{"id":6802,"date":"2024-03-29T17:26:27","date_gmt":"2024-03-29T21:26:27","guid":{"rendered":"https:\/\/labs.icahn.mssm.edu\/minervalab\/?p=6802"},"modified":"2025-05-16T15:55:27","modified_gmt":"2025-05-16T19:55:27","slug":"minerva-hpc-information-and-training-sessions-2","status":"publish","type":"post","link":"https:\/\/labs.icahn.mssm.edu\/minervalab\/minerva-hpc-information-and-training-sessions-2\/","title":{"rendered":"Minerva HPC Information and Training Sessions"},"content":{"rendered":"<p>[et_pb_section][et_pb_row][et_pb_column type=&#8221;4_4&#8243;][et_pb_text]We summarize our seven Spring 2024 training sessions for Minerva users below.<\/p>\n<ul>\n<li>There were two information\/training sessions for Minerva. These sessions are intended to familiarize you with the Minerva environment. <em><strong>Basic understanding of the general Unix operating environment and Linux commands is expected.<\/strong><\/em><\/li>\n<li>There was a<strong> training session for Data Ark<\/strong> to familiarize you with the Data Ark \u2013 Mount Sinai Data Commons data sets and environment.<\/li>\n<li>We also held <strong>four GPU\/AI training sessions for Minerva users<\/strong>, jointly presented by Minerva HPC staff and NVIDIA domain experts.<\/li>\n<li><strong>Sessions 2 and 6<\/strong> were offered in person at the Icahn Building as well as remotely through Zoom. <strong>Sessions 3, 4, 5 and 7<\/strong> were held remotely through Zoom.<\/li>\n<\/ul>\n<p><strong>Session 1: Introduction to Minerva \u2013 <\/strong><b>held on Wednesday, March 27, 2024, 1 pm-2 pm<\/b><\/p>\n<p>Training <a title=\"https:\/\/labs.icahn.mssm.edu\/minervalab\/wp-content\/uploads\/sites\/342\/2024\/03\/MinervaIntro_27Mar2024.pdf\" href=\"https:\/\/labs.icahn.mssm.edu\/minervalab\/wp-content\/uploads\/sites\/342\/2024\/03\/MinervaIntro_27Mar2024.pdf\" data-outlook-id=\"70c6a2b2-c8bd-417f-8083-38a1fe5b1ecf\">slides<\/a> and <a title=\"https:\/\/sc.u.hpc.mssm.edu\/HPC\/Minerva_Intro_Mar27_2024_Recording.mp4\" href=\"https:\/\/sc.u.hpc.mssm.edu\/HPC\/Minerva_Intro_Mar27_2024_Recording.mp4\" data-outlook-id=\"24c164d1-c44b-477e-9559-9d333c49b66d\">video<\/a> are available.<\/p>\n<p>This session covered:<\/p>\n<ul>\n<li>Minerva resources<\/li>\n<li>Account and logging in<\/li>\n<li>User software environment<\/li>\n<li>Service on file transfers, web server, TSM archive and Posit connect server<\/li>\n<\/ul>\n<p><strong>Session 2: Load Sharing Facility (LSF) Job Scheduler \u2013 <\/strong><b>Wednesday, April 3, 2024, 1 pm-2 pm<\/b><\/p>\n<p>Training\u00a0<a id=\"OWA14b574cb-1084-1413-ec8f-d5f0d756c853\" title=\"https:\/\/labs.icahn.mssm.edu\/minervalab\/wp-content\/uploads\/sites\/342\/2024\/04\/Minerva_LSF_2024-04-03.pdf\" href=\"https:\/\/labs.icahn.mssm.edu\/minervalab\/wp-content\/uploads\/sites\/342\/2024\/04\/Minerva_LSF_2024-04-03.pdf\" target=\"_blank\" rel=\"noopener noreferrer\" data-auth=\"NotApplicable\" data-loopstyle=\"linkonly\" data-linkindex=\"4\">slides<\/a>\u00a0and\u00a0<a id=\"OWAa1121421-1f47-6eaa-8246-2f5ce79e18a5\" title=\"https:\/\/sc.u.hpc.mssm.edu\/HPC\/Minerva_LSF_Apr03_2024_Recording.mp4\" href=\"https:\/\/sc.u.hpc.mssm.edu\/HPC\/Minerva_LSF_Apr03_2024_Recording.mp4\" target=\"_blank\" rel=\"noopener noreferrer\" data-auth=\"NotApplicable\" data-loopstyle=\"linkonly\" data-linkindex=\"5\">video<\/a>\u00a0are available.<\/p>\n<p>This session covered:<\/p>\n<ul>\n<li>LSF introduction and basic\/helpful LSF commands<\/li>\n<li>Dependent job<\/li>\n<li>Self-scheduler<\/li>\n<li>Parallel jobs (job arrays, parallel processing and GPUs)<\/li>\n<li>Things to avoid<\/li>\n<\/ul>\n<p><strong>Session 3. Introduction to GPU\/AI resources on Minerva \u2013 Wednesday, April 10, 2024, 1 pm -2 pm<\/strong><\/p>\n<p>Training\u00a0<a id=\"LPlnk552728\" title=\"https:\/\/labs.icahn.mssm.edu\/minervalab\/wp-content\/uploads\/sites\/342\/2024\/04\/Minerva_GPUs_2024-04-10.pdf\" href=\"https:\/\/labs.icahn.mssm.edu\/minervalab\/wp-content\/uploads\/sites\/342\/2024\/04\/Minerva_GPUs_2024-04-10.pdf\" target=\"_blank\" rel=\"noopener noreferrer\" data-auth=\"NotApplicable\" data-loopstyle=\"linkonly\" data-linkindex=\"6\">slides<\/a>\u00a0and\u00a0<a id=\"LPlnk984994\" title=\"https:\/\/sc.u.hpc.mssm.edu\/HPC\/Minerva_GPU_Apr10_2024_Recording.mp4\" href=\"https:\/\/sc.u.hpc.mssm.edu\/HPC\/Minerva_GPU_Apr10_2024_Recording.mp4\" target=\"_blank\" rel=\"noopener noreferrer\" data-auth=\"NotApplicable\" data-loopstyle=\"linkonly\" data-linkindex=\"7\">video<\/a>\u00a0are available.<\/p>\n<p>This session covered:<\/p>\n<ul>\n<li>What is a GPU<\/li>\n<li>GPU resources on Minerva<\/li>\n<li>User GPU\/AI Software environment on Minerva<\/li>\n<li>Running GPU\/AI jobs in LSF<\/li>\n<\/ul>\n<p><strong>\u00a0<\/strong><\/p>\n<p><strong>Session 4. 5 Ways to Get Started with GPUs \u2013 Friday, April 12, 2024, 1 pm-2 pm<\/strong><\/p>\n<p>Training <a href=\"https:\/\/labs.icahn.mssm.edu\/minervalab\/wp-content\/uploads\/sites\/342\/2024\/05\/FiveWays-HealthCare-April2024.pdf\">slides<\/a> and <a href=\"https:\/\/sc.u.hpc.mssm.edu\/HPC\/5_Ways_to_Get_Started_with_GPUs.mp4\">video<\/a> are available.<\/p>\n<p>This session covered:<\/p>\n<ul>\n<li>Some GPU basics<\/li>\n<li>5 ways to accelerate with GPUs (Applications, Library, OpenACC Directives, CUDA Programming, Standard Language Parallelism)<\/li>\n<\/ul>\n<p><strong>Session 5: Accelerated General Data Science in Medicine\u00a0with RAPIDS,\u00a0CuPy\u00a0and\u00a0Numba \u2013 Wednesday, April 17, 1 pm-2 pm<\/strong><\/p>\n<p>Training <a href=\"https:\/\/labs.icahn.mssm.edu\/minervalab\/wp-content\/uploads\/sites\/342\/2024\/04\/MountSinai_accelerated_general_data_science-compressed.pdf\">slides<\/a> and <a href=\"https:\/\/sc.u.hpc.mssm.edu\/HPC\/Accelerated_General_Data_Science_in_Medicine_with_RAPIDS_CuPy_and_Numba.mp4\">video<\/a> are available.<\/p>\n<p>This session covered:<\/p>\n<ul>\n<li>Overview of GPU Computing<\/li>\n<li>GPU-Accelerated Numerical Computing with CuPy<\/li>\n<li>GPU-Accelerated Data Science with RAPIDS<\/li>\n<li>Custom GPU Kernels with Numba Frameworks<\/li>\n<li>Interoperability \u2013 Data Conversion Bottleneck<\/li>\n<\/ul>\n<p><strong>Session 6: Introduction to Data Ark &#8211; Mount Sinai Data Commons \u2013 Wednesday, April 24, 2024, 1 pm-2 pm<\/strong><\/p>\n<p>Training <a href=\"https:\/\/labs.icahn.mssm.edu\/minervalab\/wp-content\/uploads\/sites\/342\/2024\/04\/MountSinai_accelerated_general_data_science-compressed.pdf\">slides<\/a> and <a href=\"https:\/\/sc.u.hpc.mssm.edu\/HPC\/Accelerated_General_Data_Science_in_Medicine_with_RAPIDS_CuPy_and_Numba.mp4\">video<\/a> are available.<\/p>\n<p>This session covered:<\/p>\n<ul>\n<li style=\"font-weight: 400\">Introduction to Data Ark<\/li>\n<li style=\"font-weight: 400\">Accessing datasets through Data Ark<\/li>\n<li style=\"font-weight: 400\">Introduction to MarketScan data<\/li>\n<li style=\"font-weight: 400\">Accessing MarketScan Data via Minerva HPC<\/li>\n<\/ul>\n<p><strong>Session 7: How to Accelerate Genome Analysis Toolkit (GATK) by using Parabricks \u2013 Wednesday, May 1, 2024, 1 pm-2 pm<\/strong><\/p>\n<p>Training <a href=\"https:\/\/labs.icahn.mssm.edu\/minervalab\/wp-content\/uploads\/sites\/342\/2024\/05\/mount_sinai_Parabricks_RAPIDS_BIONEMO-compressed.pdf\">slides<\/a> and video are available.<\/p>\n<p>This session covered:<\/p>\n<ul>\n<li>Capabilities and Performance of Parabricks<\/li>\n<li>Parabricks for secondary analysis<\/li>\n<\/ul>\n<p>Please send any questions to <a href=\"mailto:hpchelp@hpc.mssm.edu\">hpchelp@hpc.mssm.edu<\/a><\/p>\n<p>Thank you\u2014<\/p>\n<p>Scientific Computing and Data<br \/>\nIcahn School of Medicine at Mount Sinai[\/et_pb_text][\/et_pb_column][\/et_pb_row][\/et_pb_section]<\/p>\n","protected":false},"excerpt":{"rendered":"<p><div class=\"et_pb_section et_pb_section_0 et_section_regular\" >\n\t\t\t\t\n\t\t\t\t\n\t\t\t\t\n\t\t\t\t\n\t\t\t\t\n\t\t\t\t\n\t\t\t\t\n\t\t\t\t\n\t\t\t\t\n\t\t\t<\/div><div class=\"et_pb_row et_pb_row_0 et_pb_row_empty\">\n\t\t\t\t\n\t\t\t\t\n\t\t\t\t\n\t\t\t\t\n\t\t\t\t\n\t\t\t<\/div><div class=\"et_pb_module et_pb_text et_pb_text_0  et_pb_text_align_left et_pb_bg_layout_light\">\n\t\t\t\t\n\t\t\t\t\n\t\t\t\t\n\t\t\t\t\n\t\t\t\t\n\t\t\t<\/div>We summarize our seven Spring 2024 training sessions for Minerva users below. There were two information\/training sessions for Minerva. These sessions are intended to familiarize you with the Minerva environment. Basic understanding of the general Unix operating environment and Linux commands is expected. There was a training session for Data Ark to familiarize you with [&hellip;]<\/p>\n","protected":false},"author":600,"featured_media":0,"comment_status":"open","ping_status":"open","sticky":false,"template":"","format":"standard","meta":{"_et_pb_use_builder":"on","_et_pb_old_content":"We summarize our seven Spring 2024 training sessions for Minerva users below.\r\n<ul>\r\n \t<li>There were two information\/training sessions for Minerva. These sessions are intended to familiarize you with the Minerva environment. <em><strong>Basic understanding of the general Unix operating environment and Linux commands is expected.<\/strong><\/em><\/li>\r\n \t<li>There was a<strong> training session for Data Ark<\/strong> to familiarize you with the Data Ark \u2013 Mount Sinai Data Commons data sets and environment.<\/li>\r\n \t<li>We also held <strong>four GPU\/AI training sessions for Minerva users<\/strong>, jointly presented by Minerva HPC staff and NVIDIA domain experts.<\/li>\r\n \t<li><strong>Sessions 2 and 6<\/strong> were offered in person at the Icahn Building as well as remotely through Zoom. <strong>Sessions 3, 4, 5 and 7<\/strong> were held remotely through Zoom.<\/li>\r\n<\/ul>\r\n<strong>Session 1: Introduction to Minerva \u2013 <\/strong><b>held on Wednesday, March 27, 2024, 1 pm-2 pm<\/b>\r\n\r\nTraining <a title=\"https:\/\/labs.icahn.mssm.edu\/minervalab\/wp-content\/uploads\/sites\/342\/2024\/03\/MinervaIntro_27Mar2024.pdf\" href=\"https:\/\/labs.icahn.mssm.edu\/minervalab\/wp-content\/uploads\/sites\/342\/2024\/03\/MinervaIntro_27Mar2024.pdf\" data-outlook-id=\"70c6a2b2-c8bd-417f-8083-38a1fe5b1ecf\">slides<\/a> and <a title=\"https:\/\/sc.u.hpc.mssm.edu\/HPC\/Minerva_Intro_Mar27_2024_Recording.mp4\" href=\"https:\/\/sc.u.hpc.mssm.edu\/HPC\/Minerva_Intro_Mar27_2024_Recording.mp4\" data-outlook-id=\"24c164d1-c44b-477e-9559-9d333c49b66d\">video<\/a> are available.\r\n\r\nThis session covered:\r\n<ul>\r\n \t<li>Minerva resources<\/li>\r\n \t<li>Account and logging in<\/li>\r\n \t<li>User software environment<\/li>\r\n \t<li>Service on file transfers, web server, TSM archive and Posit connect server<\/li>\r\n<\/ul>\r\n<strong>Session 2: Load Sharing Facility (LSF) Job Scheduler \u2013 <\/strong><b>Wednesday, April 3, 2024, 1 pm-2 pm<\/b>\r\n\r\nTraining\u00a0<a id=\"OWA14b574cb-1084-1413-ec8f-d5f0d756c853\" title=\"https:\/\/labs.icahn.mssm.edu\/minervalab\/wp-content\/uploads\/sites\/342\/2024\/04\/Minerva_LSF_2024-04-03.pdf\" href=\"https:\/\/labs.icahn.mssm.edu\/minervalab\/wp-content\/uploads\/sites\/342\/2024\/04\/Minerva_LSF_2024-04-03.pdf\" target=\"_blank\" rel=\"noopener noreferrer\" data-auth=\"NotApplicable\" data-loopstyle=\"linkonly\" data-linkindex=\"4\">slides<\/a>\u00a0and\u00a0<a id=\"OWAa1121421-1f47-6eaa-8246-2f5ce79e18a5\" title=\"https:\/\/sc.u.hpc.mssm.edu\/HPC\/Minerva_LSF_Apr03_2024_Recording.mp4\" href=\"https:\/\/sc.u.hpc.mssm.edu\/HPC\/Minerva_LSF_Apr03_2024_Recording.mp4\" target=\"_blank\" rel=\"noopener noreferrer\" data-auth=\"NotApplicable\" data-loopstyle=\"linkonly\" data-linkindex=\"5\">video<\/a>\u00a0are available.\r\n\r\nThis session covered:\r\n<ul>\r\n \t<li>LSF introduction and basic\/helpful LSF commands<\/li>\r\n \t<li>Dependent job<\/li>\r\n \t<li>Self-scheduler<\/li>\r\n \t<li>Parallel jobs (job arrays, parallel processing and GPUs)<\/li>\r\n \t<li>Things to avoid<\/li>\r\n<\/ul>\r\n<strong>Session 3. Introduction to GPU\/AI resources on Minerva \u2013 Wednesday, April 10, 2024, 1 pm -2 pm<\/strong>\r\n\r\nTraining\u00a0<a id=\"LPlnk552728\" title=\"https:\/\/labs.icahn.mssm.edu\/minervalab\/wp-content\/uploads\/sites\/342\/2024\/04\/Minerva_GPUs_2024-04-10.pdf\" href=\"https:\/\/labs.icahn.mssm.edu\/minervalab\/wp-content\/uploads\/sites\/342\/2024\/04\/Minerva_GPUs_2024-04-10.pdf\" target=\"_blank\" rel=\"noopener noreferrer\" data-auth=\"NotApplicable\" data-loopstyle=\"linkonly\" data-linkindex=\"6\">slides<\/a>\u00a0and\u00a0<a id=\"LPlnk984994\" title=\"https:\/\/sc.u.hpc.mssm.edu\/HPC\/Minerva_GPU_Apr10_2024_Recording.mp4\" href=\"https:\/\/sc.u.hpc.mssm.edu\/HPC\/Minerva_GPU_Apr10_2024_Recording.mp4\" target=\"_blank\" rel=\"noopener noreferrer\" data-auth=\"NotApplicable\" data-loopstyle=\"linkonly\" data-linkindex=\"7\">video<\/a>\u00a0are available.\r\n\r\nThis session covered:\r\n<ul>\r\n \t<li>What is a GPU<\/li>\r\n \t<li>GPU resources on Minerva<\/li>\r\n \t<li>User GPU\/AI Software environment on Minerva<\/li>\r\n \t<li>Running GPU\/AI jobs in LSF<\/li>\r\n<\/ul>\r\n<strong>\u00a0<\/strong>\r\n\r\n<strong>Session 4. 5 Ways to Get Started with GPUs \u2013 Friday, April 12, 2024, 1 pm-2 pm<\/strong>\r\n\r\nTraining <a href=\"https:\/\/labs.icahn.mssm.edu\/minervalab\/wp-content\/uploads\/sites\/342\/2024\/05\/FiveWays-HealthCare-April2024.pdf\">slides<\/a> and <a href=\"https:\/\/sc.u.hpc.mssm.edu\/HPC\/5_Ways_to_Get_Started_with_GPUs.mp4\">video<\/a> are available.\r\n\r\nThis session covered:\r\n<ul>\r\n \t<li>Some GPU basics<\/li>\r\n \t<li>5 ways to accelerate with GPUs (Applications, Library, OpenACC Directives, CUDA Programming, Standard Language Parallelism)<\/li>\r\n<\/ul>\r\n<strong>Session 5: Accelerated General Data Science in Medicine\u00a0with RAPIDS,\u00a0CuPy\u00a0and\u00a0Numba \u2013 Wednesday, April 17, 1 pm-2 pm<\/strong>\r\n\r\nTraining <a href=\"https:\/\/labs.icahn.mssm.edu\/minervalab\/wp-content\/uploads\/sites\/342\/2024\/04\/MountSinai_accelerated_general_data_science-compressed.pdf\">slides<\/a> and <a href=\"https:\/\/sc.u.hpc.mssm.edu\/HPC\/Accelerated_General_Data_Science_in_Medicine_with_RAPIDS_CuPy_and_Numba.mp4\">video<\/a> are available.\r\n\r\nThis session covered:\r\n<ul>\r\n \t<li>Overview of GPU Computing<\/li>\r\n \t<li>GPU-Accelerated Numerical Computing with CuPy<\/li>\r\n \t<li>GPU-Accelerated Data Science with RAPIDS<\/li>\r\n \t<li>Custom GPU Kernels with Numba Frameworks<\/li>\r\n \t<li>Interoperability \u2013 Data Conversion Bottleneck<\/li>\r\n<\/ul>\r\n<strong>Session 6: Introduction to Data Ark - Mount Sinai Data Commons \u2013 Wednesday, April 24, 2024, 1 pm-2 pm<\/strong>\r\n\r\nTraining <a href=\"https:\/\/labs.icahn.mssm.edu\/minervalab\/wp-content\/uploads\/sites\/342\/2024\/04\/MountSinai_accelerated_general_data_science-compressed.pdf\">slides<\/a> and <a href=\"https:\/\/sc.u.hpc.mssm.edu\/HPC\/Accelerated_General_Data_Science_in_Medicine_with_RAPIDS_CuPy_and_Numba.mp4\">video<\/a> are available.\r\n\r\nThis session covered:\r\n<ul>\r\n \t<li style=\"font-weight: 400\">Introduction to Data Ark<\/li>\r\n \t<li style=\"font-weight: 400\">Accessing datasets through Data Ark<\/li>\r\n \t<li style=\"font-weight: 400\">Introduction to MarketScan data<\/li>\r\n \t<li style=\"font-weight: 400\">Accessing MarketScan Data via Minerva HPC<\/li>\r\n<\/ul>\r\n<strong>Session 7: How to Accelerate Genome Analysis Toolkit (GATK) by using Parabricks \u2013 Wednesday, May 1, 2024, 1 pm-2 pm<\/strong>\r\n\r\nTraining <a href=\"https:\/\/labs.icahn.mssm.edu\/minervalab\/wp-content\/uploads\/sites\/342\/2024\/05\/mount_sinai_Parabricks_RAPIDS_BIONEMO-compressed.pdf\">slides<\/a> and video are available.\r\n\r\nThis session covered:\r\n<ul>\r\n \t<li>Capabilities and Performance of Parabricks<\/li>\r\n \t<li>Parabricks for secondary analysis<\/li>\r\n<\/ul>\r\nPlease send any questions to <a href=\"mailto:hpchelp@hpc.mssm.edu\">hpchelp@hpc.mssm.edu<\/a>\r\n\r\nThank you\u2014\r\n\r\nScientific Computing and Data\r\nIcahn School of Medicine at Mount Sinai","_et_gb_content_width":"","footnotes":""},"categories":[7],"tags":[],"class_list":["post-6802","post","type-post","status-publish","format-standard","hentry","category-minerva"],"aioseo_notices":[],"_links":{"self":[{"href":"https:\/\/labs.icahn.mssm.edu\/minervalab\/wp-json\/wp\/v2\/posts\/6802","targetHints":{"allow":["GET"]}}],"collection":[{"href":"https:\/\/labs.icahn.mssm.edu\/minervalab\/wp-json\/wp\/v2\/posts"}],"about":[{"href":"https:\/\/labs.icahn.mssm.edu\/minervalab\/wp-json\/wp\/v2\/types\/post"}],"author":[{"embeddable":true,"href":"https:\/\/labs.icahn.mssm.edu\/minervalab\/wp-json\/wp\/v2\/users\/600"}],"replies":[{"embeddable":true,"href":"https:\/\/labs.icahn.mssm.edu\/minervalab\/wp-json\/wp\/v2\/comments?post=6802"}],"version-history":[{"count":24,"href":"https:\/\/labs.icahn.mssm.edu\/minervalab\/wp-json\/wp\/v2\/posts\/6802\/revisions"}],"predecessor-version":[{"id":9975,"href":"https:\/\/labs.icahn.mssm.edu\/minervalab\/wp-json\/wp\/v2\/posts\/6802\/revisions\/9975"}],"wp:attachment":[{"href":"https:\/\/labs.icahn.mssm.edu\/minervalab\/wp-json\/wp\/v2\/media?parent=6802"}],"wp:term":[{"taxonomy":"category","embeddable":true,"href":"https:\/\/labs.icahn.mssm.edu\/minervalab\/wp-json\/wp\/v2\/categories?post=6802"},{"taxonomy":"post_tag","embeddable":true,"href":"https:\/\/labs.icahn.mssm.edu\/minervalab\/wp-json\/wp\/v2\/tags?post=6802"}],"curies":[{"name":"wp","href":"https:\/\/api.w.org\/{rel}","templated":true}]}}