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

[Kutzner, Carsten]

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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