Difference between revisions of "User:DukeEgr93/SNIPR"

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(→‎Process)
Line 99: Line 99:
 
* sudo ./install
 
* sudo ./install
 
* MATLAB, Simulink, Bioinformatics, Statistics, Control System, Robust Control
 
* MATLAB, Simulink, Bioinformatics, Statistics, Control System, Robust Control
−
* Edit .bash_profile and add
 
−
export LD_LIBRARY_PATH=/usr/lib:/usr/local/lib:/usr/lib/x86_64-linux-gnu
 
 
* source ~/.bash_profile
 
* source ~/.bash_profile
 
* cd /usr/local/MATLAB/R2017b/sys/os/glnx64
 
* cd /usr/local/MATLAB/R2017b/sys/os/glnx64
Line 106: Line 104:
 
* sudo apt-get install git
 
* sudo apt-get install git
 
* git clone https://github.com/Albert09111/SNIPR
 
* 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 [https://ubuntu.com/download/desktop/thank-you?version=20.04.2.0&architecture=amd64 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 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:
 +
sudo apt-get install libgconf-2-4
 +
cd /usr/local.MATLAB/R2017a/bin/glnxa64
 +
sudo mkdir exclude
 +
sudo mv libfreetype.so.6 exclude
 +
:: From [https://www.mathworks.com/matlabcentral/answers/364551-why-is-matlab-unable-to-run-the-matlabwindow-application-on-linux#answer_288902 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'
 +
 +
* source ~/.nash_profile
 +
 +
=== NUPACK ===
 +
* [http://www.nupack.org/downloads 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

Revision as of 13:26, 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 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:
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'
  • source ~/.nash_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
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