[gmx-users] gromacs parallel doesn't work

[Yang Ye]

So, the kernel you used from Debian could be a non-SMP one. Change 
another in the boot screen if there is.
\
Yang Ye

David van der Spoel wrote:
> Beniamino Sciacca wrote:
>> with "-c 2" I've two processes, each one running at nearly 50%.
>> with "-c 4" I've four processes, each one running at nearly 25%
>> with "-c 1" I've only one process wich runs at nearly 99%
>> I tried also with mdrun_Nmpi (compiled without enabling mpi), and it 
>> runs at nearly 99%.
>> Is it possible that the software sees only one core?
>
> I think your OS only sees one processor.
> if Linux try:
> cat /proc/cpuinfo
>
>
>>
>> Beniamino
>>
>> Yang Ye ha scritto:
>>
>>> Use top to check, you shall have two processes running at nearly 
>>> 100% with "-c 2"
>>>
>>> Yang Ye
>>>
>>> Beniamino Sciacca wrote:
>>>
>>>> I've just tried "mpirun -c 2 mdrun..." (34 h/ns).
>>>> It works, but the problem is the same... the simulation time....
>>>> In fact I also tried "mpirun -c 1 mdrun" (32 h/ns) and  "mpirun -c 
>>>> 4 mdrun" (34 h/ns), but the simulation time remain the same!
>>>>
>>>>
>>>> Yang Ye ha scritto:
>>>>
>>>>> Beniamino Sciacca wrote:
>>>>>
>>>>>> I never used mprun -np 2, and I had not problem. Before I didn't 
>>>>>> use "mprun -np 2", now I don't use "mprun -np 2" but simulation 
>>>>>> time now is twice. It has changed from a day to the other.
>>>>>> However I've just tried, like you suggested,  to use " -np 2" (in 
>>>>>> grompp and in mdrun) but I obtain an error:
>>>>>> -------------------------------------------
>>>>>> "Program mdrun_d, VERSION 3.3.1
>>>>>> Source code file: init.c, line: 69
>>>>>>
>>>>>> Fatal error:
>>>>>> run input file DNA8_mdEq.tpr was made for 2 nodes,
>>>>>>              while mdrun_d expected it to be for 1 nodes.
>>>>>> "
>>>>>> -------------------------------------------
>>>>>> In fact I've only one node.
>>>>>
>>>>> Try David's mpirun -c 2 mdrun
>>>>>
>>>>>>
>>>>>> Laptop should be running in top speed, I never modified the 
>>>>>> configuration of energy profile.
>>>>>> Beniamino
>>>>>>
>>>>>>
>>>>>> 2006/6/3, Yang Ye <leafyoung81-group at yahoo.com 
>>>>>> <mailto:leafyoung81-group at yahoo.com>>:
>>>>>>
>>>>>>     First, make sure that you used mdrun -np 2.
>>>>>>     Second, check your energy profile. Is your laptop running in top
>>>>>>     speed?
>>>>>>     or does it have sleep time?
>>>>>>
>>>>>>     Yang Ye
>>>>>>
>>>>>>     Beniamino Sciacca wrote:
>>>>>>     > I don't understand what you talking about...
>>>>>>     > I didn't write any hostfile.... I'm not in a cluster. I 
>>>>>> only use my
>>>>>>     > notebook with the two cores.
>>>>>>     > In fact I type "lamboot" without -v.......
>>>>>>     >
>>>>>>     > Beniamino
>>>>>>     >
>>>>>>     > Mark Abraham ha scritto:
>>>>>>     >> Did your default LAM hostfile configuration (or whatever 
>>>>>> it is)
>>>>>>     >> change from 2 processors to one?
>>>>>>     >>
>>>>>>     >> Mark
>>>>>>     >> _______________________________________________
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>>>>>>
>>>>>>     --
>>>>>>     /Regards,/
>>>>>>     Yang Ye
>>>>>>     /Computational Biology Lab
>>>>>>     School of Biological Sciences
>>>>>>     Nanyang Technological University
>>>>>>     Singapore
>>>>>>     Tel: 6316-2884
>>>>>>     /
>>>>>>
>>>>>>     _______________________________________________
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>>>>>>
>>>>>> ------------------------------------------------------------------------ 
>>>>>>
>>>>>>
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>>>>>
>>>>>
>>>>>
>>>>>
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