/tag/chem

  • Spark and UVA HPC

     Description Spark is Hadoop MapReduce done in memory
    Software Category: devel
    For detailed information, visit the Spark website.
    Available Versions To find the available versions and learn how to load them, run:
    module spider spark The output of the command shows the available Spark module versions.
    For detailed information about a particular Spark module, including how to load the module, run the module spider command with the module’s full version label. For example:
    module spider spark/4.0.0 ModuleVersion Module Load Command spark4.0.0 module load spark/4.0.0 Using Spark interactively There are three ways to use Spark interactively:
    Shell prompt Open OnDemand JupyterLab PySpark kernel Open OnDemand Desktop If you need the Web UI you must use the third method (OOD Desktop).
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  • VASP and UVA HPC

     Description The Vienna Ab initio Simulation Package (VASP) is a computer program for atomic scale materials modelling.
    Local support is not available. The package is supported by its developers through their documentation site. VASP is licensed software and licenses are issued to individual research groups. Each group must build and maintain its own copy of the code.
    Software Category: chem
    For detailed information, visit the VASP website.
    Building VASP VASP 6 on AMD hardware Please follow the instructions on the VASP wiki. We recommend that you load intel/2025.0 and start from makefile.include.oneapi. To build for AMD (all parallel nodes are AMD), change -xHost to -march=znver4.
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  • GROMACS and UVA HPC

     Description GROMACS is a versatile package to perform molecular dynamics,
    i.e. simulate the Newtonian equations of motion for systems with hundreds to millions of particles.
    Software Category: chem
    For detailed information, visit the GROMACS website.
    Available Versions To find the available versions and learn how to load them, run:
    module spider gromacs The output of the command shows the available GROMACS module versions.
    For detailed information about a particular GROMACS module, including how to load the module, run the module spider command with the module’s full version label. For example:
    module spider gromacs/2025.3 ModuleVersion Module Load Command gromacs2025.3 module load intel-compilers/2023.
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  • Chemistry and UVA HPC

     Overview Many popular software packages for computational chemistry are available on Rivanna and Afton.
    General considerations Most computational chemistry packages utilize MPI for parallel execution. Accordingly, the Slurm job scripts should contain the following two SBATCH directives:
    #SBATCH -N <M> # request M nodes (replace with a number) #SBATCH –ntasks-per-node=<L> # request L MPI processes per node You should launch your program with srun as the MPI executor, for example for Quantum Espresso
    srun pw.x -in mymol.in Please see the page of the particular package you wish to use for more details.
    VASP Users
    The Vienna Ab-Initio Simulation Package, is licensed by individual groups and we do not have a common installation.
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  • Gaussian and UVA HPC

     Description Gaussian is a suite of electronic-structure codes.
    Software Category: chem
    For detailed information, visit the Gaussian website.
    Available Versions The current installation of Gaussian incorporates the most popular packages. To find the available versions and learn how to load them, run:
    module spider gaussian The output of the command shows the available Gaussian module versions.
    For detailed information about a particular Gaussian module, including how to load the module, run the module spider command with the module’s full version label. For example:
    module spider gaussian/g16 ModuleVersion Module Load Command gaussiang16 module load gaussian/g16 gaussiangrads16 module load gaussian/grads16 License and Permission We have a site license.
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  • LAMMPS and UVA HPC

     Description LAMMPS (Large-scale Atomic/Molecular Massively Parallel Simulator) is a molecular-dynamics code. The code is designed to be easy to modify or extend with new functionality. LAMMPS can run on a single core but is designed to be highly efficient running on a large number of cores in parallel using message-passing techniques and a spatial decomposition of the simulation domain. It solves systems ranging from single atoms through polymers and proteins to rigid collections of particles. A variety of force fields is supported.
    Local support is not available. LAMMPS has documentation and tutorials at its Website. It has a large and active community of users; to search or join the mailing list see the instructions here.
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  • NAMD and UVA HPC

     Description NAMD is a parallel molecular dynamics code designed for high-performance simulation of
    large biomolecular systems.
    Software Category: chem
    For detailed information, visit the NAMD website.
    Available Versions The current installation of NAMD incorporates the most popular packages. To find the available versions and learn how to load them, run:
    module spider namd The output of the command shows the available NAMD module versions.
    For detailed information about a particular NAMD module, including how to load the module, run the module spider command with the module’s full version label. For example:
    module spider namd/2.14 ModuleVersion Module Load Command namd2.14 module load gcc/11.
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  • ORCA and UVA HPC

     Description ORCA is a flexible, efficient and easy-to-use general purpose tool for quantum chemistry
    with specific emphasis on spectroscopic properties of open-shell molecules.
    It features a wide variety of standard quantum chemical methods ranging from semiempirical methods to DFT to single-
    and multireference correlated ab initio methods.
    It can also treat environmental and relativistic effects.
    Software Category: chem
    For detailed information, visit the ORCA website.
    Available Versions The current installation of ORCA incorporates the most popular packages. To find the available versions and learn how to load them, run:
    module spider orca The output of the command shows the available ORCA module versions.
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  • QuantumEspresso and UVA HPC

     Description Quantum ESPRESSO is an integrated suite of computer codes
    for electronic-structure calculations and materials modeling at the nanoscale.
    It is based on density-functional theory, plane waves, and pseudopotentials
    (both norm-conserving and ultrasoft).
    Local support is not available. For detailed documentation and tutorials, visit the QuantumEspresso website. QuantumEspresso (QE) has a large and active community of users; to search or join the mailing list see the instructions here. Software Category: chem
    Available Versions We built versions of QE incorporating the most popular optional packages. To find the available versions and learn how to load them, run:
    module spider quantumespresso The output of the command shows the available QuantumEspresso module versions.
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  • TeX Live and UVA HPC

     Description TeX Live is TeX Live is intended to be a straightforward way to get up and running with the TeX document production system. It provides a comprehensive TeX system with binaries for most flavors of Unix, including GNU/Linux, macOS, and also Windows. It includes all the major TeX-related programs, macro packages, and fonts that are free software, including support for many languages around the world.
    Software Category: tools
    For detailed information, visit the TeX Live website.
    Available Versions To find the available versions and learn how to load them, run:
    module spider texlive The output of the command shows the available TeX Live module versions.
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