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Nipun Sadvilkar
@nipunsadvilkar

Hi, I was running given example in plaintext using following command:
./bin/runCPE.sh examples/plaintext/PlainTextCPM_Example.xml which takes lot of memory and results into crash of system.

verbose output is as follows:
```

# nipunsadvilkar @ localhost in ~/Biomedicus [10:16:04] 
$ ./bin/runCPE.sh examples/plaintext/PlainTextCPM_Example.xml
2017-04-03 10:16:07,681 INFO  [main] SimpleRunCPE (SimpleRunCPE.java:59) - Instantiating CPE
2017-04-03 10:16:07,800 INFO  [main] GuiceInjector (GuiceInjector.java:50) - Initializing Guice Injector Resource
2017-04-03 10:16:07,809 INFO  [main] Bootstrapper (Bootstrapper.java:68) - Using configuration directory: /home/nipunsadvilkar/Biomedicus/config
2017-04-03 10:16:07,877 INFO  [main] Bootstrapper (Bootstrapper.java:109) - Using data directory: /home/nipunsadvilkar/Biomedicus/biomedicus-umls-data-1.5.0
2017-04-03 10:16:08,660 INFO  [main] VocabularyLoader (VocabularyLoader.java:50) - Loading words into term index from path: /home/nipunsadvilkar/Biomedicus/biomedicus-umls-data-1.5.0/vocabulary/words.txt
2017-04-03 10:16:10,905 INFO  [main] SpellingModel (SpellingModel.java:74) - Building BK tree for spelling model using 1491258 words.
2017-04-03 10:16:23,748 INFO  [main] SpellingModel (SpellingModel.java:79) - Loading Spelling n-grams from ARPA file: /home/nipunsadvilkar/Biomedicus/biomedicus-umls-data-1.5.0/spell/UPMC.arpa
2017-04-03 10:16:26,009 INFO  [main] TntModel$Loader (TntModel.java:142) - Loading TnT trigram model: /home/nipunsadvilkar/Biomedicus/biomedicus-umls-data-1.5.0/tnt/trigram.yml
2017-04-03 10:16:27,293 INFO  [main] TntModel$Loader$1 (TntModel.java:152) - Loading TnT word model #1: /home/nipunsadvilkar/Biomedicus/biomedicus-umls-data-1.5.0/tnt/words/8.yml
2017-04-03 10:16:43,395 INFO  [main] TntModel$Loader$1 (TntModel.java:152) - Loading TnT word model #2: /home/nipunsadvilkar/Biomedicus/biomedicus-umls-data-1.5.0/tnt/words/7.yml
2017-04-03 10:16:54,405 INFO  [main] TntModel$Loader$1 (TntModel.java:152) - Loading TnT word model #3: /home/nipunsadvilkar/Biomedicus/biomedicus-umls-data-1.5.0/tnt/words/5.yml
2017-04-03 10:16:55,719 INFO  [main] TntModel$Loader$1 (TntModel.java:152) - Loading TnT word model #4: /home/nipunsadvilkar/Biomedicus/biomedicus-umls-data-1.5.0/tnt/words/6.yml
2017-04-03 10:17:07,205 INFO  [main] TntModel$Loader$1 (TntModel.java:152) - Loading TnT word model #5: /home/nipunsadvilkar/Biomedicus/biomedicus-umls-data-1.5.0/tnt/words/9.yml
2017-04-03 10:17:14,956 INFO  [main] TntModel$Loader$1 (TntModel.java:152) - Loading TnT word model #6: /home/nipunsadvilkar/Biomedicus/biomedicus-umls-data-1.5.0/tnt/words/2.yml
2017-04-03 10:17:15,464 INFO  [main] TntModel$Loader$1 (TntModel.java:152) - Loading TnT word model #7: /home/nipunsadvilkar/Biomedicus/biomedicus-umls-data-1.5.0/tnt/words/3.yml
2017-04-03 10:17:15,909 INFO  [main] TntModel$Loader$1 (TntModel.java:152) - Loading TnT word model #8: /home/nipunsadvilkar/Biomedicus/biomedicus-umls-data-1.5.0/tnt/words/10.yml
2017-04-03 10:17:37,918 INFO  [main] TntModel$Loader$1 (TntModel.java:152) - Loading TnT word model #9: /home/nipunsadvilkar/Biomedicus/biomedicus-umls-data-1.5.0/tnt/words/1.yml
2017-04-03 10:17:38,503 INFO  [main] TntModel$Loader$1 (TntModel.java:152) - Loading TnT word model #10: /home/nipunsadvilkar/Biomedicus/biomedicus-umls-data-1.5.0/tnt/words/4.yml
2017-04-03 10:17:38,783 INFO  [main] NormalizerModelLoader (NormalizerModelLoader.java:55) - Loading normalization lexicon file: /home/nipunsadvilkar/Biomedicus/biomedicus-umls-data-1.5.0/normalization/lexicon.yml
2017-04-03 10:17:44,378 INFO  [main] NormalizerModelLoader (NormalizerModelLoader.java:59) - Loading normalization fallback lexicon file: /home/nipunsadvilkar/Biomedicus/biomedicus-umls-data-1.5.0/normalization/fallbackLexicon.yml
2017-04-03 10:17:47,304 INFO  [main] AcronymExpansionsModel$Loader (AcronymExpansionsModel.java:72) - Loading acronym expansions: /home/nipunsadvilkar/Biomedicus/biomedicus-umls-data-1.5.0/acronym/expansions.txt
2017-04-03 10:17:47,395 INFO  [main] AcronymVectorModel$Loader (AcronymVectorModel.java:281) - Loading acronym vector space: /home/nipunsadvilkar/Biomedicus/biomedicus-umls-data-1.5.0/acronym/vectorSpace.yml
2017-04-03 10:17:49,645 INFO  [main] AcronymVectorModel$Loader (AcronymVectorModel.java:285)
2017-04-03 10:17:49,645 INFO  [main] AcronymVectorModel$Loader (AcronymVectorModel.java:285) - Loading acronym sense map: /home/nipunsadvilkar/Biomedicus/biomedicus-umls-data-1.5.0/acronym/senseMap.ser
Java HotSpot(TM) 64-Bit Server VM warning: INFO: os::commit_memory(0x0000000582a00000, 1011875840, 0) failed; error='Cannot allocate memory' (errno=12)
#
# There is insufficient memory for the Java Runtime Environment to continue.
# Native memory allocation (mmap) failed to map 1011875840 bytes for committing reserved memory.
# An error report file with more information is saved as:
# /home/nipunsadvilkar/Biomedicus/hs_err_pid13674.log
I am using ubuntu x64 4 core, 8GB RAM
Ben Knoll
@benknoll-umn
To @nipunsadvilkar and anyone else reading this, that issue was caused by BioMedICUS’s high memory requirements, which we’ve worked to mitigate in the time since then. The current version of BioMedICUS, 1.8.1, requires 2 gb of memory, much less than it had previously required.
Alden
@aldencg
Hi all. I'm attempting to use biomedicus on a headless aws linux server. Installation seemed successful but running the plaintext example produces outputs with very few features (essentially just id and length) even though biomedicus seemed to run a number of detectors and annotators. Could you all offer me any guidance?
Thanks
As a side note, it looks like your example CPE descriptor doesn't work unless the command is run from the biomedicus home directory (it looks for the examples directory relative to its current path rather than via absolute path)
Alden
@aldencg
Solved the above, for future users this was an issue with parsing the XMI output. Use xmllint --format myoutput.xmi.
Alden
@aldencg
Is there a reason your negation recall might be lower than other negex implementations? Biomedicus seems to provide no negation terms for 'patient denies neuralgia', which is almost always caught by NegEx. I'm using the DefaultClinicalDocumentPipeline so modification detection should be included.
mikedemick
@mikedemick
Hi, do you have either plans or instructions for updating the data files to include post-covid-19 metathesaurus data?