How to use GROMACS on ENEA-grid

Application Name Gromacs
Discipline: Computational Biology

GROMACS is a versatile package to perform molecular dynamics, i.e. simulate the Newtonian equations of motion for systems with hundreds to millions of particles. It is primarily designed for biochemical molecules like proteins and lipids that have a lot of complicated bonded interactions, but since GROMACS is extremely fast at calculating the nonbonded interactions (that usually dominate simulations) many groups are also using it for research on non-biological systems, e.g. polymers.

In this page you can find the launching and submission syntax for Gromacs code on the ENEA-GRID. Please, read the following documentation for running serial/parallel application on CRESCO clusters using LSF framework: Batch Jobs / LSF. This is not a tutorial about using codes like Gromacs, for that, you may find documentation and tutorial on the official web site www.gromacs.org.

ENEA-GRID/CRESCO utilization rules (link).


JOB SUBMISSION SCRIPT on CRESCO6

To submit on CRESCO6 use the script named gromacs . To know the installed versions simply type:
gromacs --version
For help on how to use the script:
gromacs --help



CRESCO
Cluster
CRESCO6
front-ends
cresco6x001 cresco6x002
LSF submission
bsub -n N -q queue bsub_options -o lsf_file.out -e file.err gromacs version mode args

export OMP_NUM_THREADS=nthreads
bsub -n N -q queue -R "span[ptile=pt]" bsub_options -o lsf_file.out -e file.err gromacs version mode args
where:
version = gromacs version (e.g. 2019)
mode = par or ser
args = mdrun (or other gormacs executables) -s input.in -o trajectory.trr -c structure.gro -g md.log -e energy.edr ...


Example of job submission
  • To submit a job on CRESCO6 using the 2019 version with only MPI parallelism and using 96 processors:
    bsub -n 96 -q cresco6_48h24 -o lsf_file.out -e file.err gromacs 2019 par mdrun -s topol.tpr
  • To submit a job on CRESCO6 using the 2019 version with hybrid MPI+OpenMP parallelism and using 96 processors and 2 threads per core (pt*threads=48 since CRESCO6 has 48 cores per node):

    export OMP_NUM_THREADS=2
    bsub -n 96 -q cresco6_48h24 -R "span[ptile=24]" -o lsf_file.out -e file.err gromacs 2019 par mdrun -s topol.tpr
  • To submit a job on CRESCO6 using the intel compiler and the serial version:
    bsub -n 1 -q cresco6_h4 -o lsf_file.out -e file.err gromacs 2019 ser mdrun -s topol.tpr -ntmpi 1
N.B.. The syntax of the script to launch gromacs under CRESCO6 is different from that used in CRESCOn (with n <6).



JOB SUBMISSION SCRIPT on CRESCOn (with n <6)



CRESCO
Cluster
CRESCO4
front-end
cresco4x001
cresco4x002
LSF submission
bsub -n N -q queue bsub_options -i file.in -o file.out -e file.err gromacs5.0.7_par args
bsub -n 1 -q queue bsub_options -i file.in -o file.out -e file.err gromacs5.0.7_ser args


Gromacs version 5.0.7 (manual.pdf, manual.html)

example for submission on CRESCO4: cresco4x001, cresco4x002.
bsub -n 400 -q cresco4_256h24 -o file.out -e err.dat gromacs5.0.7_par args
bsub -n 64 -q cresco4_16h24 -o file.out -e err.dat gromacs5.0.7_par args
bsub -n 64 -q cresco4_h6 -o file.out -e err.dat gromacs5.0.7_par args

N.B.
  • Example of arguments: -s input.in -o trajectory.trr -c structure.gro -g md.log -e energy.edr
  • For the interactive submission on the front-end cresco4x002 use the command:
    • gromacs5.0.7_ser args
Some useful bsub options: -W time_in_minute, -R "span[ptile=16]", -R "span[ptile=24]",
-R "same[model]", -R K40, -R S2050, -R "select[model==xxx]",
-R "select[hname==crescoxx1 || hname==crescoxx2]", -R "select[hname!=crescoxx3]".