Getting started on Mason
Indiana University is a large memory computer cluster configured to
support data-intensive, high-performance computing tasks for
researchers using genome assembly software (particularly software
suitable for assembly of data from next-generation sequencers),
large-scale phylogenetic software, or other genome analysis
applications that require large amounts of computer memory. At IU, Mason accounts are available to IU faculty,
postdoctoral fellows, research staff, and students involved in genome
research. IU educators providing instruction on genome analysis
software, and developers of such software, are also welcome to use
Mason. IU has also made Mason available to genome researchers from the
National Science Foundation's
Extreme Science and Engineering Discovery Environment (XSEDE) project.
Mason consists of 18 Hewlett-Packard (HP) DL580 servers, each containing four Intel Xeon L7555 8-core processors and 512 GB of RAM, and two HP DL360 login nodes, each containing two Intel Xeon E5-2600 processors and 24 GB of RAM. The total RAM in the system is 9 TB. Each server chassis has a 10-gigabit Ethernet connection to the other research systems at IU and the XSEDE network (XSEDENet).
Mason nodes run Red Hat Enterprise Linux (RHEL 6.x). The system uses TORQUE integrated with Moab Workload Manager to coordinate resource management and job scheduling. The Data Capacitor II and Data Capacitor Wide Area Network (DC-WAN) parallel file systems are mounted for temporary storage of research data. The Modules environment management package on Mason allows users to dynamically customize their shell environments.
Following is a selection of IU Knowledge Base documents to help you get started using Mason. For additional documentation, search the Knowledge Base. For slides and lab files from past high-performance computing workshops, see Supercomputing quick start guides.
On this page:
- System overview
- Accounts, access, and user policies
- Programming environment
- Running jobs
- X forwarding and interactive jobs
- Application-specific help
- Getting help
Accounts, access, and user policies
- Requesting an account
- Accessing Mason
- What are my responsibilities as a computer user at IU?
- What are my responsibilities as an XSEDE user?
- Policies regarding UITS research systems
- Working with data containing PHI
- Using Modules to manage your software environment
- Genome analysis software on Mason
- Mason software installation policy
- Compiling programs on Mason
- Queue information
- Using TORQUE to submit and manage batch jobs
- Monitoring memory and CPU usage
- Using the IU Cyberinfrastructure Gateway to monitor batch jobs on Mason
X forwarding and interactive jobs
- If you have a system-specific question about Big Red II, Karst, Mason, or the Research Database Complex (RDC) contact the High Performance Systems (HPS) team.
- If you have questions about the Scholarly Data Archive (SDA), contact the Research Storage team.
- If you have questions about shared scratch or project space on the Data Capacitor II or Data Capacitor Wide Area Network (DC-WAN) file system, contact the High Performance File Systems (HPFS) team.
- If you have questions about the development tools, compilers, scientific or numerical libraries, or debuggers available on the research computing system, contact the Scientific Applications and Performance Tuning (SciAPT) team.
- If you have questions about the statistical and mathematical applications available on the research computing systems, contact the Research Analytics group.
- If you have questions about the bioinformatics and genome analysis packages available on the research computing systems, email the National Center for Genome Analysis Support (NCGAS).
For general inquiries about UITS Research Technologies systems and services, complete and submit the Research Technologies request for help form.