Re: Oh dear, 'namd2 invoked oom-killer' ...

From: Nicholas M Glykos (
Date: Fri Apr 15 2011 - 12:16:06 CDT

Hi Jim,

> You don't say how long this ran before running out of memory, but there
> is a memory leak in trajector/restart output in NAMD 2.8b1. The bug has
> been fixed so please try a nightly build.

It was ~18 hours for 6G of physical memory. Before sending the message I
tried downloading the latest pre-made Linux-x86_64-CUDA nightly build, but
what I'm getting back is the NAMD_CVS-2011-03-21_Linux-x86_64-CUDA.tar.gz
archive (md5sum 731b8d7a9aec0f9a84f15caef73d9afe) containing executables
dated from 2011-03-21, older than those contained in the
NAMD_2.8b1_Linux-x86_64-CUDA.tar.gz archive (dated 2011-03-26). I must be
missing something here (again) ...


          Dr Nicholas M. Glykos, Department of Molecular Biology
     and Genetics, Democritus University of Thrace, University Campus,
  Dragana, 68100 Alexandroupolis, Greece, Tel/Fax (office) +302551030620,
    Ext.77620, Tel (lab) +302551030615,

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