[gmx-users] essential dynamics mdrun with SD integrator yields segmentation fault
Carsten Kutzner
ckutzne at gwdg.de
Mon Dec 21 16:45:41 CET 2009
Hi Chris,
the segfault was due to the fact that with the sd integrator the constraints
have to be evaluated twice and in the second call there is no pointer to
the velocities present. I have fixed that in the master and release-4-0-
patches branches. The velocity correction is now only done when velocities
are present.
Carsten
On Dec 19, 2009, at 2:09 AM, chris.neale at utoronto.ca wrote:
> Hello,
>
> In my hands, mdrun throws a segfault when passing the -ei flag to mdrun and utilizing the sd integrator. I'll admit that I have only tried this with a single system. Nevertheless, using -linacc vs. -linfix makes no difference, neither does moving to constraints=none or parallel vs. serial mdrun. However, when I change sd to md, the run is fine.
>
> With sd and -ei, the segfault is immediate:
>
> $ mdrun -deffnm edi -nosum -dlb yes -npme -1 -cpt 30 -maxh 48 -cpi edi.cpt -ei testpositive.edi -eo testpositive.edo
> :-) G R O M A C S (-:
>
> GROup of MAchos and Cynical Suckers
>
> :-) VERSION 4.0.5 (-:
>
>
> Written by David van der Spoel, Erik Lindahl, Berk Hess, and others.
> Copyright (c) 1991-2000, University of Groningen, The Netherlands.
> Copyright (c) 2001-2008, The GROMACS development team,
> 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 General Public License
> as published by the Free Software Foundation; either version 2
> of the License, or (at your option) any later version.
>
> :-) mdrun (-:
>
> Option Filename Type Description
> ------------------------------------------------------------
> -s edi.tpr Input Run input file: tpr tpb tpa
> -o edi.trr Output Full precision trajectory: trr trj cpt
> -x edi.xtc Output, Opt. Compressed trajectory (portable xdr format)
> -cpi edi.cpt Input, Opt! Checkpoint file
> -cpo edi.cpt Output, Opt. Checkpoint file
> -c edi.gro Output Structure file: gro g96 pdb
> -e edi.edr Output Energy file: edr ene
> -g edi.log Output Log file
> -dgdl edi.xvg Output, Opt. xvgr/xmgr file
> -field edi.xvg Output, Opt. xvgr/xmgr file
> -table edi.xvg Input, Opt. xvgr/xmgr file
> -tablep edi.xvg Input, Opt. xvgr/xmgr file
> -tableb edi.xvg Input, Opt. xvgr/xmgr file
> -rerun edi.xtc Input, Opt. Trajectory: xtc trr trj gro g96 pdb cpt
> -tpi edi.xvg Output, Opt. xvgr/xmgr file
> -tpid edi.xvg Output, Opt. xvgr/xmgr file
> -ei testpositive.edi Input, Opt! ED sampling input
> -eo testpositive.edo Output, Opt! ED sampling output
> -j edi.gct Input, Opt. General coupling stuff
> -jo edi.gct Output, Opt. General coupling stuff
> -ffout edi.xvg Output, Opt. xvgr/xmgr file
> -devout edi.xvg Output, Opt. xvgr/xmgr file
> -runav edi.xvg Output, Opt. xvgr/xmgr file
> -px edi.xvg Output, Opt. xvgr/xmgr file
> -pf edi.xvg Output, Opt. xvgr/xmgr file
> -mtx edi.mtx Output, Opt. Hessian matrix
> -dn edi.ndx Output, Opt. Index file
>
> Option Type Value Description
> ------------------------------------------------------
> -[no]h bool no Print help info and quit
> -nice int 19 Set the nicelevel
> -deffnm string edi Set the default filename for all file options
> -[no]xvgr bool yes Add specific codes (legends etc.) in the output
> xvg files for the xmgrace program
> -[no]pd bool no Use particle decompostion
> -dd vector 0 0 0 Domain decomposition grid, 0 is optimize
> -npme int -1 Number of separate nodes to be used for PME, -1
> is guess
> -ddorder enum interleave DD node order: interleave, pp_pme or cartesian
> -[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 yes Dynamic load balancing (with DD): auto, no or yes
> -dds real 0.8 Minimum allowed dlb scaling of the DD cell size
> -[no]sum bool no Sum the energies at every step
> -[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 30 Checkpoint interval (minutes)
> -[no]append bool no Append to previous output files when continuing
> from checkpoint
> -[no]addpart bool yes Add the simulation part number to all output
> files when continuing from checkpoint
> -maxh real 48 Terminate after 0.99 times this time (hours)
> -multi int 0 Do multiple simulations in parallel
> -replex int 0 Attempt replica exchange every # steps
> -reseed int -1 Seed for replica exchange, -1 is generate a seed
> -[no]glas bool no Do glass simulation with special long range
> corrections
> -[no]ionize bool no Do a simulation including the effect of an X-Ray
> bombardment on your system
>
> No previous checkpoint file present, assuming this is a new run.
>
> ED sampling will be performed!
>
> Reading file edi.tpr, VERSION 4.0.5 (single precision)
> ED: Initialzing essential dynamics constraints.
> ED: Reading edi file testpositive.edi
> ED: Note: Reference and average structure are composed of the same atom indices.
> ED: Found 1 ED dataset.
> ED: Initial RMSD from reference after fit = 0.307421 nm (dataset #1)
>
> WARNING: This run will generate roughly 6031 Mb of data
>
> starting mdrun 'Generated by genbox'
> 5000 steps, 5.0 ps.
> Segmentation fault
>
> ##############################
>
> The message is a little more verbose when i run it in parallel:
>
> ...
> ...
> ED: Initialzing essential dynamics constraints.
> ED: Reading edi file testpositive.edi
> ED: Note: Reference and average structure are composed of the same atom indices.
> ED: Found 1 ED dataset.
> ED: Initial RMSD from reference after fit = 0.307421 nm (dataset #1)
> Making 1D domain decomposition 8 x 1 x 1
>
> WARNING: This run will generate roughly 6031 Mb of data
>
> starting mdrun 'Generated by genbox'
> 5000 steps, 5.0 ps.
> [gpc-f103n048:05752] *** Process received signal ***
> [gpc-f103n048:05752] Signal: Segmentation fault (11)
> [gpc-f103n048:05752] Signal code: Address not mapped (1)
> [gpc-f103n048:05752] Failing at address: 0x1abb0
> [gpc-f103n048:05750] *** Process received signal ***
> [gpc-f103n048:05750] Signal: Segmentation fault (11)
> [gpc-f103n048:05750] Signal code: Address not mapped (1)
> [gpc-f103n048:05750] Failing at address: 0x46398
> [gpc-f103n048:05746] *** Process received signal ***
> [gpc-f103n048:05746] Signal: Segmentation fault (11)
> [gpc-f103n048:05746] Signal code: Address not mapped (1)
> ...
> ...
>
> ##############################
>
> When I use md, however, things are fine.
>
> Is there some reason that I should not be combining ED mdrun and the SD integrator? It seems like a reasonable combination to me and I was unable to find and documentation suggesting that one should not be doing this.
>
> Thank you,
> Chris.
>
> PS: I repeated this with 4.0.7 and found the same behaviour:
>
> $ /scratch/cneale/GPC/exe/intel/gromacs-4.0.7/exec/bin/mdrun -deffnm edi -nosum -dlb yes -npme -1 -cpt 30 -maxh 48 -cpi edi.cpt -ei testpositive.edi -eo testpositive.edo
> :-) G R O M A C S (-:
>
> Great Red Owns Many ACres of Sand
>
> :-) VERSION 4.0.7 (-:
>
>
> Written by David van der Spoel, Erik Lindahl, Berk Hess, and others.
> Copyright (c) 1991-2000, University of Groningen, The Netherlands.
> Copyright (c) 2001-2008, The GROMACS development team,
> 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 General Public License
> as published by the Free Software Foundation; either version 2
> of the License, or (at your option) any later version.
>
> :-) /scratch/cneale/GPC/exe/intel/gromacs-4.0.7/exec/bin/mdrun (-:
>
> Option Filename Type Description
> ------------------------------------------------------------
> -s edi.tpr Input Run input file: tpr tpb tpa
> -o edi.trr Output Full precision trajectory: trr trj cpt
> -x edi.xtc Output, Opt. Compressed trajectory (portable xdr format)
> -cpi edi.cpt Input, Opt! Checkpoint file
> -cpo edi.cpt Output, Opt. Checkpoint file
> -c edi.gro Output Structure file: gro g96 pdb
> -e edi.edr Output Energy file: edr ene
> -g edi.log Output Log file
> -dgdl edi.xvg Output, Opt. xvgr/xmgr file
> -field edi.xvg Output, Opt. xvgr/xmgr file
> -table edi.xvg Input, Opt. xvgr/xmgr file
> -tablep edi.xvg Input, Opt. xvgr/xmgr file
> -tableb edi.xvg Input, Opt. xvgr/xmgr file
> -rerun edi.xtc Input, Opt. Trajectory: xtc trr trj gro g96 pdb cpt
> -tpi edi.xvg Output, Opt. xvgr/xmgr file
> -tpid edi.xvg Output, Opt. xvgr/xmgr file
> -ei testpositive.edi Input, Opt! ED sampling input
> -eo testpositive.edo Output, Opt! ED sampling output
> -j edi.gct Input, Opt. General coupling stuff
> -jo edi.gct Output, Opt. General coupling stuff
> -ffout edi.xvg Output, Opt. xvgr/xmgr file
> -devout edi.xvg Output, Opt. xvgr/xmgr file
> -runav edi.xvg Output, Opt. xvgr/xmgr file
> -px edi.xvg Output, Opt. xvgr/xmgr file
> -pf edi.xvg Output, Opt. xvgr/xmgr file
> -mtx edi.mtx Output, Opt. Hessian matrix
> -dn edi.ndx Output, Opt. Index file
>
> Option Type Value Description
> ------------------------------------------------------
> -[no]h bool no Print help info and quit
> -nice int 19 Set the nicelevel
> -deffnm string edi Set the default filename for all file options
> -[no]xvgr bool yes Add specific codes (legends etc.) in the output
> xvg files for the xmgrace program
> -[no]pd bool no Use particle decompostion
> -dd vector 0 0 0 Domain decomposition grid, 0 is optimize
> -npme int -1 Number of separate nodes to be used for PME, -1
> is guess
> -ddorder enum interleave DD node order: interleave, pp_pme or cartesian
> -[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 yes Dynamic load balancing (with DD): auto, no or yes
> -dds real 0.8 Minimum allowed dlb scaling of the DD cell size
> -[no]sum bool no Sum the energies at every step
> -[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 30 Checkpoint interval (minutes)
> -[no]append bool no Append to previous output files when continuing
> from checkpoint
> -[no]addpart bool yes Add the simulation part number to all output
> files when continuing from checkpoint
> -maxh real 48 Terminate after 0.99 times this time (hours)
> -multi int 0 Do multiple simulations in parallel
> -replex int 0 Attempt replica exchange every # steps
> -reseed int -1 Seed for replica exchange, -1 is generate a seed
> -[no]glas bool no Do glass simulation with special long range
> corrections
> -[no]ionize bool no Do a simulation including the effect of an X-Ray
> bombardment on your system
>
> No previous checkpoint file present, assuming this is a new run.
>
> ED sampling will be performed!
>
> Back Off! I just backed up testpositive.edo to ./#testpositive.edo.4#
> Reading file edi.tpr, VERSION 4.0.7 (single precision)
> ED: Initialzing essential dynamics constraints.
> ED: Reading edi file testpositive.edi
> ED: Note: Reference and average structure are composed of the same atom indices.
> ED: Found 1 ED dataset.
> ED: Initial RMSD from reference after fit = 0.307421 nm (dataset #1)
>
> WARNING: This run will generate roughly 6031 Mb of data
>
> starting mdrun 'Generated by genbox'
> 5000 steps, 5.0 ps.
> Segmentation fault
>
>
>
> --
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--
Dr. Carsten Kutzner
Max Planck Institute for Biophysical Chemistry
Theoretical and Computational Biophysics
Am Fassberg 11, 37077 Goettingen, Germany
Tel. +49-551-2012313, Fax: +49-551-2012302
http://www.mpibpc.mpg.de/home/grubmueller/ihp/ckutzne
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