[Linux-cluster] Question about GFS2 and mmap

[Steven Whitehouse]

Hi,

On Sat, 2011-01-15 at 16:46 -0800, Scooter Morris wrote:
> 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
> 
Are you sure that the noatime mount option has been used? I can't figure
out why that shouldn't work if the BLAST processes are really only
reading the files and not writing to them.

GFS2 is able to tell the difference between read and write accesses to
shared, writable mmap()ed files (unlike GFS which has to assume that all
accesses are write accesses). Some early versions of GFS2 did that too,
but anything recent (has ->page_mkwrite() in the source) and certainly
5.5 does, should be ok.

You can use the glock dump to see what mode the glock associated with
the mmap()ed inode is in. With RHEL6/Fedora/upstream you can use the
tracepoints to watch the state dynamically during the operations. I'm
afraid that isn't available on RHEL5. All you need to know is the inode
number of the file in question and then look for a type 2 glock with the
same number.

Let us know if that helps narrow down the issue. BLAST is something that
I'd like to see running well on GFS2,

Steve.

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