Sweet! That was definitely it! It's flying now (granted, our files are not in the > 1 mb realm, like it the jira issue - just in the nnn.kb realm, but still!).
Mahalo nui loa! On Tue, Sep 24, 2019 at 6:29 PM Finan, Sean < sean.fi...@childrens.harvard.edu> wrote: > Hi Greg, > > Check your log to see what component is taking all the time. > > There is a known problem with the cleartk assertion annotators: > > https://issues.apache.org/jira/browse/CTAKES-449 > > A partial fix was made in the "windowed" sub-package of ctakes-assertion: > org.apache.ctakes.assertion.medfacts.cleartk.windowed. > > Each of the normal assertion engines has a replacement in the windowed > package. > > If you are using a piper file that contains "load AttributeCleartkSubPipe" > as the Default clinical pipeline does, just replace it with "load > WindowedAttributeCleartkSubPipe". > > It isn't a full fix for the problem, and I don't know if it will make your > processing faster, but you can give it a try. > > Sean > > ________________________________________ > From: Greg Silverman <g...@umn.edu> > Sent: Tuesday, September 24, 2019 6:47 PM > To: dev@ctakes.apache.org > Subject: Large files taking forever to process [EXTERNAL] > > Any suggestions on how to speed up processing large clinical text notes > approaching 13K lines? This is a very old corpus culled from EPIC notes > back in 2009. I thought about splitting the notes into smaller chunks, but > then I would have to deal with the offsets when analyzing system output > against manual annotations that had been done. > > As is, I've tried different garbage collection options (this seemed to have > worked well with CLAMP on the same set of notes). > > TIA! > > Greg-- > > -- > Greg M. Silverman > Senior Systems Developer > NLP/IE < > https://urldefense.proofpoint.com/v2/url?u=https-3A__healthinformatics.umn.edu_research_nlpie-2Dgroup&d=DwIFaQ&c=qS4goWBT7poplM69zy_3xhKwEW14JZMSdioCoppxeFU&r=fs67GvlGZstTpyIisCYNYmQCP6r0bcpKGd4f7d4gTao&m=kVCVyGR2m-zb7CsPmrrCeBL1N-9Z6tXZOp869xqkcBQ&s=TEirYUPMXTOjZ1PoJMxTXt7M8I5axwQI9zzNrvLmGRo&e= > > > Department of Surgery > University of Minnesota > g...@umn.edu > > › evaluate-it.org ‹ > -- Greg M. Silverman Senior Systems Developer NLP/IE <https://healthinformatics.umn.edu/research/nlpie-group> Department of Surgery University of Minnesota g...@umn.edu › evaluate-it.org ‹
