<div> dear teacher </div><div>when i do remd , i got an erro ! bu i do not know how to do !</div><div>thanks!!!</div><div><br></div><div> modify it under the terms of the GNU General Public License</div><div> as published by the Free Software Foundation; either version 2</div>
<div> of the License, or (at your option) any later version.</div><div><br></div><div> :-) /export/software/bin/mdrun_mpi_4.5.5 (-:</div><div><br></div><div>Option Filename Type Description</div>
<div>------------------------------------------------------------</div><div> -s pmma.tpr Input Run input file: tpr tpb tpa</div><div> -o md.trr Output Full precision trajectory: trr trj cpt</div>
<div> -x traj.xtc Output, Opt. Compressed trajectory (portable xdr format)</div><div>-cpi state.cpt Input, Opt. Checkpoint file</div><div>-cpo state.cpt Output, Opt. Checkpoint file</div><div> -c after_md.gro Output Structure file: gro g96 pdb etc.</div>
<div> -e ener.edr Output Energy file</div><div> -g md.log Output Log file</div><div>-dhdl dhdl.xvg Output, Opt. xvgr/xmgr file</div><div>-field field.xvg Output, Opt. xvgr/xmgr file</div>
<div>-table table.xvg Input, Opt. xvgr/xmgr file</div><div>-tablep tablep.xvg Input, Opt. xvgr/xmgr file</div><div>-tableb table.xvg Input, Opt. xvgr/xmgr file</div><div>-rerun rerun.xtc Input, Opt. Trajectory: xtc trr trj gro g96 pdb cpt</div>
<div>-tpi tpi.xvg Output, Opt. xvgr/xmgr file</div><div>-tpid tpidist.xvg Output, Opt. xvgr/xmgr file</div><div> -ei sam.edi Input, Opt. ED sampling input</div><div> -eo sam.edo Output, Opt. ED sampling output</div>
<div> -j wham.gct Input, Opt. General coupling stuff</div><div> -jo bam.gct Output, Opt. General coupling stuff</div><div>-ffout gct.xvg Output, Opt. xvgr/xmgr file</div><div>-devout deviatie.xvg Output, Opt. xvgr/xmgr file</div>
<div>-runav runaver.xvg Output, Opt. xvgr/xmgr file</div><div> -px pullx.xvg Output, Opt. xvgr/xmgr file</div><div> -pf pullf.xvg Output, Opt. xvgr/xmgr file</div><div>-mtx nm.mtx Output, Opt. Hessian matrix</div>
<div> -dn dipole.ndx Output, Opt. Index file</div><div>-multidir ./0/ Input, Opt!, Mult. </div><div> ./1/ </div><div> ./2/ </div><div> ./3/ </div>
<div> ./4/ </div><div> ./5/ </div><div> ./6/ </div><div> ./7/ </div><div> ./8/ </div>
<div> ./9/ </div><div> ./10/ </div><div> ./11/ Run directory</div><div><br></div><div>Option Type Value Description</div><div>------------------------------------------------------</div>
<div>-[no]h bool no Print help info and quit</div><div>-[no]version bool no Print version info and quit</div><div>-nice int 0 Set the nicelevel</div><div>-deffnm string Set the default filename for all file options</div>
<div>-xvg enum xmgrace xvg plot formatting: xmgrace, xmgr or none</div><div>-[no]pd bool yes Use particle decompostion</div><div>-dd vector 0 0 0 Domain decomposition grid, 0 is optimize</div>
<div>-npme int -1 Number of separate nodes to be used for PME, -1</div><div> is guess</div><div>-ddorder enum interleave DD node order: interleave, pp_pme or cartesian</div>
<div>-[no]ddcheck bool yes Check for all bonded interactions with DD</div><div>-rdd real 0 The maximum distance for bonded interactions with</div><div> DD (nm), 0 is determine from initial coordinates</div>
<div>-rcon real 0 Maximum distance for P-LINCS (nm), 0 is estimate</div><div>-dlb enum auto Dynamic load balancing (with DD): auto, no or yes</div><div>-dds real 0.8 Minimum allowed dlb scaling of the DD cell size</div>
<div>-gcom int -1 Global communication frequency</div><div>-[no]v bool yes Be loud and noisy</div><div>-[no]compact bool yes Write a compact log file</div><div>-[no]seppot bool no Write separate V and dVdl terms for each</div>
<div> interaction type and node to the log file(s)</div><div>-pforce real -1 Print all forces larger than this (kJ/mol nm)</div><div>-[no]reprod bool no Try to avoid optimizations that affect binary</div>
<div> reproducibility</div><div>-cpt real 15 Checkpoint interval (minutes)</div><div>-[no]cpnum bool no Keep and number checkpoint files</div><div>-[no]append bool yes Append to previous output files when continuing</div>
<div> from checkpoint instead of adding the simulation</div><div> part number to all file names</div><div>-maxh real -1 Terminate after 0.99 times this time (hours)</div>
<div>-multi int 0 Do multiple simulations in parallel</div><div>-replex int 2000 Attempt replica exchange every # steps</div><div>-reseed int -1 Seed for replica exchange, -1 is generate a seed</div>
<div>-[no]ionize bool no Do a simulation including the effect of an X-Ray</div><div> bombardment on your system</div><div><br></div><div>NNODES=12, MYRANK=7, HOSTNAME=c0115</div><div>NNODES=12, MYRANK=1, HOSTNAME=c0101</div>
<div>NNODES=12, MYRANK=2, HOSTNAME=c0101</div><div>NODEID=1 argc=26</div><div>NNODES=12, MYRANK=5, HOSTNAME=c0113</div><div>NNODES=12, MYRANK=6, HOSTNAME=c0113</div><div>NODEID=5 argc=26</div><div>NNODES=12, MYRANK=3, HOSTNAME=c0102</div>
<div>NNODES=12, MYRANK=4, HOSTNAME=c0102</div><div>NODEID=3 argc=26</div><div>NODEID=2 argc=26</div><div>NODEID=6 argc=26</div><div>NODEID=4 argc=26</div><div>NNODES=12, MYRANK=9, HOSTNAME=c0115</div><div>NNODES=12, MYRANK=11, HOSTNAME=c0115</div>
<div>NODEID=11 argc=26</div><div>NODEID=7 argc=26</div><div>NNODES=12, MYRANK=8, HOSTNAME=c0115</div><div>NODEID=8 argc=26</div><div>NNODES=12, MYRANK=10, HOSTNAME=c0115</div><div>NODEID=9 argc=26</div><div>NODEID=10 argc=26</div>
<div><br></div><div>Back Off! I just backed up md.log to ./#md.log.1#</div><div>Getting Loaded...</div><div>Reading file pmma.tpr, VERSION 4.5.5 (single precision)</div><div><br></div><div>Back Off! I just backed up md.log to ./#md.log.1#</div>
<div><br></div><div>Back Off! I just backed up md.log to ./#md.log.1#</div><div><br></div><div>Back Off! I just backed up md.log to ./#md.log.1#</div><div><br></div><div>Back Off! I just backed up md.log to ./#md.log.1#</div>
<div><br></div><div>Back Off! I just backed up md.log to ./#md.log.1#</div><div><br></div><div>Back Off! I just backed up md.log to ./#md.log.1#</div><div><br></div><div>Back Off! I just backed up md.log to ./#md.log.1#</div>
<div>Getting Loaded...</div><div>Getting Loaded...</div><div>Loaded with Money</div><div><br></div><div>Getting Loaded...</div><div>Reading file pmma.tpr, VERSION 4.5.5 (single precision)</div><div>Reading file pmma.tpr, VERSION 4.5.5 (single precision)</div>
<div>Reading file pmma.tpr, VERSION 4.5.5 (single precision)</div><div>Getting Loaded...</div><div>Getting Loaded...</div><div>Getting Loaded...</div><div>Loaded with Money</div><div><br></div><div>Loaded with Money</div>
<div><br></div><div>Getting Loaded...</div><div>Loaded with Money</div><div><br></div><div>Reading file pmma.tpr, VERSION 4.5.5 (single precision)</div><div><br></div><div>Back Off! I just backed up traj.xtc to ./#traj.xtc.1#</div>
<div><br></div><div>Back Off! I just backed up traj.xtc to ./#traj.xtc.1#</div><div><br></div><div>Back Off! I just backed up traj.xtc to ./#traj.xtc.1#</div><div><br></div><div>Back Off! I just backed up ener.edr to ./#ener.edr.1#</div>
<div>Reading file pmma.tpr, VERSION 4.5.5 (single precision)</div><div><br></div><div>Back Off! I just backed up traj.xtc to ./#traj.xtc.1#</div><div><br></div><div>Back Off! I just backed up ener.edr to ./#ener.edr.1#</div>
<div><br></div><div>WARNING: This run will generate roughly 3150 Mb of data</div><div><br></div><div><br></div><div>WARNING: This run will generate roughly 3150 Mb of data</div><div><br></div><div><br></div><div>WARNING: This run will generate roughly 3150 Mb of data</div>
<div><br></div><div>Loaded with Money</div><div><br></div><div><br></div><div>Back Off! I just backed up ener.edr to ./#ener.edr.1#</div><div>Reading file pmma.tpr, VERSION 4.5.5 (single precision)</div><div>Loaded with Money</div>
<div><br></div><div>Loaded with Money</div><div><br></div><div><br></div><div>WARNING: This run will generate roughly 3150 Mb of data</div><div><br></div><div>Reading file pmma.tpr, VERSION 4.5.5 (single precision)</div><div>
Loaded with Money</div><div><br></div><div>MPI_Recv: process in local group is dead (rank 3, comm 6)</div><div><br></div><div>WARNING: This run will generate roughly 3150 Mb of data</div><div><br></div><div>-----------------------------------------------------------------------------</div>
<div>One of the processes started by mpirun has exited with a nonzero exit</div><div>code. This typically indicates that the process finished in error.</div><div>If your process did not finish in error, be sure to include a "return</div>
<div>0" or "exit(0)" in your C code before exiting the application.</div><div><br></div><div>PID 1498 failed on node n0 (192.168.1.251) with exit status 1.</div><div>-----------------------------------------------------------------------------</div>
<div>Rank (5, MPI_COMM_WORLD): Call stack within LAM:</div><div>Rank (5, MPI_COMM_WORLD): - MPI_Recv()</div><div>Rank (5, MPI_COMM_WORLD): - MPI_Bcast()</div><div>Rank (5, MPI_COMM_WORLD): - MPI_Allgather()</div><div>Rank (5, MPI_COMM_WORLD): - MPI_Allreduce()</div>
<div>Rank (5, MPI_COMM_WORLD): - main()</div><div><br></div><div><br></div><div>regards,</div><div><span class="Apple-style-span" style="font-family: arial, sans-serif; font-size: 14px; border-collapse: collapse; color: rgb(34, 34, 34); ">Bo Du<br>
Department of Polymer Science and Engineering,<br>School of Chemical Engineering and technology,<br>Tianjin University, Weijin Road 92, Nankai District 300072,<br>Tianjin City P. R. China<br>Tel/Fax: +86-22-27404303<br>E-mail: <a href="mailto:2008dubo@gmail.com" style="color: rgb(17, 85, 204); ">2008dubo@gmail.com</a></span></div>