[gmx-users] essential dynamics mdrun with SD integrator yields segmentation fault
chris.neale at utoronto.ca
chris.neale at utoronto.ca
Sat Dec 19 02:09:37 CET 2009
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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