From cb2f0697963d83fe33495fda6d414bc41d3268e1 Mon Sep 17 00:00:00 2001 From: Kenneth Hoste Date: Tue, 6 May 2025 11:48:25 +0200 Subject: [PATCH 1/5] add link to form for submitting software usage reports + rewording --- .../HPC/software_installation_requests.md | 46 +++++++++++-------- 1 file changed, 27 insertions(+), 19 deletions(-) diff --git a/mkdocs/docs/HPC/software_installation_requests.md b/mkdocs/docs/HPC/software_installation_requests.md index f0de930d788e..3e0253f83351 100644 --- a/mkdocs/docs/HPC/software_installation_requests.md +++ b/mkdocs/docs/HPC/software_installation_requests.md @@ -8,22 +8,30 @@ To submit a software installation request, please use the available request form ## Software usage report -By submitting a software installation request, you are committing to sending back a **software usage report**, -in which the following questions are answered: - -- 1) How many times have you used this software so far? -- 2) On which system(s) did you use this software? -- 3) Is the software working as it should? If not, please elaborate. -- 4) Is the performance of the software as you expect it to be? If not, please elaborate (and consider reporting problems). -- 5) How often will you be using this software going forward? -- 6) Describe how this software will help you with future research output. -- 7) Please provide an example of how to use this software, including the necessary information to run this example (where to get the input files, etc.), so we can consider documenting its usage. - -**Please provide the report no later than 1 month after the completion of the software installation**, -taking into account the following: - -* Send us the software usage report **in PDF format**, as attachment in the reply to the support ticket that corresponds to your software installation request; -* Keep it concise: try to limit the entire report to about one single page; -* You are welcome to consolidate the answers to the questions above for multiple related software installation requests into a single report. - For each additional tool, aim to add no more than half a page extra to the report. - Try to provide an example in which all requested software is used together (see last question above). +By submitting a software installation request, you are committing to sending back a **software usage report**. + +!!! tip "Use the form, Luke" + To submit a software usage report you should use to dedicated form that is available in the HPC-UGent web portal: + + [https://login.hpc.ugent.be/pun/sys/dashboard/support?category=swreport](https://login.hpc.ugent.be/pun/sys/dashboard/support?category=swreport) + +A software usage report provides answers to the following questions: + +- How many times have you used this software so far? +- On which system(s) did you use this software? +- Is the software working as it should? If not, please elaborate. +- Is the performance of the software as you expect it to be? If not, please elaborate (and consider reporting problems). +- How often will you be using this software going forward? +- Describe how this software will help you with future research output. +- Provide an example of how to use this software, including the necessary information to run this example (where to get the input files, etc.), so we can consider documenting its usage. + +!!! abstract "Timing" + Please provide the report **no later than 1 month** after the completion of the software installation. + +Take into account the following guidelines: + +* Make sure to use the correct ticket number in [the form to submit a software usage report](https://login.hpc.ugent.be/pun/sys/dashboard/support?category=swreport); +* Keep it concise: a couple of sentences per answer is sufficient; +* Please submit **one software usage report per ticket** that corresponds to an installation request. + Do not combine usage reports for multiple requests, unless you requested multiple (related) software installations in + a single request (single ticket number). From 74a9abf7fa3b737041d3d831d18ee573b47c0991 Mon Sep 17 00:00:00 2001 From: Kenneth Hoste Date: Tue, 6 May 2025 11:52:47 +0200 Subject: [PATCH 2/5] add link to form for software usage reports to whitelist --- scripts/link_checker/whitelist.txt | 1 + 1 file changed, 1 insertion(+) diff --git a/scripts/link_checker/whitelist.txt b/scripts/link_checker/whitelist.txt index 4f6eefd879a9..265608e303d6 100644 --- a/scripts/link_checker/whitelist.txt +++ b/scripts/link_checker/whitelist.txt @@ -24,6 +24,7 @@ http://hpc.ugent.be/clusterstate https://linux.die.net/man/1/rsync https://linux.die.net/man/1/setfacl https://login.hpc.ugent.be +https://login.hpc.ugent.be/pun/sys/dashboard/support?category=swreport # expired SSL certificate (20250120) https://elearning.vib.be/courses/alphafold From fd00e484269cbf995def9c7c120ca512c70d6c21 Mon Sep 17 00:00:00 2001 From: Kenneth Hoste Date: Tue, 6 May 2025 11:57:40 +0200 Subject: [PATCH 3/5] use Python 3.9 in GA workflow --- .github/workflows/script_module_list.yml | 4 ++-- 1 file changed, 2 insertions(+), 2 deletions(-) diff --git a/.github/workflows/script_module_list.yml b/.github/workflows/script_module_list.yml index 645ece683309..1f1e5770386f 100644 --- a/.github/workflows/script_module_list.yml +++ b/.github/workflows/script_module_list.yml @@ -22,7 +22,7 @@ jobs: - name: Set up Python environment uses: actions/setup-python@v4 with: - python-version: "3.6" + python-version: '3.9' - name: flake8 Lint uses: py-actions/flake8@v2 with: @@ -36,7 +36,7 @@ jobs: - name: Set up Python uses: actions/setup-python@v4 with: - python-version: '3.6' + python-version: '3.9' - name: Install dependencies run: | cd scripts/available_software From eae94b9f884fe0fcce408eabf6680de57e371656 Mon Sep 17 00:00:00 2001 From: Kenneth Hoste Date: Tue, 6 May 2025 12:00:37 +0200 Subject: [PATCH 4/5] use Ubuntu 24.04 --- .github/workflows/script_module_list.yml | 2 +- 1 file changed, 1 insertion(+), 1 deletion(-) diff --git a/.github/workflows/script_module_list.yml b/.github/workflows/script_module_list.yml index 1f1e5770386f..7a76476bc6ac 100644 --- a/.github/workflows/script_module_list.yml +++ b/.github/workflows/script_module_list.yml @@ -30,7 +30,7 @@ jobs: path: "scripts/available_software" pytest-tests: - runs-on: ubuntu-20.04 + runs-on: ubuntu-24.04 steps: - uses: actions/checkout@v3 - name: Set up Python From 87db8ab66fdca812104d85e3170fa2d1a058337c Mon Sep 17 00:00:00 2001 From: Kenneth Hoste Date: Tue, 6 May 2025 12:01:37 +0200 Subject: [PATCH 5/5] add GitHub links resulting in 429 to whitelist --- scripts/link_checker/whitelist.txt | 8 ++++++++ 1 file changed, 8 insertions(+) diff --git a/scripts/link_checker/whitelist.txt b/scripts/link_checker/whitelist.txt index 265608e303d6..2f874da8a174 100644 --- a/scripts/link_checker/whitelist.txt +++ b/scripts/link_checker/whitelist.txt @@ -58,3 +58,11 @@ http://www.straightrunning.com/XmingNotes/ # 404 only accessible from UGent network https://ugentbe.sharepoint.com/:u:/r/sites/intranet-personeelszaken/SitePages/en/Vrijwillig-medewerker-en-postdoctoraal-onbezoldigd-medewerker.aspx + +# 429 +https://github.com/deepmind/alphafold/blob/main/README.md +https://github.com/deepmind/alphafold/blob/main/README.md#alphafold-output +https://github.com/deepmind/alphafold/blob/main/README.md#examples +https://github.com/deepmind/alphafold/blob/main/README.md#running-alphafold +https://github.com/hpcugent/vsc-mympirun/blob/master/README.md +https://github.com/open-mpi/ompi/blob/master/examples/ring_c.c