Uima Ruta Out of Memory issue in spark context

Question

I'm running an UIMA application on apache spark. There are million of pages coming into batches to be processed by UIMA RUTA for calculation. But some time i'm facing out of memory exception.It throws exception sometime as it successfully process 2000 pages but some time fail on 500 pages.

Application Log

Caused by: java.lang.OutOfMemoryError: Java heap space
        at org.apache.uima.internal.util.IntArrayUtils.expand_size(IntArrayUtils.java:57)
        at org.apache.uima.internal.util.IntArrayUtils.ensure_size(IntArrayUtils.java:39)
        at org.apache.uima.cas.impl.Heap.grow(Heap.java:187)
        at org.apache.uima.cas.impl.Heap.add(Heap.java:241)
        at org.apache.uima.cas.impl.CASImpl.ll_createFS(CASImpl.java:2844)
        at org.apache.uima.cas.impl.CASImpl.createFS(CASImpl.java:489)
        at org.apache.uima.cas.impl.CASImpl.createAnnotation(CASImpl.java:3837)
        at org.apache.uima.ruta.rule.RuleMatch.getMatchedAnnotations(RuleMatch.java:172)
        at org.apache.uima.ruta.rule.RuleMatch.getMatchedAnnotationsOf(RuleMatch.java:68)
        at org.apache.uima.ruta.rule.RuleMatch.getLastMatchedAnnotation(RuleMatch.java:73)
        at org.apache.uima.ruta.rule.ComposedRuleElement.mergeDisjunctiveRuleMatches(ComposedRuleElement.java:330)
        at org.apache.uima.ruta.rule.ComposedRuleElement.continueMatch(ComposedRuleElement.java:213)
        at org.apache.uima.ruta.rule.ComposedRuleElement.continueOwnMatch(ComposedRuleElement.java:362)
        at org.apache.uima.ruta.rule.ComposedRuleElement.fallbackContinue(ComposedRuleElement.java:459)
        at org.apache.uima.ruta.rule.ComposedRuleElement.continueMatch(ComposedRuleElement.java:225)
        at org.apache.uima.ruta.rule.ComposedRuleElement.continueOwnMatch(ComposedRuleElement.java:362)
        at org.apache.uima.ruta.rule.ComposedRuleElement.fallbackContinue(ComposedRuleElement.java:459)
        at org.apache.uima.ruta.rule.ComposedRuleElement.continueMatch(ComposedRuleElement.java:225)
        at org.apache.uima.ruta.rule.ComposedRuleElement.continueOwnMatch(ComposedRuleElement.java:362)
        at org.apache.uima.ruta.rule.ComposedRuleElement.fallbackContinue(ComposedRuleElement.java:459)
        at org.apache.uima.ruta.rule.ComposedRuleElement.continueMatch(ComposedRuleElement.java:225)
        at org.apache.uima.ruta.rule.ComposedRuleElement.continueOwnMatch(ComposedRuleElement.java:362)
        at org.apache.uima.ruta.rule.ComposedRuleElement.fallbackContinue(ComposedRuleElement.java:459)
        at org.apache.uima.ruta.rule.ComposedRuleElement.continueMatch(ComposedRuleElement.java:225)
        at org.apache.uima.ruta.rule.ComposedRuleElement.continueOwnMatch(ComposedRuleElement.java:362)
        at org.apache.uima.ruta.rule.ComposedRuleElement.fallbackContinue(ComposedRuleElement.java:459)
        at org.apache.uima.ruta.rule.ComposedRuleElement.continueMatch(ComposedRuleElement.java:225)
        at org.apache.uima.ruta.rule.ComposedRuleElement.continueOwnMatch(ComposedRuleElement.java:362)
        at org.apache.uima.ruta.rule.ComposedRuleElement.fallbackContinue(ComposedRuleElement.java:459)
        at org.apache.uima.ruta.rule.ComposedRuleElement.continueMatch(ComposedRuleElement.java:225)
        at org.apache.uima.ruta.rule.ComposedRuleElement.continueOwnMatch(ComposedRuleElement.java:362)
        at org.apache.uima.ruta.rule.ComposedRuleElement.fallbackContinue(ComposedRuleElement.java:459)

UIMA RUTA SCRIPT

WORDLIST EnglishStopWordList = 'stopWords.txt';
WORDLIST FiltersList = 'AnchorFilters.txt';
DECLARE Filters, EnglishStopWords;
DECLARE Anchors, SpanStart,SpanClose;

DocumentAnnotation{-> ADDRETAINTYPE(MARKUP)};

DocumentAnnotation{-> MARKFAST(Filters, FiltersList)};

STRING MixCharacterRegex = "[0-9]+[a-zA-Z]+";

DocumentAnnotation{-> MARKFAST(EnglishStopWords, EnglishStopWordList,true)};
(SW | CW | CAP ) { -> MARK(Anchors, 1, 2)};
Anchors{CONTAINS(EnglishStopWords) -> UNMARK(Anchors)};

(SPECIAL{REGEXP("['\"-=()\\[\\]]")}| PM) (SW | CW | CAP ) (SPECIAL{REGEXP("['\"-=()\\[\\]]")}| PM) EnglishStopWords? { -> MARK(Anchors, 1, 4)};
(SPECIAL{REGEXP("['\"-=()\\[\\]]")}| PM)? (SW | CW | CAP ) (SPECIAL{REGEXP("['\"-=()\\[\\]]")}| PM) EnglishStopWords? { -> MARK(Anchors, 1, 4)};
(SPECIAL{REGEXP("['\"-=()\\[\\]]")}| PM) (SW | CW | CAP ) (SPECIAL{REGEXP("['\"-=()\\[\\]]")}| PM)? EnglishStopWords? { -> MARK(Anchors, 1, 4)};
(SW | CW | CAP ) (SPECIAL{REGEXP("['\"-=()\\[\\]]")}| PM) EnglishStopWords? { -> MARK(Anchors, 1, 3)};

Anchors{CONTAINS(MARKUP) -> UNMARK(Anchors)};
MixCharacterRegex -> Anchors;

"<Value>"  -> SpanStart;
"</Value>" -> SpanClose;

Anchors{-> CREATE(ExtractedData, "type" = "ANCHOR", "value" = Anchors)};

SpanStart Filters? SPACE? ExtractedData SPACE? Filters? SpanClose{-> GATHER(Data, 2, 6, "ExtractedData" = 4)};

Answer 1

Normally, the reasons for high memory usage in UIMA Ruta can be found in RutaBasic (many annotation, coverage information) or in RuleMatch (inefficient rules, many rule element matches).

This your example, the problem seems to origin somewhere else. The stacktrace indicates that the memory is used up by some disjunctive rule element, which requires to create new annotations for storing the match information.

It seems that the version of UIMA Ruta is rather old since line number do not match at all with the source I am looking at.

There are seven (!!!) calls of continueOwnMatch in the stacktrace. I was looking for a rule that could cause something like this but found none. This could be a old flaw which has been fixed in newer versions, or some preprocessing added additional CW/SW/CAP annotations.

As a first advice, I would suggest two things:

1. Update to UIMA Ruta 2.6.0
2. Get rid of all disjunctive rule elements

The disjunctive rule elements are not really needed in your script. In general, they should not used at all if not really required. I do not use them at all in productive rules.

Instead of (SW | CW | CAP ) you can simply write W.

Instead of (SPECIAL{REGEXP("['\"-=()\\[\\]]")}| PM) you can write ANY{OR(REGEXP("['\"-=()\\[\\]]"),IS(PM))}.

Using ANY as a matching condition can reduce the runtime performance. In this example, two rules instead of the rule lement rewrite might be better, e.g., something like

SPECIAL{REGEXP("['\"-=()\\[\\]]")} W ANY?{OR(REGEXP("['\"-=()\\[\\]]"),IS(PM))} EnglishStopWords? { -> MARK(Anchors, 1, 4)};
PM W ANY?{OR(REGEXP("['\"-=()\\[\\]]"),IS(PM))} EnglishStopWords? { -> MARK(Anchors, 1, 4)};

(optional rule elements at the start of a rule without any anchors in the rule are not optional)

btw, there is a lot of room for optimization in your rules. If I had to guess, I'd say you can get rid at least of half the rules and 90% of all created annotations, which would also considerably reduce the memory usage.

DISCLAIMER: I am a developer of UIMA Ruta