[gmx-users] try to restart a md run using cpt file
Thielges, Sabine
Sabine.Thielges at cnrc-nrc.gc.ca
Tue Nov 3 17:53:40 CET 2009
Hi,
One of my trajectory stop because i didn't have enough space so I made some space and i wanted to restart it using
mpiexec -np 8 mdrun.MPI -s md_20_100_s_IP_beta.tpr -cpi md_20_100_s_IP_beta.cpt -append
and also
mpiexec -np 8 mdrun.MPI -s md_20_100_s_IP_beta.tpr -cpi md_20_100_s_IP_beta_prev.cpt -append
but each time it give me an error message about the .trr file not being properly truncated!!!
there is the error.log file:
nohup: appending output to `nohup.out'
NNODES=8, MYRANK=0, HOSTNAME=fnode21
NODEID=0 argc=6
NNODES=8, MYRANK=1, HOSTNAME=fnode21
NODEID=1 argc=6
NNODES=8, MYRANK=2, HOSTNAME=fnode21
NODEID=2 argc=6
NNODES=8, MYRANK=3, HOSTNAME=fnode21
NODEID=3 argc=6
NNODES=8, MYRANK=4, HOSTNAME=fnode21
NODEID=4 argc=6
NNODES=8, MYRANK=5, HOSTNAME=fnode21
NODEID=5 argc=6
NNODES=8, MYRANK=6, HOSTNAME=fnode21
NODEID=6 argc=6
NNODES=8, MYRANK=7, HOSTNAME=fnode21
NODEID=7 argc=6
:-) G R O M A C S (-:
Gallium Rubidium Oxygen Manganese Argon Carbon Silicon
:-) VERSION 4.0.3 (-:
Written by David van der Spoel, Erik Lindahl, Berk Hess, and others.
Copyright (c) 1991-2000, University of Groningen, The Netherlands.
Copyright (c) 2001-2008, The GROMACS development team,
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 md_20_100_s_IP_beta.tpr Input Run input file: tpr tpb tpa
-o traj.trr Output Full precision trajectory: trr trj cpt
-x traj.xtc Output, Opt. Compressed trajectory (portable xdr format)
-cpi md_20_100_s_IP_beta_prev.cpt Input, Opt! Checkpoint file
-cpo state.cpt Output, Opt. Checkpoint file
-c confout.gro Output Structure file: gro g96 pdb
-e ener.edr Output Energy file: edr ene
-g md.log Output Log file
-dgdl dgdl.xvg Output, Opt. xvgr/xmgr file
-field field.xvg Output, Opt. xvgr/xmgr file
-table table.xvg Input, Opt. xvgr/xmgr file
-tablep tablep.xvg Input, Opt. xvgr/xmgr file
-tableb table.xvg Input, Opt. xvgr/xmgr file
-rerun rerun.xtc Input, Opt. Trajectory: xtc trr trj gro g96 pdb cpt
-tpi tpi.xvg Output, Opt. xvgr/xmgr file
-tpid tpidist.xvg Output, Opt. xvgr/xmgr file
-ei sam.edi Input, Opt. ED sampling input
-eo sam.edo Output, Opt. ED sampling output
-j wham.gct Input, Opt. General coupling stuff
-jo bam.gct Output, Opt. General coupling stuff
-ffout gct.xvg Output, Opt. xvgr/xmgr file
-devout deviatie.xvg Output, Opt. xvgr/xmgr file
-runav runaver.xvg Output, Opt. xvgr/xmgr file
-px pullx.xvg Output, Opt. xvgr/xmgr file
-pf pullf.xvg Output, Opt. xvgr/xmgr file
-mtx nm.mtx Output, Opt. Hessian matrix
-dn dipole.ndx Output, Opt. Index file
Option Type Value Description
------------------------------------------------------
-[no]h bool no Print help info and quit
-nice int 0 Set the nicelevel
-deffnm string Set the default filename for all file options
-[no]xvgr bool yes Add specific codes (legends etc.) in the output
xvg files for the xmgrace program
-[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
-[no]sum bool yes Sum the energies at every step
-[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]append bool yes Append to previous output files when restarting
from checkpoint
-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]glas bool no Do glass simulation with special long range
corrections
-[no]ionize bool no Do a simulation including the effect of an X-Ray
bombardment on your system
Reading file md_20_100_s_IP_beta.tpr, VERSION 4.0.3 (single precision)
Reading checkpoint file md_20_100_s_IP_beta_prev.cpt generated: Sat Oct 31 12:34:46 2009
-------------------------------------------------------
Program mdrun.MPI, VERSION 4.0.3
Source code file: checkpoint.c, line: 1238
Fatal error:
Truncation of file md_20_100_s_IP_beta.trr failed.
-------------------------------------------------------
"Do You Have a Mind of Your Own ?" (Garbage)
Error on node 0, will try to stop all the nodes
Halting parallel program mdrun.MPI on CPU 0 out of 8
gcq#280: "Do You Have a Mind of Your Own ?" (Garbage)
[fnode21:27263] MPI_ABORT invoked on rank 0 in communicator MPI_COMM_WORLD with errorcode -1
mpiexec noticed that job rank 1 with PID 27267 on node fnode21 exited on signal 15 (Terminated).
Can anyone help me understand what is the problem?
thank you in advance.
Sabine
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