[gmx-users] gromacs parallel doesn't work

[Beniamino Sciacca]

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?

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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