Skip to content

Latest commit

 

History

History
169 lines (147 loc) · 6.43 KB

WSLINSTALL.md

File metadata and controls

169 lines (147 loc) · 6.43 KB
Raw

improv in Windows Subsystem for Linux

This is a guide to installing and running improv on Windows systems using Windows Subsystem for Linux (WSL)


Setup

I. Install WSL

After completing the following WSL installation, the WSL shell can be activated by the wsl command in Command Prompt.

  1. Enable WSL via Powershell as administrator

    Enable-WindowsOptionalFeature -Online -FeatureName Microsoft-Windows-Subsystem-Linux

    -Be sure to install WSL 1 instead of WSL 2 due to unresolved network connectivity issues. In order to downgrade from WSL 2 to WSL 1, execute wsl --set-version <distro-name>

  2. Restart system

  3. Install Ubuntu 18.04 (or other distro) from Windows Store

  4. Initialize distro

    • Set username, password when prompted

WSL files can be accessed through the path: ~, which is equivalent to /home/[USER], within the WSL shell. Windows files, specifically the C: drive can be accessed through the path: /mnt/c. For RASP purposes, only the plasma store and the anaconda environment used to execute RASP is within the WSL system. The RASP code is located within Windows file system.

Furthermore, certain directories must be added to the PATH environmental variable in Linux in order for RASP to run properly. Below are the steps to "permanently" adding to the Linux $PATH.

  1. Use vim to edit ~/.profile 
    vim ~/.profile
  2. Add export PATH="[PATH]:$PATH" to end of ~/.profile
  3. Restart WSL shell

II. Install Anaconda 3 in WSL

  1. Find latest version of Anaconda 3 for Linux
  2. Install latest version within WSL 
    wget https://repo.continuum.io/archive/Anaconda3-[VERSION]-Linux-x86_64.sh
  3. Run installation script 
    bash Anaconda-[VERSION]-Linux-x86_64.sh
  4. Opt to install Visual Studio Code when prompted
  5. Update Anaconda if prompted or if necessary 
    conda update anaconda
  6. Add Anaconda to $PATH (see Section I) 
    export PATH="~/anaconda3/bin:$PATH"

III. Installing & Running X Server for any GUIs with improv

  1. Download and install VcXsrv
  2. Run XLaunch
    • Set Display number to "0"
    • Select Disable access control
    • Keep other default settings
  3. Allow access through Windows firewall if prompted
  4. Use vim to set display in ~/.profile (See Section 1) 
    export DISPLAY=:0

IV. improv Installation

  1. Clone improv 
    git clone https://github.com/pearsonlab/improv
  2. Clone improv submodules 
    git submodule update --init
  3. Create Anaconda environment
    This creates a new anaconda environment named caiman using Python 3.6, which can be used for improv installations and executions. Execute the following command in the CaImAn dir. 
    conda env create -f environment.yml -n caiman
conda activate caiman
  4. Install CaImAn module
    Execute the following command within the CaImAn directory and caiman env. 
    pip install -e .
  5. Install the following dependencies.
    • pyarrow
    • pyqtgraph
    conda install [PACKAGE]
  6. Add pyarrow plasma_store_server to path (See Section I)
    plasma_store_server is most likely located in the bin directory of the caiman conda environment: ~/anaconda3/envs/caiman/bin. You can find where your environment is installed by entering conda info --envs.

V. Run improv

See Common Issues for errors and missing dependencies that might need to be installed.

  1. Activate WSL 
    wsl
  2. Activate caiman environment 
    conda activate caiman
  3. Run XLaunch (see Section V)
  4. Run improv 
    python -m nexus.nexus demos/basic/basic_demo.yaml

Common Issues

I. WSL Installation from Windows Store

If Ubuntu cannot be downloaded and installed from the Windows Store, it can be instead manually downloaded and installed through the following instructions.

  1. Go to https://docs.microsoft.com/en-us/windows/wsl/install-manual to download distro or https://aka.ms/wsl-ubuntu-1804 to directly download Ubuntu 18.04
  2. If running the .appx file downloaded does not successfully install, rename .appx extension to .zip and uncompress
  3. Run ubuntu18.04.exe or altenerative distro executable
  4. Complete initialization and rest of installation

II. CaImAn/Anaconda Installation

Several issues can appear during the CaImAn installation process. It is recommended that if any severe issues appear, one should delete and then recreate the caiman conda environment from scratch. Or, caiman can be uninstalled (pip uinstall caiman) and installation can be reattempted. Some of the following issues might appear:

  1. Aborted (core dumped) when activating the caiman env
    • Solved by updating all packages 
      conda update --all
  2. Failed building wheel for caiman: command 'gcc' failed with exit status 1
    • This error could be due to gcc or g++ not being installed. Follow these steps to install both. 
      conda update -all
sudo apt-get update
sudo apt-get install gcc
sudo apt-get install g++

III. Errors Running improv

  1. ImportError: libGl.so.1: cannot open shared object file

    • Solved by running the following 
      sudo apt-get update
sudo apt-get install libgl1-mesa-glx

  2. ImportError: libopencv_reg.so.3.4: cannot enable executable stack as shared object

    • Solved by running the following (second line contains path of opencv installation) 
      sudo apt-get update
sudo apt-get install execstack
sudo execstack -c ~/anaconda3/envs/caiman/lib/libopencv_*

  3. This application failed to start because it could not find or load the Qt platform plugin "xcb"

    • Solved by running the following 
      sudo apt-get update
sudo apt-get install libqt5x11extras5

  4. gcc: error trying to exec 'cc1plus': execvp: No such file or directory

    • Solved by installing gcc and g++ 
      conda update -all
sudo apt-get update
sudo apt-get install gcc
sudo apt-get install g++