[gmx-users] do_dssp strange reaction
Justin Lemkul
jalemkul at vt.edu
Wed May 4 15:38:01 CEST 2016
On 5/4/16 9:20 AM, Chalaoux, Francois-Regis wrote:
> Hi everybody,
>
> Trying to use do_dssp_mpi for my MD I got an error described below.
> I gave "-ver 2" for dssp 2.0.4 but nothing changed.
>
> This is a real pain in the neck since a week to debug this message.
>
> Any tracks Guys ?
>
The usual tips are:
1. Don't compile analysis tools with MPI.
2. Verify that the dssp binary (not executed via do_dssp) actually works.
-Justin
> FRC
>
> Config:
> Linux Centos 6.7
> Gromacs mpi 5.04
>
> ==============
> CMD and Error
> ==============
> [fchalaoux at frtow0216 Complex3]$ do_dssp_mpi -f md_0_1.xtc -s md_0_1.tpr -sc scount.xvg -o ss.xpm -dt 10 -ver 2
> GROMACS: gmx do_dssp, VERSION 5.0.4
>
> GROMACS is written by:
> Emile Apol Rossen Apostolov Herman J.C. Berendsen Par Bjelkmar
> Aldert van Buuren Rudi van Drunen Anton Feenstra Sebastian Fritsch
> Gerrit Groenhof Christoph Junghans Peter Kasson Carsten Kutzner
> Per Larsson Justin A. Lemkul Magnus Lundborg Pieter Meulenhoff
> Erik Marklund Teemu Murtola Szilard Pall Sander Pronk
> Roland Schulz Alexey Shvetsov Michael Shirts Alfons Sijbers
> Peter Tieleman Christian Wennberg Maarten Wolf
> and the project leaders:
> Mark Abraham, Berk Hess, Erik Lindahl, and David van der Spoel
>
> Copyright (c) 1991-2000, University of Groningen, The Netherlands.
> Copyright (c) 2001-2014, The GROMACS development team at
> Uppsala University, Stockholm University and
> the Royal Institute of Technology, Sweden.
> check out http://www.gromacs.org for more information.
>
> GROMACS 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.
>
> GROMACS: gmx do_dssp, VERSION 5.0.4
> Executable: /site/tl/app/x86_64/discovery/academic/gromacs/5.0.4/icc-2015_mkl_openmpi-1.8.5_plumed-2.1.3-sp/bin/gmx_mpi
> Library dir: /site/tl/app/x86_64/discovery/academic/gromacs/5.0.4/icc-2015_mkl_openmpi-1.8.5_plumed-2.1.3-sp/share/gromacs/top
> Command line:
> do_dssp_mpi -f md_0_1.xtc -s md_0_1.tpr -sc scount.xvg -o ss.xpm -dt 10 -ver 2
>
> Reading file md_0_1.tpr, VERSION 5.0.4 (single precision)
> Reading file md_0_1.tpr, VERSION 5.0.4 (single precision)
> Group 0 ( System) has 47921 elements
> Group 1 ( Protein) has 2614 elements
> Group 2 ( Protein-H) has 1301 elements
> Group 3 ( C-alpha) has 163 elements
> Group 4 ( Backbone) has 489 elements
> Group 5 ( MainChain) has 653 elements
> Group 6 ( MainChain+Cb) has 805 elements
> Group 7 ( MainChain+H) has 815 elements
> Group 8 ( SideChain) has 1799 elements
> Group 9 ( SideChain-H) has 648 elements
> Group 10 ( Prot-Masses) has 2614 elements
> Group 11 ( non-Protein) has 45307 elements
> Group 12 ( Other) has 22 elements
> Group 13 ( JZ4) has 22 elements
> Group 14 ( CL) has 6 elements
> Group 15 ( Water) has 45279 elements
> Group 16 ( SOL) has 45279 elements
> Group 17 ( non-Water) has 2642 elements
> Group 18 ( Ion) has 6 elements
> Group 19 ( JZ4) has 22 elements
> Group 20 ( CL) has 6 elements
> Group 21 ( Water_and_ions) has 45285 elements
> Select a group: 5
> Selected 5: 'MainChain'
> There are 163 residues in your selected group
> dssp cmd='/site/tl/app/x86_64/discovery/dssp/2.0.4/bin -i ddEJhJwS -o ddllnW5z > /dev/null 2> /dev/null'
> Reading frame 0 time 0.000
> Back Off! I just backed up ddEJhJwS to ./#ddEJhJwS.1#
>
> -------------------------------------------------------
> Program do_dssp_mpi, VERSION 5.0.4
> Source code file: /site/tl/app/x86_64/discovery/academic/gromacs/5.0.4-src/gromacs-5.0.4/src/gromacs/gmxana/gmx_do_dssp.c, line: 670
>
> Fatal error:
> Failed to execute command: Try specifying your dssp version with the -ver option.
>
> For more information and tips for troubleshooting, please check the GROMACS
> website at http://www.gromacs.org/Documentation/Errors
> -------------------------------------------------------
>
> Halting program do_dssp_mpi
>
> gcq#48: "You Could Make More Money As a Butcher" (F. Zappa)
>
> --------------------------------------------------------------------------
> MPI_ABORT was invoked on rank 0 in communicator MPI_COMM_WORLD
> with errorcode -1.
>
> NOTE: invoking MPI_ABORT causes Open MPI to kill all MPI processes.
> You may or may not see output from other processes, depending on
> exactly when Open MPI kills them.
> --------------------------------------------------------------------------
>
--
==================================================
Justin A. Lemkul, Ph.D.
Ruth L. Kirschstein NRSA Postdoctoral Fellow
Department of Pharmaceutical Sciences
School of Pharmacy
Health Sciences Facility II, Room 629
University of Maryland, Baltimore
20 Penn St.
Baltimore, MD 21201
jalemkul at outerbanks.umaryland.edu | (410) 706-7441
http://mackerell.umaryland.edu/~jalemkul
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