Re: problem with gpu namd 2.9b3

From: Peter Jones (pm-jones_at_bigpond.com)
Date: Mon Apr 23 2012 - 01:00:11 CDT

Hi,

I just discovered that the problem was in my PBS submission script. I needed- select=(number of nodes):ncpus=12:mpiprocs=12:ngpu=1:mem=xxGB, for a machine with two 6 core processors and one gnu per node. Thanks for your help and apologies for wasting peoples time, hopefully the post will save it happening again!

Cheers,
Peter

On 23/04/2012, at 3:45 PM, Norman Geist wrote:

> Hi,
>
> ok, does the restarts also work somewhere else?
>
> Mit freundlichen Grüßen
>
> Norman Geist.
>
>> -----Ursprüngliche Nachricht-----
>> Von: Peter Jones [mailto:pm-jones_at_bigpond.com]
>> Gesendet: Freitag, 20. April 2012 07:55
>> An: Norman Geist
>> Betreff: Re: namd-l: problem with gpu namd 2.9b3
>>
>> Hi Norman,
>>
>> thanks for your reply. Yes the simulation was run to 100M steps on
>> another machine, using Namd 2.7b3 and the same protocol etc, I'm just
>> trying to restart this simulation on the new machine,
>>
>> Cheers,
>> Peter
>>
>>
>>
>>
>>
>> On 20/04/2012, at 3:45 PM, Norman Geist wrote:
>>
>>> Hi Peter,
>>>
>>> Does the same inputs work with another namd version?
>>>
>>> Best wishes
>>>
>>> Norman Geist.
>>>
>>>> -----Ursprüngliche Nachricht-----
>>>> Von: owner-namd-l_at_ks.uiuc.edu [mailto:owner-namd-l_at_ks.uiuc.edu] Im
>>>> Auftrag von Peter Jones
>>>> Gesendet: Donnerstag, 19. April 2012 11:31
>>>> An: namd-l_at_ks.uiuc.edu
>>>> Betreff: namd-l: problem with gpu namd 2.9b3
>>>>
>>>> Hello,
>>>>
>>>> I'm trying to run a simulation using Namd 2.9b3 on a cluster with
>> gpu
>>>> acceleration; its a continuation of a job that was running on
>> another
>>>> machine. Namd starts ok, prints out the energies for step 0, and
>> then
>>>> prints-
>>>>
>>>> LDB: ============= START OF LOAD BALANCING ============== 11.8193
>>>> LDB: ============== END OF LOAD BALANCING =============== 11.8194
>>>> LDB: =============== DONE WITH MIGRATION ================ 11.8197
>>>> 0:961(5) atom 32894 found 2 exclusions but expected 3
>>>> 0:1042(50) atom 40634 found 2 exclusions but expected 3
>>>>
>>>> followed by a long list of messages similar to the last two lines.
>> This
>>>> is followed by a list of errors regarding RATTLE constraint failures
>>>> and then termination. I'm new to gpu-accelerated NAMD and I do not
>> have
>>>> any idea what is wrong here, any help would be greatly appreciated,
>>>>
>>>> Thankyou,
>>>>
>>>> Kind Regards,
>>>> Peter Jones
>>>>
>>>
>>>
>>>
>
>

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