# Errors Running Gromacs Simulation on HPC **URL:** \ **Category:** User discussions\ **Tags:** mdrun\ **Created:** [April 6, 2022, 5:21pm UTC](https://gromacs.bioexcel.eu/t/errors-running-gromacs-simulation-on-hpc/3967 "2022-04-06T17:21:10Z")\ **Posts on this page:** 1\ **Page:** 1
**Author:** ![christos-efthymiou](https://avatars.discourse-cdn.com/v4/letter/c/8edcca/32.png) [@christos-efthymiou](https://gromacs.bioexcel.eu/u/christos-efthymiou)\ **Post date:** [April 6, 2022, 5:21pm UTC](https://gromacs.bioexcel.eu/t/errors-running-gromacs-simulation-on-hpc/3967/1 "2022-04-06T17:21:10Z")
Hi, I have prepared a Gromacs simulation on the Bioexcel Building Blocks website ([Homepage - BioExcel Building Blocks Workflows](https://mmb.irbbarcelona.org/biobb-wfs/)) for a protein complex. According to the help page ([Help - BioExcel Building Blocks Workflows](https://mmb.irbbarcelona.org/biobb-wfs/help/workflows-home/gmx-prod#custom)), to run the simulation on a supercomputer the tpr file generated needs to be transferred to the HPC along with a script to run the job. The example script provided is for SLURM: ```auto #!/bin/bash ###################################### # GROMACS MD Execution Script # # Usage: sbatch FILE_NAME.sh # ###################################### # ######################################################################### # To use with Slurm Queue Manager # # #SBATCH --ntasks : Number of processes to start. # # #SBATCH --cpus-per-task : Jobs CPU n = cpus_per_task * total_tasks. # # #SBATCH --ntasks-per-node : Number of tasks x node. # # #SBATCH --nodes : Number of nodes. # # #SBATCH -t : Job time limit. # # #SBATCH --qos : Queue name. # # #SBATCH -J : Job name. # # #SBATCH -e : Job standard error file. # # #SBATCH -o : Job standard output file. # # #SBATCH -D : Working directory. # ######################################################################### #SBATCH --ntasks=1 #SBATCH --cpus-per-task=48 #SBATCH --ntasks-per-node=1 #SBATCH --nodes=1 #SBATCH -t 0-2:00:00 #SBATCH --qos=debug #SBATCH -J JOB_NAME #SBATCH -o job.out #SBATCH -e job.err #SBATCH -D . module load gromacs # GROMACS production MD gmx_mpi -nobackup -nocopyright mdrun -s gppmdsim.tpr -o output_prod.trr -c output_prod.gro -e output_prod.edr -g output_prod.log -x output_prod.xtc ``` However, the HPC that I am working with uses Sun Grid Engine (SGE) rather than SLURM. Therefore, I have tried creating a script for SGE, but I am experiencing some problems: Script: ```auto # SGE job submission system #$ -S /bin/bash ##wall time for calculations #$ -l h_rt=0:10:0 # For 1 GPU #$ -l gpu=1 ##memory required #$ -l mem=4G ##name of calculation #$ -N Gromacs_2XQW_test2 ##number of cores needed for calculation. Tip: use multiples of 16 as there are 16 cores per node, ##this makes it easier for the queue system to allocate you job to the resources. #$ -pe mpi 16 ##this tells the computer where to run the calculation, cwd stands for current working directory ##meaning that the code will be run in the directory that the submisson script is submitted #$ -cwd ##these are modules and dependencies that cp2k uses to run calculations module unload -f compilers mpi module load compilers/intel/2018/update3 module load mpi/intel/2018/update3/intel module load libmatheval module load flex module load plumed/2.5.2/intel-2018 module load gromacs/2019.3/plumed/intel-2018 # GROMACS production MD gerun gmx_mpi -nobackup -nocopyright mdrun -s gppmdsim.tpr -o output_prod.trr -c output_prod.gro -e output_prod.edr -g output_prod.log -x output_prod.xtc ``` Error with Script: ```auto GERun: GERun: Note: Lines like this one prefixed with "GERun:" are for debugging GERun: purposes only and you do not need to report them to rc-support GERun: unless your job fails for other reasons. GERun: GERun: GERun: Grid Engine parallel launcher abstraction layer version iv (public) GERun: Dr Owain Kenway, RCAS, RITS, ISD, UCL, 7th of February, 2018 GERun: GERun: For licensing terms, see LICENSE.txt GERun: GERun: Using environment: intel GERun: Running on 16 slots: GERun: 16 MPI tasks GERun: 1 threads per task GERun: TMPDIR=/tmpdir/job/718657.undefined GERun: GERun: Contents of machinefile: GERun: node-e00a-016 GERun: node-e00a-016 GERun: node-e00a-016 GERun: node-e00a-016 GERun: node-e00a-016 GERun: node-e00a-016 GERun: node-e00a-016 GERun: node-e00a-016 GERun: node-e00a-016 GERun: node-e00a-016 GERun: node-e00a-016 GERun: node-e00a-016 GERun: node-e00a-016 GERun: node-e00a-016 GERun: node-e00a-016 GERun: node-e00a-016 GERun: node-e00a-016 GERun: node-e00a-016 GERun: node-e00a-016 GERun: node-e00a-016 GERun: node-e00a-016 GERun: node-e00a-016 GERun: GERun: GErun command being run: GERun: mpirun --rsh=ssh -machinefile /tmpdir/job/718657.undefined/machines.unique -np 16 -rr gmx_mpi -nobackup -nocopyright mdrun -s gppmdsim.tpr -o output_prod.trr -c output_prod.gro -e :-) GROMACS - gmx mdrun, 2019.3 (-: Executable: /shared/ucl/apps/gromacs/2019.3/plumed/intel-2018/bin/gmx_mpi Data prefix: /shared/ucl/apps/gromacs/2019.3/plumed/intel-2018 Working dir: /lustre/home/ucbtcd1/2xqw_original_10ns_test2 Command line: gmx_mpi -nobackup -nocopyright mdrun -s gppmdsim.tpr -o output_prod.trr -c output_prod.gro -e ------------------------------------------------------- Program: gmx mdrun, version 2019.3 Source file: src/gromacs/commandline/cmdlineparser.cpp (line 276) Function: void gmx::CommandLineParser::parse(int *, char **) MPI rank: 0 (out of 16) Error in user input: Invalid command-line options ------------------------------------------------------- Program: gmx mdrun, version 2019.3 Source file: src/gromacs/commandline/cmdlineparser.cpp (line 276) Function: void gmx::CommandLineParser::parse(int *, char **) MPI rank: 1 (out of 16) Error in user input: Invalid command-line options ------------------------------------------------------- Program: gmx mdrun, version 2019.3 Source file: src/gromacs/commandline/cmdlineparser.cpp (line 276) Function: void gmx::CommandLineParser::parse(int *, char **) MPI rank: 2 (out of 16) Error in user input: Invalid command-line options ------------------------------------------------------- Program: gmx mdrun, version 2019.3 Source file: src/gromacs/commandline/cmdlineparser.cpp (line 276) Function: void gmx::CommandLineParser::parse(int *, char **) MPI rank: 3 (out of 16) Error in user input: Invalid command-line options ------------------------------------------------------- Program: gmx mdrun, version 2019.3 Source file: src/gromacs/commandline/cmdlineparser.cpp (line 276) Function: void gmx::CommandLineParser::parse(int *, char **) MPI rank: 4 (out of 16) Error in user input: Invalid command-line options ------------------------------------------------------- Program: gmx mdrun, version 2019.3 Source file: src/gromacs/commandline/cmdlineparser.cpp (line 276) Function: void gmx::CommandLineParser::parse(int *, char **) MPI rank: 5 (out of 16) Error in user input: Invalid command-line options ------------------------------------------------------- Program: gmx mdrun, version 2019.3 Source file: src/gromacs/commandline/cmdlineparser.cpp (line 276) Function: void gmx::CommandLineParser::parse(int *, char **) MPI rank: 6 (out of 16) Error in user input: Invalid command-line options ------------------------------------------------------- Program: gmx mdrun, version 2019.3 Source file: src/gromacs/commandline/cmdlineparser.cpp (line 276) Function: void gmx::CommandLineParser::parse(int *, char **) MPI rank: 7 (out of 16) Error in user input: Invalid command-line options ------------------------------------------------------- Program: gmx mdrun, version 2019.3 Source file: src/gromacs/commandline/cmdlineparser.cpp (line 276) Function: void gmx::CommandLineParser::parse(int *, char **) MPI rank: 8 (out of 16) Error in user input: Invalid command-line options ------------------------------------------------------- Program: gmx mdrun, version 2019.3 Source file: src/gromacs/commandline/cmdlineparser.cpp (line 276) Function: void gmx::CommandLineParser::parse(int *, char **) MPI rank: 9 (out of 16) Error in user input: Invalid command-line options ------------------------------------------------------- Program: gmx mdrun, version 2019.3 Source file: src/gromacs/commandline/cmdlineparser.cpp (line 276) Function: void gmx::CommandLineParser::parse(int *, char **) MPI rank: 10 (out of 16) Error in user input: Invalid command-line options ------------------------------------------------------- Program: gmx mdrun, version 2019.3 Source file: src/gromacs/commandline/cmdlineparser.cpp (line 276) Function: void gmx::CommandLineParser::parse(int *, char **) MPI rank: 11 (out of 16) Error in user input: Invalid command-line options ------------------------------------------------------- Program: gmx mdrun, version 2019.3 Source file: src/gromacs/commandline/cmdlineparser.cpp (line 276) Function: void gmx::CommandLineParser::parse(int *, char **) MPI rank: 12 (out of 16) Error in user input: Invalid command-line options ------------------------------------------------------- Program: gmx mdrun, version 2019.3 Source file: src/gromacs/commandline/cmdlineparser.cpp (line 276) Function: void gmx::CommandLineParser::parse(int *, char **) MPI rank: 13 (out of 16) Error in user input: Invalid command-line options ------------------------------------------------------- Program: gmx mdrun, version 2019.3 Source file: src/gromacs/commandline/cmdlineparser.cpp (line 276) Function: void gmx::CommandLineParser::parse(int *, char **) MPI rank: 14 (out of 16) Error in user input: Invalid command-line options ------------------------------------------------------- Program: gmx mdrun, version 2019.3 Source file: src/gromacs/commandline/cmdlineparser.cpp (line 276) Function: void gmx::CommandLineParser::parse(int *, char **) MPI rank: 15 (out of 16) Error in user input: Invalid command-line options In command-line option -s File 'gppmdsim.tpr' does not exist or is not accessible. The file could not be opened. In command-line option -s File 'gppmdsim.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 ------------------------------------------------------- In command-line option -s File 'gppmdsim.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 ------------------------------------------------------- In command-line option -s File 'gppmdsim.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 ------------------------------------------------------- In command-line option -s File 'gppmdsim.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 ------------------------------------------------------- In command-line option -s File 'gppmdsim.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 ------------------------------------------------------- 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 ------------------------------------------------------- In command-line option -s File 'gppmdsim.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 ------------------------------------------------------- In command-line option -s File 'gppmdsim.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 ------------------------------------------------------- In command-line option -s File 'gppmdsim.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 ------------------------------------------------------- In command-line option -s File 'gppmdsim.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 ------------------------------------------------------- application called MPI_Abort(MPI_COMM_WORLD, 1) - process 8 In command-line option -s File 'gppmdsim.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 ------------------------------------------------------- application called MPI_Abort(MPI_COMM_WORLD, 1) - process 12 In command-line option -s File 'gppmdsim.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 ------------------------------------------------------- application called MPI_Abort(MPI_COMM_WORLD, 1) - process 14 application called MPI_Abort(MPI_COMM_WORLD, 1) - process 0 application called MPI_Abort(MPI_COMM_WORLD, 1) - process 1 application called MPI_Abort(MPI_COMM_WORLD, 1) - process 3 application called MPI_Abort(MPI_COMM_WORLD, 1) - process 4 application called MPI_Abort(MPI_COMM_WORLD, 1) - process 6 application called MPI_Abort(MPI_COMM_WORLD, 1) - process 7 application called MPI_Abort(MPI_COMM_WORLD, 1) - process 9 application called MPI_Abort(MPI_COMM_WORLD, 1) - process 13 application called MPI_Abort(MPI_COMM_WORLD, 1) - process 15 In command-line option -s File 'gppmdsim.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 ------------------------------------------------------- application called MPI_Abort(MPI_COMM_WORLD, 1) - process 11 /var/opt/sge/node-e00a-016/job_scripts/718657: line 37: output_prod.edr: command not found /var/opt/sge/node-e00a-016/job_scripts/718657: line 38: output_prod.log: command not found ``` Therefore, I am not sure what is wrong with the script or how I can resolve this issue. I have checked the documentation for the HPC that I use, and they provide a few different examples for loading the modules of gromacs: Version 1: ```auto # Example for gromacs/2021.2/gnu-7.3.0 module load beta-modules module unload -f compilers mpi gcc-libs module load gcc-libs/7.3.0 module load compilers/gnu/7.3.0 module load mpi/openmpi/3.1.4/gnu-7.3.0 module load python3 module load gromacs/2021.2/gnu-7.3.0 # Run GROMACS - replace with mdrun command line suitable for your job! gerun mdrun_mpi -v -stepout 10000 ``` Version 2: ```auto # Example for gromacs/2019.3/intel-2018 module unload -f compilers mpi module load compilers/intel/2018/update3 module load mpi/intel/2018/update3/intel module load gromacs/2019.3/intel-2018 # Run GROMACS - replace with mdrun command line suitable for your job! gerun mdrun_mpi -v -stepout 10000 ``` Version 3: ```auto # Plumed example for gromacs/2019.3/plumed/intel-2018 module unload -f compilers mpi module load compilers/intel/2018/update3 module load mpi/intel/2018/update3/intel module load libmatheval module load flex module load plumed/2.5.2/intel-2018 module load gromacs/2019.3/plumed/intel-2018 # Run GROMACS - replace with mdrun command line suitable for your job! gerun gmx_mpi -v -stepout 10000 ``` In my case, I used Version 3 for loading the modules because this is the only example which shows gmx\_mpi. The other two use mdrun\_mpi. Since the example SLURM script from Biobb uses gmx\_mpi and mdrun, I figured this would be the best option, but I am not sure. I believe my issue arises from the gerun line, so any suggestions on how to fix this would be highly appreciated.