AW: NamdMemoryReduction - genCompressedPsf

From: Norman Geist (
Date: Mon Mar 11 2013 - 01:56:40 CDT

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 []
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 ...




On Fri, Mar 8, 2013 at 6:04 PM, Norman Geist
<> wrote:

1TB memory? Could it be that you confuse memory (RAM) with disk space (HD)?


Norman Geist.


Von: [] Im Auftrag
von Sridhar Kumar Kannam
Gesendet: Freitag, 8. März 2013 04:39
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 -
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 :)

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