https://hpcwiki.uark.edu/ 2026-04-17T03:02:30+00:00 https://hpcwiki.uark.edu/ https://hpcwiki.uark.edu/lib/exe/fetch.php?media=wiki:dokuwiki.svg text/html 2026-02-24T17:51:18+00:00 dchaffin (dchaffin@undisclosed.example.com) https://hpcwiki.uark.edu/doku.php?id=singularity-apptainer&rev=1771955478&do=diff Apptainer/Singularity Apptainer from <https://apptainer.org/>, formerly Sylabs Singularity, is a container system for HPC systems. In many respects it is similar to <https://www.docker.com/>, but Docker is too insecure for use with parallel file systems. Containers allow a specific distribution and version of linux and application software to be set in the container image while running on the HPC system. Containers are very useful for applications that were written on personal workstations (o… text/html 2024-11-08T21:41:42+00:00 pwolinsk (pwolinsk@undisclosed.example.com) https://hpcwiki.uark.edu/doku.php?id=logging_in&rev=1731102102&do=diff Logging In AHPCC clusters can be access via the SSH protocol ssh hpc-portal2.hpc.uark.edu and and using the OpenOnDemand web portal <https://hpc-portal2.hpc.uark.edu>. ssh common account text login host is hpc-portal2.hpc.uark.edu. Once logged in users are redirected to on of 10 login nodes, pinnacle-l1..pinnacle-l10. text/html 2024-11-08T21:27:31+00:00 pwolinsk (pwolinsk@undisclosed.example.com) https://hpcwiki.uark.edu/doku.php?id=off-campus_access&rev=1731101251&do=diff Off-campus Access SSH access Direct Secure Shell (SSH) access to AHPCC login nodes is only allowed from: * UAF campus network * via UAF Virtual Private Network (VPN <https://its.uark.edu/network-access/vpn/index.php>) connection * Other research organization networks, with membership determined by the Arkansas Research and Education Optical Network (ARE-ON text/html 2024-11-08T21:17:36+00:00 pwolinsk (pwolinsk@undisclosed.example.com) https://hpcwiki.uark.edu/doku.php?id=portal_login&rev=1731100656&do=diff Portal Login An OpenOnDemand graphical web portal is available at <https://hpc-portal2.hpc.uark.edu>. If you go to the web page of either portal, a login popup will accept your AHPCC id and password (Your id may be the first part of your email, use “rfeynman” not “rfeynman@caltech.edu” text/html 2024-11-08T21:14:01+00:00 pwolinsk (pwolinsk@undisclosed.example.com) https://hpcwiki.uark.edu/doku.php?id=moving_data&rev=1731100441&do=diff Data Transfer to and from AHPCC Clusters Small files (<100MB) There data transfer protocols are supported to move data to and from the main storage on the AHPCC clusters: * scp (secure copy) * sftp (secure ftp) * rsync In addition the wget and text/html 2024-10-15T13:57:26+00:00 root (root@undisclosed.example.com) https://hpcwiki.uark.edu/doku.php?id=facilities&rev=1729000646&do=diff Facilities The Pinnacle Phase I (2019), Phase II (2022), and Phase III (2024) clusters are the major compute resources at AHPCC. Pinnacle Phase I consists of 106 mostly Intel Skylake based compute nodes with a total of 26 NVidia mostly Volta V100 GPUs. Phase II consists of 79 AMD Zen based compute nodes with a total of 74 NVidia mostly Ampere A100 GPUs. Phase III consists of 36 AMD Zen based compute nodes with 4 Ampere L40 GPUs. An awarded CC* grant will augment Phase III with non-GPU nodes … text/html 2024-08-13T16:36:55+00:00 jpummil (jpummil@undisclosed.example.com) https://hpcwiki.uark.edu/doku.php?id=etiquette&rev=1723567015&do=diff System Etiquette on a Shared Research Resource Welcome as users on the AHPCC Pinnacle HPC system! As Pinnacle is a shared resource used by many concurrent researchers at any given time, it's very important to observe a few basic rules so as to ensure that everyone enjoys a favorable user experience text/html 2024-08-06T22:06:28+00:00 root (root@undisclosed.example.com) https://hpcwiki.uark.edu/doku.php?id=research&rev=1722981988&do=diff HPC Researcher News 2024-07-31 Khodadadi selected for NIH Summer Course <https://news.uark.edu/articles/70822/ph-d-student-ehsan-khodadadi-accepted-into-prestigious-nih-summer-course> 2024-07-01 Research report from House, Hasan, Asnayanti, Alrubaye, Pummill, Rhoads <https://www.researchgate.net/publication/382672799_Phylogenomic_Analyses_of_Three_Distinct_Lineages_Uniting_Staphylococcus_cohnii_and_Staphylococcus_urealyticus_from_Diverse_Hosts> 2024-06-17 Research report from Yamashita, Rhoad… text/html 2024-05-02T16:38:42+00:00 root (root@undisclosed.example.com) https://hpcwiki.uark.edu/doku.php?id=abinit9&rev=1714667922&do=diff Abinit9 Production version is 9.10.3 module load intel/21.7.0 mkl/21.3.0 impi/19.0.9 hdf5/ts/1.10.8 netcdf-c-2/4.9.0 netcdf-f-2/4.6.0 libxc-2/6.0.0 wannier90-2/3.1.0 omp/1 abinit/9.10.3 Run times with a sample problem on pairs of different CPUs. In each case OMP__ text/html 2024-04-30T11:54:18+00:00 jpummil (jpummil@undisclosed.example.com) https://hpcwiki.uark.edu/doku.php?id=conda&rev=1714478058&do=diff Conda Package Manager Conda Conda is an open source package management system and environment management system. Conda as a package manager helps you find and install packages. If you need a package that requires a different version of Python, you do not need to switch to a different environment manager, because conda is also an environment manager. With just a few commands, you can set up a totally separate environment to run that different version of Python, while continuing to run your usua… text/html 2024-04-27T02:59:42+00:00 jpummil (jpummil@undisclosed.example.com) https://hpcwiki.uark.edu/doku.php?id=ollama_llm&rev=1714186782&do=diff Ollama LLM Ollama is an open source inference engine for running LLM models. <https://ollama.com>. To run a local LLM, you need two ingredients: the model itself, and the inference engine, which is a piece of software that can run the model. Conceptually, the inference engine processes the input (a text prompt), feeds it through the neural network of the model, and retrieves the response. Ollama is different than Chat-GPT and Gemini as it runs locally without accessing the internet for model da… text/html 2023-08-24T17:57:10+00:00 pwolinsk (pwolinsk@undisclosed.example.com) https://hpcwiki.uark.edu/doku.php?image=cirrusbridge1.png&ns=0&rev=1692899830&tab_details=history&media_do=diff&do=media <img src="https://hpcwiki.uark.edu/lib/exe/fetch.php?w=500&amp;h=500&amp;tok=0e0566&amp;media=cirrusbridge1.png" alt="cirrusbridge1.png" loading="lazy" width="500" height="500" /> text/html 2023-08-24T17:57:09+00:00 pwolinsk (pwolinsk@undisclosed.example.com) https://hpcwiki.uark.edu/doku.php?image=cirrusbridge2.png&ns=0&rev=1692899829&tab_details=history&media_do=diff&do=media <img src="https://hpcwiki.uark.edu/lib/exe/fetch.php?w=500&amp;h=500&amp;tok=1f0aa5&amp;media=cirrusbridge2.png" alt="cirrusbridge2.png" loading="lazy" width="500" height="500" /> text/html 2023-08-24T17:57:09+00:00 pwolinsk (pwolinsk@undisclosed.example.com) https://hpcwiki.uark.edu/doku.php?image=cirrusbridge3.png&ns=0&rev=1692899829&tab_details=history&media_do=diff&do=media <img src="https://hpcwiki.uark.edu/lib/exe/fetch.php?w=500&amp;h=500&amp;tok=29bdf5&amp;media=cirrusbridge3.png" alt="cirrusbridge3.png" loading="lazy" width="500" height="500" /> text/html 2023-08-24T17:57:09+00:00 pwolinsk (pwolinsk@undisclosed.example.com) https://hpcwiki.uark.edu/doku.php?image=cirrusbridge-g1.png&ns=0&rev=1692899829&tab_details=history&media_do=diff&do=media <img src="https://hpcwiki.uark.edu/lib/exe/fetch.php?w=500&amp;h=500&amp;tok=c461e2&amp;media=cirrusbridge-g1.png" alt="cirrusbridge-g1.png" loading="lazy" width="500" height="500" /> text/html 2023-08-24T17:57:08+00:00 pwolinsk (pwolinsk@undisclosed.example.com) https://hpcwiki.uark.edu/doku.php?image=cirrusbridge-g2.png&ns=0&rev=1692899828&tab_details=history&media_do=diff&do=media <img src="https://hpcwiki.uark.edu/lib/exe/fetch.php?w=500&amp;h=500&amp;tok=b28578&amp;media=cirrusbridge-g2.png" alt="cirrusbridge-g2.png" loading="lazy" width="500" height="500" /> text/html 2023-08-21T20:25:21+00:00 pwolinsk (pwolinsk@undisclosed.example.com) https://hpcwiki.uark.edu/doku.php?image=ssh-cert2.png&ns=0&rev=1692649521&tab_details=history&media_do=diff&do=media <img src="https://hpcwiki.uark.edu/lib/exe/fetch.php?w=500&amp;h=500&amp;tok=0f79be&amp;media=ssh-cert2.png" alt="ssh-cert2.png" loading="lazy" width="500" height="500" /> text/html 2023-08-21T20:24:56+00:00 pwolinsk (pwolinsk@undisclosed.example.com) https://hpcwiki.uark.edu/doku.php?image=ssh-cert.png&ns=0&rev=1692649496&tab_details=history&media_do=diff&do=media <img src="https://hpcwiki.uark.edu/lib/exe/fetch.php?w=500&amp;h=500&amp;tok=766093&amp;media=ssh-cert.png" alt="ssh-cert.png" loading="lazy" width="500" height="500" /> text/html 2022-07-27T14:47:56+00:00 pwolinsk (pwolinsk@undisclosed.example.com) https://hpcwiki.uark.edu/doku.php?image=globus-token.png&ns=0&rev=1658933276&tab_details=history&media_do=diff&do=media <img src="https://hpcwiki.uark.edu/lib/exe/fetch.php?w=500&amp;h=500&amp;tok=3d4c9b&amp;media=globus-token.png" alt="globus-token.png" loading="lazy" width="500" height="500" /> text/html 2022-07-27T14:20:46+00:00 pwolinsk (pwolinsk@undisclosed.example.com) https://hpcwiki.uark.edu/doku.php?image=login-uaf-idp.png&ns=0&rev=1658931646&tab_details=history&media_do=diff&do=media <img src="https://hpcwiki.uark.edu/lib/exe/fetch.php?w=500&amp;h=500&amp;tok=f10b05&amp;media=login-uaf-idp.png" alt="login-uaf-idp.png" loading="lazy" width="500" height="500" />