[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)
> BUILD_SHARED_LIBS:BOOL=OFF
> 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.
-Justin
> RHEL 5.4 gcc 4.1.2, CUDA 3.1
> yy
>
--
========================================
Justin A. Lemkul
Ph.D. Candidate
ICTAS Doctoral Scholar
MILES-IGERT Trainee
Department of Biochemistry
Virginia Tech
Blacksburg, VA
jalemkul[at]vt.edu | (540) 231-9080
http://www.bevanlab.biochem.vt.edu/Pages/Personal/justin
========================================
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