[gmx-users] g_tune_pme crashes in 5.0.1

[Oliver Schillinger]

Hi Mark,
thanks for your detailed answer.
Your hack is convenient enough to me for the moment.

For build scripts:
sed -i 's/\(gmx_bool bFirst\s*=\)\s*TRUE/\1 FALSE/g' 
src/gromacs/gmxana/gmx_tune_pme.c

Cheers,
Oliver

On 09/15/2014 10:44 PM, Mark Abraham wrote:
> Hi,
>
> Addressing this problem started back in May, but is stalled in code review
> waiting for people who care to finish reviewing it. The basic problem is
> that the optimizer would like to check that mdrun works on the .tpr, so it
> can tell you that up front before the optimization starts. But there's no
> reliable way to choose mdrun -npme for that test, since -1 is likely to
> fail at low parallelism (prime factors too common, as here) and 0 is likely
> to fail at high parallelism (domains are too small). gmx tune_pme should
> grow some more brains, but that depends on my code getting reviewed :-)
>
> The "good" news is that you can hack line 1388 of
> src/gromacs/gmxana/gmx_tune_pme.c so that
>
>      gmx_bool bFirst        = TRUE;
>
> becomes
>
>      gmx_bool bFirst        = FALSE;
>
> and the subsequent compile and install of gmx tune_pme won't do this check
> (and is otherwise normal).
>
> Mark
>
> On Mon, Sep 15, 2014 at 3:54 PM, Oliver Schillinger <
> o.schillinger at fz-juelich.de> wrote:
>
>> Hi,
>> I was using g_tune_pme successfully with the 4.6.* branch.
>> Now I switched to 5.0.1 and g_tune_pme keeps crashing.
>>
>> perf.out (default filenames used) says:
>> Cannot run the benchmark simulations! Please check the error message of
>> mdrun for the source of the problem. Did you provide a command line
>> argument that neither g_tune_pme nor mdrun understands? Offending command:
>> mpiexec -np 24 mdrun_mpi -npme 7 -s 04_prod01_bench00.tpr -resetstep 100
>> -o bench.trr -x bench.xtc -cpo bench.cpt -c bench.gro -e bench.edr -g
>> bench.log  -nsteps 1 -quiet
>>
>> bench.log contains only output of the first benchmark run with the error
>> message:
>> Fatal error:
>> The number of ranks you selected (17) contains a large prime factor 17.
>> ...
>>
>> The problem seems to me that the second run does not get started at all,
>> but the program terminates after the first unsuccessful benchmark.
>>
>> Am I alone with this problem?
>>
>> Cheers,
>> Oliver
>>
>> --
>> Oliver Schillinger
>> PhD student
>>
>> ICS-6 - Structural Biochemistry
>> Building 5.8v, Room 3010
>> Phone:  +49 2461-61-9532
>> Mobile: +49 172 53 27 914
>>
>> Forschungszentrum Juelich GmbH
>> 52425 Juelich
>> Sitz der Gesellschaft: Juelich
>> Eingetragen im Handelsregister des Amtsgerichts Dueren Nr. HR B 3498
>> Vorsitzender des Aufsichtsrats: MinDir Dr. Karl Eugen Huthmacher
>> Geschaeftsfuehrung: Prof. Dr. Achim Bachem (Vorsitzender),
>> Karsten Beneke (stellv. Vorsitzender), Prof. Dr.-Ing. Harald Bolt,
>> Prof. Dr. Sebastian M. Schmidt
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-- 
Oliver Schillinger
PhD student

ICS-6 - Structural Biochemistry
Building 5.8v, Room 3010
Phone:  +49 2461-61-9532
Mobile: +49 172 53 27 914

Forschungszentrum Juelich GmbH
52425 Juelich
Sitz der Gesellschaft: Juelich
Eingetragen im Handelsregister des Amtsgerichts Dueren Nr. HR B 3498
Vorsitzender des Aufsichtsrats: MinDir Dr. Karl Eugen Huthmacher
Geschaeftsfuehrung: Prof. Dr. Achim Bachem (Vorsitzender),
Karsten Beneke (stellv. Vorsitzender), Prof. Dr.-Ing. Harald Bolt,
Prof. Dr. Sebastian M. Schmidt