AW: NamdMemoryReduction - genCompressedPsf

From: Norman Geist (norman.geist_at_uni-greifswald.de)
Date: Tue Mar 12 2013 - 01:58:11 CDT

Can we see the input/output for/of the compression attempt?

 

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: Montag, 11. März 2013 23:18
An: Norman Geist
Cc: Namd Mailing List
Betreff: Re: namd-l: NamdMemoryReduction - genCompressedPsf

 

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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