[gmx-users] ./mdrun-gpu fatal error
Justin A. Lemkul
jalemkul at vt.edu
Sat Nov 6 01:00:38 CET 2010
lin hen 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?
No. You need to generate a sensible input file.
-Justin
> 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
> >
> > ========================================
> > --
> > gmx-users mailing list gmx-users at gromacs.org
> > http://lists.gromacs.org/mailman/listinfo/gmx-users
> > Please search the archive at
> http://www.gromacs.org/Support/Mailing_Lists/Search before posting!
> > Please don't post (un)subscribe requests to the list. Use the
> > www interface or send it to gmx-users-request at gromacs.org.
> > Can't post? Read http://www.gromacs.org/Support/Mailing_Lists
--
========================================
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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