Hi Marek, I ran the megatest with checkFirstID=False option, and it still uses almost 2.5GB memory. Maybe it would be the minimum memory requirements.
deepreds 13699 64.6 1.2 607512 420904 pts/1 R 17:24 2:58 deepreds 13699 82.1 1.6 731100 544620 pts/1 R 17:24 7:54 deepreds 13699 87.7 1.6 731100 544620 pts/1 R 17:24 12:49 deepreds 13699 90.4 1.6 731104 544624 pts/1 R 17:24 17:45 deepreds 13699 90.3 5.1 2147928 1700528 pts/1 R 17:24 22:14 deepreds 13699 91.5 5.3 2147928 1752012 pts/1 R 17:24 27:07 deepreds 13699 92.4 5.4 2147928 1804292 pts/1 R 17:24 31:59 deepreds 13699 93.0 5.6 2147928 1851724 pts/1 R 17:24 36:51 deepreds 13699 93.5 5.6 2147928 1867856 pts/1 R 17:24 41:44 deepreds 13699 93.9 5.6 2147928 1878332 pts/1 R 17:24 46:36 deepreds 13699 94.2 5.7 2147928 1899956 pts/1 R 17:24 51:28 deepreds 13699 94.5 5.7 2147928 1908628 pts/1 R 17:24 56:21 deepreds 13699 94.7 5.8 2147932 1913468 pts/1 R 17:24 61:13 deepreds 13699 94.9 5.8 2147932 1919276 pts/1 R 17:24 66:06 deepreds 13699 95.1 5.8 2147932 1921768 pts/1 R 17:24 70:58 deepreds 13699 95.2 5.8 2147932 1934852 pts/1 R 17:24 75:50 deepreds 13699 94.6 5.8 2143660 1934944 pts/1 S 17:24 80:06 deepreds 13699 92.9 6.5 2427684 2154680 pts/1 D 17:24 83:15 -- Namshin Kim On Fri, Aug 28, 2009 at 2:43 AM, Marek Szuba <[email protected]> wrote: > > Hello Namshin and everyone else, > > Chris and I talked about the megatest memory-consumption issue > yesterday and we might have found a way of addressing it. Could you > check whether passing checkFirstID=False to the AnnotationDB > constructor helps when the entire megatest is run? > > I have just tested this on llpygr using the following code: > > from pygr import sqlgraph, seqdb, worldbase > hg18 = worldbase("Bio.Seq.Genome.HUMAN.hg18") > snp_slices = sqlgraph.SQLTableClustered('PYGR_MEGATESTS.pygr_snp126_hg18', > clusterKey = 'clusterKey', maxCache = 0) > snp_db = seqdb.AnnotationDB(snp_slices, hg18, checkFirstID=XXX, > sliceAttrDict = dict(id = 'chromosome', gene_id = 'name', snp_id = > 'snp_id', score = 'score', ref_NCBI = 'ref_NCBI', ref_UCSC = > 'ref_UCSC', observed = 'observed', molType = 'molType', myClass = > 'myClass', myValid = 'myValid', avHet = 'avHet', avHetSE = > 'avHetSE', myFunc = 'myFunc', locType = 'locType', myWeight = > 'myWeight')) > > If XXX is True (the default), the prompt goes away for a few minutes, > with the amount of used memory gradually increasing from about 1.8 to > about 3 GB. If on the other hand XXX is False, the prompt comes back > instantaneously and memory usage hardly changes. > > Cheers, > -- > MS > > > > --~--~---------~--~----~------------~-------~--~----~ You received this message because you are subscribed to the Google Groups "pygr-dev" group. To post to this group, send email to [email protected] To unsubscribe from this group, send email to [email protected] For more options, visit this group at http://groups.google.com/group/pygr-dev?hl=en -~----------~----~----~----~------~----~------~--~---
