From a8967aab21b71b30ffd76c35d8962d4d0b826e38 Mon Sep 17 00:00:00 2001 From: Oa8choo2 <77433187+Oa8choo2@users.noreply.github.com> Date: Tue, 21 Oct 2025 13:33:07 +0200 Subject: [PATCH 01/12] Update alphafold.md Replace link text 'here' by something more meaningful. See also: https://archive.org/embed/designingwebusab00niel Designing Web usability, Nielsen, Jakob, 2000 https://archive.org/details/designingwebusab00niel/page/54/mode/2up?q=blue+bee The oldest web design rule is to avoid using "Click Here" as the anchor text for a hypertext link. There are two reasons for this rule. First, only mouse-using visitors do in fact click, whereas disabled users or users with a touchscreen or other alternative device don't click. Second, the words "Click" and "Here" are hardly information-carrying and, as such, should not be used as a design element that attracts the user's attention. Instead of saying For background information on the blue-nosed honeybee, click [here](dummy). It is better to say We have additional background information about [the blue-nosed honeybee](dummy). --- mkdocs/docs/HPC/alphafold.md | 8 ++++---- 1 file changed, 4 insertions(+), 4 deletions(-) diff --git a/mkdocs/docs/HPC/alphafold.md b/mkdocs/docs/HPC/alphafold.md index 0890136f8767..b653aefa23e3 100644 --- a/mkdocs/docs/HPC/alphafold.md +++ b/mkdocs/docs/HPC/alphafold.md @@ -20,8 +20,8 @@ It is therefore recommended to first familiarize yourself with AlphaFold. The fo - VSC webpage about AlphaFold: - Introductory course on AlphaFold by VIB: - "Getting Started with AlphaFold" presentation by Kenneth Hoste (HPC-UGent) - - recording available [on YouTube](https://www.youtube.com/watch?v=jP9Qg1yBGcs) - - slides available [here (PDF)](https://www.vscentrum.be/_files/ugd/5446c2_f19a8723f7f7460ebe990c28a53e56a2.pdf?index=true) + - [recording available](https://www.youtube.com/watch?v=jP9Qg1yBGcs) (on YouTube) + - [slides available](https://www.vscentrum.be/_files/ugd/5446c2_f19a8723f7f7460ebe990c28a53e56a2.pdf?index=true) (PDF) - see also @@ -130,8 +130,8 @@ Likewise for `jackhmmer`, the core count can be controlled via `$ALPHAFOLD_JACKH ### CPU/GPU comparison -The provided timings were obtained by executing the `T1050.fasta` example, as outlined in the Alphafold [README]({{readme}}). -For the corresponding jobscripts, they are available [here](./example-jobscripts). +The provided timings were obtained by executing the `T1050.fasta` example, as outlined in the [Alphafold README]({{readme}}). +The [corresponding jobscripts](#example-jobscripts) are available. Using `--db_preset=full_dbs`, the following runtime data was collected: From 604088c5513654fdf42dad0f5bf7af112c36ab7e Mon Sep 17 00:00:00 2001 From: Oa8choo2 <77433187+Oa8choo2@users.noreply.github.com> Date: Tue, 21 Oct 2025 13:41:55 +0200 Subject: [PATCH 02/12] Update getting_started.md replace "here"-link text --- mkdocs/docs/HPC/getting_started.md | 8 ++++++-- 1 file changed, 6 insertions(+), 2 deletions(-) diff --git a/mkdocs/docs/HPC/getting_started.md b/mkdocs/docs/HPC/getting_started.md index d43087486087..a5c2a2e623ce 100644 --- a/mkdocs/docs/HPC/getting_started.md +++ b/mkdocs/docs/HPC/getting_started.md @@ -79,8 +79,12 @@ Make sure you can get to a shell access to the {{hpcinfra}} before proceeding wi Now that you can login, it is time to transfer files from your local computer to your **home directory** on the {{hpcinfra}}. -Download [tensorflow_mnist.py](https://raw.githubusercontent.com/hpcugent/vsc_user_docs/main/{{exampleloc}}/tensorflow_mnist.py) -and [run.sh](https://raw.githubusercontent.com/hpcugent/vsc_user_docs/main/{{exampleloc}}/run.sh) example scripts to your computer (from [here](https://github.com/hpcugent/vsc_user_docs/tree/main/{{exampleloc}})). +Download following the example scripts to your computer: + +- [tensorflow_mnist.py](https://raw.githubusercontent.com/hpcugent/vsc_user_docs/main/{{exampleloc}}/tensorflow_mnist.py) +- [run.sh](https://raw.githubusercontent.com/hpcugent/vsc_user_docs/main/{{exampleloc}}/run.sh) + +You can also find the example scripts in our git repo: [https://github.com/hpcugent/vsc_user_docs/](https://github.com/hpcugent/vsc_user_docs/tree/4c3caefe7ac69f2476079f4b44f033e4e30ba7ab/mkdocs/docs/HPC/examples/Getting_Started/tensorflow_mnist). {%- if OS == windows %} From fa02c6a73fc23869464d9518e1794f2f29591b61 Mon Sep 17 00:00:00 2001 From: Oa8choo2 <77433187+Oa8choo2@users.noreply.github.com> Date: Tue, 21 Oct 2025 13:47:48 +0200 Subject: [PATCH 03/12] Update jupyter.md replace "here"-link --- mkdocs/docs/HPC/jupyter.md | 4 +++- 1 file changed, 3 insertions(+), 1 deletion(-) diff --git a/mkdocs/docs/HPC/jupyter.md b/mkdocs/docs/HPC/jupyter.md index 3f6776b38e7f..d24598050461 100644 --- a/mkdocs/docs/HPC/jupyter.md +++ b/mkdocs/docs/HPC/jupyter.md @@ -89,7 +89,9 @@ $ module load SciPy-bundle/2023.11-gfbf-2023b ``` This throws no errors, since this module uses a toolchain that is compatible with the toolchain used by the notebook -If we use a different SciPy module that uses an incompatible toolchain, we will get a module load conflict when trying to load it (For more info on these errors, see [here](troubleshooting.md#module-conflicts)). +If we use a different SciPy module that uses an incompatible toolchain, +we will get a module load conflict when trying to load it +(for more info on these errors, consult the [troubleshooting page](troubleshooting.md#module-conflicts)). ```shell $ module load JupyterNotebook/7.2.0-GCCcore-13.2.0 From aa48c0d7f89c6e543081ba516a4c8829210a6a46 Mon Sep 17 00:00:00 2001 From: Oa8choo2 <77433187+Oa8choo2@users.noreply.github.com> Date: Tue, 21 Oct 2025 13:57:48 +0200 Subject: [PATCH 04/12] Update multi_core_jobs.md replace "here"-link --- mkdocs/docs/HPC/multi_core_jobs.md | 2 +- 1 file changed, 1 insertion(+), 1 deletion(-) diff --git a/mkdocs/docs/HPC/multi_core_jobs.md b/mkdocs/docs/HPC/multi_core_jobs.md index 00834138cbd5..518a3f0b2a4f 100644 --- a/mkdocs/docs/HPC/multi_core_jobs.md +++ b/mkdocs/docs/HPC/multi_core_jobs.md @@ -47,7 +47,7 @@ MPI. !!! warning Just requesting more nodes and/or cores does not mean that your job will automatically run faster. - You can find more about this [here](troubleshooting.md#job_does_not_run_faster). + This is explained on the [troubleshooting page](troubleshooting.md#job_does_not_run_faster). ## Parallel Computing with threads From f35f0523af2a68bd757b65f4cc8aa39ff4f5e022 Mon Sep 17 00:00:00 2001 From: Oa8choo2 <77433187+Oa8choo2@users.noreply.github.com> Date: Tue, 21 Oct 2025 15:21:09 +0200 Subject: [PATCH 05/12] Update multi_job_submission.md replace "here"-link --- mkdocs/docs/HPC/multi_job_submission.md | 6 +++++- 1 file changed, 5 insertions(+), 1 deletion(-) diff --git a/mkdocs/docs/HPC/multi_job_submission.md b/mkdocs/docs/HPC/multi_job_submission.md index 70239ac4d433..ddebf7561cf8 100644 --- a/mkdocs/docs/HPC/multi_job_submission.md +++ b/mkdocs/docs/HPC/multi_job_submission.md @@ -159,7 +159,11 @@ a parameter instance is called a work item in Worker parlance. ``` module swap cluster/donphan ``` - We recommend using a `module swap cluster` command after submitting the jobs. Additional information about this as well as more comprehensive details concerning the 'Illegal instruction' error can be accessed [here](troubleshooting.md#multi-job-submissions-on-a-non-default-cluster). + + We recommend using a `module swap cluster` command after submitting the jobs. + Additional information about this as well as more comprehensive details + concerning the 'Illegal instruction' error can be found + on [the troubleshooting page](troubleshooting.md#multi-job-submissions-on-a-non-default-cluster). ## The Worker framework: Job arrays [//]: # (sec:worker-framework-job-arrays) From 7743e73251573dc7e23a9b4de337fdfb2b599fdb Mon Sep 17 00:00:00 2001 From: Oa8choo2 <77433187+Oa8choo2@users.noreply.github.com> Date: Tue, 21 Oct 2025 15:29:11 +0200 Subject: [PATCH 06/12] Update donphan-gallade.md replace "here"-link --- mkdocs/docs/HPC/only/gent/2023/donphan-gallade.md | 6 ++++-- 1 file changed, 4 insertions(+), 2 deletions(-) diff --git a/mkdocs/docs/HPC/only/gent/2023/donphan-gallade.md b/mkdocs/docs/HPC/only/gent/2023/donphan-gallade.md index 7d3aa9cf0ac1..5bd5f5853367 100644 --- a/mkdocs/docs/HPC/only/gent/2023/donphan-gallade.md +++ b/mkdocs/docs/HPC/only/gent/2023/donphan-gallade.md @@ -15,7 +15,7 @@ For software installation requests, please use the [request form](https://www.ug `donphan` is the new debug/interactive cluster. -It replaces `slaking`, which will be retired on **Monday 22 May 2023**. +It replaces `slaking`, which was retired on **Monday 22 May 2023**. It is primarily intended for interactive use: interactive shell sessions, using GUI applications through the [HPC-UGent web portal](../../../web_portal.md), etc. @@ -135,4 +135,6 @@ a `gallade` workernode has 128 cores (so ~7.3 GiB per core on average), while a (so ~20.5 GiB per core on average). It is important to take this aspect into account when submitting jobs to `gallade`, especially when requesting -all cores via `ppn=all`. You may need to explictly request more memory (see also [here](../../../fine_tuning_job_specifications#pbs_mem)). +all cores via `ppn=all`. +You may need to explictly request more memory by +[setting the memory parameter](../../../fine_tuning_job_specifications#pbs_mem). From 4b6fd02f5949f3da121ede1d7f02456913daba07 Mon Sep 17 00:00:00 2001 From: Oa8choo2 <77433187+Oa8choo2@users.noreply.github.com> Date: Tue, 21 Oct 2025 15:31:55 +0200 Subject: [PATCH 07/12] Update setting_up_python_virtual_environments.md replace "here"-link --- mkdocs/docs/HPC/setting_up_python_virtual_environments.md | 3 ++- 1 file changed, 2 insertions(+), 1 deletion(-) diff --git a/mkdocs/docs/HPC/setting_up_python_virtual_environments.md b/mkdocs/docs/HPC/setting_up_python_virtual_environments.md index 896d3d3f22a0..a9797c0cbe53 100644 --- a/mkdocs/docs/HPC/setting_up_python_virtual_environments.md +++ b/mkdocs/docs/HPC/setting_up_python_virtual_environments.md @@ -363,7 +363,8 @@ $ python Illegal instruction (core dumped) ``` -we are presented with the illegal instruction error. More info on this [here](troubleshooting.md#illegal-instruction-error) +we are presented with the illegal instruction error. +More info on this on the [troubleshooting page](troubleshooting.md#illegal-instruction-error) ### Error: GLIBC not found From 2e1750e174bb436bb3d7c67914d17cf99fba5d25 Mon Sep 17 00:00:00 2001 From: Oa8choo2 <77433187+Oa8choo2@users.noreply.github.com> Date: Tue, 21 Oct 2025 15:36:17 +0200 Subject: [PATCH 08/12] Update troubleshooting.md replace "here"-link --- mkdocs/docs/HPC/troubleshooting.md | 4 ++-- 1 file changed, 2 insertions(+), 2 deletions(-) diff --git a/mkdocs/docs/HPC/troubleshooting.md b/mkdocs/docs/HPC/troubleshooting.md index f3453b194e83..a463d5dd9f11 100644 --- a/mkdocs/docs/HPC/troubleshooting.md +++ b/mkdocs/docs/HPC/troubleshooting.md @@ -60,7 +60,7 @@ or because the pinning is done incorrectly and several threads/processes are bei - **Lack of sufficient memory**: When there is not enough memory available, or not enough memory bandwidth, it is likely that you will not see a significant speedup when using more cores (since each thread or process most likely requires additional memory). -More info on running multi-core workloads on the {{ hpcinfra }} can be found [here](multi_core_jobs.md). +There is more info on [running multi-core workloads](multi_core_jobs.md) on the {{ hpcinfra }}. ### Using multiple nodes When trying to use multiple (worker)nodes to improve the performance of your workloads, you may not see (significant) speedup. @@ -74,7 +74,7 @@ Actually using additional nodes is not as straightforward as merely asking for m Using the resources of multiple nodes is often done using a [Message Passing Interface (MPI)](https://en.wikipedia.org/wiki/Message_Passing_Interface) library. MPI allows nodes to communicate and coordinate, but it also introduces additional complexity. -An example of how you can make beneficial use of multiple nodes can be found [here](multi_core_jobs.md#parallel-computing-with-mpi). +We have an example of [how you can make beneficial use of multiple nodes](multi_core_jobs.md#parallel-computing-with-mpi). You can also use MPI in Python, some useful packages that are also available on the HPC are: From 51e0135dab74137943a1d2ae99743d61a513d628 Mon Sep 17 00:00:00 2001 From: Oa8choo2 <77433187+Oa8choo2@users.noreply.github.com> Date: Wed, 22 Oct 2025 07:59:20 +0200 Subject: [PATCH 09/12] Update web_portal.md replace "here"-link --- mkdocs/docs/HPC/web_portal.md | 8 +++----- 1 file changed, 3 insertions(+), 5 deletions(-) diff --git a/mkdocs/docs/HPC/web_portal.md b/mkdocs/docs/HPC/web_portal.md index c34e211625e2..986f075ece1c 100644 --- a/mkdocs/docs/HPC/web_portal.md +++ b/mkdocs/docs/HPC/web_portal.md @@ -32,11 +32,9 @@ Through this web portal, you can: - open a terminal session directly in your web browser; -More detailed information is available below, as well as in the [Open -OnDemand -documentation](https://osc.github.io/ood-documentation/latest/). A -walkthrough video is available on YouTube -[here](https://www.youtube.com/watch?v=4-w-4wjlnPk). +More detailed information is available below, as well as in the +[Open OnDemand documentation](https://osc.github.io/ood-documentation/latest/). +A [walkthrough video](https://www.youtube.com/watch?v=4-w-4wjlnPk) is available on YouTube. ## Pilot access From bfeafb5c16b6db1e44c28d6adbc7d1788931baf5 Mon Sep 17 00:00:00 2001 From: Oa8choo2 <77433187+Oa8choo2@users.noreply.github.com> Date: Wed, 22 Oct 2025 08:11:37 +0200 Subject: [PATCH 10/12] Update FAQ.md replace "here"-link --- mkdocs/docs/HPC/FAQ.md | 4 ++-- 1 file changed, 2 insertions(+), 2 deletions(-) diff --git a/mkdocs/docs/HPC/FAQ.md b/mkdocs/docs/HPC/FAQ.md index 4ac40f1f73c4..10ee104e5478 100644 --- a/mkdocs/docs/HPC/FAQ.md +++ b/mkdocs/docs/HPC/FAQ.md @@ -319,8 +319,8 @@ Please send an e-mail to {{hpcinfo}} that includes: {% endif %} -If the software is a Python package, you can manually install it in a virtual environment. -More information can be found [here](./setting_up_python_virtual_environments.md). +If the software is a Python package, you can manually +[install it in a virtual environment](./setting_up_python_virtual_environments.md). Note that it is still preferred to submit a software installation request, as the software installed by the HPC team will be optimized for the HPC environment. This can lead to dramatic performance improvements. From 0608a22c2cbc05ee934ffe2d4c7e12ab0e87e4bf Mon Sep 17 00:00:00 2001 From: =?UTF-8?q?Godfried=20Borremans=20=E2=80=94=20UGent?= Date: Wed, 22 Oct 2025 11:05:23 +0200 Subject: [PATCH 11/12] replace "here"-links --- mkdocs/docs/HPC/infrastructure.md | 4 ++-- mkdocs/docs/HPC/running_batch_jobs.md | 4 +++- 2 files changed, 5 insertions(+), 3 deletions(-) diff --git a/mkdocs/docs/HPC/infrastructure.md b/mkdocs/docs/HPC/infrastructure.md index 331fedb2b3f0..42d7c9a74787 100644 --- a/mkdocs/docs/HPC/infrastructure.md +++ b/mkdocs/docs/HPC/infrastructure.md @@ -13,8 +13,8 @@ Science and Innovation (EWI). Log in to the HPC-UGent Tier-2 infrastructure via [https://login.hpc.ugent.be](https://login.hpc.ugent.be) or using SSH via `login.hpc.ugent.be`. -More info on using the web portal you can find [here](web_portal.md), -and about connection with SSH [here](connecting.md). +Read more info on [using the web portal](web_portal.md), +and [about making a connection with SSH](connecting.md). ## Tier-2 compute clusters diff --git a/mkdocs/docs/HPC/running_batch_jobs.md b/mkdocs/docs/HPC/running_batch_jobs.md index 054d268979fd..c9ae045da310 100644 --- a/mkdocs/docs/HPC/running_batch_jobs.md +++ b/mkdocs/docs/HPC/running_batch_jobs.md @@ -833,7 +833,9 @@ The output of the various commands interacting with jobs (`qsub`, It is possible to submit jobs from a job to a cluster different than the one your job is running on. This could come in handy if, for example, the tool used to submit jobs only works on a particular cluster (or only on the login nodes), but the jobs can be run on several clusters. -An example of this is the `wsub` command of `worker`, see also [here](troubleshooting.md#multi-job-submissions-on-a-non-default-cluster). +An example of this is the `wsub` command of `worker`. +More info on these commands is in the document on [multi job submission](multi_job_submission.md) +or on the [troubleshooting page](troubleshooting.md#multi-job-submissions-on-a-non-default-cluster). To submit jobs to the `{{othercluster}}` cluster, you can change only what is needed in your session environment to submit jobs to that particular cluster by using `module swap env/slurm/{{othercluster}}` instead of using From 151d6668e3cdd35950c826158b5b611598f7a712 Mon Sep 17 00:00:00 2001 From: Oa8choo2 <77433187+Oa8choo2@users.noreply.github.com> Date: Wed, 22 Oct 2025 14:25:15 +0200 Subject: [PATCH 12/12] Update getting_started.md use latest version to tensorflow_mnist and not permalink to a particular version --- mkdocs/docs/HPC/getting_started.md | 2 +- 1 file changed, 1 insertion(+), 1 deletion(-) diff --git a/mkdocs/docs/HPC/getting_started.md b/mkdocs/docs/HPC/getting_started.md index a5c2a2e623ce..91e15ceedd9d 100644 --- a/mkdocs/docs/HPC/getting_started.md +++ b/mkdocs/docs/HPC/getting_started.md @@ -84,7 +84,7 @@ Download following the example scripts to your computer: - [tensorflow_mnist.py](https://raw.githubusercontent.com/hpcugent/vsc_user_docs/main/{{exampleloc}}/tensorflow_mnist.py) - [run.sh](https://raw.githubusercontent.com/hpcugent/vsc_user_docs/main/{{exampleloc}}/run.sh) -You can also find the example scripts in our git repo: [https://github.com/hpcugent/vsc_user_docs/](https://github.com/hpcugent/vsc_user_docs/tree/4c3caefe7ac69f2476079f4b44f033e4e30ba7ab/mkdocs/docs/HPC/examples/Getting_Started/tensorflow_mnist). +You can also find the example scripts in our git repo: [https://github.com/hpcugent/vsc_user_docs/](https://github.com/hpcugent/vsc_user_docs/tree/main/mkdocs/docs/HPC/examples/Getting_Started/tensorflow_mnist). {%- if OS == windows %}