{"id":29620522,"url":"https://github.com/bu-isciii/introduction_to_hpc","last_synced_at":"2026-02-15T15:04:29.311Z","repository":{"id":305519897,"uuid":"1023095347","full_name":"BU-ISCIII/introduction_to_hpc","owner":"BU-ISCIII","description":"In this training course you will find theory and practice material for introducing yourself to the basics of high-performance computing (HPC) environment.","archived":false,"fork":false,"pushed_at":"2025-09-10T08:22:57.000Z","size":5257,"stargazers_count":0,"open_issues_count":1,"forks_count":2,"subscribers_count":0,"default_branch":"main","last_synced_at":"2025-09-10T11:59:03.963Z","etag":null,"topics":[],"latest_commit_sha":null,"homepage":null,"language":"Shell","has_issues":true,"has_wiki":null,"has_pages":null,"mirror_url":null,"source_name":null,"license":"gpl-3.0","status":null,"scm":"git","pull_requests_enabled":true,"icon_url":"https://github.com/BU-ISCIII.png","metadata":{"files":{"readme":"README.md","changelog":null,"contributing":null,"funding":null,"license":"LICENSE","code_of_conduct":null,"threat_model":null,"audit":null,"citation":null,"codeowners":null,"security":null,"support":null,"governance":null,"roadmap":null,"authors":null,"dei":null,"publiccode":null,"codemeta":null,"zenodo":null,"notice":null,"maintainers":null,"copyright":null,"agents":null,"dco":null,"cla":null}},"created_at":"2025-07-20T14:14:40.000Z","updated_at":"2025-09-10T08:23:00.000Z","dependencies_parsed_at":"2025-09-02T16:17:54.481Z","dependency_job_id":null,"html_url":"https://github.com/BU-ISCIII/introduction_to_hpc","commit_stats":null,"previous_names":["bu-isciii/introduction_to_hpc"],"tags_count":0,"template":false,"template_full_name":null,"purl":"pkg:github/BU-ISCIII/introduction_to_hpc","repository_url":"https://repos.ecosyste.ms/api/v1/hosts/GitHub/repositories/BU-ISCIII%2Fintroduction_to_hpc","tags_url":"https://repos.ecosyste.ms/api/v1/hosts/GitHub/repositories/BU-ISCIII%2Fintroduction_to_hpc/tags","releases_url":"https://repos.ecosyste.ms/api/v1/hosts/GitHub/repositories/BU-ISCIII%2Fintroduction_to_hpc/releases","manifests_url":"https://repos.ecosyste.ms/api/v1/hosts/GitHub/repositories/BU-ISCIII%2Fintroduction_to_hpc/manifests","owner_url":"https://repos.ecosyste.ms/api/v1/hosts/GitHub/owners/BU-ISCIII","download_url":"https://codeload.github.com/BU-ISCIII/introduction_to_hpc/tar.gz/refs/heads/main","sbom_url":"https://repos.ecosyste.ms/api/v1/hosts/GitHub/repositories/BU-ISCIII%2Fintroduction_to_hpc/sbom","scorecard":null,"host":{"name":"GitHub","url":"https://github.com","kind":"github","repositories_count":275449422,"owners_count":25466837,"icon_url":"https://github.com/github.png","version":null,"created_at":"2022-05-30T11:31:42.601Z","updated_at":"2022-07-04T15:15:14.044Z","status":"online","status_checked_at":"2025-09-16T02:00:10.229Z","response_time":65,"last_error":null,"robots_txt_status":"success","robots_txt_updated_at":"2025-07-24T06:49:26.215Z","robots_txt_url":"https://github.com/robots.txt","online":true,"can_crawl_api":true,"host_url":"https://repos.ecosyste.ms/api/v1/hosts/GitHub","repositories_url":"https://repos.ecosyste.ms/api/v1/hosts/GitHub/repositories","repository_names_url":"https://repos.ecosyste.ms/api/v1/hosts/GitHub/repository_names","owners_url":"https://repos.ecosyste.ms/api/v1/hosts/GitHub/owners"}},"keywords":[],"created_at":"2025-07-21T03:14:33.359Z","updated_at":"2026-02-15T15:04:29.306Z","avatar_url":"https://github.com/BU-ISCIII.png","language":"Shell","funding_links":[],"categories":[],"sub_categories":[],"readme":"# Introduction to High-Performance Computing (HPC) environment\n\nIn this training course you will find theory and practice material for introducing yourself to the basics of high-performance computing (HPC) environment.\n\nThe material includes slides with theory concepts and practical exercises.\n\n## Slides\n\n### Day 1\n\n- **Talk 1:** [Introduction to High-Performance Computing and its components. Identifying problems that can be addressed using a computing cluster](slides/talk1_introduction_hpc.pdf)\n- **Talk 2:** [Introduction to the Linux environment. Using the shell and basic commands](slides/linux_intro.pdf).\n- **Exercise 1:** [Linux basic commands](exercises/01_handson_linux/handson_linux1_BasicCommands.md) -- [Download pdf](exercises/01_handson_linux/handson_linux1_BasicCommands.pdf)\n\n### Day 2\n\n- **Exercise 2:** [Filesystem](exercises/01_handson_linux/handson_linux2_FileProcessing.md) -- [Download pdf](exercises/01_handson_linux/handson_linux2_FileProcessing.pdf)\n- **Exercise 3:** [Users and privileges](exercises/01_handson_linux/handson_linux3_Privileges.md) -- [Download pdf](exercises/01_handson_linux/handson_linux3_Privileges.pdf)\n- **Talk 3:** [Accessing, connecting to, and transferring data to an HPC environment](slides/talk3_access_connection_datatransfer.pdf)\n- **Exercise 4:** [Accessing, connecting to, and transferring data to an HPC environment](exercises/04_access/handson_access.md) -- [Download pdf](exercises/xxx.pdf)\n\n### Day 3\n\n- **Talk 4:** [Running processes using a job scheduler (Slurm). Resource reservation, working directories, and genomic data storage protocols](slides/talk4_filesystems_slurm.pdf)\n- **Exercise 5:** [Running processes using a job scheduler (Slurm). Resource reservation, working directories, and genomic data storage protocols](exercises/05_srun/handson_srun.md) -- [Download pdf](exercises/xxx.pdf)\n- **Talk 5:** [Software installation in HPC. EasyBuild, Conda, Mamba. Introduction to container usage in HPC.](slides/talk5_SoftwareManagement_and_ContainersinHPC.pdf)\n- **Exercise 6:** [Software installation in HPC. EasyBuild, Conda, Mamba. Introduction to container usage in HPC](exercises/06_software_management_hpc/handson_software_management.md) -- [Download pdf](exercises/xxxx.pdf)\n  \n### Day 4\n\n- **Talk 6:** [Scripting and parallelization](slides/Talk6_Scripting_and_Parallelization.pdf)\n- **Exercise 7:** [Scripting and parallelization](exercises/07_handson_scripting_and_parallelization/handson_scripting_and_parallelization.md) -- [Download pdf](exercises/xxxx.pdf)\n- **Talk 7:** [Building a reliable and reproducible scientific workflow using Nextflow](slides/talk7_ReliableReproducible_ScientificWorkflows_Nextflow.pdf)\n- **Exercise 8:** [Building a reliable and reproducible scientific workflow using Nextflow](exercises/08_handson_scientific_workflows_nextflow/handson_scientificworkflows_nextflow.md) -- [Download pdf](exercises/xxx.pdf)\n\n### Day 5\n\n- **Exercise 9:** [Practical cases and common issue](exercises/09_usecase_issues/handson_usecase_issues1.md) -- [Download pdf](exercises/xxx.pdf)\n","project_url":"https://awesome.ecosyste.ms/api/v1/projects/github.com%2Fbu-isciii%2Fintroduction_to_hpc","html_url":"https://awesome.ecosyste.ms/projects/github.com%2Fbu-isciii%2Fintroduction_to_hpc","lists_url":"https://awesome.ecosyste.ms/api/v1/projects/github.com%2Fbu-isciii%2Fintroduction_to_hpc/lists"}