:-) G R O M A C S (-: GROtesk MACabre and Sinister :-) 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 assemble.tpr Input Run input file: tpr tpb tpa -o assemble.trr Output Full precision trajectory: trr trj cpt -x assemble.xtc Output, Opt. Compressed trajectory (portable xdr format) -cpi assemble.cpt Input, Opt! Checkpoint file -cpo assemble.cpt Output, Opt. Checkpoint file -c assemble.gro Output Structure file: gro g96 pdb etc. -e assemble.edr Output Energy file -g assemble.log Output Log file -dhdl assemble.xvg Output, Opt. xvgr/xmgr file -field assemble.xvg Output, Opt. xvgr/xmgr file -table assemble.xvg Input, Opt. xvgr/xmgr file -tabletf assemble.xvg Input, Opt. xvgr/xmgr file -tablep assemble.xvg Input, Opt. xvgr/xmgr file -tableb assemble.xvg Input, Opt. xvgr/xmgr file -rerun assemble.xtc Input, Opt. Trajectory: xtc trr trj gro g96 pdb cpt -tpi assemble.xvg Output, Opt. xvgr/xmgr file -tpid assemble.xvg Output, Opt. xvgr/xmgr file -ei assemble.edi Input, Opt. ED sampling input -eo assemble.xvg Output, Opt. xvgr/xmgr file -j assemble.gct Input, Opt. General coupling stuff -jo assemble.gct Output, Opt. General coupling stuff -ffout assemble.xvg Output, Opt. xvgr/xmgr file -devout assemble.xvg Output, Opt. xvgr/xmgr file -runav assemble.xvg Output, Opt. xvgr/xmgr file -px assemble.xvg Output, Opt. xvgr/xmgr file -pf assemble.xvg Output, Opt. xvgr/xmgr file -ro assemble.xvg Output, Opt. xvgr/xmgr file -ra assemble.log Output, Opt. Log file -rs assemble.log Output, Opt. Log file -rt assemble.log Output, Opt. Log file -mtx assemble.mtx Output, Opt. Hessian matrix -dn assemble.ndx Output, Opt. Index file -multidir assemble Input, Opt., Mult. Run directory -membed assemble.dat Input, Opt. Generic data file -mp assemble.top Input, Opt. Topology file -mn assemble.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 assemble 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 assemble.tpr, VERSION 4.6.5 (single precision) The number of OpenMP threads was set by environment variable OMP_NUM_THREADS to 32 Reading checkpoint file assemble.cpt generated: Sun Dec 27 04:18:43 2015 #nodes mismatch, current program: 32 checkpoint file: 1 #PME-nodes mismatch, current program: -1 checkpoint file: 0 Gromacs binary or parallel settings not identical to previous run. Continuation is exact, but is not guaranteed to be binary identical. Using 32 MPI processes ------------------------------------------------------- Program mdrun_mpi, VERSION 4.6.5 Source code file: /work/aoltu/build/gromacs-4.6.5/src/kernel/runner.c, line: 911 Fatal error: OpenMP threads have been requested with cut-off scheme Group, but these are only supported with cut-off scheme Verlet For more information and tips for troubleshooting, please check the GROMACS website at http://www.gromacs.org/Documentation/Errors ------------------------------------------------------- "These are Ideas, They are Not Lies" (Magnapop) Error on node 25, will try to stop all the nodes Halting parallel program mdrun_mpi on CPU 25 out of 32 ------------------------------------------------------- Program mdrun_mpi, VERSION 4.6.5 Source code file: /work/aoltu/build/gromacs-4.6.5/src/kernel/runner.c, line: 911 Fatal error: OpenMP threads have been requested with cut-off scheme Group, but these are only supported with cut-off scheme Verlet For more information and tips for troubleshooting, please check the GROMACS website at http://www.gromacs.org/Documentation/Errors ------------------------------------------------------- "These are Ideas, They are Not Lies" (Magnapop) Error on node 1, will try to stop all the nodes Halting parallel program mdrun_mpi on CPU 1 out of 32 ------------------------------------------------------- Program mdrun_mpi, VERSION 4.6.5 Source code file: /work/aoltu/build/gromacs-4.6.5/src/kernel/runner.c, line: 911 Fatal error: OpenMP threads have been requested with cut-off scheme Group, but these are only supported with cut-off scheme Verlet For more information and tips for troubleshooting, please check the GROMACS website at http://www.gromacs.org/Documentation/Errors ------------------------------------------------------- "These are Ideas, They are Not Lies" (Magnapop) Error on node 15, will try to stop all the nodes Halting parallel program mdrun_mpi on CPU 15 out of 32 ------------------------------------------------------- Program mdrun_mpi, VERSION 4.6.5 Source code file: /work/aoltu/build/gromacs-4.6.5/src/kernel/runner.c, line: 911 Fatal error: OpenMP threads have been requested with cut-off scheme Group, but these are only supported with cut-off scheme Verlet For more information and tips for troubleshooting, please check the GROMACS website at http://www.gromacs.org/Documentation/Errors ------------------------------------------------------- "These are Ideas, They are Not Lies" (Magnapop) Error on node 14, will try to stop all the nodes Halting parallel program mdrun_mpi on CPU 14 out of 32 ------------------------------------------------------- Program mdrun_mpi, VERSION 4.6.5 Source code file: /work/aoltu/build/gromacs-4.6.5/src/kernel/runner.c, line: 911 Fatal error: OpenMP threads have been requested with cut-off scheme Group, but these are only supported with cut-off scheme Verlet For more information and tips for troubleshooting, please check the GROMACS website at http://www.gromacs.org/Documentation/Errors ------------------------------------------------------- "These are Ideas, They are Not Lies" (Magnapop) Error on node 10, will try to stop all the nodes Halting parallel program mdrun_mpi on CPU 10 out of 32 ------------------------------------------------------- Program mdrun_mpi, VERSION 4.6.5 Source code file: /work/aoltu/build/gromacs-4.6.5/src/kernel/runner.c, line: 911 Fatal error: OpenMP threads have been requested with cut-off scheme Group, but these are only supported with cut-off scheme Verlet For more information and tips for troubleshooting, please check the GROMACS website at http://www.gromacs.org/Documentation/Errors ------------------------------------------------------- "These are Ideas, They are Not Lies" (Magnapop) Error on node 30, will try to stop all the nodes Halting parallel program mdrun_mpi on CPU 30 out of 32 ------------------------------------------------------- Program mdrun_mpi, VERSION 4.6.5 Source code file: /work/aoltu/build/gromacs-4.6.5/src/kernel/runner.c, line: 911 Fatal error: OpenMP threads have been requested with cut-off scheme Group, but these are only supported with cut-off scheme Verlet For more information and tips for troubleshooting, please check the GROMACS website at http://www.gromacs.org/Documentation/Errors ------------------------------------------------------- "These are Ideas, They are Not Lies" (Magnapop) Error on node 31, will try to stop all the nodes Halting parallel program mdrun_mpi on CPU 31 out of 32 ------------------------------------------------------- Program mdrun_mpi, VERSION 4.6.5 Source code file: /work/aoltu/build/gromacs-4.6.5/src/kernel/runner.c, line: 911 Fatal error: OpenMP threads have been requested with cut-off scheme Group, but these are only supported with cut-off scheme Verlet For more information and tips for troubleshooting, please check the GROMACS website at http://www.gromacs.org/Documentation/Errors ------------------------------------------------------- "These are Ideas, They are Not Lies" (Magnapop) ------------------------------------------------------- Program mdrun_mpi, VERSION 4.6.5 Source code file: /work/aoltu/build/gromacs-4.6.5/src/kernel/runner.c, line: 911 Fatal error: OpenMP threads have been requested with cut-off scheme Group, but these are only supported with cut-off scheme Verlet For more information and tips for troubleshooting, please check the GROMACS website at http://www.gromacs.org/Documentation/Errors ------------------------------------------------------- "These are Ideas, They are Not Lies" (Magnapop) ------------------------------------------------------- Program mdrun_mpi, VERSION 4.6.5 Source code file: /work/aoltu/build/gromacs-4.6.5/src/kernel/runner.c, line: 911 Fatal error: OpenMP threads have been requested with cut-off scheme Group, but these are only supported with cut-off scheme Verlet For more information and tips for troubleshooting, please check the GROMACS website at http://www.gromacs.org/Documentation/Errors ------------------------------------------------------- "These are Ideas, They are Not Lies" (Magnapop) Error on node 13, will try to stop all the nodes Error on node 27, will try to stop all the nodes Error on node 26, will try to stop all the nodes Halting parallel program mdrun_mpi on CPU 27 out of 32 Halting parallel program mdrun_mpi on CPU 26 out of 32 ------------------------------------------------------- Program mdrun_mpi, VERSION 4.6.5 Source code file: /work/aoltu/build/gromacs-4.6.5/src/kernel/runner.c, line: 911 Fatal error: OpenMP threads have been requested with cut-off scheme Group, but these are only supported with cut-off scheme Verlet For more information and tips for troubleshooting, please check the GROMACS website at http://www.gromacs.org/Documentation/Errors ------------------------------------------------------- "These are Ideas, They are Not Lies" (Magnapop) ------------------------------------------------------- Program mdrun_mpi, VERSION 4.6.5 Source code file: /work/aoltu/build/gromacs-4.6.5/src/kernel/runner.c, line: 911 Fatal error: OpenMP threads have been requested with cut-off scheme Group, but these are only supported with cut-off scheme Verlet For more information and tips for troubleshooting, please check the GROMACS website at http://www.gromacs.org/Documentation/Errors ------------------------------------------------------- "These are Ideas, They are Not Lies" (Magnapop) Halting parallel program mdrun_mpi on CPU 13 out of 32 ------------------------------------------------------- Program mdrun_mpi, VERSION 4.6.5 Source code file: /work/aoltu/build/gromacs-4.6.5/src/kernel/runner.c, line: 911 Fatal error: OpenMP threads have been requested with cut-off scheme Group, but these are only supported with cut-off scheme Verlet For more information and tips for troubleshooting, please check the GROMACS website at http://www.gromacs.org/Documentation/Errors ------------------------------------------------------- "These are Ideas, They are Not Lies" (Magnapop) Error on node 5, will try to stop all the nodes Error on node 16, will try to stop all the nodes Error on node 19, will try to stop all the nodes Halting parallel program mdrun_mpi on CPU 5 out of 32 Halting parallel program mdrun_mpi on CPU 16 out of 32 Halting parallel program mdrun_mpi on CPU 19 out of 32 ------------------------------------------------------- Program mdrun_mpi, VERSION 4.6.5 Source code file: /work/aoltu/build/gromacs-4.6.5/src/kernel/runner.c, line: 911 Fatal error: OpenMP threads have been requested with cut-off scheme Group, but these are only supported with cut-off scheme Verlet For more information and tips for troubleshooting, please check the GROMACS website at http://www.gromacs.org/Documentation/Errors ------------------------------------------------------- "These are Ideas, They are Not Lies" (Magnapop) gcq#221: "These are Ideas, They are Not Lies" (Magnapop) Error on node 29, will try to stop all the nodes Halting parallel program mdrun_mpi on CPU 29 out of 32 ------------------------------------------------------- Program mdrun_mpi, VERSION 4.6.5 Source code file: /work/aoltu/build/gromacs-4.6.5/src/kernel/runner.c, line: 911 Fatal error: OpenMP threads have been requested with cut-off scheme Group, but these are only supported with cut-off scheme Verlet For more information and tips for troubleshooting, please check the GROMACS website at http://www.gromacs.org/Documentation/Errors ------------------------------------------------------- "These are Ideas, They are Not Lies" (Magnapop) Error on node 24, will try to stop all the nodes Halting parallel program mdrun_mpi on CPU 24 out of 32 ------------------------------------------------------- Program mdrun_mpi, VERSION 4.6.5 Source code file: /work/aoltu/build/gromacs-4.6.5/src/kernel/runner.c, line: 911 Fatal error: OpenMP threads have been requested with cut-off scheme Group, but these are only supported with cut-off scheme Verlet For more information and tips for troubleshooting, please check the GROMACS website at http://www.gromacs.org/Documentation/Errors ------------------------------------------------------- "These are Ideas, They are Not Lies" (Magnapop) ------------------------------------------------------- Program mdrun_mpi, VERSION 4.6.5 Source code file: /work/aoltu/build/gromacs-4.6.5/src/kernel/runner.c, line: 911 Fatal error: OpenMP threads have been requested with cut-off scheme Group, but these are only supported with cut-off scheme Verlet For more information and tips for troubleshooting, please check the GROMACS website at http://www.gromacs.org/Documentation/Errors ------------------------------------------------------- "These are Ideas, They are Not Lies" (Magnapop) Error on node 12, will try to stop all the nodes ------------------------------------------------------- Program mdrun_mpi, VERSION 4.6.5 Source code file: /work/aoltu/build/gromacs-4.6.5/src/kernel/runner.c, line: 911 Fatal error: OpenMP threads have been requested with cut-off scheme Group, but these are only supported with cut-off scheme Verlet For more information and tips for troubleshooting, please check the GROMACS website at http://www.gromacs.org/Documentation/Errors ------------------------------------------------------- "These are Ideas, They are Not Lies" (Magnapop) Halting parallel program mdrun_mpi on CPU 12 out of 32 Error on node 22, will try to stop all the nodes Error on node 6, will try to stop all the nodes Halting parallel program mdrun_mpi on CPU 22 out of 32 Halting parallel program mdrun_mpi on CPU 6 out of 32 Rank 14 [Sun Dec 27 10:38:50 2015] [c1-0c1s6n3] application called MPI_Abort(MPI_COMM_WORLD, -1) - process 14 ------------------------------------------------------- Program mdrun_mpi, VERSION 4.6.5 Source code file: /work/aoltu/build/gromacs-4.6.5/src/kernel/runner.c, line: 911 Fatal error: OpenMP threads have been requested with cut-off scheme Group, but these are only supported with cut-off scheme Verlet For more information and tips for troubleshooting, please check the GROMACS website at http://www.gromacs.org/Documentation/Errors ------------------------------------------------------- "These are Ideas, They are Not Lies" (Magnapop) Error on node 3, will try to stop all the nodes Halting parallel program mdrun_mpi on CPU 3 out of 32 ------------------------------------------------------- Program mdrun_mpi, VERSION 4.6.5 Source code file: /work/aoltu/build/gromacs-4.6.5/src/kernel/runner.c, line: 911 Fatal error: OpenMP threads have been requested with cut-off scheme Group, but these are only supported with cut-off scheme Verlet For more information and tips for troubleshooting, please check the GROMACS website at http://www.gromacs.org/Documentation/Errors ------------------------------------------------------- "These are Ideas, They are Not Lies" (Magnapop) Error on node 7, will try to stop all the nodes ------------------------------------------------------- Program mdrun_mpi, VERSION 4.6.5 Source code file: /work/aoltu/build/gromacs-4.6.5/src/kernel/runner.c, line: 911 Fatal error: OpenMP threads have been requested with cut-off scheme Group, but these are only supported with cut-off scheme Verlet For more information and tips for troubleshooting, please check the GROMACS website at http://www.gromacs.org/Documentation/Errors ------------------------------------------------------- "These are Ideas, They are Not Lies" (Magnapop) Halting parallel program mdrun_mpi on CPU 7 out of 32 Error on node 17, will try to stop all the nodes Halting parallel program mdrun_mpi on CPU 17 out of 32 ------------------------------------------------------- Program mdrun_mpi, VERSION 4.6.5 Source code file: /work/aoltu/build/gromacs-4.6.5/src/kernel/runner.c, line: 911 Fatal error: OpenMP threads have been requested with cut-off scheme Group, but these are only supported with cut-off scheme Verlet For more information and tips for troubleshooting, please check the GROMACS website at http://www.gromacs.org/Documentation/Errors ------------------------------------------------------- "These are Ideas, They are Not Lies" (Magnapop) Error on node 0, will try to stop all the nodes Halting parallel program mdrun_mpi on CPU 0 out of 32 ------------------------------------------------------- Program mdrun_mpi, VERSION 4.6.5 Source code file: /work/aoltu/build/gromacs-4.6.5/src/kernel/runner.c, line: 911 Fatal error: OpenMP threads have been requested with cut-off scheme Group, but these are only supported with cut-off scheme Verlet For more information and tips for troubleshooting, please check the GROMACS website at http://www.gromacs.org/Documentation/Errors ------------------------------------------------------- "These are Ideas, They are Not Lies" (Magnapop) Error on node 18, will try to stop all the nodes Halting parallel program mdrun_mpi on CPU 18 out of 32 ------------------------------------------------------- Program mdrun_mpi, VERSION 4.6.5 Source code file: /work/aoltu/build/gromacs-4.6.5/src/kernel/runner.c, line: 911 Fatal error: OpenMP threads have been requested with cut-off scheme Group, but these are only supported with cut-off scheme Verlet For more information and tips for troubleshooting, please check the GROMACS website at http://www.gromacs.org/Documentation/Errors ------------------------------------------------------- "These are Ideas, They are Not Lies" (Magnapop) Error on node 9, will try to stop all the nodes Halting parallel program mdrun_mpi on CPU 9 out of 32 ------------------------------------------------------- Program mdrun_mpi, VERSION 4.6.5 Source code file: /work/aoltu/build/gromacs-4.6.5/src/kernel/runner.c, line: 911 Fatal error: OpenMP threads have been requested with cut-off scheme Group, but these are only supported with cut-off scheme Verlet For more information and tips for troubleshooting, please check the GROMACS website at http://www.gromacs.org/Documentation/Errors ------------------------------------------------------- "These are Ideas, They are Not Lies" (Magnapop) Error on node 11, will try to stop all the nodes Halting parallel program mdrun_mpi on CPU 11 out of 32 _pmiu_daemon(SIGCHLD): [NID 01395] [c1-0c1s6n3] [Sun Dec 27 10:38:50 2015] PE RANK 14 exit signal Aborted gcq#221: "These are Ideas, They are Not Lies" (Magnapop) Rank 9 [Sun Dec 27 10:38:50 2015] [c1-0c1s6n3] application called MPI_Abort(MPI_COMM_WORLD, -1) - process 9 [NID 01395] 2015-12-27 10:38:50 Apid 5104028: initiated application termination