Hi,
I found where annotation_hg18_megatest consumes almost all of the memory. In
mysqlannot_test(), megatest uses all the memory in following process. Does
anybody have an idea what is going on?
snp_db = seqdb.AnnotationDB(snp_slices, hg18, 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'))
Yours,
Namshin Kim
On Tue, Jul 14, 2009 at 5:36 AM, C. Titus Brown <[email protected]> wrote:
>
> On Mon, Jul 13, 2009 at 01:28:10PM -0700, Christopher Lee wrote:
> -> Hi Namshin, Marek,
> -> is there a way we can incorporate a measurement of memory usage into
> -> the megatests? This is a critical measure of performance, and we need
> -> an immediate warning if changes introduced to master break proper
> -> cache freeing. At this point, it'll be a pain in the ass trying to
> -> track down when cache clearing was broken, if it is now broken as
> -> Namshin says.
>
> You could also query the gc for # of objects, etc. and place that in the
> assertions; it shouldn't change dramatically.
>
> Or artificially limit the amount of available memory with ulimit.
>
> --titus
>
> >
>
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