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

[Viveca Lindahl]

@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.

@Mark: Do you mean that tune_pme expects the binaries to have exactly these
names gmx/gmx_mpi  (and be in the same location)?

--
Viveca


On Tue, Apr 10, 2018 at 3:54 PM, Mark Abraham <mark.j.abraham at gmail.com>
wrote:

> Hi,
>
> Yes, Cray's MPI also does not permit such nesting. This is why it's
> generally advisable that installations make both an MPI and non-MPI build,
> and to let the default suffixing of the gmx binary handle itself so both
> installations can go to the same place for convenience.
>
> Mark
>
> On Tue, Apr 10, 2018 at 3:50 PM Kutzner, Carsten <ckutzne at gwdg.de> wrote:
>
> > Hi Viveca,
> >
> > > On 10. Apr 2018, at 15:10, Viveca Lindahl <vivecalindahl at 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
> > > --
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