Weekly ReportBy: Devin Trejo

Week of July 6, 2015-> July 12, 2015

Previous Goals

• WE2 Workshop• Isip security cleared and domain name responding on world wide

web.• Purchase hardware for cluster!?• Create a list of compensation budget management issues that need to

be address.• Finish 2014 NEDC Corpus.

Accomplishments

WE2 WorkshopBudget

• Met with Dr. Picone to calculate fringe benefits. • We balanced the compensation budget sheets to date.

Accomplishments

ISIP Website: No accomplishment• Still waiting for security approval to get the server on public domain.

Git• Web server is waiting for IT security approval -> couldn't thoroughly test the

environment. • Main boot drive throwing SMART errors

Accomplishments (cont.)Cluster

• Finalized the compute cluster build configuration• Contacted several vendors (to get the best deal possible).

• WebEx session w/ Dr. Picone to discuss cluster serial job parallelization across nodes.

• If you specify a job to run on nodes=3:ppn=2 and submit a PBSJOB script with multiple serial jobs it will run on one node exclusively. The other two nodes will sit idle and the job schuelder will not submit new jobs to those idle nodes.

• If you set the ppn=2 while the node has 4 cores and submit multiple serial jobs use a PBSJOB script, it will run on all four codes on the node. The job scheduler doesn't restrict core usage for a job even when specifying a ppn count.

• I'm currently experimenting currently with a OpenMPI/pbsdsh approach to running multiple serial jobs in parallel.

Accomplishments (cont.)NEDC

• Spell check for 2014 is done. • Copied in 16 out of 44 new CDs. These are for release_2015 book_17.

Status:

Reports: Session Count

Access mModal HC Missing

Release_2014 3013 (2977 w/ Reports) 1746 971 260 35

Release_2015 490 (458 w/ Reports) 286 164 8 30

# Function Description Status 1st Pass Status 2nd Pass

1 chck_mrns Finds: No. Records Found, Duplicate MRNs, Multiple MRNs Done 05/18/2015Done 05/26/2015

2 check_fnames Checks file_name syntax (Len(MRN)=8, Len(Date)=8, appendix) Done 05/18/2015 Done 05/26/2015

3 check_dirs Checks to ensure we have all necessary files in a directory Done 05/19/2015Done 05/26/2015

4 check_prerelease outputs the files we need to exist in each directory Done 05/25/2015 Done 05/26/2015

5 check_names Compares names in NPA to reports Done 05/25/2015 Done 05/26/2015

6 check_eg Checks to see if de-identified = source Done 05/25/2015 Done 05/26/2015

7 word_frequency A tool to look for patient names, ect N/ADone 05/26/2015

8 spell_check Spell check the reports N/ADone 07/09/2015

9 check_special_words Checks for special words that correlate to identifiable information N/ADone 05/27/2015

New Goals

WebServer• Webserver security checked. • GitLab testNEDC• Rerun all the checks on 2014, including check_mrms across the entire database, to make

sure we didn't miss anything.• Digitize and store the new CDs• Move forward on 2015Cluster• Purchase hardware for cluster!? (week2)• Test further ways to parallelize jobs across multiple nodes.Poster