Difference between revisions of "Running Gromacs"
| (6 intermediate revisions by 4 users not shown) | |||
| Line 1: | Line 1: | ||
| + | '''NOTE''' MOST OF THIS IS DEPRECATED FOR GPC POST IB UPGRADE | ||
| + | |||
=====Submitting an IB GPC job using openmpi===== | =====Submitting an IB GPC job using openmpi===== | ||
| − | <source lang=" | + | <source lang="bash"> |
#!/bin/bash | #!/bin/bash | ||
| − | #PBS -l nodes=10:ib:ppn=8,walltime=40:00:00 | + | #PBS -l nodes=10:ib:ppn=8,walltime=40:00:00 |
| − | #PBS -N | + | #PBS -N test |
if [ "$PBS_ENVIRONMENT" != "PBS_INTERACTIVE" ]; then | if [ "$PBS_ENVIRONMENT" != "PBS_INTERACTIVE" ]; then | ||
if [ -n "$PBS_O_WORKDIR" ]; then | if [ -n "$PBS_O_WORKDIR" ]; then | ||
| Line 23: | Line 25: | ||
so this will not work on the non-IB nodes, even for 8 cores. | so this will not work on the non-IB nodes, even for 8 cores. | ||
| − | <source lang=" | + | <source lang="bash"> |
#!/bin/bash | #!/bin/bash | ||
| − | #PBS -l nodes=4:ib:ppn=8,walltime=30:00:00 | + | #PBS -l nodes=4:ib:ppn=8,walltime=30:00:00 |
| − | #PBS -N | + | #PBS -N test |
if [ "$PBS_ENVIRONMENT" != "PBS_INTERACTIVE" ]; then | if [ "$PBS_ENVIRONMENT" != "PBS_INTERACTIVE" ]; then | ||
if [ -n "$PBS_O_WORKDIR" ]; then | if [ -n "$PBS_O_WORKDIR" ]; then | ||
| Line 44: | Line 46: | ||
=====Submitting a non-IB GPC job using openmpi===== | =====Submitting a non-IB GPC job using openmpi===== | ||
| − | <source lang=" | + | <source lang="bash"> |
#!/bin/bash | #!/bin/bash | ||
| − | #PBS -l nodes=1:compute-eth:ppn=8,walltime=40:00:00 | + | #PBS -l nodes=1:compute-eth:ppn=8,walltime=40:00:00 |
| − | #PBS -N | + | #PBS -N test |
if [ "$PBS_ENVIRONMENT" != "PBS_INTERACTIVE" ]; then | if [ "$PBS_ENVIRONMENT" != "PBS_INTERACTIVE" ]; then | ||
if [ -n "$PBS_O_WORKDIR" ]; then | if [ -n "$PBS_O_WORKDIR" ]; then | ||
| Line 53: | Line 55: | ||
fi | fi | ||
fi | fi | ||
| − | /scinet/gpc/mpi/openmpi/1.3.2-intel-v11.0-ofed/bin/mpirun | + | /scinet/gpc/mpi/openmpi/1.3.2-intel-v11.0-ofed/bin/mpirun -mca btl_sm_num_fifos 7 |
| − | -mca btl_sm_num_fifos 7 -np $(wc -l $PBS_NODEFILE | gawk '{print $1}') | + | -np $(wc -l $PBS_NODEFILE | gawk '{print $1}') -mca btl self,sm |
| − | -mca btl self,sm -machinefile $PBS_NODEFILE | + | -machinefile $PBS_NODEFILE /scratch/cneale/exe/intel/gromacs-4.0.5/exec/bin/mdrun_openmpi |
| − | /scratch/cneale/exe/intel/gromacs-4.0.5/exec/bin/mdrun_openmpi -deffnm | + | -deffnm pagp -nosum -dlb yes -cpt 120 |
| − | pagp -nosum -dlb yes | ||
## To submit type: qsub this.sh | ## To submit type: qsub this.sh | ||
</source> | </source> | ||
| Line 67: | Line 68: | ||
=====Submitting a IB GPC job using openmpi that resubmits prior to completing===== | =====Submitting a IB GPC job using openmpi that resubmits prior to completing===== | ||
| − | <source lang=" | + | <source lang="bash"> |
#!/bin/bash | #!/bin/bash | ||
| − | #PBS -l nodes=6:ib:ppn=8,walltime=46:00:00 | + | #PBS -l nodes=6:ib:ppn=8,walltime=46:00:00 |
| − | #PBS -N | + | #PBS -N test |
if [ "$PBS_ENVIRONMENT" != "PBS_INTERACTIVE" ]; then | if [ "$PBS_ENVIRONMENT" != "PBS_INTERACTIVE" ]; then | ||
if [ -n "$PBS_O_WORKDIR" ]; then | if [ -n "$PBS_O_WORKDIR" ]; then | ||
Latest revision as of 15:34, 17 June 2013
NOTE MOST OF THIS IS DEPRECATED FOR GPC POST IB UPGRADE
Submitting an IB GPC job using openmpi
<source lang="bash">
- !/bin/bash
- PBS -l nodes=10:ib:ppn=8,walltime=40:00:00
- PBS -N test
if [ "$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 $PBS_NODEFILE /scratch/cneale/exe/intel/gromacs-4.0.5/exec/bin/mdrun_openmpi -deffnm pagp -nosum -dlb yes -npme 24 -cpt 120
- To submit type: qsub this.sh
</source>
-- cneale 18 August 2009
Submitting an IB GPC job using mvapich2-1.4rc1
Note that mvapich2-1.4rc1 is not configured to fall back to ethernet so this will not work on the non-IB nodes, even for 8 cores.
<source lang="bash">
- !/bin/bash
- PBS -l nodes=4:ib:ppn=8,walltime=30:00:00
- PBS -N test
if [ "$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 $PBS_NODEFILE /scratch/cneale/exe/intel/gromacs-4.0.5/exec/bin/mdrun_mvapich2 -deffnm pagp -nosum -dlb yes -npme 12 -cpt 120
- To submit type: qsub this.sh
</source>
-- cneale 18 August 2009
Submitting a non-IB GPC job using openmpi
<source lang="bash">
- !/bin/bash
- PBS -l nodes=1:compute-eth:ppn=8,walltime=40:00:00
- PBS -N test
if [ "$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 $PBS_NODEFILE /scratch/cneale/exe/intel/gromacs-4.0.5/exec/bin/mdrun_openmpi
-deffnm pagp -nosum -dlb yes -cpt 120
- To submit type: qsub this.sh
</source>
This is VERY IMPORTANT !!! Please read the [relevant user tips section] for information that is essential for your single node (up to 8 core) MPI GROMACS jobs.
-- cneale 14 September 2009
Submitting a IB GPC job using openmpi that resubmits prior to completing
<source lang="bash">
- !/bin/bash
- PBS -l nodes=6:ib:ppn=8,walltime=46:00:00
- PBS -N test
if [ "$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 $PBS_O_WORKDIR; qsub this.sh -v NUM=$num";
fi
- Initial submission with: qsub this.sh -v NUM=0
</source>
-- Holyoake 14 September 2009