From 91ff683a9935fd0c4809958034606f70f8593277 Mon Sep 17 00:00:00 2001
From: "andrea.giannetti" <andrea.giannetti@inaf.it>
Date: Thu, 13 Jun 2024 10:20:57 -0600
Subject: [PATCH] Added Docker files
---
.dockerignore | 10 +++++++++
Dockerfile | 33 +++++++++++++++++++++++++++++
apptainer.def | 7 +++++++
create_apptainer_image_file.sh | 3 +++
docker-compose.yaml | 36 ++++++++++++++++++++++++++++++++
documentation/radmc3d_install.sh | 28 +++++++++++++++++++++++++
6 files changed, 117 insertions(+)
create mode 100644 .dockerignore
create mode 100644 Dockerfile
create mode 100644 apptainer.def
create mode 100644 create_apptainer_image_file.sh
create mode 100644 docker-compose.yaml
create mode 100644 documentation/radmc3d_install.sh
diff --git a/.dockerignore b/.dockerignore
new file mode 100644
index 0000000..7f80558
--- /dev/null
+++ b/.dockerignore
@@ -0,0 +1,10 @@
+/etl/credentials/db_credentials*.yml
+/etl/stg/archive/*
+/etl/prs/fits/cubes/*
+/etl/prs/fits/moments/*
+/etl/prs/fits/ratios/*
+/etl/prs/fits/grids/*
+/etl/mdl/radmc_files/*
+/etl/mdl/scratches/*
+/etl/prs/output/*
+/etl/*.sif
\ No newline at end of file
diff --git a/Dockerfile b/Dockerfile
new file mode 100644
index 0000000..b0c98fa
--- /dev/null
+++ b/Dockerfile
@@ -0,0 +1,33 @@
+FROM python:3.9-slim
+
+
+# STEP 1) Setting up environment
+# apt packages
+RUN apt-get update && \
+ apt-get --yes upgrade && \
+ apt-get install --yes libgomp1 && \
+ apt-get install --yes postgresql-client && \
+ apt-get install --yes --reinstall build-essential && \
+ apt-get -y install curl vim less nano git && \
+ apt-get -y install zip unzip && \
+ apt-get clean
+
+WORKDIR /usr/src/etl
+RUN python -m pip install --upgrade pip
+COPY etl/requirements.txt .
+RUN pip install -r requirements.txt
+
+RUN mkdir /sak_user
+# RUN /usr/sbin/usermod -d /sak_user root
+RUN HOME=/sak_user
+COPY documentation/radmc3d_install.sh .
+RUN chmod 755 radmc3d_install.sh
+RUN HOME=/sak_user;./radmc3d_install.sh
+ENV PATH="/sak_user/bin:${PATH}"
+ENV PYTHONPATH="/sak_user/bin/python:${PYTHONPATH}"
+RUN chmod 755 /sak_user/bin/radmc3d
+
+# STEP 2) Bundling app
+COPY etl .
+
+CMD python main.py
\ No newline at end of file
diff --git a/apptainer.def b/apptainer.def
new file mode 100644
index 0000000..597e8c3
--- /dev/null
+++ b/apptainer.def
@@ -0,0 +1,7 @@
+Bootstrap: docker
+From: postgres:14.1-alpine
+
+%environment
+export POSTGRES_DB=$DB_NAME
+export POSTGRES_USER=$DB_USER
+export POSTGRES_PASSWORD=$DB_PASS
diff --git a/create_apptainer_image_file.sh b/create_apptainer_image_file.sh
new file mode 100644
index 0000000..724dcb1
--- /dev/null
+++ b/create_apptainer_image_file.sh
@@ -0,0 +1,3 @@
+rm swiss_army_knife_latest.sif
+singularity pull --disable-cache docker://git.ia2.inaf.it:5050/andrea.giannetti/swiss_army_knife
+
diff --git a/docker-compose.yaml b/docker-compose.yaml
new file mode 100644
index 0000000..e33c742
--- /dev/null
+++ b/docker-compose.yaml
@@ -0,0 +1,36 @@
+version: '3.8'
+services:
+ db:
+ image: postgres:14.1-alpine
+ container_name: db_container_sak
+ restart: always
+ environment:
+ - POSTGRES_DB=$DB_NAME
+ - POSTGRES_USER=$DB_USER
+ - POSTGRES_PASSWORD=$DB_PASS
+ ports:
+ - '31000:5432'
+ volumes:
+ - db:/var/lib/postgresql/data
+ networks:
+ - sak_network
+
+ etl:
+ build:
+ dockerfile: Dockerfile
+ container_name: 'etl_sak'
+ image: 'sak_etl'
+ depends_on:
+ - db
+ stdin_open: true
+ tty: true
+ networks:
+ - sak_network
+ volumes:
+ - ./etl:/usr/src/etl
+volumes:
+ db:
+ driver: local
+networks:
+ sak_network:
+ name: 'sak_app_network'
\ No newline at end of file
diff --git a/documentation/radmc3d_install.sh b/documentation/radmc3d_install.sh
new file mode 100644
index 0000000..f119cb7
--- /dev/null
+++ b/documentation/radmc3d_install.sh
@@ -0,0 +1,28 @@
+#!/bin/bash
+# Set PYCHARM_HOME, INSTALL_DEPENDENCIES environment variable
+PYCHARM_HOME=${PYCHARM_HOME:=$HOME}
+INSTALL_DEPENDENCIES="${INSTALL_DEPENDENCIES:=true}"
+echo $PYCHARM_HOME
+cd $PYCHARM_HOME
+export RADMC_HOME=$PYCHARM_HOME/radmc3d-2.0
+if [[ ! -d "$RADMC_HOME" ]]
+then
+ echo RADMC not found, cloning into "$(pwd)"
+ git clone https://github.com/dullemond/radmc3d-2.0.git
+fi
+
+if $INSTALL_DEPENDENCIES
+then
+ apt-get install -y gfortran
+fi
+
+cd $RADMC_HOME/src
+make
+echo "y\n y\n"| make install
+
+# Add this to the .bashrc configuration file (or equivalent)
+export PATH=$HOME/bin:$PATH
+export PYTHONPATH=$HOME/bin/python:$PYTHONPATH
+
+cd $RADMC_HOME/python/radmc3dPy
+python setup.py install
--
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