Java memory consumtion - Githubissues

BauerLab / ngsane

Analysis Framework for Biological Data from High Throughput Experiments

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Java memory consumtion #3

Closed allPowerde closed 11 years ago

allPowerde commented 11 years ago

The RNAseq part errors out supposedly because it is running out of memory. This issue is to test whether this has to do with the other memory setups on the cluster

allPowerde commented 11 years ago

Java parameters can be specifically unset, that way we have full control over the virtual machine set up:

JAVAPARAMS="-Xmx"$(python -c "print int($MEMORY_TOPHAT*0.8)")"g -Djava.io.tmpdir="$TMP"  -XX:ConcGCThreads=1 -XX:ParallelGCThreads=1" 
unset _JAVA_OPTIONS