[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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