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@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.
Copyright (c) 1991-2000, University of Groningen, The Netherlands.
Copyright (c) 2001-2012,2013, The GROMACS development team at
Uppsala University & The Royal Institute of Technology, Sweden.
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 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.
:-) /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
jalem...@outerbanks.umaryland.edu | (410) 706-7441
http://mackerell.umaryland.edu/~jalemkul
==================================================
--
Gromacs Users mailing list
* Please search the archive at
http://www.gromacs.org/Support/Mailing_Lists/GMX-Users_List before posting!
* Can't post? Read http://www.gromacs.org/Support/Mailing_Lists
* For (un)subscribe requests visit
https://maillist.sys.kth.se/mailman/listinfo/gromacs.org_gmx-users or send a
mail to gmx-users-requ...@gromacs.org.
