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Owens Information Transition

Owens cluster will be decommissioned on February 3, 2025. Some pages may still reference Owens after Owens is decommissioned , and we are in the process of gradually updating the content. Thank you for your patience during this transition

Software

fMRIPrep

fMRIPrep is a functional magnetic resonance imaging (fMRI) data preprocessing pipeline that is designed to provide an easily accessible, state-of-the-art interface that is robust to variations in scan acquisition protocols and that requires minimal user input, while providing easily interpretable and comprehensive error and output reporting.

Trinity

Trinity represents a novel method for the efficient and robust de novo reconstruction of transcriptomes from RNA-seq data.

Availability and Restrictions

The following versions of Trinity are available on OSC clusters:

PETSc

PETSc is a suite of data structures and routines for the scalable (parallel) solution of scientific applications modeled by partial differential equations. It supports MPI, and GPUs through CUDA or OpenCL, as well as hybrid MPI-GPU parallelism.

Software Refresh - May 2020

OSC will be refreshing the software stack for Owens and Pitzer on May 19, 2020. This will be done in a system-wide downtime. During the software refresh, some default versions will be changed to be more up-to-date. Information about the new default versions, as well as all available versions of each software package will be included on the corresponding OSC software webpage. See https://www.osc.edu/supercomputing/software-list.

NetCDF-Serial

NetCDF (Network Common Data Form) is an interface for array-oriented data access and a library that provides an implementation of the interface. The netcdf library also defines a machine-independent format for representing scientific data. Together, the interface, library, and format support the creation, access, and sharing of scientific data.

For mpi-dependent codes, use the non-serial NetCDF module.

HDF5-Serial

HDF5 is a general purpose library and file format for storing scientific data. HDF5 can store two primary objects: datasets and groups. A dataset is essentially a multidimensional array of data elements, and a group is a structure for organizing objects in an HDF5 file. Using these two basic objects, one can create and store almost any kind of scientific data structure, such as images, arrays of vectors, and structured and unstructured grids.

For mpi-dependent codes, use the non-serial HDF5 module.

Connectome Workbench

Connectome Workbench is an open source, freely available visualization and analysis tool for neuroimaging data, especially data generated by the Human Connectome Project.

Availability and Restrictions

Versions

Connectome Workbench is available on Owens and Pitzer clusters. These are the versions currently available:

LS-PrePost

LS-PrePost is an ad­vanced pre and post-proces­sor that is de­liv­ered free with LS-DY­NA.

Availability and Restrictions

Versions

The following versions of ls-prepost are available on OSC clusters:

QGIS

QGIS is a user friendly Open Source Geographic Information System (GIS) licensed under the GNU General Public License. QGIS is an official project of the Open Source Geospatial Foundation (OSGeo). It runs on Linux, Unix, Mac OSX, Windows and Android and supports numerous vector, raster, and database formats and functionalities.

Availability and Restrictions

Versions

The following versions of QGIS are available on OSC clusters:

Gaussian

Gaussian is a very popular general purpose electronic structure program. Recent versions can perform density functional theory, Hartree-Fock, Möller-Plesset, coupled-cluster, and configuration interaction calculations among others. Geometry optimizations, vibrational frequencies, magnetic properties, and solution modeling are available. It performs well as black-box software on closed-shell ground state systems. 

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