[gmx-users] mpirun: cannot open .tpr file
Justin Lemkul
jalemkul at vt.edu
Sun Mar 3 15:31:47 CET 2013
On 3/3/13 1:12 AM, Ewaru wrote:
> 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 error means that npt.tpr does not exist in the working directory.
-Justin
> 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
>
>
>
> --
> View this message in context: http://gromacs.5086.n6.nabble.com/mpirun-cannot-open-tpr-file-tp5006059.html
> Sent from the GROMACS Users Forum mailing list archive at Nabble.com.
>
--
========================================
Justin A. Lemkul, Ph.D.
Research Scientist
Department of Biochemistry
Virginia Tech
Blacksburg, VA
jalemkul[at]vt.edu | (540) 231-9080
http://www.bevanlab.biochem.vt.edu/Pages/Personal/justin
========================================
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