NAMD stalled at startup phase 0 when working on a large numbr of processors

From: lucie delemotte (
Date: Wed Mar 24 2010 - 13:07:44 CDT

Hi all,

I'm trying to run benchmarks for a large system (~1 000 000 atoms) on Jade
(SGI Altix ICE 8200 cluster, Cines computing center, Montpellier,
France). For a small number of processors (under 512), everything works fine
but when going above, the simulation stalls at:

Info: Entering startup phase 0 with 70768 kB of memory in use.

It seems that the issue does not come from NAMD but from the cluster and the
guys at the computing center are looking into it but I was wondering if
anyone can give me some indication about what might be going on to help them
go in the right direction.



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