[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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