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[Linux-cluster] Question about GFS2 and mmap



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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