Skip to content
New issue

Have a question about this project? Sign up for a free GitHub account to open an issue and contact its maintainers and the community.

Sign up for GitHub

By clicking “Sign up for GitHub”, you agree to our terms of service and privacy statement. We’ll occasionally send you account related emails.

Already on GitHub? Sign in to your account

Fix failures to allocate arrays with a very large Java heap size #1986

Open
wants to merge 1 commit into
base: master
Choose a base branch
from
Open

Fix failures to allocate arrays with a very large Java heap size #1986

Show file tree
Hide file tree
Changes from all commits
Commits
Show all changes
1 commit
Select commit
File filter

Filter by extension

Filter by extension
Conversations
Failed to load comments.
Loading
Jump to
Jump to file
Failed to load files.
Loading
Diff view
Diff view
4 changes: 2 additions & 2 deletions src/main/java/picard/sam/markduplicates/EstimateLibraryComplexity.java
View file
Open in desktop
Original file line number Diff line number Diff line change
Expand Up @@ -425,7 +425,7 @@ public EstimateLibraryComplexity() {
} else {
sizeInBytes = PairedReadSequence.getSizeInBytes();
}
MAX_RECORDS_IN_RAM = (int) (Runtime.getRuntime().maxMemory() / sizeInBytes) / 2;
MAX_RECORDS_IN_RAM = Math.min((int) (Runtime.getRuntime().maxMemory() / sizeInBytes) / 2, Integer.MAX_VALUE - 32);
}

/**
Expand Down Expand Up @@ -673,4 +673,4 @@ boolean passesQualityCheck(final byte[] bases, final byte[] quals, final int see
for (int i = 0; i < readLength; i++) total += quals[i];
return total / readLength >= minQuality;
}
}
}
6 changes: 3 additions & 3 deletions src/main/java/picard/sam/markduplicates/MarkDuplicates.java
View file
Open in desktop
Original file line number Diff line number Diff line change
Expand Up @@ -479,8 +479,8 @@ private void buildSortedReadEndLists(final boolean useBarcodes) {
} else {
sizeInBytes = ReadEndsForMarkDuplicates.getSizeOf();
}
MAX_RECORDS_IN_RAM = (int) (Runtime.getRuntime().maxMemory() / sizeInBytes) / 2;
final int maxInMemory = (int) ((Runtime.getRuntime().maxMemory() * SORTING_COLLECTION_SIZE_RATIO) / sizeInBytes);
MAX_RECORDS_IN_RAM = Math.min((int) (Runtime.getRuntime().maxMemory() / sizeInBytes) / 2, Integer.MAX_VALUE - 32);
final int maxInMemory = Math.min((int) ((Runtime.getRuntime().maxMemory() * SORTING_COLLECTION_SIZE_RATIO) / sizeInBytes), Integer.MAX_VALUE - 32);
log.info("Will retain up to " + maxInMemory + " data points before spilling to disk.");

final ReadEndsForMarkDuplicatesCodec fragCodec, pairCodec, diskCodec;
Expand Down Expand Up @@ -719,7 +719,7 @@ protected void sortIndicesForDuplicates(final boolean indexOpticalDuplicates){
entryOverhead = SortingLongCollection.SIZEOF;
}
// Keep this number from getting too large even if there is a huge heap.
int maxInMemory = (int) Math.min((Runtime.getRuntime().maxMemory() * 0.25) / entryOverhead, (double) (Integer.MAX_VALUE - 5));
int maxInMemory = (int) Math.min((Runtime.getRuntime().maxMemory() * 0.25) / entryOverhead, (double) (Integer.MAX_VALUE - 32));
// If we're also tracking optical duplicates, reduce maxInMemory, since we'll need two sorting collections
if (indexOpticalDuplicates) {
maxInMemory /= ((entryOverhead + SortingLongCollection.SIZEOF) / entryOverhead);
Expand Down
2 changes: 1 addition & 1 deletion src/main/java/picard/util/SequenceDictionaryUtils.java
View file
Open in desktop
Original file line number Diff line number Diff line change
Expand Up @@ -190,7 +190,7 @@ public static SortingCollection<String> makeSortingCollection() {
String.class,
new StringCodec(),
String::compareTo,
(int) Math.min(maxNamesInRam, Integer.MAX_VALUE),
(int) Math.min(maxNamesInRam, Integer.MAX_VALUE - 32),
tmpDir.toPath()
);
}
Expand Down
Loading