[gmx-users] gromacs parallel doesn't work

[Beniamino Sciacca]

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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