> On 10. Apr 2018, at 18:13, Viveca Lindahl <vivecalind...@gmail.com> wrote: > > Thanks. It's running now. I just had a typo in my gmx_mpi variable that > gave me the last error I posted. Using the non-mpi binary for tune_pme > solved it. BTW you might find the tune_pme -ntpr 1 switch useful if you are using the Verlet cutoff scheme. Since with Verlet, mdrun does automatically balance PME grid and cutoff settings, there is no need for tune_pme to provide .tpr files with various settings for grid and cutoff. Will make the tuning significantly faster!
Happy tuning, Carsten > > -- > Viveca > > > On Tue, Apr 10, 2018 at 5:22 PM, Mark Abraham <mark.j.abra...@gmail.com> > wrote: > >> Hi, >> >> On Tue, Apr 10, 2018 at 4:52 PM Viveca Lindahl <vivecalind...@gmail.com> >> wrote: >> >>> @Carsten: thanks for the suggestions. I needed the 'aprun -n 1' to be >> able >>> to run with my mpi-binary (otherwise I get 'illegal instruction'). I now >>> tried >>> >>> >>> export MPIRUN=aprun; $gmx tune_pme -npstring n -s topol.tpr -np 16 -mdrun >>> $gmx_mpi >>> >>> where gmx/gmx_mpi are a thread-mpi/real MPI builds and get >>> >>> Fatal error: >>> Need an MPI-enabled version of mdrun. This one >>> (/cfs/klemming/nobackup/v/vivecal/programs/gromacs/2018.1/bin/gmx) >>> seems to have been compiled without MPI support. >>> >>> referring to the mpi build. >>> >> >> It's tried out what you supplied to the -mdrun flag and found it didn't >> work. Probably for the reason below. >> >> >>> @Mark: Do you mean that tune_pme expects the binaries to have exactly >> these >>> names gmx/gmx_mpi (and be in the same location)? >>> >> >> No, but checking out gmx help tune_pme regarding -mdrun would help you >> provide what is needed, e.g. "gmx_mpi mdrun" (modulo however you built and >> suffixed your gmx binaries). >> >> Mark >> -- >> 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. -- Dr. Carsten Kutzner Max Planck Institute for Biophysical Chemistry Theoretical and Computational Biophysics Am Fassberg 11, 37077 Goettingen, Germany Tel. +49-551-2012313, Fax: +49-551-2012302 http://www.mpibpc.mpg.de/grubmueller/kutzner http://www.mpibpc.mpg.de/grubmueller/sppexa -- 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.
