME/TESTS/crystal09/tests/out/ 37 | 38 | 39 | 40 | -------------------------------------------------------------------------------- /GridEngine/crystal-09-mpi-iqtc04.sub: -------------------------------------------------------------------------------- 1 | #!/bin/bash 2 | ########################################## 3 | # SGE options and parameters 4 | ########################################## 5 | # (1) Name of the job 6 | #$ -N crystal09-MPI 7 | # (2) Requested resources 8 | # Parallel Environment and number of cores 9 | #$ -pe omp* 12 10 | # Queue 11 | #$ -q iqtc04.q 12 | # Shell 13 | #$ -S /bin/bash 14 | # (3) Output files 15 | #$ -cwd 16 | #$ -o crystal09-mpi.out 17 | #$ -e crystal09-mpi.err 18 | # (4) Remove the first '#' of the following 2 lines if you want to receive an email when the job ends. 19 | ##$ -m e 20 | ##$ -M yourmail@ub.edu 21 | ########################################## 22 | # User environment. 23 | ########################################## 24 | # Load the modules needed 25 | . /etc/profile.d/modules.sh 26 | module load crystal/09 27 | ########################################## 28 | # Run the job 29 | ######################################### 30 | runmpi.iqtc INPUT $NSLOTS 31 | 32 | ########################################## 33 | # Copy the results to our home directory 34 | ########################################## 35 | mkdir -p $HOME/TESTS/crystal09/tests/out 36 | cp -r $TMPDIR/* $HOME/TESTS/crystal09/tests/out/ 37 | 38 | 39 | 40 | -------------------------------------------------------------------------------- /GridEngine/gamess-2010r2-ompi-iqtc01.sub: -------------------------------------------------------------------------------- 1 | #!/bin/bash 2 | ########################################## 3 | # SGE options and parameters 4 | ########################################## 5 | # (1) Name of the job 6 | #$ -N GAMESS-prova01 7 | # (2) Requested resources 8 | # Parallel Environment and number of cores 9 | #$ -pe ompi 8 10 | # Queue 11 | #$ -q iqtc01.q 12 | # Shell 13 | #$ -S /bin/bash 14 | # (3) Output files 15 | #$ -cwd 16 | #$ -o gamess01.out 17 | #$ -e gamess01.err 18 | # (4) Remove the first '#' of the following 2 lines if you want to receive an email when the job ends. 19 | ##$ -m e 20 | ##$ -M yourmail@ub.edu 21 | ########################################## 22 | # User environment. 23 | ########################################## 24 | # Load the modules needed 25 | . /etc/profile.d/modules.sh 26 | module load gamess/2010r2_intel_ompi-1.3.3 27 | ########################################## 28 | # Copying files needed 29 | ########################################## 30 | # We copy the inputs to the directory where the jobs will run 31 | cd $TMPDIR 32 | cp -r $HOME/bench/GAMESS/XRQTC.Gamess_MCQDPT/input/XRQTC.Gamess_MCQDPT.inp . 33 | ########################################## 34 | # Run the job 35 | ########################################## 36 | rungms XRQTC.Gamess_MCQDPT.inp 00 $NSLOTS >& XRQTC.Gamess_MCQDPT.log 37 | ########################################## 38 | # Copy the results to our home directory 39 | ########################################## 40 | cp -r $TMPDIR $HOME/tests.out 41 | -------------------------------------------------------------------------------- /GridEngine/gamess-2010r2-ompi-iqtc02.sub: -------------------------------------------------------------------------------- 1 | #!/bin/bash 2 | ########################################## 3 | # SGE options and parameters 4 | ########################################## 5 | # (1) Name of the job 6 | #$ -N GAMESS-prova01 7 | # (2) Requested resources 8 | # Parallel Environment and number of cores 9 | #$ -pe ompi 8 10 | # Queue 11 | #$ -q iqtc02.q 12 | # Shell 13 | #$ -S /bin/bash 14 | # (3) Output files 15 | #$ -cwd 16 | #$ -o gamess01.out 17 | #$ -e gamess01.err 18 | # (4) Remove the first '#' of the following 2 lines if you want to receive an email when the job ends. 19 | ##$ -m e 20 | ##$ -M yourmail@ub.edu 21 | ########################################## 22 | # User environment. 23 | ########################################## 24 | # Load the modules needed 25 | . /etc/profile.d/modules.sh 26 | module load gamess/2010r2_ompi-1.3 27 | ########################################## 28 | # Copying files needed 29 | ########################################## 30 | # We copy the inputs to the directory where the jobs will run 31 | cd $TMPDIR 32 | cp -r $HOME/bench/GAMESS/XRQTC.Gamess_MCQDPT/input/XRQTC.Gamess_MCQDPT.inp . 33 | ########################################## 34 | # Run the job 35 | ########################################## 36 | rungms XRQTC.Gamess_MCQDPT.inp 00 $NSLOTS >& XRQTC.Gamess_MCQDPT.log 37 | ########################################## 38 | # Copy the results to our home directory 39 | ########################################## 40 | cp -r $TMPDIR $HOME/tests.out 41 | -------------------------------------------------------------------------------- /GridEngine/gamess-2010r2-ompi-iqtc03.sub: -------------------------------------------------------------------------------- 1 | #!/bin/bash 2 | ########################################## 3 | # SGE options and parameters 4 | ########################################## 5 | # (1) Name of the job 6 | #$ -N GAMESS-prova01 7 | # (2) Requested resources 8 | # Parallel Environment and number of cores 9 | #$ -pe ompi 8 10 | # Queue 11 | #$ -q iqtc03.q 12 | # Shell 13 | #$ -S /bin/bash 14 | # (3) Output files 15 | #$ -cwd 16 | #$ -o gamess01.out 17 | #$ -e gamess01.err 18 | # (4) Remove the first '#' of the following 2 lines if you want to receive an email when the job ends. 19 | ##$ -m e 20 | ##$ -M yourmail@ub.edu 21 | ########################################## 22 | # User environment. 23 | ########################################## 24 | # Load the modules needed 25 | . /etc/profile.d/modules.sh 26 | module load gamess/2010r2_ompi-1.3 27 | ########################################## 28 | # Copying files needed 29 | ########################################## 30 | # We copy the inputs to the directory where the jobs will run 31 | cd $TMPDIR 32 | cp -r $HOME/bench/GAMESS/XRQTC.Gamess_MCQDPT/input/XRQTC.Gamess_MCQDPT.inp . 33 | ########################################## 34 | # Run the job 35 | ########################################## 36 | rungms XRQTC.Gamess_MCQDPT.inp 00 $NSLOTS >& XRQTC.Gamess_MCQDPT.log 37 | ########################################## 38 | # Copy the results to our home directory 39 | ########################################## 40 | cp -r $TMPDIR $HOME/tests.out 41 | -------------------------------------------------------------------------------- /GridEngine/gamess-2010r2-ompi-iqtc04.sub: -------------------------------------------------------------------------------- 1 | #!/bin/bash 2 | ########################################## 3 | # SGE options and parameters 4 | ########################################## 5 | # (1) Name of the job 6 | #$ -N GAMESS-prova01 7 | # (2) Requested resources 8 | # Parallel Environment and number of cores 9 | #$ -pe omp* 12 10 | # Queue 11 | #$ -q iqtc04.q 12 | # Shell 13 | #$ -S /bin/bash 14 | # (3) Output files 15 | #$ -cwd 16 | #$ -o gamess01.out 17 | #$ -e gamess01.err 18 | # (4) Remove the first '#' of the following 2 lines if you want to receive an email when the job ends. 19 | ##$ -m e 20 | ##$ -M yourmail@ub.edu 21 | ########################################## 22 | # User environment. 23 | ########################################## 24 | # Load the modules needed 25 | . /etc/profile.d/modules.sh 26 | module load gamess/2010r2_intel11.1_mkl11.1_ompi-1.4.2 27 | ########################################## 28 | # Copying files needed 29 | ########################################## 30 | # We copy the inputs to the directory where the jobs will run 31 | cd $TMPDIR 32 | cp -r $HOME/bench/GAMESS/XRQTC.Gamess_MCQDPT/input/XRQTC.Gamess_MCQDPT.inp . 33 | ########################################## 34 | # Run the job 35 | ########################################## 36 | rungms XRQTC.Gamess_MCQDPT.inp 00 $NSLOTS >& XRQTC.Gamess_MCQDPT.log 37 | ########################################## 38 | # Copy the results to our home directory 39 | ########################################## 40 | cp -r $TMPDIR $HOME/tests.out 41 | -------------------------------------------------------------------------------- /GridEngine/gamess-2010r2-smp-iqtc01.sub: -------------------------------------------------------------------------------- 1 | #!/bin/bash 2 | ########################################## 3 | # SGE options and parameters 4 | ########################################## 5 | # (1) Name of the job 6 | #$ -N GAMESS-prova01 7 | # (2) Requested resources 8 | # Parallel Environment and number of cores 9 | #$ -pe smp 1 10 | # Queue 11 | #$ -q iqtc01.q 12 | # Shell 13 | #$ -S /bin/bash 14 | # (3) Output files 15 | #$ -cwd 16 | #$ -o gamess01.out 17 | #$ -e gamess01.err 18 | # (4) Remove the first '#' of the following 2 lines if you want to receive an email when the job ends. 19 | ##$ -m e 20 | ##$ -M yourmail@ub.edu 21 | ########################################## 22 | # User environment. 23 | ########################################## 24 | # Load the modules needed 25 | . /etc/profile.d/modules.sh 26 | module load gamess/2010r2_intel 27 | ########################################## 28 | # Copying files needed 29 | ########################################## 30 | # We copy the inputs to the directory where the jobs will run 31 | cd $TMPDIR 32 | cp -r $HOME/bench/GAMESS/XRQTC.Gamess_MCQDPT/input/XRQTC.Gamess_MCQDPT.inp . 33 | ########################################## 34 | # Run the job 35 | ########################################## 36 | rungms XRQTC.Gamess_MCQDPT.inp 00 $NSLOTS >& XRQTC.Gamess_MCQDPT.log 37 | ########################################## 38 | # Copy the results to our home directory 39 | ########################################## 40 | cp -r $TMPDIR $HOME/tests.out 41 | -------------------------------------------------------------------------------- /GridEngine/gamess-2010r2-smp-iqtc02.sub: -------------------------------------------------------------------------------- 1 | #!/bin/bash 2 | ########################################## 3 | # SGE options and parameters 4 | ########################################## 5 | # (1) Name of the job 6 | #$ -N GAMESS-prova01 7 | # (2) Requested resources 8 | # Parallel Environment and number of cores 9 | #$ -pe smp 1 10 | # Queue 11 | #$ -q iqtc02.q 12 | # Shell 13 | #$ -S /bin/bash 14 | # (3) Output files 15 | #$ -cwd 16 | #$ -o gamess01.out 17 | #$ -e gamess01.err 18 | # (4) Remove the first '#' of the following 2 lines if you want to receive an email when the job ends. 19 | ##$ -m e 20 | ##$ -M yourmail@ub.edu 21 | ########################################## 22 | # User environment. 23 | ########################################## 24 | # Load the modules needed 25 | . /etc/profile.d/modules.sh 26 | module load gamess/2010r2 27 | ########################################## 28 | # Copying files needed 29 | ########################################## 30 | # We copy the inputs to the directory where the jobs will run 31 | cd $TMPDIR 32 | cp -r $HOME/bench/GAMESS/XRQTC.Gamess_MCQDPT/input/XRQTC.Gamess_MCQDPT.inp . 33 | ########################################## 34 | # Run the job 35 | ########################################## 36 | rungms XRQTC.Gamess_MCQDPT.inp 00 $NSLOTS >& XRQTC.Gamess_MCQDPT.log 37 | ########################################## 38 | # Copy the results to our home directory 39 | ########################################## 40 | cp -r $TMPDIR $HOME/tests.out 41 | -------------------------------------------------------------------------------- /GridEngine/gamess-2010r2-smp-iqtc03.sub: -------------------------------------------------------------------------------- 1 | #!/bin/bash 2 | ########################################## 3 | # SGE options and parameters 4 | ########################################## 5 | # (1) Name of the job 6 | #$ -N GAMESS-prova01 7 | # (2) Requested resources 8 | # Parallel Environment and number of cores 9 | #$ -pe smp 1 10 | # Queue 11 | #$ -q iqtc03.q 12 | # Shell 13 | #$ -S /bin/bash 14 | # (3) Output files 15 | #$ -cwd 16 | #$ -o gamess01.out 17 | #$ -e gamess01.err 18 | # (4) Remove the first '#' of the following 2 lines if you want to receive an email when the job ends. 19 | ##$ -m e 20 | ##$ -M yourmail@ub.edu 21 | ########################################## 22 | # User environment. 23 | ########################################## 24 | # Load the modules needed 25 | . /etc/profile.d/modules.sh 26 | module load gamess/2010r2 27 | ########################################## 28 | # Copying files needed 29 | ########################################## 30 | # We copy the inputs to the directory where the jobs will run 31 | cd $TMPDIR 32 | cp -r $HOME/bench/GAMESS/XRQTC.Gamess_MCQDPT/input/XRQTC.Gamess_MCQDPT.inp . 33 | ########################################## 34 | # Run the job 35 | ########################################## 36 | rungms XRQTC.Gamess_MCQDPT.inp 00 $NSLOTS >& XRQTC.Gamess_MCQDPT.log 37 | ########################################## 38 | # Copy the results to our home directory 39 | ########################################## 40 | cp -r $TMPDIR $HOME/tests.out 41 | -------------------------------------------------------------------------------- /GridEngine/gamess-2010r2-smp-iqtc04.sub: -------------------------------------------------------------------------------- 1 | #!/bin/bash 2 | ########################################## 3 | # SGE options and parameters 4 | ########################################## 5 | # (1) Name of the job 6 | #$ -N GAMESS-prova01 7 | # (2) Requested resources 8 | # Parallel Environment and number of cores 9 | #$ -pe smp 1 10 | # Queue 11 | #$ -q iqtc04.q 12 | # Shell 13 | #$ -S /bin/bash 14 | # (3) Output files 15 | #$ -cwd 16 | #$ -o gamess01.out 17 | #$ -e gamess01.err 18 | # (4) Remove the first '#' of the following 2 lines if you want to receive an email when the job ends. 19 | ##$ -m e 20 | ##$ -M yourmail@ub.edu 21 | ########################################## 22 | # User environment. 23 | ########################################## 24 | # Load the modules needed 25 | . /etc/profile.d/modules.sh 26 | module load gamess/2010r2_intel11.1_mkl11.1 27 | ########################################## 28 | # Copying files needed 29 | ########################################## 30 | # We copy the inputs to the directory where the jobs will run 31 | cd $TMPDIR 32 | cp -r $HOME/bench/GAMESS/XRQTC.Gamess_MCQDPT/input/XRQTC.Gamess_MCQDPT.inp . 33 | ########################################## 34 | # Run the job 35 | ########################################## 36 | rungms XRQTC.Gamess_MCQDPT.inp 00 $NSLOTS >& XRQTC.Gamess_MCQDPT.log 37 | ########################################## 38 | # Copy the results to our home directory 39 | ########################################## 40 | cp -r $TMPDIR $HOME/tests.out 41 | -------------------------------------------------------------------------------- /GridEngine/gamess-smp.sub: -------------------------------------------------------------------------------- 1 | #!/bin/bash 2 | # Script per enviar càlculs de Gamess 3 | # amb 8 processadors sobre la mateixa maquina 4 | # - Jordi Blasco 12/08/07 - 5 | ########################################## 6 | # Opcions i parametres de l'SGE 7 | ########################################## 8 | # (1) Nom del treball (per identificar) 9 | #$ -N GAMESS-prova01 10 | # (2) Recursos sol.licitats 11 | #$ -l h_rt=0:50:0 12 | #$ -l mem_free=16.0G 13 | #$ -pe smp 8 14 | # (3) Fitxers de sortida 15 | #$ -cwd 16 | #$ -o gamess01.out 17 | #$ -e gamess01.err 18 | # (4) Envia un mail quan acava el treball. 19 | #$ -m e 20 | #$ -M jblasco@fbg.ub.es 21 | ########################################## 22 | # Entorn d.usuari 23 | ########################################## 24 | # Es carreguen els moduls a utilitzar 25 | . /etc/profile 26 | module load gamess 27 | ########################################## 28 | # transferencia de dades 29 | ########################################## 30 | # Es copien les dades al directori on es llenc,aran els calculs. 31 | cd $TMPDIR 32 | export Project=gamess_smp_8 33 | export Input=$Project 34 | cp -pr $HOME/path/amb/els/inputs/ $Input 35 | ########################################## 36 | # calcul 37 | ########################################## 38 | # Es crea un directori de sortida pels resultats. 39 | rungms JOB.inp 00 $NCPUS >& JOB.log 40 | ########################################## 41 | # Transferencia dels resultats 42 | ########################################## 43 | cp -pr $Input $HOME/path/a/on/guardar/els/outputs/ 44 | -------------------------------------------------------------------------------- /GridEngine/gamess_uk-7.0-ompi-iqtc01.sub: -------------------------------------------------------------------------------- 1 | #!/bin/sh 2 | #$ -pe ompi 4 3 | #$ -cwd 4 | #$ -V 5 | #$ -o Si8O13.log 6 | #$ -S /bin/bash 7 | #$ -q iqtc01.q 8 | # 9 | source /opt/modules/init/bash 10 | module load gamess-uk/7.0_intel10.1_ompi1.3.3 11 | jobname=Si8O13 12 | root=Si8O13 13 | executable=/aplic/gamess-uk_ompi_intel/bin/gamess-uk 14 | jobmode=openmpi 15 | flist="-k ftn058=Si8O13.pun -k ed3" 16 | nprocs=4 17 | nnodes=4 18 | jobtime=120 19 | scratchtopdir=. 20 | libdir=/aplic/gamess-uk_ompi_intel/lib 21 | tempdir=/tmp 22 | homedir=/home/rporcel/subscripts/gamessuk/Si8O13 23 | stdout=0 24 | listing=TEST.out 25 | datain=1 26 | procspernode=1 27 | project=none 28 | RUNGAMESS_DIR=/aplic/gamess-uk_ompi_intel/rungamess 29 | PROG=rungamess 30 | queueargs="" 31 | queue=iqtc01.q 32 | debug=0 33 | jobworkdir= 34 | export jobname 35 | export root 36 | export executable 37 | export jobmode 38 | export flist 39 | export nprocs 40 | export nnodes 41 | export jobtime 42 | export scratchtopdir 43 | export libdir 44 | export tempdir 45 | export homedir 46 | export stdout 47 | export listing 48 | export datain 49 | export procs_per_node 50 | export project 51 | export RUNGAMESS_DIR 52 | export PROG 53 | export queueargs 54 | export queue 55 | export debug 56 | export jobworkdir 57 | #if test -f /home/g4stefan/.profile 58 | #then 59 | #. /home/g4stefan/.profile 60 | #fi 61 | if test ${GAMESS_LIB:=unset} = unset 62 | then 63 | GAMESS_LIB=/aplic/gamess-uk_ompi_intel/lib 64 | export GAMESS_LIB 65 | fi 66 | if test ${GAMESS_SCR:=unset} = unset 67 | then 68 | GAMESS_SCR=. 69 | export GAMESS_SCR 70 | fi 71 | if test ${GAMESS_WORK:=unset} = unset 72 | then 73 | GAMESS_WORK= 74 | export GAMESS_WORK 75 | fi 76 | if test ${GAMESS_TMP:=unset} = unset 77 | then 78 | GAMESS_TMP=/tmp 79 | export GAMESS_TMP 80 | fi 81 | if test ${GAMESS_PAREXE:=unset} = unset 82 | then 83 | GAMESS_PAREXE=/aplic/gamess-uk_ompi_intel/bin/gamess-uk 84 | export GAMESS_PAREXE 85 | fi 86 | if test ${GAMESS_EXE:=unset} = unset 87 | then 88 | GAMESS_EXE=/aplic/gamess-uk_ompi_intel/bin/gamess-uk 89 | export GAMESS_EXE 90 | fi 91 | $RUNGAMESS_DIR/rg_exe.$jobmode > /home/rporcel/subscripts/gamessuk/Si8O13/Si8O13.out 92 | -------------------------------------------------------------------------------- /GridEngine/gamess_uk-7.0-ompi-iqtc02.sub: -------------------------------------------------------------------------------- 1 | #!/bin/sh 2 | #$ -pe ompi 4 3 | #$ -cwd 4 | #$ -V 5 | #$ -o Si8O13.log 6 | #$ -S /bin/bash 7 | #$ -q iqtc02.q 8 | # 9 | source /opt/modules/init/bash 10 | module load gamessuk/7.0_ompi 11 | jobname=Si8O13 12 | root=Si8O13 13 | executable=/aplic/gamess-uk/7.0_ompi/bin/gamess-uk 14 | jobmode=openmpi 15 | flist="-k ftn058=Si8O13.pun -k ed3" 16 | nprocs=4 17 | nnodes=4 18 | jobtime=120 19 | scratchtopdir=. 20 | libdir=/aplic/gamess-uk/7.0_ompi/lib 21 | tempdir=/tmp 22 | homedir=/home/rporcel/subscripts/gamessuk/Si8O13 23 | stdout=0 24 | listing=TEST.out 25 | datain=1 26 | procspernode=1 27 | project=none 28 | RUNGAMESS_DIR=/aplic/gamess-uk/7.0_ompi/rungamess 29 | PROG=rungamess 30 | queueargs="" 31 | queue=iqtc02.q 32 | debug=0 33 | jobworkdir= 34 | export jobname 35 | export root 36 | export executable 37 | export jobmode 38 | export flist 39 | export nprocs 40 | export nnodes 41 | export jobtime 42 | export scratchtopdir 43 | export libdir 44 | export tempdir 45 | export homedir 46 | export stdout 47 | export listing 48 | export datain 49 | export procs_per_node 50 | export project 51 | export RUNGAMESS_DIR 52 | export PROG 53 | export queueargs 54 | export queue 55 | export debug 56 | export jobworkdir 57 | #if test -f /home/g4stefan/.profile 58 | #then 59 | #. /home/g4stefan/.profile 60 | #fi 61 | if test ${GAMESS_LIB:=unset} = unset 62 | then 63 | GAMESS_LIB=/aplic/gamess-uk/7.0_ompi/lib 64 | export GAMESS_LIB 65 | fi 66 | if test ${GAMESS_SCR:=unset} = unset 67 | then 68 | GAMESS_SCR=. 69 | export GAMESS_SCR 70 | fi 71 | if test ${GAMESS_WORK:=unset} = unset 72 | then 73 | GAMESS_WORK= 74 | export GAMESS_WORK 75 | fi 76 | if test ${GAMESS_TMP:=unset} = unset 77 | then 78 | GAMESS_TMP=/tmp 79 | export GAMESS_TMP 80 | fi 81 | if test ${GAMESS_PAREXE:=unset} = unset 82 | then 83 | GAMESS_PAREXE=/aplic/gamess-uk/7.0_ompi/bin/gamess-uk 84 | export GAMESS_PAREXE 85 | fi 86 | if test ${GAMESS_EXE:=unset} = unset 87 | then 88 | GAMESS_EXE=/aplic/gamess-uk/7.0_ompi/bin/gamess-uk 89 | export GAMESS_EXE 90 | fi 91 | $RUNGAMESS_DIR/rg_exe.$jobmode > /home/rporcel/subscripts/gamessuk/Si8O13/Si8O13.out 92 | -------------------------------------------------------------------------------- /GridEngine/gamess_uk-7.0-ompi-iqtc03.sub: -------------------------------------------------------------------------------- 1 | #!/bin/sh 2 | #$ -pe ompi 4 3 | #$ -cwd 4 | #$ -V 5 | #$ -o Si8O13.log 6 | #$ -S /bin/bash 7 | #$ -q iqtc03.q 8 | # 9 | source /opt/modules/init/bash 10 | module load gamessuk/7.0_ompi 11 | jobname=Si8O13 12 | root=Si8O13 13 | executable=/aplic/gamess-uk/7.0_ompi/bin/gamess-uk 14 | jobmode=openmpi 15 | flist="-k ftn058=Si8O13.pun -k ed3" 16 | nprocs=4 17 | nnodes=4 18 | jobtime=120 19 | scratchtopdir=. 20 | libdir=/aplic/gamess-uk/7.0_ompi/lib 21 | tempdir=/tmp 22 | homedir=/home/rporcel/subscripts/gamessuk/Si8O13 23 | stdout=0 24 | listing=TEST.out 25 | datain=1 26 | procspernode=1 27 | project=none 28 | RUNGAMESS_DIR=/aplic/gamess-uk/7.0_ompi/rungamess 29 | PROG=rungamess 30 | queueargs="" 31 | queue=iqtc03.q 32 | debug=0 33 | jobworkdir= 34 | export jobname 35 | export root 36 | export executable 37 | export jobmode 38 | export flist 39 | export nprocs 40 | export nnodes 41 | export jobtime 42 | export scratchtopdir 43 | export libdir 44 | export tempdir 45 | export homedir 46 | export stdout 47 | export listing 48 | export datain 49 | export procs_per_node 50 | export project 51 | export RUNGAMESS_DIR 52 | export PROG 53 | export queueargs 54 | export queue 55 | export debug 56 | export jobworkdir 57 | #if test -f /home/g4stefan/.profile 58 | #then 59 | #. /home/g4stefan/.profile 60 | #fi 61 | if test ${GAMESS_LIB:=unset} = unset 62 | then 63 | GAMESS_LIB=/aplic/gamess-uk/7.0_ompi/lib 64 | export GAMESS_LIB 65 | fi 66 | if test ${GAMESS_SCR:=unset} = unset 67 | then 68 | GAMESS_SCR=. 69 | export GAMESS_SCR 70 | fi 71 | if test ${GAMESS_WORK:=unset} = unset 72 | then 73 | GAMESS_WORK= 74 | export GAMESS_WORK 75 | fi 76 | if test ${GAMESS_TMP:=unset} = unset 77 | then 78 | GAMESS_TMP=/tmp 79 | export GAMESS_TMP 80 | fi 81 | if test ${GAMESS_PAREXE:=unset} = unset 82 | then 83 | GAMESS_PAREXE=/aplic/gamess-uk/7.0_ompi/bin/gamess-uk 84 | export GAMESS_PAREXE 85 | fi 86 | if test ${GAMESS_EXE:=unset} = unset 87 | then 88 | GAMESS_EXE=/aplic/gamess-uk/7.0_ompi/bin/gamess-uk 89 | export GAMESS_EXE 90 | fi 91 | $RUNGAMESS_DIR/rg_exe.$jobmode > /home/rporcel/subscripts/gamessuk/Si8O13/Si8O13.out 92 | -------------------------------------------------------------------------------- /GridEngine/gamess_uk-7.0-ompi-iqtc04.sub: -------------------------------------------------------------------------------- 1 | #!/bin/sh 2 | #$ -pe omp* 4 3 | #$ -cwd 4 | #$ -V 5 | #$ -o Si8O13.log 6 | #$ -S /bin/bash 7 | #$ -q iqtc04.q 8 | # 9 | source /opt/modules/init/bash 10 | module load gamess-uk/7.0_intel10.1_mkl10.1_ompi1.4.2 11 | jobname=Si8O13 12 | root=Si8O13 13 | executable=/aplic/gamess-uk/gamess-uk-7.0_intel10.1_mkl10.1_ompi1.4.2/bin/gamess-uk 14 | jobmode=openmpi 15 | flist="-k ftn058=Si8O13.pun -k ed3" 16 | nprocs=4 17 | nnodes=4 18 | jobtime=120 19 | scratchtopdir=. 20 | libdir=/aplic/gamess-uk/gamess-uk-7.0_intel10.1_mkl10.1_ompi1.4.2/lib 21 | tempdir=/tmp 22 | homedir=/home/rporcel/subscripts/gamessuk/Si8O13 23 | stdout=0 24 | listing=TEST.out 25 | datain=1 26 | procspernode=1 27 | project=none 28 | RUNGAMESS_DIR=/aplic/gamess-uk/gamess-uk-7.0_intel10.1_mkl10.1_ompi1.4.2/rungamess 29 | PROG=rungamess 30 | queueargs="" 31 | queue=iqtc04.q 32 | debug=0 33 | jobworkdir= 34 | export jobname 35 | export root 36 | export executable 37 | export jobmode 38 | export flist 39 | export nprocs 40 | export nnodes 41 | export jobtime 42 | export scratchtopdir 43 | export libdir 44 | export tempdir 45 | export homedir 46 | export stdout 47 | export listing 48 | export datain 49 | export procs_per_node 50 | export project 51 | export RUNGAMESS_DIR 52 | export PROG 53 | export queueargs 54 | export queue 55 | export debug 56 | export jobworkdir 57 | #if test -f /home/g4stefan/.profile 58 | #then 59 | #. /home/g4stefan/.profile 60 | #fi 61 | if test ${GAMESS_LIB:=unset} = unset 62 | then 63 | GAMESS_LIB=/aplic/gamess-uk/gamess-uk-7.0_intel10.1_mkl10.1_ompi1.4.2/lib 64 | export GAMESS_LIB 65 | fi 66 | if test ${GAMESS_SCR:=unset} = unset 67 | then 68 | GAMESS_SCR=. 69 | export GAMESS_SCR 70 | fi 71 | if test ${GAMESS_WORK:=unset} = unset 72 | then 73 | GAMESS_WORK= 74 | export GAMESS_WORK 75 | fi 76 | if test ${GAMESS_TMP:=unset} = unset 77 | then 78 | GAMESS_TMP=/tmp 79 | export GAMESS_TMP 80 | fi 81 | if test ${GAMESS_PAREXE:=unset} = unset 82 | then 83 | GAMESS_PAREXE=/aplic/gamess-uk/gamess-uk-7.0_intel10.1_mkl10.1_ompi1.4.2/bin/gamess-uk 84 | export GAMESS_PAREXE 85 | fi 86 | if test ${GAMESS_EXE:=unset} = unset 87 | then 88 | GAMESS_EXE=/aplic/gamess-uk/gamess-uk-7.0_intel10.1_mkl10.1_ompi1.4.2/bin/gamess-uk 89 | export GAMESS_EXE 90 | fi 91 | $RUNGAMESS_DIR/rg_exe.$jobmode > /home/rporcel/subscripts/gamessuk/Si8O13/Si8O13.out 92 | -------------------------------------------------------------------------------- /GridEngine/gamess_uk-7.0-smp-iqtc01.sub: -------------------------------------------------------------------------------- 1 | #!/bin/bash 2 | ########################################## 3 | # SGE options and parameters 4 | ########################################## 5 | # (1) Name of the job 6 | #$ -N gamess-uk 7 | # (2) Requested resources 8 | # Parallel Environment and number of cores 9 | #$ -pe smp 4 10 | # Queue 11 | #$ -q iqtc01.q 12 | # Shell 13 | #$ -S /bin/bash 14 | # (3) Output files 15 | #$ -cwd 16 | #$ -o Si8O13.out 17 | #$ -e Si8O13.err 18 | # (4) Remove the first '#' of the following 2 lines if you want to receive an email when the job ends. 19 | ##$ -m e 20 | ##$ -M yourmail@ub.edu 21 | ########################################## 22 | # User environment. 23 | ########################################## 24 | # Load the modules needed 25 | . /etc/profile.d/modules.sh 26 | module load gamess-uk/7.0_intel10.1_ompi1.3.3 27 | ########################################## 28 | # GAMESS-UK cruft 29 | ########################################## 30 | 31 | jobname=Si8O13 32 | root=Si8O13 33 | executable=/aplic/gamess-uk_ompi_intel/bin/gamess-uk 34 | jobmode=openmpi 35 | flist="-k ftn058=Si8O13.pun -k ed3" 36 | nprocs=$NSLOTS 37 | nnodes=$NSLOTS 38 | jobtime=120 39 | scratchtopdir=. 40 | libdir=/aplic/gamess-uk_ompi_intel/lib 41 | tempdir=/tmp 42 | homedir=/home/rporcel/subscripts/gamessuk/tst 43 | stdout=0 44 | listing=TEST.out 45 | datain=1 46 | procspernode=1 47 | project=none 48 | RUNGAMESS_DIR=/aplic/gamess-uk_ompi_intel/rungamess 49 | PROG=rungamess 50 | queueargs="" 51 | queue=iqtc01.q 52 | debug=0 53 | jobworkdir= 54 | export jobname 55 | export root 56 | export executable 57 | export jobmode 58 | export flist 59 | export nprocs 60 | export nnodes 61 | export jobtime 62 | export scratchtopdir 63 | export libdir 64 | export tempdir 65 | export homedir 66 | export stdout 67 | export listing 68 | export datain 69 | export procs_per_node 70 | export project 71 | export RUNGAMESS_DIR 72 | export PROG 73 | export queueargs 74 | export queue 75 | export debug 76 | export jobworkdir 77 | if test ${GAMESS_LIB:=unset} = unset 78 | then 79 | GAMESS_LIB=/aplic/gamess-uk_ompi_intel/lib 80 | export GAMESS_LIB 81 | fi 82 | if test ${GAMESS_SCR:=unset} = unset 83 | then 84 | GAMESS_SCR=. 85 | export GAMESS_SCR 86 | fi 87 | if test ${GAMESS_WORK:=unset} = unset 88 | then 89 | GAMESS_WORK= 90 | export GAMESS_WORK 91 | fi 92 | if test ${GAMESS_TMP:=unset} = unset 93 | then 94 | GAMESS_TMP=/tmp 95 | export GAMESS_TMP 96 | fi 97 | if test ${GAMESS_PAREXE:=unset} = unset 98 | then 99 | GAMESS_PAREXE=/aplic/gamess-uk_ompi_intel/bin/gamess-uk 100 | export GAMESS_PAREXE 101 | fi 102 | if test ${GAMESS_EXE:=unset} = unset 103 | then 104 | GAMESS_EXE=/aplic/gamess-uk_ompi_intel/bin/gamess-uk 105 | export GAMESS_EXE 106 | fi 107 | 108 | export GAMESS_SCR=$TMPDIR 109 | cp $homedir/$jobname.in $TMPDIR 110 | 111 | $RUNGAMESS_DIR/rg_exe.$jobmode > $homedir/$jobname.out 112 | 113 | -------------------------------------------------------------------------------- /GridEngine/gamess_uk-7.0-smp-iqtc02.sub: -------------------------------------------------------------------------------- 1 | #!/bin/bash 2 | ########################################## 3 | # SGE options and parameters 4 | ########################################## 5 | # (1) Name of the job 6 | #$ -N gamess-uk 7 | # (2) Requested resources 8 | # Parallel Environment and number of cores 9 | #$ -pe smp 8 10 | # Queue 11 | #$ -q iqtc02.q 12 | # Shell 13 | #$ -S /bin/bash 14 | # (3) Output files 15 | #$ -cwd 16 | #$ -o Si8O13.out 17 | #$ -e Si8O13.err 18 | # (4) Remove the first '#' of the following 2 lines if you want to receive an email when the job ends. 19 | ##$ -m e 20 | ##$ -M yourmail@ub.edu 21 | ########################################## 22 | # User environment. 23 | ########################################## 24 | # Load the modules needed 25 | . /etc/profile.d/modules.sh 26 | module load gamessuk/7.0_ompi 27 | ########################################## 28 | # GAMESS-UK cruft 29 | ########################################## 30 | 31 | jobname=Si8O13 32 | root=Si8O13 33 | executable=/aplic/gamess-uk/7.0_ompi/bin/gamess-uk 34 | jobmode=openmpi 35 | flist="-k ftn058=Si8O13.pun -k ed3" 36 | nprocs=$NSLOTS 37 | nnodes=$NSLOTS 38 | jobtime=120 39 | scratchtopdir=. 40 | libdir=/aplic/gamess-uk/7.0_ompi/lib 41 | tempdir=/tmp 42 | homedir=/home/rporcel/subscripts/gamessuk/tst 43 | stdout=0 44 | listing=TEST.out 45 | datain=1 46 | procspernode=1 47 | project=none 48 | RUNGAMESS_DIR=/aplic/gamess-uk/7.0_ompi/rungamess 49 | PROG=rungamess 50 | queueargs="" 51 | queue=iqtc02.q 52 | debug=0 53 | jobworkdir= 54 | export jobname 55 | export root 56 | export executable 57 | export jobmode 58 | export flist 59 | export nprocs 60 | export nnodes 61 | export jobtime 62 | export scratchtopdir 63 | export libdir 64 | export tempdir 65 | export homedir 66 | export stdout 67 | export listing 68 | export datain 69 | export procs_per_node 70 | export project 71 | export RUNGAMESS_DIR 72 | export PROG 73 | export queueargs 74 | export queue 75 | export debug 76 | export jobworkdir 77 | if test ${GAMESS_LIB:=unset} = unset 78 | then 79 | GAMESS_LIB=/aplic/gamess-uk/7.0_ompi/lib 80 | export GAMESS_LIB 81 | fi 82 | if test ${GAMESS_SCR:=unset} = unset 83 | then 84 | GAMESS_SCR=. 85 | export GAMESS_SCR 86 | fi 87 | if test ${GAMESS_WORK:=unset} = unset 88 | then 89 | GAMESS_WORK= 90 | export GAMESS_WORK 91 | fi 92 | if test ${GAMESS_TMP:=unset} = unset 93 | then 94 | GAMESS_TMP=/tmp 95 | export GAMESS_TMP 96 | fi 97 | if test ${GAMESS_PAREXE:=unset} = unset 98 | then 99 | GAMESS_PAREXE=/aplic/gamess-uk/7.0_ompi/bin/gamess-uk 100 | export GAMESS_PAREXE 101 | fi 102 | if test ${GAMESS_EXE:=unset} = unset 103 | then 104 | GAMESS_EXE=/aplic/gamess-uk/7.0_ompi/bin/gamess-uk 105 | export GAMESS_EXE 106 | fi 107 | 108 | export GAMESS_SCR=$TMPDIR 109 | cp $homedir/$jobname.in $TMPDIR 110 | 111 | $RUNGAMESS_DIR/rg_exe.$jobmode > $homedir/$jobname.out 112 | -------------------------------------------------------------------------------- /GridEngine/gamess_uk-7.0-smp-iqtc03.sub: -------------------------------------------------------------------------------- 1 | #!/bin/bash 2 | ########################################## 3 | # SGE options and parameters 4 | ########################################## 5 | # (1) Name of the job 6 | #$ -N gamess-uk 7 | # (2) Requested resources 8 | # Parallel Environment and number of cores 9 | #$ -pe smp 8 10 | # Queue 11 | #$ -q iqtc03.q 12 | # Shell 13 | #$ -S /bin/bash 14 | # (3) Output files 15 | #$ -cwd 16 | #$ -o Si8O13.out 17 | #$ -e Si8O13.err 18 | # (4) Remove the first '#' of the following 2 lines if you want to receive an email when the job ends. 19 | ##$ -m e 20 | ##$ -M yourmail@ub.edu 21 | ########################################## 22 | # User environment. 23 | ########################################## 24 | # Load the modules needed 25 | . /etc/profile.d/modules.sh 26 | module load gamessuk/7.0_ompi 27 | ########################################## 28 | # GAMESS-UK cruft 29 | ########################################## 30 | 31 | jobname=Si8O13 32 | root=Si8O13 33 | executable=/aplic/gamess-uk/7.0_ompi/bin/gamess-uk 34 | jobmode=openmpi 35 | flist="-k ftn058=Si8O13.pun -k ed3" 36 | nprocs=$NSLOTS 37 | nnodes=$NSLOTS 38 | jobtime=120 39 | scratchtopdir=. 40 | libdir=/aplic/gamess-uk/7.0_ompi/lib 41 | tempdir=/tmp 42 | homedir=/home/rporcel/subscripts/gamessuk/tst 43 | stdout=0 44 | listing=TEST.out 45 | datain=1 46 | procspernode=1 47 | project=none 48 | RUNGAMESS_DIR=/aplic/gamess-uk/7.0_ompi/rungamess 49 | PROG=rungamess 50 | queueargs="" 51 | queue=iqtc03.q 52 | debug=0 53 | jobworkdir= 54 | export jobname 55 | export root 56 | export executable 57 | export jobmode 58 | export flist 59 | export nprocs 60 | export nnodes 61 | export jobtime 62 | export scratchtopdir 63 | export libdir 64 | export tempdir 65 | export homedir 66 | export stdout 67 | export listing 68 | export datain 69 | export procs_per_node 70 | export project 71 | export RUNGAMESS_DIR 72 | export PROG 73 | export queueargs 74 | export queue 75 | export debug 76 | export jobworkdir 77 | if test ${GAMESS_LIB:=unset} = unset 78 | then 79 | GAMESS_LIB=/aplic/gamess-uk/7.0_ompi/lib 80 | export GAMESS_LIB 81 | fi 82 | if test ${GAMESS_SCR:=unset} = unset 83 | then 84 | GAMESS_SCR=. 85 | export GAMESS_SCR 86 | fi 87 | if test ${GAMESS_WORK:=unset} = unset 88 | then 89 | GAMESS_WORK= 90 | export GAMESS_WORK 91 | fi 92 | if test ${GAMESS_TMP:=unset} = unset 93 | then 94 | GAMESS_TMP=/tmp 95 | export GAMESS_TMP 96 | fi 97 | if test ${GAMESS_PAREXE:=unset} = unset 98 | then 99 | GAMESS_PAREXE=/aplic/gamess-uk/7.0_ompi/bin/gamess-uk 100 | export GAMESS_PAREXE 101 | fi 102 | if test ${GAMESS_EXE:=unset} = unset 103 | then 104 | GAMESS_EXE=/aplic/gamess-uk/7.0_ompi/bin/gamess-uk 105 | export GAMESS_EXE 106 | fi 107 | 108 | export GAMESS_SCR=$TMPDIR 109 | cp $homedir/$jobname.in $TMPDIR 110 | 111 | $RUNGAMESS_DIR/rg_exe.$jobmode > $homedir/$jobname.out 112 | 113 | -------------------------------------------------------------------------------- /GridEngine/gamess_uk-7.0-smp-iqtc04.sub: -------------------------------------------------------------------------------- 1 | #!/bin/bash 2 | ########################################## 3 | # SGE options and parameters 4 | ########################################## 5 | # (1) Name of the job 6 | #$ -N gamess-uk 7 | # (2) Requested resources 8 | # Parallel Environment and number of cores 9 | #$ -pe smp 12 10 | # Queue 11 | #$ -q iqtc04.q 12 | # Shell 13 | #$ -S /bin/bash 14 | # (3) Output files 15 | #$ -cwd 16 | #$ -o Si8O13.out 17 | #$ -e Si8O13.err 18 | # (4) Remove the first '#' of the following 2 lines if you want to receive an email when the job ends. 19 | ##$ -m e 20 | ##$ -M yourmail@ub.edu 21 | ########################################## 22 | # User environment. 23 | ########################################## 24 | # Load the modules needed 25 | . /etc/profile.d/modules.sh 26 | module load gamess-uk/7.0_intel10.1_mkl10.1_ompi1.4.2 27 | ########################################## 28 | # GAMESS-UK cruft 29 | ########################################## 30 | 31 | jobname=Si8O13 32 | root=Si8O13 33 | executable=/aplic/gamess-uk/gamess-uk-7.0_intel10.1_mkl10.1_ompi1.4.2/bin/gamess-uk 34 | jobmode=openmpi 35 | flist="-k ftn058=Si8O13.pun -k ed3" 36 | nprocs=$NSLOTS 37 | nnodes=$NSLOTS 38 | jobtime=120 39 | scratchtopdir=. 40 | libdir=/aplic/gamess-uk/gamess-uk-7.0_intel10.1_mkl10.1_ompi1.4.2/lib 41 | tempdir=/tmp 42 | homedir=/home/rporcel/subscripts/gamessuk/tst 43 | stdout=0 44 | listing=TEST.out 45 | datain=1 46 | procspernode=1 47 | project=none 48 | RUNGAMESS_DIR=/aplic/gamess-uk/gamess-uk-7.0_intel10.1_mkl10.1_ompi1.4.2/rungamess 49 | PROG=rungamess 50 | queueargs="" 51 | queue=iqtc04.q 52 | debug=0 53 | jobworkdir= 54 | export jobname 55 | export root 56 | export executable 57 | export jobmode 58 | export flist 59 | export nprocs 60 | export nnodes 61 | export jobtime 62 | export scratchtopdir 63 | export libdir 64 | export tempdir 65 | export homedir 66 | export stdout 67 | export listing 68 | export datain 69 | export procs_per_node 70 | export project 71 | export RUNGAMESS_DIR 72 | export PROG 73 | export queueargs 74 | export queue 75 | export debug 76 | export jobworkdir 77 | if test ${GAMESS_LIB:=unset} = unset 78 | then 79 | GAMESS_LIB=/aplic/gamess-uk/gamess-uk-7.0_intel10.1_mkl10.1_ompi1.4.2/lib 80 | export GAMESS_LIB 81 | fi 82 | if test ${GAMESS_SCR:=unset} = unset 83 | then 84 | GAMESS_SCR=. 85 | export GAMESS_SCR 86 | fi 87 | if test ${GAMESS_WORK:=unset} = unset 88 | then 89 | GAMESS_WORK= 90 | export GAMESS_WORK 91 | fi 92 | if test ${GAMESS_TMP:=unset} = unset 93 | then 94 | GAMESS_TMP=/tmp 95 | export GAMESS_TMP 96 | fi 97 | if test ${GAMESS_PAREXE:=unset} = unset 98 | then 99 | GAMESS_PAREXE=/aplic/gamess-uk/gamess-uk-7.0_intel10.1_mkl10.1_ompi1.4.2/bin/gamess-uk 100 | export GAMESS_PAREXE 101 | fi 102 | if test ${GAMESS_EXE:=unset} = unset 103 | then 104 | GAMESS_EXE=/aplic/gamess-uk/gamess-uk-7.0_intel10.1_mkl10.1_ompi1.4.2/bin/gamess-uk 105 | export GAMESS_EXE 106 | fi 107 | 108 | export GAMESS_SCR=$TMPDIR 109 | cp $homedir/$jobname.in $TMPDIR 110 | 111 | $RUNGAMESS_DIR/rg_exe.$jobmode > $homedir/$jobname.out 112 | 113 | -------------------------------------------------------------------------------- /GridEngine/gaussian-03-linda-iqtc01.sub: -------------------------------------------------------------------------------- 1 | #!/bin/csh 2 | ########################################## 3 | # SGE options and parameters 4 | ########################################## 5 | # (1) Name of the job 6 | #$ -N test_gaus 7 | # (2) Requested resources 8 | # Parallel Environment and number of cores 9 | #$ -pe linda 8 10 | # Queue 11 | #$ -q iqtc01.q 12 | # Shell 13 | #$ -S /bin/bash 14 | # (3) Output files 15 | #$ -cwd 16 | #$ -o testl_gaus.out 17 | #$ -e testl_gaus.err 18 | # (4) Remove the first '#' of the following 2 lines if you want to receive an email when the job ends. 19 | ##$ -m e 20 | ##$ -M yourmail@ub.edu 21 | ########################################## 22 | # User environment. 23 | ########################################## 24 | # Load the modules needed 25 | module load gaussian/g03d02 26 | ########################################## 27 | # Copying files needed 28 | ########################################## 29 | # We copy the inputs to the directory where the jobs will run 30 | cd $TMPDIR 31 | cp -r $HOME/proves/h2o_opt.dat . 32 | 33 | # Es carreguen algunes variables pel Linda 34 | 35 | setenv GAUSS_SCRDIR $TMPDIR 36 | setenv NODES \"`cat $TMPDIR/tsnet.nodes`\" 37 | setenv GAUSS_LFLAGS "-v -nodelist ${NODES} -mp 4" 38 | 39 | ########################################## 40 | # Run the job 41 | ########################################## 42 | # We run gaussian g03l 43 | g03l < ./h2o_opt.dat > h2ol_opt.log 44 | ########################################## 45 | # Copy the results to our home directory 46 | ########################################## 47 | mkdir $HOME/proves/resultatl 48 | cp -r . $HOME/proves/resultatl/ 49 | 50 | -------------------------------------------------------------------------------- /GridEngine/gaussian-03-smp-iqtc01.sub: -------------------------------------------------------------------------------- 1 | #!/bin/csh 2 | ########################################## 3 | # SGE options and parameters 4 | ########################################## 5 | # (1) Name of the job 6 | #$ -N test_gaus 7 | # (2) Requested resources 8 | # Parallel Environment and number of cores 9 | #$ -pe smp 4 10 | # Queue 11 | #$ -q iqtc01.q 12 | # Shell 13 | #$ -S /bin/csh 14 | # (3) Output files 15 | #$ -cwd 16 | #$ -o testl_gaus.out 17 | #$ -e testl_gaus.err 18 | # (4) Remove the first '#' of the following 2 lines if you want to receive an email when the job ends. 19 | ##$ -m e 20 | ##$ -M yourmail@ub.edu 21 | ########################################## 22 | # User environment. 23 | ########################################## 24 | # Load the modules needed 25 | module load gaussian/g03d02 26 | ########################################## 27 | # Copying files needed 28 | ########################################## 29 | # We copy the inputs to the directory where the jobs will run 30 | cd $TMPDIR 31 | cp -r $HOME/proves/h2o_opt.dat . 32 | 33 | # Set some variables for gaussian 34 | 35 | setenv GAUSS_SCRDIR $TMPDIR 36 | 37 | ########################################## 38 | # Run the job 39 | ########################################## 40 | # We run gaussian g03 41 | g03 < ./h2o_opt.dat > h2ol_opt.log 42 | ########################################## 43 | # Copy the results to our home directory 44 | ########################################## 45 | mkdir $HOME/proves/resultatl 46 | cp -r . $HOME/proves/resultatl/ 47 | 48 | -------------------------------------------------------------------------------- /GridEngine/gaussian-03-smp-iqtc02.sub: -------------------------------------------------------------------------------- 1 | #!/bin/csh 2 | ########################################## 3 | # SGE options and parameters 4 | ########################################## 5 | # (1) Name of the job 6 | #$ -N test_gaus 7 | # (2) Requested resources 8 | # Parallel Environment and number of cores 9 | #$ -pe smp 8 10 | # Queue 11 | #$ -q iqtc02.q 12 | # Shell 13 | #$ -S /bin/csh 14 | # (3) Output files 15 | #$ -cwd 16 | #$ -o testl_gaus.out 17 | #$ -e testl_gaus.err 18 | # (4) Remove the first '#' of the following 2 lines if you want to receive an email when the job ends. 19 | ##$ -m e 20 | ##$ -M yourmail@ub.edu 21 | ########################################## 22 | # User environment. 23 | ########################################## 24 | # Load the modules needed 25 | module load gaussian/g03d02 26 | ########################################## 27 | # Copying files needed 28 | ########################################## 29 | # We copy the inputs to the directory where the jobs will run 30 | cd $TMPDIR 31 | cp -r $HOME/proves/h2o_opt.dat . 32 | 33 | # Set some variables for gaussian 34 | 35 | setenv GAUSS_SCRDIR $TMPDIR 36 | 37 | ########################################## 38 | # Run the job 39 | ########################################## 40 | # We run gaussian g03 41 | g03 < ./h2o_opt.dat > h2ol_opt.log 42 | ########################################## 43 | # Copy the results to our home directory 44 | ########################################## 45 | mkdir $HOME/proves/resultatl 46 | cp -r . $HOME/proves/resultatl/ 47 | 48 | -------------------------------------------------------------------------------- /GridEngine/gaussian-03-smp-iqtc03.sub: -------------------------------------------------------------------------------- 1 | #!/bin/csh 2 | ########################################## 3 | # SGE options and parameters 4 | ########################################## 5 | # (1) Name of the job 6 | #$ -N test_gaus 7 | # (2) Requested resources 8 | # Parallel Environment and number of cores 9 | #$ -pe smp 8 10 | # Queue 11 | #$ -q iqtc03.q 12 | # Shell 13 | #$ -S /bin/csh 14 | # (3) Output files 15 | #$ -cwd 16 | #$ -o testl_gaus.out 17 | #$ -e testl_gaus.err 18 | # (4) Remove the first '#' of the following 2 lines if you want to receive an email when the job ends. 19 | ##$ -m e 20 | ##$ -M yourmail@ub.edu 21 | ########################################## 22 | # User environment. 23 | ########################################## 24 | # Load the modules needed 25 | module load gaussian/g03d02 26 | ########################################## 27 | # Copying files needed 28 | ########################################## 29 | # We copy the inputs to the directory where the jobs will run 30 | cd $TMPDIR 31 | cp -r $HOME/proves/h2o_opt.dat . 32 | 33 | # Set some variables for gaussian 34 | 35 | setenv GAUSS_SCRDIR $TMPDIR 36 | 37 | ########################################## 38 | # Run the job 39 | ########################################## 40 | # We run gaussian g03 41 | g03 < ./h2o_opt.dat > h2ol_opt.log 42 | ########################################## 43 | # Copy the results to our home directory 44 | ########################################## 45 | mkdir $HOME/proves/resultatl 46 | cp -r . $HOME/proves/resultatl/ 47 | 48 | -------------------------------------------------------------------------------- /GridEngine/gaussian-03-smp-iqtc04.sub: -------------------------------------------------------------------------------- 1 | #!/bin/csh 2 | ########################################## 3 | # SGE options and parameters 4 | ########################################## 5 | # (1) Name of the job 6 | #$ -N test_gaus 7 | # (2) Requested resources 8 | # Parallel Environment and number of cores 9 | #$ -pe smp 12 10 | # Queue 11 | #$ -q iqtc04.q 12 | # Shell 13 | #$ -S /bin/csh 14 | # (3) Output files 15 | #$ -cwd 16 | #$ -o testl_gaus.out 17 | #$ -e testl_gaus.err 18 | # (4) Remove the first '#' of the following 2 lines if you want to receive an email when the job ends. 19 | ##$ -m e 20 | ##$ -M yourmail@ub.edu 21 | ########################################## 22 | # User environment. 23 | ########################################## 24 | # Load the modules needed 25 | . /etc/profile.d/modules.sh 26 | module load gaussian/g03d02 27 | ########################################## 28 | # Copying files needed 29 | ########################################## 30 | # We copy the inputs to the directory where the jobs will run 31 | cd $TMPDIR 32 | cp -r $HOME/proves/h2o_opt.dat . 33 | 34 | # Set some variables for gaussian 35 | 36 | setenv GAUSS_SCRDIR $TMPDIR 37 | 38 | ########################################## 39 | # Run the job 40 | ########################################## 41 | # We run gaussian g03 42 | g03 < ./h2o_opt.dat > h2ol_opt.log 43 | ########################################## 44 | # Copy the results to our home directory 45 | ########################################## 46 | mkdir $HOME/proves/resultatl 47 | cp -r . $HOME/proves/resultatl/ 48 | 49 | -------------------------------------------------------------------------------- /GridEngine/gaussian-09-linda-iqtc01.sub: -------------------------------------------------------------------------------- 1 | #!/bin/csh 2 | ########################################## 3 | # SGE options and parameters 4 | ########################################## 5 | # (1) Name of the job 6 | #$ -N test_gaus 7 | # (2) Requested resources 8 | # Parallel Environment and number of cores 9 | #$ -pe linda 8 10 | # Queue 11 | #$ -q iqtc04.q 12 | # Shell 13 | #$ -S /bin/csh 14 | # (3) Output files 15 | #$ -cwd 16 | #$ -o testl_gaus.out 17 | #$ -e testl_gaus.err 18 | # (4) Remove the first '#' of the following 2 lines if you want to receive an email when the job ends. 19 | ##$ -m e 20 | ##$ -M yourmail@ub.edu 21 | ########################################## 22 | # User environment. 23 | ########################################## 24 | # Load the modules needed 25 | module load gaussian/g09b01 26 | ########################################## 27 | # Copying files needed 28 | ########################################## 29 | # We copy the inputs to the directory where the jobs will run 30 | cd $TMPDIR 31 | cp -r $HOME/proves/h2o_opt.dat . 32 | 33 | # Es carreguen algunes variables pel Linda 34 | 35 | setenv GAUSS_SCRDIR $TMPDIR 36 | setenv NODES \"`cat $TMPDIR/tsnet.nodes`\" 37 | setenv GAUSS_LFLAGS "-v -nodelist ${NODES} -mp 4" 38 | 39 | ########################################## 40 | # Run the job 41 | ########################################## 42 | # We run gaussian g09 43 | g09 < ./h2o_opt.dat > h2ol_opt.log 44 | ########################################## 45 | # Copy the results to our home directory 46 | ########################################## 47 | mkdir $HOME/proves/resultatl 48 | cp -r . $HOME/proves/resultatl/ 49 | 50 | -------------------------------------------------------------------------------- /GridEngine/gaussian-09-linda-iqtc02.sub: -------------------------------------------------------------------------------- 1 | #!/bin/csh 2 | ########################################## 3 | # SGE options and parameters 4 | ########################################## 5 | # (1) Name of the job 6 | #$ -N test_gaus 7 | # (2) Requested resources 8 | # Parallel Environment and number of cores 9 | #$ -pe linda 16 10 | # Queue 11 | #$ -q iqtc04.q 12 | # Shell 13 | #$ -S /bin/csh 14 | # (3) Output files 15 | #$ -cwd 16 | #$ -o testl_gaus.out 17 | #$ -e testl_gaus.err 18 | # (4) Remove the first '#' of the following 2 lines if you want to receive an email when the job ends. 19 | ##$ -m e 20 | ##$ -M yourmail@ub.edu 21 | ########################################## 22 | # User environment. 23 | ########################################## 24 | # Load the modules needed 25 | module load gaussian/g09b01 26 | ########################################## 27 | # Copying files needed 28 | ########################################## 29 | # We copy the inputs to the directory where the jobs will run 30 | cd $TMPDIR 31 | cp -r $HOME/proves/h2o_opt.dat . 32 | 33 | # Es carreguen algunes variables pel Linda 34 | 35 | setenv GAUSS_SCRDIR $TMPDIR 36 | setenv NODES \"`cat $TMPDIR/tsnet.nodes`\" 37 | setenv GAUSS_LFLAGS "-v -nodelist ${NODES} -mp 8" 38 | 39 | ########################################## 40 | # Run the job 41 | ########################################## 42 | # We run gaussian g09 43 | g09 < ./h2o_opt.dat > h2ol_opt.log 44 | ########################################## 45 | # Copy the results to our home directory 46 | ########################################## 47 | mkdir $HOME/proves/resultatl 48 | cp -r . $HOME/proves/resultatl/ 49 | 50 | -------------------------------------------------------------------------------- /GridEngine/gaussian-09-linda-iqtc03.sub: -------------------------------------------------------------------------------- 1 | #!/bin/csh 2 | ########################################## 3 | # SGE options and parameters 4 | ########################################## 5 | # (1) Name of the job 6 | #$ -N test_gaus 7 | # (2) Requested resources 8 | # Parallel Environment and number of cores 9 | #$ -pe linda 16 10 | # Queue 11 | #$ -q iqtc04.q 12 | # Shell 13 | #$ -S /bin/bash 14 | # (3) Output files 15 | #$ -cwd 16 | #$ -o testl_gaus.out 17 | #$ -e testl_gaus.err 18 | # (4) Remove the first '#' of the following 2 lines if you want to receive an email when the job ends. 19 | ##$ -m e 20 | ##$ -M yourmail@ub.edu 21 | ########################################## 22 | # User environment. 23 | ########################################## 24 | # Load the modules needed 25 | module load gaussian/g09b01 26 | ########################################## 27 | # Copying files needed 28 | ########################################## 29 | # We copy the inputs to the directory where the jobs will run 30 | cd $TMPDIR 31 | cp -r $HOME/proves/h2o_opt.dat . 32 | 33 | # Es carreguen algunes variables pel Linda 34 | 35 | setenv GAUSS_SCRDIR $TMPDIR 36 | setenv NODES \"`cat $TMPDIR/tsnet.nodes`\" 37 | setenv GAUSS_LFLAGS "-v -nodelist ${NODES} -mp 8" 38 | 39 | ########################################## 40 | # Run the job 41 | ########################################## 42 | # We run gaussian g09 43 | g09 < ./h2o_opt.dat > h2ol_opt.log 44 | ########################################## 45 | # Copy the results to our home directory 46 | ########################################## 47 | mkdir $HOME/proves/resultatl 48 | cp -r . $HOME/proves/resultatl/ 49 | 50 | -------------------------------------------------------------------------------- /GridEngine/gaussian-09-linda-iqtc04.sub: -------------------------------------------------------------------------------- 1 | #!/bin/csh 2 | ########################################## 3 | # SGE options and parameters 4 | ########################################## 5 | # (1) Name of the job 6 | #$ -N test_gaus 7 | # (2) Requested resources 8 | # Parallel Environment and number of cores 9 | #$ -pe linda 24 10 | # Queue 11 | #$ -q iqtc04.q 12 | # Shell 13 | #$ -S /bin/csh 14 | # (3) Output files 15 | #$ -cwd 16 | #$ -o testl_gaus.out 17 | #$ -e testl_gaus.err 18 | # (4) Remove the first '#' of the following 2 lines if you want to receive an email when the job ends. 19 | ##$ -m e 20 | ##$ -M yourmail@ub.edu 21 | ########################################## 22 | # User environment. 23 | ########################################## 24 | # Load the modules needed 25 | . /etc/profile.d/modules.csh 26 | module load gaussian/g09b01 27 | ########################################## 28 | # Copying files needed 29 | ########################################## 30 | # We copy the inputs to the directory where the jobs will run 31 | cd $TMPDIR 32 | cp -r $HOME/proves/h2o_opt.dat . 33 | 34 | # Es carreguen algunes variables pel Linda 35 | 36 | setenv GAUSS_SCRDIR $TMPDIR 37 | setenv NODES \"`cat $TMPDIR/tsnet.nodes | uniq`\" 38 | setenv GAUSS_LFLAGS "-v -nodelist ${NODES} -mp 12" 39 | 40 | ########################################## 41 | # Run the job 42 | ########################################## 43 | # We run gaussian g09 44 | g09 < ./h2o_opt.dat > h2ol_opt.log 45 | ########################################## 46 | # Copy the results to our home directory 47 | ########################################## 48 | mkdir $HOME/proves/resultatl 49 | cp -r . $HOME/proves/resultatl/ 50 | 51 | -------------------------------------------------------------------------------- /GridEngine/gaussian-09-smp-iqtc01.sub: -------------------------------------------------------------------------------- 1 | #!/bin/csh 2 | ########################################## 3 | # SGE options and parameters 4 | ########################################## 5 | # (1) Name of the job 6 | #$ -N test_gaus 7 | # (2) Requested resources 8 | # Parallel Environment and number of cores 9 | #$ -pe smp 4 10 | # Queue 11 | #$ -q iqtc01.q 12 | # Shell 13 | #$ -S /bin/bash 14 | # (3) Output files 15 | #$ -cwd 16 | #$ -o testl_gaus.out 17 | #$ -e testl_gaus.err 18 | # (4) Remove the first '#' of the following 2 lines if you want to receive an email when the job ends. 19 | ##$ -m e 20 | ##$ -M yourmail@ub.edu 21 | ########################################## 22 | # User environment. 23 | ########################################## 24 | # Load the modules needed 25 | module load gaussian/g09b01 26 | ########################################## 27 | # Copying files needed 28 | ########################################## 29 | # We copy the inputs to the directory where the jobs will run 30 | cd $TMPDIR 31 | cp -r $HOME/proves/h2o_opt.dat . 32 | 33 | # Set some variables for gaussian 34 | 35 | setenv GAUSS_SCRDIR $TMPDIR 36 | 37 | ########################################## 38 | # Run the job 39 | ########################################## 40 | # We run gaussian g09 41 | g09 < ./h2o_opt.dat > h2ol_opt.log 42 | ########################################## 43 | # Copy the results to our home directory 44 | ########################################## 45 | mkdir $HOME/proves/resultatl 46 | cp -r . $HOME/proves/resultatl/ 47 | 48 | -------------------------------------------------------------------------------- /GridEngine/gaussian-09-smp-iqtc02.sub: -------------------------------------------------------------------------------- 1 | #!/bin/csh 2 | ########################################## 3 | # SGE options and parameters 4 | ########################################## 5 | # (1) Name of the job 6 | #$ -N test_gaus 7 | # (2) Requested resources 8 | # Parallel Environment and number of cores 9 | #$ -pe smp 8 10 | # Queue 11 | #$ -q iqtc02.q 12 | # Shell 13 | #$ -S /bin/csh 14 | # (3) Output files 15 | #$ -cwd 16 | #$ -o testl_gaus.out 17 | #$ -e testl_gaus.err 18 | # (4) Remove the first '#' of the following 2 lines if you want to receive an email when the job ends. 19 | ##$ -m e 20 | ##$ -M yourmail@ub.edu 21 | ########################################## 22 | # User environment. 23 | ########################################## 24 | # Load the modules needed 25 | module load gaussian/g09b01 26 | ########################################## 27 | # Copying files needed 28 | ########################################## 29 | # We copy the inputs to the directory where the jobs will run 30 | cd $TMPDIR 31 | cp -r $HOME/proves/h2o_opt.dat . 32 | 33 | # Set some variables for gaussian 34 | 35 | setenv GAUSS_SCRDIR $TMPDIR 36 | 37 | ########################################## 38 | # Run the job 39 | ########################################## 40 | # We run gaussian g09 41 | g09 < ./h2o_opt.dat > h2ol_opt.log 42 | ########################################## 43 | # Copy the results to our home directory 44 | ########################################## 45 | mkdir $HOME/proves/resultatl 46 | cp -r . $HOME/proves/resultatl/ 47 | 48 | -------------------------------------------------------------------------------- /GridEngine/gaussian-09-smp-iqtc03.sub: -------------------------------------------------------------------------------- 1 | #!/bin/csh 2 | ########################################## 3 | # SGE options and parameters 4 | ########################################## 5 | # (1) Name of the job 6 | #$ -N test_gaus 7 | # (2) Requested resources 8 | # Parallel Environment and number of cores 9 | #$ -pe smp 8 10 | # Queue 11 | #$ -q iqtc03.q 12 | # Shell 13 | #$ -S /bin/csh 14 | # (3) Output files 15 | #$ -cwd 16 | #$ -o testl_gaus.out 17 | #$ -e testl_gaus.err 18 | # (4) Remove the first '#' of the following 2 lines if you want to receive an email when the job ends. 19 | ##$ -m e 20 | ##$ -M yourmail@ub.edu 21 | ########################################## 22 | # User environment. 23 | ########################################## 24 | # Load the modules needed 25 | module load gaussian/g09b01 26 | ########################################## 27 | # Copying files needed 28 | ########################################## 29 | # We copy the inputs to the directory where the jobs will run 30 | cd $TMPDIR 31 | cp -r $HOME/proves/h2o_opt.dat . 32 | 33 | # Set some variables for gaussian 34 | 35 | setenv GAUSS_SCRDIR $TMPDIR 36 | 37 | ########################################## 38 | # Run the job 39 | ########################################## 40 | # We run gaussian g09 41 | g09 < ./h2o_opt.dat > h2ol_opt.log 42 | ########################################## 43 | # Copy the results to our home directory 44 | ########################################## 45 | mkdir $HOME/proves/resultatl 46 | cp -r . $HOME/proves/resultatl/ 47 | 48 | -------------------------------------------------------------------------------- /GridEngine/gaussian-09-smp-iqtc04.sub: -------------------------------------------------------------------------------- 1 | #!/bin/csh 2 | ########################################## 3 | # SGE options and parameters 4 | ########################################## 5 | # (1) Name of the job 6 | #$ -N test_gaus 7 | # (2) Requested resources 8 | # Parallel Environment and number of cores 9 | #$ -pe smp 12 10 | # Queue 11 | #$ -q iqtc04.q 12 | # Shell 13 | #$ -S /bin/csh 14 | # (3) Output files 15 | #$ -cwd 16 | #$ -o testl_gaus.out 17 | #$ -e testl_gaus.err 18 | # (4) Remove the first '#' of the following 2 lines if you want to receive an email when the job ends. 19 | ##$ -m e 20 | ##$ -M yourmail@ub.edu 21 | ########################################## 22 | # User environment. 23 | ########################################## 24 | # Load the modules needed 25 | . /etc/profile.d/modules.csh 26 | module load gaussian/g09b01 27 | ########################################## 28 | # Copying files needed 29 | ########################################## 30 | # We copy the inputs to the directory where the jobs will run 31 | cd $TMPDIR 32 | cp -r $HOME/proves/h2o_opt.dat . 33 | 34 | # Set some variables for gaussian 35 | 36 | setenv GAUSS_SCRDIR $TMPDIR 37 | 38 | ########################################## 39 | # Run the job 40 | ########################################## 41 | # We run gaussian g09 42 | g09 < ./h2o_opt.dat > h2ol_opt.log 43 | ########################################## 44 | # Copy the results to our home directory 45 | ########################################## 46 | mkdir $HOME/proves/resultatl 47 | cp -r . $HOME/proves/resultatl/ 48 | 49 | -------------------------------------------------------------------------------- /GridEngine/gaussian-linda.sub: -------------------------------------------------------------------------------- 1 | 2 | #!/bin/bash 3 | ########################################## 4 | # Opcions i parametres de l'SGE 5 | ########################################## 6 | # (1) Nom del treball (per identificar) 7 | #$ -N gaussian-linda-prova01 8 | # (2) Recursos sol.licitats 9 | #$ -l h_rt=0:50:0 10 | #$ -l h_vmem=8G 11 | #$ -pe linda 4 12 | # (3) Fitxers de sortida 13 | #$ -cwd 14 | #$ -o gaussian-linda.out 15 | #$ -e gaussian-linda.err 16 | #$ (4) Envia un mail quan acava el treball. 17 | #$ -m e 18 | #$ -M jblasco@fbg.ub.es 19 | ########################################## 20 | # Entorn d.usuari 21 | ########################################## 22 | # Es carreguen els moduls a utilitzar 23 | . /etc/profile 24 | module load gaussian 25 | ########################################## 26 | # transferencia de dades 27 | ########################################## 28 | # Es copien les dades al directori on es llenc,aran els calculs. 29 | cd $TMPDIR 30 | export Project=gaussian-linda 31 | export Input=$Project 32 | cp -pr $HOME/path/amb/els/input.com $Input 33 | # Es carreguen algunes variables pel Linda 34 | export GAUSS_SCRDIR=$TMPDIR 35 | export NODES=\"`cat $TMPDIR/machines`\" 36 | export GAUSS_LFLAGS="-v -nodelist ${NODES}" 37 | ########################################## 38 | # calcul 39 | ########################################## 40 | # executem el gaussian g03 41 | g03l g03lindatest.com > g03lindatest.log 42 | ########################################## 43 | # Transferencia dels resultats 44 | ########################################## 45 | cp -pr $Input $HOME/path/a/on/guardar/els/outputs/ 46 | 47 | 48 | Cal incloure 3 paràmetres: 49 | * '''nproc''' : número de processadors a utilitzar dins de cada node 50 | * '''NProcLinda''' : número de nodes a utilitzar 51 | * '''mem''' : quantitat de memòria necessaria per realitzar el càlcul 52 | 53 | El input de Gaussian per enviar-ho amb el PE de linda te la forma: 54 | 55 | %nproc=2 56 | %NProcLinda=4 57 | %mem=400MB 58 | %chk=t_cp 59 | #p b3lyp/cc-pvtz counterpoise=3 opt=z-matrix optcyc=999 60 | 61 | t 62 | 63 | 0 1 64 | O 1 65 | O 1 oo 2 66 | O 2 oo 1 60.0 3 67 | H 1 oh 3 hoo 2 0.0 0 1 68 | H 2 oh 1 hoo 3 0.0 0 2 69 | H 3 oh 2 hoo 1 0.0 0 3 70 | H 1 ho 2 oho 3 d1 0 1 71 | H 2 ho 3 oho 1 d2 0 2 72 | H 3 ho 1 oho 2 d2 0 3 73 | 74 | oo 2.7873 75 | oh 0.9771 76 | hoo 78.2005 77 | ho 0.9609 78 | oho 113.8022 79 | d1 112.335 80 | d2 -113.7495 81 | 82 | -------------------------------------------------------------------------------- /GridEngine/gaussian-serial.sub: -------------------------------------------------------------------------------- 1 | #!/bin/bash 2 | ########################################## 3 | # Opcions i parametres de l'SGE 4 | ########################################## 5 | # (1) Nom del treball (per identificar) 6 | #$ -N gaussian-serial-prova01 7 | # (2) Recursos sol.licitats 8 | #$ -l h_rt=0:50:0 9 | #$ -l h_vmem=6G 10 | # (3) Fitxers de sortida 11 | #$ -cwd 12 | #$ -o gaussian-serial.out 13 | #$ -e gaussian-serial.err 14 | #$ (4) Envia un mail quan acava el treball. 15 | #$ -m e 16 | #$ -M jblasco@fbg.ub.es 17 | ########################################## 18 | # Entorn d.usuari 19 | ########################################## 20 | # Es carreguen els moduls a utilitzar 21 | module load gaussian 22 | ########################################## 23 | # transferencia de dades 24 | ########################################## 25 | # Es copien les dades al directori on es llenc,aran els calculs. 26 | cd $TMPDIR 27 | export Project=gaussian-serial 28 | export Input=$Project 29 | cp -pr $HOME/path/amb/els/input.com $Input 30 | ########################################## 31 | # calcul 32 | ########################################## 33 | # executem el gaussian g03 34 | g03 < ./test001.com > test001.log 35 | ########################################## 36 | # Transferencia dels resultats 37 | ########################################## 38 | cp -pr $Input $HOME/path/a/on/guardar/els/outputs/ 39 | -------------------------------------------------------------------------------- /GridEngine/gaussian-smp.sub: -------------------------------------------------------------------------------- 1 | #!/bin/bash 2 | ########################################## 3 | # Opcions i parametres de l'SGE 4 | ########################################## 5 | # (1) Nom del treball (per identificar) 6 | #$ -N gaussian-smp-prova01 7 | # (2) Recursos sol.licitats 8 | #$ -l h_rt=0:50:0 9 | #$ -l h_vmem=8G 10 | #$ -pe smp 4 11 | # (3) Fitxers de sortida 12 | #$ -cwd 13 | #$ -o gaussian-smp.out 14 | #$ -e gaussian-smp.err 15 | #$ (4) Envia un mail quan acava el treball. 16 | #$ -m e 17 | #$ -M jblasco@fbg.ub.es 18 | ########################################## 19 | # Entorn d.usuari 20 | ########################################## 21 | # Es carreguen els moduls a utilitzar 22 | module load gaussian 23 | ########################################## 24 | # transferencia de dades 25 | ########################################## 26 | # Es copien les dades al directori on es llenc,aran els calculs. 27 | cd $TMPDIR 28 | export Project=gaussian-smp 29 | export Input=$Project 30 | cp -pr $HOME/path/amb/els/input.com $Input 31 | ########################################## 32 | # calcul 33 | ########################################## 34 | # executem el gaussian g03 35 | g03 < ./test001.com > test001.log 36 | ########################################## 37 | # Transferencia dels resultats 38 | ########################################## 39 | cp -pr $Input $HOME/path/a/on/guardar/els/outputs/ 40 | 41 | Per enviar un càlcul de Gaussian en paral·lel cal: 42 | Afegir en el input de gaussian el nombre de processadors a utilitzar %NPROCS=4 43 | Afegir en el input de gaussian la quantitat de memoria a utilitzar %MEM=8GB 44 | Afegir el Parallel Environment smp per que paral·lelitzi sobre la mateixa màquina (shared memory) 45 | Gaussian no acostuma a escalar per sobre dels 8 processadors i depenent del tipus de càlcul, inclús menys, per aquest motiu recomanem utilitzar SMP (amb un sol node) en comptes de Linda (amb varis nodes) 46 | -------------------------------------------------------------------------------- /GridEngine/gromacs-3.3.1-ompi-iqtc04.sub: -------------------------------------------------------------------------------- 1 | #!/bin/bash 2 | ########################################## 3 | # SGE options and parameters 4 | ########################################## 5 | # (1) Name of the job 6 | #$ -N XRQTC.Gromacs_9LDT-72 7 | # (2) Requested resources 8 | # Parallel Environment and number of cores 9 | #$ -pe omp* 12 10 | # Queue 11 | #$ -q iqtc04.q 12 | # Shell 13 | #$ -S /bin/bash 14 | # (3) Output files 15 | #$ -cwd 16 | #$ -o gromacs-XRQTC.Gromacs_9LDT-72.out 17 | #$ -e gromacs-XRQTC.Gromacs_9LDT-72.err 18 | # (4) Remove the first '#' of the following 2 lines if you want to receive an email when the job ends. 19 | ##$ -m e 20 | ##$ -M yourmail@ub.edu 21 | ########################################## 22 | # User environment. 23 | ########################################## 24 | # Load the modules needed 25 | . /etc/profile.d/modules.sh 26 | module load Gromacs/3.3.1_ics-11.1.072_fftw3.2.2_ompi-1.4.2 27 | ########################################## 28 | # Copying files needed 29 | ########################################## 30 | # We copy the inputs to the directory where the jobs will run 31 | cd $TMPDIR 32 | mkdir -p gromacs-ompi-XRQTC.Gromacs_9LDT-72 33 | cd gromacs-ompi-XRQTC.Gromacs_9LDT-72 34 | cp $HOME/bench/GROMACS/XRQTC.Gromacs_9LDT/* . 35 | ########################################## 36 | # Run the job 37 | ########################################## 38 | export OMP_NUM_THREADS=1 39 | ulimit -s unlimited 40 | grompp_d -f full_vdw.mdp -c 9LDT-pt-md-3.gro -p 9LDT-bu.top -o 9LDT-bu.tpr 41 | mpirun -np $NSLOTS mdrun_mpi -v -s 9LDT-bu.tpr -o 9LDT-bu.trr > mdrun.out 42 | ########################################## 43 | # Copy the results to our home directory 44 | ########################################## 45 | mkdir -p $HOME/bench/GROMACS/XRQTC.Gromacs_9LDT/OUT/gromacs 46 | cp -r $TMPDIR/* $HOME/bench/GROMACS/XRQTC.Gromacs_9LDT/OUT/gromacs/ 47 | ########################################## 48 | # Temps dels resultats 49 | ########################################## 50 | TEMPS=$(cat md.log | grep Time: | awk '{print $3}') 51 | echo "$NSLOTS $TEMPS" >> $HOME/bench/GROMACS/XRQTC.Gromacs_9LDT/benchmark-ompi-XRQTC.Gromacs_9LDT.dat 52 | -------------------------------------------------------------------------------- /GridEngine/gromacs-mpi.sub: -------------------------------------------------------------------------------- 1 | #!/bin/bash 2 | # Script per enviar càlculs de Gromacs 3 | # amb 16 processadors amb openmpi 4 | # Recomenat enviar-ho a 2 nodes de 8 cores 5 | # - Jordi Blasco 12/08/09 - 6 | ########################################## 7 | # Opcions i parametres de l'SGE 8 | ########################################## 9 | # (1) Nom del treball (per identificar) 10 | #$ -N GROMACS-OpenMPI-16 11 | # (2) Recursos sol.licitats 12 | #$ -pe ompi 16 13 | # (3) Fitxers de sortida 14 | #$ -cwd 15 | #$ -o gromacs01.out 16 | #$ -e gromacs01.err 17 | # (4) Envia un mail quan acava el treball. 18 | #$ -m e 19 | #$ -M jblasco@fbg.ub.es 20 | ########################################## 21 | # Entorn d.usuari 22 | ########################################## 23 | # Es carreguen els moduls a utilitzar 24 | . /etc/profile 25 | module load gromacs/4.0.5_ompi_fftw-3.2.1 26 | ########################################## 27 | # transferencia de dades 28 | ########################################## 29 | # Es copien les dades al directori on es llenc,aran els calculs. 30 | cd $TMPDIR 31 | cp -pr /$WORK/jblasco/d.dppc/* . 32 | ########################################## 33 | # calcul 34 | ########################################## 35 | # Es crea un directori de sortida pels resultats. 36 | export OMP_NUM_THREADS=1 37 | grompp -v &> grompp.out 38 | mpirun -np $NSLOTS mdrun_mpi -v &> mdrun.out 39 | ########################################## 40 | # Transferencia dels resultats 41 | ########################################## 42 | cp -pr mdrun.out /$WORK/jblasco/d.dppc/ -------------------------------------------------------------------------------- /GridEngine/gromacs-ompi-iqtc02.sub: -------------------------------------------------------------------------------- 1 | #!/bin/bash 2 | ########################################## 3 | # SGE options and parameters 4 | ########################################## 5 | # (1) Name of the job 6 | #$ -N GROMACS-OpenMPI-8 7 | # (2) Requested resources 8 | # Parallel Environment and number of cores 9 | #$ -pe ompi 8 10 | # Queue 11 | #$ -q iqtc02.q 12 | # Shell 13 | #$ -S /bin/bash 14 | # (3) Output files 15 | #$ -cwd 16 | #$ -o gromacs01-8.out 17 | #$ -e gromacs01-8.err 18 | # (4) Remove the first '#' of the following 2 lines if you want to receive an email when the job ends. 19 | ##$ -m e 20 | ##$ -M yourmail@ub.edu 21 | ########################################## 22 | # User environment. 23 | ########################################## 24 | # Load the modules needed 25 | . /etc/profile.d/modules.sh 26 | module load gromacs/4.0.5_ompfftw-3.2.1 27 | ########################################## 28 | # Copying files needed 29 | ########################################## 30 | # We copy the inputs to the directory where the jobs will run 31 | rm gromacs01-8.out 32 | rm gromacs01-8.err 33 | cd $TMPDIR 34 | cp /work/jblasco/d.dppc/* . 35 | ########################################## 36 | # Run the job 37 | ########################################## 38 | export OMP_NUM_THREADS=1 39 | grompp -v &> grompp.out 40 | mpirun -np $NSLOTS mdrun_mpi -v &> mdrun.out 41 | ########################################## 42 | # Copy the results to our home directory 43 | ########################################## 44 | mkdir -p /work/jblasco/bench/gromacs-8 45 | cp -r * /work/jblasco/bench/gromacs-8/ 46 | -------------------------------------------------------------------------------- /GridEngine/gromacs-ompi-iqtc04.sub: -------------------------------------------------------------------------------- 1 | #!/bin/bash 2 | ########################################## 3 | # SGE options and parameters 4 | ########################################## 5 | # (1) Name of the job 6 | #$ -N XRQTC.Gromacs_9LDT-72 7 | # (2) Requested resources 8 | # Parallel Environment and number of cores 9 | #$ -pe omp* 12 10 | # Queue 11 | #$ -q iqtc04.q 12 | # Shell 13 | #$ -S /bin/bash 14 | # (3) Output files 15 | #$ -cwd 16 | #$ -o gromacs-XRQTC.Gromacs_9LDT-72.out 17 | #$ -e gromacs-XRQTC.Gromacs_9LDT-72.err 18 | # (4) Remove the first '#' of the following 2 lines if you want to receive an email when the job ends. 19 | ##$ -m e 20 | ##$ -M yourmail@ub.edu 21 | ########################################## 22 | # User environment. 23 | ########################################## 24 | # Load the modules needed 25 | . /etc/profile.d/modules.sh 26 | module load Gromacs/4.0.7_ics-11.1.072_fftw3.2.2_ompi-1.4.2 27 | ########################################## 28 | # Copying files needed 29 | ########################################## 30 | # We copy the inputs to the directory where the jobs will run 31 | cd $TMPDIR 32 | mkdir -p gromacs-ompi-XRQTC.Gromacs_9LDT-72 33 | cd gromacs-ompi-XRQTC.Gromacs_9LDT-72 34 | cp $HOME/bench/GROMACS/XRQTC.Gromacs_9LDT/* . 35 | ########################################## 36 | # Run the job 37 | ########################################## 38 | export OMP_NUM_THREADS=1 39 | ulimit -s unlimited 40 | grompp_d -f full_vdw.mdp -c 9LDT-pt-md-3.gro -p 9LDT-bu.top -o 9LDT-bu.tpr 41 | mpirun -np $NSLOTS mdrun_mpi -v -s 9LDT-bu.tpr -o 9LDT-bu.trr > mdrun.out 42 | ########################################## 43 | # Copy the results to our home directory 44 | ########################################## 45 | mkdir -p $HOME/bench/GROMACS/XRQTC.Gromacs_9LDT/OUT/gromacs 46 | cp -r $TMPDIR/* $HOME/bench/GROMACS/XRQTC.Gromacs_9LDT/OUT/gromacs/ 47 | ########################################## 48 | # Temps dels resultats 49 | ########################################## 50 | TEMPS=$(cat md.log | grep Time: | awk '{print $3}') 51 | echo "$NSLOTS $TEMPS" >> $HOME/bench/GROMACS/XRQTC.Gromacs_9LDT/benchmark-ompi-XRQTC.Gromacs_9LDT.dat 52 | -------------------------------------------------------------------------------- /GridEngine/lammps-mpi.sub: -------------------------------------------------------------------------------- 1 | #!/bin/bash 2 | ########################################## 3 | # Opcions i parametres de l'SGE 4 | ########################################## 5 | # (1) Nom del treball (per identificar) 6 | #$ -N LAMMPS-prova01 7 | # (2) Recursos sol.licitats 8 | #$ -l h_rt=0:50:0 9 | #$ -l mem_free=16.0G 10 | #$ -l num_proc=1 11 | #$ -pe mpi 16 12 | # (3) Fitxers de sortida 13 | #$ -cwd 14 | #$ -o lammps01.out 15 | #$ -e lammps01.err 16 | #$ (4) Envia un mail quan acava el treball. 17 | #$ -m e 18 | #$ -M jblasco@fbg.ub.es 19 | ########################################## 20 | # Entorn d.usuari 21 | ########################################## 22 | # Es carreguen els moduls a utilitzar 23 | . /etc/profile 24 | module load lammps 25 | ########################################## 26 | # transferencia de dades 27 | ########################################## 28 | # Es copien les dades al directori on es llenc,aran els calculs. 29 | cd $TMPDIR 30 | export Project=lammps_mpi_16 31 | export Input=$Project 32 | cp -pr $HOME/path/amb/els/inputs/ $Input 33 | ########################################## 34 | # calcul 35 | ########################################## 36 | # Es crea un directori de sortida pels resultats. 37 | export OMP_NUM_THREADS=1 38 | lmp_mpi -np $NSLOTS < in.test > out.txt 39 | ########################################## 40 | # Transferencia dels resultats 41 | ########################################## 42 | cp -pr $Input $HOME/path/a/on/guardar/els/outputs/ 43 | -------------------------------------------------------------------------------- /GridEngine/molcas.sub: -------------------------------------------------------------------------------- 1 | #!/bin/bash 2 | # Script per enviar càlculs de Molcas 3 | # amb 4 processadors sobre la mateixa maquina 4 | # - Jordi Blasco 12/08/07 - 5 | ########################################## 6 | # Opcions i parametres de l'SGE 7 | ########################################## 8 | # (1) Nom del treball (per identificar) 9 | #$ -N Molcas-prova01 10 | # (2) Recursos sol.licitats 11 | #$ -l h_rt=0:50:0 12 | #$ -l mem_free=4.0G 13 | #$ -pe smp 4 14 | # (3) Fitxers de sortida 15 | #$ -cwd 16 | #$ -o molcas01.out 17 | #$ -e molcas01.err 18 | # (4) Envia un mail quan acava el treball. 19 | #$ -m e 20 | #$ -M jblasco@fbg.ub.es 21 | ########################################## 22 | # Entorn d.usuari 23 | ########################################## 24 | # Es carreguen els moduls a utilitzar 25 | module load molcas 26 | ########################################## 27 | # transferencia de dades 28 | ########################################## 29 | # Es copien les dades al directori on es llenc,aran els calculs. 30 | cd $TMPDIR 31 | export Project=Jobname 32 | export Input="$Project".input 33 | export Output="$Project".out 34 | cp -pr $HOME/path/amb/el/input/fitxer.input $Input 35 | ########################################## 36 | # calcul 37 | ########################################## 38 | # Es crea un directori de sortida pels resultats. 39 | export OMP_NUM_THREADS=$NSLOTS 40 | export CPUS=4 41 | molcas "$Input" >>"$Output" 42 | 43 | ########################################## 44 | # Transferencia dels resultats 45 | ########################################## 46 | cp -pr $Output $HOME/path/a/on/guardar/output/ 47 | -------------------------------------------------------------------------------- /GridEngine/molcas_7.4-ompi-iqtc04.sub: -------------------------------------------------------------------------------- 1 | #!/bin/bash 2 | ########################################## 3 | # SGE options and parameters 4 | ########################################## 5 | # (1) Name of the job 6 | #$ -N MOLCAS-mpi-ncores 7 | # (2) Requested resources 8 | # Parallel Environment and number of cores 9 | #$ -pe omp* 12 10 | # Queue 11 | #$ -q iqtc04.q 12 | # Shell 13 | #$ -S /bin/bash 14 | # (3) Output files 15 | #$ -cwd 16 | #$ -o molcas-mpi-TEST-ncores.out 17 | #$ -e molcas-mpi-TEST-ncores.err 18 | # (4) Remove the first '#' of the following 2 lines if you want to receive an email when the job ends. 19 | ##$ -m e 20 | ##$ -M yourmail@ub.edu 21 | ########################################## 22 | # User environment. 23 | ########################################## 24 | # Load the modules needed 25 | . /etc/profile.d/modules.sh 26 | module load molcas/7.4_patch045_serial_ics-11.1.072_mkl-11.1.072_ompi-1.4.2 27 | ########################################## 28 | # Copying files needed 29 | ########################################## 30 | # We copy the inputs to the directory where the jobs will run 31 | cd $TMPDIR 32 | cp -r $HOME/bench/MOLCAS/XRQTC.Molcas_caspt2/* . 33 | ########################################## 34 | # Run the job 35 | ########################################## 36 | export OMP_NUM_THREADS=1 37 | export CPUS=$NSLOTS 38 | #export MOLCASMEM=47104 39 | molcas "MOLCAS.inputmol" >> "MOLCAS.out" 40 | ########################################## 41 | # Copy the results to our home directory 42 | ########################################## 43 | mkdir -p $HOME/bench/MOLCAS/OUT/molcas 44 | #cp -r * $HOME/bench/MOLCAS/OUT/molcas 45 | cp -r $TMPDIR $HOME/bench/MOLCAS/OUT/molcas/ 46 | -------------------------------------------------------------------------------- /GridEngine/molcas_7.4-serial-iqtc01.sub: -------------------------------------------------------------------------------- 1 | #!/bin/tcsh 2 | 3 | #16/12/09 4 | #NOTA: Molcas 7.2 dona uns resultats diferents a la versió 7.4 5 | #això es degut a que la nova versió utilitza un level shift de 0.5 respecte 6 | #al level shift 1 que utilitza la versió 7.2. Si en la versió s'utilitza 7 | #un level shift de 0.5 els resultats ja son bastant concordants amb la 8 | #última versió 9 | 10 | #------------------------------------------------------------------- 11 | # Parametres del SGE 12 | # ------------------------------------------------------------------ 13 | 14 | #$ -N NOM_SCRIPT 15 | #$ -pe mpi 1 16 | #$ -cwd 17 | #$ -S /bin/tcsh 18 | #$ -o molcas.out 19 | #$ -e molcas.err 20 | #$ -m e 21 | #$ -M yourmail@ub.edu 22 | #$ -q iqtc01.q 23 | 24 | #--------------------------------------------------------------------- 25 | # Carreguem els moduls 26 | #--------------------------------------------------------------------- 27 | source /opt/Modules/3.2.3/init/tcsh 28 | module load molcas/molcas74_patch045_serial_pgi10.0_blasmolcas 29 | 30 | #--------------------------------------------------------------------- 31 | #DADES A MODIFICAR PER L'USUARI 32 | # Preparem l'entorn 33 | #--------------------------------------------------------------------- 34 | 35 | setenv CurrDir /home/jingles/tests/molcas/7.4/Albert 36 | setenv Project Ps 37 | setenv MOLCASMEM 4000 38 | setenv MOLCASDISK 12000 39 | setenv Title Titol_projecte 40 | setenv TempDir $TMPDIR 41 | setenv WorkDir $TempDir/$Project.Work 42 | setenv MOLCAS_SAVE $WorkDir 43 | 44 | #-------------------------------------------------------------------- 45 | # Preparem els directoris 46 | #-------------------------------------------------------------------- 47 | mkdir -p $WorkDir 48 | mkdir -p $TempDir 49 | 50 | cp -r $CurrDir/* $WorkDir 51 | cd $WorkDir 52 | 53 | #--------------------------------------------------------------------- 54 | # 55 | # Start executing molcas job qsub -q iqtc01.q script 56 | # 57 | #--------------------------------------------------------------------- 58 | 59 | setenv OMP_NUM_THREADS $NSLOTS 60 | set Infile=$WorkDir/$Project.input 61 | set Outfile=$WorkDir/$Project.out 62 | molcas $Infile >> $Outfile 63 | 64 | #--------------------------------------------------------------------- 65 | # 66 | # Copiem el resultat 67 | # 68 | #--------------------------------------------------------------------- 69 | 70 | cp $Outfile $CurrDir 71 | 72 | #-------------------------------------------------------------------- 73 | # 74 | # Netejem el scratch 75 | # 76 | #-------------------------------------------------------------------- 77 | 78 | cd - 79 | rm -rf $TempDir 80 | 81 | exit 82 | -------------------------------------------------------------------------------- /GridEngine/molcas_7.4-serial-iqtc02.sub: -------------------------------------------------------------------------------- 1 | #!/bin/tcsh 2 | 3 | #16/12/09 4 | #NOTA: Molcas 7.2 dona uns resultats diferents a la versió 7.4 5 | #això es degut a que la nova versió utilitza un level shift de 0.5 respecte 6 | #al level shift 1 que utilitza la versió 7.2. Si en la versió s'utilitza 7 | #un level shift de 0.5 els resultats ja son bastant concordants amb la 8 | #última versió 9 | 10 | #------------------------------------------------------------------- 11 | # Parametres del SGE 12 | # ------------------------------------------------------------------ 13 | 14 | #$ -N NOM_SCRIPT 15 | #$ -pe mpi 1 16 | #$ -cwd 17 | #$ -S /bin/tcsh 18 | #$ -o molcas.out 19 | #$ -e molcas.err 20 | #$ -m e 21 | #$ -M yourmail@ub.edu 22 | #$ -q iqtc02.q 23 | 24 | #--------------------------------------------------------------------- 25 | # Carreguem els moduls 26 | #--------------------------------------------------------------------- 27 | source /opt/modules/init/tcsh 28 | module load molcas/molcas74_patch045_serial_intel9.1_mkl9.1 29 | 30 | #--------------------------------------------------------------------- 31 | #DADES A MODIFICAR PER L'USUARI 32 | # Preparem l'entorn 33 | #--------------------------------------------------------------------- 34 | 35 | setenv CurrDir /home/jingles/tests/molcas/7.4/Albert 36 | setenv Project Ps 37 | setenv MOLCASMEM 4000 38 | setenv MOLCASDISK 12000 39 | setenv Title Titol_projecte 40 | setenv TempDir $TMPDIR #$TMP/$Project 41 | # Nota $TMP variable ja cargada pel propi sistema que conté el path /scratch/$USER 42 | setenv WorkDir $TempDir/$Project.Work 43 | setenv MOLCAS_SAVE $WorkDir 44 | 45 | #-------------------------------------------------------------------- 46 | # Preparem els directoris 47 | #-------------------------------------------------------------------- 48 | mkdir -p $WorkDir 49 | mkdir -p $TempDir 50 | 51 | cp -r $CurrDir/* $WorkDir 52 | cd $WorkDir 53 | 54 | #--------------------------------------------------------------------- 55 | # 56 | # Start executing molcas job qsub -q iqtc01.q script 57 | # 58 | #--------------------------------------------------------------------- 59 | 60 | setenv OMP_NUM_THREADS $NSLOTS 61 | set Infile=$WorkDir/$Project.input 62 | set Outfile=$WorkDir/$Project.out 63 | molcas $Infile >> $Outfile 64 | 65 | #--------------------------------------------------------------------- 66 | # 67 | # Copiem el resultat 68 | # 69 | #--------------------------------------------------------------------- 70 | 71 | cp $Outfile $CurrDir 72 | 73 | #-------------------------------------------------------------------- 74 | # 75 | # Netejem el scratch 76 | # 77 | #-------------------------------------------------------------------- 78 | 79 | cd - 80 | rm -rf $TempDir 81 | 82 | exit 83 | -------------------------------------------------------------------------------- /GridEngine/molcas_7.4-serial-iqtc03.sub: -------------------------------------------------------------------------------- 1 | #!/bin/tcsh 2 | 3 | #16/12/09 4 | #NOTA: Molcas 7.2 dona uns resultats diferents a la versió 7.4 5 | #això es degut a que la nova versió utilitza un level shift de 0.5 respecte 6 | #al level shift 1 que utilitza la versió 7.2. Si en la versió s'utilitza 7 | #un level shift de 0.5 els resultats ja son bastant concordants amb la 8 | #última versió 9 | 10 | #------------------------------------------------------------------- 11 | # Parametres del SGE 12 | # ------------------------------------------------------------------ 13 | 14 | #$ -N NOM_SCRIPT 15 | #$ -pe mpi 1 16 | #$ -cwd 17 | #$ -S /bin/tcsh 18 | #$ -o molcas.out 19 | #$ -e molcas.err 20 | #$ -m e 21 | #$ -M yourmail@ub.edu 22 | #$ -q iqtc03.q 23 | 24 | #--------------------------------------------------------------------- 25 | # Carreguem els moduls 26 | #--------------------------------------------------------------------- 27 | source /opt/modules/init/tcsh 28 | module load molcas/molcas74_patch045_serial_intel9.1_mkl9.1 29 | 30 | #--------------------------------------------------------------------- 31 | #DADES A MODIFICAR PER L'USUARI 32 | # Preparem l'entorn 33 | #--------------------------------------------------------------------- 34 | 35 | setenv CurrDir /home/jingles/tests/molcas/7.4/Albert 36 | setenv Project Ps 37 | setenv MOLCASMEM 4000 38 | setenv MOLCASDISK 12000 39 | setenv Title Titol_projecte 40 | setenv TempDir $TMPDIR #$TMP/$Project 41 | # Nota $TMP variable ja cargada pel propi sistema que conté el path /scratch/$USER 42 | setenv WorkDir $TempDir/$Project.Work 43 | setenv MOLCAS_SAVE $WorkDir 44 | 45 | #-------------------------------------------------------------------- 46 | # Preparem els directoris 47 | #-------------------------------------------------------------------- 48 | mkdir -p $WorkDir 49 | mkdir -p $TempDir 50 | 51 | cp -r $CurrDir/* $WorkDir 52 | cd $WorkDir 53 | 54 | #--------------------------------------------------------------------- 55 | # 56 | # Start executing molcas job qsub -q iqtc01.q script 57 | # 58 | #--------------------------------------------------------------------- 59 | 60 | setenv OMP_NUM_THREADS $NSLOTS 61 | set Infile=$WorkDir/$Project.input 62 | set Outfile=$WorkDir/$Project.out 63 | molcas $Infile >> $Outfile 64 | 65 | #--------------------------------------------------------------------- 66 | # 67 | # Copiem el resultat 68 | # 69 | #--------------------------------------------------------------------- 70 | 71 | cp $Outfile $CurrDir 72 | 73 | #-------------------------------------------------------------------- 74 | # 75 | # Netejem el scratch 76 | # 77 | #-------------------------------------------------------------------- 78 | 79 | cd - 80 | rm -rf $TempDir 81 | 82 | exit 83 | -------------------------------------------------------------------------------- /GridEngine/molcas_7.4-serial-iqtc04.sub: -------------------------------------------------------------------------------- 1 | #!/bin/tcsh 2 | 3 | #16/12/09 4 | #NOTA: Molcas 7.2 dona uns resultats diferents a la versió 7.4 5 | #això es degut a que la nova versió utilitza un level shift de 0.5 respecte 6 | #al level shift 1 que utilitza la versió 7.2. Si en la versió s'utilitza 7 | #un level shift de 0.5 els resultats ja son bastant concordants amb la 8 | #última versió 9 | 10 | #------------------------------------------------------------------- 11 | # Parametres del SGE 12 | # ------------------------------------------------------------------ 13 | 14 | #$ -N NOM_SCRIPT 15 | #$ -pe smp 1 16 | #$ -cwd 17 | #$ -S /bin/tcsh 18 | #$ -o molcas.out 19 | #$ -e molcas.err 20 | #$ -m e 21 | #$ -M yourmail@ub.edu 22 | #$ -q iqtc04.q 23 | 24 | #--------------------------------------------------------------------- 25 | # Carreguem els moduls 26 | #--------------------------------------------------------------------- 27 | source /opt/modules/init/tcsh 28 | module load molcas/7.4_patch045_serial_intel10.1_mkl10.1 29 | 30 | #--------------------------------------------------------------------- 31 | #DADES A MODIFICAR PER L'USUARI 32 | # Preparem l'entorn 33 | #--------------------------------------------------------------------- 34 | 35 | setenv CurrDir /home/jingles/tests/molcas/7.4/Albert 36 | setenv Project Ps 37 | setenv MOLCASMEM 4000 38 | setenv MOLCASDISK 12000 39 | setenv Title Titol_projecte 40 | setenv TempDir $TMPDIR #$TMP/$Project 41 | # Nota $TMP variable ja cargada pel propi sistema que conté el path /scratch/$USER 42 | setenv WorkDir $TempDir/$Project.Work 43 | setenv MOLCAS_SAVE $WorkDir 44 | 45 | #-------------------------------------------------------------------- 46 | # Preparem els directoris 47 | #-------------------------------------------------------------------- 48 | mkdir -p $WorkDir 49 | mkdir -p $TempDir 50 | 51 | cp -r $CurrDir/* $WorkDir 52 | cd $WorkDir 53 | 54 | #--------------------------------------------------------------------- 55 | # 56 | # Start executing molcas job qsub -q iqtc01.q script 57 | # 58 | #--------------------------------------------------------------------- 59 | 60 | setenv OMP_NUM_THREADS $NSLOTS 61 | set Infile=$WorkDir/$Project.input 62 | set Outfile=$WorkDir/$Project.out 63 | molcas $Infile >> $Outfile 64 | 65 | #--------------------------------------------------------------------- 66 | # 67 | # Copiem el resultat 68 | # 69 | #--------------------------------------------------------------------- 70 | 71 | cp $Outfile $CurrDir 72 | 73 | #-------------------------------------------------------------------- 74 | # 75 | # Netejem el scratch 76 | # 77 | #-------------------------------------------------------------------- 78 | 79 | cd - 80 | rm -rf $TempDir 81 | 82 | exit 83 | -------------------------------------------------------------------------------- /GridEngine/nwchem-ompi-iqtc04.sub: -------------------------------------------------------------------------------- 1 | #!/bin/bash 2 | ########################################## 3 | # SGE options and parameters 4 | ########################################## 5 | # (1) Name of the job 6 | #$ -N test_nwchem_iqtc04 7 | # (2) Requested resources 8 | # Parallel Environment and number of cores 9 | #$ -pe omp* 4 10 | # Queue 11 | #$ -q iqtc04.q 12 | # Shell 13 | #$ -S /bin/bash 14 | # (3) Output files 15 | #$ -cwd 16 | #$ -o iqtc04-4.out 17 | #$ -e iqtc04-4.err 18 | # (4) Remove the first '#' of the following 2 lines if you want to receive an email when the job ends. 19 | ##$ -m e 20 | ##$ -M yourmail@ub.edu 21 | ########################################## 22 | # User environment. 23 | ########################################## 24 | # Load the modules needed 25 | . /etc/profile.d/modules.sh 26 | module load nwchem/5.1.1_ics-11.1.072_ompi-1.4.2 27 | INPUT=input_m5_2x_Rqm3.nw 28 | output=$INPUT.log 29 | ########################################## 30 | # Copying files needed 31 | ########################################## 32 | # We copy the inputs to the directory where the jobs will run 33 | 34 | cd $TMPDIR 35 | cp -r $HOME/bench/NWCHEM/$INPUT . 36 | ########################################## 37 | # Run the job 38 | ########################################## 39 | export OMP_NUM_THREADS=1 40 | 41 | echo "INICI" 42 | date 43 | mpirun -np $NSLOTS nwchem $INPUT > $output 44 | echo "FI" 45 | date 46 | ########################################## 47 | # Copy the results to our home directory 48 | ########################################## 49 | mkdir -p $HOME/bench/NWCHEM/OUT_iqtc04 50 | cp -r $TMPDIR $HOME/bench/NWCHEM/OUT_iqtc04 51 | 52 | -------------------------------------------------------------------------------- /GridEngine/orca-ompi-iqtc04.sub: -------------------------------------------------------------------------------- 1 | #!/bin/bash 2 | ########################################## 3 | # SGE options and parameters 4 | ########################################## 5 | # (1) Name of the job 6 | #$ -N XRQTC.Orca_B3LYP-12 7 | # (2) Requested resources 8 | # Parallel Environment and number of cores 9 | #$ -pe omp* 12 10 | # Queue 11 | #$ -q iqtc04.q 12 | # Shell 13 | #$ -S /bin/bash 14 | # (3) Output files 15 | #$ -cwd 16 | #$ -o orca-XRQTC.Orca_B3LYP-12.out 17 | #$ -e orca-XRQTC.Orca_B3LYP-12.err 18 | # (4) Remove the first '#' of the following 2 lines if you want to receive an email when the job ends. 19 | ##$ -m e 20 | ##$ -M yourmail@ub.edu 21 | ########################################## 22 | # User environment. 23 | ########################################## 24 | # Load the modules needed 25 | . /etc/profile.d/modules.sh 26 | module load orca 27 | ########################################## 28 | # Copying files needed 29 | ########################################## 30 | # We copy the inputs to the directory where the jobs will run 31 | cd $TMPDIR 32 | cp $HOME/bench/Orca/XRQTC.Orca_B3LYP/input/* . 33 | 34 | # --------------> ATENCIO <------------------- 35 | # Cal posar % pal nprocs $NSLOTS dins de l.input! 36 | # en les seguents linies es modifica en funcio del PE 37 | mv XRQTC.Orca_B3LYP.inp XRQTC.Orca_B3LYP.inp.1 38 | echo "% pal nprocs $NSLOTS 39 | end" > XRQTC.Orca_B3LYP.inp.0 40 | cat XRQTC.Orca_B3LYP.inp.0 XRQTC.Orca_B3LYP.inp.1 > XRQTC.Orca_B3LYP.inp 41 | 42 | 43 | rm XRQTC.Orca_B3LYP.inp.* 44 | ########################################## 45 | # Run the job 46 | ########################################## 47 | export P4_RSHCOMMAND=ssh 48 | export OMP_NUM_THREADS=1 49 | /aplic/ORCA/2.7.0b/ompi-1.4.2/orca XRQTC.Orca_B3LYP.inp > XRQTC.Orca_B3LYP.out 50 | 51 | ########################################## 52 | # Copy the results to our home directory 53 | ########################################## 54 | mkdir -p $HOME/bench/Orca/XRQTC.Orca_B3LYP/OUT/orca 55 | cp -r $TMPDIR $HOME/bench/Orca/XRQTC.Orca_B3LYP/OUT/orca/ 56 | ########################################## 57 | # Temps dels resultats 58 | ########################################## 59 | TEMPS=$(cat XRQTC.Orca_B3LYP.out | grep Time: | awk '{print$3}') 60 | echo "$NSLOTS $TEMPS" >> $HOME/bench/Orca/XRQTC.Orca_B3LYP/benchmark-ompi-XRQTC.Orca_B3LYP.dat 61 | 62 | -------------------------------------------------------------------------------- /GridEngine/orca_ompi_scratch.sub: -------------------------------------------------------------------------------- 1 | #!/bin/bash 2 | #################################################### 3 | # To use this script execute next instruccion 4 | # 5 | # qsub orca_ompi_scratch.sub name_of_input (without extention) 6 | # 7 | # 8 | #################################################### 9 | #$ -S /bin/bash 10 | # 11 | # name of job 12 | #$ -N orca_ompi ### job name 13 | #$ -e orca_ompi.err ### sge error file 14 | #$ -o orca_ompi.out ### sge output file 15 | #### 16 | #### Select the cluster where you want to run your job iqtc01.q, iqtc02.q & iqtc03.q #### 17 | #$ -q iqtc01.q 18 | #$ -cwd 19 | #$ -m e 20 | #### 21 | #### change this mail to recive an alert amil when the job finishes ######## 22 | #$ -M my@mail.com 23 | # 24 | # 25 | ##### Emember that in iqtc01.q the maximum is 4 cores/node ans iqtc02.q & iqtc03.q is 8 cores/node 26 | #$ -pe ompi 4 27 | 28 | 29 | source /etc/profile 30 | . /etc/profile.d/modules.sh 31 | 32 | cwd=$PWD 33 | 34 | module load orca/ompi_r1730 35 | 36 | cp $1.inp $TMPDIR/ 37 | cd $TMPDIR 38 | 39 | /aplic/orca/orca_amd64_exe_r1730/orca $1.inp > $1.out 40 | 41 | mkdir -p $cwd/$1_out 42 | cp -r * $cwd/$1_out/ 43 | 44 | -------------------------------------------------------------------------------- /GridEngine/orca_ompi_work.sub: -------------------------------------------------------------------------------- 1 | #!/bin/bash 2 | #################################################### 3 | # To use this script execute next instruccion 4 | # 5 | # qsub orca_ompi_work.sub name_of_input (without extention) 6 | # 7 | # 8 | #################################################### 9 | #$ -S /bin/bash 10 | # 11 | # name of job 12 | #$ -N orca_ompi ### job name flag 13 | #$ -e orca_ompi.err ### sge error file 14 | #$ -o orca_ompi.out ### sge output file 15 | #### 16 | #### Select the cluster where you want to run your job iqtc01.q, iqtc02.q & iqtc03.q #### 17 | #$ -q iqtc01.q 18 | #$ -cwd 19 | #$ -m e 20 | #### 21 | #### change this mail to recive an alert amil when the job finishes ######## 22 | #$ -M my@mail.com 23 | # 24 | # 25 | ##### Emember that in iqtc01.q the maximum is 4 cores/node ans iqtc02.q & iqtc03.q is 8 cores/node 26 | #$ -pe ompi 4 27 | 28 | 29 | source /etc/profile 30 | . /etc/profile.d/modules.sh 31 | 32 | cwd=$PWD 33 | 34 | module load orca/ompi_r1730 35 | 36 | cp $1.inp $TMPDIR/ 37 | 38 | mkdir $WORK/$1_DIR 39 | cd $WORK/$1_DIR 40 | cp -r $TMPDIR/* . 41 | 42 | /aplic/orca/orca_amd64_exe_r1730/orca $1.inp > $1.out 43 | 44 | mkdir -p $cwd/$1_out 45 | cp -r * $cwd/$1_out/ 46 | 47 | cd $cwd/$1_out/ 48 | rm -r $WORK/$1_DIR 49 | -------------------------------------------------------------------------------- /GridEngine/siesta-3.0-ompi-iqtc02.sub: -------------------------------------------------------------------------------- 1 | #!/bin/bash 2 | ########################################## 3 | # SGE options and parameters 4 | ########################################## 5 | # (1) Name of the job 6 | #$ -N test_siesta_iqtc02 7 | # (2) Recursos sol.licitats 8 | # Parallel Environment and number of cores 9 | #$ -pe ompi 4 10 | # Queue 11 | #$ -q iqtc02.q 12 | # Shell 13 | #$ -S /bin/bash 14 | # (3) Output files 15 | #$ -cwd 16 | #$ -o siesta_iqtc02-4.out 17 | #$ -e siesta_iqtc02-4.err 18 | # (4) Remove the first '#' of the following 2 lines if you want to receive an email when the job ends. 19 | ##$ -m e 20 | ##$ -M yourmail@ub.edu 21 | ########################################## 22 | # User environment 23 | ########################################## 24 | # Load the modules needed 25 | . /etc/profile.d/modules.sh 26 | module load siesta/3.0-rc2_paralel_ompi 27 | 28 | INPUT=SnO2FC.fdf 29 | OUTPUT=$INPUT.log 30 | ########################################## 31 | # Copying files needed 32 | ########################################## 33 | # We copy the inputs to the directory where the jobs will run 34 | 35 | cp -r * $TMPDIR/ 36 | cd $TMPDIR 37 | #cp -r $HOME/bench/SIESTA/XRQTC.SIESTA_SnO2_FCfullBZ/input/* . 38 | ########################################## 39 | # Run the job 40 | ########################################## 41 | export OMP_NUM_THREADS=1 42 | 43 | mpirun -np $NSLOTS siesta < $INPUT > $OUTPUT 44 | ########################################## 45 | # Copy the results to our home directory 46 | ########################################## 47 | mkdir -p $HOME/bench/SIESTA/XRQTC.SIESTA_SnO2_FCfullBZ/OUT_iqtc02 48 | cp -r $TMPDIR $HOME/bench/SIESTA/XRQTC.SIESTA_SnO2_FCfullBZ/OUT_iqtc02 49 | 50 | -------------------------------------------------------------------------------- /GridEngine/siesta-3.0-ompi-iqtc02_tcsh.sub: -------------------------------------------------------------------------------- 1 | #!/bin/bash 2 | ########################################## 3 | # SGE options and parameters 4 | ########################################## 5 | # (1) Name of the job 6 | #$ -N test_siesta_iqtc02 7 | # (2) Recursos sol.licitats 8 | #$ -pe ompi 4 9 | # Queue 10 | #$ -q iqtc02.q 11 | # Shell 12 | #$ -S /bin/tcsh 13 | # (3) Output files 14 | #$ -cwd 15 | #$ -o siesta_iqtc02-4.out 16 | #$ -e siesta_iqtc02-4.err 17 | # (4) Remove the first '#' of the following 2 lines if you want to receive an email when the job ends. 18 | ##$ -m e 19 | ##$ -M yourmail@ub.edu 20 | #$ -S /bin/tcsh 21 | ########################################## 22 | # User environment 23 | ########################################## 24 | # Load the modules needed 25 | . /etc/profile.d/modules.csh 26 | module load siesta/3.0-rc2_paralel_ompi 27 | 28 | set INPUT=SnO2FC.fdf 29 | set OUTPUT=$INPUT.log 30 | ########################################## 31 | # Copying files needed 32 | ########################################## 33 | # We copy the inputs to the directory where the jobs will run 34 | 35 | cp -r * $TMPDIR/ 36 | cd $TMPDIR 37 | #cp -r $HOME/bench/SIESTA/XRQTC.SIESTA_SnO2_FCfullBZ/input/* . 38 | ########################################## 39 | # Run the job 40 | ########################################## 41 | setenv OMP_NUM_THREADS 1 42 | 43 | mpirun -np $NSLOTS siesta < $INPUT > $OUTPUT 44 | ########################################## 45 | # Copy the results to our home directory 46 | ########################################## 47 | mkdir -p $HOME/bench/SIESTA/XRQTC.SIESTA_SnO2_FCfullBZ/OUT_iqtc02 48 | cp -r $TMPDIR $HOME/bench/SIESTA/XRQTC.SIESTA_SnO2_FCfullBZ/OUT_iqtc02 49 | 50 | -------------------------------------------------------------------------------- /GridEngine/siesta-3.0-ompi-iqtc04.sub: -------------------------------------------------------------------------------- 1 | #!/bin/bash 2 | ########################################## 3 | # SGE options and parameters 4 | ########################################## 5 | # (1) Name of the job 6 | #$ -N test_siesta_iqtc04 7 | # (2) Requested resources 8 | # Parallel Environment and number of cores 9 | #$ -pe omp* 8 10 | # Queue 11 | #$ -q iqtc04.q 12 | # Shell 13 | #$ -S /bin/bash 14 | # (3) Output files 15 | #$ -cwd 16 | #$ -o siesta_iqtc04-8.out 17 | #$ -e siesta_iqtc04-8.err 18 | # (4) Remove the first '#' of the following 2 lines if you want to receive an email when the job ends. 19 | ##$ -m e 20 | ##$ -M yourmail@ub.edu.com 21 | ########################################## 22 | # User environment. 23 | ########################################## 24 | # Load the modules needed 25 | . /etc/profile.d/modules.sh 26 | module load siesta/3.0-rc2_paralel_ompi 27 | INPUT=SnO2FC.fdf 28 | output=$INPUT.log 29 | ########################################## 30 | # Copying files needed 31 | ########################################## 32 | # We copy the inputs to the directory where the jobs will run 33 | 34 | cd $TMPDIR 35 | cp -r $HOME/bench/SIESTA/XRQTC.SIESTA_SnO2_FCfullBZ/input/* . 36 | ########################################## 37 | # Run the job 38 | ########################################## 39 | export OMP_NUM_THREADS=1 40 | 41 | echo "INICI" 42 | date 43 | mpirun -np $NSLOTS siesta < $INPUT > $output 44 | echo "FI" 45 | date 46 | 47 | ########################################## 48 | # Copy the results to our home directory 49 | ########################################## 50 | mkdir -p $HOME/bench/SIESTA/XRQTC.SIESTA_SnO2_FCfullBZ/OUT_iqtc04 51 | cp -r $TMPDIR $HOME/bench/SIESTA/XRQTC.SIESTA_SnO2_FCfullBZ/OUT_iqtc04 52 | 53 | -------------------------------------------------------------------------------- /GridEngine/siesta-mpi.sub: -------------------------------------------------------------------------------- 1 | #!/bin/bash 2 | ########################################## 3 | # Opcions i parametres de l'SGE 4 | ########################################## 5 | # (1) Nom del treball (per identificar) 6 | #$ -N siesta-prova01 7 | # (2) Recursos sol.licitats 8 | #$ -l h_rt=0:50:0 9 | #$ -l mem_free=2.0G 10 | #$ -l num_proc=1 11 | #$ -pe mpi 4 12 | # (3) Fitxers de sortida 13 | #$ -cwd 14 | #$ -o siesta01.out 15 | #$ -e siesta01.err 16 | #$ (4) Envia un mail quan acava el treball. 17 | #$ -m e 18 | #$ -M jblasco@fbg.ub.es 19 | ########################################## 20 | # Entorn d.usuari 21 | ########################################## 22 | # Es carreguen els moduls a utilitzar 23 | . /etc/profile 24 | module load siesta 25 | ########################################## 26 | # transferencia de dades 27 | ########################################## 28 | # Es copien les dades al directori on es llenc,aran els calculs. 29 | cd $TMPDIR 30 | export Project=siesta_mpi_4 31 | export Input=$Project 32 | cp -pr $HOME/path/amb/els/inputs/ $Input 33 | ########################################## 34 | # calcul 35 | ########################################## 36 | # Es crea un directori de sortida pels resultats. 37 | export OMP_NUM_THREADS=1 38 | mpirun -np $NSLOTS siesta_mpi < input.fdf > output.out 39 | ########################################## 40 | # Transferencia dels resultats 41 | ########################################## 42 | cp -pr $Input $HOME/path/a/on/guardar/els/outputs/ 43 | -------------------------------------------------------------------------------- /GridEngine/stress_x86-64.sub: -------------------------------------------------------------------------------- 1 | #!/bin/bash 2 | ########################################## 3 | # SGE options and parameters 4 | ########################################## 5 | # (1) Name of the job 6 | #$ -N STRESS-ncores 7 | # (2) Requested resources 8 | # Parallel Environment and number of cores 9 | #$ -pe smp ncores 10 | # Shell 11 | #$ -S /bin/bash 12 | # (3) Output files 13 | #$ -cwd 14 | #$ -o $HOME/stress-out/stress-$HOSTNAME.out 15 | #$ -e $HOME/stress-out/stress-$HOSTNAME.err 16 | # (4) Remove the first '#' of the following 2 lines if you want to receive an email when the job ends. 17 | ##$ -m e 18 | ##$ -M yourmail@ub.edu 19 | ########################################## 20 | # User environment. 21 | ########################################## 22 | # Load the modules needed 23 | . /etc/profile.d/modules.sh 24 | module load stress/1.0.4 25 | ########################################## 26 | # Copying files needed 27 | ########################################## 28 | # We copy the inputs to the directory where the jobs will run 29 | cd $TMPDIR 30 | ########################################## 31 | # Run the job 32 | disk=$(df -hP /scratch | tail -1 | gawk '{DF=$2; if( DF ~ /G/){gsub("G","",DF); print DF/100}}') 33 | mem=$(cat /proc/meminfo | grep MemFree | gawk '{print $2/1024/20}') 34 | stress_x86-64 --cpu $NSLOTS -m 20 --vm-bytes $mem -d 100 --hdd-bytes $disk 35 | ########################################## 36 | # redirecciono un dmesg per revisar possibles errors de sistema 37 | dmesg > $HOME/stress-out/dmesg-$HOSTNAME.out 38 | -------------------------------------------------------------------------------- /GridEngine/stress_x86.sub: -------------------------------------------------------------------------------- 1 | #!/bin/bash 2 | ########################################## 3 | # SGE options and parameters 4 | ########################################## 5 | # (1) Name of the job 6 | #$ -N STRESS-ncores 7 | # (2) Requested resources 8 | # Parallel Environment and number of cores 9 | #$ -pe smp ncores 10 | # Shell 11 | #$ -S /bin/bash 12 | # (3) Output files 13 | #$ -cwd 14 | #$ -o $HOME/stress-out/stress-$HOSTNAME.out 15 | #$ -e $HOME/stress-out/stress-$HOSTNAME.err 16 | # (4) Remove the first '#' of the following 2 lines if you want to receive an email when the job ends. 17 | ##$ -m e 18 | ##$ -M yourmail@ub.edu 19 | ########################################## 20 | # User environment. 21 | ########################################## 22 | # Load the modules needed 23 | . /etc/profile.d/modules.sh 24 | module load stress/1.0.4 25 | ########################################## 26 | # Copying files needed 27 | ########################################## 28 | # We copy the inputs to the directory where the jobs will run 29 | cd $TMPDIR 30 | ########################################## 31 | # Run the job 32 | stress-x86 33 | ########################################## 34 | -------------------------------------------------------------------------------- /GridEngine/vasp-4.6-ompi-iqtc01.sub: -------------------------------------------------------------------------------- 1 | #!/bin/bash 2 | ########################################## 3 | # SGE options and parameters 4 | ########################################## 5 | # (1) Name of the job 6 | #$ -N VASP-4.6-OMPI 7 | # (2) Requested resources 8 | # Parallel Environment and number of cores 9 | #$ -pe ompi 16 10 | # Queue 11 | #$ -q iqtc01.q 12 | # Shell 13 | #$ -S /bin/bash 14 | # (3) Output files 15 | #$ -cwd 16 | #$ -o vasp-ompi.out 17 | #$ -e vasp-ompi.err 18 | # (4) Remove the first '#' of the following 2 lines if you want to receive an email when the job ends. 19 | ##$ -m e 20 | ##$ -M yourmail@ub.edu 21 | ########################################## 22 | # User environment. 23 | ########################################## 24 | # Load the modules needed 25 | . /etc/profile.d/modules.sh 26 | module load openmpi/1.3.3_intel_11.1.059 27 | module load vasp/4.6.28_openmpi_intel 28 | ########################################## 29 | # Copying files needed 30 | ########################################## 31 | # We copy the inputs to the directory where the jobs will run 32 | echo "Got $NSLOTS processors." 33 | cd $WORKDIR 34 | cp -r /home/jblasco/TESTS/vasp-4.6/tests/test-hg/* . 35 | ########################################## 36 | # Run the job 37 | ########################################## 38 | 39 | startdir=$PWD 40 | export OMP_NUM_THREADS=1 41 | 42 | # -------------> WARNING <------------------- 43 | # Check what binary fits your needs 44 | # vasp MPI parallel, charge density and wavefunction complex 45 | # vasp_gamma MPI parallel, gamma-point only (-DwNGZhalf) 46 | # vasp_vtst MPI parallel, charge density + wavefunction complex + VASP TST Tools 47 | # ------------------------------------------- 48 | 49 | mpirun -np $NSLOTS /aplic/vasp/4.6.28_ompi_intel/vasp 50 | 51 | ########################################## 52 | # Copy the results to our home directory 53 | ########################################## 54 | mkdir -p $HOME/TESTS/vasp-4.6/tests/out 55 | cp -r * $HOME/TESTS/vasp-4.6/tests/out/ 56 | -------------------------------------------------------------------------------- /GridEngine/vasp-4.6-ompi-iqtc02.sub: -------------------------------------------------------------------------------- 1 | #!/bin/bash 2 | ########################################## 3 | # SGE options and parameters 4 | ########################################## 5 | # (1) Name of the job 6 | #$ -N VASP-4.6-OMPI 7 | # (2) Requested resources 8 | # Parallel Environment and number of cores 9 | #$ -pe ompi 16 10 | # Queue 11 | #$ -q iqtc02.q 12 | # Shell 13 | #$ -S /bin/bash 14 | # (3) Output files 15 | #$ -cwd 16 | #$ -o vasp-ompi.out 17 | #$ -e vasp-ompi.err 18 | # (4) Remove the first '#' of the following 2 lines if you want to receive an email when the job ends. 19 | ##$ -m e 20 | ##$ -M yourmail@ub.edu 21 | ########################################## 22 | # User environment. 23 | ########################################## 24 | # Load the modules needed 25 | . /etc/profile.d/modules.sh 26 | module load vasp/4.6 27 | ########################################## 28 | # Copying files needed 29 | ########################################## 30 | # We copy the inputs to the directory where the jobs will run 31 | echo "Got $NSLOTS processors." 32 | cd $WORKDIR 33 | cp -r $HOME/TESTS/vasp-4.6/tests/test-hg/* . 34 | ########################################## 35 | # Run the job 36 | ########################################## 37 | 38 | startdir=$PWD 39 | export OMP_NUM_THREADS=1 40 | export MPICH_PROCESS_GROUP=no 41 | mpirun -np $NSLOTS /aplic/VASP/4.6_intel_11.0.074_openmpi/vasp.4.6/vasp 42 | 43 | ########################################## 44 | # Copy the results to our home directory 45 | ########################################## 46 | mkdir -p $HOME/TESTS/vasp-4.6/tests/out 47 | cp -r * $HOME/TESTS/vasp-4.6/tests/out/ 48 | -------------------------------------------------------------------------------- /GridEngine/vasp-4.6-ompi-iqtc03.sub: -------------------------------------------------------------------------------- 1 | #!/bin/bash 2 | ########################################## 3 | # SGE options and parameters 4 | ########################################## 5 | # (1) Name of the job 6 | #$ -N VASP-4.6-OMPI 7 | # (2) Requested resources 8 | # Parallel Environment and number of cores 9 | #$ -pe ompi 16 10 | # Queue 11 | #$ -q iqtc03.q 12 | # Shell 13 | #$ -S /bin/bash 14 | # (3) Output files 15 | #$ -cwd 16 | #$ -o vasp-ompi.out 17 | #$ -e vasp-ompi.err 18 | # (4) Remove the first '#' of the following 2 lines if you want to receive an email when the job ends. 19 | ##$ -m e 20 | ##$ -M yourmail@ub.edu 21 | ########################################## 22 | # User environment. 23 | ########################################## 24 | # Load the modules needed 25 | . /etc/profile.d/modules.sh 26 | module load vasp/4.6 27 | ########################################## 28 | # Copying files needed 29 | ########################################## 30 | # We copy the inputs to the directory where the jobs will run 31 | echo "Got $NSLOTS processors." 32 | cd $WORKDIR 33 | cp -r /home/jblasco/TESTS/vasp-4.6/tests/test-hg/* . 34 | ########################################## 35 | # Run the job 36 | ########################################## 37 | 38 | startdir=$PWD 39 | export OMP_NUM_THREADS=1 40 | export MPICH_PROCESS_GROUP=no 41 | mpirun -np $NSLOTS /aplic/VASP/4.6_intel_11.0.074_openmpi/vasp.4.6/vasp 42 | 43 | ########################################## 44 | # Copy the results to our home directory 45 | ########################################## 46 | mkdir -p $HOME/TESTS/vasp-4.6/tests/out 47 | cp -r * $HOME/TESTS/vasp-4.6/tests/out/ 48 | -------------------------------------------------------------------------------- /GridEngine/vasp-4.6-ompi-iqtc04.sub: -------------------------------------------------------------------------------- 1 | #!/bin/bash 2 | ########################################## 3 | # SGE options and parameters 4 | ########################################## 5 | # (1) Name of the job 6 | #$ -N XRQTC.VASP_ceria-surface-96 7 | # (2) Requested resources 8 | # Parallel Environment and number of cores 9 | # !!!WARNING!!!! 10 | # IF YOU'RE GOING TO USE 12 OR LESS CORES PLEASE USE THE SMP SCRIPT!!! 11 | #$ -pe omp* 24 12 | # Queue 13 | #$ -q iqtc04.q 14 | # Shell 15 | #$ -S /bin/bash 16 | # (3) Output files 17 | #$ -cwd 18 | #$ -o vasp-XRQTC.VASP_ceria-surface-96.out 19 | #$ -e vasp-XRQTC.VASP_ceria-surface-96.err 20 | # (4) Remove the first '#' of the following 2 lines if you want to receive an email when the job ends. 21 | ##$ -m e 22 | ##$ -M yourmail@ub.edu 23 | ########################################## 24 | # User environment. 25 | ########################################## 26 | # Load the modules needed 27 | . /etc/profile.d/modules.sh 28 | module load VASP/4.6.36_ics-11.1.072_ompi-1.4.2 29 | ########################################## 30 | # Copying files needed 31 | ########################################## 32 | # We copy the inputs to the directory where the jobs will run 33 | #cd $TMPDIR 34 | mkdir -p /work/jblasco/vasp-XRQTC.VASP_ceria-surface-96 35 | cd /work/jblasco/vasp-XRQTC.VASP_ceria-surface-96 36 | cp -r $HOME/bench/VASP/XRQTC.VASP_ceria-surface/input/* . 37 | ########################################## 38 | # Run the job 39 | ########################################## 40 | export OMP_NUM_THREADS=1 41 | ulimit -l unlimited 42 | 43 | # -------------> WARNING <------------------- 44 | # Check what binary fits your needs 45 | # vasp MPI parallel, charge density and wavefunction complex 46 | # vasp_cd MPI parallel, charge density: half grid mode (-DNGZhalf) 47 | # vasp_gamma MPI parallel, gamma-point only (-DwNGZhalf) 48 | # vasp_vtst MPI parallel, charge density + wavefunction complex + VASP TST Tools 49 | # vasp_vtst_cd MPI parallel, charge density: half grid mode (-DNGZhalf) + VASP TST Tools 50 | # vasp_vtst_gamma MPI parallel, gamma-point only (-DwNGZhalf) + VASP TST Tools 51 | # ------------------------------------------- 52 | 53 | mpirun -np $NSLOTS vasp_cd 54 | 55 | ########################################## 56 | # Copy the results to our home directory 57 | ########################################## 58 | mkdir -p $HOME/bench/VASP/XRQTC.VASP_ceria-surface/OUT/vasp 59 | #cp -r $TMPDIR $HOME/bench/VASP/XRQTC.VASP_ceria-surface/OUT/vasp/ 60 | cp -r /work/jblasco/vasp-XRQTC.VASP_ceria-surface-96 $HOME/bench/VASP/XRQTC.VASP_ceria-surface/OUT/vasp/ 61 | rm -fr /work/jblasco/vasp-XRQTC.VASP_ceria-surface-96 62 | ########################################## 63 | # Temps dels resultats 64 | ########################################## 65 | TEMPS=$(cat OUTCAR | grep "Total CPU time used" | awk '{print $(NF)}') 66 | echo "$NSLOTS $TEMPS" >> $HOME/bench/VASP/XRQTC.VASP_ceria-surface/benchmark-Nehalem-DP-XRQTC.VASP_ceria-surface.dat 67 | 68 | -------------------------------------------------------------------------------- /GridEngine/vasp-5.2-ompi-iqtc01.sub: -------------------------------------------------------------------------------- 1 | #!/bin/bash 2 | ########################################## 3 | # SGE options and parameters 4 | ########################################## 5 | # (1) Name of the job 6 | #$ -N VASP-5.2-OpenMPI 7 | # (2) Requested resources 8 | # Parallel Environment and number of cores 9 | #$ -pe ompi 8 10 | # Queue 11 | #$ -q iqtc01.q 12 | # Shell 13 | #$ -S /bin/bash 14 | # (3) Output files 15 | #$ -cwd 16 | #$ -o vasp-ompi.out 17 | #$ -e vasp-ompi.err 18 | # (4) Remove the first '#' of the following 2 lines if you want to receive an email when the job ends. 19 | ##$ -m e 20 | ##$ -M yourmail@ub.edu 21 | ########################################## 22 | # User environment. 23 | ########################################## 24 | # Load the modules needed 25 | . /etc/profile.d/modules.sh 26 | module load vasp/5.2_intel11.1_openmpi1.3.3 27 | ########################################## 28 | # Copying files needed 29 | ########################################## 30 | # We copy the inputs to the directory where the jobs will run 31 | echo "Got $NSLOTS processors." 32 | cd $TMPDIR 33 | cp -r /home/jblasco/TESTS/vasp5.2/tests/test-hg/* . 34 | ########################################## 35 | # Run the job 36 | ########################################## 37 | export OMP_NUM_THREADS=1 38 | mpirun -np $NSLOTS vasp 39 | 40 | ########################################## 41 | # Copy the results to our home directory 42 | ########################################## 43 | mkdir -p $HOME/TESTS/vasp5.2/tests/out 44 | cp -r * $HOME/TESTS/vasp5.2/tests/out/ 45 | -------------------------------------------------------------------------------- /GridEngine/vasp-5.2-ompi-iqtc02.sub: -------------------------------------------------------------------------------- 1 | #!/bin/bash 2 | ########################################## 3 | # SGE options and parameters 4 | ########################################## 5 | # (1) Name of the job 6 | #$ -N VASP-5.2-OpenMPI 7 | # (2) Requested resources 8 | # Parallel Environment and number of cores 9 | #$ -pe ompi 16 10 | # Queue 11 | #$ -q iqtc02.q 12 | # Shell 13 | #$ -S /bin/bash 14 | # (3) Output files 15 | #$ -cwd 16 | #$ -o vasp-ompi.out 17 | #$ -e vasp-ompi.err 18 | # (4) Remove the first '#' of the following 2 lines if you want to receive an email when the job ends. 19 | ##$ -m e 20 | ##$ -M yourmail@ub.edu 21 | ########################################## 22 | # User environment. 23 | ########################################## 24 | # Load the modules needed 25 | . /etc/profile.d/modules.sh 26 | module load vasp/5.2 27 | ########################################## 28 | # Copying files needed 29 | ########################################## 30 | # We copy the inputs to the directory where the jobs will run 31 | echo "Got $NSLOTS processors." 32 | cd $TMPDIR 33 | cp -r /home/jblasco/TESTS/vasp5.2/tests/test-hg/* . 34 | ########################################## 35 | # Run the job 36 | ########################################## 37 | export OMP_NUM_THREADS=1 38 | mpirun -np $NSLOTS vasp 39 | 40 | ########################################## 41 | # Copy the results to our home directory 42 | ########################################## 43 | mkdir -p $HOME/TESTS/vasp5.2/tests/out 44 | cp -r * $HOME/TESTS/vasp5.2/tests/out/ 45 | -------------------------------------------------------------------------------- /GridEngine/vasp-5.2-ompi-iqtc03.sub: -------------------------------------------------------------------------------- 1 | #!/bin/bash 2 | ########################################## 3 | # SGE options and parameters 4 | ########################################## 5 | # (1) Name of the job 6 | #$ -N VASP-5.2-OpenMPI 7 | # (2) Requested resources 8 | # Parallel Environment and number of cores 9 | #$ -pe ompi 16 10 | # Queue 11 | #$ -q iqtc03.q 12 | # Shell 13 | #$ -S /bin/bash 14 | # (3) Output files 15 | #$ -cwd 16 | #$ -o vasp-ompi.out 17 | #$ -e vasp-ompi.err 18 | # (4) Remove the first '#' of the following 2 lines if you want to receive an email when the job ends. 19 | ##$ -m e 20 | ##$ -M yourmail@ub.edu 21 | ########################################## 22 | # User environment. 23 | ########################################## 24 | # Load the modules needed 25 | . /etc/profile.d/modules.sh 26 | module load vasp/5.2 27 | ########################################## 28 | # Copying files needed 29 | ########################################## 30 | # We copy the inputs to the directory where the jobs will run 31 | echo "Got $NSLOTS processors." 32 | cd $TMPDIR 33 | cp -r /home/jblasco/TESTS/vasp5.2/tests/test-hg/* . 34 | ########################################## 35 | # Run the job 36 | ########################################## 37 | export OMP_NUM_THREADS=1 38 | mpirun -np $NSLOTS vasp 39 | 40 | ########################################## 41 | # Copy the results to our home directory 42 | ########################################## 43 | mkdir -p $HOME/TESTS/vasp5.2/tests/out 44 | cp -r * $HOME/TESTS/vasp5.2/tests/out/ 45 | -------------------------------------------------------------------------------- /GridEngine/vasp-5.2-ompi-iqtc04.sub: -------------------------------------------------------------------------------- 1 | #!/bin/bash 2 | ########################################## 3 | # SGE options and parameters 4 | ########################################## 5 | # (1) Name of the job 6 | #$ -N XRQTC.VASP_ceria-surface-96 7 | # (2) Requested resources 8 | # Parallel Environment and number of cores 9 | #$ -pe omp* 24 10 | # Queue 11 | #$ -q iqtc04.q 12 | # Shell 13 | #$ -S /bin/bash 14 | # (3) Output files 15 | #$ -cwd 16 | #$ -o vasp-XRQTC.VASP_ceria-surface-96.out 17 | #$ -e vasp-XRQTC.VASP_ceria-surface-96.err 18 | # (4) Remove the first '#' of the following 2 lines if you want to receive an email when the job ends. 19 | ##$ -m e 20 | ##$ -M yourmail@ub.edu 21 | ########################################## 22 | # User environment. 23 | ########################################## 24 | # Load the modules needed 25 | . /etc/profile.d/modules.sh 26 | module load VASP/5.2.12_ics-11.1.072_ompi-1.4.2 27 | ########################################## 28 | # Copying files needed 29 | ########################################## 30 | # We copy the inputs to the directory where the jobs will run 31 | #cd $TMPDIR 32 | mkdir -p /work/jblasco/vasp-XRQTC.VASP_ceria-surface-96 33 | cd /work/jblasco/vasp-XRQTC.VASP_ceria-surface-96 34 | cp -r $HOME/bench/VASP/XRQTC.VASP_ceria-surface/input/* . 35 | ########################################## 36 | # Run the job 37 | ########################################## 38 | export OMP_NUM_THREADS=1 39 | ulimit -l unlimited 40 | 41 | # -------------> WARNING <------------------- 42 | # Check what binary fits your needs 43 | # vasp MPI parallel, charge density and wavefunction complex 44 | # vasp_cd MPI parallel, charge density: half grid mode (-DNGZhalf) 45 | # vasp_gamma MPI parallel, gamma-point only (-DwNGZhalf) 46 | # vasp_vtst MPI parallel, charge density + wavefunction complex + VASP TST Tools 47 | # vasp_vtst_cd MPI parallel, charge density: half grid mode (-DNGZhalf) + VASP TST Tools 48 | # vasp_vtst_gamma MPI parallel, gamma-point only (-DwNGZhalf) + VASP TST Tools 49 | # ------------------------------------------- 50 | 51 | mpirun -np $NSLOTS vasp_cd 52 | 53 | ########################################## 54 | # Copy the results to our home directory 55 | ########################################## 56 | mkdir -p $HOME/bench/VASP/XRQTC.VASP_ceria-surface/OUT/vasp 57 | #cp -r $TMPDIR $HOME/bench/VASP/XRQTC.VASP_ceria-surface/OUT/vasp/ 58 | cp -r /work/jblasco/vasp-XRQTC.VASP_ceria-surface-96 $HOME/bench/VASP/XRQTC.VASP_ceria-surface/OUT/vasp/ 59 | rm -fr /work/jblasco/vasp-XRQTC.VASP_ceria-surface-96 60 | ########################################## 61 | # Temps dels resultats 62 | ########################################## 63 | TEMPS=$(cat OUTCAR | grep "Total CPU time used" | awk '{print $(NF)}') 64 | echo "$NSLOTS $TEMPS" >> $HOME/bench/VASP/XRQTC.VASP_ceria-surface/benchmark-Nehalem-DP-XRQTC.VASP_ceria-surface.dat 65 | 66 | -------------------------------------------------------------------------------- /GridEngine/vasp-mpi.sub: -------------------------------------------------------------------------------- 1 | #!/bin/bash 2 | ########################################## 3 | # Opcions i parametres de l'SGE 4 | ########################################## 5 | # (1) Nom del treball (per identificar) 6 | #$ -N VASP-5.2-prova01 7 | # (2) Recursos sol.licitats 8 | #$ -l h_rt=0:50:0 9 | #$ -l mem_free=4.0G 10 | #$ -pe mpi 16 11 | # (3) Fitxers de sortida 12 | #$ -cwd 13 | #$ -o molcas01.out 14 | #$ -e molcas01.err 15 | #$ (4) Envia un mail quan acava el treball. 16 | #$ -m e 17 | #$ -M jblasco@fbg.ub.es 18 | ########################################## 19 | # Entorn d.usuari 20 | ########################################## 21 | # Es carreguen els moduls a utilitzar 22 | module load vasp/5.2 23 | module load openmpi 24 | ########################################## 25 | # transferencia de dades 26 | ########################################## 27 | # Es copien les dades al directori on es llenc,aran els calculs. 28 | cd $TMPDIR 29 | export Project=vasp_mpi_16 30 | export Input=$Project 31 | cp -pr $HOME/path/amb/els/inputs/ $Input 32 | ########################################## 33 | # calcul 34 | ########################################## 35 | # Es crea un directori de sortida pels resultats. 36 | export OMP_NUM_THREADS=1 37 | mpirun -C np $NSLOTS $pe_machines vasp 38 | 39 | ########################################## 40 | # Transferencia dels resultats 41 | ########################################## 42 | cp -pr $Input $HOME/path/a/on/guardar/els/outputs/ 43 | -------------------------------------------------------------------------------- /LSF/ior.lsf: -------------------------------------------------------------------------------- 1 | #!/bin/bash 2 | #BSUB -J IOR 3 | #BSUB -W 2:00 4 | #BSUB -n 8 5 | #BSUB -e %J.err 6 | #BSUB -o %J.out 7 | #BSUB -m "hostA hostD hostB" 8 | module load openmpi/4.0.2 9 | 10 | # Options 11 | NUM_PROCS=8 12 | #BLOCK_SIZE=$((3*${RAM_SIZE_PER_STORAGE_SERVER}*${NUM_STORAGE_SERVERS})/${NUM_PROCS})) 13 | BLOCK_SIZE=4000 14 | WORKDIR=$HOME/workdir/ior 15 | mkdir -p $WORKDIR 16 | cd $WORKDIR 17 | 18 | #Multi-stream Throughput Benchmark 19 | mpirun --map-by node -np ${NUM_PROCS} ~/IOR/IOR -wr -i5 -t2m -b ${BLOCK_SIZE} -g -F -e 20 | -o $WORKDIR/ior_multi_stream_throughput.txt 21 | 22 | #Shared File Throughput Benchmark 23 | mpirun --map-by node -np ${NUM_PROCS} ~/IOR/IOR -wr -i5 -t1200k -b ${BLOCK_SIZE} -g -e 24 | -o $WORKDIR/ior_share_file_throughput.txt 25 | 26 | # IOPS Benchmark 27 | mpirun --map-by node -np ${NUM_PROCS} ~/IOR/IOR -w -i5 -t4k -b ${BLOCK_SIZE} -F -z -g 28 | -o $WORKDIR/ior_iops.txt 29 | -------------------------------------------------------------------------------- /LSF/iozone.lsf: -------------------------------------------------------------------------------- 1 | #!/bin/bash 2 | #BSUB -J IOZone 3 | #BSUB -W 2:00 4 | #BSUB -n 1 5 | #BSUB -e %J.err 6 | #BSUB -o %J.out 7 | #BSUB -m "hostA hostD hostB" 8 | module load openmpi/4.0.2 9 | WORKDIR=$HOME/workdir/iozone 10 | mkdir -p $WORKDIR 11 | cd $WORKDIR 12 | ~/iozone –Rac –g 16G > $WORKDIR/iozone.log 13 | -------------------------------------------------------------------------------- /LSF/mdtest.lsf: -------------------------------------------------------------------------------- 1 | #!/bin/bash 2 | #BSUB -J MDTest 3 | #BSUB -W 2:00 4 | #BSUB -n 1 5 | #BSUB -e %J.err 6 | #BSUB -o %J.out 7 | #BSUB -m "hostA hostD hostB" 8 | module load openmpi/4.0.2 9 | 10 | # Options 11 | # 12 | # The value for the number of processes ${NUM_PROCS} depends on the number on clients to test and the number of processes per client to test. 13 | # The number of directories can be calculated as ${NUM_DIRS} = (parameter -b ^ parameter -z). 14 | # The total amount of files should always be higher than 1 000 000, so ${FILES_PER_DIR} is calculated as: 15 | 16 | NUM_DIRS=18 17 | NUM_PROCS=1 18 | FILES_PER_DIR=$((1000000 / ${NUM_DIRS} / ${NUM_PROCS})) 19 | WORKDIR=$HOME/workdir/mdtest 20 | mkdir -p $WORKDIR 21 | cd ~/mdtest 22 | # mpirun --map-by node -np 10 mdtest -C -T -r -F -d $HOME/workdir/mdtest -i 3 -I ${FILES_PER_DIR} -z 2 -b 8 -L -u 23 | ./mdtest -d /tmp/ -b 18 -z 2 -i 1 -I ${FILES_PER_DIR} -d $WORKDIR 24 | -------------------------------------------------------------------------------- /README.md: -------------------------------------------------------------------------------- 1 | High Performance Computing Knowledge Portal 2 | ==================================================================== 3 | This GIT Project contains a collection of usefull Submit Scripts 4 | for most popular applications in HPC. 5 | 6 | Please, send us feedback and suggestions. 7 | 8 | Thanks! 9 | 10 | Learn more about HPC Knowledge Portal @ http://www.hpckp.org 11 | 12 | Learn more about HPCNow! @ http://www.hpcnow.com 13 | -------------------------------------------------------------------------------- /Slurm/GATK_multithreads.sl: -------------------------------------------------------------------------------- 1 | #!/bin/bash 2 | # GATK SubmitScript 3 | ################################################################# 4 | #SBATCH -J GATK_SHM_THREADS 5 | #SBATCH -A hpcnow # Project Account 6 | #SBATCH --time=08:00:00 # Walltime 7 | #SBATCH --mem-per-cpu=4G # memory/cpu 8 | #SBATCH --cpus-per-task=4 # 4 OpenMP Threads 9 | ################################################################# 10 | ### Load the Environment 11 | module load GATK/3.1-1 12 | ################################################################# 13 | ### The files will be allocated in the /dev/shm FS 14 | cd $SHM_DIR 15 | cp -r /sNow/test/GATK/examples/* . 16 | ################################################################# 17 | ### Run the Parallel Program 18 | ### More information about Multihreading capabilities here: 19 | ### http://gatkforums.broadinstitute.org/discussion/1975/how-can-i-use-parallelism-to-make-gatk-tools-run-faster 20 | MEM=$(($SLURM_CPUS_PER_TASK*$SLURM_MEM_PER_CPU)) 21 | srun java -Xmx${MEM}m -Djava.io.tmpdir=$SHM_DIR -jar $GATK -R exampleFASTA.fasta -I exampleBAM.bam -T CountReads 22 | # Multi-threading options 23 | # -nt / --num_threads controls the number of data threads sent to the processor 24 | # -nct / --num_cpu_threads_per_data_thread controls the number of CPU threads allocated to each data thread 25 | #srun java -Xmx${MEM}m -Djava.io.tmpdir=$SHM_DIR -jar $GATK -R exampleFASTA.fasta -I exampleBAM.bam -T CountReads -nct $SLURM_CPUS_PER_TASK 26 | #srun java -Xmx${MEM}m -Djava.io.tmpdir=$SHM_DIR -jar $GATK -R exampleFASTA.fasta -I exampleBAM.bam -T CountReads -nt $SLURM_CPUS_PER_TASK 27 | ################################################################# 28 | ### Transferring the results to the project directory 29 | #mkdir -p $HOME/OUT/GATK 30 | #cp -pr *out $HOME/OUT/GATK/ 31 | -------------------------------------------------------------------------------- /Slurm/Intel-Trace-Analyser-and-Collector-instrumented.sl: -------------------------------------------------------------------------------- 1 | #!/bin/bash 2 | #SBATCH -J ITAC 3 | #SBATCH -A hpcnow 4 | #SBATCH --time=6:00:00 5 | #SBATCH --mem-per-cpu=6144 6 | #SBATCH --ntasks=48 7 | #SBATCH --nodes=2 8 | ml 2021 9 | ml intel/2021a 10 | ml VTune/2021.6.0 11 | ml itac/2021.5.0 12 | source itacvars.sh impi5 13 | ###################################################################################### 14 | export VT_PCTRACE=4 15 | export VT_CONFIG=/sNow/SubmitScripts/slurm/trace.conf 16 | # the code needs to be compiled with -tcollect option in order to be instrumented 17 | # mpiifort -g -O3 -xhost -ip -tcollect yourcode.f -o yourcode_traces $VT_ADD_LIBS 18 | srun /path/to/instrumented/code [my apps options] 19 | -------------------------------------------------------------------------------- /Slurm/Intel-Trace-Analyser-and-Collector.sl: -------------------------------------------------------------------------------- 1 | #!/bin/bash 2 | #SBATCH -J ITAC 3 | #SBATCH -A hpcnow 4 | #SBATCH --time=6:00:00 5 | #SBATCH --mem-per-cpu=6144 6 | #SBATCH --ntasks=48 7 | #SBATCH --nodes=2 8 | ml 2021 9 | ml intel/2021a 10 | ml VTune/2021.6.0 11 | ml itac/2021.5.0 12 | source itacvars.sh impi5 13 | ###################################################################################### 14 | unset I_MPI_PMI_LIBRARY 15 | mpiexec.hydra -trace /path/to/instrumented/code [my apps options] 16 | -------------------------------------------------------------------------------- /Slurm/OpenFOAM-parallel.sl: -------------------------------------------------------------------------------- 1 | #!/bin/bash 2 | #SBATCH -J OpenFOAM 3 | #SBATCH -A hpcnow # Project account 4 | #SBATCH -D /sNow/tests/OpenFOAM/test01 5 | #SBATCH --time=06:00:00 # Walltime 6 | #SBATCH --mem-per-cpu=4G # memory/cpu 7 | #SBATCH --ntasks=256 # MPI processes 8 | 9 | module load OpenFOAM/2.3.0-ictce-5.4.0 10 | source $FOAM_BASH 11 | 12 | srun interFoam -parallel 13 | 14 | -------------------------------------------------------------------------------- /Slurm/OpenFOAM-serial.sl: -------------------------------------------------------------------------------- 1 | #!/bin/bash 2 | #SBATCH -J OpenFOAM 3 | #SBATCH -A hpcnow # Project account 4 | #SBATCH -D /projects/hpcnow/planejet 5 | #SBATCH --time=06:00:00 # Walltime 6 | #SBATCH --mem-per-cpu=4G # memory/cpu 7 | 8 | module load OpenFOAM/2.3.0-ictce-5.4.0 9 | source $FOAM_BASH 10 | 11 | srun blockMesh 12 | srun simpleFoam 13 | 14 | -------------------------------------------------------------------------------- /Slurm/OpenSees.sl: -------------------------------------------------------------------------------- 1 | #!/bin/bash 2 | #SBATCH -J example 3 | #SBATCH -A hpcnow # Project Account 4 | #SBATCH --time=00:20:00 # Walltime 5 | #SBATCH --ntasks=48 # number of tasks 6 | #SBATCH --mem-per-cpu=2G # memory/cpu 7 | #SBATCH --workdir=/sNow/test/OpenSees 8 | #SBATCH -C wm 9 | module load OpenSees 10 | srun OpenSeesMP ./example.tcl 11 | -------------------------------------------------------------------------------- /Slurm/QuantumESPRESSO-hybrid.sl: -------------------------------------------------------------------------------- 1 | #!/bin/bash 2 | #SBATCH -J QuantumESPRESSO-Hybrid 3 | #SBATCH -A hpcnow # Project Account 4 | #SBATCH --ntasks=64 # number of tasks 5 | #SBATCH --mem-per-cpu=4G # memory/cpu 6 | #SBATCH --cpus-per-task=8 # 8 OpenMP Threads 7 | #SBATCH --time=2:00:00 8 | 9 | # Load the user environment 10 | ml QuantumESPRESSO/5.0.2-intel-2015a 11 | ### The files will be allocated in the shared FS 12 | cp -pr /sNow/test/QuantumESPRESSO/Benchmarks/GRIR443/* $SCRATCH_DIR/ 13 | cd $SCRATCH_DIR 14 | ### how to run executables (not all of them are parallel) 15 | PARA_PREFIX=srun 16 | PARA_POSTFIX="-ntg 8" 17 | ### available flags: 18 | # -nimage n number of images (or -nimages) 19 | # -npool n number of pools (or -npools) 20 | # -nband n number of band groups (or -nb, -nbgrp, -nband_group ) 21 | # -ntask_groups n number of task groups (or -ntg) 22 | # -ndiag n number of processors for linear algebra (or -nproc_ortho, -northo, -nproc_diag) 23 | PW_COMMAND="$PARA_PREFIX pw.x $PARA_POSTFIX" 24 | PP_COMMAND="$PARA_PREFIX pp.x $PARA_POSTFIX" 25 | PLOTRHO_COMMAND="$PARA_PREFIX plotrho.x" 26 | BANDS_COMMAND="$PARA_PREFIX bands.x $PARA_POSTFIX" 27 | PLOTBAND_COMMAND="$PARA_PREFIX plotband.x" 28 | ### Run the Parallel Program 29 | $PW_COMMAND -in grir443.in 30 | ### Transfer output files back to the project folder 31 | #cp -pr $SCRATCH_DIR/ /your_project/folder/ 32 | -------------------------------------------------------------------------------- /Slurm/QuantumESPRESSO-mpi.sl: -------------------------------------------------------------------------------- 1 | #!/bin/bash 2 | #SBATCH -J QuantumESPRESSO-MPI 3 | #SBATCH -A hpcnow # Project Account 4 | #SBATCH --ntasks=512 # number of tasks 5 | #SBATCH --mem-per-cpu=4G # memory/cpu 6 | #SBATCH --time=2:00:00 7 | 8 | # Load the user environment 9 | ml QuantumESPRESSO/5.0.2-intel-2015a 10 | ### The files will be allocated in the shared FS 11 | cp -pr /sNow/test/QuantumESPRESSO/Benchmarks/GRIR443/* $SCRATCH_DIR/ 12 | cd $SCRATCH_DIR 13 | ### how to run executables (not all of them are parallel) 14 | PARA_PREFIX=srun 15 | PARA_POSTFIX= 16 | ### available flags: 17 | # -nimage n number of images (or -nimages) 18 | # -npool n number of pools (or -npools) 19 | # -nband n number of band groups (or -nb, -nbgrp, -nband_group ) 20 | # -ntask_groups n number of task groups (or -ntg) 21 | # -ndiag n number of processors for linear algebra (or -nproc_ortho, -northo, -nproc_diag) 22 | PW_COMMAND="$PARA_PREFIX pw.x $PARA_POSTFIX" 23 | PP_COMMAND="$PARA_PREFIX pp.x $PARA_POSTFIX" 24 | PLOTRHO_COMMAND="$PARA_PREFIX plotrho.x" 25 | BANDS_COMMAND="$PARA_PREFIX bands.x $PARA_POSTFIX" 26 | PLOTBAND_COMMAND="$PARA_PREFIX plotband.x" 27 | ### Run the Parallel Program 28 | $PW_COMMAND -in grir443.in 29 | ### Transfer output files back to the project folder 30 | #cp -pr $SCRATCH_DIR/ /your_project/folder/ 31 | -------------------------------------------------------------------------------- /Slurm/R-parallel-mpi.r: -------------------------------------------------------------------------------- 1 | library(Rmpi) 2 | 3 | id <- mpi.comm.rank(comm = 0) 4 | np <- mpi.comm.size(comm = 0) 5 | hostname <- mpi.get.processor.name() 6 | 7 | msg <- sprintf("Hello world from process %03d of %03d, on host %s\n", 8 | id, np, hostname) 9 | cat(msg) 10 | 11 | mpi.barrier(comm = 0) 12 | mpi.finalize() 13 | -------------------------------------------------------------------------------- /Slurm/R-parallel-mpi.sl: -------------------------------------------------------------------------------- 1 | #!/bin/bash 2 | #SBATCH -A hpcnow 3 | #SBATCH --ntasks=24 4 | #SBATCH --time=00:10:00 5 | #SBATCH --mem-per-cpu=2G 6 | #SBATCH --job-name=TestJob 7 | 8 | module load R/3.0.3-goolf-1.5.14 9 | mpirun Rscript R-parallel-mpi.r 10 | -------------------------------------------------------------------------------- /Slurm/R-template.sl: -------------------------------------------------------------------------------- 1 | #!/bin/bash 2 | #SBATCH -A hpcnow 3 | #SBATCH --time=7-00:00:00 4 | #SBATCH --mem-per-cpu=6G 5 | #SBATCH -J TestJob 6 | 7 | module load R/3.0.3-goolf-1.5.14 8 | 9 | srun Rscript ./PMT.R 10 | -------------------------------------------------------------------------------- /Slurm/VASP-iomkl.sl: -------------------------------------------------------------------------------- 1 | #!/bin/bash 2 | # Scalability tests 3 | # for i in {4..12}; do sbatch --ntasks=$(($i*$i)) --nodes=$((($i*$i)/12))-$((1+($i*$i)/12)) -C wm /sNow/SubmitScripts/slurm/VASP-iomkl.sl ; done 4 | #SBATCH -J VASPBench 5 | #SBATCH -A hpcnow 6 | #SBATCH --time=1:59:00 7 | ##SBATCH --ntasks=96 8 | #SBATCH --mem-per-cpu=8G 9 | ml VASP/5.3.5-iomkl-4.6.13 10 | cd $SCRATCH_DIR 11 | # 12 | # Available tests are : NeSI.VASP_BandsandDOS NeSI.VASP_SurfOpt XRQTC.VASP_ceria-surface XRQTC.VASP_DFT 13 | # 14 | TEST=KristaGSteenbergen-MD-bulk_melting 15 | cp -pr /sNow/test/VASP/$TEST/input/* . 16 | SQRTCORES=$(echo "sqrt($SLURM_NPROCS)"|bc) 17 | sed -i "s/SQRTCORES/$SQRTCORES/g" INCAR 18 | ########################################################################## 19 | ### Run the Parallel Program 20 | # -------------> WARNING <------------------- 21 | # Check what binary fits your needs 22 | # vasp MPI parallel, charge density and wavefunction complex 23 | # vasp_cd MPI parallel, charge density: half grid mode (-DNGZhalf) 24 | # vasp_md_cd MPI parallel, charge density: half grid mode (-DNGZhalf), MD 25 | # vasp_gamma MPI parallel, gamma-point only (-DwNGZhalf) 26 | # vasp_md_gamma MPI parallel, gamma-point only (-DwNGZhalf), MD 27 | # vasp_vtst MPI parallel, charge density + wavefunction complex + VASP TST Tools 28 | # vasp_vtst_cd MPI parallel, charge density: half grid mode (-DNGZhalf) + VASP TST Tools 29 | # vasp_vtst_gamma MPI parallel, gamma-point only (-DwNGZhalf) + VASP TST Tools 30 | # ------------------------------------------- 31 | export OMP_NUM_THREADS=1 32 | VASPBIN=vasp_md_cd 33 | srun $VASPBIN 34 | ########################################################################## 35 | ### Transfering the results to the home directory ($HOME) 36 | mkdir -p /sNow/test/VASP/OUT/$TEST 37 | rm WAVECAR CHG* 38 | cp -pr $SCRATCH_DIR /sNow/test/VASP/OUT/$TEST/ 39 | TEMPS=$(cat OUTCAR | grep "Total CPU time used" | awk '{print $(NF)}') 40 | echo "$SLURM_NPROCS $TEMPS" >> /sNow/test/VASP/benchmark-$TEST-$VASPBIN-5.3.5-iomkl-4.6.13-$LMOD_SYSTEM_NAME.log 41 | -------------------------------------------------------------------------------- /Slurm/VTune-MPI.sl: -------------------------------------------------------------------------------- 1 | #!/bin/bash 2 | #SBATCH -J VTuneMPI 3 | #SBATCH -A hpcnow 4 | #SBATCH --time=1:00:00 5 | #SBATCH --mem-per-cpu=8G 6 | #SBATCH -C ib 7 | #SBATCH --ntasks=48 8 | #SBATCH --nodes=2 9 | ml 2021 10 | ml intel/2021a 11 | ml VTune/2021.6.0 12 | ml itac/2021.5.0 13 | 14 | # Some sites may require to unset the following variable and use mpiexec.hydra instead of srun. 15 | #unset I_MPI_PMI_LIBRARY 16 | # The following line uses GTOOL option to instruct Intel MPI to collect the hotspots metrics using VTune only on task #11. 17 | export I_MPI_GTOOL="vtune -collect hotspots -r result:10" 18 | srun my_app [my_app_options] 19 | 20 | #To analyze a single MPI process with VTune Profiler, you must specify the relevant command in the corresponding argument set. The example below runs 47 MPI tasks where one of them is analysed with vtune: 21 | #mpiexec.hydra -n 47 ./my_app : -n 1 vtune -c hotspots -r results_dir -- ./my_app 22 | -------------------------------------------------------------------------------- /Slurm/VTune-OpenMP.sl: -------------------------------------------------------------------------------- 1 | #!/bin/bash 2 | #SBATCH -J VTuneOpenMP 3 | #SBATCH -A hpcnow 4 | #SBATCH --time=1:00:00 5 | #SBATCH --mem-per-cpu=4G 6 | #SBATCH -C ib 7 | #SBATCH --cpus-per-task=24 8 | ml 2021 9 | ml intel/2021a 10 | ml VTune/2021.6.0 11 | 12 | srun vtune -r my_profile_dir -c hotspots my_app [my_app_options] 13 | -------------------------------------------------------------------------------- /Slurm/VTune-serial.sl: -------------------------------------------------------------------------------- 1 | #!/bin/bash 2 | #SBATCH -J VTuneSerial 3 | #SBATCH -A hpcnow 4 | #SBATCH --time=1:00:00 5 | #SBATCH --mem-per-cpu=4G 6 | #SBATCH -C ib 7 | #SBATCH --cpus-per-task=1 8 | ml 2021 9 | ml intel/2021a 10 | ml VTune/2021.6.0 11 | 12 | srun vtune -r my_profile_dir -c hotspots my_app [my_app_options] 13 | -------------------------------------------------------------------------------- /Slurm/abaqus.sl: -------------------------------------------------------------------------------- 1 | #!/bin/bash 2 | # Abaqus SubmitScript 3 | # Optimized for run parallel job 4 | ###################################################### 5 | #SBATCH -J Abaqus_TEST 6 | #SBATCH -A hpcnow # Project Account 7 | #SBATCH --time=08:00:00 # Walltime 8 | #SBATCH --ntasks=24 # number of tasks 9 | #SBATCH --mem-per-cpu=1G # memory/cpu 10 | ###################################################### 11 | ### Load the Environment 12 | module load Abaqus 13 | ###################################################### 14 | ### The files will be allocated in the shared FS 15 | #cp myinput.inp $SCRATCH_DIR 16 | #cd $SCRATCH_DIR 17 | source /sNow/SubmitScripts/slurm/slurm_setup_abaqus-env.sh 18 | ###################################################### 19 | ### Run the Parallel Program 20 | abaqus job=test input=myinput.inp cpus=$SLURM_NTASKS -verbose 3 standard_parallel=all mp_mode=mpi interactive 21 | ###################################################### 22 | ### Transferring the results to the home directory ($HOME) 23 | #mkdir -p $HOME/OUT/abaqus 24 | #cp -pr $SCRATCH_DIR $HOME/OUT/abaqus 25 | -------------------------------------------------------------------------------- /Slurm/ansys-cfx.sl: -------------------------------------------------------------------------------- 1 | #!/bin/bash 2 | # ANSYS_FLUENT SubmitScript 3 | # Optimized for run parallel job 4 | ###################################################### 5 | #SBATCH -J ANSYS_CFX_TEST 6 | #SBATCH -A hpcnow # Project Account 7 | #SBATCH --time=01:00:00 # Walltime 8 | #SBATCH --ntasks=16 # number of tasks 9 | #SBATCH --mem-per-cpu=7G # memory/cpu 10 | ###################################################### 11 | 12 | ### Load the Environment 13 | module load ANSYS/15.0 14 | 15 | source /sNow/SubmitScripts/slurm/slurm_setup_cfx-env2.sh 16 | 17 | # Executable and input file. 18 | defname=example.def 19 | 20 | cfx5solve -batch -single -def $defname -par -par-dist $CFX_HOSTLIST 21 | -------------------------------------------------------------------------------- /Slurm/ansys-fluent-requeue.sl: -------------------------------------------------------------------------------- 1 | #!/bin/bash 2 | # ANSYS_FLUENT SubmitScript 3 | # Optimized for run parallel job 4 | ################################################################ 5 | #SBATCH -J FLUENT_REQUEUE 6 | #SBATCH -A hpcnow # Project Account 7 | #SBATCH --time=01:03:00 # Walltime 8 | #SBATCH --ntasks=48 # number of tasks 9 | #SBATCH --mem-per-cpu=4G # memory/cpu 10 | #SBATCH -C sb 11 | #SBATCH -p requeue 12 | ################################################################ 13 | ### Load the Environment 14 | module load ANSYS/15.0 15 | cd /sNow/test/ansys/fluent/case3/input/ 16 | ### Creating the hostfile 17 | srun hostname > FLUENT_HOSTFILE 18 | ### Run Fluent Model 19 | fluent -v3ddp -g -t $SLURM_NTASKS -mpi=pcmpi -cnf=FLUENT_HOSTFILE -pinfiniband -ssh << EOFluentInput > stats-$SLURM_NTASKS-$SLURM_JOBID.out 20 | rc a16.cas 21 | rd fluent-1-12000.dat 22 | /solve/dual-time-iterate 10 10 23 | /file/write-case-data a16-$SLURM_NTASKS-$SLURM_JOBID.out 24 | exit 25 | EOFluentInput 26 | ################################################################ 27 | -------------------------------------------------------------------------------- /Slurm/ansys-fluent.sl: -------------------------------------------------------------------------------- 1 | #!/bin/bash 2 | # ANSYS_FLUENT SubmitScript 3 | # Optimized for run parallel job 4 | ###################################################### 5 | #SBATCH -J ANSYS_FLUENT_TEST 6 | #SBATCH -A hpcnow # Project Account 7 | #SBATCH --time=01:03:00 # Walltime 8 | #SBATCH --ntasks=24 # number of tasks 9 | #SBATCH --mem-per-cpu=4G # memory/cpu 10 | #SBATCH --nodes=1-2 11 | ###################################################### 12 | ### Load the Environment 13 | module load ANSYS/15.0 14 | 15 | rm FLUENT_HOSTFILE 16 | srun hostname > FLUENT_HOSTFILE 17 | cat FLUENT_HOSTFILE 18 | 19 | ######################################################### 20 | ## Run the Parallel Program 21 | # the following is a generic command. In order to get this command working 22 | # please decide if you want to run the 2d or 2ddp OR 3d OR 3ddp solver and 23 | # please use ONLY one of the options in the <> shown below 24 | # fluent <2d|2ddp|3d|3ddp> -g -t2 25 | fluent -v3ddp -g -t$SLURM_NTASKS -mpi=pcmpi -cnf=FLUENT_HOSTFILE -pib -ssh << EOFluentInput > output1.stat.dat 26 | rcd testCase.cas 27 | /solve/dual-time-iterate 201 28 | /file/write-case-data cdfiner.out.cas 29 | exit 30 | EOFluentInput 31 | ###################################################### 32 | ### Transferring the results to the home directory ($HOME) 33 | -------------------------------------------------------------------------------- /Slurm/array-io.sl: -------------------------------------------------------------------------------- 1 | #!/bin/bash 2 | #SBATCH -J JobArray 3 | #SBATCH --time=01:00:00 # Walltime 4 | #SBATCH -A hpcnow # Project Account 5 | #SBATCH --ntasks=1 # number of tasks 6 | #SBATCH --mem-per-cpu=8G # memory/cpu 7 | #SBATCH --cpus-per-task=4 # 4 OpenMP Threads 8 | #SBATCH --array=1-1000 # Array definition 9 | #SBATCH --gres=io # IO intensive jobs 10 | srun sleep $SLURM_ARRAY_TASK_ID 11 | srun echo running on $(hostname) 12 | -------------------------------------------------------------------------------- /Slurm/array-mpi.sl: -------------------------------------------------------------------------------- 1 | #!/bin/bash 2 | #SBATCH -J JobArray 3 | #SBATCH --time=01:00:00 # Walltime 4 | #SBATCH -A hpcnow # Project Account 5 | #SBATCH --ntasks=2 # number of tasks 6 | #SBATCH --mem-per-cpu=8G # memory/cpu 7 | #SBATCH --cpus-per-task=2 # 4 OpenMP Threads 8 | #SBATCH --array=20-180 # Array definition 9 | srun sleep $SLURM_ARRAY_TASK_ID 10 | srun echo running on $(hostname) 11 | #srun stress --cpu 1 --vm-bytes 128M --timeout 10s 12 | module load intel/2015a 13 | srun /sNow/utils/bin/pi_mpi 14 | -------------------------------------------------------------------------------- /Slurm/array.sl: -------------------------------------------------------------------------------- 1 | #!/bin/bash 2 | #SBATCH -J JobArray 3 | #SBATCH --time=01:00:00 # Walltime 4 | #SBATCH -A hpcnow # Project Account 5 | #SBATCH --ntasks=1 # number of tasks 6 | #SBATCH --mem-per-cpu=8G # memory/cpu 7 | #SBATCH --cpus-per-task=2 # 4 OpenMP Threads 8 | #SBATCH --array=100-120 # Array definition 9 | srun sleep $SLURM_ARRAY_TASK_ID 10 | srun echo running on $(hostname) 11 | -------------------------------------------------------------------------------- /Slurm/array_builder.sh: -------------------------------------------------------------------------------- 1 | #!/bin/bash 2 | for o in $(seq 2 2 2); do 3 | for po in $(seq 2.5 0.5 10.000); do 4 | for osc in $(seq 2 .25 2.00); do 5 | for freq in $(seq .6 .2 .800); do 6 | echo "${osc} ${freq} ${po} 1500 ${o}" >> params.dat 7 | done 8 | done 9 | done 10 | done 11 | -------------------------------------------------------------------------------- /Slurm/array_multi_parameters.sl: -------------------------------------------------------------------------------- 1 | #!/bin/bash 2 | #SBATCH -J JobArray 3 | #SBATCH --time=01:00:00 # Walltime 4 | #SBATCH -A hpcnow # Project Account 5 | #SBATCH --mem-per-cpu=1G # memory/cpu 6 | #SBATCH --array=1-1000 # Array definition 7 | #SBATCH -n 64 8 | 9 | # If you need to explore several parameters or to use several input files 10 | # you can create a mapping file like params.dat and use a single array 11 | # job description file to run all the simulations. 12 | # The script array_builder.sh is a simple example that generates the params.dat file 13 | 14 | PARAMETERS=$(sed -n ${SLURM_ARRAY_TASK_ID}p params.dat) 15 | 16 | #srun your_binary $PARAMETERS 17 | srun -n 1 sleep 120 18 | -------------------------------------------------------------------------------- /Slurm/blast+_array.sl: -------------------------------------------------------------------------------- 1 | #!/bin/bash 2 | # NCBI-BLAST+ SubmitScript 3 | # Optimized for run 500 array jobs using single core each. 4 | ################################################################# 5 | #SBATCH -J BLAST-SHM 6 | #SBATCH -A hpcnow # Project Account 7 | #SBATCH --time=08:00:00 # Walltime 8 | #SBATCH --mem-per-cpu=4G # memory/cpu 9 | #SBATCH --cpus-per-task=1 # 1 OpenMP Threads 10 | #SBATCH --array=1-500 # Array definition 11 | ################################################################# 12 | ### Load the Environment 13 | module load BLAST/2.2.29-intel-2015a 14 | ################################################################# 15 | ### The files will be allocated in the /dev/shm FS 16 | echo $SHM_DIR 17 | mkdir $SHM_DIR/{queries,results} 18 | QUERY=frag_$(printf "%03d\n" $SLURM_ARRAY_TASK_ID) 19 | cp -r /sNow/test/blast/queries/$QUERY $SHM_DIR/queries/ 20 | cd $SHM_DIR 21 | ################################################################# 22 | ### Run the Parallel Program 23 | echo $SLURM_ARRAY_TASK_ID 24 | srun blastn -query queries/$QUERY \ 25 | -db nt -task blastn -num_alignments 5 \ 26 | -num_descriptions 5 -evalue 0.0001 \ 27 | -out results/$QUERY.out 28 | ################################################################# 29 | ### Transferring the results to the project directory 30 | mkdir -p $HOME/OUT/BLAST 31 | cp -pr results/$QUERY.out $HOME/OUT/BLAST/ 32 | -------------------------------------------------------------------------------- /Slurm/blast+_array_multithreads.sl: -------------------------------------------------------------------------------- 1 | #!/bin/bash 2 | # NCBI-BLAST+ SubmitScript 3 | # Optimized for run 1000 array jobs using 4 Threads each. 4 | ################################################################# 5 | #SBATCH -J BLAST_SHM_THREADS 6 | #SBATCH -A hpcnow # Project Account 7 | #SBATCH --time=08:00:00 # Walltime 8 | #SBATCH --mem-per-cpu=4G # memory/cpu 9 | #SBATCH --cpus-per-task=4 # 4 OpenMP Threads 10 | #SBATCH --array=1-1000 # Array definition 11 | ################################################################# 12 | ### Load the Environment 13 | module load BLAST/2.2.29-intel-2015a 14 | ################################################################# 15 | ### The files will be allocated in the /dev/shm FS 16 | echo $SHM_DIR 17 | mkdir $SHM_DIR/{queries,results} 18 | QUERY=frag_$(printf "%03d\n" $SLURM_ARRAY_TASK_ID) 19 | cp -r /sNow/test/blast/queries/$QUERY $SHM_DIR/queries/ 20 | cd $SHM_DIR 21 | ################################################################# 22 | ### Run the Parallel Program 23 | echo $SLURM_ARRAY_TASK_ID 24 | srun blastn -query queries/$QUERY \ 25 | -db nt -task blastn -num_alignments 5 \ 26 | -num_threads 3 -num_descriptions 5 -evalue 0.0001 \ 27 | -out results/$QUERY.out 28 | ################################################################# 29 | ### Transferring the results to the project directory 30 | mkdir -p $HOME/OUT/BLAST 31 | cp -pr results/$QUERY.out $HOME/OUT/BLAST/ 32 | -------------------------------------------------------------------------------- /Slurm/checkpoint-blcr.sl: -------------------------------------------------------------------------------- 1 | #!/bin/bash 2 | #SBATCH -J OpenMP_JOB 3 | #SBATCH -A hpcnow # Project Account 4 | #SBATCH --time=01:05:00 # Walltime 5 | #SBATCH --mem-per-cpu=6G # memory/cpu 6 | #SBATCH --cpus-per-task=12 # 12 OpenMP Threads 7 | export SLURM_CHECKPOINT=12:00:00 8 | export SLURM_CHECKPOINT_DIR=$CHK_DIR/$SLURM_JOB_NAME 9 | #export SLURM_RESTART_DIR=$SLURM_CHECKPOINT_DIR 10 | 11 | mkdir $SLURM_CHECKPOINT_DIR 12 | 13 | cd $SCRATCH_DIR 14 | 15 | srun_cr sleep 3600 16 | #srun_cr stress --vm 1 --vm-bytes 128M --timeout 3600s 17 | -------------------------------------------------------------------------------- /Slurm/cuda-mpi.sl: -------------------------------------------------------------------------------- 1 | #!/bin/bash 2 | #SBATCH -J GPU_JOB 3 | #SBATCH --time=01:00:00 # Walltime 4 | #SBATCH -A hpcnow # Project Account 5 | #SBATCH --ntasks=4 # number of tasks 6 | #SBATCH --ntasks-per-node=2 # number of tasks per node 7 | #SBATCH --mem-per-cpu=8G # memory/cpu 8 | #SBATCH --cpus-per-task=4 # 4 OpenMP Threads 9 | #SBATCH --gres=gpu:2 # GPUs per node 10 | srun binary_cuda_mpi 11 | -------------------------------------------------------------------------------- /Slurm/cuda.sl: -------------------------------------------------------------------------------- 1 | #!/bin/bash 2 | # CUDA SubmitScript 3 | ########################################################################## 4 | #SBATCH -J CUDA_JOB 5 | #SBATCH --time=01:00:00 # Walltime 6 | #SBATCH -A hpcnow # Project Account 7 | #SBATCH --mem-per-cpu=2G # memory/cpu 8 | #SBATCH --cpus-per-task=2 # 2 OpenMP Threads 9 | #SBATCH --ntasks=1 10 | #SBATCH --gres=gpu:2 11 | ########################################################################## 12 | ### Load the Enviroment Modules 13 | module load CUDA/5.5 14 | ########################################################################## 15 | ### The files will be allocated in the shared FS ($SCRATCH_DIR) 16 | cd $SCRATCH_DIR 17 | ########################################################################## 18 | ### Run the Parallel Program 19 | srun cuda_binary 20 | -------------------------------------------------------------------------------- /Slurm/easybuild.sl: -------------------------------------------------------------------------------- 1 | #!/bin/bash 2 | ###################################################### 3 | #SBATCH -J EasyBuild 4 | #SBATCH -A hpcnow 5 | #SBATCH --time=06:00:00 6 | #SBATCH --mem-per-cpu=4G 7 | #SBATCH --cpus-per-task=4 8 | #SBATCH -D /sNow/easybuild/jobs 9 | #SBATCH --uid=5674 10 | ###################################################### 11 | ## Call the Easy Build 12 | srun eb GROMACS-4.6.5-ictce-5.5.0-mt.eb --try-toolchain=ictce,5.4.0 --robot --force 13 | srun eb WRF-3.4-goalf-1.1.0-no-OFED-dmpar.eb -r 14 | ###################################################### 15 | ## Update the LMOD cache 16 | /sNow/apps/lmod/utils/BuildSystemCacheFile/createSystemCacheFile.sh 17 | -------------------------------------------------------------------------------- /Slurm/flexpart.sl: -------------------------------------------------------------------------------- 1 | #!/bin/bash 2 | # FLEXPART-WRF SubmitScript 3 | ###################################################### 4 | #SBATCH -J FLEXPART-WRF 5 | #SBATCH -A hpcnow # Project Account 6 | #SBATCH --time=00:10:00 # Walltime 7 | #SBATCH --mem-per-cpu=1G # memory/cpu 8 | ###################################################### 9 | ### Load the Environment 10 | module load flexpart-wrf/2006-intel-2015a 11 | ###################################################### 12 | ### The files will be allocated in the shared FS 13 | cd /sNow/src/flexpart-wrf/run.example2 14 | ###################################################### 15 | ### Run the Parallel Program 16 | srun flexpart_wrf 17 | -------------------------------------------------------------------------------- /Slurm/gaussian.sl: -------------------------------------------------------------------------------- 1 | #!/bin/bash 2 | # Gaussian SubmitScript 3 | # Optimized for run parallel job of 8 Cores 4 | ###################################################### 5 | #SBATCH -J Gaussian 6 | #SBATCH -A hpcnow # Project Account 7 | #SBATCH --time=01:00:00 # Walltime 8 | #SBATCH --cpus-per-task=8 # 8 OpenMP Threads 9 | #SBATCH --mem-per-cpu=8G # memory/cpu 10 | ###################################################### 11 | ### Load the Environment Modules for Gaussian 12 | module load Gaussian/D.01 13 | ###################################################### 14 | ### Transferring the data to the local disk ($SCRATCH_DIR) 15 | cd $SCRATCH_DIR 16 | cp /sNow/test/Gaussian/test0324.com . 17 | export GAUSS_SCRDIR=$SCRATCH_DIR 18 | ###################################################### 19 | ### Run the Parallel Program 20 | srun g09 < ./test0324.com > test0324.out 21 | ###################################################### 22 | ### Transferring the results to the project directory 23 | cp -pr $SCRATCH_DIR $HOME/OUT/gaussian/ 24 | -------------------------------------------------------------------------------- /Slurm/gromacs-cuda-mpi.sl: -------------------------------------------------------------------------------- 1 | #!/bin/bash 2 | # Gromacs MPI+OpenMP+CUDA SubmitScript 3 | ########################################################################## 4 | #SBATCH -J GROMACS_JOB 5 | #SBATCH --time=01:00:00 # Walltime 6 | #SBATCH -A hpcnow # Project Account 7 | #SBATCH --mem-per-cpu=8G # memory/cpu 8 | #SBATCH --ntasks=4 # number of tasks 9 | #SBATCH --ntasks-per-node=2 # number of tasks per node 10 | #SBATCH --cpus-per-task=4 # 4 OpenMP Threads 11 | #SBATCH --gres=gpu:2 # GPUs per node 12 | ########################################################################## 13 | ### Load the Enviroment Modules for Gromacs 4.5.4 14 | module load GROMACS/4.5.4 15 | ########################################################################## 16 | ### Transfering the data to the local disk ($SCRATCH_DIR) 17 | cd $SCRATCH_DIR 18 | cp $HOME/Gromacs_9LDT/input/* . 19 | ########################################################################## 20 | ### Run the Parallel Program 21 | srun grompp -f full_vdw.mdp -c 9LDT-pt-md-3.gro -p 9LDT-bu.top -o 9LDT-bu.tpr 22 | srun mdrun_mpi -v -s 9LDT-bu.tpr -o 9LDT-bu.trr > mdrun.out 23 | ########################################################################## 24 | ### Transfering the results to the home directory ($HOME) 25 | cp -pr $SCRATCH_DIR $HOME/results/ 26 | -------------------------------------------------------------------------------- /Slurm/gromacs-mpi.sl: -------------------------------------------------------------------------------- 1 | #!/bin/bash 2 | # Gromacs MPI SubmitScript 3 | ########################################################################## 4 | #SBATCH -J GROMACS_JOB 5 | #SBATCH --time=01:00:00 # Walltime 6 | #SBATCH -A hpcnow # Project Account 7 | #SBATCH --mem-per-cpu=2G # memory/cpu 8 | #SBATCH --ntasks=24 # number of tasks 9 | ########################################################################## 10 | ### Load the Enviroment Modules for Gromacs 4.5.4 11 | module load GROMACS/4.5.4 12 | ########################################################################## 13 | ### Transfering the data to the local disk ($SCRATCH_DIR) 14 | cd $SCRATCH_DIR 15 | cp $HOME/Gromacs_9LDT/input/* . 16 | ########################################################################## 17 | ### Run the Parallel Program 18 | srun grompp -f full_vdw.mdp -c 9LDT-pt-md-3.gro -p 9LDT-bu.top -o 9LDT-bu.tpr 19 | srun mdrun_mpi -v -s 9LDT-bu.tpr -o 9LDT-bu.trr > mdrun.out 20 | ########################################################################## 21 | ### Transfering the results to the home directory ($HOME) 22 | cp -pr $SCRATCH_DIR $HOME/results/ 23 | -------------------------------------------------------------------------------- /Slurm/gromacs-openmp.sl: -------------------------------------------------------------------------------- 1 | #!/bin/bash 2 | # Gromacs OpenMP SubmitScript 3 | ########################################################################## 4 | #SBATCH -J GROMACS_JOB 5 | #SBATCH --time=01:00:00 # Walltime 6 | #SBATCH -A hpcnow # Project Account 7 | #SBATCH --mem-per-cpu=2G # memory/cpu 8 | #SBATCH --cpus-per-task=12 # 4 OpenMP Threads 9 | ########################################################################## 10 | ### Load the Enviroment Modules for Gromacs 4.5.4 11 | module load GROMACS/4.5.4 12 | ########################################################################## 13 | ### Transfering the data to the local disk ($SCRATCH_DIR) 14 | cd $SCRATCH_DIR 15 | cp $HOME/Gromacs_9LDT/input/* . 16 | ########################################################################## 17 | ### Run the Parallel Program 18 | srun grompp -f full_vdw.mdp -c 9LDT-pt-md-3.gro -p 9LDT-bu.top -o 9LDT-bu.tpr 19 | srun mdrun_mpi -v -s 9LDT-bu.tpr -o 9LDT-bu.trr > mdrun.out 20 | ########################################################################## 21 | ### Transfering the results to the home directory ($HOME) 22 | cp -pr $SCRATCH_DIR $HOME/results/ 23 | -------------------------------------------------------------------------------- /Slurm/hello_world-array.sl: -------------------------------------------------------------------------------- 1 | #!/bin/bash 2 | ###################################################### 3 | #SBATCH -J JobName 4 | ##SBATCH -A # Project Account 5 | #SBATCH --time=00:10:00 # Walltime 6 | #SBATCH --mem-per-cpu=1G # memory/cpu 7 | #SBATCH -a 1-96 # array of 96 jobs 8 | #SBATCH -n 1 # 1 core means serial 9 | ###################################################### 10 | ### Run the Parallel Program 11 | srun echo "hello from SLURM_ARRAY_TASK_ID : $SLURM_ARRAY_TASK_ID" 12 | srun sleep 10 13 | -------------------------------------------------------------------------------- /Slurm/hello_world.sl: -------------------------------------------------------------------------------- 1 | #!/bin/bash 2 | ###################################################### 3 | #SBATCH -J JobName 4 | #SBATCH -A # Project Account 5 | #SBATCH --time=00:10:00 # Walltime 6 | #SBATCH --mem-per-cpu=1G # memory/cpu 7 | #SBATCH -n 1 # 1 core means serial 8 | #SBATCH -o serial.out # OPTIONAL 9 | #SBATCH -e serial.err # OPTIONAL 10 | ###################################################### 11 | ### Run the Parallel Program 12 | srun echo "hello" 13 | -------------------------------------------------------------------------------- /Slurm/hybrid.sl: -------------------------------------------------------------------------------- 1 | #!/bin/bash 2 | #SBATCH -J Hybrid_JOB 3 | #SBATCH -A hpcnow # Project Account 4 | #SBATCH --time=01:00:00 # Walltime 5 | #SBATCH --ntasks=4 # number of tasks 6 | #SBATCH --mem-per-cpu=4G # memory/cpu 7 | #SBATCH --cpus-per-task=8 # 8 OpenMP Threads 8 | module load intel/intel-2015a 9 | srun /sNow/utils/bin/pi_hybrid 10 | -------------------------------------------------------------------------------- /Slurm/intel-mpi.sl: -------------------------------------------------------------------------------- 1 | #!/bin/bash 2 | #SBATCH -J MPI_JOB 3 | #SBATCH -A hpcnow # Project Account 4 | #SBATCH --time=10:00:00 # Walltime 5 | #SBATCH --ntasks=16 # number of tasks 6 | #SBATCH --mem-per-cpu=1G # memory/cpu 7 | module load intel/2015a 8 | srun /sNow/utils/bin/pi_mpi 9 | -------------------------------------------------------------------------------- /Slurm/intel-mpitune.sl: -------------------------------------------------------------------------------- 1 | #!/bin/bash 2 | #SBATCH -J MPITUNE 3 | #SBATCH -A hpcnow # Project Account 4 | #SBATCH --time=1:00:00 # Walltime 5 | ##SBATCH --ntasks=48 # number of tasks 6 | #SBATCH --mem-per-cpu=2048 # memory/cpu (in MB) 7 | 8 | ml VTune/2015_update2 9 | ml supermagic/20130104-intel-2015a 10 | ml itac/9.0.3.051 11 | source itacvars.sh impi5 12 | unset I_MPI_PMI_LIBRARY 13 | export I_MPI_FABRICS=shm:dapl 14 | 15 | mpitune -a \"mpiexec.hydra -n 16 supermagic -a -m 2M -w $SCRATCH_DIR/ -n 10 \" -of tune.conf 16 | -------------------------------------------------------------------------------- /Slurm/lammps-hybrid.sl: -------------------------------------------------------------------------------- 1 | #!/bin/bash 2 | # LAMMPS SubmitScript 3 | # Optimized for run parallel job of 1024 Cores 4 | ###################################################### 5 | #SBATCH -J LAMMPS 6 | #SBATCH -A hpcnow # Project Account 7 | #SBATCH --time=00:30:00 # Walltime 8 | #SBATCH --mem-per-cpu=4G # memory/cpu 9 | #SBATCH --ntasks=128 # Number of tasks 10 | #SBATCH --cpus-per-task=8 # Number of OpenMP threads 11 | ###################################################### 12 | ### Load the Environment 13 | module load lammps 14 | ###################################################### 15 | ### The files will be allocated in the shared FS 16 | cd $SCRATCH_DIR 17 | cp -pr /sNow/test/LAMMPS/* . 18 | ###################################################### 19 | ### Run the Parallel Program 20 | #Lennard Jones Benchmark input parameters: Weak Scaling 21 | srun lmp_mpi -var x 10 -var y 40 -var z 40 -in in.lj 22 | ###################################################### 23 | ### Transferring the results to the home directory 24 | cp -pr $SCRATCH_DIR $HOME/OUT/lammps/ 25 | -------------------------------------------------------------------------------- /Slurm/launcher.sl: -------------------------------------------------------------------------------- 1 | #!/bin/bash 2 | #SBATCH -J Launcher 3 | #SBATCH --time=01:00:00 # Walltime 4 | #SBATCH -A hpcnow # Project Account 5 | #SBATCH --nodes=2 # 2 nodes 6 | #SBATCH --ntasks=128 # number of tasks 7 | #SBATCH --mem-per-cpu=6G # memory/cpu 8 | #SBATCH -o Parametric.%j.out 9 | #SBATCH -e Parametric.%j.err 10 | # 11 | # Simple SLURM script for submitting multiple serial 12 | # jobs (e.g. parametric studies) using a script wrapper 13 | # to launch the jobs. 14 | # 15 | # To use, build the launcher executable and your 16 | # serial application(s) and place them in your WORKDIR 17 | # directory. Then, edit the LAUNCHER_JOB_FILE to specify 18 | # each executable per process. 19 | #------------------------------------------------------ 20 | 21 | # Load user environment 22 | module load launcher 23 | export LAUNCHER_RMI=SLURM 24 | export LAUNCHER_WORKDIR=/home/easybuild/launcher_test 25 | export LAUNCHER_JOB_FILE=helloworld_multi 26 | 27 | # Run the job file 28 | paramrun 29 | -------------------------------------------------------------------------------- /Slurm/matlab.sl: -------------------------------------------------------------------------------- 1 | #!/bin/bash 2 | #SBATCH -J Serial_Job 3 | #SBATCH -A hpcnow # Project Account 4 | #SBATCH --time=00:10:00 # Walltime 5 | #SBATCH --mem-per-cpu=4G # memory/cpu 6 | #SBATCH --cpus-per-task=5 7 | module load MATLAB/R2012b 8 | srun matlab -nodesktop -nosplash -r myLu 9 | -------------------------------------------------------------------------------- /Slurm/mb.sl: -------------------------------------------------------------------------------- 1 | #!/bin/bash 2 | #SBATCH -J nex 3 | #SBATCH -A hpcnow # Project Account 4 | #SBATCH --time=2:00:00 # Walltime 5 | #SBATCH --mem-per-cpu=4G # memory/cpu 6 | #SBATCH --ntasks=6 7 | 8 | module load MrBayes/3.1.2-ictce-5.4.0 9 | srun mb k86_07.nex 10 | -------------------------------------------------------------------------------- /Slurm/migrate-benchmark-serial.sl: -------------------------------------------------------------------------------- 1 | #!/bin/bash 2 | # MIGRATE Benchmark SubmitScript 3 | # Optimized for run parallel job of Cores 4 | # for j in {2..4} ; do sbatch --ntasks=$((16*$j)) --ntasks-per-node=16 --array=1-100 /sNow/SubmitScripts/slurm/migrate-benchmark.sl ; done 5 | ###################################################### 6 | #SBATCH -J MIGRATE_TEST 7 | #SBATCH -A hpcnow 8 | #SBATCH --time=08:00:00 9 | ##SBATCH --ntasks-per-node=24 10 | #SBATCH --mem-per-cpu=60000 11 | ###################################################### 12 | ###################################################### 13 | ### The files will be allocated in the shared FS 14 | cp -pr /sNow/test/migrate/parmfile* $SCRATCH_DIR/ 15 | cp -pr /sNow/test/migrate/infile $SCRATCH_DIR/ 16 | ###################################################### 17 | ### Run the Parallel Program 18 | for i in 3.4.4-ictce-5.4.0 3.6.6-ictce-5.4.0 3.4.4-goolf-1.4.10 3.6.6-goolf-1.4.10 3.4.4-goolf-1.5.14 3.6.6-goolf-1.5.14 19 | do 20 | echo "version $i" 21 | ml MIGRATE/$i 22 | cd $SCRATCH_DIR 23 | mkdir $i 24 | cp parmfile* $i/ 25 | cp infile $i/ 26 | cd $i 27 | echo "version $i" 28 | /usr/bin/time -f "real %e" -a -o benchmark-$LMOD_SYSTEM_NAME-$i-$SLURM_NTASKS.dat srun migrate-n parmfile.short -nomenu 29 | ml purge 30 | done 31 | ###################################################### 32 | ### Transferring the results to the home directory ($HOME) 33 | mkdir -p $HOME/OUT/migrate 34 | cp -pr $SCRATCH_DIR $HOME/OUT/migrate 35 | -------------------------------------------------------------------------------- /Slurm/migrate-benchmark-tuned.sl: -------------------------------------------------------------------------------- 1 | #!/bin/bash 2 | # MIGRATE Benchmark SubmitScript 3 | # Optimized for run parallel job of Cores 4 | # for j in {2..4} ; do sbatch --ntasks=$((16*$j)) --ntasks-per-node=16 --array=1-100 /sNow/SubmitScripts/slurm/migrate-benchmark.sl ; done 5 | ###################################################### 6 | #SBATCH -J MIGRATE_TEST 7 | #SBATCH -A hpcnow 8 | #SBATCH --time=01:00:00 9 | ##SBATCH --ntasks-per-node=16 10 | #SBATCH --mem-per-cpu=4G 11 | ##SBATCH -C sb 12 | #SBATCH -x compute-bigmem-[001,003-004],compute-chem-001 13 | ###################################################### 14 | ###################################################### 15 | ### The files will be allocated in the shared FS 16 | cp -pr /sNow/test/migrate/parmfile* $SCRATCH_DIR/ 17 | cp -pr /sNow/test/migrate/infile $SCRATCH_DIR/ 18 | ###################################################### 19 | ### Run the Parallel Program 20 | #for i in 3.4.4-ictce-5.4.0 3.6.6-ictce-5.4.0 21 | for i in 3.4.4-ictce-5.4.0 22 | do 23 | export I_MPI_FABRICS="shm:dapl" 24 | #export I_MPI_FALLBACK=disable 25 | #export I_MPI_DAPL_UD=enable 26 | #export I_MPI_ADJUST_COLLECTIVES="bcast:0;reduce:2" 27 | #export I_MPI_DAPL_SCALABLE_PROGRESS=1 28 | #export I_MPI_WAIT_MODE=enable 29 | export I_MPI_PIN_PROCESSOR_LIST="grain=cache2,shift=sock" 30 | #export I_MPI_WAIT_MODE=enable 31 | #export I_MPI_SHM_BYPASS=enable 32 | #export I_MPI_INTRANODE_EAGER_THRESHOLD=262144 33 | #export I_MPI_SHM_CACHE_BYPASS_THRESHOLDS=,[,,] 34 | #export I_MPI_SHM_CACHE_BYPASS_THRESHOLDS=16384,16384,-1,16384,-1,16384 35 | echo "version $i" 36 | ml MIGRATE/$i 37 | #cd $SCRATCH_DIR 38 | cd $SCRATCH_DIR 39 | mkdir -p $i 40 | cp parmfile* $i/ 41 | cp infile $i/ 42 | cd $i 43 | echo "version $i" 44 | /usr/bin/time -f "real %e" -a -o /home/jbla572/OUT/migrate/benchmark-95r1-tuned-$LMOD_SYSTEM_NAME-$i-$SLURM_NTASKS.dat srun migrate-n-mpi parmfile.short -nomenu 45 | ml purge 46 | done 47 | ###################################################### 48 | ### Transferring the results to the home directory ($HOME) 49 | #mkdir -p $HOME/OUT/migrate 50 | #cp -pr $SCRATCH_DIR $HOME/OUT/migrate 51 | -------------------------------------------------------------------------------- /Slurm/migrate-benchmark.sl: -------------------------------------------------------------------------------- 1 | #!/bin/bash 2 | # MIGRATE Benchmark SubmitScript 3 | # Optimized for run parallel job of Cores 4 | # for j in {2..4} ; do sbatch --ntasks=$((16*$j)) --ntasks-per-node=16 --array=1-100 /sNow/SubmitScripts/slurm/migrate-benchmark.sl ; done 5 | ###################################################### 6 | #SBATCH -J MIGRATE_TEST 7 | #SBATCH -A hpcnow 8 | #SBATCH --time=08:00:00 9 | ##SBATCH --ntasks-per-node=24 10 | #SBATCH --mem-per-cpu=2048 11 | ##SBATCH -C ib 12 | #SBATCH -x compute-bigmem-[001,003-004],compute-chem-001 13 | ###################################################### 14 | ###################################################### 15 | ### The files will be allocated in the shared FS 16 | cp -pr /sNow/test/migrate/parmfile* $SCRATCH_DIR/ 17 | cp -pr /sNow/test/migrate/infile $SCRATCH_DIR/ 18 | ###################################################### 19 | ### Run the Parallel Program 20 | for i in 3.4.4-ictce-5.4.0 3.6.6-ictce-5.4.0 3.4.4-goolf-1.4.10 3.6.6-goolf-1.4.10 3.4.4-goolf-1.5.14 3.6.6-goolf-1.5.14 21 | #for i in 3.4.4-goolf-1.4.10 3.6.6-goolf-1.4.10 22 | #for i in 3.4.4-goolf-1.5.14 3.6.6-goolf-1.5.14 23 | #export I_MPI_FABRICS=shm:dapl 24 | #export I_MPI_ADJUST_COLLECTIVES = bcast:0;reduce:2 25 | #export I_MPI_DAPL_SCALABLE_PROGRESS=1 26 | #export I_MPI_PIN_PROCESSOR_LIST='grain=cache2,shift=sock' 27 | #for i in 3.4.4-ictce-5.4.0 28 | do 29 | echo "version $i" 30 | ml MIGRATE/$i 31 | cd $SCRATCH_DIR 32 | mkdir $i 33 | cp parmfile* $i/ 34 | cp infile $i/ 35 | cd $i 36 | echo "version $i" 37 | /usr/bin/time -f "real %e" -a -o /home/jbla572/OUT/migrate/benchmark-10r-$LMOD_SYSTEM_NAME-$i-$SLURM_NTASKS.dat srun migrate-n-mpi parmfile.short -nomenu 38 | ml purge 39 | done 40 | ###################################################### 41 | ### Transferring the results to the home directory ($HOME) 42 | #mkdir -p $HOME/OUT/migrate 43 | #cp -pr $SCRATCH_DIR $HOME/OUT/migrate 44 | -------------------------------------------------------------------------------- /Slurm/migrate-mpi.sl: -------------------------------------------------------------------------------- 1 | #!/bin/bash 2 | # MIGRATE Benchmark SubmitScript 3 | # Optimized for run parallel job of 96 Cores 4 | ###################################################### 5 | #SBATCH -J MIGRATE_TEST 6 | #SBATCH -A hpcnow 7 | #SBATCH --time=08:00:00 8 | #SBATCH --ntasks=ncores 9 | #SBATCH --ntasks-per-node=16 10 | #SBATCH --mem-per-cpu=4G 11 | ###################################################### 12 | ###################################################### 13 | ### The files will be allocated in the shared FS 14 | cp -pr /sNow/test/migrate/parmfile.* $SCRATCH_DIR/ 15 | cp -pr /sNow/test/migrate/infile $SCRATCH_DIR/ 16 | ###################################################### 17 | ### Run the Parallel Program 18 | for i in 3.4.4-goolf-1.4.10 3.4.4-ictce-5.4.0 3.6.6-goolf-1.4.10 3.6.6-ictce-5.4.0 19 | do 20 | echo "version $i" 21 | cd $SCRATCH_DIR 22 | mkdir $i 23 | cp parmfile.* $i/ 24 | cp infile $i/ 25 | cd $i 26 | time srun migrate-n-mpi parmfile -nomenu 27 | done 28 | sstat -j $SLURM_JOBID -o JobID,MaxVMSize,AveVMSize,MinCPU,AveCPU,NTasks 29 | ###################################################### 30 | ### Transferring the results to the home directory ($HOME) 31 | mkdir -p $HOME/OUT/migrate 32 | cp -pr $SCRATCH_DIR $HOME/OUT/migrate 33 | -------------------------------------------------------------------------------- /Slurm/migrate-profile.sl: -------------------------------------------------------------------------------- 1 | #!/bin/bash 2 | # MIGRATE Benchmark SubmitScript 3 | # Optimized for run parallel job of Cores 4 | ###################################################### 5 | #SBATCH -J MIGRATE_Profile 6 | #SBATCH -A hpcnow 7 | #SBATCH --time=01:00:00 8 | #SBATCH --ntasks-per-node=16 9 | #SBATCH --mem-per-cpu=4G 10 | #SBATCH -C sb 11 | ###################################################### 12 | ###################################################### 13 | ### The files will be allocated in the shared FS 14 | cp -pr /sNow/test/migrate/parmfile* $SCRATCH_DIR/ 15 | cp -pr /sNow/test/migrate/infile $SCRATCH_DIR/ 16 | ###################################################### 17 | ### Run the Parallel Program 18 | for i in 3.4.4-ictce-5.4.0 3.6.6-ictce-5.4.0 19 | do 20 | #export I_MPI_FABRICS=shm:dapl 21 | #export I_MPI_ADJUST_COLLECTIVES = bcast:0;reduce:2 22 | #export I_MPI_DAPL_SCALABLE_PROGRESS=1 23 | #export I_MPI_STATS=3 24 | #export I_MPI_STATS_SCOPE=coll 25 | echo "version $i" 26 | ml MIGRATE/$i 27 | ml VTune/2013_update8 28 | ml itac/8.1.4.045 29 | source itacvars.sh impi4 30 | #export VT_PCTRACE=4 31 | #export VT_CONFIG=/sNow/SubmitScripts/slurm/trace.conf 32 | cd $SCRATCH_DIR 33 | mkdir $i 34 | cp parmfile* $i/ 35 | cp infile $i/ 36 | cd $i 37 | #srun migrate-n-mpi parmfile.short -nomenu 38 | unset I_MPI_PMI_LIBRARY 39 | srun amplxe-cl -collect hotspots -- migrate-n-mpi parmfile.short -nomenu 40 | ml purge 41 | done 42 | sstat -j $SLURM_JOBID -o JobID,MaxVMSize,AveVMSize,MinCPU,AveCPU,NTasks 43 | ###################################################### 44 | ### Transferring the results to the home directory ($HOME) 45 | mkdir -p $HOME/OUT/migrate-profile 46 | cp -pr $SCRATCH_DIR $HOME/OUT/migrate-profile/ 47 | -------------------------------------------------------------------------------- /Slurm/migrate-traces.sl: -------------------------------------------------------------------------------- 1 | #!/bin/bash 2 | # MIGRATE Benchmark SubmitScript 3 | # Optimized for run parallel job of Cores 4 | ###################################################### 5 | #SBATCH -J MIGRATE_traces 6 | #SBATCH -A hpcnow 7 | #SBATCH --time=08:00:00 8 | ##SBATCH --ntasks-per-node=16 9 | #SBATCH --mem-per-cpu=4G 10 | ##SBATCH -C sb 11 | ###################################################### 12 | ###################################################### 13 | ### The files will be allocated in the shared FS 14 | cp -pr /sNow/test/migrate/parmfile* $SCRATCH_DIR/ 15 | cp -pr /sNow/test/migrate/infile $SCRATCH_DIR/ 16 | ###################################################### 17 | ### Run the Parallel Program 18 | mkdir -p $HOME/OUT/migrate-traces/tuned-c 19 | #for i in 3.4.4-ictce-5.4.0 3.6.6-ictce-5.4.0 3.4.4-goolf-1.4.10 3.6.6-goolf-1.4.10 20 | for i in 3.4.4-ictce-5.4.0 3.6.6-ictce-5.4.0 21 | do 22 | export I_MPI_FABRICS=shm:dapl 23 | #export I_MPI_ADJUST_COLLECTIVES = bcast:0;reduce:2 24 | export I_MPI_FALLBACK=disable 25 | export I_MPI_DAPL_UD=enable 26 | export I_MPI_DAPL_SCALABLE_PROGRESS=1 27 | export I_MPI_PIN_PROCESSOR_LIST='grain=cache2,shift=sock' 28 | export I_MPI_WAIT_MODE=enable 29 | export I_MPI_SHM_BYPASS=enable 30 | export I_MPI_INTRANODE_EAGER_THRESHOLD=262144 31 | #export I_MPI_SHM_CACHE_BYPASS_THRESHOLDS=,[,,] 32 | export I_MPI_SHM_CACHE_BYPASS_THRESHOLDS=16384,16384,-1,16384,-1,16384 33 | #export I_MPI_STATS=3 34 | #export I_MPI_STATS_SCOPE=coll 35 | echo "version $i" 36 | ml MIGRATE/$i 37 | ml VTune/2013_update8 38 | ml itac/8.1.4.045 39 | source itacvars.sh impi4 40 | #export VT_PCTRACE=4 41 | #export VT_CONFIG=/sNow/SubmitScripts/slurm/trace.conf 42 | cd $SCRATCH_DIR 43 | mkdir $i 44 | cp parmfile* $i/ 45 | cp infile $i/ 46 | cd $i 47 | #srun migrate-n-mpi parmfile.short -nomenu 48 | unset I_MPI_PMI_LIBRARY 49 | mpiexec.hydra -trace migrate-n-mpi parmfile.short -nomenu 50 | #mpiexec.hydra -trace migrate-n-mpi parmfile.short -nomenu 51 | #mpirun itcpin --run -- migrate-n-mpi parmfile.short -nomenu 52 | ml purge 53 | cp -pr $SCRATCH_DIR $HOME/OUT/migrate-traces/tuned-c/$i-$SLURM_NTASKS 54 | done 55 | #sstat -j $SLURM_JOBID -o JobID,MaxVMSize,AveVMSize,MinCPU,AveCPU,NTasks 56 | ###################################################### 57 | ### Transferring the results to the home directory ($HOME) 58 | -------------------------------------------------------------------------------- /Slurm/mpi-all.sl: -------------------------------------------------------------------------------- 1 | #!/bin/bash 2 | #SBATCH -J MPI_JOB 3 | #SBATCH -A hpcnow # Project Account 4 | #SBATCH --time=1:00:00 # Walltime 5 | #SBATCH --nodes=200 6 | #SBATCH --tasks-per-node=16 7 | #SBATCH --mem-per-cpu=1G # memory/cpu 8 | module load intel/ics-2013 9 | srun hostname 10 | srun /sNow/training/slurm/bin/pi_mpi 11 | -------------------------------------------------------------------------------- /Slurm/mpi.sl: -------------------------------------------------------------------------------- 1 | #!/bin/bash 2 | #SBATCH -J MPI_JOB 3 | #SBATCH -A hpcnow 4 | #SBATCH --time=00:15:00 5 | #SBATCH --ntasks=32 6 | #SBATCH --mem-per-cpu=1G 7 | module load ictce/5.4.0 8 | srun hostname 9 | srun /sNow/training/slurm/bin/pi_mpi 10 | -------------------------------------------------------------------------------- /Slurm/multi-mpi.conf: -------------------------------------------------------------------------------- 1 | 0 echo 'I am the Master' 2 | 1 sleep 120 3 | 2-3 printenv SLURM_PROCID 4 | 4-47 hostname 5 | -------------------------------------------------------------------------------- /Slurm/multi-prog-mpi.sl: -------------------------------------------------------------------------------- 1 | #!/bin/bash 2 | #SBATCH -J MasterSlave 3 | #SBATCH -A hpcnow # Project Account 4 | #SBATCH --time=01:00:00 # Walltime 5 | #SBATCH --ntasks=48 # number of tasks 6 | #SBATCH --mem-per-cpu=1G # memory/cpu 7 | /sNow/SubmitScripts/slurm/multi-prog-mpi.sl 8 | srun --multi-prog multi-mpi.conf 9 | -------------------------------------------------------------------------------- /Slurm/multi-prog.sl: -------------------------------------------------------------------------------- 1 | #!/bin/bash 2 | #SBATCH -J MasterSlave 3 | #SBATCH -A hpcnow # Project Account 4 | #SBATCH --time=01:00:00 # Walltime 5 | #SBATCH --ntasks=48 # number of tasks 6 | #SBATCH --mem-per-cpu=1G # memory/cpu 7 | srun --multi-prog multi.conf 8 | -------------------------------------------------------------------------------- /Slurm/multi.conf: -------------------------------------------------------------------------------- 1 | 0 echo 'I am the Master' 2 | 1 sleep 120 3 | 2-3 printenv SLURM_PROCID 4 | 4-47 hostname 5 | -------------------------------------------------------------------------------- /Slurm/multistage.sl: -------------------------------------------------------------------------------- 1 | #!/bin/bash 2 | #SBATCH -J OpenMP_JOB 3 | #SBATCH -A hpcnow # Project Account 4 | #SBATCH --time=01:00:00 # Walltime 5 | #SBATCH --mem-per-cpu=8G # memory/cpu 6 | #SBATCH --cpus-per-task=8 # 8 OpenMP Threads 7 | srun openmp_binary stage1.dat 8 | srun openmp_binary stage2.dat 9 | srun openmp_binary stage3.dat 10 | srun openmp_binary stage4.dat 11 | srun openmp_binary stage5.dat 12 | srun openmp_binary stage6.dat 13 | srun openmp_binary stage7.dat 14 | srun openmp_binary stage7.dat 15 | -------------------------------------------------------------------------------- /Slurm/namd-cuda.sl: -------------------------------------------------------------------------------- 1 | #!/bin/bash 2 | # NAMD CUDA SubmitScript 3 | ########################################################################## 4 | #SBATCH -J NAMD 5 | #SBATCH --time=01:00:00 # Walltime 6 | #SBATCH -A hpcnow # Project Account 7 | #SBATCH --mem-per-cpu=2G # memory/cpu 8 | #SBATCH --cpus-per-task=2 # 2 OpenMP Threads 9 | #SBATCH --gres=gpu:2        # GPUs per node 10 | ########################################################################## 11 | ### Load the Enviroment Modules for NAMD 12 | module load NAMD/2.9 13 | ########################################################################## 14 | ### The files will be allocated in the shared FS ($SCRATCH_DIR) 15 | cp -pr /sNow/test/NAMD/apoa1/* $SCRATCH_DIR 16 | cd $SCRATCH_DIR 17 | ########################################################################## 18 | ### Run the Parallel Program 19 | export OMP_NUM_THREADS=1 20 | srun namd2 apoa1.namd 21 | ########################################################################## 22 | ### Transfering the results to the home directory ($HOME) 23 | cp -pr $SCRATCH_DIR $HOME/OUT/namd 24 | -------------------------------------------------------------------------------- /Slurm/namd-mpi.sl: -------------------------------------------------------------------------------- 1 | #!/bin/bash 2 | # NAMD MPI SubmitScript 3 | ########################################################################## 4 | #SBATCH -J NAMD 5 | #SBATCH --time=01:00:00 # Walltime 6 | #SBATCH -A hpcnow # Project Account 7 | #SBATCH --mem-per-cpu=2G # memory/cpu 8 | #SBATCH --ntasks=24 # number of tasks 9 | ########################################################################## 10 | ### Load the Enviroment Modules for Gromacs 4.5.4 11 | module load NAMD/2.9 12 | ########################################################################## 13 | ### The files will be allocated in the shared FS ($SCRATCH_DIR) 14 | cp -pr /sNow/test/NAMD/apoa1/* $SCRATCH_DIR 15 | cd $SCRATCH_DIR 16 | ########################################################################## 17 | ### Run the Parallel Program 18 | export OMP_NUM_THREADS=1 19 | srun namd2 apoa1.namd 20 | ########################################################################## 21 | ### Transfering the results to the home directory ($HOME) 22 | cp -pr $SCRATCH_DIR $HOME/OUT/namd 23 | -------------------------------------------------------------------------------- /Slurm/nextflow.config: -------------------------------------------------------------------------------- 1 | process { 2 | executor='slurm' 3 | queueSize = 15 4 | pollInterval = '5 min' 5 | dumpInterval = '6 min' 6 | queueStatInterval = '5 min' 7 | exitReadTimeout = '13 min' 8 | killBatchSize = 30 9 | submitRateLimit = '20 min' 10 | clusterOptions = '-p short -t 00:30:00 -C ilk' 11 | } 12 | -------------------------------------------------------------------------------- /Slurm/node_stress.sl: -------------------------------------------------------------------------------- 1 | #!/bin/bash 2 | ###################################################### 3 | #SBATCH -J STRESS_TEST 4 | #SBATCH -A hpcnow # Project Account 5 | #SBATCH --time=12:00:00 # Walltime 6 | #SBATCH --mem-per-cpu=4G # memory/cpu 7 | #SBATCH --cpus-per-task=12 # 12 OpenMP Threads 8 | #SBATCH --nodes=1 # number nodes 9 | ###################################################### 10 | ### Load the Environment 11 | ###################################################### 12 | cd $SHM_DIR 13 | #srun stress -v --cpu 12 --vm 12 --vm-bytes 4096M --timeout 1800s 14 | srun stress -v --cpu 12 15 | ###################################################### 16 | -------------------------------------------------------------------------------- /Slurm/octave.sl: -------------------------------------------------------------------------------- 1 | #!/bin/bash 2 | #SBATCH -J Serial_Job 3 | #SBATCH --job-name=octave 4 | #SBATCH -A hpcnow # Project Account 5 | #SBATCH --time=00:10:00 # Walltime 6 | #SBATCH --mem-per-cpu=2G # memory/cpu 7 | #SBATCH --mail-user=b.verleye@auckland.ac.nz 8 | #SBATCH --mail-type=ALL 9 | module load Octave 10 | octave 'myTest.m' 11 | -------------------------------------------------------------------------------- /Slurm/open-mpi.sl: -------------------------------------------------------------------------------- 1 | #!/bin/bash 2 | #SBATCH -J MPI_JOB 3 | #SBATCH -A hpcnow # Project Account 4 | #SBATCH --time=10:00:00 # Walltime 5 | #SBATCH --ntasks=96 # number of tasks 6 | #SBATCH --mem-per-cpu=1G # memory/cpu 7 | ml load OpenMPI/1.6.5-GCC-4.8.2 8 | srun /sNow/training/slurm/bin/pi_openmpi-1.6.5-GCC-4.8.2 9 | -------------------------------------------------------------------------------- /Slurm/openmp.sl: -------------------------------------------------------------------------------- 1 | #!/bin/bash 2 | #SBATCH -J OpenMP_JOB 3 | #SBATCH -A hpcnow # Project Account 4 | #SBATCH --time=01:00:00 # Walltime 5 | #SBATCH --mem-per-cpu=8G # memory/cpu 6 | #SBATCH --cpus-per-task=8 # 8 OpenMP Threads 7 | srun openmp_binary 8 | -------------------------------------------------------------------------------- /Slurm/orca-mpi.sl: -------------------------------------------------------------------------------- 1 | #!/bin/bash 2 | #SBATCH -J ORCA 3 | #SBATCH -A hpcnow # Project Account 4 | #SBATCH --time=01:00:00 # Walltime 5 | #SBATCH --mem-per-cpu=8G # memory/cpu 6 | #SBATCH --ntasks=48 # number of tasks 7 | 8 | # Load the user environment 9 | ml ORCA/3_0_2-linux_x86-64 10 | export P4_RSHCOMMAND=ssh 11 | export OMP_NUM_THREADS=1 12 | ### The files will be allocated in the shared FS 13 | cd $SCRATCH_DIR 14 | cp /sNow/test/benchmarks/Orca/XRQTC.Orca_localCCSD/input/* . 15 | # --------------> WARNING <------------------- 16 | # The number of CPUs needs to be specified in 17 | # the input file : % pal nprocs $SLURM_NTASKS 18 | mv XRQTC.Orca_localCCSD.inp XRQTC.Orca_localCCSD.inp.1 19 | echo "% pal nprocs $SLURM_NTASKS 20 | end" > XRQTC.Orca_localCCSD.inp.0 21 | cat XRQTC.Orca_localCCSD.inp.0 XRQTC.Orca_localCCSD.inp.1 > XRQTC.Orca_localCCSD.inp 22 | rm XRQTC.Orca_localCCSD.inp.* 23 | ########################################## 24 | # Run the job 25 | ########################################## 26 | srun orca XRQTC.Orca_localCCSD.inp > XRQTC.Orca_localCCSD.out 27 | ########################################## 28 | # Copy the results to our home directory 29 | ########################################## 30 | mkdir -p /sNow/test/benchmarks/Orca/XRQTC.Orca_localCCSD/OUT/orca 31 | cp -r $SCRATCH_DIR /sNow/test/benchmarks/Orca/XRQTC.Orca_localCCSD/OUT/orca/ 32 | ########################################## 33 | # Temps dels resultats 34 | ########################################## 35 | TEMPS=$(cat XRQTC.Orca_localCCSD.out | grep "Time:" | awk '{print $3}') 36 | echo "$SLURM_NTASKS $TEMPS" >> /sNow/test/benchmarks/Orca/XRQTC.Orca_localCCSD/benchmark-ompi-XRQTC.Orca_localCCSD.dat 37 | -------------------------------------------------------------------------------- /Slurm/orca-smp.sl: -------------------------------------------------------------------------------- 1 | #!/bin/bash 2 | #SBATCH -J ORCA 3 | #SBATCH -A hpcnow # Project Account 4 | #SBATCH --time=01:00:00 # Walltime 5 | #SBATCH --mem-per-cpu=8G # memory/cpu 6 | #SBATCH --cpus-per-task=8 # 8 OpenMP Threads 7 | 8 | # Load the user environment 9 | ml ORCA/3_0_2-linux_x86-64 10 | export P4_RSHCOMMAND=ssh 11 | export OMP_NUM_THREADS=1 12 | ### The files will be allocated in the shared FS 13 | cd $TMP_DIR 14 | cp /sNow/test/benchmarks/Orca/XRQTC.Orca_B3LYP/input/* . 15 | # --------------> WARNING <------------------- 16 | # The number of CPUs needs to be specified in 17 | # the input file : % pal nprocs $SLURM_NPROCS 18 | mv XRQTC.Orca_B3LYP.inp XRQTC.Orca_B3LYP.inp.1 19 | echo "% pal nprocs $NSLOTS 20 | end" > XRQTC.Orca_B3LYP.inp.0 21 | cat XRQTC.Orca_B3LYP.inp.0 XRQTC.Orca_B3LYP.inp.1 > XRQTC.Orca_B3LYP.inp 22 | rm XRQTC.Orca_B3LYP.inp.* 23 | ########################################## 24 | # Run the job 25 | ########################################## 26 | srun orca XRQTC.Orca_B3LYP.inp > XRQTC.Orca_B3LYP.out 27 | ########################################## 28 | # Copy the results to our home directory 29 | ########################################## 30 | mkdir -p /sNow/test/benchmarks/Orca/XRQTC.Orca_B3LYP/OUT/orca 31 | cp -r $TMP_DIR /sNow/test/benchmarks/Orca/XRQTC.Orca_B3LYP/OUT/orca/ 32 | ########################################## 33 | # Temps dels resultats 34 | ########################################## 35 | TEMPS=$(cat XRQTC.Orca_B3LYP.out | grep Time: | awk '{print$3}') 36 | echo "$NSLOTS $TEMPS" >> /sNow/test/benchmarks/Orca/XRQTC.Orca_B3LYP/benchmark-ompi-XRQTC.Orca_B3LYP.dat 37 | -------------------------------------------------------------------------------- /Slurm/params.dat: -------------------------------------------------------------------------------- 1 | 2.00 0.6 10 1500 2 2 | 2.00 0.8 10 1500 2 3 | 2.00 0.6 2.5 1500 2 4 | 2.00 0.8 2.5 1500 2 5 | 2.00 0.6 3.0 1500 2 6 | 2.00 0.8 3.0 1500 2 7 | 2.00 0.6 3.5 1500 2 8 | 2.00 0.8 3.5 1500 2 9 | 2.00 0.6 4.0 1500 2 10 | 2.00 0.8 4.0 1500 2 11 | 2.00 0.6 4.5 1500 2 12 | 2.00 0.8 4.5 1500 2 13 | 2.00 0.6 5.0 1500 2 14 | 2.00 0.8 5.0 1500 2 15 | 2.00 0.6 5.5 1500 2 16 | 2.00 0.8 5.5 1500 2 17 | 2.00 0.6 6.0 1500 2 18 | 2.00 0.8 6.0 1500 2 19 | 2.00 0.6 6.5 1500 2 20 | 2.00 0.8 6.5 1500 2 21 | 2.00 0.6 7.0 1500 2 22 | 2.00 0.8 7.0 1500 2 23 | 2.00 0.6 7.5 1500 2 24 | 2.00 0.8 7.5 1500 2 25 | 2.00 0.6 8.0 1500 2 26 | 2.00 0.8 8.0 1500 2 27 | 2.00 0.6 8.5 1500 2 28 | 2.00 0.8 8.5 1500 2 29 | 2.00 0.6 9.0 1500 2 30 | 2.00 0.8 9.0 1500 2 31 | 2.00 0.6 9.5 1500 2 32 | 2.00 0.8 9.5 1500 2 33 | 2.00 0.6 10.0 1500 2 34 | 2.00 0.8 10.0 1500 2 35 | 2.00 0.6 2.5 1500 2 36 | 2.00 0.8 2.5 1500 2 37 | 2.00 0.6 3.0 1500 2 38 | 2.00 0.8 3.0 1500 2 39 | 2.00 0.6 3.5 1500 2 40 | 2.00 0.8 3.5 1500 2 41 | 2.00 0.6 4.0 1500 2 42 | 2.00 0.8 4.0 1500 2 43 | 2.00 0.6 4.5 1500 2 44 | 2.00 0.8 4.5 1500 2 45 | 2.00 0.6 5.0 1500 2 46 | 2.00 0.8 5.0 1500 2 47 | 2.00 0.6 5.5 1500 2 48 | 2.00 0.8 5.5 1500 2 49 | 2.00 0.6 6.0 1500 2 50 | 2.00 0.8 6.0 1500 2 51 | 2.00 0.6 6.5 1500 2 52 | 2.00 0.8 6.5 1500 2 53 | 2.00 0.6 7.0 1500 2 54 | 2.00 0.8 7.0 1500 2 55 | 2.00 0.6 7.5 1500 2 56 | 2.00 0.8 7.5 1500 2 57 | 2.00 0.6 8.0 1500 2 58 | 2.00 0.8 8.0 1500 2 59 | 2.00 0.6 8.5 1500 2 60 | 2.00 0.8 8.5 1500 2 61 | 2.00 0.6 9.0 1500 2 62 | 2.00 0.8 9.0 1500 2 63 | 2.00 0.6 9.5 1500 2 64 | 2.00 0.8 9.5 1500 2 65 | 2.00 0.6 10.0 1500 2 66 | 2.00 0.8 10.0 1500 2 67 | -------------------------------------------------------------------------------- /Slurm/platform-mpi.sl: -------------------------------------------------------------------------------- 1 | #!/bin/bash 2 | #SBATCH -J MPI_JOB 3 | #SBATCH -A hpcnow # Project Account 4 | #SBATCH --time=10:00:00 # Walltime 5 | #SBATCH --ntasks=14 # number of tasks 6 | #SBATCH --mem-per-cpu=1G # memory/cpu 7 | module load Abaqus/6.13 8 | mpirun -srun uname 9 | #mpirun -srun pi_platform-mpi-08.3.0.0 10 | -------------------------------------------------------------------------------- /Slurm/post-processing.sl: -------------------------------------------------------------------------------- 1 | #!/bin/bash 2 | #SBATCH -J Post-ProcessingJob 3 | #SBATCH -A hpcnow # Project Account 4 | #SBATCH --time=01:00:00 # Walltime 5 | #SBATCH --mem-per-cpu=8G # memory/cpu 6 | srun echo "Post-Processing done." 7 | -------------------------------------------------------------------------------- /Slurm/pre-processing.sl: -------------------------------------------------------------------------------- 1 | #!/bin/bash 2 | #SBATCH -J Pre-ProcessingJob 3 | #SBATCH -A hpcnow # Project Account 4 | #SBATCH --time=01:00:00 # Walltime 5 | #SBATCH --mem-per-cpu=8G # memory/cpu 6 | srun echo "Pre-Processing done. Run the job dependencies" 7 | -------------------------------------------------------------------------------- /Slurm/profile.sl: -------------------------------------------------------------------------------- 1 | #!/bin/bash 2 | #SBATCH -J Slurm-Profiler 3 | #SBATCH -A hpcnow 4 | ##SBATCH --time=24:00:00 # Walltime 5 | #SBATCH --time=00:15:00 # Walltime 6 | #SBATCH --mem-per-cpu=8G # memory/cpu 7 | #SBATCH --cpus-per-task=4 # 4 OpenMP Threads 8 | srun --profile=task stress --vm 4 --vm-bytes 2GB --timeout 900s 9 | -------------------------------------------------------------------------------- /Slurm/serial.sl: -------------------------------------------------------------------------------- 1 | #!/bin/bash 2 | #SBATCH -J Serial_Job 3 | #SBATCH -A hpcnow # Project Account 4 | #SBATCH --time=01:00:00 # Walltime 5 | #SBATCH --mem-per-cpu=8G # memory/cpu 6 | srun sleep 30 7 | srun echo "My first serial Slurm job" 8 | -------------------------------------------------------------------------------- /Slurm/slurm_setup_abaqus-env.sh: -------------------------------------------------------------------------------- 1 | # This script will create the User Environment to run Abaqus under Slurm 2 | # Created by Jordi Blasco 3 | # The previous releases of Abaqus was using HPMPI but the current one 6.13 uses Platform/IBM MPI which is not fully integrated with srun 4 | # According to the slurm website, it seems that HP-MPI only needs -srun flag, and we can avoid to use the following lines of code. 5 | # http://slurm.schedmd.com/mpi_guide.html#hp_mpi 6 | envFile=abaqus_v6.env 7 | if [[ -f $envFile ]]; then 8 | rm $envFile 9 | fi 10 | echo "import os">>$envFile 11 | srun hostname -s | sort > slurm.hosts 12 | mp_host_list="[" 13 | for i in $(cat slurm.hosts) ; do 14 | mp_host_list="${mp_host_list}['$i', 1]," 15 | done 16 | #mp_host_list=`echo ${mp_host_list} | sed -e "s/,$//" | sed -e "s/\-p/\-ib/g"` 17 | mp_host_list=`echo ${mp_host_list}` 18 | mp_host_list="${mp_host_list}]" 19 | export mp_host_list 20 | #echo "mp_host_list=${mp_host_list}" >>$envFile 21 | echo "mp_host_list=${mp_host_list}" >>$envFile 22 | echo "max_history_requests=0" >> $envFile 23 | echo "mp_rsh_command = 'ssh -x -n -l %U %H %C'" >> $envFile 24 | alias mpirun='mpirun -srun' 25 | #echo "mp_mpirun_path = {HP:'/sNow/apps/Abaqus/6.13/installation/6.13-2/code/bin/SMAExternal/pmpi-8.3/bin/mpirun -srun'}" >> $envFile 26 | #echo "mp_rsh_command = 'ssh -x -n -l %U %H %C'" >> $envFile 27 | -------------------------------------------------------------------------------- /Slurm/slurm_setup_cfx-env.sh: -------------------------------------------------------------------------------- 1 | #!/bin/bash 2 | # This script will create the User Environment to run ANSYS CFX under Slurm 3 | # Created by Jordi Blasco , Bart Verleye 4 | export CFX5RSH=ssh 5 | export MPI_REMSH=ssh 6 | export MPI_IC_ORDER="udapl:ibv:tcp" 7 | #export MPI_CPU_AFFINITY=SLURM 8 | 9 | envFile=ansys.env 10 | rm $envFile 11 | srun hostname -s | sort > slurm.hosts 12 | for i in $(cat slurm.hosts) ; do 13 | mp_host_list="${mp_host_list}$i," 14 | done 15 | mp_host_list=`echo ${mp_host_list} | sed -e "s/,$//"` 16 | export mp_host_list 17 | echo "${mp_host_list}" >>$envFile 18 | unset mp_host_list 19 | -------------------------------------------------------------------------------- /Slurm/slurm_setup_cfx-env2.sh: -------------------------------------------------------------------------------- 1 | #!/bin/bash 2 | # This script will create the User Environment to run ANSYS CFX under Slurm 3 | # Created by Jordi Blasco , Bart Verleye 4 | export CFX5RSH=ssh 5 | export MPI_REMSH=ssh 6 | export MPI_IC_ORDER="udapl:ibv:tcp" 7 | #export MPI_CPU_AFFINITY=SLURM 8 | 9 | CFX_HOSTLIST_TMP=`srun hostname -s | sort ` 10 | CFX_HOSTLIST_TMP=`echo $CFX_HOSTLIST_TMP | sed -e 's/ /,/g'` 11 | export CFX_HOSTLIST=$CFX_HOSTLIST_TMP 12 | -------------------------------------------------------------------------------- /Slurm/slurm_setup_cfx-env3.sh: -------------------------------------------------------------------------------- 1 | #!/bin/bash 2 | # This script will create the User Environment to run ANSYS CFX under Slurm 3 | # Created by Jordi Blasco , Bart Verleye 4 | #export CFX5RSH=ssh 5 | #export MPI_REMSH=ssh 6 | #export MPI_IC_ORDER="udapl:ibv:tcp" 7 | #export MPI_CPU_AFFINITY=SLURM 8 | 9 | CFX_HOSTLIST_TMP=`srun hostname -s | sort ` 10 | CFX_HOSTLIST_TMP=`echo $CFX_HOSTLIST_TMP | sed -e 's/ /,/g'` 11 | export CFX_HOSTLIST=$CFX_HOSTLIST_TMP 12 | -------------------------------------------------------------------------------- /Slurm/slurm_setup_fluent.sh: -------------------------------------------------------------------------------- 1 | #!/usr/bin/env bash 2 | export MPI_IC_ORDER="udapl:ibv:tcp" 3 | HOSTSFILE=.hostlist-job$SLURM_JOB_ID 4 | if [ "$SLURM_PROCID" == "0" ]; then 5 | srun hostname -f > $HOSTSFILE 6 | fi 7 | -------------------------------------------------------------------------------- /Slurm/star-ccm+-platform.sl: -------------------------------------------------------------------------------- 1 | #!/bin/bash 2 | # STAR-CCM+ SubmitScript 3 | # Optimized for run parallel job with Platform MPI 4 | ###################################################### 5 | #SBATCH -J STAR-CCM+PMPI 6 | #SBATCH -A hpcnow 7 | #SBATCH -D /sNow/test/Star-CCM+/case06/input 8 | #SBATCH --time=06:00:00 9 | #SBATCH --mem-per-cpu=2048 10 | #SBATCH --nodes=10 11 | #SBATCH --ntasks=160 12 | ###################################################### 13 | 14 | export SIM_FILE=Test7.1-Fn-0.45-layers1.5-timestep15.sim 15 | export BATCH_FILE=Run.java 16 | export PATH=$PATH:/projects/hpcnow/STAR-CCM+9.04.009-R8/star/bin 17 | 18 | cp -pr * $SCRATCH_DIR 19 | cd $SCRATCH_DIR 20 | 21 | echo "JOB_ID:" $SLURM_JOB_ID 22 | echo '#!/bin/bash' >$(echo "star-connect-"$SLURM_JOB_ID) 23 | echo "/projects/hpcnow/STAR-CCM+9.04.009-R8/star/bin/starccm+ -host" $SLURMD_NODENAME "-port 47827 &" >>$(echo "star-connect-"$SLURM_JOB_ID) 24 | chmod +x $(echo "star-connect-"$SLURM_JOB_ID) 25 | 26 | # Build node list 27 | srun hostname -s | sort >slurm.hosts 28 | 29 | # Start Star-CCM+ server in batch mode 30 | echo "Starting Star-CCM+" 31 | echo 32 | 33 | #starccm+ -power -rsh ssh -licpath 1999@flex.cd-adapco.com -np $SLURM_NPROCS -cpubind off -podkey $PODKEY -machinefile slurm.hosts -batch $BATCH_FILE $SIM_FILE 34 | starccm+ -power -collab -np $SLURM_NPROCS -licpath $LICENSE -podkey $PODKEY -cpubind off -machinefile slurm.hosts -time -mppflags "-srun" -fabric UDAPL -batch $BATCH_FILE -rsh ssh $SIM_FILE 35 | # Where: 36 | # -collab is an option necessary to avoid user name checking. my.java is an optional java file. 37 | # mycase.sim is the STAR-CCM+ simulation file. 38 | 39 | rm slurm.hosts 40 | rm $(echo "star-connect-"$SLURM_JOB_ID) 41 | 42 | mv Resistance_Data.csv $(echo $SIM_FILE".csv") 43 | 44 | cp -pr $SCRATCH_DIR /sNow/test/Star-CCM+/case06/output/ 45 | 46 | -------------------------------------------------------------------------------- /Slurm/stress.sl: -------------------------------------------------------------------------------- 1 | #!/bin/bash 2 | #SBATCH -J STRESS 3 | #SBATCH -A hpcnow 4 | #SBATCH --time=1:05:00 5 | #SBATCH --mem-per-cpu=4G 6 | ##SBATCH --cpus-per-task=12 7 | #srun stress --cpu 12 --vm-bytes 2GB --timeout 3600s 8 | cd $SCRATCH_DIR 9 | srun stress --cpu 1 -d 10 --timeout 3600s 10 | -------------------------------------------------------------------------------- /Slurm/supermagic.sl: -------------------------------------------------------------------------------- 1 | #!/bin/bash 2 | #SBATCH -J MPI_SuperMagic 3 | #SBATCH -A hpcnow 4 | #SBATCH --time=02:00:00 5 | #SBATCH --mem-per-cpu=7800M 6 | #SBATCH --ntasks=1024 7 | # 8 | # options: 9 | # [-a|--all] run all tests in suite 10 | # [-h|--help] display this message 11 | # [-m|--msg-size x[B,k,M,G]] change message size 12 | # [-M|--file-size B[B,k,M,G]] change file size (per rank) 13 | # [-n|--n-iters X] run X iterations of a test suite 14 | # [-q|--quiet] run in quiet mode 15 | # [-s|--stat /a/path] add /a/path to stat list 16 | # [-t|--with-tests t1[,t2,tn]] run tests in requested order 17 | # [-w|--write /a/path] add /a/path to IO tests 18 | # [-V|--verbose] display verbose output 19 | # 20 | 21 | for i in 20130104-goolf-1.5.14 20130104-ictce-5.4.0 20130104-iomkl-4.6.13 20130104-iomkl-6.5.4 20130104-foss-2015a 20130104-intel-2015a 22 | do 23 | module load supermagic/$i 24 | echo "Tool Chain $i" 25 | srun supermagic -a -m 2M -w $SCRATCH_DIR/ -n 10 > supermagic-$i-$SLURM_JOB_ID.dat 26 | module purge 27 | done 28 | -------------------------------------------------------------------------------- /Slurm/trace.conf: -------------------------------------------------------------------------------- 1 | LOGFILE-FORMAT STFSINGLE 2 | ACTIVITY MPI ON 3 | STATE MPI:* ON 4 | PROCESS 0:N OFF 5 | PROCESS 0:3 ON 6 | TIME-WINDOWS 0:300000l 7 | --------------------------------------------------------------------------------