[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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