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  • Michael
    replied
    So no other ideas then? I tried it on another box too and experienced the same failures.

    Leave a comment:


  • uncle_fungus
    replied
    Just installed afresh from the latest git code and all the tests work fine for me.

    Leave a comment:


  • uncle_fungus
    replied
    OK. I'll try it on a fresh install from git later on today.

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  • Michael
    replied
    Hmmm I still can't get it working for me. I've wiped out everything and did a fresh install, etc.

    Leave a comment:


  • uncle_fungus
    replied
    The tests all work for me.

    This is the problem:
    cd: 30: can't cd to /home/michael/pts-benchmark-env/md-gromacs/gmxbench/d.poly-ch2/
    It looks like the gmxbench-3.0.tar.gz isn't being extracted to the right place.

    Edit: I've tried it on another machine which is using the latest git code and it works fine too.
    Last edited by uncle_fungus; 05-07-2008, 02:24 PM. Reason: New info

    Leave a comment:


  • uncle_fungus
    replied
    Oh dear. I'm not sure what's broken that.

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  • Michael
    replied
    -------------------------------------------------------
    Program mdrun_single, VERSION 3.3.3
    Source code file: gmxfio.c, line: 706

    Can not open file:
    topol.tpr
    -------------------------------------------------------



    Err I've now tried it with all four and they all fail.

    Leave a comment:


  • Michael
    replied
    Poly-CH2 single threaded

    and it also occurs with the villin.

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  • uncle_fungus
    replied
    Which test did you try to run?

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  • Michael
    replied
    Pushed it into git, but it seems broken for at least the test I tried:

    -------------------------------------------------------
    Program grompp, VERSION 3.3.3
    Source code file: futil.c, line: 345

    File input/output error:
    grompp.mdp
    -------------------------------------------------------

    "Got Coffee, Got Donuts, Got Wasted" (F. Black)

    :-) G R O M A C S (-:

    God Rules Over Mankind, Animals, Cosmos and Such

    :-) VERSION 3.3.3 (-:


    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.

    :-) /home/michael/pts-benchmark-env/md-gromacs/gromacs333_/bin/mdrun_single (-:

    Option Filename Type Description
    ------------------------------------------------------------
    -s topol.tpr Input Generic run input: tpr tpb tpa xml
    -o traj.trr Output Full precision trajectory: trr trj
    -x traj.xtc Output, Opt. Compressed trajectory (portable xdr format)
    -c confout.gro Output Generic structure: gro g96 pdb xml
    -e ener.edr Output Generic energy: 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
    -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 no 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 md.log to ./#md.log.1#

    -------------------------------------------------------
    Program mdrun_single, VERSION 3.3.3
    Source code file: gmxfio.c, line: 706

    Can not open file:
    topol.tpr
    -------------------------------------------------------

    "Got Coffee, Got Donuts, Got Wasted" (F. Black)

    :-) G R O M A C S (-:

    God Rules Over Mankind, Animals, Cosmos and Such

    :-) VERSION 3.3.3 (-:


    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.

    :-) /home/michael/pts-benchmark-env/md-gromacs/gromacs333_/bin/grompp (-:

    creating statusfile for 1 node...
    d.dppc/
    d.dppc/conf.gro
    d.dppc/grompp.mdp
    d.dppc/topol.top
    d.lzm/
    d.lzm/conf.gro
    d.lzm/cutoff.mdp
    d.lzm/topol.top
    d.lzm/pme.mdp
    d.poly-ch2/
    d.poly-ch2/grompp.mdp
    d.poly-ch2/conf.gro
    d.poly-ch2/topol.top
    d.villin/
    d.villin/conf.gro
    d.villin/topol.top
    d.villin/grompp.mdp

    ====================================
    GROMACS MD Benchmark (Run 3 of 3)
    ====================================

    cd: 30: can't cd to /home/michael/pts-benchmark-env/md-gromacs/gmxbench/d.poly-ch2/
    Option Filename Type Description
    ------------------------------------------------------------
    -f grompp.mdp Input, Opt. grompp input file with MD parameters
    -po mdout.mdp Output grompp input file with MD parameters
    -c conf.gro Input Generic structure: gro g96 pdb tpr tpb tpa
    xml
    -r conf.gro Input, Opt. Generic structure: gro g96 pdb tpr tpb tpa
    xml
    -rb conf.gro Input, Opt. Generic structure: gro g96 pdb tpr tpb tpa
    xml
    -n index.ndx Input, Opt. Index file
    -deshuf deshuf.ndx Output, Opt. Index file
    -p topol.top Input Topology file
    -pp processed.top Output, Opt. Topology file
    -o topol.tpr Output Generic run input: tpr tpb tpa xml
    -t traj.trr Input, Opt. Full precision trajectory: trr trj
    -e ener.edr Input, Opt. Generic energy: edr ene

    Option Type Value Description
    ------------------------------------------------------
    -[no]h bool no Print help info and quit
    -nice int 0 Set the nicelevel
    -[no]v bool no Be loud and noisy
    -time real -1 Take frame at or first after this time.
    -np int 1 Generate statusfile for # nodes
    -[no]shuffle bool no Shuffle molecules over nodes
    -[no]sort bool no Sort molecules according to X coordinate
    -[no]rmvsbds bool yes Remove constant bonded interactions with virtual
    sites
    -load string Releative load capacity of each node on a
    parallel machine. Be sure to use quotes around
    the string, which should contain a number for
    each node
    -maxwarn int 10 Number of warnings after which input processing
    stops
    -[no]check14 bool no Remove 1-4 interactions without Van der Waals
    -[no]zero bool no Set parameters for bonded interactions without
    defaults to zero instead of generating an error
    -[no]renum bool yes Renumber atomtypes and minimize number of
    atomtypes


    -------------------------------------------------------
    Program grompp, VERSION 3.3.3
    Source code file: futil.c, line: 345

    File input/output error:
    grompp.mdp
    -------------------------------------------------------

    Leave a comment:

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