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September 01, 2004

Setting up your .tcshrc file

The .tcshrc file is a resource file in your home directory that sets up certain environment variables. To set it up just copy and paste the following commands once you are logged in to miles:


echo "setenv FSLDIR /Volumes/local/fsl" > ~/.tcshrc
echo " set path = ( ~/bin /Volumes/local/bin /usr/bin /bin /usr/local/sbin /usr/sbin /sbin /usr/X11R6/bin $FSLDIR/bin . )" >> ~/.tcshrc

Cluster Benchmarking Results

I ran an FSL group analysis of 4 subjects with very long runs, and 7 copes.

Regular feat on Miles - 8h55m
feat_sge (FLAME split with Sun Grid Engine across 10 processors) - 1h13m

That's a speed increase of approx. 86%. For some reason the analysis only used 10 processors so this is fairly close to linear, which would be 90%. It should be able to take advantage of 14 (possibly 16 depending on configuration). I reran Feat on Miles just to duplicate the results, and got a time of 8h44m, which is a difference of about 2%. I also reran feat_sge and got 1h8m, a difference of about 10%. These increases simply represent what happens when nothing else is happening on Miles, as I was still working on Miles during the first runs.