memory leak

Brian LaMere blamere at
Tue Dec 17 18:43:18 PST 2002

Having not gotten very far, I thought I'd ask you all for some advice...

I have a memory leak ... somewhere.  It *appears* to be an nfs file caching
issue.  The nodes pick up 750Mb files from an NFS server, and crunch on
them.  They're only doing this to one at a time.

After about a week, they've used up all the memory on the systems.  I say
all.../almost/ all.  Never all.  Never is the swap used, and of the 2Gb ram
on each node, there's always 16-40Mb free minimum.  Problem is that the
nodes lose the ability to cache those 750Mb files, and have to then start
going out and grabbing it after each and every run.  Since a job takes only
a couple seconds, having to grab it each time is terribly inefficient.

The master (which has 3.25Gb ram) exhibits the same behavior - for whatever
reason, almost all of its memory is used up too.  Nothing short of (blech)
rebooting the systems will clear out the memory.  Then, after about a week,
they're all full again.

The particular file they're caching right now has been the same since Sep24,
and absolutely nothing non-data related has changed on the cluster (ie, OS
files, modules, settings, whatnot) since the beginning of September.  There
have been some external changes, but...  This problem has only been
occurring for about a month.

Top doesn't report anything using a lot of memory (a few 0.2's, a few 0.1's,
then 0.0's percentage-wise for master), and when sorted by memory usage
nothing over 1% is listed.  "free" doesn't even show an exorbitant amount
being used for cacheing, I'm just led to believe its that due to the fact
that the memory never gets 100% used (I can increase the load, even when
there is only 16M free of memory, and swap won't be touched).

Instead of going through and telling everyone all the things I've tried for
the last month (would take a long while), I'd rather just see what sort of
suggestions people might have.  Where does one find a memory hole?
Malicious code is, I suppose, theoretically possible.  Unfortunately (damn
it) I don't have tripwire up, but I'm not terribly sure that would matter.
It just doesn't feel like that's the right direction.

Suggestions?  Thoughts?  Advice?  I'm open for anything.  Rebooting the
cluster once a week hurts...have to though, cause it takes down the nfs
server otherwise (what with constant requests for 750Mb files).  I can't
think of anywhere else to look other than where I have already.  I've stared
at the proc tree so long I'm goin crazy.

basic info:
Nodes are dual 1ghz p3's, with 2Gb ram and a 18gb local disk.
Master is dual 1ghz p3 with 3.25Gb ram and mirrored 36 Gb disk.
Running Scyld 28cz4rc3
Running nfs version 3

/proc/sys/vm/bdflush (not changed, at default):
40	0	0	0	500	3000	60	0	0

(hopeful) pre-emptive thanks,
Brian LaMere
Diversa Corp

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