User:DukeEgr93/SNIPR

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Ubuntu on a VirtualBox

Virtual Machine

  • Created a machine in VirtualBox Manager using New; 8 GB Ram; 100 GB VDI drive fixed size for speed
  • Downloaded Ubuntu from Ubuntu and installed it
    • After installation, stop the machine and remove the optical ISO if need be
  • Need to install:
sudo apt-get install gcc
sudo apt-get install g++
sudo apt-get install cmake
sudo apt-get install mlocate 
sudo apt-get install git
  • Also need to be using gcc-9; if 10 is installed:
sudo apt install gcc-9 g++-9
sudo update-alternatives --install /usr/bin/gcc gcc /usr/bin/gcc-9 100 --slave /usr/bin/g++ g++ /usr/bin/g++-9 --slave /usr/bin/gcov gcov /usr/bin/gcov-9
sudo update-alternatives --install /usr/bin/gcc gcc /usr/bin/gcc-10 90 --slave /usr/bin/g++ g++ /usr/bin/g++-10 --slave /usr/bin/gcov gcov /usr/bin/gcov-10


MATLAB

  • Used Firefox to connect to MATLAB, downloaded and saved to Downloads
  • Extract and install:
cd ~/.Downloads
unzip matlab_R2017b_glnxa64.zip
sudo ./install
  • Need to have MATLAB, Simulink, Bioinformatics, Robust Control, Statistics and Machine Learning, and Control System Toolbox.
    • Note: To be able to add toolboxes later, in UNIX:
sudo apt-get install libgconf-2-4
cd /usr/local.MATLAB/R2017a/bin/glnxa64
sudo mkdir exclude
sudo mv libfreetype.so.6 exclude
From MATLAB's help site
  • Move libstdc++.so so it does not interfere with the new one
cd /usr/local/MATLAB/R2017b/sys/os/glnxa64
sudo mv libstdc++.so.6 libstdc++.so.6.OLD

NUPACK

  • NUPACK
    • Registered
    • Downloaded and saved to Downloads
cd ~/Downloads
gunzip nupack3.2.2.tar.gz
tar -xvf nupack3.2.2.tar
cd nupack3.2.2
mkdir build
cd build
sudo cmake ../
sudo make
sudo make install
Sooooo many warnings with make

Prepare Shell

  • Edit ~/.bash_profile and add lines; use
pico ~/.bash_terminal
in the terminal, add the lines:
export LD_LIBRARY_PATH=/usr/lib:/usr/local/lib:/usr/lib/x86_64-linux-gnu
alias matlab='/usr/local/MATLAB/R2017b/bin/matlab'
then save and exit
  • First time you do this, in the terminal type
source ~/.bash_profile

Check MATLAAB

  • Run MATLAB
matlab
  • Try to run multitubedesign
system('multitubedesign')


SNIPR

  • Change into home
cd 
  • Get github repository
git clone https://github.com/Albert09111/SNIPR/
  • Change into SNIPR Folder
cd SNIPR
  • Run MATLAB (assumes alias is working)
matlab &
  • In MATLAB, run SNIPR
SNIPR