Parallelization of mutation annotation

broadinstitute / oncotator

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Parallelization of mutation annotation #239

Open alexramos opened 10 years ago

alexramos commented 10 years ago

Parallelization of mutation annotation would dramatically improve performance of Oncotator on a single machine.

LeeTL1220 commented 10 years ago

Issue

No multicore support for annotation -- Only some datasource initialization can be done multicore

Solution

Use chunking and proxy managers to annotate multicore
Proof-of-concept tested in experimental GAF code
This will give us a large speed boost for everything -- except Firehose (or whenever --no-multicore specified)
Must be aware of potential concurrency issues, but most are identified already. Few concurrency issues exist, because the datasources are read-only once annotation starts

LeeTL1220 commented 10 years ago

Somehow this escaped getting assigned an issue.

On Thu, Nov 20, 2014 at 11:48 AM, Alex Ramos notifications@github.com wrote:

Parallelization of mutation annotation would dramatically improve performance of Oncotator on a single machine.

— Reply to this email directly or view it on GitHub https://github.com/broadinstitute/oncotator/issues/239.

Lee Lichtenstein Broad Institute 75 Ames Street, Room 7003M Cambridge, MA 02142 617 714 8632