documentation update and fixes

Data/README.md

 # Data Descriptions
 
-Purpose: list available data at the department of Meteorology and Geophysics.
+Purpose: list available data at the Department of Meteorology and Geophysics.
 
 Edit this file here or on [gitlab](https://gitlab.phaidra.org/imgw/computer-resources/-/blob/master/Data/README.md)
 

Dockerfile

+FROM python:3.10-buster
+ADD requirements.txt /requirements.txt
+RUN apt-get update -y \
+ && apt-get install -y -qq graphviz sshpass openssh-client rsync \
+ && pip install -r requirements.txt

Fortran/Compilers.md

 # Compiling & Building
 
-under development :)
+There are a number of tools to build an application. Very often `make` or `cmake` is used to build applications with different complexity.
 
-## Makefile
+![](../mkdocs/img/cmake-explanation.png)
 
+To use Make, you have to manually create the Makefile, but with CMake, the Makefile is automatically created.
 
-### Environmental Modules & Makefile
+## Environmental Modules & Makefile
 
 It is quite handy to use environmental modules and load different version of libraries, but how to make use of these ever changing **PATHs**. Take a look at the following examples to help with making your `Makefile` ready for modules.
 
-```
-# use the environmental variable $INCLUDE
+```makefile
+# use the environmental variable $INCLUDE or $CPATH
 # split the paths separated by :
 INC = $(subst :, ,$(INCLUDE))
+INC = $(subst :, ,$(CPATH))
 # add a -I/path/to/include
 INC := $(INC:%=-I%)
 # use the environmental variable $LIBRARY_PATH
@@ -20,4 +22,86 @@ LIBS = $(subst :, ,$(LIBRARY_PATH))
 LIBS := $(LIBS:%=-L%)
 ```
 
-With this code snippet in your Makefile you should be able to use environmental variables such as `$INCLUDE` or `$LIBRARY_PATH` efficiently. These paths adapt to your loaded modules.
+With this code snippet in your Makefile you should be able to use environmental variables such as `$INCLUDE`/`$CPATH` or `$LIBRARY_PATH` efficiently. These paths adapt to your loaded modules.
+
+When using `cmake` these paths are found automatically.
+
+important is when writing a makefile is to use tabs
+
+```makefile
+target: dependencies
+<tab>    command
+```
+
+here is an example of a makefile:
+
+```makefile title="Makefile"
+triangle: circle.o age.o
+    gfortran circle.o triangle.o -o triangle
+
+triangle.o: triangle.f90
+    gfortran -c triangle.f90
+
+circle.o: circle.f90
+    gfortran -c circle.f90  
+
+clean:
+    rm *.o triangle
+```
+
+```sh title="running the Makefile
+$ make
+gfortran -c circle.f90  
+gfortran -c triangle.f90
+gfortran circle.o triangle.o -o triangle
+$ ./triangle
+Enter the radius of the circle:  34
+Area of circle with radius   34.00 is      3631.68
+```
+
+or writing a cmake `CMakeLists.txt` file
+
+```cmake title="CMakeLists.txt"
+cmake_minimum_required(VERSION 3.10.0)
+
+enable_language(Fortran)
+
+project (triangle)
+
+add_executable(triangle triangle.f90 circle.f90)
+```
+
+building the application is a bit different
+
+```sh title='running cmake'
+$ mkdir build
+$ cd build
+$ cmake ...
+-- The Fortran compiler identification is GNU 13.2.1
+-- Detecting Fortran compiler ABI info
+-- Detecting Fortran compiler ABI info - done
+-- Check for working Fortran compiler: /usr/bin/f95 - skipped
+-- The C compiler identification is GNU 13.2.1
+-- The CXX compiler identification is GNU 13.2.1
+-- Detecting C compiler ABI info
+-- Detecting C compiler ABI info - done
+-- Check for working C compiler: /usr/bin/cc - skipped
+-- Detecting C compile features
+-- Detecting C compile features - done
+-- Detecting CXX compiler ABI info
+-- Detecting CXX compiler ABI info - done
+-- Check for working CXX compiler: /usr/bin/c++ - skipped
+-- Detecting CXX compile features
+-- Detecting CXX compile features - done
+-- Configuring done (0.6s)
+-- Generating done (0.0s)
+-- Build files have been written to: ./Fortran/build
+$ make
+[ 33%] Building Fortran object CMakeFiles/triangle.dir/circle.f90.o
+[ 66%] Building Fortran object CMakeFiles/triangle.dir/triangle.f90.o
+[100%] Linking Fortran executable triangle
+[100%] Built target triangle
+$ ./triangle
+Enter the radius of the circle:  34
+Area of circle with radius   34.00 is      3631.68
+```
\ No newline at end of file

Fortran/README.md

@@ -26,6 +26,15 @@ There are a few compilers, but most commonly GNU (Gfortran) and INTEL (ifort) ar
 | highest recommended optimisation | `-O3`| `-O2` maybe `-O3` or `-fast`|
 
 
+Please take a look into the compiler options guidelines from AMD or Intel, which might be very helpful for finding the right compiler flags for certain CPUs
+
+- Servers such as Aurora [AMD EPYC ZEN3](compiler-options-quick-ref-guide-epyc-7xx3-series-processors.pdf)
+- Servers such as VSC5, LUMI, ... [AMD EPYC ZEN4](compiler-options-quick-ref-guide-amd-epyc-9xx4-series-processors.pdf)
+- Servers such as SRVX1, JET, VSC4 [Intel](quick-reference-guide-intel-compilers-v19-1-final.pdf)
+
+more information on how to find good options can be found on the PRACE (Partnership for advanced computing in Europe) [website](https://prace-ri.eu/training-support/best-practice-guides/)
+![](https://prace-ri.eu/wp-content/uploads/logo-main.png)
+
 ## Intel Compiler
 
 from P. Seibert using ifort for the fastest code (srvx1):
@@ -51,24 +60,15 @@ gfortran man page says:
 Specify the length of record markers for unformatted files. Valid values for length are 4 and 8. Default is 4. This is different from previous versions of gfortran, which specified a default record marker length of 8 on most systems. If you want to read or write files compatible with earlier versions of gfortran, use -frecord-marker=8.
 ```
 
-# Trainings
-
-online training courses ?
-
 
 # Code Testing
 pFUnit - python Parallel Fortran Unit Testing Framework [GitHub](https://github.com/Goddard-Fortran-Ecosystem/pFUnit)
 
 
-# Documentation
-
-## Automatic Documentation Generation
-FORD: [Overview in Fortran Wiki](http://fortranwiki.org/fortran/show/FORD) | [Code on Github](https://github.com/cmacmackin/ford)
-
-## Documentation 
+# Documentation and other resources
 
-- Fortran wikibook [DE](https://de.wikibooks.org/wiki/Fortran) [EN](https://en.wikibooks.org/wiki/Fortran)
-
-### Books
 
+Fortran wikibook [DE](https://de.wikibooks.org/wiki/Fortran) [EN](https://en.wikibooks.org/wiki/Fortran)
 
+## Automatic Documentation Generation
+FORD: [Overview in Fortran Wiki](http://fortranwiki.org/fortran/show/FORD) | [Code on Github](https://github.com/cmacmackin/ford)

Fortran/check_cpu_extensions.sh

+#!/bin/bash
+# By MB
+# Check a compiled program and its dependencies on micro architecture extensions
+# this can be useful to understand if a certain program will be terminated because it does
+# not support the correct architecture. and its libraries too.
+
+
+install() {
+    echo "Downloading elfx86exts tool ..."
+    curl -s -L https://github.com/pkgw/elfx86exts/releases/download/elfx86exts%400.6.2/elfx86exts-0.6.2-x86_64-unknown-linux-gnu.tar.gz | tar xvz -C /tmp
+}
+
+dependencies(){
+    combined=""
+    while IFS="\n" read ilib
+    do
+        # is there a path?
+        nobjects=$(echo "$ilib" | wc -w)
+        if [ $nobjects -eq 4 ]; then
+            # libeccodes.so => /usr/local/lib64/libeccodes.so (0x00007f12b462b000)
+            ilibpath=$(echo "$ilib" | cut -d' ' -f3)
+            ilibname=$(echo "$ilib" | cut -d' ' -f1)
+            if [ -e "$ilibpath" ]; then
+                echo "-- dependency: $ilibname"
+                ilibextensions=$($CMD "$ilibpath" 2>&1 | grep "Instruction set extensions used:" | sed "s/Instruction set extensions used:/${LIBNAME}/")
+                echo "$ilibextensions"
+                combined="$combined $ilibextensions"
+            fi
+        fi
+        echo "------------------------------------------------------------"
+    done < <(ldd "$1")
+    echo "All combined extensions found:"
+    ALL_COMBINED=$(echo "$combined" | tr -d , | tr ' ' '\n'| sort -u | tr '\n' ' ')
+    echo "$ALL_COMBINED"
+    echo
+}
+
+CMD=/tmp/elfx86exts
+#
+# check local executable
+#
+if [ ! -e "$CMD" ]; then
+    install
+fi
+echo "using: $CMD"
+
+if [ $# -ne 1 ]; then
+    cat <<EOF
+CPU micro architecture tool
+
+Usage: $0 [EXECUTABLE/LIBRARY]
+
+Please supply an executable or library to be analysed.
+EOF
+    exit 1
+fi
+
+if [ ! -e "$1" ]; then
+    echo "Error: $1"
+    exit 1
+fi
+
+file_type=$(file "$1")
+
+if echo "$file_type"| grep -q executable; then
+    echo "Analysing executable: $1"
+    echo "$file_type"
+    echo -------------------------------------------------------------
+    echo Analysing: "$1"
+    $CMD "$1"
+    echo -------------------------------------------------------------
+    echo Analysing: dependencies
+    dependencies "$1"
+    echo -------------------------------------------------------------
+else
+    echo "Analysing library: $1"
+    echo "$file_type"
+    echo -------------------------------------------------------------
+    echo Analysing: "$1"
+    $CMD "$1"
+    echo -------------------------------------------------------------
+fi
+
+if command -v lscpu; then
+    echo "Your current CPU:"
+    lscpu | grep -E 'Model name|Socket|Thread|NUMA|CPU\(s\)' 
+    lscpu | grep -E 'Flags' | grep --color -iE "$(echo $ALL_COMBINED | tr ' ' '|')"
+    echo -------------------------------------------------------------
+fi

Fortran/circle.f90

+MODULE Circle
+   !---------------------------------------------------------------------
+   !
+   !  Module containing definitions of variables needed to
+   !  compute the area of a circle of radius r
+   !
+   !---------------------------------------------------------------------
+   REAL, PARAMETER :: Pi = 3.1415927
+   REAL :: radius
+END MODULE Circle

Fortran/triangle.f90

+PROGRAM Area
+!---------------------------------------------------------------------
+!
+!  This program computes the area of a circle given the input radius
+!
+!  Uses:  MODULE Circle
+!         FUNCTION Area_Circle (r)
+!
+!---------------------------------------------------------------------
+   USE Circle, ONLY : radius
+   IMPLICIT NONE
+
+   INTERFACE
+      FUNCTION Area_Circle (r)
+         REAL, INTENT(IN) :: r
+      END FUNCTION Area_Circle
+   END INTERFACE
+
+
+!  Prompt user for radius of circle
+   write(*, '(A)', ADVANCE = "NO") "Enter the radius of the circle:  "
+   read(*,*) radius
+
+! Write out area of circle using function call
+   write(*,100) "Area of circle with radius", radius, " is", &
+      Area_Circle(radius)
+100 format (A, 2x, F6.2, A, 2x, F11.2)
+
+END PROGRAM Area
+!-----Area_Circle----------------------------------------------------
+!
+!  Function to compute the area of a circle of given radius
+!
+!---------------------------------------------------------------------
+FUNCTION Area_Circle(r)
+   USE Circle, ONLY : Pi
+
+   IMPLICIT NONE
+   REAL :: Area_Circle
+   REAL, INTENT(IN) :: r
+
+   Area_Circle = Pi * r * r
+
+END FUNCTION Area_Circle

Getting Started.md

@@ -19,6 +19,7 @@ Tasks to complete for newcomers, it is recommended that you print this page an t
  - Login in to all servers:
       * [ ] srvx1 .img.univie.ac.at
       * [ ] srvx8
+      * [ ] aurora
       * [ ] jet01/jet02
       * [ ] (optional) connect to vsc5.vsc.ac.at
 
@@ -46,4 +47,4 @@ The Department of Meteorology and Geophysics has access to the following computi
 - Vienna Scientific Cluster ([VSC](VSC.md))
 - European Center for Medium-Range Weather Forecast ([ECMWF](ECMWF.md))
 
-Please read about access, hardware and quotas at these different resources. A good starting point is [here](./Servers/)
\ No newline at end of file
+Please read about access, hardware and quotas at these different resources. A good starting point is [here](./Servers/README.md)
\ No newline at end of file

Latex/README.md

@@ -5,7 +5,7 @@
 What you need to get started:
 
 1. A latex distribution, e.g. texlive or Miktex
-    * Or a online latex service, e.g. [Overleaf](www.overleaf.de), [latex4technics](https://www.latex4technics.com)
+    * Or a online latex service, e.g. [Overleaf](https://www.overleaf.de), [latex4technics](https://www.latex4technics.com)
 2. An Editor, e.g. TexStudio or Texshop, ...
 3. Examples:
     * Open [Seminararbeit.tex ](Seminararbeit.tex) or as [PDF](Seminararbeit.pdf) or online [on Overleaf](https://de.overleaf.com/read/whhnjmbwsvpy)

Python/README.md

@@ -131,6 +131,6 @@ Ever needed to backup a conda environment or copy from a colleague or designing
 You just need to add a configuration option and then you can open the Dashboard in any Jupyterhub. Works on SRVX1 and JET.
 
 ## Q: How to profile memory and exeution time of functions?
-[Profile](/QA-009-Memory-Profiling.ipynb)
+[Profile](QA-009-Memory-Profiling.ipynb)
 
 If you need to get a better understanding of you functions memory and execution time, try these profiling options.
\ No newline at end of file

README.md

@@ -5,18 +5,26 @@
 
 Find help here with your computer related problems. A mkdocs rendered version is available here: [wolke](https://wolke.img.univie.ac.at/documentation/general/index.html)
 
+
+    🚧🚧🚧🚧🚧🚧🚧🚧🚧🚧🚧
+    Please note that this documentation is under active development and things might shift a bit.
+    🚧🚧🚧🚧🚧🚧🚧🚧🚧🚧🚧
+
 Search with the top bar or go through the directories:
 
-- [Python related Problems](./Python/)
-- [SSH, VNC, VPN related Problems](./SSH-VPN-VNC/)
-- [Editors](./Editors/) and [remote connection](./SSH-VPN-VNC/)
-- [Data availability and location](./Data/)
+- [Python related Problems](./Python/README.md)
+- [SSH, VNC, VPN related Problems](./SSH-VPN-VNC/README.md)
+- [Editors](./Editors/) and [remote connection](./SSH-VPN-VNC/README.md)
+- [Data availability and location](./Data/README.md)
 - [Git related problems](https://gitlab.phaidra.org/imgw/computer-resources/-/issues)
 
-for new employees or students, you could start with the [Getting Started](./Getting%20Started.md) section
+for new employees or students, you could start with the [Getting Started](./Getting%20Started.md) section or the [Student](./Students.md) section.
+
+A useful summary of all resources is given by the [IMGW Cheat sheet](./mkdocs/imgw-cheatsheet.pdf)
+
 
-If you care to participate please do so.
+**If you care to participate please do so:**
 
-- Raise an [Issue on Gitlab](https://gitlab.phaidra.org/imgw/computer-resources/-/issues) :earth_africa:
+- Raise an [Issue on Gitlab](https://gitlab.phaidra.org/imgw/computer-resources/-/issues/?sort=created_date&state=all&first_page_size=20) :earth_africa:
 - Give some feedback ([mail](mailto:it.img-wien@univie.ac.at), [mattermost](https://discuss.phaidra.org/imgw/channels/bugs)) :snowman:
 - Write to [individual members of the department](https://img.univie.ac.at/en/about-us/staff/). :frog:

SSH-VPN-VNC/README.md

@@ -6,7 +6,7 @@ Please find here some details on how to connect using SSH or VPN or VNC. And som
 Please use these methods to access the servers:
 
 1. Connect using [SSH](SSH.md) or [MOSH](https://mosh.org/#) (Mobile Secure Shell)
-2. Connect using [TeachingHub](../TeachingHub.md) or [ResearchHub](../Jet-Cluster.md#jupyterhub)
+2. Connect using [TeachingHub](../TeachingHub.md) or [ResearchHub](../Servers/JET.md#jupyterhub)
 3. Connect using [VNC](VNC.md)
 4. Access from outside the UNI, [VPN](VPN.md)
 

SSH-VPN-VNC/connect2vpn

 #!/bin/bash
 # By Michael Blaschek
-# Date 23.03.2021
+# Date 31.07.2023
 # CC BY 4.0 International
 # University of Vienna, Austria
+# Department of Meteorology and Geophysics
+# img.univie.ac.at
 
 # Description:
 # Connect to VPN from the University of Vienna
-# Watch connection
+# You need to download the F5 VPN Client from the ZID website (zid.univie.ac.at/vpn)
+# The executable works only for VPN@UNIVIE. Follow the instructions on the ZID website
+# on how to install the package depending on your Linux distro.
+# Maybe this download link works directly:
+# https://vpn.univie.ac.at/public/share/BIGIPLinuxClient.tgz
+#
+# Steps:
+# 1. run connect2vpn script
+# 1.1. Checks if it can find f5fpc exe 
+# 1.2. Asks for credentials
+# 1.3. Asks for TOTP Code
+# 1.4. Watch connection
 
 vpninfos() {
 	infos=$(f5fpc --info)
@@ -38,6 +51,9 @@ else
 	echo "[VPN] $(f5fpc -v | head -n1)"
 fi
 
+echo
+echo "[VPN] Notice: This script will continue to run in foreground!"
+echo
 read -p "[VPN] Full (1) or split (None) tunnel? (1/None): " REPLY
 if [ "$REPLY" == "" ]; then
 	echo "[VPN] Connecting split-tunnel ..."
@@ -60,7 +76,8 @@ do
 		fi
 		echo "[VPN] Starting connection ..."
 		if [ -z "$VPN_PWD" ]; then
-			read -p "[VPN] u:account password:" VPN_PWD
+			read -sp "[VPN] u:account password:" VPN_PWD
+			echo
 		fi
 		read -p "[VPN] TOTP Code (6 digits/empty):" VPN_TOTP
 		if [ -n "$VPN_TOTP" ]; then

Servers/JET.md

@@ -142,7 +142,7 @@ enstools/v2020.11  enstools/v2021.11  teleport/10.1.4
 --------- /opt/spack-jet01/share/spack/lmod/linux-rhel8-skylake_avx512 ---------
 anaconda3/2020.11-gcc-8.3.1-bqubbbt  
 ```
-on how to use environment modules go to [Using Environment Modules](Misc/Environment-Modules.md)
+on how to use environment modules go to [Using Environment Modules](../Misc/Environment-Modules.md)
 
 
 ## Jupyterhub

Servers/README.md

@@ -16,7 +16,7 @@ Locations:
 - Staff + Remote Desktop [SRVX8](SRVX8.md)
 - Staff + Remote Desktop + Jupyterhub [Jet Cluster](JET.md)
 - Staff + Students, Jupyterhub called [TeachingHub](../TeachingHub.md)
-- Staff [Vienna Scientific Cluster (VSC)](VSC.md)
+- Staff [Vienna Scientific Cluster (VSC)](../VSC.md)
     - [VSC Training](https://vsc.ac.at/training)
     - [VSC Trainings @ IMGW](https://gitlab.phaidra.org/imgw/trainings-course)
 
@@ -25,42 +25,12 @@ Locations:
 
 ## How to connect from Home or Abroad?
 
-```graphviz dot attack_plan.png
-digraph Servers {
-    users [shape=none image="./mkdocs/img/student_sm.png" label="User" labelloc="b" height="1" imagepos="tc"]
-    srvx1 [shape=none image="./mkdocs/img/server_sm.png" label="SRVX1" labelloc="b" height="1" imagepos="tc"]
-    srvx8 [shape=none image="./mkdocs/img/server_sm.png" label="SRVX8" labelloc="b" height="1" imagepos="tc"]
-    jet [shape=none image="./mkdocs/img/server_sm.png" label="JET" labelloc="b" height="1" imagepos="tc"]
-    VPN [shape=none image="./mkdocs/img/local-area-network_sm.png" label="VPN" labelloc="b" height="1" imagepos="tc"]
-    vsc [shape=none image="./mkdocs/img/logo_vsc_sm.png" label="VSC" labelloc="b" height=".8" imagepos="tc"]
-
-    users -> srvx1
-    users -> VPN
-    srvx1 -> srvx8
-    srvx1 -> jet
-    srvx1 -> vsc
-    VPN -> jet
-    VPN -> vsc
-    VPN -> srvx8
-}
-```
+![IMGW Connection Diagramm](../mkdocs/img/IMGW-connection-diagram.png)
 
 ## How to connect from the Office?
 
-```graphviz dot attack_plan.png
-digraph Servers {
-    users [shape=none image="./mkdocs/img/student_sm.png" label="User" labelloc="b" height="1" imagepos="tc"]
-    srvx1 [shape=none image="./mkdocs/img/server_sm.png" label="SRVX1" labelloc="b" height="1" imagepos="tc"]
-    srvx8 [shape=none image="./mkdocs/img/server_sm.png" label="SRVX8" labelloc="b" height="1" imagepos="tc"]
-    jet [shape=none image="./mkdocs/img/server_sm.png" label="JET" labelloc="b" height="1" imagepos="tc"]
-    vsc [shape=none image="./mkdocs/img/logo_vsc_sm.png" label="VSC" labelloc="b" height=".8" imagepos="tc"]
-
-    users -> srvx1
-    users -> srvx8
-    users -> jet
-    users -> vsc
-}
-```
+![IMGW Connection Diagramm2](../mkdocs/img/IMGW-connection-diagram2.png)
+
 
 # Containers & Services
 

Servers/SRVX8.md

@@ -8,7 +8,7 @@
 Steps:
 
 1. Request access
-2. Access using SSH - [How to SSH / VNC / VPN](SSH-VPN-VNC/README.md)
+2. Access using SSH - [How to SSH / VNC / VPN](../SSH-VPN-VNC/README.md)
 
 ## System Information
 
@@ -55,11 +55,11 @@ Major Libraries:
 
 These software libraries are usually handled by environment modules.
 
-![](./mkdocs/img/envmodules.png)
+![](../mkdocs/img/envmodules.png)
 
 ## Currently installed modules
 
-on how to use environment modules go to [Using Environment Modules](Misc/Environment-Modules.md)
+on how to use environment modules go to [Using Environment Modules](../Misc/Environment-Modules.md)
 
 ```sh title="Environment Modules"
 module av

mkdocs.yml

+#
+# mkdocs serve -a localhost:3000 --dirtyreload
+#
+
 site_name: Computer Resources @ IMGW
-# default is ./site/
+
 # could change this to /var/www/html/docs
-site_url: "https://wolke.img.univie.ac.at/documentation/general/"
+site_url: "https://wolke.img.univie.ac.at/doc/general/"
 site_dir: "./site/"
-# site_dir: "/var/www/html/documentation/general/"
 docs_dir: "."
 repo_url: https://gitlab.phaidra.org/imgw/computer-resources
 repo_name: IMGW/Computer-Resources
+
+
 # this makes relative links  valid
 use_directory_urls: false
+
 # this adds the feature to directly edit the file on gitlab
+
 edit_uri: edit/master/
-copyright: Copyright © 2022 - 2022 IMGW, Michael Blaschek
+
+copyright: Copyright © 2023 - 2023 IMGW, Michael Blaschek
 
 theme:
   name: material
@@ -20,9 +28,13 @@ theme:
   features:
     - navigation.indexes
     - navigation.top
+    - content.code.copy
   logo: mkdocs/img/favicon.ico
   favicon: mkdocs/img/favicon.ico
   custom_dir: mkdocs/overrides
+  font:
+    text: Roboto
+    code: Roboto Mono
 plugins:
   - same-dir
   - search