[gmx-users] ./mdrun-gpu fatal error

Justin A. Lemkul jalemkul at vt.edu
Sat Nov 6 00:29:09 CET 2010

lin hen wrote:
> Hi,
> I am new for gromacs, I am trying to run the mdrun-gpu executable:
> the step to build the mdrun-gpu:
> 1. disable the shared libraries:
>    //disable shared libraries (can be problematic with MPI, Windows)
> 2. export LD_LIBRARY_PATH=/path to openmm2.0-Linux64/lib:$ LD_LIBRARY_PATH
> 3. export OPENMM_PLUGIN_DIR=/path to openmm2.0-Linux64/plugins
> 4. export OPENMM_ROOT_DIR=/path to openmm2.0-Linux64
> 5. ./configure
> 6. cmake -DGMX_OPENMM=ON
> 7. make mdrun
> 8. make install
> when I got the mdrun-gpu in /src/kernel.
> I put all the shared libs in one folder, point the LD_LIBRARY_PATH to 
> this folder, also openmm libs
> The attached is the .tpr file I use in the same folder with mdrun-gpu.
> when i run ./mdrun-gpu
> it shows:
>                          :-)  G  R  O  M  A  C  S  (-:
>                    GROningen MAchine for Chemical Simulation
>                             :-)  VERSION 4.5.1  (-:
>         Written by Emile Apol, Rossen Apostolov, Herman J.C. Berendsen,
>       Aldert van Buuren, Pär Bjelkmar, Rudi van Drunen, Anton Feenstra,
>         Gerrit Groenhof, Peter Kasson, Per Larsson, Peiter Meulenhoff,
>           Teemu Murtola, Szilard Pall, Sander Pronk, Roland Schultz,
>                 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) 2001-2010, The GROMACS development team at
>         Uppsala University & The Royal Institute of Technology, Sweden.
>             check out http://www.gromacs.org <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 General Public License
>          as published by the Free Software Foundation; either version 2
>              of the License, or (at your option) any later version.
>                              :-)  ./mdrun-gpu  (-:
> Option     Filename  Type         Description
> ------------------------------------------------------------
>   -s      topol.tpr  Input        Run input file: tpr tpb tpa
>   -o       traj.trr  Output       Full precision trajectory: trr trj cpt
>   -x       traj.xtc  Output, Opt. Compressed trajectory (portable xdr 
> format)
> -cpi      state.cpt  Input, Opt.  Checkpoint file
> -cpo      state.cpt  Output, Opt. Checkpoint file
>   -c    confout.gro  Output       Structure file: gro g96 pdb etc.
>   -e       ener.edr  Output       Energy file
>   -g         md.log  Output       Log file
> -dhdl      dhdl.xvg  Output, Opt. xvgr/xmgr file
> -field    field.xvg  Output, Opt. xvgr/xmgr file
> -table    table.xvg  Input, Opt.  xvgr/xmgr file
> -tablep  tablep.xvg  Input, Opt.  xvgr/xmgr file
> -tableb   table.xvg  Input, Opt.  xvgr/xmgr file
> -rerun    rerun.xtc  Input, Opt.  Trajectory: xtc trr trj gro g96 pdb cpt
> -tpi        tpi.xvg  Output, Opt. xvgr/xmgr file
> -tpid   tpidist.xvg  Output, Opt. xvgr/xmgr file
>  -ei        sam.edi  Input, Opt.  ED sampling input
>  -eo        sam.edo  Output, Opt. ED sampling output
>   -j       wham.gct  Input, Opt.  General coupling stuff
>  -jo        bam.gct  Output, Opt. General coupling stuff
> -ffout      gct.xvg  Output, Opt. xvgr/xmgr file
> -devout   deviatie.xvg  Output, Opt. xvgr/xmgr file
> -runav  runaver.xvg  Output, Opt. xvgr/xmgr file
>  -px      pullx.xvg  Output, Opt. xvgr/xmgr file
>  -pf      pullf.xvg  Output, Opt. xvgr/xmgr file
> -mtx         nm.mtx  Output, Opt. Hessian matrix
>  -dn     dipole.ndx  Output, 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         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
> -npme        int    -1      Number of separate nodes to be used for PME, -1
>                             is guess
> -ddorder     enum   interleave  DD node order: interleave, pp_pme or 
> cartesian
> -[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
> -[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
> -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 every # steps
> -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
> -device      string         Device option string
> Back Off! I just backed up md.log to ./#md.log.14#
> Reading file topol.tpr, VERSION 4.0.5 (single precision)
> Note: tpx file_version 58, software version 73
> Back Off! I just backed up ener.edr to ./#ener.edr.14#
> WARNING: OpenMM does not support leap-frog, will use velocity-verlet 
> integrator.
> -------------------------------------------------------
> Program mdrun-gpu, VERSION 4.5.1
> *Source code file: 
> /root/BioWorkBench/TPPS/GROMACS/GROMACS-final/gromacs-4.5.1/src/kernel/openmm_wrapper.cpp, 
> line: 555*
> *Fatal error:
> OpenMM supports only the following methods for electrostatics: NoCutoff 
> (i.e. rcoulomb = rvdw = 0 ),Reaction-Field, Ewald or PME.
> *For more information and tips for troubleshooting, please check the GROMACS
> website at http://www.gromacs.org/Documentation/Errors
> -------------------------------------------------------
> "Breaking the Law, Breaking the Law" (Judas Priest)
> Could you please help take a look at it? Is there anything wrong with my 
> input file? 

Yes, your .mdp file has something set wrong, either coulombtype, rcoulomb, etc. 
  The error message lists the only relevant options.


> RHEL 5.4  gcc  4.1.2,  CUDA 3.1
> yy


Justin A. Lemkul
Ph.D. Candidate
ICTAS Doctoral Scholar
Department of Biochemistry
Virginia Tech
Blacksburg, VA
jalemkul[at]vt.edu | (540) 231-9080


More information about the gromacs.org_gmx-users mailing list