[gmx-users] genbox_mpi and "Error: Invalid number of threads defined"

[Justin Lemkul]

On 7/25/14, 11:20 AM, lswierczewski . wrote:
> Dear GROMACS Users,
>
> I have a problem when running genbox_mpi.
>
> Below is information from the console.
>
>
>
> [lswiercz at nostromo ~/gromacs]$ srun --nodes 1 genbox_mpi -cp
> 1AKI_newbox.gro -cs spc216.gro -p topol.top -o solvated.gro
> srun: job 5026 queued and waiting for resources
> srun: job 5026 has been allocated resources
>                           :-)  G  R  O  M  A  C  S  (-:
>
>              Georgetown Riga Oslo Madrid Amsterdam Chisinau Stockholm
>
>                              :-)  VERSION 4.6.3  (-:
>
>          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.
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>
>                    :-)  /opt/gromacs/4.6.3/bin/genbox_mpi  (-:
>
> Option     Filename  Type         Description
> ------------------------------------------------------------
>   -cp 1AKI_newbox.gro  Input, Opt!  Structure file: gro g96 pdb tpr etc.
>   -cs     spc216.gro  Input, Opt!, Lib. Structure file: gro g96 pdb tpr etc.
>   -ci     insert.gro  Input, Opt.  Structure file: gro g96 pdb tpr etc.
>    -o   solvated.gro  Output       Structure file: gro g96 pdb etc.
>    -p      topol.top  In/Out, Opt! Topology 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    19      Set the nicelevel
> -box         vector 0 0 0   Box size
> -nmol        int    0       Number of extra molecules to insert
> -try         int    10      Try inserting -nmol times -try times
> -seed        int    1997    Random generator seed
> -vdwd        real   0.105   Default van der Waals distance
> -shell       real   0       Thickness of optional water layer around solute
> -maxsol      int    0       Maximum number of solvent molecules to add if
>                              they fit in the box. If zero (default) this is
>                              ignored
> -[no]vel     bool   no      Keep velocities from input solute and solvent
>
> Reading solute configuration
> LYSOZYME
> Containing 2194 atoms in 207 residues
> Initialising van der waals distances...
>
> WARNING: Masses and atomic (Van der Waals) radii will be guessed
>           based on residue and atom names, since they could not be
>           definitively assigned from the information in your input
>           files. These guessed numbers might deviate from the mass
>           and radius of the atom type. Please check the output
>           files if necessary.
>
> Reading solvent configuration
> "216H2O,WATJP01,SPC216,SPC-MODEL,300K,BOX(M)=1.86206NM,WFVG,MAR. 1984"
> solvent configuration contains 648 atoms in 216 residues
>
> Initialising van der waals distances...
> Will generate new solvent configuration of 4x4x4 boxes
> Generating configuration
> Sorting configuration
> Found 1 molecule type:
>      SOL (   3 atoms): 13824 residues
> Calculating Overlap...
> box_margin = 0.315
> Removed 0 atoms that were outside the box
> 1587-119 Error: Invalid number of threads defined.
>
>
> Why does the system returns the "Error: Invalid number of threads defined"?
>

None of the tools are MPI-aware.  The error is probably a result of incorrect 
compilation.

-Justin

-- 
==================================================

Justin A. Lemkul, Ph.D.
Ruth L. Kirschstein NRSA Postdoctoral Fellow

Department of Pharmaceutical Sciences
School of Pharmacy
Health Sciences Facility II, Room 601
University of Maryland, Baltimore
20 Penn St.
Baltimore, MD 21201

jalemkul at outerbanks.umaryland.edu | (410) 706-7441
http://mackerell.umaryland.edu/~jalemkul

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