The GC is a memory handling subsystem of the JVM that scans through the currently used heap and frees up memory by removing contents no longer in use. The larger the maximum heap, which is what this memory setting is affecting, the longer each check through the heap will take. The JVM has to suspend all other activities while running the GC. These suspensions are normally on the scale of milliseconds to a few seconds, and in this range, they are generally not noticeable. In combination with the GC subystem of the JVM, the CLC Workbenches and Servers use a sophisticated caching system, moving unneeded data out of memory and into temporary disk storage. The result of this caching system means that there will not be any noticeable performance improvement with a Java heap space larger than 50GB, while GC pauses may become more noticeable. The suggestion to limit memory use to a maximum of 50% of the physical RAM is made because most CLC Workbenches and CLC Servers have some optimized external binaries responsible for compute-heavy tasks such as read mapping and de novo assembly. These external binaries are not affected by the maximum heap space limit. They request memory from the OS, just like any other executable. Thus, the suggested 50% limit for the heap space setting for the Java Virtual Machine (JVM) is to try to ensure that the machine will have sufficient free memory to run the external binaries.įootnotes. ![]() 1 For releases before CLC Genomics Workbench 8.0, Biomedical Genomics Workbench 2.1 and CLC Main Workbench 7.6, the -Xmx setting for macOS was in the ist file, which is also under the Contents folder.One thing different in the new release is that there is no longer a minimum contig length of 200 bases.
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