[gmx-users] Error when for gmx tune_pme on Cray

[Kutzner, Carsten]

> 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 
significantly faster!

Happy tuning,
  Carsten

> 
> --
> Viveca
> 
> 
> On Tue, Apr 10, 2018 at 5:22 PM, Mark Abraham <mark.j.abraham at gmail.com>
> wrote:
> 
>> Hi,
>> 
>> On Tue, Apr 10, 2018 at 4:52 PM Viveca Lindahl <vivecalindahl at 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-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
http://www.mpibpc.mpg.de/grubmueller/kutzner
http://www.mpibpc.mpg.de/grubmueller/sppexa