> ## Documentation Index > Fetch the complete documentation index at: https://docs.nyc-ai.app/llms.txt > Use this file to discover all available pages before exploring further. # Applications & software catalog > Scientific applications, compilers, MPI libraries, and languages available at CUNY HPCC. The HPCC maintains a broad software stack through the Lmod environment module system. Load packages with `module load ` after checking availability with `module spider ` or `module avail`. See [Software & modules](/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](mailto:HPCHelp@csi.cuny.edu) 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. | ```bash theme={null} 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: ```bash theme={null} 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. | ```bash theme={null} 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 ```bash theme={null} 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/` (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](mailto: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.