Dump heap on memory error in realignment

Adding these options to help us get to the bottom of memory issues in P5. They should not have any impact if there is no OOM error.
hartwigmedical · Feb 7, 2019 · 0fbd40a · 0fbd40a
1 parent 2616d8f
commit 0fbd40a
Showing 1 changed file with 2 additions and 0 deletions.
diff --git a/templates/Realignment.sh.tt b/templates/Realignment.sh.tt
@@ -9,6 +9,8 @@ cd "[% dirs.tmp %]"
 assert_not_empty "[% sample_bam_path %]"
 
 java -Xmx[% opt.REALIGNMENT_MASTER_MEM %]G \
+    -XX:+HeapDumpOnOutOfMemoryError \
+    -XX:HeapDumpPath="[% opt.OUTPUT_DIR %]" \
     -Djava.io.tmpdir="[% dirs.tmp %]" \
     -jar "[% opt.GATK_QUEUE_PATH %]/Queue.jar" \
     -jobQueue [% opt.REALIGNMENT_QUEUE %] \