Steve, are you using the ctakes-rest-service https://github.com/GoTeamEpsilon/ctakes-rest-service?
If so, do you have any pointers as to how to configure a custom dictionary (such as for ICD10) after installing the ctakes-rest-service. Because the ctakes-rest-service installation procedure involves building ctakes from source, the runCustomDictionary tool does not work…I have logged an issue here: https://github.com/GoTeamEpsilon/ctakes-rest-service/issues/56 I was wondering if you had any pointers in this regard, or know anything about how to implement their suggested solution of creating custom tables etc. From: Steve Evans <[email protected]> Sent: Tuesday, January 29, 2019 10:23 AM To: [email protected] Subject: RE: Processing large batches of files in cTAKES Leah, I run my ctakes work load using docker containers. I have built a container that serves ctakes requests via tomcat webservices. That’s not for the feint of heart and not for non-programmer types. But you might be able to install the ctakes software in a container with the input/output directories on the host and then run in parallel using file input/output. I run 10 containers to get the thru put we need (5/second). This is on a 16 cpu 64GB host (each container consumes about 2GB of ram) Not a slam dunk type answer but I thought it might help gen ideas Steve From: Baas,Leah <[email protected] <mailto:[email protected]> > Sent: Tuesday, January 29, 2019 12:59 PM To: [email protected] <mailto:[email protected]> Subject: Processing large batches of files in cTAKES Hi all, I would like to process a batch of 13,414 files (avg file size 6.2 KB) using the default clinical pipeline. I am new to cTAKES and computer programming, and I’m looking for guidance on how to process these files with maximum time/CPU efficiency. I am currently running my program on an Ubuntu VM with 3 CPUs. It takes me 28 seconds (real time) to process one 6.0 KB file. I’m reading up on parallel processing strategies, but would be grateful for any suggestions, tips, etc. that you might have! Thanks, Leah ----------------------------------------------------------------------- Confidentiality Notice: This e-mail message, including any attachments, is for the sole use of the intended recipient(s) and may contain privileged and confidential information. Any unauthorized review, use, disclosure or distribution is prohibited. If you are not the intended recipient, please contact the sender by reply e-mail and destroy all copies of the original message.
