[gmx-users] Assistance needed running gromacs 4.6.3 on Blue Gene/P

Prentice Bisbal prentice.bisbal at rutgers.edu
Wed Aug 7 17:04:59 CEST 2013



On 08/07/2013 05:51 AM, Bogdan Costescu wrote:
> Hi Prentice,
> The subject and first phrase mention version 4.6.3, but all scripts
> refer to 4.6.2. Are you sure you are not mixing versions ? Do you have
> another 4.6.x version working already ?

Your correct - I'm working with version 4.6.2. the 4.6.3 in the subject 
line was a mistake.
>>    -DCMAKE_C_FLAGS="-O3 -qarch=450d -qtune=450" \
> Could you try with a lower optimization level ?

-O3 should be safe, but yes, I can try it with a lower optimization.
>> <Aug 06 17:25:55.303940> BE_MPI (ERROR):   "killed with signal 6"
> What is signal 6 on this platform ?

I couldn't find anything explicit in the documentation, The compute node 
kernel (CNK) is proprietary, but is said to be very Linux-like, so a 
signal 6 should be the same as on Linux, which would be an abort signal.
> Cheers,
> Bogdan

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