Hi Steven,
As near as I can tell, the access times aren't getting updated, but when
I run BLAST on a second node, it also gets an EX lock on the inode. On
the other hand, if I run them simultaneously, they both get shared (SH)
locks (!?!):
node1:
lsof:
blastp 21730 root mem REG 253,8 46265880 88699363
/databases/mol/blast/db_current/nr.00.pin
lockdump:
G: s:SH n:2/54971e3 f:q t:SH d:EX/0 l:0 a:0 r:3
I: n:1055306/88699363 t:8 f:0x10 d:0x00000000 s:46265880/46265880
node2:
blastp 18052 root mem REG 253,0 46265880 88699363
/databases/mol/blast/db_current/nr.00.pin
G: s:SH n:2/54971e3 f:q t:SH d:EX/0 l:0 a:0 r:3
I: n:1055306/88699363 t:8 f:0x10 d:0x00000000 s:46265880/46265880
It seems like the mmap proactively grabs an exclusive lock (perhaps in
preparation to update the atime?) if it can. The problem with this
strategy, is that it appears as though when the lock gets demoted from
an exclusive lock to a shared lock, any cached pages are flushed,
resulting in a significant decrease in repeated performance. The
biggest issue from out perspective is what appears to be the flush of
the cached pages since that a huge impact on the performance of this
particular application.
Thanks again for your help on this!
-- scooter
On 01/18/2011 03:41 AM, Steven Whitehouse wrote:
Hi,
On Mon, 2011-01-17 at 11:06 -0800, Scooter Morris wrote:
Steven,
Thanks for getting back to me. Yes, I've checked and noatime is
definitely set. While blast was running, I did a lockdump and the
mmaped files had EX locks on them:
G: s:EX n:2/5497229 f:q t:EX d:EX/0 l:0 a:0 r:3
I: n:1055314/88699433 t:8 f:0x10 d:0x00000000 s:55237024/55237024
where inode 88699433 is one of the mapped files:
[root@crick blast]# ls -li /databases/mol/blast/db_current/nr.01.pin
88699433 -rw-r--r-- 1 rpcuser sacs 55237024 Jan 17 02:53
/databases/mol/blast/db_current/nr.01.pin
so that explains the behavior. What I don't understand is why they had
EX locks. I did an strace of the blast, and what I see when the files
are mmaped is something like:
stat("/databases/mol/blast/db/nr.01.pin", {st_mode=S_IFREG|0644,
st_size=55237024, ...}) = 0
open("/databases/mol/blast/db/nr.01.pin", O_RDONLY) = 8
mmap(NULL, 55237024, PROT_READ, MAP_SHARED, 8, 0) = 0x2b9ec1a14000
Where /databases/mol/blast is the gfs2 filesystem. So, the files are
not opened read/write, and the mmap'ed segment is not read/write. It's
not clear why gfs2 would create an exclusive glock for this file? Does
this make any sense to you?
-- scooter
Well it depends on the history of the glock in question. Once a glock
has been cached in exclusive mode, it will never be dropped unless (a)
there is memory pressure and the glock is reclaimed or (b) another node
requests it.
So if there has been only a single node doing read only work on the
inode and previous to that something on that same node wrote to that
inode, then it will still be in exclusive mode. A read only request from
a different node should push the glock into shared mode (on both nodes)
and if that isn't happening correctly, then it sounds like something has
gone awry somewhere.
The other thing, is that mmap() itself does grab an exclusive lock on
the inode - it has to update atime if that is turned on (but it doesn't
take any locks if atime is turned off as in your case). Note that this
is only the initial call to mmap() though, and the locks taken during
page faults are either shared or exclusive according to the type of
fault (read or write).
If you could check the atime before the mmap and after it, that should
tell us if there is a problem with the noatime check here.
If that still doesn't work, I'll try and duplicate what you are doing
with a small test program and see if I can reproduce the problem,
Steve.
On 01/16/2011 07:32 AM, Steven Whitehouse wrote:
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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