[gmx-users] mpirun: cannot open .tpr file

Ewaru edina_wang at yahoo.com
Sun Mar 3 07:12:21 CET 2013


Hi,

I'm trying to test mpirun, so I tried with the NPT equilibration. From the
tutorial of:

http://www.bevanlab.biochem.vt.edu/Pages/Personal/justin/gmx-tutorials/lysozyme/07_equil2.html

I run this command: mpirun --np 10 --hostfile ~/hostfile mdrun_mpi -npme 3
-deffnm npt

and obtained an error saying "Cannot open file: npt.tpr". However, if I run
it with just mdrun, it goes fine. Can someone please advice what went wrong?
:( 

The output for the mpirun is as below:

NNODES=10, MYRANK=2, HOSTNAME=wizztjh-Presario-CQ42-Notebook-PC
NNODES=10, MYRANK=3, HOSTNAME=wizztjh-Presario-CQ42-Notebook-PC
NNODES=10, MYRANK=6, HOSTNAME=wizztjh-Presario-CQ42-Notebook-PC
NNODES=10, MYRANK=1, HOSTNAME=wizztjh-Presario-CQ42-Notebook-PC
NNODES=10, MYRANK=7, HOSTNAME=wizztjh-Presario-CQ42-Notebook-PC
NNODES=10, MYRANK=4, HOSTNAME=wizztjh-Presario-CQ42-Notebook-PC
NNODES=10, MYRANK=9, HOSTNAME=wizztjh-Presario-CQ42-Notebook-PC
NNODES=10, MYRANK=5, HOSTNAME=wizztjh-Presario-CQ42-Notebook-PC
NNODES=10, MYRANK=0, HOSTNAME=wizztjh-Presario-CQ42-Notebook-PC
NODEID=0 argc=5
NODEID=4 argc=5
NNODES=10, MYRANK=8, HOSTNAME=wizztjh-Presario-CQ42-Notebook-PC
NODEID=2 argc=5
NODEID=1 argc=5
NODEID=3 argc=5
                         :-)  G  R  O  M  A  C  S  (-:

NODEID=5 argc=5
NODEID=9 argc=5
               NODEID=6 argc=5
NODEID=8 argc=5
Gromacs Runs One Microsecond At Cannonball Speeds

                            :-)  VERSION 4.5.4  (-:

        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, 
NODEID=7 argc=5
           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  (-:

Option     Filename  Type         Description
------------------------------------------------------------
  -s        npt.tpr  Input        Run input file: tpr tpb tpa
  -o        npt.trr  Output       Full precision trajectory: trr trj cpt
  -x        npt.xtc  Output, Opt. Compressed trajectory (portable xdr
format)
-cpi        npt.cpt  Input, Opt.  Checkpoint file
-cpo        npt.cpt  Output, Opt. Checkpoint file
  -c        npt.gro  Output       Structure file: gro g96 pdb etc.
  -e        npt.edr  Output       Energy file
  -g        npt.log  Output       Log file
-dhdl       npt.xvg  Output, Opt. xvgr/xmgr file
-field      npt.xvg  Output, Opt. xvgr/xmgr file
-table      npt.xvg  Input, Opt.  xvgr/xmgr file
-tablep     npt.xvg  Input, Opt.  xvgr/xmgr file
-tableb     npt.xvg  Input, Opt.  xvgr/xmgr file
-rerun      npt.xtc  Input, Opt.  Trajectory: xtc trr trj gro g96 pdb cpt
-tpi        npt.xvg  Output, Opt. xvgr/xmgr file
-tpid       npt.xvg  Output, Opt. xvgr/xmgr file
 -ei        npt.edi  Input, Opt.  ED sampling input
 -eo        npt.edo  Output, Opt. ED sampling output
  -j        npt.gct  Input, Opt.  General coupling stuff
 -jo        npt.gct  Output, Opt. General coupling stuff
-ffout      npt.xvg  Output, Opt. xvgr/xmgr file
-devout     npt.xvg  Output, Opt. xvgr/xmgr file
-runav      npt.xvg  Output, Opt. xvgr/xmgr file
 -px        npt.xvg  Output, Opt. xvgr/xmgr file
 -pf        npt.xvg  Output, Opt. xvgr/xmgr file
-mtx        npt.mtx  Output, Opt. Hessian matrix
 -dn        npt.ndx  Output, Opt. Index file
-multidir       npt  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 npt     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    3       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    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]ionize  bool   no      Do a simulation including the effect of an X-Ray
                            bombardment on your system


Back Off! I just backed up npt.log to ./#npt.log.8#

-------------------------------------------------------
Program mdrun_mpi, VERSION 4.5.4
Source code file: /build/buildd/gromacs-4.5.4/src/gmxlib/gmxfio.c, line: 519

Can not open file:
npt.tpr
For more information and tips for troubleshooting, please check the GROMACS
website at http://www.gromacs.org/Documentation/Errors
-------------------------------------------------------

"I like to wait, then I feel like I do something" (Carl Caleman)

Error on node 0, will try to stop all the nodes
--------------------------------------------------------------------------
MPI_ABORT was invoked on rank 0 in communicator MPI_COMM_WORLD 
with errorcode -1.

NOTE: invoking MPI_ABORT causes Open MPI to kill all MPI processes.
You may or may not see output from other processes, depending on
exactly when Open MPI kills them.
--------------------------------------------------------------------------
Halting parallel program mdrun_mpi on CPU 0 out of 10

gcq#361: "I like to wait, then I feel like I do something" (Carl Caleman)

--------------------------------------------------------------------------
mpirun has exited due to process rank 0 with PID 6917 on
node 192.168.1.252 exiting without calling "finalize". This may
have caused other processes in the application to be
terminated by signals sent by mpirun (as reported here).


Thanking you in advance!

Best wishes



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