[gmx-users] Gromacs 2020 fails to run adh_cubic_vsites
Rolly Ng
rollyng at gmail.com
Sat Mar 7 17:04:46 CET 2020
Dear Gromacs developers,
I am new to Gromacs and I have recently compiled Gromacs 2020.
I tried to run the ADH benchmarks from
ftp://ftp.gromacs.org/pub/benchmarks/ADH_bench_systems.tar.gz
The adh_cubic and adh_dodec completed successfully, but the adh_cubic_vsites
and adh_dodec_vsites failed at grompp.
Could you please have a look at the following output log?
Thanks,
Rolly Ng
PhD, Former Research Fellow,
Department of Materials Science and Engineering
City University of Hong Kong
:-) GROMACS - gmx grompp, 2020-UNCHECKED (-:
GROMACS is written by:
Emile Apol Rossen Apostolov Paul Bauer Herman J.C.
Berendsen
Par Bjelkmar Christian Blau Viacheslav Bolnykh Kevin Boyd
Aldert van Buuren Rudi van Drunen Anton Feenstra Alan Gray
Gerrit Groenhof Anca Hamuraru Vincent Hindriksen M. Eric Irrgang
Aleksei Iupinov Christoph Junghans Joe Jordan Dimitrios
Karkoulis
Peter Kasson Jiri Kraus Carsten Kutzner Per Larsson
Justin A. Lemkul Viveca Lindahl Magnus Lundborg Erik Marklund
Pascal Merz Pieter Meulenhoff Teemu Murtola Szilard Pall
Sander Pronk Roland Schulz Michael Shirts Alexey Shvetsov
Alfons Sijbers Peter Tieleman Jon Vincent Teemu Virolainen
Christian Wennberg Maarten Wolf Artem Zhmurov
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) 2001-2019, 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 grompp, version 2020-UNCHECKED
Executable: /home/rolly/Gromacs/gromacs-2020/install/bin/gmx_mpi
Data prefix: /home/rolly/Gromacs/gromacs-2020/install
Working dir: /home/rolly/Gromacs/ADH_bench/adh_cubic_vsites
Command line:
gmx_mpi grompp -f pme_verlet_vsites.mdp -c conf.gro -p topol.top
Ignoring obsolete mdp entry 'ns_type'
Replacing old mdp entry 'nstxtcout' by 'nstxout-compressed'
Setting the LD random seed to -1974193353
Generated 2145 of the 2145 non-bonded parameter combinations
Generating 1-4 interactions: fudge = 0.5
Generated 2145 of the 2145 1-4 parameter combinations
Excluding 3 bonded neighbours molecule type 'Protein_chain_A'
turning all bonds into constraints...
Excluding 3 bonded neighbours molecule type 'Protein_chain_B'
turning all bonds into constraints...
Excluding 3 bonded neighbours molecule type 'Protein_chain_C'
turning all bonds into constraints...
Excluding 3 bonded neighbours molecule type 'Protein_chain_D'
turning all bonds into constraints...
Excluding 2 bonded neighbours molecule type 'SOL'
turning all bonds into constraints...
Excluding 2 bonded neighbours molecule type 'SOL'
Excluding 2 bonded neighbours molecule type 'SOL'
Excluding 2 bonded neighbours molecule type 'SOL'
Excluding 2 bonded neighbours molecule type 'SOL'
Excluding 1 bonded neighbours molecule type 'NA'
turning all bonds into constraints...
WARNING 1 [file topol.top, line 55]:
The following macros were defined in the 'define' mdp field with the -D
prefix, but were not used in the topology:
VSITE
If you haven't made a spelling error, either use the macro you defined,
or don't define the macro
Cleaning up constraints and constant bonded interactions with virtual sites
Removed 1683 Angles with virtual sites, 8136 left
Removed 1587 Proper Dih.s with virtual sites, 16689 left
Converted 2918 Constraints with virtual sites to connections, 2473 left
Warning: removed 896 Constraints with vsite with Virtual site 3out
construction
This vsite construction does not guarantee constant bond-length
If the constructions were generated by pdb2gmx ignore this warning
Cleaning up constraints and constant bonded interactions with virtual sites
Removed 1683 Angles with virtual sites, 8136 left
Removed 1587 Proper Dih.s with virtual sites, 16689 left
Converted 2918 Constraints with virtual sites to connections, 2473 left
Warning: removed 896 Constraints with vsite with Virtual site 3out
construction
This vsite construction does not guarantee constant bond-length
If the constructions were generated by pdb2gmx ignore this warning
Cleaning up constraints and constant bonded interactions with virtual sites
Removed 1683 Angles with virtual sites, 8136 left
Removed 1587 Proper Dih.s with virtual sites, 16689 left
Converted 2918 Constraints with virtual sites to connections, 2473 left
Warning: removed 896 Constraints with vsite with Virtual site 3out
construction
This vsite construction does not guarantee constant bond-length
If the constructions were generated by pdb2gmx ignore this warning
Cleaning up constraints and constant bonded interactions with virtual sites
Removed 1683 Angles with virtual sites, 8136 left
Removed 1587 Proper Dih.s with virtual sites, 16689 left
Converted 2918 Constraints with virtual sites to connections, 2473 left
Warning: removed 896 Constraints with vsite with Virtual site 3out
construction
This vsite construction does not guarantee constant bond-length
If the constructions were generated by pdb2gmx ignore this warning
Analysing residue names:
There are: 1408 Protein residues
There are: 37600 Water residues
There are: 12 Ion residues
Analysing Protein...
Analysing residues not classified as Protein/DNA/RNA/Water and splitting
into groups...
Number of degrees of freedom in T-Coupling group System is 247713.00
Determining Verlet buffer for a tolerance of 0.005 kJ/mol/ps at 300 K
NOTE 1 [file pme_verlet_vsites.mdp]:
There are 9592 non-linear virtual site constructions. Their contribution
to the energy error is approximated. In most cases this does not affect
the error significantly.
Calculated rlist for 1x1 atom pair-list as 1.013 nm, buffer size 0.113 nm
Set rlist, assuming 4x4 atom pair-list, to 0.935 nm, buffer size 0.035 nm
Note that mdrun will redetermine rlist based on the actual pair-list setup
Calculating fourier grid dimensions for X Y Z
Using a fourier grid of 100x100x100, spacing 0.110 0.110 0.110
Estimate for the relative computational load of the PME mesh part: 0.28
This run will generate roughly 10 Mb of data
There was 1 note
There was 1 warning
-------------------------------------------------------
Program: gmx grompp, version 2020-UNCHECKED
Source file: src/gromacs/gmxpreprocess/grompp.cpp (line 2352)
Fatal error:
Too many warnings (1).
If you are sure all warnings are harmless, use the -maxwarn option.
For more information and tips for troubleshooting, please check the GROMACS
website at http://www.gromacs.org/Documentation/Errors
-------------------------------------------------------
application called MPI_Abort(MPI_COMM_WORLD, 1) - process 0
[unset]: write_line error; fd=-1 buf=:cmd=abort exitcode=1
:
system msg for write_line failure : Bad file descriptor
:-) GROMACS - gmx mdrun, 2020-UNCHECKED (-:
GROMACS is written by:
Emile Apol Rossen Apostolov Paul Bauer Herman J.C.
Berendsen
Par Bjelkmar Christian Blau Viacheslav Bolnykh Kevin Boyd
Aldert van Buuren Rudi van Drunen Anton Feenstra Alan Gray
Gerrit Groenhof Anca Hamuraru Vincent Hindriksen M. Eric Irrgang
Aleksei Iupinov Christoph Junghans Joe Jordan Dimitrios
Karkoulis
Peter Kasson Jiri Kraus Carsten Kutzner Per Larsson
Justin A. Lemkul Viveca Lindahl Magnus Lundborg Erik Marklund
Pascal Merz Pieter Meulenhoff Teemu Murtola Szilard Pall
Sander Pronk Roland Schulz Michael Shirts Alexey Shvetsov
Alfons Sijbers Peter Tieleman Jon Vincent Teemu Virolainen
Christian Wennberg Maarten Wolf Artem Zhmurov
and the project leaders:
srun: Job step aborted: Waiting up to 32 seconds for job step to finish.
Mark Abraham, Berk Hess, Erik Lindahl, and David van der Spoel
Copyright (c) 1991-2000, University of Groningen, The Netherlands.
Copyright (c) 2001-2019, 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 mdrun, version 2020-UNCHECKED
Executable: /home/rolly/Gromacs/gromacs-2020/install/bin/gmx_mpi
Data prefix: /home/rolly/Gromacs/gromacs-2020/install
Working dir: /home/rolly/Gromacs/ADH_bench/adh_cubic_vsites
Command line:
gmx_mpi mdrun -g adh_cubic_vsites.log -pin on -v -noconfout -nsteps 10000
-s topol.tpr -ntomp 1
-------------------------------------------------------
Program: gmx mdrun, version 2020-UNCHECKED
Source file: src/gromacs/commandline/cmdlineparser.cpp (line 275)
Function: void gmx::CommandLineParser::parse(int *, char **)
MPI rank: 0 (out of 176)
Error in user input:
Invalid command-line options
In command-line option -s
File 'topol.tpr' does not exist or is not accessible.
The file could not be opened.
Reason: No such file or directory
(call to fopen() returned error code 2)
For more information and tips for troubleshooting, please check the GROMACS
website at http://www.gromacs.org/Documentation/Errors
-------------------------------------------------------
srun: error: node11: tasks
0-8,10-11,14,18-19,22-24,29,35,37,46,48,53-54,58-59,64,66-69,71,73-74,76,78-
79,85,90,93,95,98,101-103,105-106,108-109,111-113,115,118-121,123-124,126,12
8-129,131,135-136,138-142,144-145,147,152,154-156,158-159: Exited with exit
code 1
-------------------------------------------------------
Program: gmx mdrun, version 2020-UNCHECKED
Source file: src/gromacs/commandline/cmdlineparser.cpp (line 275)
Function: void gmx::CommandLineParser::parse(int *, char **)
MPI rank: 1 (out of 176)
Error in user input:
Invalid command-line options
srun: error: node11: tasks
9,12-13,15-17,20-21,25-28,30-34,36,38-45,47,49-52,55-57,60-63,65,70,72,75,77
,80-84,86-89,91-92,94,96-97,99-100,104,107,110,114,116-117,122,125,127,130,1
32-134,137,143,146,148-151,153,157,160-175: Killed
-------------------------------------------------------
Program: gmx mdrun, version 2020-UNCHECKED
Source file: src/gromacs/commandline/cmdlineparser.cpp (line 275)
Function: void gmx::CommandLineParser::parse(int *, char **)
MPI rank: 3 (out of 176)
Error in user input:
Invalid command-line options
In command-line option -s
-------------------------------------------------------
Program: gmx mdrun, version 2020-UNCHECKED
Source file: src/gromacs/commandline/cmdlineparser.cpp (line 275)
Function: void gmx::CommandLineParser::parse(int *, char **)
MPI rank: 4 (out of 176)
Error in user input:
Invalid command-line options
In command-line option -s
File 'topol.tpr' does not exist or is not accessible.
The file could not be opened.
Reason: No such file or directory
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