[khmer] exceeding defined RAM limits?

[Oh, Julia (NIH/NHGRI) [F]]

[ohjs at helix khmer]$ git checkout master
Branch master set up to track remote branch master from origin.
Switched to a new branch 'master'
[ohjs at helix khmer]$ make

===> lots of stuff, ending with:

copying build/lib.linux-x86_64-2.6/khmer/_khmermodule.so -> khmer
make[1]: Leaving directory `/home/ohjs/khmer/python'


[ohjs at helix khmer]$ git branch
  bleeding-edge
* master





On Dec 18, 2013, at 8:10 AM, C. Titus Brown <ctb at msu.edu> wrote:

> On Wed, Dec 18, 2013 at 03:07:57AM +0000, Oh, Julia (NIH/NHGRI) [F] wrote:
>> Titus?thanks for the tip on variable coverage; will definitely try that out.
> 
> Great -- should significantly improve sensitivity to low coverage "stuff"!
> 
>> Michael?pretty sure I did a git clone. The last date in my directory is Sept 5th?but not sure if that would be pull date or your last modified date.
> 
> OK, and then one last check... did you check out the 'master' or 'legacy'
> branch?  What does 'git branch' report?
> 
> To check out master, do:
> 
> git checkout master
> make
> 
> cheers,
> --titus
> 
>> On Dec 17, 2013, at 8:16 PM, Michael R. Crusoe <mcrusoe at msu.edu<mailto:mcrusoe at msu.edu>> wrote:
>> 
>> Hello Julia,
>> 
>> What version of khmer are you using?
>> 
>> That is, did you install via `pip` or a `git clone`?
>> 
>> 
>> On Tue, Dec 17, 2013 at 5:14 PM, C. Titus Brown <ctb at msu.edu<mailto:ctb at msu.edu>> wrote:
>> 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 [0] -- but would require you to modify
>>> the script at the moment.  If you're up for that, put
>>> 
>>>      ht.set_use_bigcount(False)
>>> 
>>> 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?!
>> 
>> cheers,
>> --titus
>> --
>> C. Titus Brown, ctb at msu.edu<mailto:ctb at msu.edu>
>> 
>> _______________________________________________
>> khmer mailing list
>> khmer at lists.idyll.org<mailto:khmer at lists.idyll.org>
>> http://lists.idyll.org/listinfo/khmer
>> 
>> 
>> 
>> --
>> Michael R. Crusoe: Software Engineer and Bioinformatician  mcrusoe at msu.edu<mailto:mcrusoe at msu.edu>
>> @ the Genomics, Evolution, and Development lab; Michigan State University
>> http://ged.msu.edu/     http://orcid.org/0000-0002-2961-9670    @biocrusoe<http://twitter.com/biocrusoe>
>> 
> 
> -- 
> C. Titus Brown, ctb at msu.edu