Setting heap size in Java

Question

I am trying to run a Java tool in Linux Ubuntu system and I keep getting the following error after the program imports 12% of the data:

Fata Error:
Exception in thread 'Thread-l" java.lang.OutOfMemoryError: java heap space

I tried to set the heap size using

java -Xms8G -Xmx16G -jar Haploview.jar

but the error appears again exactly at same point after just using less than 500M Of the allocated Ram. Using the command 'free -m' I can see that there are lots of free RAM memory left but I don't know why Java do not use it

Answer 1

• According to the specification Haploview allocates 512 MB of memory by default. You can increase the memory up to 2000 MB via java -jar Haploview.jar -memory 2000. For details see https://www.broadinstitute.org/haploview/frequent-questions
• But a memory larger than 2 GB is most likely not possible because Haploview seems to be a 32-bit application which is limited to a memory of 2 GB independent of the underlying OS (32 Bit or 64 Bit). See https://haploview.software.informer.com/download/ and Memory limit to a 32-bit process running on a 64-bit Linux OS