Computing and Visualization

The Brain Image Library provides several ways to access data without having to download it:


BIL Login Node

The BIL login node provides command line (ssh terminal) access to BIL data. Everyone who requests a BIL account has access to the login node using their BIL Username and Password. The login node is not intended for heavy computation or visualization, but rather to provide convenient shell access to BIL data and enable interactive and batch use of the BIL Computational Cluster. The BIL computational cluster provides a suitable resource for both computation and visualization.

To request a BIL account and gain access to the login node, follow these instructions to create an XSEDE portal Account. Then, send email to bil-support@psc.edu along with your XSEDE Portal Account and the subject "Access to BIL Login Node for data exploration". You will receive an email message once access has been enabled with instructions to set your password. Please allow 24 hours for access to be granted.

Once access has been granted you may connect using ssh to login.brainimagelibrary.org and log in with your username/password combination.

BIL VM System

The BIL VM system is a flexible resource that is made up of several large memory machines equiped with modern GPUS. The VM system is remote desktop capable, can host user-licenced commercial, and can host web gateways to provide project-specific data views, support web-based visualization, and compute-in-place applications.

The VM system can be set up to support two different remote-desktop models: X2Go and for high-resolution graphics TGX.

There is a rich suite of open-source and commercial software availiable on the VMs through the modules package. The suite available includes: C/C++, Java, Python, R, Matlab, Fiji, Vaa3d, and others.

VMs can also be configured to host web gateways to provide project specific views of data in BIL and to support visualization, APIs, and compute-in-place applications.

Since customization is involved, existing BIL users should send email to bil-support@psc.edu describing their proposed VM usage. BIL staff will then contact the enailer and set up a time to discuss various VM options in more detail.

Bridges-2 HPC Access

The Brain Image Library data (the /bil filesystem) is directly accessable on the Bridges-2 Platform (bridges2.psc.edu)

The Bridges-2 system is a high performance computing system designed to support familiar, convenient software and environments for both traditional and non-traditional HPC users. Bridges-2 is the ideal system for resource-intensive applications as well as applications targeting HPC + AI + Data. Additional information about Bridges-2 capabilities can be found here. In addition there is a Bridges-2 User Guide available which provides user-specific information.

Bridges-2 is allocated through XSEDE. There are three types of allocations that can be requested for open research:

Multiple users can use a single allocation. To be added to an existing allocation by the allocation owner, you must have an XSEDE Portal account (create one here if you don't already have one); once you do, the Allocation owner can submit a request through the Portal to add you to the allocation.

Proprietary research on Bridges-2 can be accommodated through the Corporate Affiliates program

Neocortex

Neocortex is a highly innovative resource that will accelerate AI-powered scientific discovery by vastly shortening the time required for deep learning training, foster greater integration of artificial deep learning with scientific workflows, and provide revolutionary new hardware for the development of more efficient algorithms for artificial intelligence and graph analytics.

Additional information about Neocortex is available here.