Difference between revisions of "Running Gromacs"
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-- [[User:Cneale|cneale]] 14 September 2009 | -- [[User:Cneale|cneale]] 14 September 2009 | ||
+ | |||
+ | =====Submitting a IB GPC job using openmpi that resubmits prior to completing===== | ||
+ | <source lang="sh"> | ||
+ | #!/bin/bash | ||
+ | #PBS -l nodes=6:ib:ppn=8,walltime=46:00:00,os=centos53computeA | ||
+ | #PBS -N 1 | ||
+ | if [ "$PBS_ENVIRONMENT" != "PBS_INTERACTIVE" ]; then | ||
+ | if [ -n "$PBS_O_WORKDIR" ]; then | ||
+ | cd $PBS_O_WORKDIR | ||
+ | fi | ||
+ | fi | ||
+ | /scinet/gpc/mpi/openmpi/1.3.2-intel-v11.0-ofed/bin/mpirun -np $(wc -l $PBS_NODEF | ||
+ | ILE | gawk '{print $1}') -machinefile $PBS_NODEFILE /scratch/cneale/GPC/exe/inte | ||
+ | l/gromacs-4.0.5/exec/bin/mdrun_openmpi -deffnm X3_LDAO_0.5MNaCl -cpi X3_LDAO_0.5 | ||
+ | MNaCl -nosum -dlb yes -cpt 120 -maxh 46 -npme 16 | ||
+ | |||
+ | num=$NUM | ||
+ | if [ $num -lt 100 ]; then | ||
+ | num=$(($num+1)) | ||
+ | ssh gpc01 "cd $PBS_O_WORKDIR; qsub run48cpu.sh -v NUM=$num"; | ||
+ | fi | ||
+ | |||
+ | ## Initial submission with: qsub this.sh -v NUM=0 | ||
+ | </source> | ||
+ | |||
+ | -- [[User:Holyoake|Holyoake]] 14 September 2009 |
Revision as of 13:04, 8 October 2009
Submitting an IB GPC job using openmpi
<source lang="sh">
- !/bin/bash
- PBS -l nodes=10:ib:ppn=8,walltime=40:00:00,os=centos53computeA
- PBS -N 1
if [ "$PBS_ENVIRONMENT" != "PBS_INTERACTIVE" ]; then
if [ -n "$PBS_O_WORKDIR" ]; then cd $PBS_O_WORKDIR fi
fi /scinet/gpc/mpi/openmpi/1.3.2-intel-v11.0-ofed/bin/mpirun -np $(wc -l $PBS_NODEFILE | gawk '{print $1}') -machinefile $PBS_NODEFILE /scratch/cneale/exe/intel/gromacs-4.0.5/exec/bin/mdrun_openmpi -deffnm pagp -nosum -dlb yes -npme 24 -cpt 120
- To submit type: qsub this.sh
</source>
-- cneale 18 August 2009
Submitting an IB GPC job using mvapich2-1.4rc1
Note that mvapich2-1.4rc1 is not configured to fall back to ethernet so this will not work on the non-IB nodes, even for 8 cores.
<source lang="sh">
- !/bin/bash
- PBS -l nodes=4:ib:ppn=8,walltime=30:00:00,os=centos53computeA
- PBS -N 1
if [ "$PBS_ENVIRONMENT" != "PBS_INTERACTIVE" ]; then
if [ -n "$PBS_O_WORKDIR" ]; then cd $PBS_O_WORKDIR fi
fi module purge module load mvapich2 intel /scratch/cneale/exe/mvapich2-1.4rc1/bin/mpirun_rsh -np $(wc -l $PBS_NODEFILE | gawk '{print $1}') -hostfile $PBS_NODEFILE /scratch/cneale/exe/intel/gromacs-4.0.5/exec/bin/mdrun_mvapich2 -deffnm pagp -nosum -dlb yes -npme 12 -cpt 120
- To submit type: qsub this.sh
</source>
-- cneale 18 August 2009
Submitting a non-IB GPC job using openmpi
<source lang="sh">
- !/bin/bash
- PBS -l nodes=1:compute-eth:ppn=8,walltime=40:00:00,os=centos53computeA
- PBS -N 1
if [ "$PBS_ENVIRONMENT" != "PBS_INTERACTIVE" ]; then
if [ -n "$PBS_O_WORKDIR" ]; then cd $PBS_O_WORKDIR fi
fi /scinet/gpc/mpi/openmpi/1.3.2-intel-v11.0-ofed/bin/mpirun -mca btl_sm_num_fifos 7 -np $(wc -l $PBS_NODEFILE | gawk '{print $1}') -mca btl self,sm -machinefile $PBS_NODEFILE /scratch/cneale/exe/intel/gromacs-4.0.5/exec/bin/mdrun_openmpi -deffnm pagp -nosum -dlb yes -npme 24 -cpt 120
- To submit type: qsub this.sh
</source>
This is VERY IMPORTANT !!! Please read the [relevant user tips section] for information that is essential for your single node (up to 8 core) MPI GROMACS jobs.
-- cneale 14 September 2009
Submitting a IB GPC job using openmpi that resubmits prior to completing
<source lang="sh">
- !/bin/bash
- PBS -l nodes=6:ib:ppn=8,walltime=46:00:00,os=centos53computeA
- PBS -N 1
if [ "$PBS_ENVIRONMENT" != "PBS_INTERACTIVE" ]; then
if [ -n "$PBS_O_WORKDIR" ]; then cd $PBS_O_WORKDIR fi
fi /scinet/gpc/mpi/openmpi/1.3.2-intel-v11.0-ofed/bin/mpirun -np $(wc -l $PBS_NODEF ILE | gawk '{print $1}') -machinefile $PBS_NODEFILE /scratch/cneale/GPC/exe/inte l/gromacs-4.0.5/exec/bin/mdrun_openmpi -deffnm X3_LDAO_0.5MNaCl -cpi X3_LDAO_0.5 MNaCl -nosum -dlb yes -cpt 120 -maxh 46 -npme 16
num=$NUM if [ $num -lt 100 ]; then
num=$(($num+1)) ssh gpc01 "cd $PBS_O_WORKDIR; qsub run48cpu.sh -v NUM=$num";
fi
- Initial submission with: qsub this.sh -v NUM=0
</source>
-- Holyoake 14 September 2009