/tag/chem
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.
Available Versions To find the available versions and learn how to load them, run:
module spider vasp The output of the command shows the available VASP
module versions.
For detailed information about a particular VASP
AlphaFold and UVA HPC
Description Open source code for AlphaFold
Software Category: bio
For detailed information, visit the AlphaFold
website.
Available Versions The current installation of AlphaFold
incorporates the most popular packages. To find the available versions and learn how to load them, run:
module spider alphafold The output of the command shows the available AlphaFold
module versions.
For detailed information about a particular AlphaFold
module, including how to load the module, run the module spider command with the module’s full version label. For example:
module spider alphafold/2.3.0 ModuleVersion Module Load Command alphafold2.3.0 module load apptainer/1.2.2 alphafold/2.3.0 AlphaFold Installation Details Dockerfile We prepared a Docker image based on the official Dockerfile with some modifications.
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.
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.
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/2023.2 ModuleVersion Module Load Command gromacs2023.2 module load gcc/11.
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.
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/3.4.1 ModuleVersion Module Load Command spark3.4.1 module load spark/3.4.1 Using Spark interactively There are three ways to use Spark interactively:
Shell prompt Open OnDemand PySpark Open OnDemand Desktop If you need the Web UI you must use the third method (OOD Desktop).
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.
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
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
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
