Knowledge Base

MSI's information hub

MSI's Knowledge Base is a collection of reference material on topics such as 

  • Creating and Managing an MSI group, 
  • Setting up your MSI Environment, 
  • Interactive Computing, 
  • Batch Job Computing, and 
  • Data Transfer and Storage

Access and Connecting

Getting Started

Access to MSI resources is available to Principal Investigators (PIs) and their research groups.

Duo 2-Factor Authentication at MSI

All researchers using secure shell (ssh) to connect to MSI high-performance computing cluster Mesabi, Mangi, and (very soon) Agate are required to use Duo 2-factor authentication.

Connecting to HPC Resources

MSI provides access to a variety of High-Performance Computing (HPC) systems designed to tackle a wide range of computational needs.

Connecting to Interactive HPC Resources

Interactive sessions provide direct access to software modules hosted by MSI.

Job Scheduling

Slurm Job Submission and Scheduling

MSI uses Slurm as its job queueing and resource management system to efficiently and fairly manage the resources used by all users.

Software and Environments

Accessing Software Resources

MSI provides access to approximately 400 software packages.

Galaxy
Services

The Galaxy web application is an integrated informatics solution that supports both data analysis and research discovery.

FAQs

Access FAQs

Your one-stop resource for everything related to access at the Minnesota Supercomputing Institute.

Additional FAQs

Quick solutions for specific queries on citation guidelines, email settings, Citrix Receiver errors, SSH access, RSA key updates, HIPAA data storage, Firefox troubleshooting, and more.

Data Storage FAQs

Explore quick answers to storage options, directory access, data safety, quotas, file sharing, troubleshooting, Galaxy usage, Second Tier Storage (S3), data interfaces, transfers, S3 bucket sharing, data management upon departure, and Google Drive to Panasas transfers.

Environment FAQs

Your resource for navigating user environment settings efficiently.

File Transfer FAQs

Your guide to effortless data movement.

Interactive Connections FAQs

Get quick solutions for SSH, remote desktop, and accessing MSI servers from Windows, Unix, and Mac.

Jobs FAQs

Get solutions for queue submissions, job start issues, supercomputer efficiency, job failures, walltime extension, email output, group changes, GNU Parallel usage, calculation terminations, job arrays, and understanding job exit statuses..

Network FAQs

Find solutions and insights on using your laptop on the wired network in MSI's Walter space.

Software FAQs

Find answers on accessing, tutorials, new software requests, modules, license issues, MSI-developed software, private modules, Singularity, R packages, compilers, updates, and software library migrations.

Stratus FAQs

Get Stratus cloud platform answers on logging in, setting up authentication, Horizon interface navigation, VM management, SSH setup, volume handling, storage tiers, dbGaP data access, encryption, software installation, Docker usage, port configurations, RDP connections, security groups, and local user password setup..

MSI Glossary

The following words and phrases are used throughout the MSI website and unless otherwise stated, the meaning of these terms is defined as follows. Please be aware that the definitions given here are not intended to be universal; rather, the definitions are specifically tailored to fit the environment at MSI.

Allocated Resources
The resources that are provided to each PI group free of charge each year. Groups will receive an allocation of storage (GBs/TBs) each year, and must submit their Annual Renewal form each year to retain access to allocated resources. With additional justification, additional resources can be allocated or purchased for the PI group (see definition "Purchased Resources").

See also:
Storage Allocations

Annual Renewal
The process by which research groups renew their access to MSI's HPC services for the next calendar year. Each Principal Investigator or Group Administrator is responsible for renewing their group's access, and annual renewal is required to maintain access.

See also:
When and how does a research group renew MSI access?

Group Administrator (Group Admin)
A member of a Principal Investigator's group who has privileges to carry out administrative functions for the group, such as adding new users and giving group members access to HPC resources. The PI may assign this role to any MSI user in their group.

See also:
How does a PI set a group admin?

Modules 
A software used to provide users with access to software-on-demand through Linux systems. Modules allow users to load and unload different software versions to meet their computational needs. Users may also create private software modules of software installed within their home or group directories.

See also:
What is a module?
How can I create private software modules?
Accessing Software Resources

Partition
The scheduling partitions used to efficiently allocate MSI hardware and resources to different types of jobs. The job partitions on our systems manage different sets of hardware, and have different limits for quantities such as walltime, available processors, and available memory. Partitions act as a sort of "waiting list" for jobs with similar hardware and resource needs, ensuring fairness and efficiency in job completion.

See also:
Queues
Choosing a Job Queue
How do I submit jobs to a queue?

Primary Storage
A global high-performance network file system that contains user home directories and shared group directories. The file system is available (exported) on all of MSI's computational resources, so that users will see the same files and directories no matter what system they are using.

See also:
High Performance Storage
Storage Allocations

Principal Investigator (PI)
The primary individual responsible for access and research conducted using MSI systems. Pricipal investigators can apply for MSI accounts for themselves and members of their research groups.

Individuals that may be eligible to become a PI include faculty, instructor faculty, emeritus faculty, and academic professionals at the University of Minnesota, as well as faculty researchers from other accredited institutions of post-secondary education in the state of Minnesota.

See also:
Eligibility Information

Purchased Resources
Resources that may be purchased beyond the allocations given to each PI group. PIs may request to purchase dedicated resources, such as additional storage and hardware, to suit the needs of their research that normal allocations may not be able to meet. Additional justification may be needed for some purchases.

See also:
Service Catalog
Can I purchase dedicated resources for my research?

Scratch Storage
Shared temporary storage used while applications are running on the supercomputer. Analogous to "scratch paper," scratch storage is not intended for valuable, long-term, or backup data storage, but instead is available for temporary file storage while executing a job. MSI offers both large capacity and high performance temporary storage.

See also:
Scratch Storage

Second Tier Storage
An object storage system in place for storing inactive data, supporting data lifecycles and workflows, and facilitating data management and sharing. Second tier storage is ideal for those looking to share data with colleagues around the world, including some storage through Amazons S3 (Simple Storage Service) interface.

See also:
Second Tier Storage

Service Units (SUs)
A unit of time on MSI HPC resources. The SU to CPU-hour conversion rates for various systems are listed on the Queues page.

Slurm Script
Script used in a small text file when submitting a job through the MSI queuing system, Slurm. This script includes information about requested resources and commands for executing the calculation. Slurm Scripts help ensure that jobs are submitted to a relevant partition, allocated the correct amount of resources, and perform the desired functions of the user.

See also:
Job Submission and Scheduling (Slurm)
Why does my job fail after only a couple of seconds?

Snapshots
A read-only copy of data stored at a particular point in time, maintaining the same permissions for each file at that point in time. These snapshots static backups of a volume can be used to restore a file to its location in the case that it was inadvertently deleted. You can also snapshot while running Virtual Machines (VM).

See also:
How do I snapshot a volume?
How do I restore a snapshot on a volume?

Supercomputer
Another given name for a machine capable of High Performance Computing (HPC). Supercomputers, including the ones at MSI, have access to the high speed networks, high performance storage, powerful GPUs, and large amounts of memory needed to execute large-scale computations and programs. MSI has two main HPC units, Mesabi and Mangi, designed to support complex computation and memory-intensive programs used in research across the University as well as the state of Minnesota.

See also:
What is HPC?
Mesabi
Mangi

Tape Storage
Off-line storage is used to remove and archive large amounts of data from MSI systems. Data is compressed and stored.

See also:
Dedicated Hardware

Tutorial
MSI hosts various tutorial seminars to assist users with a variety of topics, including how to utilize MSI's services and various software packages. These tutorials are free, and are hosted both in person and online via YouTube.

See also:
Tutorials
MSI YouTube channel

Discover Advanced Computing and Data Solutions at MSI

Our Services

Related topics

Governance

The Minnesota Supercomputing Institute is a core research facility of the University within the Research Computing umbrella group of the Research and Innovation Office.

Policies

The Minnesota Supercomputing Institute (MSI) strives to support the research and scholarship of a diverse user community.

Helpdesk

Submit a ticket via the MSI Helpdesk for General Support and Software Purchase requests, apply for Class Accounts, complete a Non-faculty PI Eligibility Form, request a purchase for Dedicated Computing or, request access to Citrix.