diff --git a/doc.zih.tu-dresden.de/docs/software/fem_software.md b/doc.zih.tu-dresden.de/docs/software/fem_software.md
index bd65ea9832462bae475841f2e3ed2fa8193e3355..843530a570593edb7e74790aece6f8385da63134 100644
--- a/doc.zih.tu-dresden.de/docs/software/fem_software.md
+++ b/doc.zih.tu-dresden.de/docs/software/fem_software.md
@@ -1,247 +1,238 @@
# FEM Software
-For an up-to-date list of the installed software versions on our
-cluster, please refer to SoftwareModulesList **TODO LINK** (SoftwareModulesList).
+!!! hint "Its all in the modules"
-## Abaqus
-
-[ABAQUS](http://www.hks.com) **TODO links to realestate site** is a general-purpose finite-element program
-designed for advanced linear and nonlinear engineering analysis
-applications with facilities for linking-in user developed material
-models, elements, friction laws, etc.
-
-Eike Dohmen (from Inst.f. Leichtbau und Kunststofftechnik) sent us the
-attached description of his ABAQUS calculations. Please try to adapt
-your calculations in that way.\<br />Eike is normally a Windows-User and
-his description contains also some hints for basic Unix commands. (
-ABAQUS-SLURM.pdf **TODO LINK** (%ATTACHURL%/ABAQUS-SLURM.pdf) - only in German)
-
-Please note: Abaqus calculations should be started with a batch script.
-Please read the information about the Batch System **TODO LINK ** (BatchSystems)
-SLURM.
-
-The detailed Abaqus documentation can be found at
-abaqus **TODO LINK MISSING** (only accessible from within the
-TU Dresden campus net).
+ All packages described in this section, are organized in so-called modules. To list the available versions of a package and load a
+ particular, e.g., ANSYS, version, invoke the commands
-**Example - Thanks to Benjamin Groeger, Inst. f. Leichtbau und
-Kunststofftechnik) **
-
-1. Prepare an Abaqus input-file (here the input example from Benjamin)
-
-Rot-modell-BenjaminGroeger.inp **TODO LINK** (%ATTACHURL%/Rot-modell-BenjaminGroeger.inp)
-
-2. Prepare a batch script on taurus like this
-
-```
-#!/bin/bash<br>
-### Thanks to Benjamin Groeger, Institut fuer Leichtbau und Kunststofftechnik, 38748<br />### runs on taurus and needs ca 20sec with 4cpu<br />### generates files:
-### yyyy.com
-### yyyy.dat
-### yyyy.msg
-### yyyy.odb
-### yyyy.prt
-### yyyy.sim
-### yyyy.sta
-#SBATCH --nodes=1 ### with >1 node abaqus needs a nodeliste
-#SBATCH --ntasks-per-node=4
-#SBATCH --mem=500 ### memory (sum)
-#SBATCH --time=00:04:00
-### give a name, what ever you want
-#SBATCH --job-name=yyyy
-### you get emails when the job will finished or failed
-### set your right email
-#SBATCH --mail-type=END,FAIL
-#SBATCH --mail-user=xxxxx.yyyyyy@mailbox.tu-dresden.de
-### set your project
-#SBATCH -A p_xxxxxxx
-### Abaqus have its own MPI
-unset SLURM_GTIDS
-### load and start
-module load ABAQUS/2019
-abaqus interactive input=Rot-modell-BenjaminGroeger.inp job=yyyy cpus=4 mp_mode=mpi
+ ```console
+ marie@login$ module avail ANSYS
+ [...]
+ marie@login$ module load ANSYS/<version>
+ ```
-```
+ The section [runtime environment](runtime_environment.md) provides a comprehensive overview
+ on the module system and relevant commands.
-3. Start the batch script (name of our script is
-"batch-Rot-modell-BenjaminGroeger")
+## Abaqus
-```
-sbatch batch-Rot-modell-BenjaminGroeger --->; you will get a jobnumber = JobID (for example 3130522)
-```
+[Abaqus](https://www.3ds.com/de/produkte-und-services/simulia/produkte/abaqus/) is a general-purpose
+finite element method program designed for advanced linear and nonlinear engineering analysis
+applications with facilities for linking-in user developed material models, elements, friction laws,
+etc.
-4. Control the status of the job
+### Guide by User
-```
-squeue -u your_login -->; in column "ST" (Status) you will find a R=Running or P=Pending (waiting for resources)
-```
+Eike Dohmen (from Inst. f. Leichtbau und Kunststofftechnik) sent us the description of his
+Abaqus calculations. Please try to adapt your calculations in that way. Eike is normally a
+Windows user and his description contains also some hints for basic Unix commands:
+[Abaqus-Slurm.pdf (only in German)](misc/ABAQUS-SLURM.pdf).
-## ANSYS
+### General
-ANSYS is a general-purpose finite-element program for engineering
-analysis, and includes preprocessing, solution, and post-processing
-functions. It is used in a wide range of disciplines for solutions to
-mechanical, thermal, and electronic problems. [ANSYS and ANSYS
-CFX](http://www.ansys.com) used to be separate packages in the past and
-are now combined.
+Abaqus calculations should be started using a job file (aka. batch script). Please refer to the
+page covering the [batch system Slurm](../jobs_and_resources/slurm.md) if you are not familiar with
+Slurm or [writing job files](../jobs_and_resources/slurm.md#job-files).
-ANSYS, like all other installed software, is organized in so-called
-modules **TODO LINK** (RuntimeEnvironment). To list the available versions and load a
-particular ANSYS version, type
+??? example "Usage of Abaqus"
-```
-module avail ANSYS
-...
-module load ANSYS/VERSION
-```
+ (Thanks to Benjamin Groeger, Inst. f. Leichtbau und Kunststofftechnik)).
-In general, HPC-systems are not designed for interactive "GUI-working".
-Even so, it is possible to start a ANSYS workbench on Taurus (login
-nodes) interactively for short tasks. The second and recommended way is
-to use batch files. Both modes are documented in the following.
+ 1. Prepare an Abaqus input-file. You can start with the input example from Benjamin:
+ [Rot-modell-BenjaminGroeger.inp](misc/Rot-modell-BenjaminGroeger.inp)
+ 2. Prepare a job file on ZIH systems like this
+ ```bash
+ #!/bin/bash
+ ### needs ca 20 sec with 4cpu
+ ### generates files:
+ ### yyyy.com
+ ### yyyy.dat
+ ### yyyy.msg
+ ### yyyy.odb
+ ### yyyy.prt
+ ### yyyy.sim
+ ### yyyy.sta
+ #SBATCH --nodes=1 # with >1 node Abaqus needs a nodeliste
+ #SBATCH --ntasks-per-node=4
+ #SBATCH --mem=500 # total memory
+ #SBATCH --time=00:04:00
+ #SBATCH --job-name=yyyy # give a name, what ever you want
+ #SBATCH --mail-type=END,FAIL # send email when the job finished or failed
+ #SBATCH --mail-user=<name>@mailbox.tu-dresden.de # set your email
+ #SBATCH -A p_xxxxxxx # charge compute time to your project
+
+
+ # Abaqus has its own MPI
+ unset SLURM_GTIDS
+
+ # load module and start Abaqus
+ module load ABAQUS/2019
+ abaqus interactive input=Rot-modell-BenjaminGroeger.inp job=yyyy cpus=4 mp_mode=mpi
+ ```
+ 3. Start the job file (e.g., name `batch-Rot-modell-BenjaminGroeger.sh`)
+ ```
+ marie@login$ sbatch batch-Rot-modell-BenjaminGroeger.sh # Slurm will provide the Job Id (e.g., 3130522)
+ ```
+ 4. Control the status of the job
+ ```
+ marie@login squeue -u your_login # in column "ST" (Status) you will find a R=Running or P=Pending (waiting for resources)
+ ```
+
+## Ansys
+
+Ansys is a general-purpose finite element method program for engineering analysis, and includes
+preprocessing, solution, and post-processing functions. It is used in a wide range of disciplines
+for solutions to mechanical, thermal, and electronic problems.
+[Ansys and Ansys CFX](http://www.ansys.com) used to be separate packages in the past and are now
+combined.
+
+In general, HPC systems are not designed for interactive working with GUIs. Even so, it is possible to
+start a Ansys workbench on the login nodes interactively for short tasks. The second and
+**recommended way** is to use job files. Both modes are documented in the following.
+
+!!! note ""
+
+ Since the MPI library that Ansys uses internally (Platform MPI) has some problems integrating
+ seamlessly with Slurm, you have to unset the enviroment variable `SLURM_GTIDS` in your
+ environment bevor running Ansysy workbench in interactive andbatch mode.
### Using Workbench Interactively
-For fast things, ANSYS workbench can be invoked interactively on the
-login nodes of Taurus. X11 forwarding needs to enabled when establishing
-the SSH connection. For OpenSSH this option is '-X' and it is valuable
-to use compression of all data via '-C'.
+Ansys workbench (`runwb2`) an be invoked interactively on the login nodes of ZIH systems for short tasks.
+[X11 forwarding](../access/ssh_login.md#x11-forwarding) needs to enabled when establishing the SSH
+connection. For OpenSSH the corresponding option is `-X` and it is valuable to use compression of
+all data via `-C`.
-```
-# Connect to taurus, e.g. ssh -CX
-module load ANSYS/VERSION
-runwb2
+```console
+# SSH connection established using -CX
+marie@login$ module load ANSYS/<version>
+marie@login$ runwb2
```
-If more time is needed, a CPU has to be allocated like this (see topic
-batch systems **TODO LINK** (BatchSystems) for further information):
+If more time is needed, a CPU has to be allocated like this (see
+[batch systems Slurm](../jobs_and_resources/slurm.md) for further information):
+```console
+marie@login$ module load ANSYS/<version>
+marie@login$ srun -t 00:30:00 --x11=first [SLURM_OPTIONS] --pty bash
+[...]
+marie@login$ runwb2
```
-module load ANSYS/VERSION
-srun -t 00:30:00 --x11=first [SLURM_OPTIONS] --pty bash
-runwb2
-```
-
-**Note:** The software NICE Desktop Cloud Visualization (DCV) enables to
-remotly access OpenGL-3D-applications running on taurus using its GPUs
-(cf. virtual desktops **TODO LINK** (Compendium.VirtualDesktops)). Using ANSYS
-together with dcv works as follows:
-
-- Follow the instructions within virtual
- desktops **TODO LINK** (Compendium.VirtualDesktops)
-```
-module load ANSYS
-```
+!!! hint "Better use DCV"
-```
-unset SLURM_GTIDS
-```
+ The software NICE Desktop Cloud Visualization (DCV) enables to
+ remotly access OpenGL-3D-applications running on ZIH systems using its GPUs
+ (cf. [virtual desktops](virtual_desktops.md)).
-- Note the hints w.r.t. GPU support on dcv side
+Ansys can be used under DCV to make use of GPU acceleration. Follow the instructions within
+[virtual desktops](virtual_desktops.md) to set up a DCV session. Then, load a Ansys module, unset
+the environment variable `SLURM_GTIDS`, and finally start the workbench:
-```
-runwb2
+```console
+marie@gpu$ module load ANSYS
+marie@gpu$ unset SLURM_GTIDS
+marie@gpu$ runwb2
```
### Using Workbench in Batch Mode
-The ANSYS workbench (runwb2) can also be used in a batch script to start
-calculations (the solver, not GUI) from a workbench project into the
-background. To do so, you have to specify the -B parameter (for batch
-mode), -F for your project file, and can then either add different
-commands via -E parameters directly, or specify a workbench script file
-containing commands via -R.
+The Ansys workbench (`runwb2`) can also be used in a job file to start calculations (the solver,
+not GUI) from a workbench project into the background. To do so, you have to specify the `-B`
+parameter (for batch mode), `-F` for your project file, and can then either add different commands via
+`-E parameters directly`, or specify a workbench script file containing commands via `-R`.
-**NOTE:** Since the MPI library that ANSYS uses internally (Platform
-MPI) has some problems integrating seamlessly with SLURM, you have to
-unset the enviroment variable SLURM_GTIDS in your job environment before
-running workbench. An example batch script could look like this:
+??? example "Ansys Job File"
+ ```bash
#!/bin/bash
#SBATCH --time=0:30:00
#SBATCH --nodes=1
#SBATCH --ntasks=2
#SBATCH --mem-per-cpu=1000M
+ unset SLURM_GTIDS # Odd, but necessary!
- unset SLURM_GTIDS # Odd, but necessary!
-
- module load ANSYS/VERSION
+ module load ANSYS/<version>
runwb2 -B -F Workbench_Taurus.wbpj -E 'Project.Update' -E 'Save(Overwrite=True)'
#or, if you wish to use a workbench replay file, replace the -E parameters with: -R mysteps.wbjn
+ ```
### Running Workbench in Parallel
-Unfortunately, the number of CPU cores you wish to use cannot simply be
-given as a command line parameter to your runwb2 call. Instead, you have
-to enter it into an XML file in your home. This setting will then be
-used for all your runwb2 jobs. While it is also possible to edit this
-setting via the Mechanical GUI, experience shows that this can be
-problematic via X-Forwarding and we only managed to use the GUI properly
-via DCV **TODO LINK** (DesktopCloudVisualization), so we recommend you simply edit
-the XML file directly with a text editor of your choice. It is located
+Unfortunately, the number of CPU cores you wish to use cannot simply be given as a command line
+parameter to your `runwb2` call. Instead, you have to enter it into an XML file in your `home`
+directory. This setting will then be **used for all** your `runwb2` jobs. While it is also possible
+to edit this setting via the Mechanical GUI, experience shows that this can be problematic via
+X11-forwarding and we only managed to use the GUI properly via [DCV](virtual_desktops.md), so we
+recommend you simply edit the XML file directly with a text editor of your choice. It is located
under:
-'$HOME/.mw/Application Data/Ansys/v181/SolveHandlers.xml'
+`$HOME/.mw/Application Data/Ansys/v181/SolveHandlers.xml`
-(mind the space in there.) You might have to adjust the ANSYS Version
-(v181) in the path. In this file, you can find the parameter
+(mind the space in there.) You might have to adjust the Ansys version
+(here `v181`) in the path to your preferred version. In this file, you can find the parameter
- <MaxNumberProcessors>2</MaxNumberProcessors>
+`<MaxNumberProcessors>2</MaxNumberProcessors>`
-that you can simply change to something like 16 oder 24. For now, you
-should stay within single-node boundaries, because multi-node
-calculations require additional parameters. The number you choose should
-match your used --cpus-per-task parameter in your sbatch script.
+that you can simply change to something like 16 oder 24. For now, you should stay within single-node
+boundaries, because multi-node calculations require additional parameters. The number you choose
+should match your used `--cpus-per-task` parameter in your job file.
## COMSOL Multiphysics
-"[COMSOL Multiphysics](http://www.comsol.com) (formerly FEMLAB) is a
-finite element analysis, solver and Simulation software package for
-various physics and engineering applications, especially coupled
-phenomena, or multiphysics."
-[\[http://en.wikipedia.org/wiki/COMSOL_Multiphysics Wikipedia\]](
- http://en.wikipedia.org/wiki/COMSOL_Multiphysics Wikipedia)
+[COMSOL Multiphysics](http://www.comsol.com) (formerly FEMLAB) is a finite element analysis, solver
+and Simulation software package for various physics and engineering applications, especially coupled
+phenomena, or multiphysics.
-Comsol may be used remotely on ZIH machines or locally on the desktop,
-using ZIH license server.
+COMSOL may be used remotely on ZIH systems or locally on the desktop, using ZIH license server.
-For using Comsol on ZIH machines, the following operating modes (see
-Comsol manual) are recommended:
+For using COMSOL on ZIH systems, we recommend the interactive client-server mode (see COMSOL
+manual).
-- Interactive Client Server Mode
+### Client-Server Mode
-In this mode Comsol runs as server process on the ZIH machine and as
-client process on your local workstation. The client process needs a
-dummy license for installation, but no license for normal work. Using
-this mode is almost undistinguishable from working with a local
-installation. It works well with Windows clients. For this operation
-mode to work, you must build an SSH tunnel through the firewall of ZIH.
-For further information, see the Comsol manual.
+In this mode, COMSOL runs as server process on the ZIH system and as client process on your local
+workstation. The client process needs a dummy license for installation, but no license for normal
+work. Using this mode is almost undistinguishable from working with a local installation. It also works
+well with Windows clients. For this operation mode to work, you must build an SSH tunnel through the
+firewall of ZIH. For further information, please refer to the COMSOL manual.
-Example for starting the server process (4 cores, 10 GB RAM, max. 8
-hours running time):
+### Usage
- module load COMSOL
- srun -c4 -t 8:00 --mem-per-cpu=2500 comsol -np 4 server
+??? example "Server Process"
-- Interactive Job via Batchsystem SLURM
+ Start the server process with 4 cores, 10 GB RAM and max. 8 hours running time using an
+ interactive Slurm job like this:
-<!-- -->
+ ```console
+ marie@login$ module load COMSOL
+ marie@login$ srun -n 1 -c 4 --mem-per-cpu=2500 -t 8:00 comsol -np 4 server
+ ```
- module load COMSOL
- srun -n1 -c4 --mem-per-cpu=2500 -t 8:00 --pty --x11=first comsol -np 4
+??? example "Interactive Job"
+
+ If you'd like to work interactively using COMSOL, you can request for an interactive job with,
+ e.g., 4 cores and 2500 MB RAM for 8 hours and X11 forwarding to open the COMSOL GUI:
+
+ ```console
+ marie@login$ module load COMSOL
+ marie@login$ srun -n 1 -c 4 --mem-per-cpu=2500 -t 8:00 --pty --x11=first comsol -np 4
+ ```
-Man sollte noch schauen, ob das Rendering unter Options -> Preferences
--> Graphics and Plot Windows auf Software-Rendering steht - und dann
-sollte man campusintern arbeiten knnen.
+ Please make sure, that the option *Preferences* --> Graphics --> *Renedering* is set to *software
+ rendering*. Than, you can work from within the campus network.
-- Background Job via Batchsystem SLURM
+??? example "Background Job"
-<!-- -->
+ Interactive working is great for debugging and setting experiments up. But, if you have a huge
+ workload, you should definitively rely on job files. I.e., you put the necessary steps to get
+ the work done into scripts and submit these scripts to the batch system. These two steps are
+ outlined:
+ 1. Create a [job file](../jobs_and_resources/slurm.md#job-files), e.g.
+ ```bash
#!/bin/bash
#SBATCH --time=24:00:00
#SBATCH --nodes=2
@@ -251,21 +242,33 @@ sollte man campusintern arbeiten knnen.
module load COMSOL
srun comsol -mpi=intel batch -inputfile ./MyInputFile.mph
-
-Submit via: `sbatch <filename>`
+ ```
## LS-DYNA
-Both, the shared memory version and the distributed memory version (mpp)
-are installed on all machines.
+[LS-DYNA](https://www.dynamore.de/de) is a general-purpose, implicit and explicit FEM software for
+nonlinear structural analysis. Both, the shared memory version and the distributed memory version
+(`mpp`) are installed on ZIH systems.
+
+You need a job file (aka. batch script) to run the MPI version.
-To run the MPI version on Taurus or Venus you need a batchfile (sumbmit
-with `sbatch <filename>`) like:
+??? example "Minimal Job File"
+ ```bash
#!/bin/bash
- #SBATCH --time=01:00:00 # walltime
- #SBATCH --ntasks=16 # number of processor cores (i.e. tasks)
+ #SBATCH --time=01:00:00 # walltime
+ #SBATCH --ntasks=16 # number of processor cores (i.e. tasks)
#SBATCH --mem-per-cpu=1900M # memory per CPU core
-
+
module load ls-dyna
srun mpp-dyna i=neon_refined01_30ms.k memory=120000000
+ ```
+
+ Submit the job file to the batch system via
+
+ ```console
+ marie@login$ sbatch <filename>
+ ```
+
+ Please refer to the section [Slurm](../jobs_and_resources.md/slurm.md) for further details and
+ options on the batch system as well as monitoring commands.
diff --git a/Compendium_attachments/FEMSoftware/ABAQUS-SLURM.pdf b/doc.zih.tu-dresden.de/docs/software/misc/ABAQUS-SLURM.pdf
similarity index 100%
rename from Compendium_attachments/FEMSoftware/ABAQUS-SLURM.pdf
rename to doc.zih.tu-dresden.de/docs/software/misc/ABAQUS-SLURM.pdf
diff --git a/Compendium_attachments/FEMSoftware/Rot-modell-BenjaminGroeger.inp b/doc.zih.tu-dresden.de/docs/software/misc/Rot-modell-BenjaminGroeger.inp
similarity index 100%
rename from Compendium_attachments/FEMSoftware/Rot-modell-BenjaminGroeger.inp
rename to doc.zih.tu-dresden.de/docs/software/misc/Rot-modell-BenjaminGroeger.inp
diff --git a/doc.zih.tu-dresden.de/wordlist.aspell b/doc.zih.tu-dresden.de/wordlist.aspell
index 038262ca7b5a4418ceefb66b0d14f57d61582609..053c349ba619d18174a0784066fbc68618eaf8ce 100644
--- a/doc.zih.tu-dresden.de/wordlist.aspell
+++ b/doc.zih.tu-dresden.de/wordlist.aspell
@@ -5,6 +5,7 @@ Amber
Amdahl's
analytics
anonymized
+Ansys
APIs
AVX
BeeGFS
@@ -17,11 +18,13 @@ CCM
ccNUMA
centauri
CentOS
+CFX
cgroups
checkpointing
Chemnitz
citable
CLI
+COMSOL
conda
CPU
CPUID
@@ -36,6 +39,7 @@ dataframes
DataFrames
datamover
DataParallel
+DCV
DDP
DDR
DFG
@@ -80,6 +84,7 @@ gnuplot
GPU
GPUs
GROMACS
+GUIs
hadoop
haswell
HBM
@@ -112,9 +117,11 @@ JupyterHub
JupyterLab
Keras
KNL
+Kunststofftechnik
LAMMPS
LAPACK
lapply
+Leichtbau
LINPACK
linter
Linter
@@ -144,6 +151,8 @@ mpif
mpifort
mpirun
multicore
+multiphysics
+Multiphysics
multithreaded
Multithreading
MultiThreading
@@ -199,6 +208,7 @@ Pre
Preload
preloaded
preloading
+preprocessing
PSOCK
Pthreads
pymdownx
@@ -271,6 +281,7 @@ tracefile
tracefiles
transferability
Trition
+undistinguishable
unencrypted
uplink
userspace