Hi Viveca, > On 10. Apr 2018, at 15:10, Viveca Lindahl <vivecalind...@gmail.com> wrote: > > Hi users, > > I never used gmx tune_pme before and thought I'd try. On a Cray machine, > using aprun instead of mpirun, I did > > args="/cfs/klemming/nobackup/v/vivecal/programs/gromacs/2018.1/bin/gmx > mdrun -pin on -quiet -stepout 5000 -ntomp 2 -noconfout" > export MPIRUN=aprun; aprun -n 1 $gmx tune_pme -npstring n -s topol.tpr -np > 32 -mdrun "$args” You don’t need to use aprun -n 1 on $gmx tune_pme, as this is just a serial program that itself calls aprun on mdrun_mpi. Does the following work:
export MPIRUN=aprun $gmx tune_pme -npstring n -s topol.tpr -np 32 -mdrun /path/to/mdrun_mpi I don’t know if on Cray it is allowed that one MPI executable (tune_pme) starts another MPI executable (mdrun), IBM PE e.g. does not allow it. There, tune_pme must be compiled without MPI, only mdrun can be linked to the MPI lib. Best, Carsten > > It hangs (no output) for some minutes, then I get the error > > Program: gmx tune_pme, version 2018.1-dev-20180315-3dfa11852 > Source file: src/gromacs/gmxana/gmx_tune_pme.cpp (line 740) > > Fatal error: > Cannot execute mdrun. Please check benchtest.log for problems! > > For more information and tips for troubleshooting, please check the GROMACS > website at http://www.gromacs.org/Documentation/Errors > ------------------------------------------------------- > Making sure that mdrun can be executed. Trying 'aprun -n 32 > /cfs/klemming/nobackup/v/vivecal/programs/gromacs/2018.1/bin/gmx mdrun -pin > on -quiet -stepout 5000 -ntomp 2 -noconfout -version -maxh 0.001 1> > benchtest.log 2>&1' ... Rank 0 [Tue Apr 10 14:58:12 2018] [c1-0c0s4n0] > application called MPI_Abort(MPI_COMM_WORLD, 1) - process 0 > > the suggested log file to look in has > > craylog: WARNING: log tmp dir /var/spool/cray/llm is not writable > aprun: Unable to contact apsys > aprun: Exiting due to errors. Application aborted > > Am I doing something wrong or is this a bug/limitation of the system I am > trying to run on? > > Thanks, > -- > Viveca > -- > 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.