From 9b2d04ec3bbeef6b8f943848cb2518d7630ab4cb Mon Sep 17 00:00:00 2001
From: mrorro <mrorro@users.noreply.github.com>
Date: Wed, 14 Dec 2022 14:51:45 +0100
Subject: [PATCH] Update AI4PP (#129)

* Update ai4pp

* Add ai4pp image to workflow

* Tensorflow looks for gpu lib in ld_library_path
---
 .github/workflows/egi-images.yml |  1 +
 single-user-ai4pp/Dockerfile     | 93 ++++++++++++++------------------
 2 files changed, 41 insertions(+), 53 deletions(-)

diff --git a/.github/workflows/egi-images.yml b/.github/workflows/egi-images.yml
index 890be310..a9b0737b 100644
--- a/.github/workflows/egi-images.yml
+++ b/.github/workflows/egi-images.yml
@@ -52,6 +52,7 @@ jobs:
         image:
         - single-user
         - single-user-panosc
+        - single-user-ai4pp
 
     steps:
       - name: try to make free space
diff --git a/single-user-ai4pp/Dockerfile b/single-user-ai4pp/Dockerfile
index 48d0609f..a0c7b347 100644
--- a/single-user-ai4pp/Dockerfile
+++ b/single-user-ai4pp/Dockerfile
@@ -5,29 +5,15 @@ FROM $BASE_IMAGE
 SHELL ["/bin/bash", "-o", "pipefail", "-c"]
 
 RUN mamba install -y --quiet \
-        cftime \
-        ipympl \
-        jmespath \
-	psycopg2 \
-	boto3 \
-	folium \
-	tensorflow \
-	tqdm \
-	lxml \
-	pymongo \
-	rasterstats \
-	geopandas \
-	ipywidgets \
-	matplotlib \
-	scipy \
-	lightgbm \
-	eo-learn \
-	plotly \
-	graphviz \
-	jq \
-        jupyterlab-git \
-    && mamba install pytorch==1.12.1=*cuda* torchvision==0.13.1 torchaudio==0.12.1 cudatoolkit=11.3 -c pytorch \
-    && mamba install -y --quiet fastai mlflow -c fastai \
+	nb_conda_kernels \
+	cudatoolkit=11.4.2 \
+	cudnn \
+        matplotlib \
+        lightgbm \
+        eo-learn \
+        plotly \
+        graphviz \
+        jq \
     && conda clean --all
 
 # Octave, install on a different environment
@@ -44,44 +30,45 @@ RUN apt-get update \
 USER $NB_UID
 
 RUN mamba install -y --quiet octave_kernel=0.32.0 \
-    && SITE_PACKAGES=$(python -c 'import site; print(site.getsitepackages().pop())') \
-    && jupyter kernelspec install "$SITE_PACKAGES/octave_kernel" --name octave --prefix /opt/conda \
     && conda clean --all
 
-#RUN conda config --add channels bioconda \
-#    && mamba install -y --quiet \
-#        biopython \
-#        blast \
-#        clustalw \
-#        emboss \
-#    && conda clean --all
-
-# packages not in conda
-RUN pip install --no-cache-dir \
-        git+https://github.com/EGI-Foundation/egi-notebooks-addons@0.1.3 \
-        h5glance \
-        nbtop \
-        tflearn
-
-# EMSO
-# python3.7, install on a different environment
-#RUN mamba create --name python3.7 -y --quiet -c conda-forge ipython python=3.7 ipykernel \
-#    && $(conda run -n python3.7 /bin/bash -c "which python") -m ipykernel install --prefix /tmp --name Python-3.7 \
-#    && jupyter kernelspec install /tmp/share/jupyter/kernels/python-3.7/ --name Python-3.7 --prefix /opt/conda \
-#    && rm -rf /tmp/share \
-#    && conda clean --all
-
+# Rstudio
 USER root
-
 RUN apt-get update \
-    && apt-get install --no-install-recommends -y \
-        libsndfile1 \
+    && apt-get install -y gdebi-core \
+    && wget -q https://download2.rstudio.org/server/jammy/amd64/rstudio-server-2022.07.2-576-amd64.deb \
+    && gdebi -n rstudio-server-2022.07.2-576-amd64.deb \
+    && rm rstudio-server-2022.07.2-576-amd64.deb \
+    && apt-get remove -y gdebi \
     && apt-get clean \
     && rm -rf /var/lib/apt/lists/*
 
 USER $NB_UID
 
-# Avoid a broken extension to show up
-RUN jupyter labextension disable @pyviz/jupyterlab_pyviz
+RUN mamba install -y --quiet \
+       -c conda-forge jupyter-rsession-proxy \
+    && conda clean --all
+
+
+# packages not in conda
+RUN pip install --no-cache-dir \
+        git+https://github.com/EGI-Foundation/egi-notebooks-addons@0.1.3 \
+	bokeh==3.0.2 \
+	panel \
+	jupyterlab-git \
+	jupyterlab-github \
+	mlflow \
+	fastai \
+	papermill \
+	tensorflow \
+	jupyter-tensorboard-proxy \
+	mlflow-server-proxy \
+	protobuf==4.21.9 \
+	torch==1.12.1+cu113 \
+	torchvision==0.13.1+cu113 \
+	torchaudio==0.12.1 \
+	--extra-index-url https://download.pytorch.org/whl/cu113 	
+
+ENV LD_LIBRARY_PATH="${CONDA_DIR}/lib:${LD_LIBRARY_PATH}"
 
 RUN rmdir work