[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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