Applications & software catalog

The HPCC maintains a broad software stack through the Lmod environment module system. Load packages with module load <name> after checking availability with module spider <name> or module avail. See Software & modules for the full workflow.

This catalog is a practical orientation, not a guarantee that every package is installed on every HPCC system. New packages are added over time and some may be retired. Always verify with module avail or module spider on the system you’re using, then contact the HPC Helpline if something you need is missing.

Compilers

Package	Notes
GNU Compiler Collection (GCC)	Multiple versions. `gcc`, `g++`, `gfortran`. Default compiler on most nodes.
Intel compiler suite / oneAPI	Check the module for current compiler names such as `icx`, `icpx`, `ifx`, or legacy `icc` / `ifort`; includes MKL.
NVIDIA HPC SDK (nvhpc)	`nvc`, `nvc++`, `nvfortran`. OpenACC and CUDA Fortran support.
Cray compilers	Legacy Cray environments only; verify current availability before using Cray-specific examples.

module spider gcc
module load GCC/12.3.0

MPI libraries

Package	Notes
OpenMPI	Recommended default for most CPU jobs.
Intel MPI	Pairs with Intel compilers; typically faster on Intel nodes.
Cray MPICH	Legacy Cray environments only; verify current availability before use.

Choose the MPI that matches your compiler:

module load GCC/12.3.0
module load OpenMPI/4.1.5-GCC-12.3.0
mpicc -o my_prog my_prog.c

Math and scientific libraries

Package	Notes
FFTW	Fast Fourier Transforms; single- and double-precision.
Intel MKL	BLAS, LAPACK, ScaLAPACK, FFTW wrappers bundled with Intel oneAPI.
OpenBLAS	Open-source optimized BLAS/LAPACK.
HDF5	Hierarchical data format; parallel (MPI) and serial builds available.
NetCDF	Network Common Data Form; critical for climate and earth-science codes.
PETSc	Parallel sparse linear algebra for PDEs.
SLEPc	Scalable eigenvalue solvers built on PETSc.
ELPA	Eigenvalue solvers for dense matrices, popular in quantum chemistry.

GPU and CUDA

Package	Notes
CUDA Toolkit	Multiple versions. Required for raw CUDA C/C++ development.
cuDNN	Deep learning primitives on top of CUDA (required by PyTorch / TensorFlow).
NCCL	Collective communication for multi-GPU training.

module spider CUDA
module load CUDA/12.2.0
nvcc -o my_kernel kernel.cu

Languages and runtimes

Package	Notes
Python	Multiple versions (3.8, 3.10, 3.11, …). Includes pip; use `venv` or `conda` for isolation.
Julia	Recommended for scientific computing newcomers to HPC.
R	Statistical computing with access to CRAN packages.
Perl	Available for bioinformatics pipelines that require it.
Java / JDK	Needed by some bioinformatics tools (e.g., Trimmomatic, Picard).

Managing Python environments

module load Python/3.10.4
python -m venv ~/envs/myproject
source ~/envs/myproject/bin/activate
pip install numpy scipy matplotlib

Store environments in /global/u/<username> (home), not in /scratch, so they survive scratch purges.

Machine learning and AI

Package	Notes
PyTorch	Install in a user environment after loading a compatible CUDA module unless a site module is available.
TensorFlow	Install in a user environment after loading a compatible CUDA module unless a site module is available.
JAX	Install via pip in a user environment; GPU builds require a matching CUDA stack.

GPU-enabled frameworks typically require module load CUDA and matching cuDNN before installing or importing the package.

Visualization and post-processing

Package	Notes
ParaView	Parallel visualization, client-server mode supported.
VisIt	Visualization and analysis for large datasets.
gnuplot	Lightweight 2-D and 3-D plotting from scripts.
ImageMagick	Command-line image processing.

GUI visualization tools require X11 forwarding (ssh -Y) or an off-cluster workflow where you copy results back to your laptop. Rendering is usually more practical done in batch using off-screen backends.

Chemistry and materials

Package	Notes
Gaussian	Licensed to CUNY; restricted to approved QOS/partition (e.g., `qoschem`).
GAMESS	Free ab initio quantum chemistry.
ORCA	Widely used for DFT and coupled-cluster calculations.
NAMD	Molecular dynamics; highly optimized for GPU.
GROMACS	Molecular dynamics; GPU-accelerated.
LAMMPS	Classical MD; many interatomic potential packages.
Quantum ESPRESSO	Plane-wave DFT for materials.
CP2K	Electronic structure and MD.

Bioinformatics

Package	Notes
BLAST	Sequence alignment.
BWA / Bowtie2	Short-read alignment to reference genomes.
STAR	RNA-seq alignment.
SAMtools / BCFtools	SAM/BAM processing and variant calling.
GATK	Variant calling pipeline (requires Java).
Trimmomatic / Fastp	Read quality trimming.
SPAdes	Genome assembly.

Other domain applications

Package	Notes
MATLAB	Licensed for academic use; launched with `matlab -nodisplay -nojvm` in batch.
WRF	Weather Research & Forecasting model.
OpenFOAM	Open-source CFD; multiple versions.
LS-DYNA	Structural and crash analysis; licensed academic use on supported systems.

Requesting new software

Email HPCHelp@csi.cuny.edu with:

The software name and the version you need.
A link to its install documentation or source.
A one-line justification (what research it enables).

Staff prioritize packages that benefit multiple research groups. For personal Python / Julia / R packages, you can usually manage them yourself inside your home directory without waiting for a ticket.

Getting started

Systems

Running jobs

Reference

Compilers

MPI libraries

Math and scientific libraries

GPU and CUDA

Languages and runtimes

Managing Python environments

Machine learning and AI

Visualization and post-processing

Chemistry and materials

Bioinformatics

Other domain applications

Requesting new software

​Compilers

​MPI libraries

​Math and scientific libraries

​GPU and CUDA

​Languages and runtimes

​Managing Python environments

​Machine learning and AI

​Visualization and post-processing

​Chemistry and materials

​Bioinformatics

​Other domain applications

​Requesting new software

Compilers

MPI libraries

Math and scientific libraries

GPU and CUDA

Languages and runtimes

Managing Python environments

Machine learning and AI

Visualization and post-processing

Chemistry and materials

Bioinformatics

Other domain applications

Requesting new software