Merge branch 'merge-preview-in-main' into 'main'

Automated merge from preview to main

See merge request !563

doc.zih.tu-dresden.de/docs/application/project_request_form_jards.md

@@ -16,29 +16,27 @@ Due to the structuring there are different ways to access [HPC resources](https:
 
 ## Workflow
 
-  ``` mermaid
-  graph LR
-    A(NHR Type) --> |National| B(Login);
-    A --> |Saxony| B;
-    A --> |TU Dresden| B;
-    B --> |ZIH Login| H(Jards Frontend);
-    B --> |E-Mail Callback| H;
-    J --> |show| J;
-    J--> |copy| J;
-    H --> |create| J(Application);
-    J --> |edit| J;
-    J --> | submit | L(Finalized Application);
-
-    click A href "http://localhost:8000/application/project_request_form_jards/#application-type" _self;
-    click E href "http://localhost:8000/application/project_request_form_jards/#nhr" _self;
-    click F href "http://localhost:8000/application/project_request_form_jards/#saxony" _self;
-    click G href "http://localhost:8000/application/project_request_form_jards/#tu-dresden" _self;
-    click B href "http://localhost:8000/application/project_request_form_jards/#login" _self;
-    click C href "http://localhost:8000/application/project_request_form_jards/#with-tu-dresden-idm-account" _self;
-    click D href "http://localhost:8000/application/project_request_form_jards/#with-tu-dresden-idm-account" _self;
-  ```
-
-{: align="center"}
+``` mermaid
+graph LR
+A(NHR Type) --> |National| B(Login);
+A --> |Saxony| B;
+A --> |TU Dresden| B;
+B --> |ZIH Login| H(Jards Frontend);
+B --> |E-Mail Callback| H;
+J --> |show| J;
+J--> |copy| J;
+H --> |create| J(Application);
+J --> |edit| J;
+J --> | submit | L(Finalized Application);
+
+click A href "http://localhost:8000/application/project_request_form_jards/#application-type" _self;
+click E href "http://localhost:8000/application/project_request_form_jards/#nhr" _self;
+click F href "http://localhost:8000/application/project_request_form_jards/#saxony" _self;
+click G href "http://localhost:8000/application/project_request_form_jards/#tu-dresden" _self;
+click B href "http://localhost:8000/application/project_request_form_jards/#login" _self;
+click C href "http://localhost:8000/application/project_request_form_jards/#with-tu-dresden-idm-account" _self;
+click D href "http://localhost:8000/application/project_request_form_jards/#with-tu-dresden-idm-account" _self;
+```
 
 === "NHR Type"
 

doc.zih.tu-dresden.de/docs/software/python_virtual_environments.md

@@ -66,6 +66,37 @@ the environment as follows:
 (env) marie@compute$ deactivate    #Leave the virtual environment
 ```
 
+??? example
+
+    This is an example on partition Alpha. The example creates a conda virtual environment, and
+    installs the package `torchvision` with conda.
+    ```console
+    marie@login$ srun --partition=alpha-interactive --nodes=1 --gres=gpu:1 --time=01:00:00 --pty bash
+    marie@alpha$ ws_allocate -F scratch my_python_virtualenv 100    # use a workspace for the environment
+    marie@alpha$ cd /scratch/ws/1/marie-my_python_virtualenv
+    marie@alpha$ module load modenv/hiera GCC/10.2.0 CUDA/11.1.1 OpenMPI/4.0.5 PyTorch/1.9.0
+    Module GCC/10.2.0, CUDA/11.1.1, OpenMPI/4.0.5, PyTorch/1.9.0 and 54 dependencies loaded.
+    marie@alpha$ which python
+    /sw/installed/Python/3.8.6-GCCcore-10.2.0/bin/python
+    marie@alpha$ pip list
+    [...]
+    marie@alpha$ virtualenv --system-site-packages my-torch-env
+    created virtual environment CPython3.8.6.final.0-64 in 42960ms
+    creator CPython3Posix(dest=[...]/my-torch-env, clear=False, global=True)
+    seeder FromAppData(download=False, pip=bundle, setuptools=bundle, wheel=bundle, via=copy, app_data_dir=~/.local/share/virtualenv)
+        added seed packages: pip==21.1.3, setuptools==57.2.0, wheel==0.36.2
+    activators BashActivator,CShellActivator,FishActivator,PowerShellActivator,PythonActivator,XonshActivator
+    marie@alpha$ source my-torch-env/bin/activate
+    (my-torch-env) marie@alpha$ pip install torchvision==0.10.0
+    [...]
+    Installing collected packages: torchvision==0.10.0
+    Successfully installed torchvision-0.10.0
+    [...]
+    (my-torch-env) marie@alpha$ python -c "import torchvision; print(torchvision.__version__)"
+    0.10.0+cu102
+    (my-torch-env) marie@alpha$ deactivate
+    ```
+
 ### Persistence of Python Virtual Environment
 
 To persist a virtualenv, you can store the names and versions of installed
@@ -134,34 +165,41 @@ can deactivate the conda environment as follows:
 (conda-env) marie@compute$ conda deactivate    #Leave the virtual environment
 ```
 
+!!! warning
+    When installing conda packages via `conda install`, ensure to have enough main memory requested
+    in your job allocation.
+
+!!! hint
+    We do not recommend to use conda environments together with EasyBuild modules due to
+    dependency conflicts. Nevertheless, if you need EasyBuild modules, consider installing conda
+    packages via `conda install --no-deps [...]` to prevent conda from installing dependencies.
+
 ??? example
 
-    This is an example on partition Alpha. The example creates a virtual environment, and installs
-    the package `torchvision` with pip.
+    This is an example on partition Alpha. The example creates a conda virtual environment, and
+    installs the package `torchvision` with conda.
     ```console
     marie@login$ srun --partition=alpha-interactive --nodes=1 --gres=gpu:1 --time=01:00:00 --pty bash
-    marie@alpha$ mkdir python-environments                               # please use workspaces
-    marie@alpha$ module load modenv/hiera GCC/10.2.0 CUDA/11.1.1 OpenMPI/4.0.5 PyTorch
-    Module GCC/10.2.0, CUDA/11.1.1, OpenMPI/4.0.5, PyTorch/1.9.0 and 54 dependencies loaded.
-    marie@alpha$ which python
-    /sw/installed/Python/3.8.6-GCCcore-10.2.0/bin/python
-    marie@alpha$ pip list
+    marie@alpha$ ws_allocate -F scratch my_conda_virtualenv 100    # use a workspace for the environment
+    marie@alpha$ cd /scratch/ws/1/marie-my_conda_virtualenv
+    marie@alpha$ module load Anaconda3
+    Module Anaconda3/2021.11 loaded.
+    marie@alpha$ conda create --prefix my-torch-env python=3.8
+    Collecting package metadata (current_repodata.json): done
+    Solving environment: done
     [...]
-    marie@alpha$ virtualenv --system-site-packages python-environments/my-torch-env
-    created virtual environment CPython3.8.6.final.0-64 in 42960ms
-    creator CPython3Posix(dest=~/python-environments/my-torch-env, clear=False, global=True)
-    seeder FromAppData(download=False, pip=bundle, setuptools=bundle, wheel=bundle, via=copy, app_data_dir=~/.local/share/virtualenv)
-        added seed packages: pip==21.1.3, setuptools==57.2.0, wheel==0.36.2
-    activators BashActivator,CShellActivator,FishActivator,PowerShellActivator,PythonActivator,XonshActivator
-    marie@alpha$ source python-environments/my-torch-env/bin/activate
-    (my-torch-env) marie@alpha$ pip install torchvision
+    Proceed ([y]/n)? y
     [...]
-    Installing collected packages: torchvision
-    Successfully installed torchvision-0.10.0
+    marie@alpha$ conda activate my-torch-env
+    (my-torch-env) marie@alpha$ conda install -c pytorch torchvision
+    Collecting package metadata (current_repodata.json): done
     [...]
+    Preparing transaction: done
+    Verifying transaction: done
+    (my-torch-env) marie@alpha$ which python    # ensure to use the correct Python
     (my-torch-env) marie@alpha$ python -c "import torchvision; print(torchvision.__version__)"
-    0.10.0+cu102
-    (my-torch-env) marie@alpha$ deactivate
+    0.12.0
+    (my-torch-env) marie@alpha$ conda deactivate
     ```
 
 ### Persistence of Conda Virtual Environment

doc.zih.tu-dresden.de/tud_theme/stylesheets/extra.css

@@ -36,6 +36,8 @@
     /* interaction color */
     --tud-red-90:                 rgb(221, 29, 29);
     --fg-color--light:              rgba(0, 0, 0, 0.6);
+
+    --icon-external-link: url('data:image/svg+xml, <svg xmlns="http://www.w3.org/2000/svg"  viewBox="0 0 20 20"> <g style="stroke:rgb(35,82,124);stroke-width:1"> <line x1="5" y1="5" x2="5" y2="14" /> <line x1="14" y1="9" x2="14" y2="14" /> <line x1="5" y1="14" x2="14" y2="14" /> <line x1="5" y1="5" x2="9" y2="5"  /> <line x1="10" y1="2" x2="17" y2="2"  /> <line x1="17" y1="2" x2="17" y2="9" /> <line x1="10" y1="9" x2="17" y2="2" style="stroke-width:1.5" /> </g> </svg>');
 }
 
 .md-typeset h1,
@@ -192,7 +194,26 @@ p {
 	margin: 0.2em;
 }
 /* main */
-
+/* style external links as found on https://stackoverflow.com/questions/5379752/css-style-external-links */
+.md-content a[href]:where([href*="\."]):not(:where(
+  /* exclude hash only links */
+  [href^="#"],
+  /* exclude relative but not double slash only links */
+  [href^="/"]:not([href^="//"]),
+  /* exclude page itself */
+  [href*="//doc.zih.tu-dresden.de"],
+  /* exclude relative links beginning with ../ */
+  [href^="\.\./"],
+  [href^="misc/"],
+  /* exclude buttons */
+  .md-content__button,
+  /* exclude icons */
+  .md-icon
+)):after {
+  content: '';
+  background: no-repeat var(--icon-external-link);
+  padding-right: 1em;
+}
 /* footer */
 .md-footer * {
     justify-content: flex-start;