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<!DOCTYPE html>
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<title>Brain Image Library: Computing and Visualization</title>
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<h1>Computing and Visualization</H1>
<p>The Brain Image Library provides several ways to access data without having to download it: </p>
<ul>
<li><b>BIL Login Node:</b> All users of the BIL systems have ssh access to the BIL login node<./li>
<li><b>BIL Computational Cluster:</b> The BIL Computational cluster consists of eight nodes
with 3 terabytes of RAM. The computational cluster runs SLURM and is avaiable for
both batch and interactive access from the BIL login node.</li>
<li><b>BIL VM System:</b>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.</li>
<li><b>Bridges-2:</b> Bridges-2 is a high performance computing system designed
to support familiar, convenient software and environments for both traditional and non-traditional
HPC users. Its richly-connected set of interacting systems offers exceptional flexibility for data
analytics, simulation, workflows and gateways, leveraging interactivity, parallel computing, Spark
and Hadoop.</li>
<li><b>NeoCortex:</b> Neocortex is a Cerebras CS-1 system.</li>
</ul>
<hr />
<div id="login"></div>
<h3>BIL Login Node</h3>
<p>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 <i>BIL Computational Cluster</i>. The BIL
computational cluster provides a suitable resource for both computation and visualization.</p>
<p>To request a BIL account and gain access to the login node, follow
<a href="http://www.brainimagelibrary.org/XSEDEportal.html">these instructions</a> to create an
XSEDE portal Account. Then, send email to <i>[email protected]</i> 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.</p>
<p> Once access has been granted you may connect using ssh to login.brainimagelibrary.org and log in
with your username/password combination.</p>
<h3>BIL VM System</h3>
<p>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.</p>
<p>The VM system can be set up to support two different remote-desktop models: X2Go and for high-resolution
graphics TGX.</a>
<p>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.
<p>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.</p>
<p>Since customization is involved, existing BIL users should send email to <i>[email protected]</i>
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. </p>
<H3>Bridges-2 HPC Access</h3>
<p>The Brain Image Library data (the /bil filesystem) is directly accessable
on the Bridges-2 Platform (bridges2.psc.edu)</b></p>
<p>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
<a href="https://www.psc.edu/resources/bridges-2/">here.</a> In addition there is a
<a href="https://www.psc.edu/resources/bridges-2/user-guide-2/">Bridges-2 User Guide</a>
available which provides user-specific information.</p>
<p>Bridges-2 is allocated through XSEDE. There are three types of allocations that can be
requested for open research:
<ul>
<li><em>Start-up allocations</em> allow you to explore high-performance computing and Bridges-2.
The application process is streamlined. See
<a href="https://portal.xsede.org/allocations/startup" target="_blank" rel="noopener noreferrer">https://portal.xsede.org/allocations/startup</a>
for details on applying.</li>
<li><em>Research allocations</em> provide expanded resource limits when you are ready to scale up your work. See
<a href="https://portal.xsede.org/allocations/research" target="_blank" rel="noopener noreferrer">https://portal.xsede.org/allocations/research</a>
for details on applying.</li>
<li><em>Coursework allocations</em> supplement educational activities from workshops to semester
courses that benefit from the use of high-performance computing. See
<a href="https://portal.xsede.org/allocations/education" target="_blank" rel="noopener noreferrer">https://portal.xsede.org/allocations/education</a>
for details on applying.</li>
</ul>
</p>
<p>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
(<a href="https://portal.xsede.org" target="_blank" rel="noopener noreferrer">create
one here if you don't already have one</a>); once you do, the
<a href="https://portal.xsede.org/knowledge-base/-/kb/document/aswb" target="_blank" rel="noopener noreferrer">Allocation
owner can submit a request through the Portal to add you to the allocation</a>.<p>
<p>Proprietary research on Bridges-2 can be accommodated through the
<a href="https://www.psc.edu/resources/computing/bridges/services/corporate-programs">Corporate
Affiliates program</a></p>
<H3>Neocortex</h3>
<p>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.</p>
<p>Additional information about Neocortex is available
<a href="https://www.cmu.edu/psc/aibd/neocortex/">here</a>.
<p> </p>
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