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howto:gromacs [2013/11/25 17:07]
swyngaard [Example Expected Output] 		howto:gromacs [2024/08/12 13:29] (current)
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 ====== Gromacs ====== ====== Gromacs ======
  
-===== Initial Setup ===== +The available **Easy Scripts** (cpu and gpu versions) for Gromacs are: 
-In order to use Gromacs append the following lines to your .profile file: +
-<code bash> +
-export MODULEPATH=/opt/gridware/applications/gromacs/modules:$MODULEPATH +
-module add gromacs/4.6.1 mpich2/1.5 +
-</code>+
  
-To complete the setup log out of the cluster and back in again (or just ''source'' your .profile file) to update your environment variables. +**qgromacs_2024-1,  qgromacs_2023-1, qgromacs_2022-4, qgromacs_2020-1,qgromacs_2019-4, qgromacs_2018-6, qgromacs_2018-2 and qgromacs_2018 **
  
-===== Example Job Submission Script ===== +**qgromacs_2024-1_gpu,  qgromacs_2023-1_gpu, qgromacs_2021-1_gpu, qgromacs_2020-1_gpu, qgromacs_2019-4_gpu and qgromacs_2018-6_gpu**
-The following file is a Gromacs template job submission script that can used as a starting point for creating your own scripts: +
-<file bash 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` +Execute any of these **Easy Scripts** on the login node (on a lustre subdirectory) and follow the prompts. 
-BIN=mdrun_mpi +This script handles PBS setup and submission. 
-ARGS="-s min.steep0.tpr -deffnm min.steep0 -npme 4"+Sets up the mpi environment variables allowing you to run over multiple processors and nodes. 
 +Examples of script execution are provided below.
  
-mpirun -np $NP -machinefile $PBS_NODEFILE $BIN $ARGS 
-</file> 
  
-This job submission script requires that the file ''{{howto:min.steep0.tpr}}'' be in the working directory specified above.+**Note**, please first include this **module load** - even better if your add this line to your .bashrc, then the Easy Scripts should be visible and available:
  
-**NOTE:** Please ensure that all file I/O associated with your job only occurs in a sub-directory of the ''scratch5'' partition.+  module load chpc/easy_scripts
  
-===== Job Submission ===== 
-Submit the job using the following command: 
-<code bash> 
-msub gromacs.job 
-</code> 
  
-===== Example Expected Output ===== +                    EXAMPLE1 
-<file text out.log> +  Enter project name/shortname 
-                         :-)  G  R  O  M  A  C  S  (-:+  CHEM0100 
 +  Enter default filename for all file options (without any extension to the file) 
 +  test 
 +  Enter number of nodes on which to run job 
 +  1 
 +  Enter total walltime (hour:minute) 
 +  2:00 
 +  Enter email address 
 +  testing@gmail.com 
 +  Generated pbs file for test 
 +  Do you wish to submit job to cluster (y/n) 
 +  y 
 +   
 +  
  
-               Giant Rising Ordinary Mutants for A Clerical Setup+    EXAMPLE2 [PLEASE TAKE NOTE OF EMPTY SPACES] 
 +  Enter project name/shortname 
 +  CHEM0100 
 +  Enter default filename for all file options (without any extension to the file) 
 +  test 
 +  Enter number of nodes on which to run job 
 +   
 +  Enter total walltime (hour:minute) 
 +   
 +  Enter email address 
 +  testing@gmail.com 
 +  Generated pbs file for test 
 +  Do you wish to submit job to cluster (y/n) 
 +  y
  
-                            :-)  VERSION 4.6.1  (-:+====== Gromacs on GPU ======
  
-        Contributions from Mark Abraham, Emile Apol, Rossen Apostolov,  +** //Please note that you need to first be added to the gpu_1 queue before you can submit jobs to the GPU cluster// **
-           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.+Execute **qgromacs_2018-2_gpu**, **qgromacs_2018-6_gpu**, **qgromacs_2019-4_gpu**, **qgromacs_2020-1_gpu** or **qgromacs_2021-1** on the login node and follow the prompts. 
 +Examples of script execution are provided below.
  
-       Copyright (c) 1991-2000, University of Groningen, The Netherlands. +                    EXAMPLE1 
-         Copyright (c) 2001-2012,2013, The GROMACS development team at +  Enter research programme name 
-        Uppsala University & The Royal Institute of Technology, Sweden. +  CHEM0100 
-            check out http://www.gromacs.org for more information.+  Enter default filename for all file options (without any extension to the file) 
 +  test 
 +  Enter total walltime (hour:minute) 
 +  2:00 
 +  Enter email address 
 +  testing@gmail.com 
 +  Generated pbs file for test 
 +  Do you wish to submit job to cluster (y/n) 
 +  y 
 +   
  
-         This program is free software; you can redistribute it and/or +    EXAMPLE2 [PLEASE TAKE NOTE OF EMPTY SPACES] 
-       modify it under the terms of the GNU Lesser General Public License +  Enter research programme name 
-        as published by the Free Software Foundation; either version 2.1 +  CHEM0100 
-             of the License, or (at your option) any later version. +  Enter default filename for all file options (without any extension to the file) 
- +  test 
-                              :-)  mdrun_mpi  (-: +  Enter total walltime (hour:minute) 
- +   
-Option     Filename  Type         Description +  Enter email address 
------------------------------------------------------------- +  testing@gmail.com 
-  -s min.steep0.tpr  Input        Run input file: tpr tpb tpa +  Generated pbs file for test 
-  -o min.steep0.trr  Output       Full precision trajectory: trr trj cpt +  Do you wish to submit job to cluster (y/n) 
-  -x min.steep0.xtc  Output, Opt. Compressed trajectory (portable xdr format) +  y
--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 +
-</file>+
  
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