Big Red II at Indiana University
On this page:
- System overview
- System access
- Available software
- Setting up your user environment
- File storage options
- Working with data containing PHI
- Running jobs on Big Red II
- Queue information
- Requesting single user time
- Acknowledging grant support
Big Red II features a hybrid architecture based on two Cray, Inc., supercomputer platforms. As configured upon entering production in August 2013, Big Red II comprised 344 XE6 (CPU-only) compute nodes and 676 XK7 "GPU-accelerated" compute nodes, all connected through Cray's Gemini scalable interconnect, providing a total of 1,020 compute nodes, 21,824 processor cores, and 43,648 GB of RAM. Each XE6 node has two AMD Opteron 16-core Abu Dhabi x86_64 CPUs and 64 GB of RAM; each XK7 node has one AMD Opteron 16-core Interlagos x86_64 CPU, 32 GB of RAM, and one NVIDIA Tesla K20 GPU accelerator.
Although Big Red II is a local resource for use by the IU community, its presence has an important effect on the national cyberinfrastructure ecosystem. By providing IU researchers the same technology, software environment, and hybrid architecture used in national supercomputer resources, such as Blue Waters at the National Center of Supercomputing Applications (NCSA), Big Red II meets relatively modest scientific computing needs locally, allowing larger national supercomputing assets to be efficiently used on challenging compute- and data-intensive projects. Big Red II also helps conserve nationally funded supercomputing assets by providing a powerful hybrid system IU scientists can use to fully optimize and tune their applications before migrating them to an Extreme Science and Engineering Discovery Environment (XSEDE) computational service.
Access is available to IU graduate students, faculty, and staff. Undergraduates and non-IU collaborators must have IU faculty sponsors. For details, see the "Research system accounts (all campuses)" section of What computing accounts are available at IU, and for whom?
Once your account is created, you can use your IU username and passphrase to log into Big Red II (
bigred2.uits.iu.edu) with any SSH2 client. Public key authentication also is permitted; see How do I set up SSH public-key authentication to connect to a remote system?
For a list of packages available on Big Red II, see Big Red II Modules in the IU Cyberinfrastructure Gateway.
Big Red II users can request software using the Software Request form.
Setting up your user environment
On the research computing resources at Indiana University, the Modules environment management system provides a convenient method for dynamically customizing your software environment.
For more about the Modules package, see the
module manual page
page. Additionally, see On Big Red II, Karst, and Mason at IU, how do I use Modules to
manage my software environment?
File storage options
For file storage information, see On IU's research systems, how much allocated and short-term storage capacity is available to me?
Working with data containing PHI
The Health Insurance Portability and Accountability Act of 1996 (HIPAA) established rules protecting the privacy and security of individually identifiable health information. The HIPAA Privacy Rule and Security Rule set national standards requiring organizations and individuals to implement certain administrative, physical, and technical safeguards to maintain the confidentiality, integrity, and availability of protected health information (PHI).
This system meets certain requirements established in the HIPAA Security Rule that enable its use for research involving data that contain protected health information (PHI). You may use this resource for research involving data that contain PHI only if you institute additional administrative, physical, and technical safeguards that complement those UITS already has in place. For more, see When using UITS Research Technologies systems and services, what are my legal responsibilities for protecting the privacy and security of data containing protected health information (PHI)? If you need help or have questions, contact UITS HIPAA Consulting.
Running jobs on Big Red II
Big Red II runs a proprietary variant of Linux called Cray Linux Environment (CLE) that provides two separate execution environments for running batch and large interactive jobs: Extreme Scalability Mode (ESM) and Cluster Compatibility Mode (CCM). Software optimized for a Cray environment (e.g., AMBER, OpenFOAM, and NAMD) will usually run in the ESM environment. If you compile your own applications, you should target the ESM environment first. Applications developed to run on a standard Linux cluster or on a single server (e.g., MATLAB or Ansys) can run in the CCM environment. In general, the CCM environment will support any standard Linux application.
Big Red II uses the TORQUE resource manager (based on OpenPBS) and the Moab Workload Manager to manage and schedule jobs. TORQUE job scripts must be tailored specifically for the Cray Linux Environment on Big Red II; see How do I run batch jobs on Big Red II at IU? Moab uses fairshare scheduling to track usage and prioritize jobs. For information on fairshare scheduling and using Moab to check the status of batch jobs, see:
aprunfor ESM jobs;
ccmrunfor CCM jobs). Additionally, for CCM jobs, you must load the
module load ccmto your
~/.modulesfile), and use the
-l gres=ccmTORQUE directive in your job script. TORQUE scripts for batch jobs on Karst or Mason will not work on Big Red II without the proper modifications. If your script's executable line does not begin with the appropriate launch command, your application will execute on an
aprunservice node, not a compute node, and may likely cause a service disruption for all users on the system. The
aprunnodes are shared by all currently running jobs, and are intended only for passing job requests. Any memory- or computationally-intensive jobs running on
aprunnodes will be terminated.
For details, see:
- Compiling C, C++, and Fortran programs on Big Red II at IU
- On Big Red II at IU, how do I run OpenMP or hybrid OpenMP/MPI jobs?
- On Big Red II at IU, how do I use PCP to bundle multiple serial jobs to run them in parallel?
- How do I run interactive jobs on Big Red II at IU?
Big Red II has the following queues configured to accept jobs that will run on the 32-core dual-Opteron (CPU-only) nodes:
- cpu: The routing queue for all "production" jobs; each job is routed, based on its resource requirements, to one of the execution queues (normal, serial, or long)
- debug_cpu: An execution queue reserved for testing and debugging purposes only
Maximum values for each execution queue are defined in the following table.
|32-core dual-Opteron (CPU-only) nodes|
|Execution queue||Cores/node||Nodes/job||Wall time/job||Nodes/user|
|(normal) *||32||128||2 days||128|
|(serial) *||32||1||7 days||128|
|(long) *||32||8||14 days||32|
|* Do not submit jobs directly to the normal, serial, or long execution queues. Always use the cpu routing queue when submitting jobs for "production" runs. Use the debug queue for testing or debugging purposes only.|
Big Red II has the following queues configured to accept jobs that will run on the 16-core Opteron/NVIDIA (CPU/GPU) nodes:
- gpu: The main execution queue for jobs on the CPU/GPU nodes
- opengl: An execution queue reserved for OpenGL jobs
- cpu16: An execution queue that lets non-GPU jobs run on the CPU/GPU nodes
- debug_gpu: An execution queue reserved for testing and debugging CPU/GPU codes
Maximum values for each queue are defined as follows:
|16-core Opteron/NVIDIA (CPU/GPU) nodes|
|Execution queue||Cores/node||Nodes/job||Wall time/job||Nodes/user|
Requesting single user time
Although UITS Research Technologies cannot provide dedicated access to an entire compute system during the course of normal operations, "single user time" is made available by request one day a month during each system's regularly scheduled maintenance window to accommodate IU researchers with tasks requiring dedicated access to an entire compute system. To request such single user time, complete and submit the Research Technologies Ask RT for Help form, requesting to run jobs in single user time on HPS systems. If you have questions, email the HPS team.
Acknowledging grant support
The Indiana University cyberinfrastructure, managed by the Research Technologies division of UITS, is supported by funding from several grants, each of which requires you to acknowledge its support in all presentations and published works stemming from research it has helped to fund. Conscientious acknowledgment of support from past grants also enhances the chances of IU's research community securing funding from grants in the future. For the acknowledgment statement(s) required for scholarly printed works, web pages, talks, online publications, and other presentations that make use of this and/or other grant-funded systems at IU, see If I use IU's research cyberinfrastructure, what sources of funding do I need to acknowledge in my published work?
For an overview of Big Red II documentation, see Getting started on Big Red II.
For tutorials on how to effectively use Big Red II's hybrid architecture, see Supercomputing quick start guides.
Support for users of IU's research computing systems and software is provided by various UITS Research Technologies units; see Research computing support at IU.
This is document bcqt in the Knowledge Base.
Last modified on 2017-03-15 13:18:05.
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