[gmx-users] segfault when running the alchemistry.org ethanol solvation free energy tutorial
Christopher Neale
chris.neale at mail.utoronto.ca
Thu Sep 26 21:00:19 CEST 2013
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.
More information about the gromacs.org_gmx-users
mailing list