GROMACS v5.0.4

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 v5.0.4. The following flavours are available:

5.0.4 for all Intel node types

Note: ability to run on all Intel nodes implies lower optimization.

• 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.

5.0.4 for Sandybridge and Ivybridge (and Haswell, Broadwell nodes) only

Note: ability to run on only Sandybridge, Ivybridge (and Haswell) nodes implies higher optimization. Note that an even higher level of optimization, and an MPI version, is available for Haswell nodes (see below).

• 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 (single-node, multicore) jobs for these types nodes.
• There are no MPI versions of 5.0.4 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.

5.0.4 for Haswell and Broadwell nodes only

Note: ability to run on only Haswell and Broadwell nodes implies higher optimization.

• Single and double precision single-node, multi-threaded (OpenMP) versions: mdrun and mdrun_d
• Single and double precision multi-node (MPI) versions: mdrun_mpi and mdrun_mpi_d
• Compiled with Intel 14.0.3 compiler with the associated Intel MKL providing the FFT functions and with AVX2_256 (an instruction set specific to these nodes which provides further optimization than AVX_256) so WILL NOT work on Westmere, Sandybridge and Ivybridge nodes.
• Single-node multi-core smp.pe jobs can use these nodes.
• Multi-core MPI orte-24-ib.pe jobs can use these nodes – the Haswell and Broadwell nodes have InfiniBand networking.
• This version will not run on highmem, twoday or short nodes (they are all Westmere).
• ngmx has been included.

Bugfix for g_hbond

Version 5.0.4 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.

Please NOTE the following which important for running jobs correctly and efficiently:

Ensure you inform gromacs how many cores it can use. This is done using either

mpiexec -n $NSLOTS mdrun_mpi            # Multi-node MPI job

or

export OMP_NUM_THREADS=$NSLOTS          # Single-node multi-threaded job
mdrun

in your jobscript (see below for which to use).

The examples below can be used for single precision or double precision gromacs. Simply run mdrun (single precision) or mdrun_d (double precision).

Multi-threaded single-precision on Intel nodes, 2 to 24 cores

Note that GROMACS v5.0.4 (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            # Can specify 2 to 24 cores in smp.pe
                            # 2-12 includes Westmere, Sandybridge, Ivybridge, Haswell
                            # 13-16 forces use of Ivybridge.
                            # 17-24 forces use of Haswell.
                            # Can force use of a particular architecture (see below)

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 double-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               # Force use of sandybridge nodes

export OMP_NUM_THREADS=$NSLOTS
mdrun_d

Submit with the command: qsub scriptname

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

Note that GROMACS v5.0.4 (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 16 threads:

#!/bin/bash
#$ -S /bin/bash
#$ -cwd
#$ -V
#$ -pe smp.pe 16
#$ -l ivybridge                 # Force use of Ivybridge nodes

export OMP_NUM_THREADS=$NSLOTS
mdrun

Submit with the command: qsub scriptname

Multi-threaded single-precision, AVX2 on Haswell nodes, 2 to 24 cores

Note that GROMACS v5.0.4 (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 16 threads:

#!/bin/bash
#$ -S /bin/bash
#$ -cwd
#$ -V
#$ -pe smp.pe 24
#$ -l haswell                  # Force use of Haswell nodes

export OMP_NUM_THREADS=$NSLOTS
mdrun

Submit with the command: qsub scriptname

Single precision MPI (single-node), 2 to 24 cores

An example batch submission script to run the double-precision mdrun_mpi executable on 8 cores using mpi:

#!/bin/bash
#$ -S /bin/bash
#$ -cwd
#$ -V
#$ -pe smp.pe 8            
                                          
mpiexec -n $NSLOTS mdrun_mpi

Submit with the command: qsub scriptname

Double precision MPI (single-node), 2 to 24 cores

An example batch submission script to run the double-precision mdrun_mpi_d executable on 8 cores using mpi:

#!/bin/bash
#$ -S /bin/bash
#$ -cwd
#$ -V
#$ -pe smp.pe 4             
                                          
mpiexec -n $NSLOTS mdrun_mpi_d

Submit with the command: qsub scriptname

Single-precision AVX2, 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 48 MPI processes (48 cores on two 24-core nodes) with the orte-24-ib.pe parallel environment (Intel Haswell nodes using infiniband):

#!/bin/bash
#$ -S /bin/bash
#$ -cwd
#$ -V
#$ -pe orte-24-ib.pe 48           # EG: Two 24-core Intel Haswell nodes

mpiexec -n $NSLOTS mdrun_mpi

Submit with the command: qsub scriptname

Illegal instruction

If during a batch job you try to run gromacs and get the following error:

Illegal instruction

This is because you have an AVX or AVX2 only version of the modulefile loaded which is not compatible with the compute nodes on which your job is running. Ensure your jobscript requests the correct type of compute node.

Error about OpenMP and cut-off scheme

If you encounter the following error:

OpenMP threads have been requested with cut-off scheme Group, but these 
are only supported with cut-off scheme Verlet

then please try using the mpi version of the software. Note that is is possible to run mpi versions on a single node (example above).

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

Apr 2015 – 5.0.4 installed with AVX support (GPU support with Intel compiler not possible)
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.