I found the -multi version of that tutorial a bit temperamental... Michael Shirts suggested that double precision is more reliable for expanded ensemble. Hopefully he can chime in in a day or two.
Mark On Thu, Sep 26, 2013 at 9:00 PM, Christopher Neale <chris.ne...@mail.utoronto.ca> wrote: > Dear Users: > > Has anyone successfully run the free energy tutorial at > http://www.alchemistry.org/wiki/GROMACS_4.6_example:_Direct_ethanol_solvation_free_energy > ? > > I just tried it and I get a segmentation fault immediately (see output at the > end of this post). > > I get a segfault with both 4.6.3 and 4.6.1. > > Note that if I modify the .mdp file to set free-energy = no , then the > simulation runs just fine. (I have, of course, set init-lambda-state in the > .mdp file that I downloaded from the aforementioned site and I get a segfault > with any value of init-lambda-state from 0 to 8). > > gpc-f103n084-$ mdrun -nt 1 -deffnm ethanol.1 -dhdl ethanol.1.dhdl.xvg > :-) G R O M A C S (-: > > GROup of MAchos and Cynical Suckers > > :-) VERSION 4.6.3 (-: > > Contributions from Mark Abraham, Emile Apol, Rossen Apostolov, > Herman J.C. Berendsen, Aldert van Buuren, Pär Bjelkmar, > Rudi van Drunen, Anton Feenstra, Gerrit Groenhof, Christoph Junghans, > Peter Kasson, Carsten Kutzner, Per Larsson, Pieter Meulenhoff, > Teemu Murtola, Szilard Pall, Sander Pronk, Roland Schulz, > 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) 2001-2012,2013, The GROMACS development team at > Uppsala University & The Royal Institute of Technology, Sweden. > check out 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 Lesser General Public License > as published by the Free Software Foundation; either version 2.1 > of the License, or (at your option) any later version. > > :-) mdrun (-: > > Option Filename Type Description > ------------------------------------------------------------ > -s ethanol.1.tpr Input Run input file: tpr tpb tpa > -o ethanol.1.trr Output Full precision trajectory: trr trj cpt > -x ethanol.1.xtc Output, Opt. Compressed trajectory (portable xdr format) > -cpi ethanol.1.cpt Input, Opt. Checkpoint file > -cpo ethanol.1.cpt Output, Opt. Checkpoint file > -c ethanol.1.gro Output Structure file: gro g96 pdb etc. > -e ethanol.1.edr Output Energy file > -g ethanol.1.log Output Log file > -dhdl ethanol.1.dhdl.xvg Output, Opt! xvgr/xmgr file > -field ethanol.1.xvg Output, Opt. xvgr/xmgr file > -table ethanol.1.xvg Input, Opt. xvgr/xmgr file > -tabletf ethanol.1.xvg Input, Opt. xvgr/xmgr file > -tablep ethanol.1.xvg Input, Opt. xvgr/xmgr file > -tableb ethanol.1.xvg Input, Opt. xvgr/xmgr file > -rerun ethanol.1.xtc Input, Opt. Trajectory: xtc trr trj gro g96 pdb cpt > -tpi ethanol.1.xvg Output, Opt. xvgr/xmgr file > -tpid ethanol.1.xvg Output, Opt. xvgr/xmgr file > -ei ethanol.1.edi Input, Opt. ED sampling input > -eo ethanol.1.xvg Output, Opt. xvgr/xmgr file > -j ethanol.1.gct Input, Opt. General coupling stuff > -jo ethanol.1.gct Output, Opt. General coupling stuff > -ffout ethanol.1.xvg Output, Opt. xvgr/xmgr file > -devout ethanol.1.xvg Output, Opt. xvgr/xmgr file > -runav ethanol.1.xvg Output, Opt. xvgr/xmgr file > -px ethanol.1.xvg Output, Opt. xvgr/xmgr file > -pf ethanol.1.xvg Output, Opt. xvgr/xmgr file > -ro ethanol.1.xvg Output, Opt. xvgr/xmgr file > -ra ethanol.1.log Output, Opt. Log file > -rs ethanol.1.log Output, Opt. Log file > -rt ethanol.1.log Output, Opt. Log file > -mtx ethanol.1.mtx Output, Opt. Hessian matrix > -dn ethanol.1.ndx Output, Opt. Index file > -multidir ethanol.1 Input, Opt., Mult. Run directory > -membed ethanol.1.dat Input, Opt. Generic data file > -mp ethanol.1.top Input, Opt. Topology file > -mn ethanol.1.ndx Input, 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 ethanol.1 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 > -ddorder enum interleave DD node order: interleave, pp_pme or cartesian > -npme int -1 Number of separate nodes to be used for PME, -1 > is guess > -nt int 1 Total number of threads to start (0 is guess) > -ntmpi int 0 Number of thread-MPI threads to start (0 is guess) > -ntomp int 0 Number of OpenMP threads per MPI process/thread > to start (0 is guess) > -ntomp_pme int 0 Number of OpenMP threads per MPI process/thread > to start (0 is -ntomp) > -pin enum auto Fix threads (or processes) to specific cores: > auto, on or off > -pinoffset int 0 The starting logical core number for pinning to > cores; used to avoid pinning threads from > different mdrun instances to the same core > -pinstride int 0 Pinning distance in logical cores for threads, > use 0 to minimize the number of threads per > physical core > -gpu_id string List of GPU id's to use > -[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 > -nb enum auto Calculate non-bonded interactions on: auto, cpu, > gpu or gpu_cpu > -[no]tunepme bool yes Optimize PME load between PP/PME nodes or GPU/CPU > -[no]testverlet bool no Test the Verlet non-bonded scheme > -[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 > -nsteps step -2 Run this number of steps, overrides .mdp file > option > -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 periodically with this > period (steps) > -nex int 0 Number of random exchanges to carry out each > exchange interval (N^3 is one suggestion). -nex > zero or not specified gives neighbor replica > exchange. > -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 > > > Back Off! I just backed up ethanol.1.log to ./#ethanol.1.log.1# > Reading file ethanol.1.tpr, VERSION 4.6.3 (single precision) > Using 1 MPI thread > > starting mdrun 'Ethanol' > 3000000 steps, 6000.0 ps. > Segmentation fault > > Thank you, > Chris. > -- > 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-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? 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