SuiteSparse Matrix Collection

A web interface for the SuiteSparse Matrix Collection, formerly known as the University of Florida Sparse Matrix Collection. It is currently deployed at https://sparse.tamu.edu.

Features and Functionality

The SuiteSparse Matrix Collection web application provides a variety of features to help the scientific computing community access the Collection more easily.

Matrix Property Search, Sorting, and Filtering

The SuiteSparse Matrix Collection web application allows real-time filtering by the following matrix properties:

Matrix Size and Shape

• Rows - The number of rows in the matrix.
• Columns - The number of columns in the matrix.
• Nonzeros - The number of nonzero entries in the matrix.

Matrix Structure and Entry Type

• Pattern symmetry - The percent of entries that are mirrored across the matrix diagonal. The numeric value of the entries is irrelevant.
• Numerical symmetry - The percent of entries that are mirrored across the matrix diagonal with the identical numeric value.
• Number of strongly connected components - The number of strongly connected components present in the resulting graph of this sparse matrix.
• Rutherford-Boeing type - The type of entry in the sparse matrix. One of either Real, Complex, Integer, or Binary.
• Structure - Special matrix structure, including square, rectangular, symmetric, skew-symmetric, Hermitian, and unsymmetric.
• Positive definiteness

Matrix Metadata

• Matrix name - The specific name of the matrix.
• Matrix group - The group name the matrix belongs to.
• Matrix ID - The numeric identification number of the matrix.
• Matrix Year - The year the matrix was added to the Collection.

Additionally, matrix details are displayed on each matrix's individual page, including the matrix's rank, condition number, and information regarding its singular value decomposition. A variety of visualizations are also presented, including sparsity patterns, force-directed graph (or bipartite graph) visualizations (courtesy of Yifan Hu), Dulmage-Mendelsohn permuted sparsity patterns, and singular values plotted in decreasing size.

Quick Access via URL Routing

Matrices can also be quickly accessed by URL route matching using the following URL routes:

• Group name and matrix name to go directly to a matrix page
  • https://sparse.tamu.edu/<Group Name>/<Matrix Name>
  • https://sparse.tamu.edu/HB/west0479
• Matrix ID number to go directly to a matrix page
  • https://sparse.tamu.edu/<Matrix ID>
  • https://sparse.tamu.edu/1230 redirects to https://sparse.tamu.edu/GHS_indef/copter2
• Group name to go directly to a group information page
  • https://sparse.tamu.edu/<Group Name>
  • https://sparse.tamu.edu/Mycielski

Other Interfaces to the Collection

For more information about interfaces to the Collection, see the Interfaces page.

Bugs and Feature Requests

Find a problem with the website? Report it as an Issue, or suggest a fix via a Pull Request.

Building Locally

While the canonical deployment can be found at https://sparse.tamu.edu, you may wish to deploy a version of the SuiteSparse Matrix Collection website locally for testing or convenience.

The only dependencies for running the application are listed below. They can be installed using your package manager (like apt-get or yum for Linux or brew for macOS):

• Ruby 2.7.1 or later
• PostgreSQL 9.3 or later (and permissions to create a database)
• A JavaScript runtime environment such as node.js 12.17.0 or later

Many operating systems come with Ruby installed, and you can check which version you have with ruby -v. If no Ruby installation is found, or the version is incorrect, you can use your package manager to install a compatible version (see ruby-lang.org for more information regarding obtaining and installing Ruby). You may also find Ruby Version Manager (rvm.io) to be helpful if you need to maintain multiple versions of Ruby.

Installing PostgreSQL and node.js also varies greatly from system to system. For example, to install PostgreSQL and node.js (required by Rails) on Ubuntu 18, you can use the following commands:

sudo apt install postgresql postgresql-contrib libpq-dev nodejs
sudo -u postgres createuser -s $(whoami); createdb $(whoami)

Note that after installing PostgreSQL, one needs to start it up so it is running in the background. The status can be checked using pg_isready. If this fails, the installation can be started manually, e.g. via pg_ctl -D /usr/local/var/postgres -l /usr/local/var/postgres/server.log start, depending on the location of your installation. If PostgreSQL was installed from a package manager, post-install information is usually displayed about how to start the PostgreSQL daemon on your platform.

For running the test suite, the following additional dependencies are required:

• Firefox 46 or later

The application is a standard Ruby on Rails web application, and can be installed with the following commands:

ruby -v                              # Check that Ruby 2.7.1+ is installed
pg_isready                           # Check that PostgreSQL database is ready
git clone https://github.com/ScottKolo/suitesparse-matrix-collection-website.git
cd suitesparse-matrix-collection-website
gem install bundler                  # Dependency manager
bundle config set without 'development test'
bundle install                       # Download and install dependencies
bundle exec rails db:setup           # Generate and seed the database
bundle exec rails server             # Start the Ruby on Rails server application

Once the Rails server starts, you can navigate in a web browser to localhost:3000 to view the web application running locally.

Test Suite

After building and running the application locally, you can run the test suite by running

bundle exec rake

This will run a variety of Cucumber, rspec, and Brakeman tests that ensure the backend and user interface frontend function correctly, and that no (obvious) security issues exist. It will also report test coverage, with a detailed report generated in the /coverage directory.

Acknowledgements

This website was originally part of a Software Engineering course project. The original team members are listed below:

• Scott Kolodziej (current maintainer)
• Read Sandström
• Mohsen Aznaveh
• Jarrett David
• Matthew Bullock
• Matthew Henderson

We would also like to thank Dr. Jeff Huang, who taught that Software Enigneering course and impressed upon us the importance of software engineering practices, such as test-driven development and Agile.

We also owe a significant debt to Dr. Tim Davis for his input and guidance, as well as for creating many of the tools (and the original website) that made this project possible.

License

Overview: This website software (except for ssget) is under the MIT License. The matrices themselves are under the CC-BY 4.0 License.

ssget (available in SuiteSparse/ssget in the ssget folder is under the BSD 3-clause License.

The matrices themselves are under the CC-BY 4.0 license. Note that this license asks you to cite the source of the matrices. That citation can be made to these references:

• Kolodziej et al., (2019). The SuiteSparse Matrix Collection Website Interface. Journal of Open Source Software, 4(35), 1244, DOI

• Timothy A. Davis and Yifan Hu. 2011. The University of Florida sparse matrix collection. ACM Trans. Math. Softw. 38, 1, Article 1 (November 2011), 25 pages. DOI

You should also preserve the metadata in the matrices themselves, which includes additional citations for specific matrices. For example, the LAW set of matrices (from the Laboratory for Web Algorithmics, Universita degli Studi di Milano) includes specific instructions on how to properly cite the matrices. See sparse.tamu.edu/LAW for details. For the Matrix Market format, most of the metadata appears in the header of the *.mtx themselves.

Ideally, if you redistribute the matrices in your own applications, you should not change them at all. This is essential for repeatability of experiments that rely on these matrices. Modification is permitted under the CC-BY 4.0 License, but that license requires you to state the modifications you make. If you make any such modifications, please change the filename and matrix name to indicate that it differs from the copy of the matrix from sparse.tamu.edu. Carefully describe any modifications you make.

Last update: Mar 14, 2022.