[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
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