Thanks Mark for your response. I looked into the PBS script and it does have a line pointing to the PBS workdir.
But what you said seems right. Somehow, the execution of the script is not happening correctly. As it turns out, I realized that I was submitting the script within a qlogin session, the same I had to use for compilations. Seems to me that PBS env variables were not set correctly within that session. When I submit the job outside of qlogin session, it works as expected. Thank again for pointing towards the right direction. Abhishek Acharya Research Associate, Department of Molecular Nutrition CSIR-Central Food Technological Research Institute, Mysuru-570020 On Tue, Jun 19, 2018 at 1:12 PM, Mark Abraham <mark.j.abra...@gmail.com> wrote: > Hi, > > You aren't running mdrun_mpi from the working directory in which > testfile.tpr is found. Probably you need to set some flag in your > submission script to change to the directory from which you submitted > > Mark > > On Tue, Jun 19, 2018 at 7:41 AM Abhishek Acharya <abhi117acha...@gmail.com > > > wrote: > > > Dear GROMACS users, > > > > I installed mpi-enabled GROMACS (mdrun only) on a linux cluster. The > > administrators recommended using Intel MPI so I used that. I also > installed > > a local version of gcc-5.5.0 (with required dependencies), as the version > > available system-wide (4.4.6 I believe) was not compatible with C11 > > standard. Using FFTW-3.3.7 and latest BLAS and LAPACK libraries. The > > compilation ran without any errors. > > > > I could not run any regtests as runs are only allowed via PBS scripts. > > However, I tried to run a test simulation using a tpr file generated > using > > the same gromacs version. > > > > On submitting the job using qsub, I find that the queue status is C. The > > output err file shows the following error, which I have never seen > before. > > > > ..... > > ..... > > GROMACS: mdrun_mpi, VERSION 5.1.4 > > Executable: /home/acusers/pbalaji/install/ > gromacs-514-impi/bin/mdrun_mpi > > > > ------------------------------------------------------- > > Program: mdrun_mpi, VERSION 5.1.4 > > > > ------------------------------------------------------- > > Program: mdrun_mpi, VERSION 5.1.4 > > Source file: src/gromacs/commandline/cmdlineparser.cpp (line 234) > > Function: void gmx::CommandLineParser::parse(int*, char**) > > > > > > ------------------------------------------------------- > > Program: mdrun_mpi, VERSION 5.1.4 > > Source file: src/gromacs/commandline/cmdlineparser.cpp (line 234) > > Function: void gmx::CommandLineParser::parse(int*, char**) > > > > > > ------------------------------------------------------- > > Program: mdrun_mpi, VERSION 5.1.4 > > Source file: src/gromacs/commandline/cmdlineparser.cpp (line 234) > > Function: void gmx::CommandLineParser::parse(int*, char**) > > > > Error in user input: > > > > ------------------------------------------------------- > > Program: mdrun_mpi, VERSION 5.1.4 > > Source file: src/gromacs/commandline/cmdlineparser.cpp (line 234) > > Function: void gmx::CommandLineParser::parse(int*, char**) > > > > Error in user input: > > > > ------------------------------------------------------- > > Program: mdrun_mpi, VERSION 5.1.4 > > Source file: src/gromacs/commandline/cmdlineparser.cpp (line 234) > > Function: void gmx::CommandLineParser::parse(int*, char**) > > > > Error in user input: > > Source file: src/gromacs/commandline/cmdlineparser.cpp (line 234) > > Function: void gmx::CommandLineParser::parse(int*, char**) > > > > Error in user input: > > Invalid command-line options > > Error in user input: > > Invalid command-line options > > Error in user input: > > Invalid command-line options > > Invalid command-line options > > Invalid command-line options > > Invalid command-line options > > In command-line option -s > > File 'testfile.tpr' does not exist or is not accessible. > > > > For more information and tips for troubleshooting, please check the > GROMACS > > website at http://www.gromacs.org/Documentation/Errors > > ------------------------------------------------------- > > Halting parallel program mdrun_mpi on rank 3 out of 12 > > In command-line option -s > > File 'testfile.tpr' does not exist or is not accessible. > > > > For more information and tips for troubleshooting, please check the > GROMACS > > website at http://www.gromacs.org/Documentation/Errors > > ------------------------------------------------------- > > Halting parallel program mdrun_mpi on rank 5 out of 12 > > In command-line option -s > > File 'testfile.tpr' does not exist or is not accessible. > > > > For more information and tips for troubleshooting, please check the > GROMACS > > website at http://www.gromacs.org/Documentation/Errors > > ------------------------------------------------------- > > Halting parallel program mdrun_mpi on rank 6 out of 12 > > > > ------------------------------------------------------- > > Program: mdrun_mpi, VERSION 5.1.4 > > Source file: src/gromacs/commandline/cmdlineparser.cpp (line 234) > > Function: void gmx::CommandLineParser::parse(int*, char**) > > > > In command-line option -s > > File 'testfile.tpr' does not exist or is not accessible. > > > > For more information and tips for troubleshooting, please check the > GROMACS > > website at http://www.gromacs.org/Documentation/Errors > > ------------------------------------------------------- > > Halting parallel program mdrun_mpi on rank 11 out of 12 > > ..... > > ..... > > and more of the same. > > > > Some clues to how this issue can be solved would certainly help. > > > > Thanks in advance. > > > > Abhishek > > -- > > 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. > > > -- > 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. > -- 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.