[khmer] exceeding defined RAM limits?
C. Titus Brown
ctb at msu.edu
Tue Dec 17 17:14:09 PST 2013
On Tue, Dec 17, 2013 at 04:36:34PM -0800, C. Titus Brown wrote:
> On Tue, Dec 17, 2013 at 07:53:18PM +0000, Oh, Julia (NIH/NHGRI) [F] wrote:
> Now, on to your real question :)
> > $python2.7 /home/ohjs/khmer/scripts/normalize-by-median.py -C 5 -k 20 -N 4 -x 16e9 round2.unaligned.keep.abundfilt;
> > I thought I would be maxing out at 64 GB ram for the hash table (I?ve also used 32e9), but I get the following RAM usage report of
> > 4986693.biobos elapsed time: 23358 seconds
> > 4986693.biobos walltime: 06:28:36 hh:mm:ss
> > 4986693.biobos memory limit: 249.00 GB
> > 4986693.biobos memory used: 249.76 GB
> > 4986693.biobos cpupercent used: 98.00 %
> What the heck!? That's not supposed to happen!
> This is either a bug, or (most likely) is being caused by an overabundance of
> high-abundance k-mers. The latter is easy to fix -- I've filed a bug report to
> fix the latter in the software overall  -- but would require you to modify
> the script at the moment. If you're up for that, put
> at line 186 of normalize-by-median:
Darn it, that can't be the problem; I just wrote a test against this
behavior and we actually did things right in the script and ignored
high abundance k-mers.
So, this must be a bug of some sort. Umm... Michael, any ideas?!
C. Titus Brown, ctb at msu.edu
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