Container repronim-reprostim

Overview

This container is designed to provide a reproducible environment to execute the reprostim tool/package commands.

ReproStim Singularity Container

Install Singularity

On Linux (Ubuntu 24.04) :

wget -O- http://neuro.debian.net/lists/noble.de-m.libre | sudo tee /etc/apt/sources.list.d/neurodebian.sources.list
sudo apt-key adv --recv-keys --keyserver hkps://keyserver.ubuntu.com 0xA5D32F012649A5A9

sudo apt-get update

sudo apt-get install singularity-container

$ singularity --version
  singularity-ce version 4.1.1

Check that X11 system is used by default in Linux (Ubuntu 24.04), psychopy will not work well with Wayland:

echo $XDG_SESSION_TYPE

It should return x11. If not, switch to X11:

• At the login screen, click on your username.

• Before entering your password, look for a gear icon or “Options” button at the bottom right corner of the screen.

• Click the gear icon, and a menu should appear where you can select either “Ubuntu on Xorg” or “Ubuntu on Wayland.”

• Choose “Ubuntu on Xorg” to switch to X11.

• Enter your password and log in. You should now be running the X11 session.

Install Pre-Built Container

On Linux (Ubuntu 24.04) :

Ensure DataLad is installed:

sudo apt-get install datalad

As next step install and download ReproNim containers:

datalad install https://datasets.datalad.org/repronim/containers
datalad update
cd ./containers/images/repronim
datalad get .

Build

To generate the container instructions like Dockerfile and Singularity use the following command:

cd containers/repronim-reprostim
./generate_container.sh

This will generate container Dockerfile/Singularity files in format like ***.repronim-reprostim-{VERSION}, where VERSION is the latest git tag version when specified, or 0.0.1 otherwise.

To build singularity container, use the following command:

cd containers/repronim-reprostim
./build_singularity.sh

To test the singularity container and run reprostim, use the following command:

cd containers/repronim-reprostim
./run_reprostim.sh --help

Run

To test reprostim package version in singularity container run:

singularity exec ./containers/repronim-reprostim/repronim-reprostim-0.7.27.sing reprostim --version

To run timesync-stimuli command with audio codes use the following command:

export REPROSTIM_PATH=$(pwd)

singularity exec \
  --cleanenv --contain \
  -B /run/user/$(id -u)/pulse \
  -B ${REPROSTIM_PATH} \
  --env DISPLAY=$DISPLAY \
  --env PULSE_SERVER=unix:/run/user/$(id -u)/pulse/native \
  ./containers/repronim-reprostim/repronim-reprostim-0.7.27.sing \
  reprostim timesync-stimuli -t 10 --mode interval

Debug & Patch Notes

Optionally, you can update the container locally for development and debugging purposes (with overlay):

singularity overlay create \
  --size 1024 \
  repronim-reprostim-0.7.27.overlay

sudo singularity exec \
  --overlay repronim-reprostim-0.7.27.overlay \
  --cleanenv --contain -B ${REPROSTIM_PATH} \
  repronim-reprostim-0.7.27.sing \
  bash

As sample install some package:

apt-get update
apt-get install pulseaudio-utils
pactl
exit

Optionally also uninstall current reprostim and install it from the local path:

sudo singularity exec \
  --overlay repronim-reprostim-0.7.27.overlay \
  --cleanenv --contain -B ${REPROSTIM_PATH} \
  repronim-reprostim-0.7.27.sing \
  /opt/psychopy/psychopy_2024.2.5_py3.10/bin/pip uninstall reprostim


sudo singularity exec \
  --overlay repronim-reprostim-0.7.27.overlay \
  --cleanenv --contain -B ${REPROSTIM_PATH} \
  repronim-reprostim-0.7.27.sing \
  /opt/psychopy/psychopy_2024.2.5_py3.10/bin/pip install ${REPROSTIM_PATH}/dist/reprostim-0.7.27.tar.gz[all,disp_mon]

And now run the script with overlay:

```shell
singularity exec \
  --cleanenv --contain \
  -B /run/user/$(id -u)/pulse \
  -B ${REPROSTIM_PATH} \
  --env DISPLAY=$DISPLAY \
  --env PULSE_SERVER=unix:/run/user/$(id -u)/pulse/native \
  --overlay ./repronim-reprostim-0.7.27.overlay \
  ./repronim-reprostim-0.7.27.sing \
  ${REPROSTIM_PATH}/tools/reprostim-timesync-stimuli output.log 1

Where /run/user/321/pulse is sample external pulseaudio device path bound to the container. Usually when you run the script w/o binding it will report error like:

Failed to create secure directory (/run/user/321/pulse): No such file or directory

NOTE: Make sure PULSE_SERVER is specified in the container environment and points to the host pulseaudio server. e.g.:

export PULSE_SERVER=unix:/run/user/321/pulse/native

REPROSTIM_PATH is the local clone of https://github.com/ReproNim/reprostim repository.

And all notes for local PC altogether:

cd ~/Projects/Dartmouth/branches/datalad/containers/images/repronim
export REPROSTIM_PATH=~/Projects/Dartmouth/branches/reprostim

singularity overlay create \
  --size 1024 \
  repronim-reprostim-0.7.27.overlay

sudo singularity exec \
  --overlay repronim-reprostim-0.7.27.overlay \
  repronim-reprostim-0.7.27.sing \
  bash

# execute in shell
apt-get update
apt-get install portaudio19-dev pulseaudio pavucontrol pulseaudio-utils
pactl
exit

# make sure all python packages are installed
sudo singularity exec \
  --overlay repronim-reprostim-0.7.27.overlay \
  repronim-reprostim-0.7.27.sing \
  python3 -m pip install pyzbar opencv-python numpy click pydantic sounddevice scipy pydub pyaudio reedsolo psychopy-sounddevice

# and run the script
rm output.log
singularity exec \
  --cleanenv --contain \
  -B /run/user/$(id -u)/pulse \
  -B ${REPROSTIM_PATH} \
  --env DISPLAY=$DISPLAY \
  --env PULSE_SERVER=unix:/run/user/$(id -u)/pulse/native \
  --overlay ./repronim-reprostim-0.7.27.overlay \
  ./repronim-reprostim-0.7.27.sing \
  reprostim timesync-stimuli --display 1