[gmx-users] Error when for gmx tune_pme on Cray
ckutzne at gwdg.de
Tue Apr 10 18:18:02 CEST 2018
> On 10. Apr 2018, at 18:13, Viveca Lindahl <vivecalindahl at 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
> On Tue, Apr 10, 2018 at 5:22 PM, Mark Abraham <mark.j.abraham at gmail.com>
>> On Tue, Apr 10, 2018 at 4:52 PM Viveca Lindahl <vivecalindahl at gmail.com>
>>> @Carsten: thanks for the suggestions. I needed the 'aprun -n 1' to be
>>> to run with my mpi-binary (otherwise I get 'illegal instruction'). I now
>>> export MPIRUN=aprun; $gmx tune_pme -npstring n -s topol.tpr -np 16 -mdrun
>>> where gmx/gmx_mpi are a thread-mpi/real MPI builds and get
>>> Fatal error:
>>> Need an MPI-enabled version of mdrun. This one
>>> 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
>>> 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).
>> 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-request at 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-request at 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
More information about the gromacs.org_gmx-users