Using OpenMatrix in Atom on Linux

  1. After installing it on Linux, invoke OpenMatrix in Atom using the shell scripts run_atom_oml.sh, located in the scripts/installation folder.
  2. From the Atom OML menu, select Start OML.
  3. In the OML command window, enter any OML command. See the Reference Guide for more information on commands.
  4. You may need to adapt the run_atom_oml.sh file to specific paths on your machine. Specifically, OpenMatrix offers a bridge between OML and Python. This bridge is disabled by default.

Enable the bridge between OML and Python

  1. Install/build Python 3.5.2 , Numpy 1.14.5.
  2. Enable omlpythonbridge toolbox loading.
    1. Add the command loadtoolbox omlpythonbridge in the file <INSTALLATION_HOME>\OpenMatrix\scripts\loadtoolboxes.oml.
  3. In file <INSTALLATION_HOME>\OpenMatrix\scripts\run_atom_oml.sh, adapt the .sh file to specific paths on your machine.
    1. Set the environment variable OML_PYTHONHOME to point to the Python home.
      Example
      export OML_PYTHONHOME=/usr/local/python3.5.2
    2. Add the Python library file (libpython3.5m.so.1.0) location to the environment variable “LD_LIBRARY_PATH”.
      Example
      LD_LIBRARY_PATH=/usr/local/python3.5.2/lib:$LD_LIBRARY_PATH
    Note: The omlpythonbridge toolbox is built using Python binaries, which are built using RedHat Linux 6.6 devtoolset-3 compilers, Intel 2016 Update 2 Fortran and C++ compilers. It is recommended that you use Python binaries built using same compiler versions.
    Note: OpenMatrix binaries are built using RedHat Linux 6.6 devtoolset-3 compilers, Intel 2016 Update 2 Fortran and C++ compilers with the following:
    Compilation Options
    g++ -O2 -fPIC -std=c++11 -DLINUX -DOS_UNIX
    Link Options
    g++ -shared -Wl,-Bsymbolic –fPIC
    Note: Verified using Python 3.5.2 binaries installed from the source. Installed Numpy, Scipy, Matplotlib using pip. The steps are as follows (may vary):
    CentOS 6.6
    cd /opt

    wget https://www.python.org/ftp/python/3.5.2/Python-3.5.2.tgz

    tar xzf Python-3.5.2.tgz

    cd Python-3.5.2

    ./configure --enable-shared --prefix=/usr/local/python352

    make altinstall

    export LD_LIBRARY_PATH=/usr/local/python352/lib:$LD_LIBRARY_PATH

    cd /usr/local/python352/bin

    python3.5 -m pip install --upgrade pip

    python3.5 -m pip install numpy==1.14.5

    python3.5 -m pip install scipy==1.1.0

    python3.5 -m pip install matplotlib==2.2.2

    CentOS 7.2

    yum install zlib*

    yum install openssl-devel

    yum install tkinter tk-devel

    cd /opt

    wget https://www.python.org/ftp/python/3.5.2/Python-3.5.2.tgz

    tar xzf Python-3.5.2.tgz

    cd Python-3.5.2

    ./configure --enable-shared --prefix=/usr/local/python352

    make altinstall

    export LD_LIBRARY_PATH=/usr/local/python352/lib:$LD_LIBRARY_PATH

    cd /usr/local/python352/bin

    python3.5 -m pip install --upgrade pip

    python3.5 -m pip install numpy==1.14.5

    python3.5 -m pip install scipy==1.1.0

    python3.5 -m pip install matplotlib=2.2.2