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: [email protected] > To: [email protected] > 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: [email protected] > > > To: [email protected] > > > 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 [email protected] > > > 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 [email protected]. > > > 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 > > ======================================== > -- > gmx-users mailing list [email protected] > 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 [email protected]. > Can't post? Read http://www.gromacs.org/Support/Mailing_Lists
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