/tag/gpu
AlphaFold and UVA HPC
Description This package provides an implementation of the inference pipeline of AlphaFold 3.
Software Category: bio
For detailed information, visit the AlphaFold
website.
Available Versions To find the available versions, run:
module spider alphafold For detailed information about a particular version, including the load command, run module spider <name/version>. For example:
module spider alphafold/3.0.0 ModuleVersion Module Load Command alphafold3.0.0 module load gcc/11.4.0 alphafold/3.0.0 alphafold2.3.0 module load apptainer/1.2.2 alphafold/2.3.0 AlphaFold 3 Model Parameters The AlphaFold 3 model parameters are subject to the Terms of Use defined here. Our module does not contain the model parameters; instead, each user must submit their own request to DeepMind.
BerkeleyGW and UVA HPC
Description Local support is not available. For detailed documentation and tutorials, visit the BerkeleyGW website. The user forum can be found here. Software Category:
Available Versions To find the available versions and learn how to load them, run:
module spider berkeleygw The output of the command shows the available BerkeleyGW
module versions.
For detailed information about a particular BerkeleyGW
module, including how to load the module, run the module spider command with the module’s full version label. For example:
module spider ModuleVersion Module Load Command Users may build their own versions of BerkeleyGW if they wish to use a different compiler+MPI combination, or to choose individual optional packages.
Yambo and UVA HPC
Description YAMBO implements Many-Body Perturbation Theory (MBPT) methods (such as GW and BSE) and Time-Dependent Density Functional Theory (TDDFT), which allows for accurate prediction of fundamental properties as band gaps of semiconductors, band alignments, defect quasi-particle energies, optics and out-of-equilibrium properties of materials.
Local support is not available. For detailed documentation and tutorials, visit the Yambo
website. The user forum can be found here.
Software Category: phys
Available Versions To find the available versions and learn how to load them, run:
module spider yambo The output of the command shows the available Yambo
module versions.
For detailed information about a particular Yambo
FastX Web Portal
Overview FastX is a commercial solution that enables users to start an X11 desktop environment on a remote system. It is available on the UVA HPC frontends. Using it is equivalent to logging in at the console of the frontend.
Using FastX for the Web We recommend that most users access FastX through its Web interface. To connect, point a browser to:
https://fastx.hpc.virginia.edu
Off Campus? Connecting to Rivanna and Afton HPC systems from off Grounds via Secure Shell Access (SSH) or FastX requires a VPN connection. We recommend using the UVA More Secure Network if available. The UVA Anywhere VPN can be used if the UVA More Secure Network is not available.
Open OnDemand
Overview Open OnDemand is a graphical user interface that allows access to UVA HPC via a web browser. Within the Open OnDemand environment users have access to a file explorer; interactive applications like JupyterLab, RStudio Server & FastX Web; a command line interface; and a job composer and job monitor.
Logging in to UVA HPC The HPC system is accessible through the Open OnDemand web client at https://ood.hpc.virginia.edu. Your login is your UVA computing ID and your password is your Netbadge password. Some services, such as FastX Web, require the Eservices password. If you do not know your Eservices password you must change it through ITS by changing your Netbadge password (see instructions).
Open OnDemand: File Explorer
Open OnDemand provides an integrated file explorer to browse and manage small files. Rivanna and Afton have multiple locations to store your files with different limits and policies. Specifically, each user has a relatively small amount of permanent storage in his/her home directory and a large amount of temporary storage (/scratch) where large data sets can be staged for job processing. Researchers can also lease storage that is accessible on Rivanna. Contact Research Computing or visit the storage website for more information.
The file explorer provides these basic functions:
Renaming of files Viewing of text and small image files Editing text files Downloading & uploading small files To see the storage locations that you have access to from within Open OnDemand, click on the Files menu.
Open OnDemand: Job Composer
Open OnDemand allows you to submit Slurm jobs to the cluster without using shell commands.
The job composer simplifies the process of:
Creating a script Submitting a job Downloading results Submitting Jobs We will describe creating a job from a template provided by the system.
Open the Job Composer tab from the Open OnDemand Dashboard.
Go to the New Job tab and from the dropdown, select From Template. You can choose the default template or you can select from the list.
Click on Create New Job. You will need to edit the file that pops up, so click the light blue Open Editor button at the bottom.
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
NVHPC
Compiling for a GPU Using a GPU can accelerate a code, but requires special programming and compiling. Several options are available for GPU-enabled programs.
OpenACC OpenACC is a standard
Available NVIDIA CUDA Compilers ModuleVersion Module Load Command cuda10.2.89 module load cuda/10.2.89 cuda11.4.2 module load cuda/11.4.2 cuda11.8.0 module load cuda/11.8.0 cuda12.2.2 module load cuda/12.2.2 cuda12.4.1 module load cuda/12.4.1 ModuleVersion Module Load Command nvhpc24.1 module load nvhpc/24.1 nvhpc24.5 module load nvhpc/24.5 GPU architecture According to the CUDA documentation, “in the CUDA naming scheme, GPUs are named sm_xy, where x denotes the GPU generation number, and y the version in that generation.
