1. Software๏ƒ

HPC3 serves researchers from all corners of the UCI campus. At the heart of the value that RCIC adds to HPC3, is wide range of applications software that is compiled and ready for use. There are literally hundreds of domain-specific, community-supported, applications maintained on the cluster.

How it is built

Some software is quick and easy to compile, install, and make available to users. Others have numerous (often undocumented) software dependencies, unique build methods, and conflicting requirements. The size of the problem is quite large, and grows with each new application.

RCIC uses a multi-factor approach to provide a stable and flexible environment

  • Adoption of a declarative, repeatable YAML2RPM build methodology designed by RCIC which generates reusable RPM that can installed on any compatible CentOS system.

  • Nearly all installed software is packaged as RPMs with encoded dependencies. Exceptions generally are very large footprint software like the Intel Compiler or MATLAB.

Why use RPMS?

For us, itโ€™s one extra step that comes a wide variety of benefits:

  • The complete stack is fairly complex and captures needed dependencies.

  • Enable installation of multiple versions of same software.

  • Use native operating system tools to get information about installed software.

  • The package manager will not allow two different RPMs to claim ownership of the same file (or have conflicting permissions on a shared directory path).

  • Properly encoded dependencies help to ensure that removal of a particular package wonโ€™t leave other software in a broken state.

  • Ease of transitioning to container definitions. We can easily put a subsets of the HPC3 software stack in the form of a singularity containers.

The deployed software stack is generally added to on weekly basis. This is in response to a near-continuous stream of requests.

A Software Map (PDF) shows a snapshot of the collections of software, software modules they provide, and build dependencies.

Cluster Operating System

Important

HPC3 operating system is Rocky Linux 8.10 (as of December 18, 2024).
All installed software is compiled specifically for this OS.

Attention

  • Docker is not available per security vulnerability, use singularity. See Create Singularity Containers guide.

  • sudo and su commands are not available per security vulnerability.

Installed software

Most software is accessed only after loading the appropriate software modules. Cluster users simply need to know or discover the already available application environment module and load it prior to using the application. Please see:

Licensed Software

Access to the following applications requires a license:

Abaqus

COMSOL

Gaussian

MATLAB [1]

Stata 16

Stata 17

VASP 5.x

VASP 6.x

Note

While all users can view and load modules for licensed software only registered users (users must be in specific groups) can use such software.

  • RCIC does not purchase or provide licenses, we only enable an access to the licenses.

  • The departments/PIs buy licenses for their labs and the access must be approved by a PI.

  • Users must submit a ticket reqesting Access to Licensend Software in order to use to licensed applications.

Request New Software

Please see User installed software before requesting new software install.

You may submit a request for new software to be added to HPC3, however we cannot and do not say yes to every request. RCIC is simply not large enough to handle all software requests.

RCIC prioritizes all software requests as follows:

  1. Fix a compilation problem, security issue, or functionality issue of existing software.

  2. A new release of an already-installed software provides significant new capability.

  3. New software has a demonstrated need by multiple labs.

RCIC says NO to the following types of requests:

  1. When a request does not meet the above priority criteria.

  2. Software that the user wants to evaluate.

  3. Licensed software that does not use the FlexLM license manager or requires RCIC to run the license server.

  4. Software that will only be used by one or two users.

  5. Software that requires MySQL, PostgreSQL, HTTP or similar server setup.