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 -- Gromacs Users mailing list * Please search the archive at http://www.gromacs.org/Support/Mailing_Lists/GMX-Users_List before posting! * Can't post? Read http://www.gromacs.org/Support/Mailing_Lists * For (un)subscribe requests visit https://maillist.sys.kth.se/mailman/listinfo/gromacs.org_gmx-users or send a mail to gmx-users-requ...@gromacs.org.