Thank you Ross
pmemd.MPI -np 12 runs fine. Thanks Jason for the hint
I am running Amber 11. I installed the program only two days ago and it is running with the latest bugfixes
Best regards
George
On Dec 12, 2010, at 7:09 PM, Ross Walker wrote:
> Hi George,
>
> Firstly it is NOT advisable to run sander.MPI with the number of processors
> not being a power of 2. Sander uses a different way of collating the forces
> when there is a non-power of 2 cpus and thus the efficiency is often a LOT
> lower. You may find that using 8 cores is actually faster than 12. What I
> suspect is happening is that there is a bug in the code used when the number
> of MPI processes is not a power of 2. PMEMD is unaffected by this because it
> uses point to point communications.
>
> The non-power of 2 code in sander is probably very rarely tested so it is
> possible there is a bug in there.
>
> Can you let me know the exact version of AMBER you are running along with
> what bugfixes have been applied.
>
> All the best
> Ross
>
>> -----Original Message-----
>> From: George Tzotzos [mailto:gtzotzos.me.com]
>> Sent: Sunday, December 12, 2010 8:10 AM
>> To: AMBER Mailing List
>> Subject: Re: [AMBER] error on running sander.MPI
>>
>> Apologies. Fingers are sometimes quicker than the mind.
>>
>> The installed compilers is gcc44.
>>
>> Just in case this helps in the diagnostics.
>>
>> Setting -np to 8 works.
>>
>> pmemd.MPI with -np 12 also works.
>>
>> Cheers
>>
>> George
>>
>>
>> On Dec 12, 2010, at 3:46 PM, George Tzotzos wrote:
>>
>>> Many thanks for the prompt reply.
>>>
>>> I'm using OSX 10.6.5 (2 x 2.93 GHz 6-Core Intel Xeon)
>>>
>>> The MPI is mpich2 and the compiler gcc installed from MacPorts
>>>
>>> The output file is attached.
>>>
>>> Many thanks
>>>
>>> George<heat.out>
>>>
>>>
>>>
>>>
>>> On Dec 12, 2010, at 3:32 PM, case wrote:
>>>
>>>> On Sun, Dec 12, 2010, George Tzotzos wrote:
>>>>>
>>>>> In the previous message mpirun -np was set to 12.
>>>>> Setting -np to 4 does not produce the same error. sander.MPI works.
>>>>
>>>> Can you tell us what version of MPI you are using, and which compilers
>> and OS?
>>>> Also, what was in the output file? (That is, did the failure occur
> right
>>>> away?)
>>>>
>>>> Second, could you try the simulation without the &rst namelist? That
>> facility
>>>> doesn't get used with minimization, and is not often used, so there
> might
>> be a
>>>> bug lurking related to that.
>>>>
>>>> ...thanks...dac
>>>>
>>>>
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>>>
>>
>>
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Received on Sun Dec 12 2010 - 10:30:05 PST
