diff --git a/doc.zih.tu-dresden.de/docs/archive/bioinformatics.md b/doc.zih.tu-dresden.de/docs/archive/bioinformatics.md index 0a8a337417e5cfe7d5c78166d85254cc71229ef7..7d2335d93c4e095552b323cc1e09f42727d9db5e 100644 --- a/doc.zih.tu-dresden.de/docs/archive/bioinformatics.md +++ b/doc.zih.tu-dresden.de/docs/archive/bioinformatics.md @@ -6,10 +6,10 @@ | Software | Module | |-----------------------------------|-------------------------------------------| -| **[Infernal](#Infernal)** | infernal | -| **[OpenProspect](#OpenProspect)** | openprospect, openprospect/885-mpi | -| **[Phylip](#Phylip)** | phylip | -| **[PhyML](#PhyML)** | phyml/2.4.4, phyml/2.4.5-mpi, phyml/3.0.0 | +| **[Infernal](#infernal)** | infernal | +| **[OpenProspect](#openprospect)** | openprospect, openprospect/885-mpi | +| **[Phylip](#phylip)** | phylip | +| **[PhyML](#phyml)** | phyml/2.4.4, phyml/2.4.5-mpi, phyml/3.0.0 | ## Infernal diff --git a/doc.zih.tu-dresden.de/docs/contrib/content_rules.md b/doc.zih.tu-dresden.de/docs/contrib/content_rules.md index f054c5fa3594c219807e9eed301db0d43d610128..c4660744c8feca5681b94b2a48db23bccc0c5334 100644 --- a/doc.zih.tu-dresden.de/docs/contrib/content_rules.md +++ b/doc.zih.tu-dresden.de/docs/contrib/content_rules.md @@ -130,7 +130,7 @@ We follow this rules regarding prompts: * **Always use a prompt**, even there is no output provided for the shown command. * All code blocks should use long parameter names (e.g. Slurm parameters), if available. * All code blocks which specify some general command templates, e.g. containing `<` and `>` - (see [Placeholders](#mark-placeholders)), should use `bash` for the code block. Additionally, + (see [Placeholders](#placeholders)), should use `bash` for the code block. Additionally, an example invocation, perhaps with output, should be given with the normal `console` code block. See also [Code Block description below](#code-blocks-and-syntax-highlighting). * Using some magic, the prompt as well as the output is identified and will not be copied! @@ -157,7 +157,7 @@ bar Make sure that shell session and console code blocks are executable on the login nodes of HPC system. -Command templates use [Placeholders](#mark-placeholders) to mark replaceable code parts. Command +Command templates use [Placeholders](#placeholders) to mark replaceable code parts. Command templates should give a general idea of invocation and thus, do not contain any output. Use a `bash` code block followed by an invocation example (with `console`): @@ -257,6 +257,10 @@ drwxr-xr-x 3 marie p_marie 4096 Feb 12 2020 data -rw-rw---- 1 marie p_marie 4096 Jan 24 2020 readme.md ``` +### Placeholders + +TODO! + ## Mark Omissions If showing only a snippet of a long output, omissions are marked with `[...]`. diff --git a/doc.zih.tu-dresden.de/docs/data_lifecycle/overview.md b/doc.zih.tu-dresden.de/docs/data_lifecycle/overview.md index 1b5561db6c93052bd4ee68fc119ac796e0a3c4c9..6aca684354ab9beb0b0f338c86f0524bf9827e48 100644 --- a/doc.zih.tu-dresden.de/docs/data_lifecycle/overview.md +++ b/doc.zih.tu-dresden.de/docs/data_lifecycle/overview.md @@ -35,7 +35,7 @@ filesystems. !!! hint "Recommendations to choose of storage system" * For data that seldom changes but consumes a lot of space, the - [warm_archive](file_systems.md#warm_archive) can be used. + [warm_archive](warm_archive.md) can be used. (Note that this is mounted **read-only** on the compute nodes). * For a series of calculations that works on the same data please use a `scratch` based [workspace](workspaces.md). diff --git a/doc.zih.tu-dresden.de/docs/data_transfer/export_nodes.md b/doc.zih.tu-dresden.de/docs/data_transfer/export_nodes.md index 5e4abf29b8b90f560fcd6dbbebbb2541bb76ae57..b4a22c95e3193bc9ff1a7c43b107fe5f7f74f953 100644 --- a/doc.zih.tu-dresden.de/docs/data_transfer/export_nodes.md +++ b/doc.zih.tu-dresden.de/docs/data_transfer/export_nodes.md @@ -137,7 +137,7 @@ the local machine. Windows 10 (1809 and higher) comes with a [built-in OpenSSH support](https://docs.microsoft.com/en-us/windows-server/administration/openssh/openssh_overview) -including the above described [SCP](#SCP) and [SFTP](#SFTP). +including the above described [SCP](#scp) and [SFTP](#sftp). ### GUI - Using WinSCP diff --git a/doc.zih.tu-dresden.de/docs/jobs_and_resources/checkpoint_restart.md b/doc.zih.tu-dresden.de/docs/jobs_and_resources/checkpoint_restart.md index 38d6686d7a655c1c5d7161d6607be9d6f55d8b5c..f05e5a3dd78795aca1541a7bf0cfaa02904ff545 100644 --- a/doc.zih.tu-dresden.de/docs/jobs_and_resources/checkpoint_restart.md +++ b/doc.zih.tu-dresden.de/docs/jobs_and_resources/checkpoint_restart.md @@ -49,7 +49,7 @@ make it easier to utilize DMTCP together with Slurm. ## Using w.r.t. Chain Jobs For long-running jobs that you wish to split into multiple shorter jobs -([chain jobs](../jobs_and_resources/slurm.md#chain-jobs)), thereby enabling the job scheduler to +([chain jobs](slurm_examples.md#chain-jobs)), thereby enabling the job scheduler to fill the cluster much more efficiently and also providing some level of fault-tolerance, we have written a script that automatically creates a number of jobs for your desired runtime and adds the checkpoint/restart bits transparently to your batch script. You just have to specify the targeted diff --git a/doc.zih.tu-dresden.de/docs/jobs_and_resources/overview.md b/doc.zih.tu-dresden.de/docs/jobs_and_resources/overview.md index 1a96fc97145d5ee5587f2b9b216ffba004f4f9d8..d3e9674ced87e57dc6f45ccafccd71383c86d921 100644 --- a/doc.zih.tu-dresden.de/docs/jobs_and_resources/overview.md +++ b/doc.zih.tu-dresden.de/docs/jobs_and_resources/overview.md @@ -6,9 +6,10 @@ research environment especially in the area of data analytics and machine learni processing extremely large data sets. Moreover it is also a perfect platform for highly scalable, data-intensive and compute-intensive applications. -With shared [login nodes](#login-nodes) and [filesystems](../data_lifecycle/file_systems.md) our -HPC system enables users to easily switch between [the components](hardware_overview.md), each -specialized for different application scenarios. +With shared [login nodes](hardware_overview.md#login-nodes) and +[filesystems](../data_lifecycle/file_systems.md) our HPC system enables users to easily switch +between [the components](hardware_overview.md), each specialized for different application +scenarios. When log in to ZIH systems, you are placed on a login node where you can [manage data life cycle](../data_lifecycle/overview.md), diff --git a/doc.zih.tu-dresden.de/docs/software/containers.md b/doc.zih.tu-dresden.de/docs/software/containers.md index 5d96ea37fb34bc3a9a76fb7fd3d40635ebb65d21..ca9e3a14d360521660604a372dba15241c1e4d78 100644 --- a/doc.zih.tu-dresden.de/docs/software/containers.md +++ b/doc.zih.tu-dresden.de/docs/software/containers.md @@ -33,7 +33,7 @@ environment. However, new containers can be created on your local workstation and moved to ZIH systems for execution. Follow the instructions for [locally installing Singularity](#local-installation) and [container creation](#container-creation). Moreover, existing Docker container can easily be -converted, see [Import a docker container](#importing-a-docker-container). +converted, see [Import a docker container](#import-a-docker-container). If you are already familiar with Singularity, you might be more interested in our [singularity recipes and hints](singularity_recipe_hints.md). diff --git a/doc.zih.tu-dresden.de/docs/software/data_analytics_with_r.md b/doc.zih.tu-dresden.de/docs/software/data_analytics_with_r.md index 1f6be0614fc728f88212a5192fb1b11277ac8454..c7334d918cdba1ff5e97c2f4cd0ea3b788b2c26d 100644 --- a/doc.zih.tu-dresden.de/docs/software/data_analytics_with_r.md +++ b/doc.zih.tu-dresden.de/docs/software/data_analytics_with_r.md @@ -260,7 +260,7 @@ is limited to the number of cores on a single node. The maximum number of cores be found in our [hardware documentation](../jobs_and_resources/hardware_overview.md). Submitting a multicore R job to Slurm is very similar to submitting an -[OpenMP Job](../jobs_and_resources/slurm.md#binding-and-distribution-of-tasks), +[OpenMP Job](../jobs_and_resources/binding_and_distribution_of_tasks.md), since both are running multicore jobs on a **single** node. Below is an example: ```Bash @@ -292,7 +292,7 @@ This way of the R parallelism uses the [Rmpi](http://cran.r-project.org/web/packages/Rmpi/index.html) package and the [MPI](https://en.wikipedia.org/wiki/Message_Passing_Interface) (Message Passing Interface) as a "back-end" for its parallel operations. The MPI-based job in R is very similar to submitting an -[MPI Job](../jobs_and_resources/slurm.md#binding-and-distribution-of-tasks) since both are running +[MPI Job](../jobs_and_resources/binding_and_distribution_of_tasks.md) since both are running multicore jobs on multiple nodes. Below is an example of running R script with the Rmpi on the ZIH system: diff --git a/doc.zih.tu-dresden.de/docs/software/overview.md b/doc.zih.tu-dresden.de/docs/software/overview.md index 9d2d86d7c06989acfcb9415f908fc1453538b6a8..2c560c30951ae3ec3419e01a19ce8716c8d441da 100644 --- a/doc.zih.tu-dresden.de/docs/software/overview.md +++ b/doc.zih.tu-dresden.de/docs/software/overview.md @@ -12,7 +12,7 @@ so called dotfiles in your home directory, e.g., `~/.bashrc` or `~/.bash_profile ## Software Environment There are different options to work with software on ZIH systems: [modules](#modules), -[Jupyter Notebook](#jupyternotebook) and [containers](#containers). Brief descriptions and related +[Jupyter Notebook](#jupyter-notebook) and [containers](#containers). Brief descriptions and related links on these options are provided below. !!! note diff --git a/doc.zih.tu-dresden.de/docs/software/tensorflow.md b/doc.zih.tu-dresden.de/docs/software/tensorflow.md index db6b97596a153b852dabec4d5d9a1e73aa1aa19b..016d6aa25634a89fb7746dcb0117a8cb15a1116e 100644 --- a/doc.zih.tu-dresden.de/docs/software/tensorflow.md +++ b/doc.zih.tu-dresden.de/docs/software/tensorflow.md @@ -96,7 +96,7 @@ the notebook by pre-loading a specific TensorFlow module: You can also define your own Jupyter kernel for more specific tasks. Please read about Jupyter kernels and virtual environments in our - [JupyterHub](../access/jupyterhub.md#creating-and-using-your-own-environment) documentation. + [JupyterHub](../access/jupyterhub.md#creating-and-using-a-custom-environment) documentation. ## TensorFlow in Containers diff --git a/doc.zih.tu-dresden.de/docs/software/visualization.md b/doc.zih.tu-dresden.de/docs/software/visualization.md index b1a103a0c1ab1c999a002c2584eefa1a1813916b..f9de3764e32ca78381c7e22a38d3bda5fe6bdd32 100644 --- a/doc.zih.tu-dresden.de/docs/software/visualization.md +++ b/doc.zih.tu-dresden.de/docs/software/visualization.md @@ -6,7 +6,7 @@ application. The ParaView package comprises different tools which are designed to meet interactive, batch and in-situ workflows. -ParaView is available on ZIH systems from the [modules system](modules.md#modules-environment). The +ParaView is available on ZIH systems from the [modules system](modules.md#module-environments). The following command lists the available versions ```console diff --git a/doc.zih.tu-dresden.de/mkdocs.yml b/doc.zih.tu-dresden.de/mkdocs.yml index 346a6ac7319a80dd813cf101ca9d7dbbf5ca18f8..4c02af0be34a12b492e00d136d16c7c33949b364 100644 --- a/doc.zih.tu-dresden.de/mkdocs.yml +++ b/doc.zih.tu-dresden.de/mkdocs.yml @@ -138,7 +138,7 @@ site_name: ZIH HPC Compendium site_description: ZIH HPC Compendium site_author: ZIH Team site_dir: public -site_url: https://doc.zih.tu-dresden.de/ +site_url: https://gitlab.hrz.tu-chemnitz.de/zih/hpcsupport/hpc-compendium # uncomment next 3 lines if link to repo should not be displayed in the navbar @@ -200,6 +200,26 @@ markdown_extensions: # - mkdocs-video +plugins: + - search + # https://github.com/manuzhang/mkdocs-htmlproofer-plugin + - htmlproofer: + # True by default + # Toggle via env. var. ENABLED_HTMLPROOFER=false + enabled: !ENV [ENABLED_HTMLPROOFER, True] + # Check URLs before serving. Build fails in case of bad URLs. + raise_error: True + # Ignore errors + #raise_error_excludes: + # 504: ['https://www.mkdocs.org/'] + # Toggle validating external URLs + validate_external_urls: False + # Validate the entire rendered template, slow! + validate_rendered_template: True + +# Enable cross-page anchor validation +use_directory_urls: False + extra: tud_homepage: https://tu-dresden.de tud_name: "TU Dresden" @@ -219,7 +239,3 @@ extra: name: "Data Protection Declaration / Datenschutzerklärung" - link: https://tu-dresden.de/zertifikate name: "Certificates" - -plugins: - - search - - markdown-caption \ No newline at end of file