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

From: Peter Freddolino (
Date: Mon Jan 19 2009 - 07:41:43 CST

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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