:-) G R O M A C S (-: Good gRace! Old Maple Actually Chews Slate :-) VERSION 4.6.5 (-: Contributions from Mark Abraham, Emile Apol, Rossen Apostolov, Herman J.C. Berendsen, Aldert van Buuren, Pär Bjelkmar, Rudi van Drunen, Anton Feenstra, Gerrit Groenhof, Christoph Junghans, Peter Kasson, Carsten Kutzner, 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) 2001-2012,2013, 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 Lesser General Public License as published by the Free Software Foundation; either version 2.1 of the License, or (at your option) any later version. :-) mdrun_mpi (-: Option Filename Type Description ------------------------------------------------------------ -s dynamic.tpr Input Run input file: tpr tpb tpa -o dynamic.trr Output Full precision trajectory: trr trj cpt -x dynamic.xtc Output, Opt. Compressed trajectory (portable xdr format) -cpi dynamic.cpt Input, Opt! Checkpoint file -cpo dynamic.cpt Output, Opt. Checkpoint file -c dynamic.gro Output Structure file: gro g96 pdb etc. -e dynamic.edr Output Energy file -g dynamic.log Output Log file -dhdl dynamic.xvg Output, Opt. xvgr/xmgr file -field dynamic.xvg Output, Opt. xvgr/xmgr file -table dynamic.xvg Input, Opt. xvgr/xmgr file -tabletf dynamic.xvg Input, Opt. xvgr/xmgr file -tablep dynamic.xvg Input, Opt. xvgr/xmgr file -tableb dynamic.xvg Input, Opt. xvgr/xmgr file -rerun dynamic.xtc Input, Opt. Trajectory: xtc trr trj gro g96 pdb cpt -tpi dynamic.xvg Output, Opt. xvgr/xmgr file -tpid dynamic.xvg Output, Opt. xvgr/xmgr file -ei dynamic.edi Input, Opt. ED sampling input -eo dynamic.xvg Output, Opt. xvgr/xmgr file -j dynamic.gct Input, Opt. General coupling stuff -jo dynamic.gct Output, Opt. General coupling stuff -ffout dynamic.xvg Output, Opt. xvgr/xmgr file -devout dynamic.xvg Output, Opt. xvgr/xmgr file -runav dynamic.xvg Output, Opt. xvgr/xmgr file -px dynamic.xvg Output, Opt. xvgr/xmgr file -pf dynamic.xvg Output, Opt. xvgr/xmgr file -ro dynamic.xvg Output, Opt. xvgr/xmgr file -ra dynamic.log Output, Opt. Log file -rs dynamic.log Output, Opt. Log file -rt dynamic.log Output, Opt. Log file -mtx dynamic.mtx Output, Opt. Hessian matrix -dn dynamic.ndx Output, Opt. Index file -multidir dynamic Input, Opt., Mult. Run directory -membed dynamic.dat Input, Opt. Generic data file -mp dynamic.top Input, Opt. Topology file -mn dynamic.ndx Input, Opt. Index file 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 dynamic 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 -ddorder enum interleave DD node order: interleave, pp_pme or cartesian -npme int -1 Number of separate nodes to be used for PME, -1 is guess -nt int 0 Total number of threads to start (0 is guess) -ntmpi int 0 Number of thread-MPI threads to start (0 is guess) -ntomp int 0 Number of OpenMP threads per MPI process/thread to start (0 is guess) -ntomp_pme int 0 Number of OpenMP threads per MPI process/thread to start (0 is -ntomp) -pin enum auto Fix threads (or processes) to specific cores: auto, on or off -pinoffset int 0 The starting logical core number for pinning to cores; used to avoid pinning threads from different mdrun instances to the same core -pinstride int 0 Pinning distance in logical cores for threads, use 0 to minimize the number of threads per physical core -gpu_id string List of GPU device id-s to use, specifies the per-node PP rank to GPU mapping -[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 1.2 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 -nb enum auto Calculate non-bonded interactions on: auto, cpu, gpu or gpu_cpu -[no]tunepme bool yes Optimize PME load between PP/PME nodes or GPU/CPU -[no]testverlet bool no Test the Verlet non-bonded scheme -[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 -nsteps step -2 Run this number of steps, overrides .mdp file option -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 periodically with this period (steps) -nex int 0 Number of random exchanges to carry out each exchange interval (N^3 is one suggestion). -nex zero or not specified gives neighbor replica exchange. -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 dynamic.tpr, VERSION 4.6.5 (single precision) Reading checkpoint file dynamic.cpt generated: Wed Dec 31 16:56:34 2014 Using 32 MPI processes Non-default thread affinity set probably by the OpenMP library, disabling internal thread affinity WARNING: This run will generate roughly 2917 Mb of data starting mdrun 'Protein in a POPC bilayer' 250000000 steps, 5000000.0 ps (continuing from step 64893340, 1297866.8 ps). A list of missing interactions: G96Angle of 4249 missing 1 Molecule type 'POPC' the first 10 missing interactions, except for exclusions: G96Angle atoms 10 11 12 global 253 254 255 Back Off! I just backed up dd_dump_err_0_n18.pdb to ./#dd_dump_err_0_n18.pdb.1# Back Off! I just backed up dd_dump_err_0_n11.pdb to ./#dd_dump_err_0_n11.pdb.1# Back Off! I just backed up dd_dump_err_0_n23.pdb to ./#dd_dump_err_0_n23.pdb.1# Back Off! I just backed up dd_dump_err_0_n8.pdb to ./#dd_dump_err_0_n8.pdb.1# Back Off! I just backed up dd_dump_err_0_n29.pdb to ./#dd_dump_err_0_n29.pdb.1# Back Off! I just backed up dd_dump_err_0_n22.pdb to ./#dd_dump_err_0_n22.pdb.1# Back Off! I just backed up dd_dump_err_0_n28.pdb to ./#dd_dump_err_0_n28.pdb.1# Back Off! I just backed up dd_dump_err_0_n9.pdb to ./#dd_dump_err_0_n9.pdb.1# Back Off! I just backed up dd_dump_err_0_n12.pdb to ./#dd_dump_err_0_n12.pdb.1# Back Off! I just backed up dd_dump_err_0_n27.pdb to ./#dd_dump_err_0_n27.pdb.1# Back Off! I just backed up dd_dump_err_0_n13.pdb to ./#dd_dump_err_0_n13.pdb.1# Back Off! I just backed up dd_dump_err_0_n1.pdb to ./#dd_dump_err_0_n1.pdb.1# Back Off! I just backed up dd_dump_err_0_n7.pdb to ./#dd_dump_err_0_n7.pdb.1# Back Off! I just backed up dd_dump_err_0_n19.pdb to ./#dd_dump_err_0_n19.pdb.1# Back Off! I just backed up dd_dump_err_0_n4.pdb to ./#dd_dump_err_0_n4.pdb.1# Back Off! I just backed up dd_dump_err_0_n14.pdb to ./#dd_dump_err_0_n14.pdb.1# Back Off! I just backed up dd_dump_err_0_n0.pdb to ./#dd_dump_err_0_n0.pdb.1# Back Off! I just backed up dd_dump_err_0_n6.pdb to ./#dd_dump_err_0_n6.pdb.1# Back Off! I just backed up dd_dump_err_0_n24.pdb to ./#dd_dump_err_0_n24.pdb.1# Back Off! I just backed up dd_dump_err_0_n3.pdb to ./#dd_dump_err_0_n3.pdb.1# Back Off! I just backed up dd_dump_err_0_n26.pdb to ./#dd_dump_err_0_n26.pdb.1# Back Off! I just backed up dd_dump_err_0_n20.pdb to ./#dd_dump_err_0_n20.pdb.1# Back Off! I just backed up dd_dump_err_0_n25.pdb to ./#dd_dump_err_0_n25.pdb.1# Back Off! I just backed up dd_dump_err_0_n31.pdb to ./#dd_dump_err_0_n31.pdb.1# Back Off! I just backed up dd_dump_err_0_n10.pdb to ./#dd_dump_err_0_n10.pdb.1# Back Off! I just backed up dd_dump_err_0_n21.pdb to ./#dd_dump_err_0_n21.pdb.1# Back Off! I just backed up dd_dump_err_0_n30.pdb to ./#dd_dump_err_0_n30.pdb.1# Back Off! I just backed up dd_dump_err_0_n2.pdb to ./#dd_dump_err_0_n2.pdb.1# Back Off! I just backed up dd_dump_err_0_n17.pdb to ./#dd_dump_err_0_n17.pdb.1# Back Off! I just backed up dd_dump_err_0_n16.pdb to ./#dd_dump_err_0_n16.pdb.1# Back Off! I just backed up dd_dump_err_0_n15.pdb to ./#dd_dump_err_0_n15.pdb.1# Back Off! I just backed up dd_dump_err_0_n5.pdb to ./#dd_dump_err_0_n5.pdb.1# ------------------------------------------------------- Program mdrun_mpi, VERSION 4.6.5 Source code file: /work/aoltu/build/gromacs-4.6.5/src/mdlib/domdec_top.c, line: 393 Fatal error: 1 of the 16494 bonded interactions could not be calculated because some atoms involved moved further apart than the multi-body cut-off distance (1.2 nm) or the two-body cut-off distance (1.2 nm), see option -rdd, for pairs and tabulated bonds also see option -ddcheck For more information and tips for troubleshooting, please check the GROMACS website at http://www.gromacs.org/Documentation/Errors ------------------------------------------------------- "Have a Nice Day" (R. McDonald) Error on node 0, will try to stop all the nodes Halting parallel program mdrun_mpi on CPU 0 out of 32 gcq#177: "Have a Nice Day" (R. McDonald) Rank 0 [Wed Dec 31 23:02:28 2014] [c4-0c0s0n2] application called MPI_Abort(MPI_COMM_WORLD, -1) - process 0 _pmiu_daemon(SIGCHLD): [NID 00222] [c4-0c0s0n2] [Wed Dec 31 23:02:28 2014] PE RANK 0 exit signal Aborted [NID 00222] 2014-12-31 23:02:28 Apid 352395: initiated application termination