[gmx-users] Gromacs 2020 fails to run adh_cubic_vsites
David van der Spoel
spoel at xray.bmc.uu.se
Sat Mar 7 17:46:58 CET 2020
Den 2020-03-07 kl. 17:04, skrev Rolly Ng:
> 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?
>
It actually tells you what is wrong in the input. -maxwarn 1 is your friend.
>
>
> 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
>
>
>
--
David van der Spoel, Ph.D., Professor of Biology
Head of Department, Cell & Molecular Biology, Uppsala University.
Box 596, SE-75124 Uppsala, Sweden. Phone: +46184714205.
http://www.icm.uu.se
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