From 2b972bc861a3dd7ecb1593e39cdf8c6d79a68f3b Mon Sep 17 00:00:00 2001
From: Tru HUYNH <tru@pasteur.fr>
Date: Fri, 10 Sep 2021 13:42:00 +0200
Subject: [PATCH] Update Dockerfile
---
docker/Dockerfile | 18 ++++++++++--------
1 file changed, 10 insertions(+), 8 deletions(-)
diff --git a/docker/Dockerfile b/docker/Dockerfile
index 1ff78c6..ded1fed 100644
--- a/docker/Dockerfile
+++ b/docker/Dockerfile
@@ -13,7 +13,7 @@
# limitations under the License.
ARG CUDA=11.0
-FROM nvidia/cuda:${CUDA}-base
+FROM nvidia/cuda:${CUDA}-cudnn8-runtime-ubuntu18.04
# FROM directive resets ARGS, so we specify again (the value is retained if
# previously set).
ARG CUDA
@@ -34,14 +34,15 @@ RUN apt-get update && DEBIAN_FRONTEND=noninteractive apt-get install -y \
# Compile HHsuite from source.
RUN git clone --branch v3.3.0 https://github.com/soedinglab/hh-suite.git /tmp/hh-suite \
- && mkdir /tmp/hh-suite/build
-WORKDIR /tmp/hh-suite/build
-RUN cmake -DHAVE_AVX2=1 -DCMAKE_INSTALL_PREFIX=/opt/hhsuite .. \
+ && mkdir /tmp/hh-suite/build \
+ && pushd /tmp/hh-suite/build \
+ && cmake -DHAVE_AVX2=1 -DCMAKE_INSTALL_PREFIX=/opt/hhsuite .. \
&& make -j 4 && make install \
&& ln -s /opt/hhsuite/bin/* /usr/bin \
+ && popd \
&& rm -rf /tmp/hh-suite
-# Install Miniconda package manger.
+# Install Miniconda package manager.
RUN wget -q -P /tmp \
https://repo.anaconda.com/miniconda/Miniconda3-latest-Linux-x86_64.sh \
&& bash /tmp/Miniconda3-latest-Linux-x86_64.sh -b -p /opt/conda \
@@ -52,9 +53,10 @@ ENV PATH="/opt/conda/bin:$PATH"
RUN conda update -qy conda \
&& conda install -y -c conda-forge \
openmm=7.5.1 \
- cudatoolkit==${CUDA}.3 \
+ cudatoolkit==${CUDA_VERSION} \
pdbfixer \
- pip
+ pip \
+ python=3.7
COPY . /app/alphafold
RUN wget -q -P /app/alphafold/alphafold/common/ \
@@ -67,7 +69,7 @@ RUN pip3 install --upgrade pip \
https://storage.googleapis.com/jax-releases/jax_releases.html
# Apply OpenMM patch.
-WORKDIR /opt/conda/lib/python3.8/site-packages
+WORKDIR /opt/conda/lib/python3.7/site-packages
RUN patch -p0 < /app/alphafold/docker/openmm.patch
# We need to run `ldconfig` first to ensure GPUs are visible, due to some quirk
--
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