Review content

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

@@ -10,16 +10,18 @@ ParaView can be used in [interactive mode](#interactive-mode) as well as in
 [batch mode](#batch-mode-pvbatch). Both modes are documented in more details in the following
 subsections.
 
-!!! note WLOG ParaView module and Cluster
+!!! warning WLOG ParaView module and cluster
 
     Without loss of generality, we stick to a certain ParaView module (from a certain module
-    release) in the following documentation and provided examples. Do not blind copy the examples.
+    release) in the following documentation and provided examples. **Do not blind copy the
+    examples.**
     Furthermore, please **adopt the commands to your needs**, e.g., the concrete ParaView module you
     want to use.
 
-    The same holds for the cluster. The documentation refers to
-    [`Barnard`](../jobs_and_resources/hardware_overview.md#barnard). If you need to use ParaView on one of the other
-    cluster, this documentation should hold too.
+    The same holds for the cluster used in the documentation and examples. The documentation refers
+    to the cluster [`Barnard`](../jobs_and_resources/hardware_overview.md#barnard). If you want to
+    use ParaView on [one of the other clusters](../jobs_and_resources/hardware_overview.md), this
+    documentation should hold too.
 
 ### ParaView Modules
 
@@ -42,7 +44,7 @@ The command `module spider <module-name>` will show you, how to load a certain P
 
 ??? example "Example on how to load a ParaView module"
 
-    For example, to obtain information on how to properly load the `ParaView/5.10.1-mpi` module, you
+    For example, to obtain information on how to properly load the module `ParaView/5.10.1-mpi`, you
     need to invoke the `module spider` command as follows:
 
     ```console
@@ -55,17 +57,18 @@ The command `module spider <module-name>` will show you, how to load a certain P
     [...]
     ```
 
-    Obvisouly, the `ParaView/5.10.1-mpi` module is available within two releases and depends in
+    Obviously, the `ParaView/5.10.1-mpi` module is available within two releases and depends in
     both cases on the two modules `GCC/11.3.0` and `OpenMPI/4.1.4`. Without loss of generality, a
     valid command to load `ParaView/5.10.1-mpi` is
 
     ```console
-    marie@login$ module load release/23.10  GCC/11.3.0  OpenMPI/4.1.4
+    marie@login$ module load release/23.10 GCC/11.3.0 OpenMPI/4.1.4
     ```
 
 ### Interactive Mode
 
-There are three different ways of using ParaView interactively on ZIH systems:
+There are three different ways of using ParaView interactively on ZIH systems, which are described
+in more details in the following subsections:
 
 - [GUI via NICE DCV](#using-the-gui-via-nice-dcv)
 - [Client-Server mode with MPI-parallel off-screen-rendering](#using-client-server-mode-with-mpi-parallel-offscreen-rendering)
@@ -79,7 +82,7 @@ handling. First, you need to open a DCV session on the Visualization cluster (us
 profiles, then click on the *DCV* tile in the lower section named *Other*). Please
 find further instructions on how to start DCV on the [virtual desktops page](virtual_desktops.md).
 In your virtual desktop session, start a terminal (right-click on desktop ->
-Terminal), then load the ParaView module as usual and start the GUI:
+Terminal or *Activities -> Terminal*), then load the ParaView module as usual and start the GUI:
 
 ```console
 marie@dcv$ module load release/23.10 GCC/11.3.0 OpenMPI/4.1.4 ParaView/5.11.1-mpi
@@ -107,13 +110,13 @@ The *pvserver* can be run in parallel using MPI. To do so, load the desired Para
 start the `pvserver` executable in offscreen rendering mode within an interactive allocation via
 `srun`.
 
-???+ example "Start pvserver"
+???+ example "Start `pvserver`"
 
     Here, we ask for 8 MPI tasks on one node for 4 hours within an interactive allocation. Please
     adopt the time limit and ressources to your needs.
 
     ```console
-    marie@login$ module load release/23.10 GCC/11.3.0 OpenMPI/4.1.4 ParaView/5.10.1-mpi
+    marie@login$ module load release/23.10 GCC/11.3.0 OpenMPI/4.1.4 ParaView/5.11.1-mpi
     marie@login$ srun --nodes=1 --ntasks=8 --mem-per-cpu=2500 --time=04:00:00 --pty pvserver --force-offscreen-rendering
     srun: job 1730359 queued and waiting for resources
     srun: job 1730359 has been allocated resources
@@ -128,16 +131,16 @@ are printed.
 !!! tip "Custom port"
 
     If the default port `11111` is already in use, an alternative or custom port can be specified
-    via the commandline option `-sp=port` to `pvserver`.
+    via the commandline option `-sp=<PORT>` to `pvserver`.
 
 The output from `pvserver` contains the node name which your job and server runs on. However, since
 the node names of the cluster are not present in the public domain name system (only
 cluster-internally), you cannot just use this line as-is for connection with your client. Instead,
-you need to establish a so-called forward SSH tunnel to localhost. You first have to resolve the
-name to an IP address on ZIH systems using `host` in another SSH
-session. Then, the SSH tunnel can be created from your workstation. The following example will
-depict both steps: Resolve the IP of the compute node and finaly create a
-forward SSH tunnel to localhost on port 22222 (or what ever port is preferred).
+you need to establish a so-called forward SSH tunnel to your local host. You first have to resolve
+the name to an IP address on ZIH systems using `host` in another SSH session. Then, the SSH tunnel
+can be created from your workstation. The following example will
+depict both steps: Resolve the IP of the compute node and finally create a
+forward SSH tunnel to local host on port 22222 (or what ever port is preferred).
 
 ???+ example "SSH tunnel"
 
@@ -221,7 +224,7 @@ it into thinking your provided GL rendering version is higher than what it actua
     marie@login$ srun --ntasks=1 --cpus-per-task=1 --mem-per-cpu=2500 --pty --x11=first paraview
     ```
 
-### Batch Mode - pvbatch
+### Batch Mode (`pvbatch`)
 
 ParaView can run in batch mode, i.e., without opening the ParaView GUI, executing a Python script.
 This way, common visualization tasks can be automated. There are two Python interfaces: `pvpython`
@@ -232,7 +235,7 @@ parallel, if it was built using MPI.
 
     ParaView is shipped with a prebuild MPI library and **pvbatch has to be
     invoked using this very mpiexec** command. Make sure to not use `srun`
-    or `mpiexec` from another MPI module, e.g., check what `mpiexec` is in
+    or `mpiexec` from another MPI module, i.e., check what `mpiexec` is in
     the path:
 
     ```console
@@ -280,15 +283,13 @@ interactive allocation.
     salloc: Pending job allocation 336202
     salloc: job 336202 queued and waiting for resources
     salloc: job 336202 has been allocated resources
-    salloc: Granted job allocation 336202
-    salloc: Waiting for resource configuration
-    salloc: Nodes taurusi6605 are ready for job
+    [...]
 
     # Make sure to only use ParaView
     marie@compute$ module purge
     marie@compute$ module load release/23.10 GCC/11.3.0 OpenMPI/4.1.4 ParaView/5.11.1-mpi
 
-    # Go to working directory, e.g., workspace
+    # Go to working directory, e.g., your workspace
     marie@compute$ cd /path/to/workspace
 
     # Execute pvbatch using 16 MPI processes in parallel on allocated resources
@@ -316,7 +317,5 @@ and pass the option `--displays $CUDA_VISIBLE_DEVICES` to `pvbatch`.
     module purge
     module load release/23.10 GCC/11.3.0 OpenMPI/4.1.4 ParaView/5.11.1-mpi
 
-    mpiexec -n $SLURM_CPUS_PER_TASK --bind-to core pvbatch --mpi --displays $CUDA_VISIBLE_DEVICES --force-offscreen-rendering pvbatch-script.py
-    #or
     pvbatch --mpi --displays $CUDA_VISIBLE_DEVICES --force-offscreen-rendering pvbatch-script.py
     ```