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

Christopher Neale chris.neale at mail.utoronto.ca
Fri Sep 27 00:07:24 CEST 2013


Thank you Mark.

I actually found that it crashed wihout the -multi part (no hamiltonian exchange). 
The command that I used was: mdrun -nt 1 -deffnm ethanol.1 -dhdl ethanol.1.dhdl.xvg

If I use the double precision version, there is no segfault. That's a working solution, but it is worrysome.

Thank you,
Chris.


-- original message --

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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