Difference between revisions of "User:DukeEgr93/SNIPR"

From PrattWiki
Jump to navigation Jump to search
(→‎MATLAB)
Line 119: Line 119:
  
 
=== MATLAB ===
 
=== MATLAB ===
−
* Used Firefox to connect to MATLAB and installed R2017b with "sudo ./install" to have access to /usr/local folders; MATLAB, Simulink, Bioinformatics, Robust Control. To be able to add toolboxes later, in UNIX:
+
* 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
 
  sudo apt-get install libgconf-2-4
 
  cd /usr/local.MATLAB/R2017a/bin/glnxa64
 
  cd /usr/local.MATLAB/R2017a/bin/glnxa64
Line 128: Line 134:
 
  export LD_LIBRARY_PATH=/usr/lib:/usr/local/lib:/usr/lib/x86_64-linux-gnu
 
  export LD_LIBRARY_PATH=/usr/lib:/usr/local/lib:/usr/lib/x86_64-linux-gnu
 
  alias matlab='/usr/local/MATLAB/R2017b/bin/matlab'
 
  alias matlab='/usr/local/MATLAB/R2017b/bin/matlab'
−
 
+
* First time you do this,
−
* source ~/.nash_profile
+
source ~/.bash_profile
  
 
=== NUPACK ===
 
=== NUPACK ===

Revision as of 13:47, 23 February 2021

  • Installed VirtualBox 6.1.18 from [1] using all defaults
  • Created a machine in VirtualBox Manager using New; 4 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
  • Used Firefox to connect to MATLAB and installed R2017a with "sudo ./install" to have access to folders; MATLAB, Simulink, Bioinformatics, Robust Control. 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
  • NUPACK
    • Registered
    • Downloaded and opened with archive manager
    • Extracted to /home/ID
    • Installed cmake with
sudo apt install cmake
  • Installed g++ with
sudo apt install g++
  • Change to nupack folder, make build, change to build,
sudo cmake -DCMAKE_C_COMPILER=gcc -DCMAKE_CXX_COMPILER=g++ ../
sudo make
sudo make install
Sooooo many warnings...
  • Install most recent version of libstdc++
sudo apt install compat-libstdc++-33.x86_64
  • Find most recent version of libstdc++
locate libstdc++
If locate does not work, use
sudo apt install mlocate
first. Find the one that is in /usr/lib/x86_64-linux-gnu
  • Add lines to bash profile and run it:
 pico ~/.bash_profile
and add
export NUPACKHOME=/home/mrg/nupack3.2.2
export PATH=$PATH":${NUPACKHOME}/bin"
export LD_PRELOAD="/usr/lib/x86_64-linux-gnu/libstdc++.so.6.0.28"
then
source ~/.bash_profile
Not sure if required since these live on /usr/local
  • Start MATLAB from terminal
cd /usr/local/MATLAB/R2017a/bin
./matlab &
  • Check to see if things are working
system('musltitubedesign')
  • SNIPR
    • Change into home
cd
  • Get github repository
sudo apt install git
git clone https://github.com/Albert09111/SPIPR/
  • Change into SNIPR Folder
cd SNIPR
  • Run MATLAB
/usr/local/MATLAB/R2017a/bin/matlab &
  • In MATLAB, run SNIPR
SNIPR

Round Two

Fedora

Made a Virtualbox with Fedora, downloaded ISO, connected to optical first time around, disconnected from optical second time around, etc

cmake

  • Opened terminal
  • sudo dnf install cmake
  • sudo yum install gcc-c++

NUPACK

  • NUPACK
    • Registered
    • Downloaded and moved to home directory
    • gunzip nupack3.2.2.tar.gz
    • tar -xvf nupack3.2.2.tar
    • cd nupack3.2.2
    • mkdir build
    • cd build
    • sudo cmake ../
    • sudo make
    • Fail...

Round Three

Debian 64

IBID; all the defaults

Process

  • opened the terminal
  • su -
  • apt-get install cmake
  • apt get-install gcc
  • apt-get install g++
  • Download zip from Firefox
  • gunzip nupack3.2.2.tar.gz
  • tar -xvf nupack3.2.2.tar
  • cd nupack3.2.2
  • mkdir build
  • cd build
  • cmake ../
  • make
  • make install
  • Download R2017b installer
  • gunzip
  • https://linuxize.com/post/how-to-add-user-to-sudoers-in-debian/ to add sudo rights
  • sudo ./install
  • MATLAB, Simulink, Bioinformatics, Statistics, Control System, Robust Control
  • source ~/.bash_profile
  • cd /usr/local/MATLAB/R2017b/sys/os/glnx64
  • sudo mv libstdc++.so.6 libstdc++.so.6.old
  • sudo apt-get install git
  • git clone https://github.com/Albert09111/SNIPR

Round 4

Trying UBUNTU again...

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


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
  • Edit ~/.bash_profile and add
export LD_LIBRARY_PATH=/usr/lib:/usr/local/lib:/usr/lib/x86_64-linux-gnu
alias matlab='/usr/local/MATLAB/R2017b/bin/matlab'
  • First time you do this,
source ~/.bash_profile

NUPACK

  • NUPACK
    • Registered
    • Downloaded and opened with archive manager
    • Extracted to /home/ID
  • Change to nupack folder, make build, change to build,
sudo cmake -DCMAKE_C_COMPILER=gcc -DCMAKE_CXX_COMPILER=g++ ../
sudo make
sudo make install
Sooooo many warnings...
  • Install most recent version of libstdc++
sudo apt install compat-libstdc++-33.x86_64
  • Find most recent version of libstdc++
locate libstdc++
If locate does not work, use
first. Find the one that is in /usr/lib/x86_64-linux-gnu
  • Add lines to bash profile and run it:
 pico ~/.bash_profile
and add
export NUPACKHOME=/home/mrg/nupack3.2.2
export PATH=$PATH":${NUPACKHOME}/bin"
export LD_PRELOAD="/usr/lib/x86_64-linux-gnu/libstdc++.so.6.0.28"
then
source ~/.bash_profile
Not sure if required since these live on /usr/local
  • Start MATLAB from terminal
cd /usr/local/MATLAB/R2017a/bin
./matlab &
  • Check to see if things are working
system('musltitubedesign')

SNIPR

  • Change into home
cd
  • Get github repository
git clone https://github.com/Albert09111/SPIPR/
  • Change into SNIPR Folder
cd SNIPR
  • Run MATLAB (assumes alias is working)
matlab &
  • In MATLAB, run SNIPR
SNIPR
Retrieved from "https://pundit.pratt.duke.edu/piki/index.php?title=User:DukeEgr93/SNIPR&oldid=26417"