You can try the systems we provided on the GROMACS-GPU page: http://www.gromacs.org/gpu#GPU_Benchmarks
-- Szilárd On Sat, Nov 6, 2010 at 12:59 AM, lin hen <cutey...@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: jalem...@vt.edu >> To: gmx-users@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: 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 >> > > >> > > ======================================== >> > > -- >> > > gmx-users mailing list gmx-users@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-requ...@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 >> >> ======================================== >> -- >> gmx-users mailing list gmx-users@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-requ...@gromacs.org. >> Can't post? Read http://www.gromacs.org/Support/Mailing_Lists > > -- > gmx-users mailing list gmx-us...@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-requ...@gromacs.org. > Can't post? Read http://www.gromacs.org/Support/Mailing_Lists > -- gmx-users mailing list gmx-users@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-requ...@gromacs.org. Can't post? Read http://www.gromacs.org/Support/Mailing_Lists