From d135edf6073e898121ecd036d9dedea31003a86a Mon Sep 17 00:00:00 2001
From: LocNgu <loc.nguyen_dang_duc@tu-dresden.de>
Date: Wed, 23 Jun 2021 13:36:28 +0200
Subject: [PATCH] Add missing markdown fixes

---
 .../docs/software/FEMSoftware.md              | 85 ++++++++++++++-----
 1 file changed, 64 insertions(+), 21 deletions(-)

diff --git a/doc.zih.tu-dresden.de/docs/software/FEMSoftware.md b/doc.zih.tu-dresden.de/docs/software/FEMSoftware.md
index 6566d8302..3c0250c19 100644
--- a/doc.zih.tu-dresden.de/docs/software/FEMSoftware.md
+++ b/doc.zih.tu-dresden.de/docs/software/FEMSoftware.md
@@ -24,30 +24,56 @@ The detailed Abaqus documentation can be found at
 abaqus **TODO LINK MISSING** (only accessible from within the
 TU Dresden campus net).
 
-\*Example - Thanks to Benjamin Groeger, Inst. f. Leichtbau und
-Kunststofftechnik) \*
+**Example - Thanks to Benjamin Groeger, Inst. f. Leichtbau und
+Kunststofftechnik) **
 
-1\. Prepare an Abaqus input-file (here the input example from Benjamin)
+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
+2. Prepare a batch script on taurus like this
 
 ```
-#!/bin/bash<br /><br />### Thanks to Benjamin Groeger, Institut fuer Leichtbau und Kunststofftechnik, 38748<br />### runs on taurus and needs ca 20sec with 4cpu<br />### generates files:<br />###  yyyy.com<br />###  yyyy.dat<br />###  yyyy.msg<br />###  yyyy.odb<br />###  yyyy.prt<br />###  yyyy.sim<br />###  yyyy.sta<br /><br />#SBATCH --nodes=1  ### with &gt;1 node abaqus needs a nodeliste<br />#SBATCH --ntasks-per-node=4<br />#SBATCH --mem=500  ### memory (sum)<br />#SBATCH --time=00:04:00<br />### give a name, what ever you want<br />#SBATCH --job-name=yyyy<br />### you get emails when the job will finished or failed<br />### set your right email<br />#SBATCH --mail-type=END,FAIL<br />#SBATCH --mail-user=xxxxx.yyyyyy@mailbox.tu-dresden.de<br />### set your project<br />#SBATCH -A p_xxxxxxx<br /><br />### Abaqus have its own MPI<br />unset SLURM_GTIDS<br /><br />### load and start<br />module load ABAQUS/2019<br />abaqus interactive input=Rot-modell-BenjaminGroeger.inp job=yyyy cpus=4 mp_mode=mpi<br /><br />
+#!/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 &gt;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
+
 ```
 
-3\. Start the batch script (name of our script is
+3. Start the batch script (name of our script is
 "batch-Rot-modell-BenjaminGroeger")
 
 ```
-sbatch batch-Rot-modell-BenjaminGroeger      ---&gt; you will get a jobnumber = JobID (for example 3130522)
+sbatch batch-Rot-modell-BenjaminGroeger      --->; you will get a jobnumber = JobID (for example 3130522)
 ```
 
-4\. Control the status of the job
+4. Control the status of the job
 
 ```
-squeue -u your_login     --&gt; in column "ST" (Status) you will find a R=Running or P=Pending (waiting for resources)
+squeue -u your_login     -->; in column "ST" (Status) you will find a R=Running or P=Pending (waiting for resources)
 ```
 
 ## ANSYS
@@ -64,7 +90,9 @@ modules **TODO LINK** (RuntimeEnvironment). To list the available versions and l
 particular ANSYS version, type
 
 ```
-module avail ANSYS<br />...<br />module load ANSYS/VERSION
+module avail ANSYS
+...
+module load ANSYS/VERSION
 ```
 
 In general, HPC-systems are not designed for interactive "GUI-working".
@@ -80,7 +108,8 @@ the SSH connection. For OpenSSH this option is '-X' and it is valuable
 to use compression of all data via '-C'.
 
 ```
-# Connect to taurus, e.g. ssh -CX<br />module load ANSYS/VERSION
+# Connect to taurus, e.g. ssh -CX
+module load ANSYS/VERSION
 runwb2
 ```
 
@@ -100,10 +129,20 @@ together with dcv works as follows:
 
 -   Follow the instructions within virtual
     desktops **TODO LINK** (Compendium.VirtualDesktops)
--   \<pre> module load ANSYS\</pre>
--   \<pre> unset SLURM_GTIDS\</pre>
+
+```
+module load ANSYS
+```
+
+```
+unset SLURM_GTIDS
+```
+
 -   Note the hints w.r.t. GPU support on dcv side
--   \<pre>runwb2\</pre>
+
+```
+runwb2
+```
 
 ### Using Workbench in Batch Mode
 
@@ -145,12 +184,12 @@ via DCV **TODO LINK** (DesktopCloudVisualization), so we recommend you simply ed
 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
 
-    &lt;MaxNumberProcessors&gt;2&lt;/MaxNumberProcessors&gt;
+    <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
@@ -159,13 +198,11 @@ match your used --cpus-per-task parameter in your sbatch script.
 
 ## COMSOL Multiphysics
 
-" [COMSOL Multiphysics](http://www.comsol.com) (formerly FEMLAB) is a
+"[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."
-[\[http://en.wikipedia.org/wiki/COMSOL_Multiphysics Wikipedia]
-([http://en.wikipedia.org/wiki/COMSOL_Multiphysics Wikipedia)
-\]
+[\[http://en.wikipedia.org/wiki/COMSOL_Multiphysics Wikipedia\]](http://en.wikipedia.org/wiki/COMSOL_Multiphysics Wikipedia)
 
 Comsol may be used remotely on ZIH machines or locally on the desktop,
 using ZIH license server.
@@ -224,4 +261,10 @@ are installed on all machines.
 To run the MPI version on Taurus or Venus you need a batchfile (sumbmit
 with `sbatch <filename>`) like:
 
-    #!/bin/bash<br />#SBATCH --time=01:00:00   # walltime<br />#SBATCH --ntasks=16   # number of processor cores (i.e. tasks)<br />#SBATCH --mem-per-cpu=1900M   # memory per CPU core<br /><br />module load ls-dyna<br />srun mpp-dyna i=neon_refined01_30ms.k memory=120000000
+    #!/bin/bash
+    #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
-- 
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