From d93991289726fb67442db012a668ca277539ca6f Mon Sep 17 00:00:00 2001
From: Dimitrios Bellos <34098719+DimitriosBellos@users.noreply.github.com>
Date: Mon, 7 Feb 2022 15:16:45 +0000
Subject: [PATCH] Support for Docker and Singularity (#24)

* Support for Docker and Singularity

* Rephrasing of certain sentences for a better clarity of meaning.
---
 .dockerignore | 23 +++++++++++++++++++++++
 Dockerfile    | 16 ++++++++++++++++
 README.md     | 36 ++++++++++++++++++++++++++++++++++++
 3 files changed, 75 insertions(+)
 create mode 100644 .dockerignore
 create mode 100644 Dockerfile

diff --git a/.dockerignore b/.dockerignore
new file mode 100644
index 0000000..68d2cc1
--- /dev/null
+++ b/.dockerignore
@@ -0,0 +1,23 @@
+**/__pycache__
+**/.classpath
+**/.dockerignore
+**/.env
+**/.project
+**/.settings
+**/.toolstarget
+**/.vs
+**/.vscode
+**/*.*proj.user
+**/*.dbmdl
+**/*.jfm
+**/bin
+**/charts
+**/docker-compose*
+**/compose*
+**/Dockerfile*
+**/node_modules
+**/npm-debug.log
+**/obj
+**/secrets.dev.yaml
+**/values.dev.yaml
+README.md
diff --git a/Dockerfile b/Dockerfile
new file mode 100644
index 0000000..94c7adb
--- /dev/null
+++ b/Dockerfile
@@ -0,0 +1,16 @@
+FROM nvidia/cuda:11.3.1-devel-ubuntu20.04
+
+WORKDIR /app
+COPY . .
+
+RUN apt update
+RUN apt install -y git
+RUN apt install -y libfftw3-dev
+RUN apt install -y g++
+RUN apt install -y python3
+RUN apt install -y python3-pip
+RUN export CXX=$(which g++)
+RUN export CUDACXX=$(which nvcc)
+RUN git submodule update --init --recursive
+RUN pip install .
+
diff --git a/README.md b/README.md
index c3f8eb8..90908e9 100644
--- a/README.md
+++ b/README.md
@@ -79,6 +79,42 @@ To run the tests, follow the installation instructions for developers and then d
 pytest
 ```
 
+## Docker
+
+Parakeet can also be installed and used via Docker (https://www.docker.com/get-started). To download parakeet's docker container you can do the following:
+
+```sh
+docker pull quay.io/rosalindfranklininstitute/parakeet:master
+```
+
+To use parakeet with docker with GPU support the host machine should have the approprate Nvidia drivers installed.
+
+To easily input and output data from the container the volume mechanism can be used, where a workspace directory of the host machine is mounted to a directory in the container (in the folder /mnt in the example below). For this reason it is advised that all the relevent files (e.g. config.yaml, sample.h5, etc.) should be present in the host workspace directory.
+
+Below is an example on how to use parakeet with docker to simulate the exit wave:
+
+```sh
+docker run --gpus all -v <host_workspace>:/mnt --rm -i -t parakeet:master parakeet.simulate.exit_wave -c /mnt/config.yaml -d gpu -s /mnt/sample.h5 -e /mnt/exit_wave.h5
+```
+
+## Singularity
+
+Parakeet can also be installed and used via Singularity (https://sylabs.io/guides/2.6/user-guide/installation.html). To download parakeet's singularity container you can do the following:
+
+```sh
+singularity pull library://rosalindfranklininstitute/parakeet/parakeet:master
+```
+
+Again similar to docker, to use parakeet with singularity and GPU support, the host machine should have the approprate Nvidia drivers installed.
+
+To easily input and output data from the container, a workspace directory in the host machine, where all the relevent files (e.g. config.yaml, sample.h5, etc.) should be present, can be binded to a directory in the container.
+
+Below is an example on how to use parakeet with singularity to simulate the exit wave:
+
+```sh
+singularity run --nv --bind <host_workspace>:/mnt parakeet.sif parakeet.simulate.exit_wave -c /mnt/config_new.yaml -d gpu -s /mnt/sample.h5 -e /mnt/exit_wave.h5
+```
+
 ## Usage
 
 Simulation of datasets is split into a number of different commands. Each