Subject: Linux kernel 2.4 parallel scaling

From: Rick Venable <[email-masked]>
Date: Sat, 15 Dec 2001 13:58:39 -0500

Myself and others here at NIH have been benchmarking CHARMM and other
parallel chemistry codes on Linux clusters using MPICH libs with an
ethernet network.  Tests on 2.4.12 kernel nodes with 2, 4, and 8 procs
showed terrible parallel scaling, compared to the same tests run with
the 2.2.16-tcpfix kernel.

I'd expect that other people using Linux clusters for computational
chemistry may have encountered this already, and may have looked into
possible solutions.

For instance, are there some kernel parameters in /proc that can be used
to tune the communications performance?

Are there any other software solutions to this problem?

Suggestions appreciated; I will summarize.

=+=+=+=+=+=+=+=+=+=+=+=+=+=+=+=+=+=+=
Rick Venable
FDA/CBER/OVRR Biophysics Lab
1401 Rockville Pike    HFM-419
Rockville, MD  20852-1448  U.S.A.
(301) 496-1905   [email-masked]
ALT email:  [email-masked]
=+=+=+=+=+=+=+=+=+=+=+=+=+=+=+=+=+=+=

---

From: David Konerding <[email-masked]>
Date: Sat, 15 Dec 2001 13:45:36 -0800

>Are there any other software solutions to this problem?

Can you please let us know what sort of network card you are using,
whether zero-copy networking is enabled, and how many errors you
see on your link (run ifconfig).   I missed the fact earlier that
you got better scaling with 2.2.16-tcpfix.  This suggests to me that
you need to look into how you configured the kernel and what
other variables changed (or didn't change).  How do simple programs like
FTP compare between the two kernels?  That's the first thing I'd check.

Dave