[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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