When GROMACS with MPI is in use, plugin doe not start and following error is returned:
Detected OpenGL version 2.0 or greater. Shaders available.
Detected GLSL version 4.50.
OpenGL graphics engine:
GL_VENDOR: NVIDIA Corporation
GL_RENDERER: GeForce GT 630/PCIe/SSE2
GL_VERSION: 4.5.0 NVIDIA 375.82
Detected 16 CPU cores. Enabled multithreaded rendering.
Searching for GROMACS installation
Running command: gmx_mpi_d -version; STDIN: None; STDOUT: test_gromacs.txt
Found GROMACS VERSION 5.0.7
Reading available force fields and water models
Running command: gmx_mpi_d pdb2gmx -f test_gromacs.pdb -o test_gromacs.gro -p test_gromacs.top; STDIN: gromacs_stdin.txt; STDOUT: test_gromacs.txt
<type 'exceptions.IndexError'> Exception in Tk callback
Function: <function <lambda> at 0x7faee124cb90> (type: <type 'function'>)
Args: ()
Traceback (innermost last):
File "/usr/lib/python2.7/dist-packages/Pmw/Pmw_1_3/lib/PmwBase.py", line 1747, in __call__
return apply(self.func, args)
File "/usr/lib/python2.7/dist-packages/pmg_tk/startup/pymol_plugin_dynamics.py", line 867, in <lambda>
command = lambda: init_function(parent=self.root))
File "/usr/lib/python2.7/dist-packages/pmg_tk/startup/pymol_plugin_dynamics.py", line 1080, in init_function
gromacs = Gromacs_output()
File "/usr/lib/python2.7/dist-packages/pmg_tk/startup/pymol_plugin_dynamics.py", line 79, in __init__
self.init2()
File "/usr/lib/python2.7/dist-packages/pmg_tk/startup/pymol_plugin_dynamics.py", line 105, in init2
while lista_gromacs[force_start_line] != "Select the Force Field:\n":
<type 'exceptions.IndexError'>: list index out of range
test_gromacs.txt looks like:
GROMACS: gmx pdb2gmx, VERSION 5.0.7 (double precision)
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 pdb2gmx, VERSION 5.0.7 (double precision)
Executable: /usr/local/gromacs/bin/gmx_mpi_d
Library dir: /usr/local/gromacs/share/gromacs/top
Command line:
gmx_mpi_d pdb2gmx -f test_gromacs.pdb -o test_gromacs.gro -p test_gromacs.top
Opening force field file /usr/local/gromacs/share/gromacs/top/amber03.ff/watermodels.dat
1: TIP3P TIP 3-point, recommended
2: TIP4P TIP 4-point
3: TIP4P-Ew TIP 4-point optimized with Ewald
4: TIP5P TIP 5-point (see http://redmine.gromacs.org/issues/1348 for issues)
5: SPC simple point charge
6: SPC/E extended simple point charge
7: None
Opening force field file /usr/local/gromacs/share/gromacs/top/amber03.ff/aminoacids.r2b
Opening force field file /usr/local/gromacs/share/gromacs/top/amber03.ff/dna.r2b
Opening force field file /usr/local/gromacs/share/gromacs/top/amber03.ff/rna.r2b
All occupancies are one
Opening force field file /usr/local/gromacs/share/gromacs/top/amber03.ff/atomtypes.atp
Atomtype 1
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Opening force field file /usr/local/gromacs/share/gromacs/top/amber03.ff/aminoacids.rtp
Residue 1
Residue 2
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Sorting it all out...
Opening force field file /usr/local/gromacs/share/gromacs/top/amber03.ff/dna.rtp
Residue 94
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Sorting it all out...
Opening force field file /usr/local/gromacs/share/gromacs/top/amber03.ff/rna.rtp
Residue 110
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Sorting it all out...
Opening force field file /usr/local/gromacs/share/gromacs/top/amber03.ff/aminoacids.hdb
Opening force field file /usr/local/gromacs/share/gromacs/top/amber03.ff/dna.hdb
Opening force field file /usr/local/gromacs/share/gromacs/top/amber03.ff/rna.hdb
Opening force field file /usr/local/gromacs/share/gromacs/top/amber03.ff/aminoacids.n.tdb
Opening force field file /usr/local/gromacs/share/gromacs/top/amber03.ff/aminoacids.c.tdb
Back Off! I just backed up test_gromacs.top to ./#test_gromacs.top.1#
8 out of 8 lines of specbond.dat converted successfully
-------------------------------------------------------
Program gmx_mpi_d, VERSION 5.0.7
Source code file: /opt/gromacs-5.0.7/src/gromacs/gmxpreprocess/pdb2gmx.c, line: 317
Fatal error:
In the chosen force field there is no residue type for 'LYS' as a standalone (starting & ending) residue
For more information and tips for troubleshooting, please check the GROMACS
website at http://www.gromacs.org/Documentation/Errors
-------------------------------------------------------
Halting program gmx_mpi_d
gcq#288: "The Candlelight Was Just Right" (Beastie Boys)
--------------------------------------------------------------------------
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.
--------------------------------------------------------------------------
The error is conncted to MPI output at the end of the log. Both plugin version 2.2 and currect master are affected.
When GROMACS with MPI is in use, plugin doe not start and following error is returned:
test_gromacs.txt looks like:
The error is conncted to MPI output at the end of the log. Both plugin version 2.2 and currect master are affected.