[gmx-users] segfault when running the alchemistry.org ethanol solvation free energy tutorial

Michael Shirts mrshirts at gmail.com
Fri Sep 27 00:20:15 CEST 2013


Just to be clear, is this the expanded ensemble version of the calculation?

On Thu, Sep 26, 2013 at 5:25 PM, Mark Abraham <mark.j.abraham at gmail.com> wrote:
> 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.neale at 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.
>> --
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