Welcome to the DeepThought HPC ========================================= The Flinders University High Performance Computing (HPC) cluster is called DeepThought and runs on RedHat Enterprise Linux 10. .. tip:: If you've never used Linux before or are a bit rusty with the command line interface and would like a refresher we have a new `Intro to Linux`_ page that may be helpful DeepThought is available to all Researchers at Flinders University including Staff, HDR Students, Full Academic Status holders and Emeritus Professors. .. note:: Staff and Students falling outside of the classifications above may still request access to DeepThought but we'll need appropriate justification and sponsorship/authorisation. Please contact the IDS Research Success team via Service One if you don't have access but require it DeepThought is primarily intended to be used by our HDR Students and Early/Middle-Career Researchers as a way to familiarise themselves with the tools that they will likely be using during their Research Projects and to allow access to computational services prior to working on projects that would be eligible for schemes like `NCMAS`_. .. _NCMAS: https://ncmas.nci.org.au Having a local compute cluster also allows us to cater for other Research-active Staff who have specific requirements for grants and projects, including those that are working with ``UNCLASSIFIED`` Defence-related materials and ``DEIDENTIFIED`` health data. We also have enough capacity to cater for more experienced Researchers, with many preferring to prototype their designs and pipelines using DeepThought before moving them to other providers for their final compute run. DeepThought is intended as a stepping stone towards the use of the larger HPC providers (such as our partners at `NCI`_ and `Pawsey`_ as Researchers progressing through their career will find that their requirements eventually outstrip what we can provide locally at the University. Pawsey in particular uses much of the same tooling as DeepThought and allows for a relatively seamless transition when the extra compute power is needed. .. _NCI: https://nci.org.au .. _Pawsey: https://pawsey.org.au .. attention:: These pages are currently a Work In Progress while we update them to include information about the upgraded HPC Cluster. Please email researchsupport@flinders.edu.au if you require assistance and we also welcome user contributions to this documentation .. _Intro to Linux: GettingStarted/IntroToLinux.html Attribution ---------------------- If you use the HPC to form a part of your research, you should attribute your usage. Flinders has minted a DOI that points to this documentation, specific for the HPC Service. It will also allow for tracking the research outputs that the HPC has contributed to. Text Citation ++++++++++++++ .. _ARDC Data Citation: https://ardc.edu.au/resources/working-with-data/citation-identifiers/data-citation/ The below text citation follows the standard Australian Research Data Commons (ARDC) format for attributing data and software. For more information on this type of attribution, visit the `ARDC Data Citation`_ page. ``Flinders University (2021). DeepThought (HPC). Retrieved from https://doi.org/10.25957/FLINDERS.HPC.DEEPTHOUGHT`` Reference Managers +++++++++++++++++++ The following files are provided for integration into your reference manager of choice. To save the file, 'Right Click -> Save Link As..'. .. _BibTex: https://raw.githubusercontent.com/flindersuni/DeepThoughtHPC-docs/master/docs/source/flindershpc2021-bibtex.bib .. _EndNote: https://raw.githubusercontent.com/flindersuni/DeepThoughtHPC-docs/master/docs/source/flindershpc2021-endnote.xml .. _RIS: https://raw.githubusercontent.com/flindersuni/DeepThoughtHPC-docs/master/docs/source/flindershpc2021-ris.ris - BibTex_ - EndNote_ - RIS_ .. _Default URL: https://deepweb.flinders.edu.au/ .. _Public Dashboard: https://deepweb.flinders.edu.au/public-dashboards/9f967160b3d0441c8fe9c7eee9f231c5 .. _Full Version: https://deepweb.flinders.edu.au/dtdash Table of Contents ==================== .. toctree:: :maxdepth: 1 :caption: Getting Started GettingStarted/ConnectingToDeepThought.md GettingStarted/UsingTheWebPortal.md GettingStarted/WorkingWithFiles.md GettingStarted/UsingSoftware.md GettingStarted/RunningJobs.md GettingStarted/IntroToLinux.md GettingStarted/MovingFromLegacyDeepThought.md .. toctree:: :maxdepth: 1 :caption: FAQ & Known Issues FAQ/FrequentlyAskedQuestions.md FAQ/KnownIssues.md .. toctree:: :maxdepth: 1 :caption: System Information SystemInformation/DeepThoughtSpecifications.md SystemInformation/StorageUsage.md SystemInformation/SoftwareModules.md SystemInformation/SLURM.md SystemInformation/HPCJobDataFlow.md SystemInformation/HPCResearchDataFlow.md SystemInformation/LegacyDeepThoughtSpecifications.md .. toctree:: :maxdepth: 1 :caption: Software Software/SoftwareOverview.md Software/OpenOnDemand.md Software/EasyBuildAndModules.md Software/Containers.md Software/EPI2ME.md Software/Gaussian16.md Software/LLMs.md Software/Miniconda.md Software/WRF.md .. toctree:: :maxdepth: 1 :caption: Software & Support Policies Policies/FairUse.md Policies/AccessAndPermissions.md .. toctree:: :maxdepth: 1 :caption: Legacy Software Software/ANSYS.md Software/CSTStudio.md Software/Delft3D.md Software/GROMACS.md Software/Jupyter.md Software/LAMMPS.md Software/MATLAB.md Software/VASP.md Software/OpenDataCube.md Legacy HPC Visual Dashboard +++++++++++++++++++++++++++ The legacy DeepThought cluster has a time-series based visual statistics dashboard that be viewed via a web-browser while on campus. The 'Default' and 'Public' URL's are using an *Alpha Release* feature set, and may not display correctly. In that case, please use the 'Full Version' link, and any display strangeness will be resolved. The following URLS all link to the dashboard. 1. `Default URL`_ 2. `Public Dashboard`_ 3. `Full Version`_ The 'Full Version' has the capability to change the time-period viewed, and will be removed when the 'Public' and 'Default' feature set reach maturity. A screen shot of a small portion of the Dashboard is below. .. figure:: _static/GrafanaDashSnapshot.png :align: center :alt: HPC Visual Statistics Dashboard Acknowledgements ---------------- We recognise the respect the trademarks of all third-party providers referenced in this documentation. Please see the respective EULAs for software packages used in configuring your own environment based on this knowledgebase. License ---------- This documentation is released under the `Creative-Commons: Attribution-ShareAlike 4.0 International `_ license.