1.2. Installation History

1.2.1. Remove message

touch ~/.sudo_as_admin_successful

1.2.6. How to create extension .foam with paraFoam -touch?

$ nano OpenFOAM/OpenFOAM-2.4.0/bin/paraFoam

# reader extension
extension=foam

1.2.7. Kate

sudo apt-get update
sudo apt-get install kate

Show line numbers:

Settings -> configure kate -> appearance -> borders

1.2.8. Dropbox

Ubuntu Software Centre then Daemon

sudo apt-get update  //update package list - need to log out and log in to restart Nautilius

1.2.9. Texmaker

sudo apt-get update
sudo apt-get install texlive-full
sudo apt-get install texmaker
http://www.artfiles.org/openoffice.org/contrib/dictionaries/en_GB.zip
Unzip the archive
cd /usr/share/hunspell
sudo cp -rv /home/apr207/Downloads/en_GB.dic .
sudo cp -rv /home/apr207/Downloads/en_GB.aff .

1.2.10. SSH

sudo apt-get install openssh-server
from laptop: ssh -XC user@IP address

Start ssh: sudo service ssh start
Stop ssh: service ssh stop

1.2.11. Gimp

Ubuntu Software Centre

(Evince gave an error)

1.2.12. Pointwise

Downloaded pw-V18.0R2-linux_x86_64-jre.sh
sh pw-V18.0R2-linux_x86_64-jre.sh
Next
Accept
/home/apr207/Pointwise/PointwiseV18.0R2 is installation directory
Run Pointwise
(Won't find license)
Specify license server
server: emps-pointwise
port: 2385

Added this to .bashrc:
# Pointwise
alias pointwise="/home/apr207/Pointwise/PointwiseV18.0R2/pointwise"

1.2.13. Tree

sudo apt-get install tree

1.2.14. LIGGGHTS

## [optional] 1. Install Voro++ 0.4.x by compiling
sudo apt install g++
cd ~
wget http://math.lbl.gov/voro++/download/dir/voro++-0.4.6.tar.gz
tar -zxvf voro++-0.4*.tar.gz
cd $HOME/voro++-0.4.*
make all
sudo make install
which voro++
# /usr/local/bin/voro++ <- comes up
#
## 2 Install Liggghts 3.x by compiling
## 2.1 Install Packages
sudo apt install git libvtk5-dev libeigen2-dev openmpi-bin openmpi-doc libopenmpi-dev
which mpirun
#/usr/bin/mpirun comes up
which mpic++
#/usr/bin/mpic++ comes up
## 2.2 Get Liggghts via Git
cd ~
git clone https://github.com/CFDEMproject/LIGGGHTS-PUBLIC $HOME/LIGGGHTS-PUBLIC3.6.0
## 2.3 Compiling Liggghts with VORONOI and jpg, png support
cd $HOME/LIGGGHTS-PUBLIC3.6.0/src
# [optional] if you want to use voro++ in LIGGGHTS:
make yes-voronoi
# [optional] if you need extra packages install with sudo make yes-packagename
gedit /$HOME/LIGGGHTS-PUBLIC3.6.0/src/MAKE/Makefile.ubuntuVTK
add "-DLAMMPS_JPEG -DLAMMPS_PNG" in line 32
add "-I/usr/include" in line 63
add "-ljpeg -lpng" in line 65
change line 73 to "VTK_INC = -I/usr/include/vtk-5.10"
change line 74 to "VTK_LIB = -lvtkCommon -lvtkFiltering -lvtkIO -lvtkParallel -lvtkGraphics"
# save and close gedit
# [optional] changes on the source code
make clean-all
make ubuntuVTK
# create system wide shortcut liggghts360 for compiled binary (I used to have different versions parallel)
sudo ln -s /$HOME/LIGGGHTS-PUBLIC3.6.0/src/lmp_ubuntuVTK /usr/bin/liggghts360
liggghts360

# Liggghts comes up, telling version, compiling date etc., press Ctr+d to quit
#
## [optional] 3. Install LPP for post processing (converts LIGGGHTS Dumps to vtk-files) - doesn't work?
cd ~
sudo apt-get install python-numpy
#already newest version
sudo git clone https://github.com/CFDEMproject/LPP.git $HOME/LPP
./install
gedit ~/.bashrc
#add:
alias lpp="python $HOME/LPP/src/lpp.py"
#sudo chown -R andrew:andrew LPP
#open new Terminal: lpp
#
## [optional] 4. Install Syntax Highlighting for xed (gedit)
cd ~
wget https://www.dropbox.com/s/78elqj4i2dn52wt/liggghts3.lang
sudo mv liggghts3.lang /usr/share/gtksourceview-3.0/language-specs
#
## [optional] 5. Install ParaView 5.0.1
sudo apt-get install paraview
# already newest version
## [optional] 6. Install GNUplot 5.0.3
sudo apt-get install gnuplot-x11
gnuplot
plot sin(x)
# window with sin graph comes up, press Ctr+d to quit.
#
## [optional] 7. Install Povray 3.7.1
# Alternative: http://www.conoce3000.com/html/espaniol/Apuntes/2014-06-20-CompilarInstalarPOV-Ray37LinuxMintCinnamon64bitsCompilarInstalarPOV-Ray37LinuxMintCinnamon64bits.php?Arch=20
cd ~
sudo apt-get install autoconf automake libboost-all-dev libboost-dev libopenexr-dev libsdl-dev zlib1g-dev libpng-dev libjpeg-dev libtiff-dev
git clone https://github.com/POV-Ray/povray.git $HOME/POV-Ray3.7
cd $HOME/POV-Ray3.7/unix
./prebuild.sh
cd ..
./configure COMPILED_BY="andrew"
make check
# windows with cup and cookies comes up, click picture
sudo make install
# done!

# Test LIGGHTS

Copy all tutorials to LIGGGHTS_User folder

cd $HOME/LIGGGHTS_User/chute_wear

liggghts360 < in.chute_wear

cd post

lpp dump*.chute

1.2.15. VIM

sudo apt-get install vim

1.2.16. INKSCAPE

sudo apt-get install inkscape

1.2.17. LAMMPS

sudo add-apt-repository ppa:gladky-anton/lammps
sudo apt-get update

sudo apt-get install lammps-daily

lammps-daily < in.lj

sudo apt-get update

sudo apt-get install lammps-daily-doc

1.2.18. CFMesh

Downloaded CFMesh:

https://sourceforge.net/projects/cfmesh/

Copied cfMesh-v1.1.2 to /home

Set environment to $ two (OpenFOAM version 2.4 - as this is installed on Rodrigo and is possible on Callisto - no instruction for 2.3.1)

$ ./Allwmake

Copy the tutorial files:

$ cp -rf tutorials $FOAM_RUN


$ file file.stl

file.stl: ASCII text

1.2.19. Mesh Lab

Ubuntu Software Centre

1.2.20. FreeCAD

Ubuntu Software Centre

1.2.21. Pizza.py

Downloaded Pizza.py from

https://sourceforge.net/projects/pizza-py/?source=typ_redirect

Extracted the file
Copied to /home

Added this to .bashrc

#Pizza.py
alias pizza="python -i $HOME/pizza/src/pizza.py"

1.2.22. Installed Redshift

Ubuntu Software Centre

1.2.23. Install Heekes CAD

Add heekscnc-devel PPA to your repositories list:

sudo add-apt-repository ppa:neomilium/heekscnc-devel

Update your packages list:

sudo apt-get update

1.2.24. Install HeeksCNC

sudo apt-get install heekscnc

1.2.25. Install Mendeley

Ubuntu Software Centre 64 bit version of Mendeley: https://www.mendeley.com/download-mendeley-desktop/ubuntu/instructions/ Install automatically

1.2.26. Install Pinta

Ubuntu Software Centre

1.2.27. Install Curl

sudo apt install curl

1.2.28. Check for Updates

To check for updates: Start > Software Updater

1.2.29. Check packages have been updated

/usr/lib/update-notifier/apt-check -p

1.2.30. Install Scipy stack

$ sudo apt-get install python-numpy python-scipy python-matplotlib ipython ipython-notebook python-pandas python-sympy python-nose

1.2.31. Remove gedit

Ubuntu Software Centre

1.2.32. Terminator

Ubuntu Software Centre

1.2.33. Sublime

sudo rpm -v --import https://download.sublimetext.com/sublimehq-rpm-pub.gpg

sudo dnf config-manager --add-repo https://download.sublimetext.com/rpm/stable/x86_64/sublime-text.repo

sudo dnf install sublime-text

Edit sublime_text.desktop

[Desktop Entry]
Encoding=UTF-8
Version=1.0
Type=Application
Name=Sublime Text
Icon=sublime_text.png
Path=/
Exec=/opt/sublime_text/sublime_text %f
StartupNotify=false
StartupWMClass=Sublime_text
OnlyShowIn=Unity;
X-UnityGenerated=true

1.2.34. OpenFOAM 2.1.x

FROM: http://openfoamwiki.net/index.php/Installation/Linux/OpenFOAM-2.1.x/Ubuntu

Up to step 7.

FROM: https://www.cfd-online.com/Forums/openfoam-installation/168746-problems-installing-openfoam-2-4-0-ubuntu-16-04-a.html


#Go into OpenFOAM's main source folder
cd $WM_PROJECT_DIR

#Change how the flex version is checked
find src applications -name "*.L" -type f | xargs sed -i -e 's=\(YY\_FLEX\_SUBMINOR\_VERSION\)=YY_FLEX_MINOR_VERSION < 6 \&\& \1='

#Still better be certain that the correct Qt version is being used
export QT_SELECT=qt4

#Back to step 8

cd $WM_PROJECT_DIR

# This next command will take a while... somewhere between 30 minutes to 3-6 hours.
./Allwmake > make.log 2>&1

#Run it a second time for getting a summary of the installation
./Allwmake > make.log 2>&1

1.2.35. OpenFOAM 2.1.0

Till step 4:

http://openfoamwiki.net/index.php/Installation/Linux/OpenFOAM-2.1.x/Ubuntu#Ubuntu_14.04

sudo -s

apt-get update

apt-get install build-essential cmake flex bison zlib1g-dev qt4-dev-tools libqt4-dev gnuplot libreadline-dev \
libncurses-dev libxt-dev libopenmpi-dev openmpi-bin git-core gcc-4.7 g++-4.7

apt-get install libscotch-dev

exit

https://openfoam.org/download/2-1-0-source/

download OpenFOAM-2.1.0 and ThirdParty-2.1.0

cd ThirdParty-2.1.0
mkdir download
wget -P download http://www.paraview.org/files/v3.12/ParaView-3.12.0.tar.gz
wget -P download https://gforge.inria.fr/frs/download.php/28043/scotch_5.1.11.tar.gz
tar -xzf download/ParaView-3.12.0.tar.gz
tar -xzf download/scotch_5.1.11.tar.gz
cd ..

Now step 6:

uname -m
sed -i -e 's/gcc/\$(WM_CC)/' OpenFOAM-2.1.0/wmake/rules/linux64Gcc/c
sed -i -e 's/g++/\$(WM_CXX)/' OpenFOAM-2.1.0/wmake/rules/linux64Gcc/c++
source $HOME/OpenFOAM/OpenFOAM-2.1.0/etc/bashrc WM_NCOMPPROCS=8 WM_MPLIB=SYSTEMOPENMPI
export WM_CC='gcc-4.7'
export WM_CXX='g++-4.7'

FULL_SETTINGS="$FOAM_SETTINGS; export WM_CC=gcc-4.7; export WM_CXX=g++-4.7"
echo "alias of210='source \$HOME/OpenFOAM/OpenFOAM-2.1.0/etc/bashrc $FULL_SETTINGS'" >> $HOME/.bashrc
unset FULL_SETTINGS

cd OpenFOAM-2.1.0
./Allwmake > log.make 2>&1
./Allwmake > log.make 2>&1

FROM: http://openfoamwiki.net/index.php/Installation/Linux/OpenFOAM-2.1.x/Ubuntu

Up to step 7.

FROM: https://www.cfd-online.com/Forums/openfoam-installation/168746-problems-installing-openfoam-2-4-0-ubuntu-16-04-a.html

#Go into OpenFOAM's main source folder
cd $WM_PROJECT_DIR

#Change how the flex version is checked
find src applications -name "*.L" -type f | xargs sed -i -e 's=\(YY\_FLEX\_SUBMINOR\_VERSION\)=YY_FLEX_MINOR_VERSION < 6 \&\& \1='

#Still better be certain that the correct Qt version is being used
export QT_SELECT=qt4

#Back to step 8

cd $WM_PROJECT_DIR

# This next command will take a while... somewhere between 30 minutes to 3-6 hours.
./Allwmake > make.log 2>&1

#Run it a second time for getting a summary of the installation
./Allwmake > make.log 2>&1

1.2.36. Generate OpenFOAM 2.2.2 doxygen

sudo apt-get install doxygen graphviz

./Allmake

1.2.37. OpenFOAM 2.3.0

# The following lines shouldn't do anything:

sudo -s

apt-get update

apt-get install build-essential cmake flex bison zlib1g-dev qt4-dev-tools libqt4-dev libqtwebkit-dev gnuplot \
libreadline-dev libncurses5-dev libxt-dev libopenmpi-dev openmpi-bin libboost-system-dev libboost-thread-dev libgmp-dev \
libmpfr-dev python python-dev

apt-get install libglu1-mesa-dev libqt4-opengl-dev

exit

# download OpenFOAM-2.3.0 and ThirdParty-2.3.0:

cd ~

cd OpenFOAM

wget "http://downloads.sourceforge.net/foam/OpenFOAM-2.3.0.tgz?use_mirror=mesh" -O OpenFOAM-2.3.0.tgz

wget "http://downloads.sourceforge.net/foam/ThirdParty-2.3.0.tgz?use_mirror=mesh" -O ThirdParty-2.3.0.tgz

tar -xzf OpenFOAM-2.3.0.tgz
tar -xzf ThirdParty-2.3.0.tgz

# Symbolic links:

ln -s /usr/bin/mpicc.openmpi OpenFOAM-2.3.0/bin/mpicc
ln -s /usr/bin/mpirun.openmpi OpenFOAM-2.3.0/bin/mpirun

uname -m

source $HOME/OpenFOAM/OpenFOAM-2.3.0/etc/bashrc WM_NCOMPPROCS=8 WM_MPLIB=SYSTEMOPENMPI

echo "alias of230='source \$HOME/OpenFOAM/OpenFOAM-2.3.0/etc/bashrc $FOAM_SETTINGS'" >> $HOME/.bashrc

# Open new terminal:

of230

# Paraview

cd $WM_THIRD_PARTY_DIR

#make very certain that the correct Qt version is being used, by running this command:
export QT_SELECT=qt4

# This next command will take a while... somewhere between 5 minutes to 30 minutes.
./Allwmake > log.make 2>&1

#update the shell environment
wmSET $FOAM_SETTINGS

#Go into OpenFOAM's main source folder
cd $WM_PROJECT_DIR

#Change how the flex version is checked
find src applications -name "*.L" -type f | xargs sed -i -e 's=\(YY\_FLEX\_SUBMINOR\_VERSION\)=YY_FLEX_MINOR_VERSION < 6 \&\& \1='

#Still better be certain that the correct Qt version is being used
export QT_SELECT=qt4

#Go into OpenFOAM's main source folder
cd $WM_PROJECT_DIR

#Still better be certain that the correct Qt version is being used
export QT_SELECT=qt4

# This next command will take a while... somewhere between 30 minutes to 3-6 hours.
./Allwmake > log.make 2>&1

#Run it a second time for getting a summary of the installation
./Allwmake > log.make 2>&1

icoFoam -help

1.2.38. OpenFOAM 2.2.x

http://openfoamwiki.net/index.php/Installation/Linux/OpenFOAM-3.0.1/Ubuntu#Ubuntu_16.04

sudo -s

apt-get update

apt-get install build-essential flex bison zlib1g-dev qt4-dev-tools libqt4-dev gnuplot libreadline-dev \
libncurses-dev libxt-dev libopenmpi-dev openmpi-bin

exit

cd OpenFOAM

download from github OpenFOAM-2.2.x-master and ThirdParty-2.2.x-master

unzip using archive manager

remove master from the folder names

uname -m

source $HOME/OpenFOAM/OpenFOAM-2.2.x/etc/bashrc WM_NCOMPPROCS=2 WM_MPLIB=SYSTEMOPENMPI

echo "alias of22x='source \$HOME/OpenFOAM/OpenFOAM-2.2.x/etc/bashrc $FOAM_SETTINGS'" >> $HOME/.bashrc

sed -i -e 's=-lz -lm -lrt=-Xlinker --no-as-needed -lz -lm -lrt=' \
  ThirdParty-2.2.x/etc/wmakeFiles/scotch/Makefile.inc.i686_pc_linux2.shlib-OpenFOAM-*

#Go into OpenFOAM's main source folder
cd $WM_PROJECT_DIR

#Change how the flex version is checked
find src applications -name "*.L" -type f | xargs sed -i -e 's=\(YY\_FLEX\_SUBMINOR\_VERSION\)=YY_FLEX_MINOR_VERSION < 6 \&\& \1='

#Still better be certain that the correct Qt version is being used
export QT_SELECT=qt4

./Allwmake > log.make 2>&1

./Allwmake > log.make 2>&1

1.2.39. To create a desktop shortcut for Doxygen

Ubuntu software centre: install gnome panel

$ gnome-desktop-item-edit --create-new ~/Desktop

1.2.41. DOS2UNIX

sudo apt install dos2unix

1.2.42. Mencoder

Ubuntu Software Centre

1.2.43. Engauge Digitiser

Ubuntu Software Centre

1.2.45. Sphinx

sudo apt-get install python-sphinx

1.2.46. Filezilla

Ubuntu Software Centre

1.2.47. Gitk

Ubuntu Software Centre

1.2.48. Ubuntu Freezes Randomly Solution

https://askubuntu.com/questions/761706/ubuntu-15-10-and-16-04-keep-freezing-randomly

sudo nano /etc/default/grub There is a line in that: GRUB_CMDLINE_LINUX_DEFAULT=”quiet splash” (like this), replace with: GRUB_CMDLINE_LINUX_DEFAULT=”quiet splash intel_idle.max_cstate=1” Save it (CTRL+O) sudo update-grub sudo reboot

I think this makes the mouse disappear (!)