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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.<BR>
<BR>
So is there any other way I could modify?<BR>
Thanks,<BR>
<BR>
YY<BR> <BR>
> Date: Fri, 5 Nov 2010 19:54:10 -0400<BR>> From: jalemkul@vt.edu<BR>> To: gmx-users@gromacs.org<BR>> Subject: Re: [gmx-users] ./mdrun-gpu fatal error<BR>> <BR>> <BR>> <BR>> lin hen wrote:<BR>> > Thanks a lot for your reply, I didn't have this .mdp file, and I <BR>> > attached the log file, how to modify?<BR>> > <BR>> <BR>> You don't have an .mdp file? Then how did you create your input .tpr file? <BR>> This is the only way to fix your problem - specify proper input parameters in <BR>> the .mdp file.<BR>> <BR>> > Just wonder the gcc compiler, I am using gcc 4.1.2, but I saw the <BR>> > requirements listed for gcc is 4.4, is it a problem?<BR>> > <BR>> <BR>> I think there have been some issues associated with gcc-4.1.x, but I am not sure <BR>> that they were specifically related to the compiler or some incompatibility with <BR>> the code that was addressed. In any case, your compiler is not your problem. <BR>> You have an error in your input file, and the fatal error is very clear about this.<BR>> <BR>> -Justin<BR>> <BR>> > Thanks,<BR>> > <BR>> > yy<BR>> > <BR>> > > Date: Fri, 5 Nov 2010 19:29:09 -0400<BR>> > > From: jalemkul@vt.edu<BR>> > > To: gmx-users@gromacs.org<BR>> > > Subject: Re: [gmx-users] ./mdrun-gpu fatal error<BR>> > ><BR>> > ><BR>> > ><BR>> > > lin hen wrote:<BR>> > > > Hi,<BR>> > > ><BR>> > > > I am new for gromacs, I am trying to run the mdrun-gpu executable:<BR>> > > ><BR>> > > > the step to build the mdrun-gpu:<BR>> > > ><BR>> > > > 1. disable the shared libraries:<BR>> > > > //disable shared libraries (can be problematic with MPI, Windows)<BR>> > > > BUILD_SHARED_LIBS:BOOL=OFF<BR>> > > > 2. export LD_LIBRARY_PATH=/path to openmm2.0-Linux64/lib:$ <BR>> > LD_LIBRARY_PATH<BR>> > > > 3. export OPENMM_PLUGIN_DIR=/path to openmm2.0-Linux64/plugins<BR>> > > > 4. export OPENMM_ROOT_DIR=/path to openmm2.0-Linux64<BR>> > > > 5. ./configure<BR>> > > > 6. cmake -DGMX_OPENMM=ON<BR>> > > > 7. make mdrun<BR>> > > > 8. make install<BR>> > > ><BR>> > > > when I got the mdrun-gpu in /src/kernel.<BR>> > > ><BR>> > > > I put all the shared libs in one folder, point the LD_LIBRARY_PATH to<BR>> > > > this folder, also openmm libs<BR>> > > ><BR>> > > > The attached is the .tpr file I use in the same folder with mdrun-gpu.<BR>> > > ><BR>> > > > when i run ./mdrun-gpu<BR>> > > > it shows:<BR>> > > ><BR>> > > > :-) G R O M A C S (-:<BR>> > > > GROningen MAchine for Chemical Simulation<BR>> > > > :-) VERSION 4.5.1 (-:<BR>> > > > Written by Emile Apol, Rossen Apostolov, Herman J.C. Berendsen,<BR>> > > > Aldert van Buuren, Pär Bjelkmar, Rudi van Drunen, Anton Feenstra,<BR>> > > > Gerrit Groenhof, Peter Kasson, Per Larsson, Peiter Meulenhoff,<BR>> > > > Teemu Murtola, Szilard Pall, Sander Pronk, Roland Schultz,<BR>> > > > Michael Shirts, Alfons Sijbers, Peter Tieleman,<BR>> > > > Berk Hess, David van der Spoel, and Erik Lindahl.<BR>> > > > Copyright (c) 1991-2000, University of Groningen, The Netherlands.<BR>> > > > Copyright (c) 2001-2010, The GROMACS development team at<BR>> > > > Uppsala University & The Royal Institute of Technology, Sweden.<BR>> > > > check out http://www.gromacs.org <http://www.gromacs.org/><BR>> > > > for more information.<BR>> > > > This program is free software; you can redistribute it and/or<BR>> > > > modify it under the terms of the GNU General Public License<BR>> > > > as published by the Free Software Foundation; either version 2<BR>> > > > of the License, or (at your option) any later version.<BR>> > > > :-) ./mdrun-gpu (-:<BR>> > > > Option Filename Type Description<BR>> > > > ------------------------------------------------------------<BR>> > > > -s topol.tpr Input Run input file: tpr tpb tpa<BR>> > > > -o traj.trr Output Full precision trajectory: trr trj cpt<BR>> > > > -x traj.xtc Output, Opt. Compressed trajectory (portable xdr<BR>> > > > format)<BR>> > > > -cpi state.cpt Input, Opt. Checkpoint file<BR>> > > > -cpo state.cpt Output, Opt. Checkpoint file<BR>> > > > -c confout.gro Output Structure file: gro g96 pdb etc.<BR>> > > > -e ener.edr Output Energy file<BR>> > > > -g md.log Output Log file<BR>> > > > -dhdl dhdl.xvg Output, Opt. xvgr/xmgr file<BR>> > > > -field field.xvg Output, Opt. xvgr/xmgr file<BR>> > > > -table table.xvg Input, Opt. xvgr/xmgr file<BR>> > > > -tablep tablep.xvg Input, Opt. xvgr/xmgr file<BR>> > > > -tableb table.xvg Input, Opt. xvgr/xmgr file<BR>> > > > -rerun rerun.xtc Input, Opt. Trajectory: xtc trr trj gro g96 pdb cpt<BR>> > > > -tpi tpi.xvg Output, Opt. xvgr/xmgr file<BR>> > > > -tpid tpidist.xvg Output, Opt. xvgr/xmgr file<BR>> > > > -ei sam.edi Input, Opt. ED sampling input<BR>> > > > -eo sam.edo Output, Opt. ED sampling output<BR>> > > > -j wham.gct Input, Opt. General coupling stuff<BR>> > > > -jo bam.gct Output, Opt. General coupling stuff<BR>> > > > -ffout gct.xvg Output, Opt. xvgr/xmgr file<BR>> > > > -devout deviatie.xvg Output, Opt. xvgr/xmgr file<BR>> > > > -runav runaver.xvg Output, Opt. xvgr/xmgr file<BR>> > > > -px pullx.xvg Output, Opt. xvgr/xmgr file<BR>> > > > -pf pullf.xvg Output, Opt. xvgr/xmgr file<BR>> > > > -mtx nm.mtx Output, Opt. Hessian matrix<BR>> > > > -dn dipole.ndx Output, Opt. Index file<BR>> > > > Option Type Value Description<BR>> > > > ------------------------------------------------------<BR>> > > > -[no]h bool no Print help info and quit<BR>> > > > -[no]version bool no Print version info and quit<BR>> > > > -nice int 0 Set the nicelevel<BR>> > > > -deffnm string Set the default filename for all file options<BR>> > > > -xvg enum xmgrace xvg plot formatting: xmgrace, xmgr or none<BR>> > > > -[no]pd bool no Use particle decompostion<BR>> > > > -dd vector 0 0 0 Domain decomposition grid, 0 is optimize<BR>> > > > -npme int -1 Number of separate nodes to be used for PME, -1<BR>> > > > is guess<BR>> > > > -ddorder enum interleave DD node order: interleave, pp_pme or<BR>> > > > cartesian<BR>> > > > -[no]ddcheck bool yes Check for all bonded interactions with DD<BR>> > > > -rdd real 0 The maximum distance for bonded interactions<BR>> > > > with<BR>> > > > DD (nm), 0 is determine from initial coordinates<BR>> > > > -rcon real 0 Maximum distance for P-LINCS (nm), 0 is estimate<BR>> > > > -dlb enum auto Dynamic load balancing (with DD): auto, no<BR>> > > > or yes<BR>> > > > -dds real 0.8 Minimum allowed dlb scaling of the DD cell size<BR>> > > > -gcom int -1 Global communication frequency<BR>> > > > -[no]v bool no Be loud and noisy<BR>> > > > -[no]compact bool yes Write a compact log file<BR>> > > > -[no]seppot bool no Write separate V and dVdl terms for each<BR>> > > > interaction type and node to the log file(s)<BR>> > > > -pforce real -1 Print all forces larger than this (kJ/mol nm)<BR>> > > > -[no]reprod bool no Try to avoid optimizations that affect binary<BR>> > > > reproducibility<BR>> > > > -cpt real 15 Checkpoint interval (minutes)<BR>> > > > -[no]cpnum bool no Keep and number checkpoint files<BR>> > > > -[no]append bool yes Append to previous output files when continuing<BR>> > > > from checkpoint instead of adding the simulation<BR>> > > > part number to all file names<BR>> > > > -maxh real -1 Terminate after 0.99 times this time (hours)<BR>> > > > -multi int 0 Do multiple simulations in parallel<BR>> > > > -replex int 0 Attempt replica exchange every # steps<BR>> > > > -reseed int -1 Seed for replica exchange, -1 is generate a seed<BR>> > > > -[no]ionize bool no Do a simulation including the effect of an X-Ray<BR>> > > > bombardment on your system<BR>> > > > -device string Device option string<BR>> > > ><BR>> > > > Back Off! I just backed up md.log to ./#md.log.14#<BR>> > > > Reading file topol.tpr, VERSION 4.0.5 (single precision)<BR>> > > > Note: tpx file_version 58, software version 73<BR>> > > > Back Off! I just backed up ener.edr to ./#ener.edr.14#<BR>> > > > WARNING: OpenMM does not support leap-frog, will use velocity-verlet<BR>> > > > integrator.<BR>> > > ><BR>> > > > -------------------------------------------------------<BR>> > > > Program mdrun-gpu, VERSION 4.5.1<BR>> > > > *Source code file:<BR>> > > > <BR>> > /root/BioWorkBench/TPPS/GROMACS/GROMACS-final/gromacs-4.5.1/src/kernel/openmm_wrapper.cpp, <BR>> > <BR>> > > > line: 555*<BR>> > > > *Fatal error:<BR>> > > > OpenMM supports only the following methods for electrostatics: <BR>> > NoCutoff<BR>> > > > (i.e. rcoulomb = rvdw = 0 ),Reaction-Field, Ewald or PME.<BR>> > > > *For more information and tips for troubleshooting, please check <BR>> > the GROMACS<BR>> > > > website at http://www.gromacs.org/Documentation/Errors<BR>> > > > -------------------------------------------------------<BR>> > > > "Breaking the Law, Breaking the Law" (Judas Priest)<BR>> > > ><BR>> > > ><BR>> > > > Could you please help take a look at it? Is there anything wrong <BR>> > with my<BR>> > > > input file?<BR>> > > ><BR>> > ><BR>> > > Yes, your .mdp file has something set wrong, either coulombtype, <BR>> > rcoulomb, etc.<BR>> > > The error message lists the only relevant options.<BR>> > ><BR>> > > -Justin<BR>> > ><BR>> > > > RHEL 5.4 gcc 4.1.2, CUDA 3.1<BR>> > > > yy<BR>> > > ><BR>> > ><BR>> > > --<BR>> > > ========================================<BR>> > ><BR>> > > Justin A. Lemkul<BR>> > > Ph.D. Candidate<BR>> > > ICTAS Doctoral Scholar<BR>> > > MILES-IGERT Trainee<BR>> > > Department of Biochemistry<BR>> > > Virginia Tech<BR>> > > Blacksburg, VA<BR>> > > jalemkul[at]vt.edu | (540) 231-9080<BR>> > > http://www.bevanlab.biochem.vt.edu/Pages/Personal/justin<BR>> > ><BR>> > > ========================================<BR>> > > --<BR>> > > gmx-users mailing list gmx-users@gromacs.org<BR>> > > http://lists.gromacs.org/mailman/listinfo/gmx-users<BR>> > > Please search the archive at <BR>> > http://www.gromacs.org/Support/Mailing_Lists/Search before posting!<BR>> > > Please don't post (un)subscribe requests to the list. Use the<BR>> > > www interface or send it to gmx-users-request@gromacs.org.<BR>> > > Can't post? Read http://www.gromacs.org/Support/Mailing_Lists<BR>> > <BR>> <BR>> -- <BR>> ========================================<BR>> <BR>> Justin A. Lemkul<BR>> Ph.D. Candidate<BR>> ICTAS Doctoral Scholar<BR>> MILES-IGERT Trainee<BR>> Department of Biochemistry<BR>> Virginia Tech<BR>> Blacksburg, VA<BR>> jalemkul[at]vt.edu | (540) 231-9080<BR>> http://www.bevanlab.biochem.vt.edu/Pages/Personal/justin<BR>> <BR>> ========================================<BR>> -- <BR>> gmx-users mailing list gmx-users@gromacs.org<BR>> http://lists.gromacs.org/mailman/listinfo/gmx-users<BR>> Please search the archive at http://www.gromacs.org/Support/Mailing_Lists/Search before posting!<BR>> Please don't post (un)subscribe requests to the list. Use the <BR>> www interface or send it to gmx-users-request@gromacs.org.<BR>> Can't post? Read http://www.gromacs.org/Support/Mailing_Lists<BR> </body>
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