Running Directory is pwd NNODES=32, MYRANK=5, HOSTNAME=tyrone-cluster NNODES=32, MYRANK=7, HOSTNAME=tyrone-cluster NNODES=32, MYRANK=9, HOSTNAME=tyrone-cluster NNODES=32, MYRANK=10, HOSTNAME=tyrone-cluster NNODES=32, MYRANK=11, HOSTNAME=tyrone-cluster NNODES=32, MYRANK=13, HOSTNAME=tyrone-cluster NNODES=32, MYRANK=14, HOSTNAME=tyrone-cluster NNODES=32, MYRANK=15, HOSTNAME=tyrone-cluster NNODES=32, MYRANK=0, HOSTNAME=tyrone-cluster NODEID=0 argc=5 NNODES=32, MYRANK=1, HOSTNAME=tyrone-cluster NODEID=1 argc=5 NNODES=32, MYRANK=2, HOSTNAME=tyrone-cluster NODEID=2 argc=5 NNODES=32, MYRANK=3, HOSTNAME=tyrone-cluster NODEID=3 argc=5 NNODES=32, MYRANK=8, HOSTNAME=tyrone-cluster NODEID=8 argc=5 NODEID=9 argc=5 NODEID=10 argc=5 NNODES=32, MYRANK=17, HOSTNAME=tyrone-cluster NNODES=32, MYRANK=19, HOSTNAME=tyrone-cluster NNODES=32, MYRANK=21, HOSTNAME=tyrone-cluster NNODES=32, MYRANK=23, HOSTNAME=tyrone-cluster NNODES=32, MYRANK=24, HOSTNAME=tyrone-cluster NNODES=32, MYRANK=27, HOSTNAME=tyrone-cluster NNODES=32, MYRANK=28, HOSTNAME=tyrone-cluster NNODES=32, MYRANK=29, HOSTNAME=tyrone-cluster :-) G R O M A C S (-: NNODES=32, MYRANK=4, HOSTNAME=tyrone-cluster NODEID=4 argc=5 NNODES=32, MYRANK=6, HOSTNAME=tyrone-cluster NODEID=6 argc=5 NODEID=11 argc=5 NNODES=32, MYRANK=25, HOSTNAME=tyrone-cluster NNODES=32, MYRANK=26, HOSTNAME=tyrone-cluster NNODES=32, MYRANK=31, HOSTNAME=tyrone-cluster NODEID=5 argc=5 NODEID=7 argc=5 NNODES=32, MYRANK=18, HOSTNAME=tyrone-cluster NNODES=32, MYRANK=16, HOSTNAME=tyrone-cluster NNODES=32, MYRANK=22, HOSTNAME=tyrone-cluster NODEID=16 argc=5 NODEID=18 argc=5 NODEID=19 argc=5 NODEID=24 argc=5 NODEID=26 argc=5 NODEID=17 argc=5 NODEID=25 argc=5 NODEID=27 argc=5 NODEID=28 argc=5 NODEID=29 argc=5 NNODES=32, MYRANK=30, HOSTNAME=tyrone-cluster NODEID=30 argc=5 NODEID=31 argc=5 NNODES=32, MYRANK=20, HOSTNAME=tyrone-cluster NODEID=20 argc=5 NODEID=21 argc=5 NODEID=22 argc=5 NODEID=23 argc=5 NNODES=32, MYRANK=12, HOSTNAME=tyrone-cluster NODEID=12 argc=5 NODEID=13 argc=5 NODEID=14 argc=5 NODEID=15 argc=5 GROup of MAchos and Cynical Suckers :-) VERSION 4.5.4 (-: Written by Emile Apol, Rossen Apostolov, Herman J.C. Berendsen, Aldert van Buuren, Pär Bjelkmar, Rudi van Drunen, Anton Feenstra, Gerrit Groenhof, Peter Kasson, Per Larsson, Pieter Meulenhoff, Teemu Murtola, Szilard Pall, Sander Pronk, Roland Schulz, Michael Shirts, Alfons Sijbers, Peter Tieleman, Berk Hess, David van der Spoel, and Erik Lindahl. Copyright (c) 1991-2000, University of Groningen, The Netherlands. Copyright (c) 2001-2010, The GROMACS development team at Uppsala University & The Royal Institute of Technology, Sweden. 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. :-) /home/proj/11/mbumasha/programs/gromacs-4.5.4/bin/mdrun_mpi_d (double precision) (-: Option Filename Type Description ------------------------------------------------------------ -s triglc-MD5.tpr Input Run input file: tpr tpb tpa -o triglc-MD5.trr Output Full precision trajectory: trr trj cpt -x triglc-MD5.xtc Output, Opt. Compressed trajectory (portable xdr format) -cpi triglc-MD5.cpt Input, Opt. Checkpoint file -cpo triglc-MD5.cpt Output, Opt. Checkpoint file -c triglc-MD5.pdb Output Structure file: gro g96 pdb etc. -e triglc-MD5.edr Output Energy file -g triglc-MD5.log Output Log file -dhdl triglc-MD5.xvg Output, Opt. xvgr/xmgr file -field triglc-MD5.xvg Output, Opt. xvgr/xmgr file -table triglc-MD5.xvg Input, Opt. xvgr/xmgr file -tablep triglc-MD5.xvg Input, Opt. xvgr/xmgr file -tableb triglc-MD5.xvg Input, Opt. xvgr/xmgr file -rerun triglc-MD5.xtc Input, Opt. Trajectory: xtc trr trj gro g96 pdb cpt -tpi triglc-MD5.xvg Output, Opt. xvgr/xmgr file -tpid triglc-MD5.xvg Output, Opt. xvgr/xmgr file -ei triglc-MD5.edi Input, Opt. ED sampling input -eo triglc-MD5.edo Output, Opt. ED sampling output -j triglc-MD5.gct Input, Opt. General coupling stuff -jo triglc-MD5.gct Output, Opt. General coupling stuff -ffout triglc-MD5.xvg Output, Opt. xvgr/xmgr file -devout triglc-MD5.xvg Output, Opt. xvgr/xmgr file -runav triglc-MD5.xvg Output, Opt. xvgr/xmgr file -px triglc-MD5.xvg Output, Opt. xvgr/xmgr file -pf triglc-MD5.xvg Output, Opt. xvgr/xmgr file -mtx triglc-MD5.mtx Output, Opt. Hessian matrix -dn triglc-MD5.ndx Output, Opt. Index file -multidir triglc-MD5 Input, Opt., Mult. 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 triglc-MD5 Set the default filename for all file options -xvg enum xmgrace xvg plot formatting: xmgrace, xmgr or none -[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 -gcom int -1 Global communication frequency -[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]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 0 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 Reading file triglc-MD5.tpr, VERSION 4.5.4 (double precision) ------------------------------------------------------- Program mdrun_mpi_d, VERSION 4.5.4 Source code file: domdec.c, line: 6436 Fatal error: There is no domain decomposition for 32 nodes that is compatible with the given box and a minimum cell size of 1.33444 nm Change the number of nodes or mdrun option -rdd or -dds Look in the log file for details on the domain decomposition For more information and tips for troubleshooting, please check the GROMACS website at http://www.gromacs.org/Documentation/Errors ------------------------------------------------------- "Sort Of" (Urban Dance Squad)