GROMACS v4.6.7

Overview

GROMACS is a package for computing molecular dynamics, simulating Newtonian equations of motion for systems with hundreds to millions of particles. GROMACS is designed for biochemical molecules with complicated bonded interactions (e.g. proteins, lipids, nucleic acids) but can also be used for non-biological systems (e.g. polymers).

This version is v4.6.7. The following flavours are available:

4.6.7 for all intel node types

• Single and double precision multi-threaded (OpenMP) versions: mdrun and mdrun_d
• Single and double precision MPI (not threaded) versions: mdrun_mpi and mdrun_d_mpi
• Compiled with Intel 14.0.3 compiler with the associated Intel MKL providing the FFT functions.
• ngmx has been included.

4.6.7 for Sandybridge and Ivybridge nodes only

• Single and double precision multi-threaded (OpenMP) versions: mdrun and mdrun_d
• Compiled with Intel 14.0.3 compiler with the associated Intel MKL providing the FFT functions and with AVX_256 (an instruction set specific to these nodes) so WILL NOT work on Westmere nodes and NONE of the commands can be run on the login nodes.
• We have no Sandybridge or Ivybridge nodes connected by Infiniband which means ONLY smp.pe job for this install.
• There are no mpi versions of 4.6.7 for Sandybridge and Ivybridge nodes available on the CSF.
• This version will not run on highmem, twoday or short nodes (they are all Westmere).
• ngmx has been included.

Bugfix for g_hbond

Version 4.6.7 has the g_hbond fix included by default and so no separate build has been made for this version. See the GROMACS v4.5.4 CSF documentation for a description of that issue.

Restrictions on use

GROMACS is free software, available under the GNU General Public License.

Set up procedure

You must load the appropriate modulefile:

module load modulefile

replacing modulefile with one of the modules listed in the table below.

qrsh -l inter -l short -l sandybridge

Running the application in batch

First load the required module (see above) and create a directory containing the required input data files.

You MUST ensure that as well as requesting a number of cores from a suitable parallel environment you also tell gromacs how many cores it may use. These two numbers must be the same, which can be ensured through correct use of some variables and/or flags depending on the version of gromacs being used. Failure to set this information causes gromacs to run incorrectly, overload compute nodes and potentially trample on jobs belonging to other users. All of the examples below ensure that jobs use the cores requested.

If you are running a different version to those used in the examples below ensure you replace the executable, e.g. mdrun with the executable appropriate to the version based on the table above.

Multi-threaded single-precision on intel nodes, 2 to 16 cores

Note that GROMACS v4.6.7 (unlike v4.5.4) does not support the -nt flag to set the number of threads when using the multithreaded OpenMP (non-MPI) verison. Instead set the OMP_NUM_THREADS environment variable as shown below.

An example batch submission script to run the single-precision mdrun executable with 12 threads:

#!/bin/bash
#$ -S /bin/bash
#$ -cwd
#$ -V
#$ -pe smp.pe 12

export OMP_NUM_THREADS=$NSLOTS
mdrun

Submit with the command: qsub scriptname

The system will run your job on a Westmere, a Sandybridge or an Ivybridge node depending on what is available. This option goes to the biggest pool of nodes. To get a more optimised run on Sandybridge or Ivybridge you should be using a modulefile with ‘avx’ in the name and using the instructions below.

Multi-threaded single-precision AVX on Sandybridge nodes 2 to 12 cores

An example batch submission script to run the double-precision mdrun_d executable with 8 threads:

#!/bin/bash
#$ -S /bin/bash
#$ -cwd
#$ -V
#$ -pe smp.pe 8
#$ -l sandybridge

export OMP_NUM_THREADS=$NSLOTS
mdrun

Submit with the command: qsub scriptname

Multi-threaded single-precision AVX on Ivybridge nodes, 2 to 16 cores

Note that GROMACS v4.6.7 (unlike v4.5.4) does not support the -nt flag to set the number of threads when using the multithreaded OpenMP (non-MPI) verison. Instead set the OMP_NUM_THREADS environment variable as shown below.

An example batch submission script to run the single-precision mdrun executable with 12 threads:

#!/bin/bash
#$ -S /bin/bash
#$ -cwd
#$ -V
#$ -pe smp.pe 12
#$ -l ivybridge

export OMP_NUM_THREADS=$NSLOTS
mdrun

Submit with the command: qsub scriptname

Single-precision MPI with Infiniband, 48 cores or more in multiples of 24

An example batch submission script to run the single precision mdrun_mpi executable with 24 MPI processes on 24 cores with the orte-24-ib.pe parallel environment (Intel nodes using infiniband):

#!/bin/bash
#$ -S /bin/bash
#$ -cwd
#$ -V
#$ -pe orte-24-ib.pe 48

mpiexec -n $NSLOTS mdrun_mpi

Submit with the command: qsub scriptname

Illegal instruction

If during job setup/post-processing you try to run gromacs commands on the login nodes and get the following error:

Illegal instruction

this is because you have an AVX only version of the modulefile loaded which is not compatible with the login node. You should load the non-AVX version and then unload it and reload the AVX version at job submission time.

If you get it in a batch job then it is because you did not specify whether to run on a sandybridge or ivybridge node in your job script.

Further info

• You can see a list of all the installed GROMACS utilities with the command: ls $GMXDIR/bin
• GROMACS web page
• GROMACS manuals
• GROMACS user mailing list

Updates

Dec 2014 – 4.6.7 installed with AVX support (specific user request for this) and documentation written.
Nov 2013 – Documentation for 4.5.4 and 4.6.1 split in to two pages.
May 2013 – Gromacs 4.6.1 and Plumed 1.3 installed.