From: Sridhar Kumar Kannam (srisriphy_at_gmail.com)
Date: Mon Mar 11 2013 - 17:18:12 CDT
Hi Norman and NAMD community
The node has 16 cores with 1024 GB memory.
For compression I am using the normal version only not the memory optimized
version.
I still have the same problem....
Any suggestions please ..
On Mon, Mar 11, 2013 at 5:56 PM, Norman Geist <
norman.geist_at_uni-greifswald.de> wrote:
> Hi Sridhar,****
>
> ** **
>
> didn’t know, shame on me, that 1TB nodes are already used out there. By
> the way, how many cores does your node has?****
>
> Please make sure that for compressing the PSF you did not used the memory
> optimized compile of namd. This feature is already implemented in the
> normal namd versions. I guess the memopt namd does only read compressed psf
> files so it fails cause of that maybe.****
>
> ** **
>
> Norman Geist.****
>
> ** **
>
> *Von:* Sridhar Kumar Kannam [mailto:srisriphy_at_gmail.com]
> *Gesendet:* Samstag, 9. März 2013 06:39
> *An:* Norman Geist
> *Betreff:* Re: namd-l: NamdMemoryReduction - genCompressedPsf****
>
> ** **
>
> Hi Norman,****
>
> ** **
>
> Yes I tried on a node with 1TB RAM memory.****
>
> ** **
>
> Can anyone please suggest a way around ..****
>
> ** **
>
> Thanks.****
>
> ** **
>
> On Fri, Mar 8, 2013 at 6:04 PM, Norman Geist <
> norman.geist_at_uni-greifswald.de> wrote:****
>
> 1TB memory? Could it be that you confuse memory (RAM) with disk space
> (HD)? ****
>
> ****
>
> Norman Geist.****
>
> ****
>
> *Von:* owner-namd-l_at_ks.uiuc.edu [mailto:owner-namd-l_at_ks.uiuc.edu] *Im
> Auftrag von *Sridhar Kumar Kannam
> *Gesendet:* Freitag, 8. März 2013 04:39
> *An:* namd-l_at_ks.uiuc.edu
> *Betreff:* namd-l: NamdMemoryReduction - genCompressedPsf****
>
> ****
>
> Hi All,****
>
>
>
> I am having a system with 3 million atoms. To use memory optimised version
> of NAMD, first I need to compress psf file.
> I followed the instructions on this web page -
> http://www.ks.uiuc.edu/Research/namd/wiki/?NamdMemoryReduction
> I am running the first step - genCompressedPsf - on a node with 1 TB
> memory, still it is giving the error - {snd:8,rcv:0} Reason: FATAL ERROR:
> Memory allocation failed on processor 0.
>
> Any suggestions please
>
>
>
> --
> Cheers !!!
> Sridhar Kumar Kannam :)
>
> ****
>
>
>
> ****
>
> ** **
>
> --
> Cheers !!!
> Sridhar Kumar Kannam :)
>
>
> ****
>
-- Cheers !!! Sridhar Kumar Kannam :)
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