[gmx-users] gromacs parallel doesn't work

[Yang Ye]

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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