Cardinal

System Downtime August 6 2024

A downtime for OSC HPC systems is scheduled from 7 a.m. to 9 p.m., Tuesday, August 6 2024. The downtime will affect the Pitzer, Owens and Ascend Clusters, web portals, and HPC file servers. There will be a short outage of the state-wide licenses; MyOSC (the client portal) will be available during the downtime. In preparation for the downtime, the batch scheduler will not start jobs that cannot be completed before 7 a.m., August 6. Jobs that are not started on clusters will be held until after the downtime and then started once the system is returned to production status.

AutoDock

AutoDock is a a suite of automated docking tools. It is designed to predict how small molecules, such as substrates or drug candidates, bind to a receptor of known 3D structure. AutoDock has applications in X-ray crystallography, structure-based drug design, lead optimization, etc.

Nodejs

Nodejs is used to create server-side web applications, and it is perfect for data-intensive applications since it uses an asynchronous, event-driven model

MRIcroGL

MRIcroGL is medical image viewer that allows you to load overlays (e.g. statistical maps), draw regions of interest (e.g. create lesion maps).

Availability and Restrictions

Versions

MRIcroGL is available on Pitzer cluster. These are the versions currently available:

dcm2nii

dcm2niix is designed to convert neuroimaging data from the DICOM format to the NIfTI format. The DICOM format is the standard image format generated by modern medical imaging devices. However, DICOM is very complicated and has been interpreted differently by different vendors. The NIfTI format is popular with scientists, it is very simple and explicit. However, this simplicity also imposes limitations (e.g. it demands equidistant slices).

nccl

The NVIDIA Collective Communication Library (NCCL) implements multi-GPU and multi-node communication primitives optimized for NVIDIA GPUs and Networking. NCCL provides routines such as all-gather, all-reduce, broadcast, reduce, reduce-scatter as well as point-to-point send and receive that are optimized to achieve high bandwidth and low latency over PCIe and NVLink high-speed interconnects within a node and over NVIDIA Mellanox Network across nodes.

oneAPI

oneAPI is an open, cross-industry, standards-based, unified, multiarchitecture, multi-vendor programming model that delivers a common developer experience across accelerator architectures – for faster application performance, more productivity, and greater innovation. The oneAPI initiative encourages collaboration on the oneAPI specification and compatible oneAPI implementations across the ecosystem.

Availability and Restrictions

Versions

oneAPI is available on Owens, Pitzer and Ascend. The versions currently available at OSC are:

Miniconda3

Miniconda3 is a free minimal installer for conda. It is a small, bootstrap version of Anaconda that includes only conda, Python, the packages they depend on, and a small number of other useful packages, including pip, zlib and a few others.

Availability and Restrictions

Versions

Miniconda is available on the Ascend Cluster. The versions currently available at OSC are:

VisIt

VisIt is an Open Source, interactive, scalable, visualization, animation and analysis tool for visualizing data defined on two- and three-dimensional structured and unstructured meshes.

 

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