RE: Automatic GPU selection in NAMD ?

From: Jesper Sørensen (lists_at_jsx.dk)
Date: Tue May 17 2011 - 05:41:03 CDT

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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