From: Sridhar Kumar Kannam (srisriphy_at_gmail.com)
Date: Wed Apr 03 2013 - 00:05:39 CDT
Hi Norman,
Thanks for the suggestions. I am trying all possible ways.
Running on 1 core also didn't help.
Yes, I am using the queuing system and we don't have any restrictions on
the memory, we can use the total 16GB for each job.
I don't think its a bug in the psf/pdb file, I created a entirely different
system and tried to compress the psf files, but still got the same errors.
The error could be due to the configuration of the machine. Actually I
tried on two different machines, but got the same error.
On Fri, Mar 22, 2013 at 6:28 PM, Norman Geist <
norman.geist_at_uni-greifswald.de> wrote:
> Hi again,****
>
> ** **
>
> First of all, to create the compressed psf, you could also try just to run
> it with only 1 core, I think there’s not much to be parallelized in that
> case anyway, and the ram of one node should be sufficient.****
>
> ** **
>
> If that doesn’t help, maybe it would be worth it, to find to code part
> that prints the message, and to add a print to the size it tries to
> allocate. Maybe we can see something there. Are you using a queuing system?
> Could there be some restrictions to the maximum memory a job can use. Or
> check the output of “ulimit –a” on the nodes, to see if you are allowed to
> use enough of the ram. I think if it would be possibly that this is a bug,
> the developers would have already turned in. So it is whether some weird
> thing in the psf or pdb (maybe try to recreate them) or the configuration
> of your machine, IMHO. ****
>
> ** **
>
> Norman Geist.****
>
> ** **
>
> *Von:* Sridhar Kumar Kannam [mailto:srisriphy_at_gmail.com]
> *Gesendet:* Freitag, 22. März 2013 05:31
>
> *An:* Norman Geist
> *Cc:* Namd Mailing List
> *Betreff:* Re: namd-l: NamdMemoryReduction - genCompressedPsf****
>
> ** **
>
> Hi Norman,****
>
> ** **
>
> I actually run the compression on 1 node too but I sent you the output
> with 32 nodes.****
>
> Here I have attached output with 1 node.****
>
> ** **
>
> On each node we have 16G ram, and each node can do 64 tasks at a time. If
> we say 16 tasks per node in the script each task would take 1GB of memory--f46d0434c06018824804d96dce38--
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