Thanks,
yy
> Date: Fri, 5 Nov 2010 19:29:09 -0400
> From: jalem...@vt.edu
> To: gmx-users@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
>
> ========================================
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