[gmx-users] TestBed in MPI not working

[Justin A. Lemkul]

Justin A. Lemkul wrote:
> 
> 
> Jones de Andrade wrote:
>> Hi Justin
>>
>>     This has been discussed several times on the list.  The -np flag is
>>     no longer necessary with grompp.  You don't get an mdrun.out because
>>     the .tpr file is likely never created, since grompp fails.
>>
>>
>> Yes, I know that and that is what I would have expected. But what I'm 
>> running is the gmxtest.pl script. Even using the 4.0.4 version, it 
>> explicit states that I must use "-np N" to make parallel works on its 
>> own command line.
>>
>> ************
>> gmxtest.pl
>> Usage: ./gmxtest.pl [ -np N ] [-verbose ] [ -double ] [ simple | 
>> complex | kernel | pdb2gmx | all ]
>>    or: ./gmxtest.pl clean | refclean | dist
>> ************
>>
>> I would expect that the script would use it only for mdrun and not for 
>> grompp, but it seems to try to use on both. What becomes really 
>> strange it the testbed really works. So, gmxtest.pl has a bug on 
>> 4.0.4? Or how should I really tell gmxtest.pl to test in a growing 
>> number of cores?
>>  
>>
> 
> Ah, sorry for the mis-read :)  There is a simple fix that you can apply 
> to the gmxtest.pl script:
> 
> % diff gmxtest.pl gmxtest_orig.pl
> 161c161
> <         system("$grompp -maxwarn 10 $ndx > grompp.out 2>&1");
> ---
>  >         system("$grompp -maxwarn 10 $ndx $par > grompp.out 2>&1");
> 
> -Justin
> 
>>
>>
>>         Version 3.3.3 on the other hand already failed in so many
>>         different places that I'm really thinking IF I'll make it
>>         available in the new cluster. :P
>>
>>
>>     What messages are you getting from 3.3.3?  I thought you said the
>>     3.3.x series worked fine.
>>
>>
>> I'll login for those and try to get any reproducible error here. ;) As 
>> soon as I have these, I post back in this thread.
>>
>> Thanks a lot again,
>>
>> Jones
> 

-- 
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Justin A. Lemkul
Ph.D. Candidate
ICTAS Doctoral Scholar
Department of Biochemistry
Virginia Tech
Blacksburg, VA
jalemkul[at]vt.edu | (540) 231-9080
http://www.bevanlab.biochem.vt.edu/Pages/Personal/justin

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