Available Software Modules

The cluster maintains a comprehensive catalog of software modules across multiple categories.

# List all available modules
module avail

# Search for a specific module
module avail python

# Get module details
module show python3/3.8.5

Categories

Biology (27+ modules)

Bioinformatics and structural biology tools:

  • Sequence Analysis: BLAST, HMMER, MAFFT

  • Structural Biology: Chimera, IMOD

  • Cryo-EM: EMAN2, Relion, cryoSPARC

  • Phylogenetics: OrthoFinder, OrthoMCL

Chemistry (17+ modules)

Molecular dynamics and quantum chemistry:

  • Molecular Dynamics: GROMACS, LAMMPS, NAMD (various CUDA/MPI versions)

  • Quantum Chemistry: ORCA (versions 4.0-4.2)

Compilers (6+ modules)

  • GCC: 6.4, 7.3, 8.3, 9.2

  • Clang: 7.0.0

  • Intel: 16.3, 17.4, 18.3, 19.1

Data (9+ modules)

  • HDF4, HDF5

  • NetCDF (C, Fortran, C++)

  • MongoDB

  • Parallel I/O formats

Development (4+ modules)

  • Bazel

  • Julia (1.0, 1.3)

  • Googletest

  • SWIG

Geology (6+ modules)

  • GMT (Generic Mapping Tools)

  • GDAL

  • Dedalus

  • OpenSees

Languages (7+ modules)

  • Go

  • Java

  • Python (2.7, 3.x)

  • R (3.5, 3.6)

  • Jupyter

Libraries (21+ modules)

Scientific computing libraries:

  • Linear Algebra: BLAS, LAPACK, OpenBLAS

  • FFT: FFTW

  • General: Boost, Eigen

  • GPU: CUDA (8.0, 9.0, 10.0, 10.1, 11.x)

Math (9+ modules)

  • Mathematica

  • MATLAB (r2016b through r2023a)

  • Sage

  • FLINT, MPFR

MPI Libraries (11+ modules)

  • OpenMPI (1.10 through 4.x)

  • MPICH

  • MVAPICH2 (various compiler/CUDA combinations)

Tools (52+ modules)

Diverse applications:

  • Build: CMake, Make, Autotools

  • Scientific: PETSc, Relion

  • Containers: Singularity, Apptainer

  • Simulation: FDTD

  • Utilities: Git, FFmpeg, ImageMagick

Visualization (3+ modules)

  • OVITO

  • VMD (1.9.2, 1.9.3)

Cloud & Testing (7+ modules)

  • AWS CLI

  • Google Cloud SDK

  • Testing utilities

Requesting New Software

To request installation of software not currently available:

  1. Check if it can be installed via Conda or containers

  2. Email help-hpc@caltech.edu with:

    • Software name and version

    • Download URL

    • Use case and research group

See Also