NNODES=1, MYRANK=0, HOSTNAME=lilligrid.na.iac.cnr.it :-) G R O M A C S (-: Gromacs Runs One Microsecond At Cannonball Speeds :-) VERSION 3.3.1 (-: Written by David van der Spoel, Erik Lindahl, Berk Hess, and others. Copyright (c) 1991-2000, University of Groningen, The Netherlands. Copyright (c) 2001-2006, 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. :-) mdrun (-: NNODES=1, MYRANK=0, HOSTNAME=lilligrid.na.iac.cnr.it :-) G R O M A C S (-: Gromacs Runs One Microsecond At Cannonball Speeds :-) VERSION 3.3.1 (-: Written by David van der Spoel, Erik Lindahl, Berk Hess, and others. Copyright (c) 1991-2000, University of Groningen, The Netherlands. Copyright (c) 2001-2006, 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. :-) mdrun (-: Option Filename Type Description ------------------------------------------------------------ -s full.tpr Input Generic run input: tpr tpb tpa xml -o full.trr Output Full precision trajectory: trr trj -x traj.xtc Output, Opt. Compressed trajectory (portable xdr format) -c after_full.gro Output Generic structure: gro g96 pdb xml -e full.edr Output Generic energy: edr ene -g flog.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 -rerun rerun.xtc Input, Opt. Generic trajectory: xtc trr trj gro g96 pdb -tpi tpi.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 -pi pull.ppa Input, Opt. Pull parameters -po pullout.ppa Output, Opt. Pull parameters -pd pull.pdo Output, Opt. Pull data output -pn pull.ndx Input, Opt. Index 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 19 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 -np int 1 Number of nodes, must be the same as used for grompp -nt int 1 Number of threads to start on each node -[no]v bool yes Be loud and noisy -[no]compact bool yes Write a compact log file -[no]sepdvdl bool no Write separate V and dVdl terms for each interaction type and node to the log file(s) -[no]multi bool no Do multiple simulations in parallel (only with -np > 1) -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 full.tpr, VERSION 3.3.1 (single precision) NNODES=1, MYRANK=0, HOSTNAME=lilligrid2.local :-) G R O M A C S (-: NNODES=1, MYRANK=0, HOSTNAME=lilligrid2.local :-) G R O M A C S (-: Gromacs Runs One Microsecond At Cannonball Speeds :-) VERSION 3.3.1 (-: Written by David van der Spoel, Erik Lindahl, Berk Hess, and others. Copyright (c) 1991-2000, University of Groningen, The Netherlands. Copyright (c) 2001-2006, 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. :-) mdrun (-: Gromacs Runs One Microsecond At Cannonball Speeds :-) VERSION 3.3.1 (-: Written by David van der Spoel, Erik Lindahl, Berk Hess, and others. Copyright (c) 1991-2000, University of Groningen, The Netherlands. Copyright (c) 2001-2006, 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. :-) mdrun (-: NNODES=1, MYRANK=0, HOSTNAME=lilligrid3.local :-) G R O M A C S (-: NNODES=1, MYRANK=0, HOSTNAME=lilligrid3.local NNODES=1, MYRANK=0, HOSTNAME=lilligrid4.local :-) G R O M A C S (-: Gromacs Runs One Microsecond At Cannonball Speeds :-) VERSION 3.3.1 (-: Written by David van der Spoel, Erik Lindahl, Berk Hess, and others. Copyright (c) 1991-2000, University of Groningen, The Netherlands. Copyright (c) 2001-2006, 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 NNODES=1, MYRANK=0, HOSTNAME=lilligrid4.local of the License, or (at your option) any later version. :-) G R O M A C S (-: :-) mdrun (-: Gromacs Runs One Microsecond At Cannonball Speeds :-) VERSION 3.3.1 (-: Written by David van der Spoel, Erik Lindahl, Berk Hess, and others. Copyright (c) 1991-2000, University of Groningen, The Netherlands. Copyright (c) 2001-2006, 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. :-) mdrun (-: Option Filename Type Description ------------------------------------------------------------ -s full.tpr Input Generic run input: tpr tpb tpa xml -o full.trr Output Full precision trajectory: trr trj -x traj.xtc Output, Opt. Compressed trajectory (portable xdr format) -c after_full.gro Output Generic structure: gro g96 pdb xml -e full.edr Output Generic energy: edr ene -g flog.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 -rerun rerun.xtc Input, Opt. Generic trajectory: xtc trr trj gro g96 pdb -tpi tpi.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 -pi pull.ppa Input, Opt. Pull parameters -po pullout.ppa Output, Opt. Pull parameters -pd pull.pdo Output, Opt. Pull data output -pn pull.ndx Input, Opt. Index 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 19 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 -np int 1 Number of nodes, must be the same as used for grompp -nt int 1 Number of threads to start on each node -[no]v bool yes Be loud and noisy -[no]compact bool yes Write a compact log file -[no]sepdvdl bool no Write separate V and dVdl terms for each interaction type and node to the log file(s) -[no]multi bool no Do multiple simulations in parallel (only with -np > 1) -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 Option Filename Type Description ------------------------------------------------------------ -s full.tpr Input Generic run input: tpr tpb tpa xml -o full.trr Output Full precision trajectory: trr trj -x traj.xtc Output, Opt. Compressed trajectory (portable xdr format) -c after_full.gro Output Generic structure: gro g96 pdb xml -e full.edr Output Generic energy: edr ene -g flog.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 -rerun rerun.xtc Input, Opt. Generic trajectory: xtc trr trj gro g96 pdb -tpi tpi.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 -pi pull.ppa Input, Opt. Pull parameters -po pullout.ppa Output, Opt. Pull parameters -pd pull.pdo Output, Opt. Pull data output -pn pull.ndx Input, Opt. Index 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 19 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 -np int 1 Number of nodes, must be the same as used for grompp -nt int 1 Number of threads to start on each node -[no]v bool yes Be loud and noisy -[no]compact bool yes Write a compact log file -[no]sepdvdl bool no Write separate V and dVdl terms for each interaction type and node to the log file(s) -[no]multi bool no Do multiple simulations in parallel (only with -np > 1) -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 NNODES=1, MYRANK=0, HOSTNAME=lilligrid5.local :-) G R O M A C S (-: -[no]ionize bool no Do a simulation including the effect of an X-Ray bombardment on your system Back Off! I just backed up flog.log to ./#flog.log.1# Getting Loaded... Gromacs Runs One Microsecond At Cannonball Speeds :-) VERSION 3.3.1 (-: Written by David van der Spoel, Erik Lindahl, Berk Hess, and others. Copyright (c) 1991-2000, University of Groningen, The Netherlands. Copyright (c) 2001-2006, 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. :-) mdrun (-: NNODES=1, MYRANK=0, HOSTNAME=lilligrid5.local :-) G R O M A C S (-: Option Filename Type Description Option Filename Type Description ------------------------------------------------------------ -s full.tpr Input Generic run input: tpr tpb tpa xml -o full.trr Output Full precision trajectory: trr trj -x traj.xtc Output, Opt. Compressed trajectory (portable xdr format) -c after_full.gro Output Generic structure: gro g96 pdb xml -e full.edr Output Generic energy: edr ene -g flog.log Output Log file -dgdl dgdl.xvg Output, Opt. xvgr/xmgr file Gromacs Runs One Microsecond At Cannonball Speeds :-) VERSION 3.3.1 (-: -field field.xvg Output, Opt. xvgr/xmgr file -table table.xvg Input, Opt. xvgr/xmgr file -tablep tablep.xvg Input, Opt. xvgr/xmgr file -rerun rerun.xtc Input, Opt. Generic trajectory: xtc trr trj gro g96 pdb -tpi tpi.xvg Output, Opt. xvgr/xmgr file -ei sam.edi Input, Opt. ED sampling input Written by David van der Spoel, Erik Lindahl, Berk Hess, and others. Copyright (c) 1991-2000, University of Groningen, The Netherlands. Copyright (c) 2001-2006, 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. :-) mdrun (-: -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 -pi pull.ppa Input, Opt. Pull parameters -po pullout.ppa Output, Opt. Pull parameters -pd pull.pdo Output, Opt. Pull data output -pn pull.ndx Input, Opt. Index 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 19 Set the nicelevel -deffnm string Set the default filename for all file options Reading file full.tpr, VERSION 3.3.1 (single precision) ------------------------------------------------------------ -[no]xvgr bool yes Add specific codes (legends etc.) in the output xvg files for the xmgrace program -np int 1 Number of nodes, must be the same as used for grompp -nt int 1 Number of threads to start on each node -[no]v bool yes Be loud and noisy -[no]compact bool yes Write a compact log file -[no]sepdvdl bool no Write separate V and dVdl terms for each interaction type and node to the log file(s) -[no]multi bool no Do multiple simulations in parallel (only with -np > 1) -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 -s full.tpr Input Generic run input: tpr tpb tpa xml -o full.trr Output Full precision trajectory: trr trj -x traj.xtc Output, Opt. Compressed trajectory (portable xdr format) -c after_full.gro Output Generic structure: gro g96 pdb xml -e full.edr Output Generic energy: edr ene -g flog.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 -rerun rerun.xtc Input, Opt. Generic trajectory: xtc trr trj gro g96 pdb -tpi tpi.xvg Output, Opt. xvgr/xmgr file -ei sam.edi Input, Opt. ED sampling input -eo sam.edo Output, Opt. ED sampling output ------------------------------------------------------- Program mdrun, VERSION 3.3.1 Source code file: init.c, line: 69 Fatal error: run input file full.tpr was made for 10 nodes, while mdrun expected it to be for 1 nodes. ------------------------------------------------------- "The Candlelight Was Just Right" (Beastie Boys) Halting program mdrun gcq#302: "The Candlelight Was Just Right" (Beastie Boys) [0] MPI Abort by user Aborting program ! [0] Aborting program! p4_error: latest msg from perror: No such file or directory p0_32408: p4_error: : -1 -j wham.gct Input, Opt. General coupling stuff -jo bam.gct Output, Opt. General coupling stuff -ffout gct.xvg Output, Opt. xvgr/xmgr file ----------------------------------------------------------------------------- It seems that [at least] one of the processes that was started with mpirun did not invoke MPI_INIT before quitting (it is possible that more than one process did not invoke MPI_INIT -- mpirun was only notified of the first one, which was on node n0). mpirun can *only* be used with MPI programs (i.e., programs that invoke MPI_INIT and MPI_FINALIZE). You can use the "lamexec" program to run non-MPI programs over the lambooted nodes. ----------------------------------------------------------------------------- p0_32409: p4_error: interrupt SIGx: 15 -devout deviatie.xvg Output, Opt. xvgr/xmgr file -runav runaver.xvg Output, Opt. xvgr/xmgr file p0_6670: p4_error: interrupt SIGx: 15 -pi pull.ppa Input, Opt. Pull parameters -po pullout.ppa Output, Opt. Pull parameters -pd pull.pdo Output, Opt. Pull data output -pn pull.ndx Input, Opt. Index 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 19 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 -np int 1 Number of nodes, must be the same as used for grompp -nt int 1 Number of threads to start on each node -[no]v bool yes Be loud and noisy -[no]compact bool yes Write a compact log file -[no]sepdvdl bool no Write separate V and dVdl terms for each interaction type and node to the log file(s) -[no]multi bool no Do multiple simulations in parallel (only with -np > 1) -replex int 0 Attempt replica exchange every # steps p0_6669: p4_error: interrupt SIGx: 15 Option Filename Type Description ------------------------------------------------------------ -s full.tpr Input Generic run input: tpr tpb tpa xml -o full.trr Output Full precision trajectory: trr trj -x traj.xtc Output, Opt. Compressed trajectory (portable xdr format) -c after_full.gro Output Generic structure: gro g96 pdb xml -e full.edr Output Generic energy: edr ene -g flog.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 -rerun rerun.xtc Input, Opt. Generic trajectory: xtc trr trj gro g96 pdb -tpi tpi.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 -pi pull.ppa Input, Opt. Pull parameters -po pullout.ppa Output, Opt. Pull parameters -pd pull.pdo Output, Opt. Pull data output -pn pull.ndx Input, Opt. Index 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 19 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 -np int 1 Number of nodes, must be the same as used for grompp -nt int 1 Number of threads to start on each node -[no]v bool yes Be loud and noisy -[no]compact bool yes Write a compact log file -[no]sepdvdl bool no Write separate V and dVdl terms for each interaction type and node to the log file(s) -[no]multi bool no Do multiple simulations in parallel (only with -np > 1) -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 Option Filename Type Description ------------------------------------------------------------ -s full.tpr Input Generic run input: tpr tpb tpa xml -o full.trr Output Full precision trajectory: trr trj -x traj.xtc Output, Opt. Compressed trajectory (portable xdr format) -c after_full.gro Output Generic structure: gro g96 pdb xml -e full.edr Output Generic energy: edr ene -g flog.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 -rerun rerun.xtc Input, Opt. Generic trajectory: xtc trr trj gro g96 pdb -tpi tpi.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 -pi pull.ppa Input, Opt. Pull parameters -po pullout.ppa Output, Opt. Pull parameters -pd pull.pdo Output, Opt. Pull data output -pn pull.ndx Input, Opt. Index 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 19 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 -np int 1 Number of nodes, must be the same as used for grompp -nt int 1 Number of threads to start on each node -[no]v bool yes Be loud and noisy -[no]compact bool yes Write a compact log file -[no]sepdvdl bool no Write separate V and dVdl terms for each interaction type and node to the log file(s) -[no]multi bool no Do multiple simulations in parallel (only with -np > 1) -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 flog.log to ./#flog.log.3# Getting Loaded... Reading file full.tpr, VERSION 3.3.1 (single precision) Back Off! I just backed up flog.log to ./#flog.log.3# Getting Loaded... Reading file full.tpr, VERSION 3.3.1 (single precision) ------------------------------------------------------- Program mdrun, VERSION 3.3.1 Source code file: init.c, line: 69 Fatal error: run input file full.tpr was made for 10 nodes, while mdrun expected it to be for 1 nodes. ------------------------------------------------------- "The Candlelight Was Just Right" (Beastie Boys) Halting program mdrun gcq#302: "The Candlelight Was Just Right" (Beastie Boys) [0] MPI Abort by user Aborting program ! [0] Aborting program! p4_error: latest msg from perror: No such file or directory p0_5157: p4_error: : -1 ------------------------------------------------------- Program mdrun, VERSION 3.3.1 Source code file: init.c, line: 69 Fatal error: run input file full.tpr was made for 10 nodes, while mdrun expected it to be for 1 nodes. ------------------------------------------------------- "The Candlelight Was Just Right" (Beastie Boys) Halting program mdrun gcq#302: "The Candlelight Was Just Right" (Beastie Boys) [0] MPI Abort by user Aborting program ! [0] Aborting program! p4_error: latest msg from perror: No such file or directory p0_5156: p4_error: : -1 :-) G R O M A C S (-: Gromacs Runs One Microsecond At Cannonball Speeds :-) VERSION 3.3.1 (-: Written by David van der Spoel, Erik Lindahl, Berk Hess, and others. Copyright (c) 1991-2000, University of Groningen, The Netherlands. Copyright (c) 2001-2006, 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. :-) mdrun (-: Gromacs Runs One Microsecond At Cannonball Speeds :-) VERSION 3.3.1 (-: Written by David van der Spoel, Erik Lindahl, Berk Hess, and others. Copyright (c) 1991-2000, University of Groningen, The Netherlands. Copyright (c) 2001-2006, 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. :-) mdrun (-: Option Filename Type Description ------------------------------------------------------------ -s full.tpr Input Generic run input: tpr tpb tpa xml -o full.trr Output Full precision trajectory: trr trj -x traj.xtc Output, Opt. Compressed trajectory (portable xdr format) -c after_full.gro Output Generic structure: gro g96 pdb xml -e full.edr Output Generic energy: edr ene -g flog.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 -rerun rerun.xtc Input, Opt. Generic trajectory: xtc trr trj gro g96 pdb -tpi tpi.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 -pi pull.ppa Input, Opt. Pull parameters -po pullout.ppa Output, Opt. Pull parameters -pd pull.pdo Output, Opt. Pull data output -pn pull.ndx Input, Opt. Index 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 19 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 -np int 1 Number of nodes, must be the same as used for grompp -nt int 1 Number of threads to start on each node -[no]v bool yes Be loud and noisy -[no]compact bool yes Write a compact log file -[no]sepdvdl bool no Write separate V and dVdl terms for each interaction type and node to the log file(s) -[no]multi bool no Do multiple simulations in parallel (only with -np > 1) -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 Option Filename Type Description ------------------------------------------------------------ -s full.tpr Input Generic run input: tpr tpb tpa xml -o full.trr Output Full precision trajectory: trr trj -x traj.xtc Output, Opt. Compressed trajectory (portable xdr format) -c after_full.gro Output Generic structure: gro g96 pdb xml -e full.edr Output Generic energy: edr ene -g flog.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 -rerun rerun.xtc Input, Opt. Generic trajectory: xtc trr trj gro g96 pdb -tpi tpi.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 -pi pull.ppa Input, Opt. Pull parameters -po pullout.ppa Output, Opt. Pull parameters -pd pull.pdo Output, Opt. Pull data output -pn pull.ndx Input, Opt. Index 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 19 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 -np int 1 Number of nodes, must be the same as used for grompp -nt int 1 Number of threads to start on each node -[no]v bool yes Be loud and noisy -[no]compact bool yes Write a compact log file -[no]sepdvdl bool no Write separate V and dVdl terms for each interaction type and node to the log file(s) -[no]multi bool no Do multiple simulations in parallel (only with -np > 1) -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 flog.log to ./#flog.log.2# p0_5728: p4_error: interrupt SIGx: 15 Sorry couldn't backup flog.log to ./#flog.log.2# Getting Loaded... Reading file full.tpr, VERSION 3.3.1 (single precision) ------------------------------------------------------- Program mdrun, VERSION 3.3.1 Source code file: init.c, line: 69 Fatal error: run input file full.tpr was made for 10 nodes, while mdrun expected it to be for 1 nodes. ------------------------------------------------------- "The Candlelight Was Just Right" (Beastie Boys) Halting program mdrun gcq#302: "The Candlelight Was Just Right" (Beastie Boys) [0] MPI Abort by user Aborting program ! [0] Aborting program! p4_error: latest msg from perror: No such file or directory p0_5729: p4_error: : -1 -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 Sorry couldn't backup flog.log to ./#flog.log.2# Sorry couldn't backup flog.log to ./#flog.log.2# Getting Loaded... Reading file full.tpr, VERSION 3.3.1 (single precision) ------------------------------------------------------- Program mdrun, VERSION 3.3.1 Source code file: init.c, line: 69 Fatal error: run input file full.tpr was made for 10 nodes, while mdrun expected it to be for 1 nodes. ------------------------------------------------------- "The Candlelight Was Just Right" (Beastie Boys) Halting program mdrun Getting Loaded... gcq#302: "The Candlelight Was Just Right" (Beastie Boys) [0] MPI Abort by user Aborting program ! [0] Aborting program! p4_error: latest msg from perror: No such file or directory p0_5521: p4_error: : -1 Reading file full.tpr, VERSION 3.3.1 (single precision) ------------------------------------------------------- Program mdrun, VERSION 3.3.1 Source code file: init.c, line: 69 Fatal error: run input file full.tpr was made for 10 nodes, while mdrun expected it to be for 1 nodes. ------------------------------------------------------- "The Candlelight Was Just Right" (Beastie Boys) Halting program mdrun gcq#302: "The Candlelight Was Just Right" (Beastie Boys) [0] MPI Abort by user Aborting program ! [0] Aborting program! p4_error: latest msg from perror: No such file or directory p0_5520: p4_error: : -1