From 013de05eb76554cfd8e9391fb762e435da3de106 Mon Sep 17 00:00:00 2001
From: Javier Castellanos <javierbq@gmail.com>
Date: Thu, 31 Aug 2023 14:38:25 -0700
Subject: [PATCH 1/2] Update Dockerfile to use conda

---
 docker/Dockerfile | 58 +++++++++++++++++++++++++----------------------
 1 file changed, 31 insertions(+), 27 deletions(-)

diff --git a/docker/Dockerfile b/docker/Dockerfile
index 8364cb10..5ef063db 100644
--- a/docker/Dockerfile
+++ b/docker/Dockerfile
@@ -19,32 +19,36 @@
 
 FROM nvcr.io/nvidia/cuda:11.6.2-cudnn8-runtime-ubuntu20.04
 
+# Install base utilities
+RUN apt-get update \
+    && apt-get install -y build-essential \
+    && apt-get install -y wget git \
+    && apt-get clean \
+    && rm -rf /var/lib/apt/lists/*
+
+# Install miniconda
+ENV CONDA_DIR /opt/conda
+RUN wget --quiet https://repo.anaconda.com/miniconda/Miniconda3-latest-Linux-x86_64.sh -O ~/miniconda.sh && \
+    /bin/bash ~/miniconda.sh -b -p /opt/conda
+
+# install mamba
+RUN wget --quiet https://github.com/conda-forge/miniforge/releases/latest/download/Mambaforge-$(uname)-$(uname -m).sh -O ~/mamba.sh  && \
+    /bin/bash  ~/mamba.sh -b
+# Put conda in path so we can use conda activate
+ENV PATH $CONDA_DIR/bin:$PATH
+
+COPY env/SE3nv.yml /tmp/SE3nv.yml 
+
+RUN  /root/mambaforge/bin/mamba  env create -f /tmp/SE3nv.yml 
+
+ENV PATH /root/mambaforge/envs/SE3nv/bin:$PATH
+
+
 COPY . /app/RFdiffusion/
 
-RUN apt-get -q update \ 
-  && DEBIAN_FRONTEND=noninteractive apt-get install --no-install-recommends -y \
-  git \
-  python3.9 \
-  python3-pip \
-  && python3.9 -m pip install -q -U --no-cache-dir pip \
-  && rm -rf /var/lib/apt/lists/* \
-  && apt-get autoremove -y \
-  && apt-get clean \
-  && pip install -q --no-cache-dir \
-  dgl==1.0.2+cu116 -f https://data.dgl.ai/wheels/cu116/repo.html \
-  torch==1.12.1+cu116 --extra-index-url https://download.pytorch.org/whl/cu116 \
-  e3nn==0.3.3 \
-  wandb==0.12.0 \
-  pynvml==11.0.0 \
-  git+https://github.com/NVIDIA/dllogger#egg=dllogger \
-  decorator==5.1.0 \
-  hydra-core==1.3.2 \
-  pyrsistent==0.19.3 \
-  /app/RFdiffusion/env/SE3Transformer \
-  && pip install --no-cache-dir /app/RFdiffusion --no-deps
-  
-WORKDIR /app/RFdiffusion
-
-ENV DGLBACKEND="pytorch"
-
-ENTRYPOINT ["python3.9", "scripts/run_inference.py"]
+WORKDIR /app/RFdiffusion/env/SE3Transformer
+RUN pip install --no-cache-dir -r requirements.txt
+RUN python setup.py install 
+RUN pip install /app/RFdiffusion
+
+CMD /app/RFdiffusion/scripts/run_inference.py 

From c5877f3ffb1d34476c423e4da666326d19186e90 Mon Sep 17 00:00:00 2001
From: Javier Castellanos <javierbq@gmail.com>
Date: Thu, 31 Aug 2023 22:56:11 -0700
Subject: [PATCH 2/2] added linker path for singularity

---
 docker/Dockerfile | 6 +++---
 1 file changed, 3 insertions(+), 3 deletions(-)

diff --git a/docker/Dockerfile b/docker/Dockerfile
index 5ef063db..00c9d823 100644
--- a/docker/Dockerfile
+++ b/docker/Dockerfile
@@ -39,10 +39,9 @@ ENV PATH $CONDA_DIR/bin:$PATH
 
 COPY env/SE3nv.yml /tmp/SE3nv.yml 
 
-RUN  /root/mambaforge/bin/mamba  env create -f /tmp/SE3nv.yml 
-
-ENV PATH /root/mambaforge/envs/SE3nv/bin:$PATH
+RUN  /root/mambaforge/bin/mamba  env create -f /tmp/SE3nv.yml  --prefix /opt/conda/envs/SE3nv
 
+ENV PATH /opt/conda/envs/SE3nv/bin:$PATH
 
 COPY . /app/RFdiffusion/
 
@@ -51,4 +50,5 @@ RUN pip install --no-cache-dir -r requirements.txt
 RUN python setup.py install 
 RUN pip install /app/RFdiffusion
 
+ENV LD_LIBRARY_PATH $LD_LIBRARY_PATH:/opt/conda/envs/SE3nv/lib/
 CMD /app/RFdiffusion/scripts/run_inference.py