About Quartz at IU

On this page:

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

System overview

Quartz is Indiana University's high-throughput computing cluster. Designed to deliver large amounts of processing capacity over long periods of time, Quartz provides the advanced supercomputing performance needed to run high-end, data-intensive applications that are critical to scientific discovery and innovation.

Quartz features 92 compute nodes, each equipped with two 64-core AMD EPYC 7742 2.25 GHz CPUs and 512 GB of RAM, with a peak per-node performance of greater than 4,608 gigaFLOPS. All Quartz nodes are housed in the IU Bloomington Data Center, run Red Hat Enterprise 8.x, and are connected to the IU Science DMZ via 10-gigabit Ethernet. The Slate, Slate-Project, and Slate-Scratch high-throughput file systems are mounted for temporary storage of computational data. The Lmod environment management package allows users to dynamically customize their shell environments.

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.

Important:

Before storing data on any of Indiana University's research computing or storage systems, make sure you understand the information in Types of sensitive institutional data appropriate for UITS Research Technologies services.

Make sure you do not include sensitive institutional data as part of a file's filename or pathname.

System access

IU students, faculty, and staff can create Quartz 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 quartz.uits.iu.edu. Log in with your IU username and passphrase.

Notes:

Two-factor authentication using Two-Step Login (Duo) is required for access to the login nodes on IU research supercomputers, and for SCP and SFTP file transfers to those systems. SSH public key authentication remains an option for researchers who submit the "SSH public key authentication to HPS systems" agreement (log into HPC everywhere using your IU username and passphrase), in which you agree to set a passphrase on your private key when you generate your key pair. If you have questions about how two-factor authentication may impact your workflows, contact the UITS Research Applications and Deep Learning team. For help, see Get started with Two-Step Login (Duo) at IU and Help for Two-Step Login (Duo).
For enhanced security, SSH connections that have been idle for 60 minutes will be disconnected. To protect your data from misuse, remember to log off or lock your computer whenever you leave it.
The scheduled monthly maintenance window for IU's high performance computing systems is the second Sunday of each month, 7am-7pm.

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.

Quartz uses the Lmod module management system.

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

Quartz provides programming environments for the GNU, Intel, and NVIDIA HPC compilers. The default environment includes GNU compilers, OpenBLAS math libraries, and MVAPICH communication libraries. For more, see Compile programs on Quartz 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

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 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.

Note:

Although PHI is classified as Critical data, other types of institutional data classified as Critical are not permitted on Research Technologies systems. For help determining which institutional data elements classified as Critical are considered PHI, see About protected health information (PHI) data elements in the classifications of institutional data.

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 Quartz

To set up access to run jobs on Quartz, 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.

Quartz uses 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.

Acknowledge 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 Sources of funding to acknowledge in published work if you use IU's research cyberinfrastructure.

Get help

Support for IU research supercomputers, software, and services is provided by various teams within the Research Technologies division of UITS.

If you have a technical issue or system-specific question, contact the High Performance Systems (HPS) team.
If you have a programming question about compilers, scientific/numerical libraries, or debuggers, contact the UITS Research Applications and Deep Learning team.

For general questions about research computing at IU, contact UITS Research Technologies.

For more options, see Research computing support at IU.