Java memory allocation issues

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Recently an issue was discovered when trying to run a java with a large heap allocation.

In this case we were trying to allocate 2Gb to the java VM instance. Even when specifying large memory allocations in SGE java would always complain there was not enough space to allocate the heap.

A few people online have reported similar issues with SGE and java, it seems to stem from differences in the way java and SGE allocate memory to threads. Their solution is included on this page, but for more details see https://wiki.york.ac.uk/pages/viewpage.action?pageId=66126798

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