About Carbonate at Indiana University

• System overview
• System access
• HPC software
• Set up your user environment
• File storage options
• Work with data containing PHI
• Run jobs on Carbonate
• Acknowledge grant support
• Get help

System overview

Besides being available to IU students, faculty, and staff for standard, cluster-based, high-throughput computing, Carbonate offers a colocation service to the IU community. IU schools and departments can purchase nodes that are compatible with IU's Carbonate cluster, have them installed in the very secure IUB Data Center, have them available when members want to use them, and have them managed and secured by UITS Research Technologies staff. This colocation service gives schools and departments access to compute nodes that are dedicated solely to their use within Carbonate's physical, electrical, and network framework while leveraging the security and energy efficiency benefits provided by location within the IU Data Center.

To inquire about the colocation service on Carbonate, email the UITS High Performance Systems (HPS) team.

System access

IU students, faculty, staff, and sponsored affiliates can create Carbonate accounts using the instructions in Get additional IU computing accounts. For details, see the Research system accounts (all campuses) section of Computing accounts at IU.

Once your account is created, you can use any SSH2 client to access carbonate.uits.iu.edu.

Log in with your IU username and passphrase.

HPC software

The Research Applications and Deep Learning (RADL) group, within the Research Technologies division of UITS, maintains and supports the high performance computing (HPC) software on IU's research supercomputers. To see which applications are available on a particular system, log into the system, and then, on the command line, enter module avail.

For information on requesting software, see Software requests in Policies regarding UITS research systems.

Set up your user environment

The IU research supercomputers use module-based environment management systems that provide a convenient method for dynamically customizing your software environment.

Carbonate uses the Modules module management system.

For more, see Use modules to manage your software environment on IU research supercomputers.

The GNU Compiler Collection (GCC), the Intel Compiler Suite, and Portland Group (PGI) compilers are available on Carbonate. Open MPI and MPICH compilers also are available for compiling parallel programs. For more, see Compile programs on Carbonate at IU.

File storage options

For file storage information, see Available access to allocated and short-term storage capacity on IU's research systems.

To check your quota, use the quota command from the command line of any IU research supercomputer. If the quota command is not already loaded by default, use the module load quota command to add it to your environment. Alternatively, log in to HPC everywhere and, in the "HPC Status" pane, look under "Storage". The quota command and HPC everywhere both display disk (data) quotas and usage for your home directory space on the research supercomputers, your space on Slate, and your space on the Scholarly Data Archive (SDA), as applicable. HPC everywhere additionally displays your inode (file) quotas for these spaces.

Before storing data on this system, make sure you understand the information in the Work with data containing PHI section (below).

Work with data containing PHI

This UITS system or service meets certain requirements established in the HIPAA Security Rule thereby enabling its use for work involving data that contain protected health information (PHI). However, using this system or service does not fulfill your legal responsibilities for protecting the privacy and security of data that contain PHI. You may use this system or service for work 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 Your legal responsibilities for protecting data containing protected health information (PHI) when using UITS Research Technologies systems and services.

If you have questions about securing HIPAA-regulated research data at IU, email securemyresearch@iu.edu. SecureMyResearch provides self-service resources and one-on-one consulting to help IU researchers, faculty, and staff meet cybersecurity and compliance requirements for processing, storing, and sharing regulated and unregulated research data; for more, see About SecureMyResearch. To learn more about properly ensuring the safe handling of PHI on UITS systems, see the UITS IT Training video Securing HIPAA Workflows on UITS Systems. To learn about division of responsibilities for securing PHI, see Shared responsibility model for securing PHI on UITS systems.

Run jobs on Carbonate

To set up access to run jobs on Carbonate, IU faculty, staff, and graduate students can use RT Projects to create projects, request allocations, and add users (research collaborators, lab members, and/or students) who should be permitted to user their allocations.

For more about RT Projects, see Use RT Projects to request and manage access to specialized Research Technologies resources.

The Indiana University research supercomputers use the Slurm workload manager for resource management and job scheduling; see Use Slurm to submit and manage jobs on IU's research computing systems.

In Slurm, compute resources are grouped into logical sets called partitions, which are essentially job queues. To view details about available partitions and nodes, use the sinfo command; for more about using sinfo, see the View partition and node information section of Use Slurm to submit and manage jobs on IU's research computing systems.

• general: If your job requires up to 251 GB of memory, submit it to the general partition by including -p general either as an SBATCH directive in your job script or as an option in your srun command.
• largememory: If your job requires from 251 GB to 503 GB of memory, submit it to the largememory partition by including -p largememory either as an SBATCH directive in your batch job script or as an option in your srun command.

Acknowledge grant support

Get help