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Running GROMACS on Legion

GROMACS on Legion was built with FFTW, the OpenMPI library and the GNU compilers. It is therefore strongly recommended that you have these modules loaded when running it:

  • sge/6.2u3
  • compilers/gnu/4.6.3
  • mpi/openmpi/1.4.5/gnu.4.6.3
  • gromacs/4.6.1/openmpi/gnu.4.6.3

Which version you require depends on the problem you wish to solve. For both single and double precisions version builds, serial binaries and an MPI binary for mdrun (mdrun_mpi) are provided. Double precision binaries have a _d suffix (so mdrun_d, mdrun_mpi_d etc). The MPI binaries should be run in the OpenMPI (openmpi) parallel environment with the OpenMPI implementation.

Job Script§

```

```#!/bin/bash -l```

```# Batch script to run an MPI parallel GROMACS job on Legion with the upgraded software```
```# stack under SGE with OpenMPI.```

```# 1. Force bash as the executing shell.```
```#$ -S /bin/bash```

```# 2. Request ten minutes of wallclock time (format hours:minutes:seconds).```
```#$ -l h_rt=0:10:0```

```# 3. Request 1 gigabyte of RAM per process.```
```#$ -l mem=1G```

```# 4. Request 15 gigabyte of TMPDIR space per node (default is 10 GB)```
```#$ -l tmpfs=15G```

```# 5. Set the name of the job.```
```#$ -N GROMACS_1_16_OpenMPI```

```# 6. Select the OpenMPI parallel environment and 16 processes.```
```#$ -pe openmpi 16```

```# 7. Select the project that this job will run under.```
```# Find `````` by running the command "groups"```
```#$ -P ```

```# 8. Set the working directory of the job to the current directory```
```#     containing your input files.```
```#    This *has* to be somewhere in your Scratch space, or else your```
```#     job will go into the Eqw state.```
```#$ -cwd```

```module unload compilers/intel/11.1/072```
```module unload mpi/qlogic/1.2.7/intel```
```module unload mkl/10.2.5/035```
```module load compilers/gnu/4.6.3```
```module load mpi/openmpi/1.4.5/gnu.4.6.3```
```module load gromacs/4.6.1/openmpi/gnu.4.6.3```

```# Run GROMACS - replace with mdrun command line suitable for your job!```

```gerun mdrun_mpi -v -stepout 10000```

```

Category:Bash script pages Category:Legion