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Software Installation on Palmetto

Palmetto2, our High Performance Computing cluster, offers a variety of software installation options to accommodate the diverse needs of our users.

Centrally Installed Software​

Centrally installed software includes widely used packages and dependencies that are essential for many scientific applications. These core modules are maintained to be easily accessible by all cluster users.

Software for Research Groups and Courses​

Custom optimized software installations are available for research groups and courses. Benefits include:

  • Uniform access to the same software version for all group members
  • Elimination of the need for individual installations in personal directories

To request a group installation, research group advisors or course instructors should fill out the software support form.

Software for Single Users​

Individual users may require software for personal use or short-term testing. Assistance with installation in home directories is available through the software support form.

Self-installation is possible by following the provided documentation for installing from source, or by using the "spack" module if the package is available through "spack".

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Important Notes

  • Privileged Commands: Users are not permitted to run “sudo” or use OS-specific package managers like “apt” or “yum”.
  • Module Updates: If you are using “spack” or linking against centrally provided modules, you may need to recompile your software after module updates post-maintenance.

Self-Installation via Spack​

Many pieces of software are available via Spack. Users can install Spack packages themselves by following the instructions below.

Basic Example​

Installing pre-packaged software via Spack is as easy as loading the module and running the spack install command.

module load spack
spack install [package-name]

Then, follow the self-installation usage instructions to use the software after installation.

Advanced Example​

In this example, we are going to install an optimized version of mfem for the AMD CPU nodes.

  1. Request for an AMD node

    salloc --nodes=1 --ntasks-per-node=1 --cpus-per-task=16 --mem=32G --time=03:00:00 -p work1 --constraint cpu_gen_genoa

  2. Load the spack module

    module load spack

    Verify that spack has loaded

    spack --version

  3. Check information of the package to be installed to determine what variants you want to install

    spack info mfem

  4. After determining the variants, "concretize" the installation. Note: This does not install the package. It gives you list of dependencies and packages to be installed.

    spack spec -Il mfem+examples+mpi

  5. Install the package

    spack install mfem+examples+mpi
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Note: This package is optimized for running on AMD CPU nodes. If you run this on an Intel node you may get segmentation faults or other errors.

Using Software Self-Installed via Spack​

  1. Load the spack module

    module load spack

  2. Use spack to load the installed module

    spack load mfem

    If you have multiple versions installed, use spack find [package] to find the version you want.

  3. Change into the mfem example directory

    Note: The following example steps are specific to mfem. Other

    packages will have different commands and options to run them. :::

    cd `spack location -i mfem`/share/mfem/examples

  4. Run the installed application. In this case, we are running mfem

    mpirun -np 4 ex1p -m ../data/square-disc.mesh