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Gromacs

Initial Setup

In order to use Gromacs append the following lines to your .profile file:

export MODULEPATH=/opt/gridware/applications/gromacs/modules:$MODULEPATH
module add gromacs/4.6.1 mpich2/1.5

To complete the setup log out of the cluster and back in again (or just source your .profile file) to update your environment variables.

Example Job Submission Script

The following file is a Gromacs template job submission script that can used as a starting point for creating your own scripts:

gromacs.job
#This job tests GROMACS, it requires the input file min.steep0.tpr to be in the working directory.
 
#MSUB -l nodes=2:ppn=12
#MSUB -l feature=dell
#MSUB -l walltime=24:00:00
#MSUB -j oe
#MSUB -o out.log
#MSUB -d /export/home/username/scratch5/gromacs
#MSUB -V
 
NP=`cat $PBS_NODEFILE | wc -l`
BIN=mdrun_mpi
ARGS="-s min.steep0.tpr -deffnm min.steep0 -npme 4"
 
mpirun -np $NP -machinefile $PBS_NODEFILE $BIN $ARGS

This job submission script requires that the file min.steep0.tpr be in the working directory specified above.

NOTE: Please ensure that all file I/O associated with your job only occurs in a sub-directory of the scratch5 partition.

Job Submission

Submit the job using the following command:

msub gromacs.job

Example Expected Output

                         :-)  G  R  O  M  A  C  S  (-:
 
               Giant Rising Ordinary Mutants for A Clerical Setup
 
                            :-)  VERSION 4.6.1  (-:
 
        Contributions from Mark Abraham, Emile Apol, Rossen Apostolov, 
           Herman J.C. Berendsen, Aldert van Buuren, Pär Bjelkmar,  
     Rudi van Drunen, Anton Feenstra, Gerrit Groenhof, Christoph Junghans, 
        Peter Kasson, Carsten Kutzner, Per Larsson, Pieter Meulenhoff, 
           Teemu Murtola, Szilard Pall, Sander Pronk, Roland Schulz, 
                Michael Shirts, Alfons Sijbers, Peter Tieleman,
 
               Berk Hess, David van der Spoel, and Erik Lindahl.
 
       Copyright (c) 1991-2000, University of Groningen, The Netherlands.
         Copyright (c) 2001-2012,2013, The GROMACS development team at
        Uppsala University & The Royal Institute of Technology, Sweden.
            check out http://www.gromacs.org for more information.
 
         This program is free software; you can redistribute it and/or
       modify it under the terms of the GNU Lesser General Public License
        as published by the Free Software Foundation; either version 2.1
             of the License, or (at your option) any later version.
 
                              :-)  mdrun_mpi  (-:
 
Option     Filename  Type         Description
------------------------------------------------------------
  -s min.steep0.tpr  Input        Run input file: tpr tpb tpa
  -o min.steep0.trr  Output       Full precision trajectory: trr trj cpt
  -x min.steep0.xtc  Output, Opt. Compressed trajectory (portable xdr format)
-cpi min.steep0.cpt  Input, Opt.  Checkpoint file
-cpo min.steep0.cpt  Output, Opt. Checkpoint file
  -c min.steep0.gro  Output       Structure file: gro g96 pdb etc.
  -e min.steep0.edr  Output       Energy file
  -g min.steep0.log  Output       Log file
-dhdl min.steep0.xvg  Output, Opt. xvgr/xmgr file
-field min.steep0.xvg  Output, Opt. xvgr/xmgr file
-table min.steep0.xvg  Input, Opt.  xvgr/xmgr file
-tabletf min.steep0.xvg  Input, Opt.  xvgr/xmgr file
-tablep min.steep0.xvg  Input, Opt.  xvgr/xmgr file
-tableb min.steep0.xvg  Input, Opt.  xvgr/xmgr file
-rerun min.steep0.xtc  Input, Opt.  Trajectory: xtc trr trj gro g96 pdb cpt
-tpi min.steep0.xvg  Output, Opt. xvgr/xmgr file
-tpid min.steep0.xvg  Output, Opt. xvgr/xmgr file
 -ei min.steep0.edi  Input, Opt.  ED sampling input
 -eo min.steep0.xvg  Output, Opt. xvgr/xmgr file
  -j min.steep0.gct  Input, Opt.  General coupling stuff
 -jo min.steep0.gct  Output, Opt. General coupling stuff
-ffout min.steep0.xvg  Output, Opt. xvgr/xmgr file
-devout min.steep0.xvg  Output, Opt. xvgr/xmgr file
-runav min.steep0.xvg  Output, Opt. xvgr/xmgr file
 -px min.steep0.xvg  Output, Opt. xvgr/xmgr file
 -pf min.steep0.xvg  Output, Opt. xvgr/xmgr file
 -ro min.steep0.xvg  Output, Opt. xvgr/xmgr file
 -ra min.steep0.log  Output, Opt. Log file
 -rs min.steep0.log  Output, Opt. Log file
 -rt min.steep0.log  Output, Opt. Log file
-mtx min.steep0.mtx  Output, Opt. Hessian matrix
 -dn min.steep0.ndx  Output, Opt. Index file
-multidir     min.steep0  Input, Opt., Mult. Run directory
-membed min.steep0.dat  Input, Opt.  Generic data file
 -mp min.steep0.top  Input, Opt.  Topology file
 -mn min.steep0.ndx  Input, Opt.  Index file
 
Option       Type   Value   Description
------------------------------------------------------
-[no]h       bool   no      Print help info and quit
-[no]version bool   no      Print version info and quit
-nice        int    0       Set the nicelevel
-deffnm      string min.steep0  Set the default filename for all file options
-xvg         enum   xmgrace  xvg plot formatting: xmgrace, xmgr or none
-[no]pd      bool   no      Use particle decompostion
-dd          vector 0 0 0   Domain decomposition grid, 0 is optimize
-ddorder     enum   interleave  DD node order: interleave, pp_pme or cartesian
-npme        int    4       Number of separate nodes to be used for PME, -1
                            is guess
-nt          int    0       Total number of threads to start (0 is guess)
-ntmpi       int    0       Number of thread-MPI threads to start (0 is guess)
-ntomp       int    0       Number of OpenMP threads per MPI process/thread
                            to start (0 is guess)
-ntomp_pme   int    0       Number of OpenMP threads per MPI process/thread
                            to start (0 is -ntomp)
-pin         enum   auto    Fix threads (or processes) to specific cores:
                            auto, on or off
-pinoffset   int    0       The starting logical core number for pinning to
                            cores; used to avoid pinning threads from
                            different mdrun instances to the same core
-pinstride   int    0       Pinning distance in logical cores for threads,
                            use 0 to minimize the number of threads per
                            physical core
-gpu_id      string         List of GPU id's to use
-[no]ddcheck bool   yes     Check for all bonded interactions with DD
-rdd         real   0       The maximum distance for bonded interactions with
                            DD (nm), 0 is determine from initial coordinates
-rcon        real   0       Maximum distance for P-LINCS (nm), 0 is estimate
-dlb         enum   auto    Dynamic load balancing (with DD): auto, no or yes
-dds         real   0.8     Minimum allowed dlb scaling of the DD cell size
-gcom        int    -1      Global communication frequency
-nb          enum   auto    Calculate non-bonded interactions on: auto, cpu,
                            gpu or gpu_cpu
-[no]tunepme bool   yes     Optimize PME load between PP/PME nodes or GPU/CPU
-[no]testverlet bool   no      Test the Verlet non-bonded scheme
-[no]v       bool   no      Be loud and noisy
-[no]compact bool   yes     Write a compact log file
-[no]seppot  bool   no      Write separate V and dVdl terms for each
                            interaction type and node to the log file(s)
-pforce      real   -1      Print all forces larger than this (kJ/mol nm)
-[no]reprod  bool   no      Try to avoid optimizations that affect binary
                            reproducibility
-cpt         real   15      Checkpoint interval (minutes)
-[no]cpnum   bool   no      Keep and number checkpoint files
-[no]append  bool   yes     Append to previous output files when continuing
                            from checkpoint instead of adding the simulation
                            part number to all file names
-nsteps      int    -2      Run this number of steps, overrides .mdp file
                            option
-maxh        real   -1      Terminate after 0.99 times this time (hours)
-multi       int    0       Do multiple simulations in parallel
-replex      int    0       Attempt replica exchange periodically with this
                            period (steps)
-nex         int    0       Number of random exchanges to carry out each
                            exchange interval (N^3 is one suggestion).  -nex
                            zero or not specified gives neighbor replica
                            exchange.
-reseed      int    -1      Seed for replica exchange, -1 is generate a seed
-[no]ionize  bool   no      Do a simulation including the effect of an X-Ray
                            bombardment on your system
 
Reading file min.steep0.tpr, VERSION 4.0.5 (single precision)
Note: file tpx version 58, software tpx version 83
Using 24 MPI processes
 
Steepest Descents:
   Tolerance (Fmax)   =  1.00000e+02
   Number of steps    =       100000
=>> PBS: job killed: walltime 3620 exceeded limit 3600
/var/www/wiki/data/attic/howto/gromacs.1385392038.txt.gz · Last modified: 2013/11/25 17:07 by swyngaard