Before I compiled gromacs enabling mpi, and mdrun used both the cpu
starting only one process.
I need one process because in my case if I use two processes mdrun
return an error (I use constraint forces).
I'm not sure, but maybe this version doesn't support native multithreaded...
Beniamino Sciacca
Andrew Friedley ha scritto:
> Beniamino Sciacca wrote:
>
>> I don't know what is changed.. but I partially resolved the problem:
>> is not an hardware problem (installing smp kernel it works).
>> Now I've to use mpirun (before I didn't use it), and I don't succeed to
>> tell the system to use both processors for only one process.
>> In fact using "mpirun -c 2" it makes two processes, each for one cpu.
>> I need to work with only one process, and before I succeeded in this.
>> (with another computer dual core I'm able to do this.
>> Thanks
>>
>
> Apologies, I'm not sure I understand what you're saying here.
>
> You weren't using mpirun before? What were you using?
>
> I don't see why two processes is bad - this to me is expected behavior,
> as LAM/MPI will start one process per processor. Why do you need only
> one process?
>
> Another note.. does gromacs support some sort of native multithreaded
> mode? This might perform better for you than using MPI would if you're
> only using the one system.
>
> Andrew
>
>
>> Andrew Friedley ha scritto:
>>
>>
>>> Beniamino Sciacca wrote:
>>>
>>>
>>>
>>>> Hi community!
>>>> I've a great problem:
>>>> two months ago I installed LAM on my centrino duo, debian -kernel 2.6.
>>>> Later I compiled gromacs enabling mpi, and everything was working well
>>>> until four days ago.
>>>> Now the simulation time is increased like if there is only one processor
>>>> (it takes twice time than before).
>>>> I don't understand why.
>>>> I disinstalled and then reinstalled LAM and gromacs (LAM 7.1.2 (I
>>>> compiled it on my own) + gromacs 3.3.1).
>>>> Nothing has changed.
>>>> I disinstalled linux and then reinstalled (debian kernel 2.6), and again
>>>> LAM and gromacs: I've the same problem, like if one of the two cores
>>>> doesn't work.
>>>> I tried also to install gromacs NON mpi-enabled, and I've the same
>>>> simulation time (respect to the enabled-mpi gromacs).
>>>> In all these cases LAM seems to work (when I type lamboot LAM starts
>>>> without problem).
>>>>
>>>> What's happened?
>>>> How can I understand if it's a software problem or an hardware one?
>>>> thank you very much for the reply!
>>>>
>>>>
>>> The first question I always ask is - what changed? You say it was
>>> working properly up to some point, something must have happened at or
>>> before that point.
>>>
>>> It's hard to tell based on the information you've given, but the first
>>> thing I would do is make sure linux has both CPU's enabled, and that any
>>> power management stuff isn't affecting your performance.
>>>
>>> Can you test any other applications, to see if this problem is specific
>>> to LAM/gromacs?
>>>
>>> You might consider other support channels as well - I can't recommend a
>>> good place for you off the top of my head, but LAM is not likely the
>>> problem here.
>>>
>>> Andrew
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>>>
>>>
>>>
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