CodeOcean is a cloud-based computational reproducibility platform. This post shows how you can utilize SReachTools in your CodeOcean capsule for repeatability. We list few examples that show SReachTools setup for CodeOcean. Then, we detail the procedure to set up a new capsule.

Examples

  1. Dubins’ car: SReachSet demonstration — <2 min runtime.
  2. ARCH 2019: Automated anesthesia delivery — <1 min runtime.
  3. ARCH 2019: Building automation system — <1 min runtime.

Detailed procedure

We choose MATLAB 2017b and the follow the installation instructions given in the installation page to setup GMP, GeoCalcLib, YALMIP, CVX, MPT3, and finally SReachTools.

  1. Create a new capsule
  2. Choose MATLAB 2017b environment
    1. At the time of writing, this was the latest MATLAB environment available.
  3. In additional packages, add the following:
    1. bzip2 (tested with 1.0.6-8) — for unzipping MATLAB toolboxes
    2. build-essential (tested with 12.1ubuntu2) — for GeoCalcLib installation (gcc and make)
    3. m4 (tested with 1.4.17-5) — for GeoCalcLib installation
  4. Next, copy the following text into post-install script section: 
     #!/bin/bash
    
 ### Install GMP
 # Requires packages build-essentials for gcc and make, and package m4 (don't know why)
 curl -sL https://gmplib.org/download/gmp/gmp-6.1.2.tar.bz2 | tar xj
 echo 'Downloaded GMP'
 cd gmp-6.1.2
 # Setup gmp
 ./configure 
 make 
 make install
 cd ..
 echo 'Installed GMP'
    
 ### GeoCalcLib (Download and setup)
 # Requires installation of gmp and packages build-essentials for gcc and make 
 curl -sL https://github.com/worc4021/GeoCalcLib/archive/master.zip --output GeoCalcLib.zip
 unzip -qq GeoCalcLib.zip
 mv GeoCalcLib-master GeoCalcLib
 rm GeoCalcLib.zip
 echo 'Downloaded GeoCalcLib'
 # Setup GeoCalcLib
 cd GeoCalcLib
 mkdir mexfiles
 echo 'MATLABROOT = /MATLAB' > User.make
 echo 'INSTALLDIR = /GeoCalcLib/mexfiles' >> User.make
 make
 cd ..
 echo 'Installed GeoCalcLib'
    
 ### YALMIP (Download only)
 # MATLAB simply adds the files to the path to complete the setup
 YALMIP_RELEASE=R20181012
 curl -sL https://github.com/yalmip/YALMIP/archive/$YALMIP_RELEASE.tar.gz | tar xz
 mv YALMIP-$YALMIP_RELEASE YALMIP
 echo 'Downloaded YALMIP'
    
 ### CVX (Download only)
 # We call cvx_setup in MATLAB to complete the setup
 curl -sL http://web.cvxr.com/cvx/cvx-a64.tar.gz | tar zx
 echo 'Downloaded CVX'
    
 ### SReachTools (Download only)
 # Call srtinit in MATLAB to complete the setup
 ## OPTION 1: Fetch a tagged release
 #
 SREACHTOOLS_RELEASE=1.2
 curl -sL https://github.com/unm-hscl/SReachTools/archive/v$SREACHTOOLS_RELEASE.zip --output SReachTools.zip
 unzip -qq SReachTools.zip
 mv SReachTools-$SREACHTOOLS_RELEASE SReachTools
 rm SReachTools.zip
 echo 'Downloaded SReachTools'
 #
 # ## OPTION 2: Fetch bleeding edge
 #
 # curl -sL https://github.com/unm-hscl/SReachTools/archive/master.zip --output SReachTools.zip
 # unzip -qq SReachTools.zip
 # mv SReachTools-master SReachTools
 # rm SReachTools.zip
 # echo 'Downloaded SReachTools'
    
 ### Setup MATLAB env for GeoCalcLib, YALMIP, CVX, MPT3, and SReachTools
 # Trailing \ implies newline in bash. MATLAB executes the commands in the quotes.
 # Make sure each line ends with ;\ to avoid MATLAB throwing errors
 # Use GPLK instead of LCP to avoid wierd shifting | Don't do mpt_init again
 # 1. Add GeoCalcLib to path
 # 2. Add YALMIP to the path
 # 3. Setup CVX
 # 4. Fetch and install MPT3 using tbxmanager; Initialize MPT3
 # 5. Setup SReachTools
 # Even though, we do not recommend using savepath, we have to do it here due to
 # CodeOcean's setup
 matlab -nodisplay -r "\
 addpath('/GeoCalcLib/mexfiles');\
 disp('Installed GeoCalcLib');\
 addpath(genpath('/YALMIP'));\
 disp('Installed YALMIP');\
 cd('/cvx');\
 evalc('cvx_setup()');\
 disp('Installed CVX (Standard bundle)');\
 mkdir('/tbxmanager');\
 cd('/tbxmanager');\
 urlwrite('http://www.tbxmanager.com/tbxmanager.m', 'tbxmanager.m');\
 a=evalc('tbxmanager');\
 disp('Installed tbxmanager');\
 evalc('tbxmanager install mpt mptdoc cddmex fourier glpkmex hysdel lcp sedumi espresso');\
 evalc('mpt_init');\
 a=mptopt('lpsolver','glpk','qpsolver','quadprog');\
 disp('Installed MPT3');\
 cd('/SReachTools');\
 srtinit;\
 disp('Installed SReachTools');\
 savepath;"
  5. Create a file run.sh in the code folder. 
     #!/bin/bash
 matlab -nodisplay -nosoftwareopengl -r "dubinsSReachSetGauss;"

    This runs a default example in SReachTools. If you wish to run a separate MATLAB script main.m, you can upload it the code folder, and overwrite run.sh with

     #!/bin/bash
 matlab -nodisplay -nosoftwareopengl -r "main;"

Notes

  • The first run will take about 3 minutes for setting up of the environment. However, if the post-install script is left untouched, then subsequent runs will be significantly faster.
  • CodeOcean, by default, does not save figures. Use the following lines to save a figure as a png or fig file. 
    saveas(gcf, '../results/FILENAME.png');
saveas(gcf, '../results/FILENAME.fig');