[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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