Re: The limit of atom number on Blue Gene/L

From: Peter Freddolino (
Date: Mon Jan 19 2009 - 18:40:24 CST

Hi Fred,
where does it say on the wiki that this functionality has been
incorporated into the released binaries? As noted on the wiki, you need
to compile from source (and you'll need to get the cvs version, at least
until 2.7 releases start showing up).

Fred (Rui FENG) wrote:
> Hi Peter,
> Thank you for your reply.
> I tried to generate the compressed PSF but failed. I downloaded a
> binary version for AMD64 and added the "genCompressedPsf on" in the
> configuration file. When I ran the command ./namd abc.txt (the conf
> file name), an error occurred:
> ERROR: The following variables were set in the
> ERROR: configuration file but are NOT VALID
> ERROR: genCompressedPsf
> It seems that the pre-compiled version of NAMD doesn't support the
> parameter "genCompressedPsf", but in the wiki it says the function has
> been integrated in the binary. Do you think it's necessary to compile
> the source code? Thank you!
> Fred
> On Mon, Jan 19, 2009 at 8:41 AM, Peter Freddolino <> wrote:
>> Hi Fred,
>> you should be able to simulate meaningful systems that are a bit larger
>> by using NAMD's compressedPsf features; please follow the directions at
>> Fred (Rui FENG) wrote:
>>> Hi All,
>>> Is there anyone who tested the limit of atom number on Blue Gene/L? My
>>> answer is 1 million (no bonds) on 512/1024/2048 nodes, no matter the
>>> scale of partitions. For example, when I submit a job that has more
>>> than 1 million particles (say, 1.1 million) on 512 nodes with VN mode,
>>> the NAMD crashes. But When I submit the same job on 1024 nodes or 2048
>>> nodes, it still crashes.
>>> Can you give me some experience about how to run millions of particles
>>> (no bonds) on Blue Gene/L? Is there any compile option or argument I
>>> can set? Thank you so much!
>>> Have a nice day!
>>> Fred

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