[BioBrew Users] zombie HPL processes, was: disabling non-SGE access to the cluster

Bill Barnard bill at barnard-engineering.com
Tue Sep 2 18:00:04 EDT 2003

On Fri, 2003-08-29 at 19:37, Glen Otero wrote:


I'm happy to report you were exactly correct. HPL is now running
properly for me. I hope to have more interesting things to write about
soon! I am extremely grateful for your help.



> WRT to HPL zombie processes, if the compute nodes are not pentium
> 4processors, then you might see zombie process behavior. The
> binariesfor hpl were optimized for the
> Pentium 4 and uses instructions (SSE2) not available on Pentium III or
> Athlon. The solution is to recompile the ATLAS library, install it and
> rebuild hpl against it. It is easiest to just download the
> Atlaslibraries from netlib (prebuilt)
> http://www.netlib.org/atlas/archives/linux/
> But if you want to rebuild atlas and hpl from scratch, you shouldstart
> by checking out a Rocks CVS source tree.
> # cvs -d :pserver:anonymous at cvs.rocksclusters.org: /home/cvs/CVSROOT/
> \
> checkout -r ROCKS_2_3_2_i386 rocks-src
> and make sure to get the 2_3_2 version and not the HEAD
> Rebuild and install ATLAS:
> # cd rocks/src/contrib/atlas
> # make rpm
> # rpm -Uvh --force /usr/src/redhat/RPMS/i386/atlas*rpm
> Rebuild HPL (no need to install it on the frontend if you don't runhpl
> on the frontend):
> # cd rocks/src/contrib/hpl
> # make rpm
> Rebuild your distribution:
> # cd /home/install
> # rocks-dist dist
> Reinstall your compute nodes:
> #shoot-node compute-0-1 compute-0-1...

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