charmm scalability on 2.4 kernels

Steve Fellini steve at
Sat Jan 5 10:10:30 PST 2002

Hi All,

Many of our users run charmm dynamics using Ewald/PME calculations,
which require 3D FFTs.  When run in parallel on a cluster, these
calculations scale moderately well to around 2-4 nodes (4-8
processors) when run on either nodes on a Myrinet network, or on nodes
running on fast ethernet with Linux 2.2.16 kernels with Josip
Loncaric's tcp fix (see

However for nodes running on ethernet with Linux 2.4.12 (i.e., without
the tcp fix) scalability is very poor - so much so that there's no
point in running on more than one node (see and image005.gif).

Has anyone successfully configured/tuned the 2.4 kernel to improve
scalability of parallel jobs with non-trivial communications?


Steven Fellini
Center for Information Technology
National Institutes of Health 
steven.fellini at

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