• Manuals

Browse the manual

• Introduction
  • System requirements
  • Licensing
  • Latest improvements
• Installation
  • Quick installation guide
  • Installing and running the Server
    • Installing the Server software
  • Silent installation
  • Upgrading an existing installation
    • Upgrading major versions
  • Allowing access through your firewall
  • Downloading a license
    • Windows license download
    • Mac OS license download
    • Linux license download
  • Starting and stopping the server
    • Microsoft Windows
    • Mac OS X
    • Linux
  • Installing relevant plugins in the Workbench
• Configuring and administering the server
  • Logging into the administrative interface
  • Adding locations for saving data
    • Adding a file system location
    • Rebuilding the index
  • Accessing files on, and writing to, areas of the server filesystem
  • Changing the listening port
  • Changing the tmp directory
    • Job node setups
  • Setting the amount of memory available for the JVM
  • Limiting the number of cpus available for use
  • Other configurations
    • HTTP settings
    • Audit log settings
    • Deployment of server information to CLC Workbenches
  • Server plugins
  • Queue
• Managing users and groups
  • Logging in the first time and the root password
  • User authentication using the web interface
    • Managing users using the web interface
    • Managing groups using the web interface
  • User authentication using the Workbench
    • Managing users through the Workbench
    • Managing groups through the Workbench
    • Adding users to a group
  • User statistics
• Access privileges and permissions
  • Controlling access to data
    • Setting permissions on a folder
    • Recycle bin
    • Technical notes about permissions and security
  • Global permissions
  • Customized attributes on data locations
    • Configuring which fields should be available
    • Editing lists
    • Removing attributes
    • Changing the order of the attributes
  • Filling in values
    • What happens when the sequence is copied to another data location?
    • Searching
• Job Distribution
  • Model I: Master server with execution nodes
    • Master and job nodes explained
    • User credentials on a master-job node setup
    • Configuring your setup
    • Installing Server plug-ins
  • Model II: Master server submitting to grid nodes
    • Requirements for CLC Grid Integration
    • Technical overview
    • Setting up the grid integration
    • Licensing of grid workers
    • Configuring licenses as a consumable resource
    • Configure grid presets
    • Controlling the number of cores utilized
    • Other grid worker options
    • Testing a Grid Preset
    • Client-side: starting CLC jobs on the grid
    • Grid Integration Tips
    • Understanding memory settings
• External applications
  • External applications integration: Basic configuration
  • External applications integration: Post-processing
  • External applications integration: Stream handling
  • External applications integration: Environment
    • Environmental Variables
    • Working directory
    • Execute as master process
  • External applications integration: Parameter flow
  • External applications integration: Velvet
    • Installing Velvet
    • Running Velvet from the Workbench
    • Understanding the Velvet configuration
  • External applications integration: Bowtie
    • Installing Bowtie
    • Understanding the Bowtie configuration
    • Parameter overview
    • Setting path for temporary data
    • Tools for building index files
  • Troubleshooting
    • Checking the configuration
    • Check your third party application
    • Is your Import/Export directory configured?
    • Check your naming
• Workflows
  • Installing and configuring workflows
  • Executing workflows
  • Automatic update of workflow elements
• Appendix
  • Use of multi-core computers
  • Troubleshooting
    • Check set-up
    • Bug reporting
  • Database configurations
    • Getting and installing JDBC drivers
    • Configurations for MySQL
  • SSL and encryption
    • Enabling SSL on the server
    • Logging in using SSL from the Workbench
    • Logging in using SSL from the CLC Server Command Line Tools
  • DRMAA libraries
    • DRMAA for LSF
    • DRMAA for PBS Pro
    • DRMAA for OGE or SGE
  • Consumable Resources
  • Third party libraries
• Bibliography

Setting the amount of memory available for the JVM

When running the CLC Genomics Server, the Java Virtual Machine (JVM) needs to know how much memory it can use. This depends on the amount of physical memory (RAM) and can thus be different from computer to computer. Therefore, the installer investigates the amount of RAM during installation and sets the amount of memory that the JVM can use.

On Windows and Linux, this value is stored in a property file called ServerType.vmoptions (e.g. CLCGenomicsServer.vmoptions) which contains a text like this:

    -Xmx8000m

The number (8000) is the amount of memory the CLC Genomics Server is allowed to use. This file is located in the installation folder of the CLC Genomics Server software.

By default, he value is set to 50% of the available RAM on the system you have installed the software on.

You can manually change the number contained in the relevant line of the vmoptions file for your CLC Genomics Server if you wish to raise or lower the amount of RAM allocated to the Java Virtual Machine.

---