NNODES=8, MYRANK=4, HOSTNAME=maginet-ii188 NNODES=8, MYRANK=2, HOSTNAME=maginet-ii188 NNODES=8, MYRANK=1, HOSTNAME=maginet-ii188 NNODES=8, MYRANK=6, HOSTNAME=maginet-ii188 NNODES=8, MYRANK=7, HOSTNAME=maginet-ii188 NNODES=8, MYRANK=0, HOSTNAME=maginet-ii188 NODEID=0 argc=12 :-) G R O M A C S (-: NODEID=2 argc=12 NODEID=4 argc=12 NODEID=1 argc=12 NODEID=6 argc=12 NNODES=8, MYRANK=5, HOSTNAME=maginet-ii188 NODEID=5 argc=12 NNODES=8, MYRANK=3, HOSTNAME=maginet-ii188 NODEID=3 argc=12 NODEID=7 argc=12 Gromacs Runs On Most of All Computer Systems :-) VERSION 4.0.5 (-: 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/gromacs-4.0.5-fftw3/bin/mdrun_mpi (-: Option Filename Type Description ------------------------------------------------------------ -s minIons2.tpr Input Run input file: tpr tpb tpa -o minIons_traj2.trr Output Full precision trajectory: trr trj cpt -x minIons_traj2.xtc Output, Opt! Compressed trajectory (portable xdr format) -cpi state.cpt Input, Opt. Checkpoint file -cpo state.cpt Output, Opt. Checkpoint file -c minIons_final2.gro Output Structure file: gro g96 pdb -e minIons_ener2.edr Output Energy file: edr ene -g md.log Output Log file -dgdl dgdl.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 Option Type Value Description ------------------------------------------------------ -[no]h bool no Print help info and quit -nice int 0 Set the nicelevel -deffnm string 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 continuing from checkpoint -[no]addpart bool yes Add the simulation part number to all output files when continuing 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 Back Off! I just backed up md.log to ./#md.log.14# Getting Loaded... Reading file minIons2.tpr, VERSION 4.0.5 (single precision) Loaded with Money ------------------------------------------------------- Program mdrun_mpi, VERSION 4.0.5 Source code file: domdec.c, line: 5873 Fatal error: There is no domain decomposition for 8 nodes that is compatible with the given box and a minimum cell size of 38.1122 nm Change the number of nodes or mdrun option -rdd Look in the log file for details on the domain decomposition ------------------------------------------------------- "Baby, It Aint Over Till It's Over" (Lenny Kravitz) Error on node 0, will try to stop all the nodes Halting parallel program mdrun_mpi on CPU 0 out of 8 gcq#285: "Baby, It Aint Over Till It's Over" (Lenny Kravitz) -------------------------------------------------------------------------- mpirun has exited due to process rank 5 with PID 23201 on node maginet-ii188 exiting without calling "finalize". This may have caused other processes in the application to be terminated by signals sent by mpirun (as reported here). --------------------------------------------------------------------------