[Bioperl-l] load_seqdatabase.pl memory requirements unusually large

Hilmar Lapp hlapp at gmx.net
Fri Feb 6 14:34:16 EST 2009


Something seems to cause Perl to be crapping out. It it were a  
programmatic exception you would see the message and the trace.

Could you run these tests by themselves:

	./Build test --test-files t/11locuslink.t

If that doesn't reveal the error, add a verbose=1 argument.

Let us know what you find.

	-hilmar

On Feb 6, 2009, at 11:03 AM, Michael Muratet wrote:

> Greetings
>
> I have use bioperl-db and load_seqdatabase.pl many times in the past  
> and it's worked pretty much out of the box.
>
> I have been trying to load fasta files from hg18. For chr1, the  
> virtual and resident memory quickly builds to 14 GB or so, then  
> starts using up the 2GB swap until it's full and then the system  
> hangs. The system is an 8-core Dell with 16GB of physical memory.  
> chr1.fa is ~242MB. All of the disk storage is network mounted on an  
> EMC system which (I am told) has a proprietary version of something  
> that's NFS-like.
>
> I loaded chrM (~17kb) and load_seqdatabase grew to over 4 GB before  
> it completed.
>
> I am using MySQL 5.0.51a-community, DBI 1.607, perl 5.85, bioperl  
> 1.6.0, bioperl-db 1.006900.
>
> I have the innodb engine enabled in MySQL and the buffers and caches  
> set for a 'large' system.
>
> I had some errors during the bioperl-db install:
>
> Test Summary Report
> -------------------
> t/01dbadaptor.t (Wstat: 256 Tests: 23 Failed: 1)
>  Failed test:  23
>  Non-zero exit status: 1
> t/10ensembl.t   (Wstat: 65280 Tests: 5 Failed: 0)
>  Non-zero exit status: 255
>  Parse errors: Bad plan.  You planned 18 tests but ran 5.
> t/11locuslink.t (Wstat: 65280 Tests: 7 Failed: 0)
>  Non-zero exit status: 255
>  Parse errors: Bad plan.  You planned 113 tests but ran 7.
> t/15cluster.t   (Wstat: 65280 Tests: 7 Failed: 0)
>  Non-zero exit status: 255
>  Parse errors: Bad plan.  You planned 162 tests but ran 7.
> Files=16, Tests=1205, 21 wallclock secs ( 0.51 usr  0.12 sys + 14.90  
> cusr  2.69 csys = 18.22 CPU)
> Result: FAIL
> Failed 4/16 test programs. 1/1205 subtests failed.
>
> The most recent bioperl-db documentation says that a workable  
> version may be possible after some errors and so I went ahead with  
> the install.
>
> The mailing list archive has some discussion about throughput but  
> nothing really about filling up memory.
>
> Can anyone offer any clues about what's going on or where to start  
> looking?
>
> Thanks
>
> Mike
> _______________________________________________
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> Bioperl-l at lists.open-bio.org
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-- 
===========================================================
: Hilmar Lapp  -:-  Durham, NC  -:-  hlapp at gmx dot net :
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