From: Sridhar Kumar Kannam (srisriphy_at_gmail.com)
Date: Thu Mar 21 2013 - 23:31:06 CDT
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.
I have run the script with just one node and one task per node, which means
I have a total of 16G memory, which is more than enough for a system with a
few million atoms.
but I got the same memory error ....
On Tue, Mar 19, 2013 at 6:50 PM, Norman Geist <
norman.geist_at_uni-greifswald.de> wrote:
> Hi Sridhar,****
>
> ** **
>
> I guess I know what the problem is. It seems that you confused a cluster
> as “one machine” which is not true. The output you posted says you are
> using 32 physical nodes, which points to a cluster, maybe a IBM super
> computer. But it’s not one machine, it’s a cluster. And here’s the
> problem. Some parts of the initialization phase of namd are only done at
> one processor, mostly zero, and this processor needs more ram to read your
> huge files. So this single processor cannot use the distributed memory of a
> cluster in the way it is currently implemented in namd.****
>
> ** **
>
> You should try to find a node that has enough local memory available.****
>
> ** **
>
> Another, but unlikely, option would be the malloc() command. If it has the
> same weakness in c++ as it had in fortran, it can only allocate 2GB at
> once, as the input parameter is a signed int, but that’s really unlikely,
> IMHO it’s the local memory. ****
>
> ** **
>
> How big is this psf file?****
>
> ** **
>
> Best wishes****
>
> ** **
>
> Norman Geist.****
>
> ** **
>
> *Von:* Sridhar Kumar Kannam [mailto:srisriphy_at_gmail.com]
> *Gesendet:* Dienstag, 19. März 2013 01:04
> *An:* Norman Geist
> *Betreff:* Re: namd-l: NamdMemoryReduction - genCompressedPsf****
>
> ** **
>
> Hi Norman,****
>
> ** **
>
> Sorry for the late response, I was on vacation.****
>
> ** **
>
> I have attached the config and log files.****
>
> ** **
>
> Best,****
>
> ** **
>
> ** **
>
> On Wed, Mar 13, 2013 at 5:54 PM, Norman Geist <
> norman.geist_at_uni-greifswald.de> wrote:****
>
> Ok sorry, I just meant the namd config file, not the pdb and parameter,
> and also the output file, which can’t be big as it crashes.****
>
> ****
>
> Norman Geist.****
>
> ****
>
> *Von:* Sridhar Kumar Kannam [mailto:srisriphy_at_gmail.com]
> *Gesendet:* Mittwoch, 13. März 2013 06:09****
>
>
> *An:* Norman Geist
> *Betreff:* Re: namd-l: NamdMemoryReduction - genCompressedPsf****
>
> ****
>
> Hi Norman,****
>
> ****
>
> Thank you very much for your help ....****
>
> The files are too big to send over an email...****
>
> I will send you the tcl script to build the system and other necessary
> files to your email ID only in a day or two.****
>
> If we find the solution, then we can post back to NAMD.****
>
> ****
>
> Best,****
>
> ****
>
> ****
>
> On Tue, Mar 12, 2013 at 5:58 PM, Norman Geist <
> norman.geist_at_uni-greifswald.de> wrote:****
>
> 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 :)****
>
>
>
> ****
>
> ****
>
> --
> Cheers !!!
> Sridhar Kumar Kannam :)
>
> ****
>
>
>
> ****
>
> ** **
>
> --
> Cheers !!!
> Sridhar Kumar Kannam :)
>
>
> ****
>
-- Cheers !!! Sridhar Kumar Kannam :)
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