Dockerfile

@@ -14,7 +14,7 @@ RUN pip install mkdocs>=1.1.2 mkdocs-material>=7.1.0 mkdocs-htmlproofer-plugin==
 
 RUN apt-get update && apt-get install -y nodejs npm aspell git git-lfs
 
-RUN npm install -g markdownlint-cli markdown-link-check
+RUN npm install -g markdownlint-cli@0.32.2 markdown-link-check
 
 ###########################################
 # prepare git for automatic merging in CI #
@@ -38,6 +38,9 @@ RUN echo 'test \! -e /docs/tud_theme/javascripts/mermaid.min.js && test -x /docs
 RUN echo 'exec "$@"' >> /entrypoint.sh
 RUN chmod u+x /entrypoint.sh
 
+# Workaround https://gitlab.com/gitlab-org/gitlab-runner/-/issues/29022
+RUN git config --global --add safe.directory /docs
+
 WORKDIR /docs
 
 CMD ["mkdocs", "build", "--verbose", "--strict"]

doc.zih.tu-dresden.de/docs/jobs_and_resources/slurm.md

@@ -328,8 +328,8 @@ specifications for each component of the heterogeneous job should be separated w
 Running a job step on a specific component is supported by the option `--het-group`.
 
 ```console
-marie@login$ salloc --ntasks 1 --cpus-per-task 4 --partition <partition> --mem=200G : \
-                    --ntasks 8 --cpus-per-task 1 --gres=gpu:8 --mem=80G --partition <partition>
+marie@login$ salloc --ntasks=1 --cpus-per-task=4 --partition <partition> --mem=200G : \
+                    --ntasks=8 --cpus-per-task=1 --gres=gpu:8 --mem=80G --partition <partition>
 [...]
 marie@login$ srun ./my_application <args for master tasks> : ./my_application <args for worker tasks>
 ```
@@ -340,16 +340,16 @@ components by a line containing the directive `#SBATCH hetjob`.
 ```bash
 #!/bin/bash
 
-#SBATCH --ntasks 1
-#SBATCH --cpus-per-task 4
-#SBATCH --partition <partition>
+#SBATCH --ntasks=1
+#SBATCH --cpus-per-task=4
+#SBATCH --partition=<partition>
 #SBATCH --mem=200G
 #SBATCH hetjob # required to separate groups
-#SBATCH --ntasks 8
-#SBATCH --cpus-per-task 1
+#SBATCH --ntasks=8
+#SBATCH --cpus-per-task=1
 #SBATCH --gres=gpu:8
 #SBATCH --mem=80G
-#SBATCH --partition <partition>
+#SBATCH --partition=<partition>
 
 srun ./my_application <args for master tasks> : ./my_application <args for worker tasks>
 
@@ -474,7 +474,7 @@ at no extra cost.
     ??? example "Show all jobs since the beginning of year 2021"
 
         ```console
-        marie@login$ sacct -S 2021-01-01 [-E now]
+        marie@login$ sacct --starttime 2021-01-01 [--endtime now]
         ```
 
 ## Jobs at Reservations

doc.zih.tu-dresden.de/docs/jobs_and_resources/slurm_examples.md

@@ -186,7 +186,7 @@ When `srun` is used within a submission script, it inherits parameters from `sba
 `--ntasks=1`, `--cpus-per-task=4`, etc. So we actually implicitly run the following
 
 ```bash
-srun --ntasks=1 --cpus-per-task=4 ... --partition=ml some-gpu-application
+srun --ntasks=1 --cpus-per-task=4 [...] --partition=ml <some-gpu-application>
 ```
 
 Now, our goal is to run four instances of this program concurrently in a single batch script. Of
@@ -237,7 +237,7 @@ inherited from the surrounding `sbatch` context. The following line would be suf
 job in this example:
 
 ```bash
-srun --exclusive --gres=gpu:1 --ntasks=1 some-gpu-application &
+srun --exclusive --gres=gpu:1 --ntasks=1 <some-gpu-application> &
 ```
 
 Yet, it adds some extra safety to leave them in, enabling the Slurm batch system to complain if not
@@ -278,7 +278,8 @@ use up all resources in the nodes:
     #SBATCH --exclusive    # ensure that nobody spoils my measurement on 2 x 2 x 8 cores
     #SBATCH --time=00:10:00
     #SBATCH --job-name=Benchmark
-    #SBATCH --mail-user=your.name@tu-dresden.de
+    #SBATCH --mail-type=end
+    #SBATCH --mail-user=<your.email>@tu-dresden.de
 
     srun ./my_benchmark
     ```
@@ -313,14 +314,14 @@ name specific to the job:
 
     ```Bash
     #!/bin/bash
-    #SBATCH --array 0-9
+    #SBATCH --array=0-9
     #SBATCH --output=arraytest-%A_%a.out
     #SBATCH --error=arraytest-%A_%a.err
     #SBATCH --ntasks=864
     #SBATCH --time=08:00:00
     #SBATCH --job-name=Science1
     #SBATCH --mail-type=end
-    #SBATCH --mail-user=your.name@tu-dresden.de
+    #SBATCH --mail-user=<your.email>@tu-dresden.de
 
     echo "Hi, I am step $SLURM_ARRAY_TASK_ID in this array job $SLURM_ARRAY_JOB_ID"
     ```

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

@@ -66,7 +66,7 @@ marie@login$ srun --ntasks 1 --partition <partition> mpicc -g -o fancy-program f
 # Allocate interactive session with 1 extra process for MUST
 marie@login$ salloc --ntasks 5 --partition <partition>
 
-marie@login$ mustrun --must:mpiexec srun --must:np --ntasks --ntasks 4 --must:stacktrace backward ./fancy-program
+marie@login$ mustrun --must:mpiexec srun --must:np --ntasks --must:stacktrace backward --ntasks 4 ./fancy-program
 [MUST] MUST configuration ... centralized checks with fall-back application crash handling (very slow)
 [MUST] Weaver ... success
 [MUST] Code generation ... success

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-a-custom-environment) documentation.
+    [JupyterHub](../access/jupyterhub_custom_environments.md) documentation.
 
 ## TensorFlow in Containers
 

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

@@ -73,7 +73,17 @@ Launching VampirServer...
 Submitting slurm 30 minutes job (this might take a while)...
 ```
 
+This way, a job with a timelimit of 30 minutes and default resources is submitted. This might fit
+your needs. If not, please feel free to request a customized job running VampirServer, e.g.
+
+```console
+marie@login$ vampirserver start --ntasks=8 --time=01:00:00 --mem-per-cpu=3000M --partition=romeo
+Launching VampirServer...
+Submitting slurm 01:00:00 minutes job (this might take a while)...
+```
+
 Above automatically allocates its resources via the respective batch system. If you want to start
+
 VampirServer without a batch allocation or from inside an interactive allocation, use
 
 ```console

doc.zih.tu-dresden.de/util/download-newest-mermaid.js.sh

@@ -6,4 +6,4 @@ scriptpath=${BASH_SOURCE[0]}
 basedir=`dirname "$scriptpath"`
 basedir=`dirname "$basedir"`
 cd $basedir/tud_theme/javascripts
-wget https://unpkg.com/mermaid/dist/mermaid.min.js
+wget https://unpkg.com/mermaid@9.4.0/dist/mermaid.min.js