CCR centerwide downtime is scheduled for Tuesday 24 August 2021. CCR resources (Globus, UB-HPC, submit) will be unavailable. Details: https://ubccr.freshdesk.com/support/discussions/topics/13000027917 close

GHub tool users: please note that these tools are currently being moved to Debian10 containers, and may not run as expected: cmctgm; cmcthistplot; crevasseoib; gisplot2. Thanks for your patience! close

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Welcome GHub users!

Feel free to look around and bookmark our direct URL, theghub.org.

You are welcome to register--use your academic or official email address and indicate your affiliation!

Any questions or concerns, feel free to enter a ticket.

Introduction to Tool Development

Any registered member of GHub can develop and share tools on the HUBzero platform--this is one of its greatest strengths. Tools can be based on Jupyter notebooks running Python 3, which makes them both easy to assemble and computationally powerful.

Example

For a recently-deployed example of GHub tools, check out Denis Felikson's modgrnld. Load the page and click "Launch Tool".

If you're not familiar with this kind of thing, just select the first block of code ("cell") and click the "Run" button. You can page through the whole notebook, running each cell, and making the computations.

The power of this tool is: a user can see the code; can run the code and tinker with it--but any changes they make will not be permanent.

Starting Out

The overall workflow you use when building a Jupyter notebook tool is outlined here:
    https://vhub.org/kb/development/pubjnotebook

If you need additional Python packages, refer here (feel free to ask me if you need package installs):
    https://vhub.org/kb/development/pythonj

For an introduction to Jupyter Notebooks, creating tools, running jobs at CCR, and packages available on GHub:
    Jupyter Notebooks Examples and Documentation (Debian10 and Python3)

For development and testing, use these GHub tools, which give you the most recent container environment, Debian 10:


User Interface Elements

Hubzero has created a package with user interface elements for interacting with data, downloading and uploading, etc. This is available to use from your Jupyter notebooks and tools. Documentation is here:
    https://hubzero.github.io/hublib/intro.html

Note: don't use the Rappture module, that's old school. You want the UI module here.

More Info

This page presents a general guide to developing tools on GHub:
    https://vhub.org/groups/ghub/developing_tools_on_ghub

Additional articles about environment variables, submitting jobs to the CCR cluster, and so forth, are here:
    https://vhub.org/kb/development

Citing GHub

To cite GHub please use the following, published 10 December 2020:

Sperhac, JM, Poinar, K, Jones‐Ivey, R, et al. GHub: Building a glaciology gateway to unify a community. Concurrency Computat Pract Exper. 2020;e6130. https://doi.org/10.1002/cpe.6130

Please note that GHub now enjoys priority access to CCR compute nodes. This change is transparent to you (but should result in shorter wait times for resources, both regular 'submit' jobs and Pegasus jobs). Any issues, problems, or questions, please enter a ticket.

3 November 2020

General

  • We now have our own domain name: theghub.org.
  • The new Debian10 Workspace tool is available.

Collaborate

  • Documentation and About include tips about running and developing tools, accessing your Dashboard, and registering for membership.
  • GHub member registration links have been added to most site pages. You'll need to register (free!) to run tools.
  • Google Drive integration is now in place for GHub Projects
  • Feel free to post on the GHub wiki, forum, blog, calendar, etc. This space is for us!

Related GHub team tools

Send me an email (jsperhac-at-buffalo-dot-edu) to join (or with any questions):

9 October 2020

Tool news:

  • Support for a Debian10 workspace based in a Docker container: coming soon.
  • Fresh install of Anaconda will be in the Debian 10 environment, should fix some tool UI issues.
  • Google Drive integration problem is being investigated and fixed.

UI and site appearance:

  • We can apply for our own domain name for ghub. What would we like to use?
    • glacierhub.net, theghub.org are two available options
  • We are are fixing up some UI issues in Projects.
  • GHub Team page is updated; check it out.

We are excited to announce new ISMIP6 data access!

ISMIP6 collaborators can now access the data store at CCR and UB using Globus for efficient, easy file transfer.

Most datasets stored on 1km grids can be found on UB Geology's Thule server (endpoint name: Thule_ISMIP6); larger grids are stored on CCR's own project space.

Access Globus using your own institutional credentials. This utility makes data access fast, secure, and easy. Just contact us by creating a ticket with your user details to get set up.

Welcome GHub users!

Please check out our newly published tools, which make use of the CCR high-performance computing cluster:

A few GHub updates:

All GHub content pages are now browsable by any visitor. Resources, tools, data access, and project materials remain secured to group membership.

Feel free to post on the wiki, forum, blog, calendar, etc. Play around--this space is for the collaboration.

Documentation has been expanded--including tips about using and developing tools, accessing the Dashboard, and registering for membership.

Please comment or inquire if you have questions or remarks.