[gmx-users] do_dssp strange reaction

[Justin Lemkul]

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

==================================================