-------------------------------------- Running PBS prologue script -------------------------------------- User and Job Data: -------------------------------------- Job ID: 72960.tezpur2 Username: sbale1 Group: Users Date: 11-Dec-2009 21:37 Node: tezpur331 (4424) -------------------------------------- PBS has allocated the following nodes: tezpur331 A total of 4 processors on 1 nodes allocated --------------------------------------------- Check nodes and clean them of stray processes --------------------------------------------- Checking node tezpur331 21:37:32 Done clearing all the allocated nodes ------------------------------------------------------ Concluding PBS prologue script - 11-Dec-2009 21:37:32 ------------------------------------------------------ Fri Dec 11 21:37:32 CST 2009 NNODES=4, MYRANK=2, HOSTNAME=tezpur331 NNODES=4, MYRANK=0, HOSTNAME=tezpur331 NNODES=4, MYRANK=1, HOSTNAME=tezpur331 NNODES=4, MYRANK=3, HOSTNAME=tezpur331 NODEID=0 argc=4 NODEID=1 argc=4 :-) G R O M A C S (-: NODEID=2 argc=4 NODEID=3 argc=4 Gyas ROwers Mature At Cryogenic Speed :-) 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. :-) /usr/local/packages/gromacs-4.0.3-mvapich-1.0-intel-10.1/bin/mdrun_mpi (double precision) (-: Option Filename Type Description ------------------------------------------------------------ -s md.tpr Input Run input file: tpr tpb tpa -o md.trr Output Full precision trajectory: trr trj cpt -x md.xtc Output, Opt. Compressed trajectory (portable xdr format) -cpi md.cpt Input, Opt. Checkpoint file -cpo md.cpt Output, Opt. Checkpoint file -c md.gro Output Structure file: gro g96 pdb -e md.edr Output Energy file: edr ene -g md.log Output Log file -dgdl md.xvg Output, Opt. xvgr/xmgr file -field md.xvg Output, Opt. xvgr/xmgr file -table md.xvg Input, Opt. xvgr/xmgr file -tablep md.xvg Input, Opt. xvgr/xmgr file -tableb md.xvg Input, Opt. xvgr/xmgr file -rerun md.xtc Input, Opt. Trajectory: xtc trr trj gro g96 pdb cpt -tpi md.xvg Output, Opt. xvgr/xmgr file -tpid md.xvg Output, Opt. xvgr/xmgr file -ei md.edi Input, Opt. ED sampling input -eo md.edo Output, Opt. ED sampling output -j md.gct Input, Opt. General coupling stuff -jo md.gct Output, Opt. General coupling stuff -ffout md.xvg Output, Opt. xvgr/xmgr file -devout md.xvg Output, Opt. xvgr/xmgr file -runav md.xvg Output, Opt. xvgr/xmgr file -px md.xvg Output, Opt. xvgr/xmgr file -pf md.xvg Output, Opt. xvgr/xmgr file -mtx md.mtx Output, Opt. Hessian matrix -dn md.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 md 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 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]append bool no 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 Getting Loaded... Reading file md.tpr, VERSION 4.0.3 (double precision) Loaded with Money Making 1D domain decomposition 4 x 1 x 1 starting mdrun 'CB' 6000000 steps, 6000.0 ps. step 0 NOTE: Turning on dynamic load balancing mpispawn.c:303 Unexpected exit status Child exited abnormally! Killing remote processes...DONE Fri Dec 11 21:37:36 CST 2009 ------------------------------------------------------ Running PBS epilogue script - 11-Dec-2009 21:37:36 ------------------------------------------------------ Checking node tezpur331 (MS) Checking node tezpur331 ok ------------------------------------------------------ Concluding PBS epilogue script - 11-Dec-2009 21:37:37 ------------------------------------------------------ Exit Status: Job ID: 72960.tezpur2 Username: sbale1 Group: Users Job Name: CB_20Bulk Session Id: 4423 Resource Limits: ncpus=1,nodes=1:ppn=4,walltime=48:00:00 Resources Used: cput=00:00:00,mem=6592kb,vmem=187780kb,walltime=00:00:06 Queue Used: checkpt Account String: sbale1 Node: tezpur331 Process id: 5011 ------------------------------------------------------