diff --git a/Dockerfile b/Dockerfile
index 4b11d882809ca6eb1d574e20306bb2cd279f5a42..ec246a77566bbbba03b613ce49ec745a82f46f51 100644
--- a/Dockerfile
+++ b/Dockerfile
@@ -1,4 +1,4 @@
-FROM python:3.8-bullseye
+FROM python:3.12-bookworm
SHELL ["/bin/bash", "-c"]
@@ -6,7 +6,7 @@ SHELL ["/bin/bash", "-c"]
# Base #
########
-RUN pip install mkdocs>=1.1.2 mkdocs-material==8.5.11 mkdocs-htmlproofer-plugin==1.2.1 mkdocs-video==1.3.0
+RUN pip install mkdocs>=1.6.0 mkdocs-material==9.5.22 mkdocs-htmlproofer-plugin==1.2.1 mkdocs-video==1.5.0
##########
# Linter #
@@ -14,7 +14,7 @@ RUN pip install mkdocs>=1.1.2 mkdocs-material==8.5.11 mkdocs-htmlproofer-plugin=
RUN apt-get update && apt-get install -y nodejs npm aspell git git-lfs
-RUN npm install -g markdownlint-cli@0.32.2 markdown-link-check
+RUN npm install -g markdownlint-cli@0.40.0 markdown-link-check
###########################################
# prepare git for automatic merging in CI #
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 80dbdbaeb0d3eb07690c8ddb16fbae0b0fc4b82e..7ded65dcd5782ae242607313c14feb8373c9cbb9 100644
--- a/doc.zih.tu-dresden.de/docs/contrib/content_rules.md
+++ b/doc.zih.tu-dresden.de/docs/contrib/content_rules.md
@@ -336,6 +336,7 @@ The table also holds a second placeholder, if, e.g., you need a second login to
| E-mail | marie@tu-dresden.de | martin@tu-dresden.de |
| Project title | `p_number_crunch` | `p_long_computations` |
| Workspace title | `number_crunch` | `long_computations` |
+| Job ID | `123456` | `456789` |
{: summary="Generic placeholders", align="bottom"}
!!! example "Output of `ls` command"
diff --git a/doc.zih.tu-dresden.de/docs/jobs_and_resources/hardware_overview.md b/doc.zih.tu-dresden.de/docs/jobs_and_resources/hardware_overview.md
index 3bf43c019f85446223119d6e7c2405e04edcc250..c8d49918b8f905b92951b01427d5639f2bbdc465 100644
--- a/doc.zih.tu-dresden.de/docs/jobs_and_resources/hardware_overview.md
+++ b/doc.zih.tu-dresden.de/docs/jobs_and_resources/hardware_overview.md
@@ -110,7 +110,7 @@ CPUs.
- 630 nodes, each with
- 2 x Intel Xeon Platinum 8470 (52 cores) @ 2.00 GHz, Multithreading enabled
- - 512 GB RAM
+ - 512 GB RAM (8 x 32 GB DDR5-4800 MT/s per socket)
- 12 nodes provide 1.8 TB local storage on NVMe device at `/tmp`
- All other nodes are diskless and have no or very limited local storage (i.e. `/tmp`)
- Login nodes: `login[1-4].barnard.hpc.tu-dresden.de`
@@ -126,7 +126,7 @@ and is designed for AI and ML tasks.
- 34 nodes, each with
- 8 x NVIDIA A100-SXM4 Tensor Core-GPUs
- 2 x AMD EPYC CPU 7352 (24 cores) @ 2.3 GHz, Multithreading available
- - 1 TB RAM
+ - 1 TB RAM (16 x 32 GB DDR4-2933 MT/s per socket)
- 3.5 TB local memory on NVMe device at `/tmp`
- Login nodes: `login[1-2].alpha.hpc.tu-dresden.de`
- Hostnames: `i[8001-8037].alpha.hpc.tu-dresden.de`
@@ -139,7 +139,7 @@ The cluster `Romeo` is a general purpose cluster by NEC based on AMD Rome CPUs.
- 192 nodes, each with
- 2 x AMD EPYC CPU 7702 (64 cores) @ 2.0 GHz, Multithreading available
- - 512 GB RAM
+ - 512 GB RAM (8 x 32 GB DDR4-3200 MT/s per socket)
- 200 GB local memory on SSD at `/tmp`
- Login nodes: `login[1-2].romeo.hpc.tu-dresden.de`
- Hostnames: `i[7001-7190].romeo.hpc.tu-dresden.de`
@@ -153,7 +153,7 @@ architecture.
- 1 node, with
- 32 x Intel(R) Xeon(R) Platinum 8276M CPU @ 2.20 GHz (28 cores)
- - 47 TB RAM
+ - 47 TB RAM (12 x 128 GB DDR4-2933 MT/s per socket)
- Configured as one single node
- 48 TB RAM (usable: 47 TB - one TB is used for cache coherence protocols)
- 370 TB of fast NVME storage available at `/nvme/<projectname>`
@@ -168,7 +168,7 @@ The cluster `Power9` by IBM is based on Power9 CPUs and provides NVIDIA V100 GPU
- 32 nodes, each with
- 2 x IBM Power9 CPU (2.80 GHz, 3.10 GHz boost, 22 cores)
- - 256 GB RAM DDR4 2666 MHz
+ - 256 GB RAM (8 x 16 GB DDR4-2666 MT/s per socket)
- 6 x NVIDIA VOLTA V100 with 32 GB HBM2
- NVLINK bandwidth 150 GB/s between GPUs and host
- Login nodes: `login[1-2].power9.hpc.tu-dresden.de`
diff --git a/doc.zih.tu-dresden.de/docs/jobs_and_resources/slurm.md b/doc.zih.tu-dresden.de/docs/jobs_and_resources/slurm.md
index ff2a9ceb43aca51cedecf234ca67b680799eabab..f96168d8dc01b2ce9425d0f5b226f59bf35aa800 100644
--- a/doc.zih.tu-dresden.de/docs/jobs_and_resources/slurm.md
+++ b/doc.zih.tu-dresden.de/docs/jobs_and_resources/slurm.md
@@ -165,30 +165,44 @@ allocation with desired switch count or the time limit expires. Acceptable time
## Interactive Jobs
Interactive activities like editing, compiling, preparing experiments etc. are normally limited to
-the login nodes. For longer interactive sessions, you can allocate cores on the compute node with
-the command `salloc`. It takes the same options as `sbatch` to specify the required resources.
+the login nodes. For longer interactive sessions, you can allocate resources on the compute node
+with the command `salloc`. It takes the same options as `sbatch` to specify the required resources.
`salloc` returns a new shell on the node where you submitted the job. You need to use the command
`srun` in front of the following commands to have these commands executed on the allocated
-resources. If you allocate more than one task, please be aware that `srun` will run the command on
-each allocated task by default! To release the allocated resources, invoke the command `exit` or
+resources. If you request for more than one task, please be aware that `srun` will run the command
+on each allocated task by default! To release the allocated resources, invoke the command `exit` or
`scancel <jobid>`.
-```console
-marie@login$ salloc --nodes=2
-salloc: Pending job allocation 27410653
-salloc: job 27410653 queued and waiting for resources
-salloc: job 27410653 has been allocated resources
-salloc: Granted job allocation 27410653
-salloc: Waiting for resource configuration
-salloc: Nodes taurusi[6603-6604] are ready for job
-marie@login$ hostname
-tauruslogin5.taurus.hrsk.tu-dresden.de
-marie@login$ srun hostname
-taurusi6604.taurus.hrsk.tu-dresden.de
-taurusi6603.taurus.hrsk.tu-dresden.de
-marie@login$ exit # ending the resource allocation
-```
+!!! example "Example: Interactive allocation using `salloc`"
+
+ The following code listing depicts the allocation of two nodes with two tasks on each node with a
+ time limit of one hour on the cluster `Barnard` for interactive usage.
+
+ ```console linenums="1"
+ marie@login.barnard$ salloc --nodes=2 --ntasks-per-node=2 --time=01:00:00
+ salloc: Pending job allocation 1234567
+ salloc: job 1234567 queued and waiting for resources
+ salloc: job 1234567 has been allocated resources
+ salloc: Granted job allocation 1234567
+ salloc: Waiting for resource configuration
+ salloc: Nodes n[1184,1223] are ready for job
+ [...]
+ marie@login.barnard$ hostname
+ login1
+ marie@login.barnard$ srun hostname
+ n1184
+ n1184
+ n1223
+ n1223
+ marie@login.barnard$ exit # ending the resource allocation
+ ```
+
+ After Slurm successfully allocated resources for the job, a new shell is created on the submit
+ host (cf. lines 9-10).
+
+ In order to use the allocated resources, you need to invoke your commands with `srun` (cf. lines
+ 11 ff).
The command `srun` also creates an allocation, if it is running outside any `sbatch` or `salloc`
allocation.
@@ -218,13 +232,6 @@ taurusi6604.taurus.hrsk.tu-dresden.de
shell, as shown in the example above. If you missed adding `-l` at submitting the interactive
session, no worry, you can source this files also later on manually (`source /etc/profile`).
-!!! note "Partition `interactive`"
-
- A dedicated partition `interactive` is reserved for short jobs (< 8h) with no more than one job
- per user. An interactive partition is available for every regular partition, e.g.
- `alpha-interactive` for `alpha`. Please check the availability of nodes there with
- `sinfo |grep 'interactive\|AVAIL' |less`
-
### Interactive X11/GUI Jobs
Slurm will forward your X11 credentials to the first (or even all) node for a job with the
diff --git a/doc.zih.tu-dresden.de/docs/quickstart/getting_started.md b/doc.zih.tu-dresden.de/docs/quickstart/getting_started.md
index 95af8dde2310081e23e24c56ce092561e723aa3a..7296a067140c885708fc5de6fadf021651206dbc 100644
--- a/doc.zih.tu-dresden.de/docs/quickstart/getting_started.md
+++ b/doc.zih.tu-dresden.de/docs/quickstart/getting_started.md
@@ -148,9 +148,9 @@ To start we recommend the Lustre filesystem **horse**.
The following command creates a workspace
```console
- marie@login$ ws_allocate -F horse -r 7 -m marie@tu-dresden.de -n test-workspace -d 90
+ marie@login$ ws_allocate -F horse -r 7 -m marie@tu-dresden.de -n number_crunch -d 90
Info: creating workspace.
- /data/horse/ws/marie-test-workspace
+ /data/horse/ws/marie-number_crunch
remaining extensions : 10
remaining time in days: 90
```
@@ -160,10 +160,10 @@ To start we recommend the Lustre filesystem **horse**.
- `ws_allocate` - command to allocate
- `-F horse` - on the horse filesystem
- `-r 7 -m marie@tu-dresden.de` - send a reminder to `marie@tu-dresden.de` 7 days before expiration
- - `-n test-workspace` - workspace name
+ - `-n number_crunch` - workspace name
- `-d 90` - a life time of 90 days
- The path to this workspace is `/data/horse/ws/marie-test-workspace`. You will need it when
+ The path to this workspace is `/data/horse/ws/marie-number_crunch`. You will need it when
transferring data or running jobs.
Find more [information on workspaces in the compendium](../data_lifecycle/workspaces.md).
@@ -177,7 +177,7 @@ The approach depends on the data volume: up to 100 MB or above.
Use the command `cp` to copy the file `example.R` from your ZIH home directory to a workspace:
```console
- marie@login$ cp /home/marie/example.R /data/horse/ws/marie-test-workspace
+ marie@login$ cp /home/marie/example.R /data/horse/ws/marie-number_crunch
```
Analogously use command `mv` to move a file.
@@ -191,7 +191,7 @@ The approach depends on the data volume: up to 100 MB or above.
filesystem location to another:
```console
- marie@login$ dtcp -r /walrus/ws/large-dataset /data/horse/ws/marie-test-workspace/data
+ marie@login$ dtcp -r /walrus/ws/large-dataset /data/horse/ws/marie-number_crunch/data
```
Analogously use the command `dtmv` to move a file or folder.
@@ -199,31 +199,32 @@ The approach depends on the data volume: up to 100 MB or above.
transfer section.
### Transferring Data *To/From* ZIH HPC Systems
-<!-- [NT] currently not available
+
???+ example "`scp` for transferring data to ZIH HPC systems"
Copy the file `example.R` from your local machine to a workspace on the ZIH systems:
```console
- marie@local$ scp /home/marie/Documents/example.R marie@dataport1.hpc.tu-dresden.de:/data/horse/ws/your_workspace/
+ marie@local$ scp /home/marie/Documents/example.R marie@dataport1.hpc.tu-dresden.de:/data/horse/ws/marie-number_crunch/
Password:
- example.R 100% 312 32.2KB/s 00:00``
+ example.R 100% 312 32.2KB/s 00:00
```
Note, the target path contains `dataport1.hpc.tu-dresden.de`, which is one of the
- so called [dataport nodes](../data_transfer/dataport_nodes.md) that allows for data transfer from/to the outside.
+ so called [dataport nodes](../data_transfer/dataport_nodes.md) that allows for data transfer
+ from/to the outside.
???+ example "`scp` to transfer data from ZIH HPC systems to local machine"
Copy the file `results.csv` from a workspace on the ZIH HPC systems to your local machine:
```console
- marie@local$ scp marie@dataport1.hpc.tu-dresden.de:/data/horse/ws/marie-test-workspace/results.csv /home/marie/Documents/
+ marie@local$ scp marie@dataport1.hpc.tu-dresden.de:/data/horse/ws/marie-number_crunch/results.csv /home/marie/Documents/
```
Feel free to explore further [examples](http://bropages.org/scp) of the `scp` command
and possibilities of the [dataport nodes](../data_transfer/dataport_nodes.md).
--->
+
!!! caution "Terabytes of data"
If you are planning to move terabytes or even more from an outside machine into ZIH systems,
@@ -423,7 +424,7 @@ See [Slurm documentation](../jobs_and_resources/slurm.md#interactive-jobs) for m
```console
marie@login$ srun --ntasks=1 --cpus-per-task=4 --time=1:00:00 --mem-per-cpu=1700 --pty bash -l #allocate 4 cores for the interactive job
marie@compute$ module load Python #load necessary packages
-marie@compute$ cd /data/horse/ws/marie-test-workspace/ #go to your created workspace
+marie@compute$ cd /data/horse/ws/marie-number_crunch/ #go to your created workspace
marie@compute$ python test.py #execute your file
Hello, World!
```
diff --git a/doc.zih.tu-dresden.de/docs/software/cfd.md b/doc.zih.tu-dresden.de/docs/software/cfd.md
index 7e0eebc74081f188a1441eea1136df0ba636458e..5fcd9082f7aed6e738cbe1463b6445dedfcc9152 100644
--- a/doc.zih.tu-dresden.de/docs/software/cfd.md
+++ b/doc.zih.tu-dresden.de/docs/software/cfd.md
@@ -76,11 +76,10 @@ geometry and mesh generator cfx5pre, and the post-processor cfx5post.
#SBATCH --mail-user=marie@tu-dresden.de # email address (only tu-dresden)
#SBATCH --mail-type=ALL
- module load ANSYS
-
- nodeset -e $SLURM_JOB_NODELIST | xargs -n1 > hostsfile_job_$SLURM_JOBID.txt
-
- fluent 2ddp -t$SLURM_NTASKS -g -mpi=intel -pinfiniband -cnf=hostsfile_job_$SLURM_JOBID.txt < input.in
+ module purge
+ module load release/23.10
+ module load ANSYS/2023R1
+ fluent 2ddp -t$SLURM_NTASKS -g -mpi=openmpi -pinfiniband -cnf=$(/software/util/slurm/bin/create_rankfile -f CCM) -i input.jou
```
To use fluent interactively, please try:
diff --git a/doc.zih.tu-dresden.de/docs/software/python_virtual_environments.md b/doc.zih.tu-dresden.de/docs/software/python_virtual_environments.md
index 0b2f334437718c53e50109079b27633a9ee3bab5..5c4759850caf8d705b9880d05d1da22a4bb116a7 100644
--- a/doc.zih.tu-dresden.de/docs/software/python_virtual_environments.md
+++ b/doc.zih.tu-dresden.de/docs/software/python_virtual_environments.md
@@ -200,13 +200,14 @@ can deactivate the conda environment as follows:
marie@alpha$ ws_allocate my_conda_virtualenv 100 # use a workspace for the environment
marie@alpha$ cd /data/horse/ws/marie-my_conda_virtualenv
marie@alpha$ module load Anaconda3
- Module Anaconda3/2021.11 loaded.
+ Module Anaconda3/2022.05 loaded.
marie@alpha$ conda create --prefix my-torch-env python=3.8
Collecting package metadata (current_repodata.json): done
Solving environment: done
[...]
Proceed ([y]/n)? y
[...]
+ marie@alpha$ source $EBROOTANACONDA3/etc/profile.d/conda.sh
marie@alpha$ conda activate my-torch-env
(my-torch-env) marie@alpha$ conda install -c pytorch torchvision
Collecting package metadata (current_repodata.json): done
diff --git a/doc.zih.tu-dresden.de/docs/software/visualization.md b/doc.zih.tu-dresden.de/docs/software/visualization.md
index 427bf746840383e69c9a4a85a84997d618cc9b15..3a4ce5b05caa6fbd6bff94c184304de30f151db2 100644
--- a/doc.zih.tu-dresden.de/docs/software/visualization.md
+++ b/doc.zih.tu-dresden.de/docs/software/visualization.md
@@ -158,7 +158,7 @@ processes.
```console
marie@login$ module ParaView/5.7.0-osmesa
- marie@login$ srun --nodes=1 --ntasks=8 --mem-per-cpu=2500 --partition=interactive --pty pvserver --force-offscreen-rendering
+ marie@login$ srun --nodes=1 --ntasks=8 --mem-per-cpu=2500 --pty pvserver --force-offscreen-rendering
srun: job 2744818 queued and waiting for resources
srun: job 2744818 has been allocated resources
Waiting for client...
@@ -254,5 +254,5 @@ it into thinking your provided GL rendering version is higher than what it actua
marie@login$ export MESA_GL_VERSION_OVERRIDE=3.2
# 3rd, start the ParaView GUI inside an interactive job. Don't forget the --x11 parameter for X forwarding:
- marie@login$ srun --ntasks=1 --cpus-per-task=1 --partition=interactive --mem-per-cpu=2500 --pty --x11=first paraview
+ marie@login$ srun --ntasks=1 --cpus-per-task=1 --mem-per-cpu=2500 --pty --x11=first paraview
```
diff --git a/doc.zih.tu-dresden.de/mkdocs.yml b/doc.zih.tu-dresden.de/mkdocs.yml
index d2b2bc9feb444046b96ee93b84c0826418e0985a..06d4aee3a10cd19514cbf93a1c920439cdd678a1 100644
--- a/doc.zih.tu-dresden.de/mkdocs.yml
+++ b/doc.zih.tu-dresden.de/mkdocs.yml
@@ -173,7 +173,6 @@ edit_uri: blob/preview/doc.zih.tu-dresden.de/docs/
theme:
# basetheme
-
name: material
# disable fonts being loaded from google fonts
@@ -221,7 +220,8 @@ markdown_extensions:
plugins:
- - search
+ - search:
+ separator: '[\s\-,:!=\[\]\(\)"/]+|(?!\b)(?=[A-Z][a-z])|\.(?!\d)|&[lg]t;'
- markdown-caption
# https://github.com/manuzhang/mkdocs-htmlproofer-plugin
- htmlproofer:
diff --git a/doc.zih.tu-dresden.de/tud_theme/partials/header.html b/doc.zih.tu-dresden.de/tud_theme/partials/header.html
index 4b28fab9289088db78f1a0ee519a7f5594ad8d38..9fad2d191b113d4367536ec342f6a95d7438b8f6 100644
--- a/doc.zih.tu-dresden.de/tud_theme/partials/header.html
+++ b/doc.zih.tu-dresden.de/tud_theme/partials/header.html
@@ -69,7 +69,7 @@
</div>
<!-- Button to open search modal -->
- {% if "search" in config["plugins"] %}
+ {% if "material/search" in config["plugins"] %}
<label class="md-header__button md-icon" for="__search">
{% include ".icons/material/magnify.svg" %}
</label>