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

Szilárd Páll szilard.pall at cbr.su.se
Sat Nov 6 18:23:50 CET 2010 

You can try the systems we provided on the GROMACS-GPU page:
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--
Szilárd




On Sat, Nov 6, 2010 at 12:59 AM, lin hen <cuteyy83 at live.com> wrote:
> Yeah, I think my problem is the input, but I don't have the .mpd file,  I am
> using the existing input which has no problem with Gromacs 4.0.5
> using ./mdrun-openmm.
>
> So is there any other way I could modify?
> Thanks,
>
> YY
>
>> Date: Fri, 5 Nov 2010 19:54:10 -0400
>> From: jalemkul at vt.edu
>> To: gmx-users at gromacs.org
>> Subject: Re: [gmx-users] ./mdrun-gpu fatal error
>>
>>
>>
>> lin hen wrote:
>> > Thanks a lot for your reply, I didn't have this .mdp file, and I
>> > attached the log file, how to modify?
>> >
>>
>> You don't have an .mdp file? Then how did you create your input .tpr file?
>> This is the only way to fix your problem - specify proper input parameters
>> in
>> the .mdp file.
>>
>> > Just wonder the gcc compiler, I am using gcc 4.1.2, but I saw the
>> > requirements listed for gcc is 4.4, is it a problem?
>> >
>>
>> I think there have been some issues associated with gcc-4.1.x, but I am
>> not sure
>> that they were specifically related to the compiler or some
>> incompatibility with
>> the code that was addressed. In any case, your compiler is not your
>> problem.
>> You have an error in your input file, and the fatal error is very clear
>> about this.
>>
>> -Justin
>>
>> > Thanks,
>> >
>> > yy
>> >
>> > > Date: Fri, 5 Nov 2010 19:29:09 -0400
>> > > From: jalemkul at vt.edu
>> > > To: gmx-users at gromacs.org
>> > > Subject: Re: [gmx-users] ./mdrun-gpu fatal error
>> > >
>> > >
>> > >
>> > > 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
>> > >
>> > > ========================================
>> > > --
>> > > gmx-users mailing list gmx-users at gromacs.org
>> > > http://lists.gromacs.org/mailman/listinfo/gmx-users
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>> >
>>
>> --
>> ========================================
>>
>> 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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