[gmx-users] remd :One of the processes started by mpirun has exited with a nonzero exit code.
杜波
2008dubo at gmail.com
Sun Nov 13 14:29:22 CET 2011
dear teacher
when i do remd , i got an erro ! bu i do not know how to do !
thanks!!!
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.
:-) /export/software/bin/mdrun_mpi_4.5.5 (-:
Option Filename Type Description
------------------------------------------------------------
-s pmma.tpr Input Run input file: tpr tpb tpa
-o md.trr Output Full precision trajectory: trr trj cpt
-x traj.xtc Output, Opt. Compressed trajectory (portable xdr
format)
-cpi state.cpt Input, Opt. Checkpoint file
-cpo state.cpt Output, Opt. Checkpoint file
-c after_md.gro Output Structure file: gro g96 pdb etc.
-e ener.edr Output Energy file
-g md.log Output Log file
-dhdl dhdl.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
-multidir ./0/ Input, Opt!, Mult.
./1/
./2/
./3/
./4/
./5/
./6/
./7/
./8/
./9/
./10/
./11/ 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 Set the default filename for all file options
-xvg enum xmgrace xvg plot formatting: xmgrace, xmgr or none
-[no]pd bool yes 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 yes 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 2000 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
NNODES=12, MYRANK=7, HOSTNAME=c0115
NNODES=12, MYRANK=1, HOSTNAME=c0101
NNODES=12, MYRANK=2, HOSTNAME=c0101
NODEID=1 argc=26
NNODES=12, MYRANK=5, HOSTNAME=c0113
NNODES=12, MYRANK=6, HOSTNAME=c0113
NODEID=5 argc=26
NNODES=12, MYRANK=3, HOSTNAME=c0102
NNODES=12, MYRANK=4, HOSTNAME=c0102
NODEID=3 argc=26
NODEID=2 argc=26
NODEID=6 argc=26
NODEID=4 argc=26
NNODES=12, MYRANK=9, HOSTNAME=c0115
NNODES=12, MYRANK=11, HOSTNAME=c0115
NODEID=11 argc=26
NODEID=7 argc=26
NNODES=12, MYRANK=8, HOSTNAME=c0115
NODEID=8 argc=26
NNODES=12, MYRANK=10, HOSTNAME=c0115
NODEID=9 argc=26
NODEID=10 argc=26
Back Off! I just backed up md.log to ./#md.log.1#
Getting Loaded...
Reading file pmma.tpr, VERSION 4.5.5 (single precision)
Back Off! I just backed up md.log to ./#md.log.1#
Back Off! I just backed up md.log to ./#md.log.1#
Back Off! I just backed up md.log to ./#md.log.1#
Back Off! I just backed up md.log to ./#md.log.1#
Back Off! I just backed up md.log to ./#md.log.1#
Back Off! I just backed up md.log to ./#md.log.1#
Back Off! I just backed up md.log to ./#md.log.1#
Getting Loaded...
Getting Loaded...
Loaded with Money
Getting Loaded...
Reading file pmma.tpr, VERSION 4.5.5 (single precision)
Reading file pmma.tpr, VERSION 4.5.5 (single precision)
Reading file pmma.tpr, VERSION 4.5.5 (single precision)
Getting Loaded...
Getting Loaded...
Getting Loaded...
Loaded with Money
Loaded with Money
Getting Loaded...
Loaded with Money
Reading file pmma.tpr, VERSION 4.5.5 (single precision)
Back Off! I just backed up traj.xtc to ./#traj.xtc.1#
Back Off! I just backed up traj.xtc to ./#traj.xtc.1#
Back Off! I just backed up traj.xtc to ./#traj.xtc.1#
Back Off! I just backed up ener.edr to ./#ener.edr.1#
Reading file pmma.tpr, VERSION 4.5.5 (single precision)
Back Off! I just backed up traj.xtc to ./#traj.xtc.1#
Back Off! I just backed up ener.edr to ./#ener.edr.1#
WARNING: This run will generate roughly 3150 Mb of data
WARNING: This run will generate roughly 3150 Mb of data
WARNING: This run will generate roughly 3150 Mb of data
Loaded with Money
Back Off! I just backed up ener.edr to ./#ener.edr.1#
Reading file pmma.tpr, VERSION 4.5.5 (single precision)
Loaded with Money
Loaded with Money
WARNING: This run will generate roughly 3150 Mb of data
Reading file pmma.tpr, VERSION 4.5.5 (single precision)
Loaded with Money
MPI_Recv: process in local group is dead (rank 3, comm 6)
WARNING: This run will generate roughly 3150 Mb of data
-----------------------------------------------------------------------------
One of the processes started by mpirun has exited with a nonzero exit
code. This typically indicates that the process finished in error.
If your process did not finish in error, be sure to include a "return
0" or "exit(0)" in your C code before exiting the application.
PID 1498 failed on node n0 (192.168.1.251) with exit status 1.
-----------------------------------------------------------------------------
Rank (5, MPI_COMM_WORLD): Call stack within LAM:
Rank (5, MPI_COMM_WORLD): - MPI_Recv()
Rank (5, MPI_COMM_WORLD): - MPI_Bcast()
Rank (5, MPI_COMM_WORLD): - MPI_Allgather()
Rank (5, MPI_COMM_WORLD): - MPI_Allreduce()
Rank (5, MPI_COMM_WORLD): - main()
regards,
Bo Du
Department of Polymer Science and Engineering,
School of Chemical Engineering and technology,
Tianjin University, Weijin Road 92, Nankai District 300072,
Tianjin City P. R. China
Tel/Fax: +86-22-27404303
E-mail: 2008dubo at gmail.com
-------------- next part --------------
An HTML attachment was scrubbed...
URL: <http://maillist.sys.kth.se/pipermail/gromacs.org_gmx-users/attachments/20111113/7adb3568/attachment.html>
More information about the gromacs.org_gmx-users
mailing list