[gmx-users] Extending REMD simulations problem
Kenny Bravo Rodriguez
kenny at mpi-muelheim.mpg.de
Fri Dec 7 16:01:10 CET 2012
Hi all,
i want to extend a remd simulation that finished correctly, but i always
get the same segmentation fault error.
This is what i am doing with a test system.
I run the REMD simulation with:
mdrun_mpi_d -s test_.tpr -deffnm test_ -multi 2 -replex 500
After the simulation correctly finished i extend the number of time
steps in each .tpr file with:
tpbconv_d -s test_1.tpr -extend 20 -o testl_1.tpr
tpbconv_d -s test_0.tpr -extend 20 -o testl_0.tpr
And then i try to continue the REMD simulation with:
mdrun_mpi_d -s testl_.tpr -deffnm test_ -cpi test_.cpt -multi 2 -replex 500
but i only got the error message show below.
What am i doing wrong?
Thanks in advanced
Kenny
NNODES=6, MYRANK=1, HOSTNAME=hydra02
NNODES=6, MYRANK=3, HOSTNAME=hydra02
NNODES=6, MYRANK=4, HOSTNAME=hydra02
NNODES=6, MYRANK=0, HOSTNAME=hydra02
NODEID=0 argc=11
NODEID=1 argc=11
NODEID=4 argc=11
:-) G R O M A C S (-:
NNODES=6, MYRANK=5, HOSTNAME=hydra02
NODEID=5 argc=11
GROningen Mixture of Alchemy and Childrens' Stories
:-) VERSION 4.5.5 (-:
Written by Emile Apol, Rossen Apostolov, Herman J.C. Berendsen,
Aldert van Buuren, Pär Bjelkmar, Rudi van Drunen, Anton Feenstra,
Gerrit Groenhof, Peter Kasson, 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) 2001-2010, 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 General Public License
as published by the Free Software Foundation; either version 2
of the License, or (at your option) any later version.
:-) mdrun_mpi_d (double precision) (-:
NNODES=6, MYRANK=2, HOSTNAME=hydra02
NODEID=2 argc=11
NODEID=3 argc=11
node 0 par_fn 'testl_0.tpr'
node 0 par_fn 'test_0.trr'
node 0 par_fn 'test_0.xtc'
node 0 par_fn 'test_0.cpt'
node 0 par_fn 'test_0.cpt'
node 0 par_fn 'test_0.gro'
node 0 par_fn 'test_0.edr'
Option Filename Type Description
------------------------------------------------------------
-s testl_.tpr Input Run input file: tpr tpb tpa
-o test_.trr Output Full precision trajectory: trr trj cpt
-x test_.xtc Output, Opt. Compressed trajectory (portable xdr
format)
-cpi test_.cpt Input, Opt! Checkpoint file
-cpo test_.cpt Output, Opt. Checkpoint file
-c test_.gro Output Structure file: gro g96 pdb etc.
-e test_.edr Output Energy file
-g test_.log Output Log file
-dhdl test_.xvg Output, Opt. xvgr/xmgr file
-field test_.xvg Output, Opt. xvgr/xmgr file
-table test_.xvg Input, Opt. xvgr/xmgr file
-tablep test_.xvg Input, Opt. xvgr/xmgr file
-tableb test_.xvg Input, Opt. xvgr/xmgr file
-rerun test_.xtc Input, Opt. Trajectory: xtc trr trj gro g96 pdb cpt
-tpi test_.xvg Output, Opt. xvgr/xmgr file
-tpid test_.xvg Output, Opt. xvgr/xmgr file
-ei test_.edi Input, Opt. ED sampling input
-eo test_.edo Output, Opt. ED sampling output
-j test_.gct Input, Opt. General coupling stuff
-jo test_.gct Output, Opt. General coupling stuff
-ffout test_.xvg Output, Opt. xvgr/xmgr file
-devout test_.xvg Output, Opt. xvgr/xmgr file
-runav test_.xvg Output, Opt. xvgr/xmgr file
-px test_.xvg Output, Opt. xvgr/xmgr file
-pf test_.xvg Output, Opt. xvgr/xmgr file
-mtx test_.mtx Output, Opt. Hessian matrix
-dn test_.ndx Output, Opt. Index file
-multidir test_ Input, Opt., Mult. Run directory
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 test_ 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
-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 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
-[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
-maxh real -1 Terminate after 0.99 times this time (hours)
-multi int 2 Do multiple simulations in parallel
-replex int 500 Attempt replica exchange every # steps
-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
node 0 par_fn 'testl_1.tpr'
node 0 par_fn 'test_1.trr'
node 0 par_fn 'test_1.xtc'
node 0 par_fn 'test_1.cpt'
node 0 par_fn 'test_1.cpt'
node 0 par_fn 'test_1.gro'
node 0 par_fn 'test_1.edr'
node 0 par_fn 'test_1.log'
log
node 0 par_fn 'test_1.xvg'
node 0 par_fn 'test_1.xvg'
node 0 par_fn 'test_1.xtc'
node 0 par_fn 'test_1.xvg'
node 0 par_fn 'test_1.xvg'
node 0 par_fn 'test_1.edo'
node 0 par_fn 'test_1.gct'
node 0 par_fn 'test_1.xvg'
node 0 par_fn 'test_1.xvg'
node 0 par_fn 'test_0.log'
log
node 0 par_fn 'test_0.xvg'
node 0 par_fn 'test_0.xvg'
node 0 par_fn 'test_0.xtc'
node 0 par_fn 'test_0.xvg'
node 0 par_fn 'test_0.xvg'
node 0 par_fn 'test_0.edo'
node 0 par_fn 'test_0.gct'
node 0 par_fn 'test_0.xvg'
node 0 par_fn 'test_0.xvg'
node 0 par_fn 'test_0.xvg'
node 0 par_fn 'test_0.xvg'
node 0 par_fn 'test_0.xvg'
node 0 par_fn 'test_0.mtx'
node 0 par_fn 'test_0.ndx'
node 0 par_fn 'test_1.xvg'
node 0 par_fn 'test_1.xvg'
node 0 par_fn 'test_1.xvg'
node 0 par_fn 'test_1.mtx'
node 0 par_fn 'test_1.ndx'
Multi-checking simulation part ... OK
Multi-checking simulation part ... OK
Reading file testl_0.tpr, VERSION 4.5.5 (double precision)
Reading file testl_1.tpr, VERSION 4.5.5 (double precision)
Multi-checking simulation part ... Multi-checking simulation part ...
Multi-checking simulation part ... Multi-checking simulation part ...
ERROR: 0031-250 task 4: Segmentation fault
ERROR: 0031-250 task 5: Segmentation fault
ERROR: 0031-250 task 0: Terminated
ERROR: 0031-250 task 3: Terminated
ERROR: 0031-250 task 1: Segmentation fault
ERROR: 0031-250 task 2: Segmentation fault
--
Kenny Bravo Rodriguez
Max-Planck-Institut für Kohlenforschung
Kaiser-Wilhelm-Platz 1
D-45470 Mülheim an der Ruhr
Germany
Phone: +49 (0)208 306 2160
Email:kenny at mpi-muelheim.mpg.de
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