We have a RedHat cluster (5.5 currently) with 3 nodes, and are sharing a
number of gfs2 filesystems across all nodes. One of the applications we
run is a standard bioinformatics application called BLAST that searches
large indexed files to find similar dna (or protein) sequences. BLAST
will typically mmap a fair amount of data into memory from the index
files. Normally, this significantly speeds up subsequent executions of
BLAST. This doesn't appear to work on gfs2, however, when I involve
other nodes. For example, if I run blast three times on a single node,
the first execution is very slow, but subsequent executions are
significantly quicker. If I then run it on another node in the cluster
(accessing the same data files over gfs2), the first execution is slow,
and subsequent executions are quicker. This makes sense. The problem
is that when I run it on multiple nodes, the speeds of subsequent runs
on the same node are no quicker. It almost seems as if gfs2 is flushing
the in-memory copy (which is read only) immediately when the file is
accessed on another node. Is this the case? If so, is there a reason
for this, or is it a bug? If it's a known bug, is there a workaround?
Any help would be appreciated! This is a critical application for us.
Thanks in advance,
-- scooter
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