[gmx-users] ./mdrun-gpu fatal error

Justin A. Lemkul jalemkul at vt.edu
Sat Nov 6 00:54:10 CET 2010 


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
>  >
>  > ========================================
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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

========================================

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