Setting the amount of memory available for the JVM
During the installation of the CLC Server, the maximum amount of memory the Java Virtual Machine (JVM) can make use of is specified. By default, the value is set to 50% of the available RAM on the system you have installed the software on, or 50 Gb, whichever is smallest.
Recommended memory limit
We generally recommend that the default settings, described above, are used. These settings take into account that:
- Memory must be available for other system operations, as well as for CLC tools with binary phases, i.e. phases that do not run as part of the java process. Such binary phases do not run within the JVM, and thus are not affected by this limit. Examples of analysis types with binary phases include de novo assembly, BLAST, and tools that include a read mapping stage.
- Raising the memory level higher than 50 Gb may not substantially improve analysis speeds or capacity, while potentially degrading performance. For further details about this aspect, please see:
https://qiagen.my.salesforce-sites.com/KnowledgeBase/KnowledgeNavigatorPage?id=kA41i000000L5t3CAC
Adjusting the maximum JVM memory use after installation
The maximum amount of memory the JVM can use is recorded in the CLCGenomicsServer.vmoptions file, located in the CLC Server installation directory. The entry looks like the following, where in this example, "8192m" means 8192 Megabytes.
-Xmx8192m
The value for this setting in the CLCGenomicsServer.vmoptions file can be changed. The new value will take effect after the CLC Server is restarted.