Re: Automatic GPU selection in NAMD ?

From: David McGiven (davidmcgivenn_at_gmail.com)
Date: Tue May 17 2011 - 06:02:29 CDT

Hi Jesper,

But I don't want to use all the avaliable gpu's. I want to use only 1
or 2 out of 4, but not knowing which of them are free.

I am wondering if there's a simple solution for that or if I will have
to create a script that parses through nvidia-smi output and crafts a
+devices argument with the avaliable GPU's. Not easy, nor elegant
solution though.

D.

On 17/05/2011, at 12:41, Jesper Sørensen wrote:

> Hi David,
>
> I meant use:
> namd ++idlepoll [...]
>
> Do not add the +devices flag. I assume that the way it works is that
> if you
> don't add it, NAMD will default to read "+devices all"
>
> Best,
> Jesper
>
>
> -----Original Message-----
> From: owner-namd-l_at_ks.uiuc.edu [mailto:owner-namd-l_at_ks.uiuc.edu] On
> Behalf
> Of David McGiven
> Sent: 17. maj 2011 12:34
> To: Jesper Sørensen
> Cc: 'namd-l'
> Subject: Re: namd-l: Automatic GPU selection in NAMD ?
>
> Thanks Jesper,
>
> It's strange ...
>
> If I use : namd ++idplepoll [...] +devices 0
>
> It works.
>
> If I use : namd ++idplepoll [...] +devices x
>
> It doesn't : Fatal error on PE 2> FATAL ERROR: CUDA error on Pe 2 (alf
> device 0): All CUDA devices are in prohibited mode, of compute
> capability
> 1.0, or otherwise unusable.
>
> I, of course, have checked the COMPUTE mode ruleset for the devices,
> and
> it's in 0, Default. I have set the two last GPU's to 1 and 2, so
> NAMD has
> all kinds of compute ruleset GPU's to chose from, but it still gives
> the
> same error.
>
> # nvidia-smi -s
> COMPUTE mode rules for GPU 0: 0
> COMPUTE mode rules for GPU 1: 0
> COMPUTE mode rules for GPU 2: 1
> COMPUTE mode rules for GPU 3: 2
>
> Do you know what might be happening ?
>
> Thanks.
>
> D.
>
>
> On 17/05/2011, at 12:05, Jesper Sørensen wrote:
>
>> Hi David,
>>
>> If you just leave out the "+devices x,x,x" it will use any available
>> GPU's on the nodes that you have requested, at least that works for
>> us
>> and we have
>> 3 GPU's per node. I will say that we have compiled NAMD with MPI
>> and I
>> don't know if that makes a difference.
>>
>> Best,
>> Jesper
>>
>>
>> -----Original Message-----
>> From: owner-namd-l_at_ks.uiuc.edu [mailto:owner-namd-l_at_ks.uiuc.edu] On
>> Behalf Of David McGiven
>> Sent: 17. maj 2011 11:59
>> To: namd-l
>> Subject: namd-l: Automatic GPU selection in NAMD ?
>>
>> Dear NAMD Users,
>>
>> Is there any way to tell NAMD to use a number of GPU's, but not the
>> specific device numbers ?
>>
>> Normally one would do :
>>
>> namd ++idplepoll [...] +devices 0,1 (for 2 GPU's) or namd +
>> +idplepoll [...]
>> +devices 0,1,2,3 (for 4 GPU's)
>>
>> But I would like not to state the specific device numbers, but
>> rather,
>> just "use 2 GPU's".
>>
>> This is because the cluster users do not know which GPU's are in use
>> or not.
>>
>> I know the best setup is to have one GPU per machine, and then one
>> avoids this kind of problems. But it's now like that and I would like
>> to know if someone has found any simple solution, or if NAMD has a
>> command for that (I Haven't found it in documentation).
>>
>> Thanks.
>>
>> Regards,
>> D.
>>
>

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