Update dockerfiles

DiamondLightSource · Aug 13, 2024 · 83f1fb4 · 83f1fb4
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diff --git a/Dockerfiles/cryoemservices_relion → Dockerfiles/class_selection b/Dockerfiles/cryoemservices_relion → Dockerfiles/class_selection
@@ -1,4 +1,4 @@
-# This Dockerfile is used for class selection and Relion's own motion correction
+# This Dockerfile is used for Relion class selection
 # First stage builds relion
 FROM rockylinux:8 AS relion-build
 
@@ -23,7 +23,7 @@ RUN curl -L -O "https://github.com/conda-forge/miniforge/releases/latest/downloa
 RUN bash Mambaforge-$(uname)-$(uname -m).sh -b -p "conda"
 
 RUN source "/conda/etc/profile.d/conda.sh" && conda install -c conda-forge conda-pack
-RUN source "/conda/etc/profile.d/conda.sh" && source "/conda/etc/profile.d/mamba.sh" && mamba create -c conda-forge -p /install/pythonenv python=3.9 pip libtiff=4.4.0 htcondor pytorch-cpu=1.10.0 numpy=1.25.2 --override-channels -y
+RUN source "/conda/etc/profile.d/conda.sh" && source "/conda/etc/profile.d/mamba.sh" && mamba create -c conda-forge -p /install/pythonenv python=3.9 pip libtiff=4.4.0 pytorch-cpu=1.10.0 numpy=1.25.2 --override-channels -y
 
 # Install cryoem-services and pipeliner
 RUN mkdir /install/cryoem-services
@@ -60,11 +60,5 @@ ENV PATH="/install/relion4.0/bin:${PATH}"
 COPY --from=conda-build /install/venv /install/venv
 ENV PATH="/install/venv/bin:${PATH}"
 
-# Add cryolo files
-RUN mkdir -p /dls_sw/apps/EM/crYOLO/phosaurus_models
-COPY cryolo_models/* /dls_sw/apps/EM/crYOLO/phosaurus_models
-
 # Change permissions
 RUN chown -R "${userid}":"${groupid}" install
-RUN chown -R "${userid}":"${groupid}" /dls_sw
-
diff --git a/Dockerfiles/cryoemservices_cpu b/Dockerfiles/cryoemservices_cpu
@@ -1,4 +1,4 @@
-# This dockerfile is used for the services that need only cpu and no extra executables
+# This Dockerfile is used for the services that can run on CPU
 FROM python:3.10
 
 ENV VIRTUAL_ENV=/venv

diff --git a/Dockerfiles/cryolo b/Dockerfiles/cryolo
@@ -1,3 +1,4 @@
+# This Dockerfile is used for cryolo
 FROM continuumio/miniconda
 
 ARG groupid

diff --git a/Dockerfiles/ctffind b/Dockerfiles/ctffind
@@ -1,3 +1,4 @@
+# This Dockerfile is used for CTFFind4
 FROM python:3.10
 
 ENV VIRTUAL_ENV=/venv

diff --git a/Dockerfiles/cryoemservices_gpu → Dockerfiles/motioncor2 b/Dockerfiles/cryoemservices_gpu → Dockerfiles/motioncor2
@@ -1,5 +1,5 @@
-# This Dockerfile is used as a base for the motioncorr and tomo_align Dockerfiles
-FROM nvidia/cuda:10.2-devel-centos7
+# This Dockerfile is used for MotionCor2
+FROM nvidia/cuda:12.4.1-runtime-rockylinux8
 
 # Create EM user
 ARG groupid
@@ -12,21 +12,18 @@ RUN curl -L -O "https://github.com/conda-forge/miniforge/releases/latest/downloa
 RUN bash Mambaforge-$(uname)-$(uname -m).sh -b -p "conda"
 
 RUN source "/conda/etc/profile.d/conda.sh" && source "/conda/etc/profile.d/mamba.sh" && mamba create -c conda-forge -p /install/pythonenv python=3.10 pip libtiff=4.4.0 --override-channels -y
-
 RUN chmod -R a+x /install/pythonenv/bin
 
-# Install cryoem-services and ccp-em pipeliner
-RUN mkdir /install/cryoem-services && mkdir /install/ccpem-pipeliner
+# Install cryoem-services
+RUN mkdir /install/cryoem-services
 COPY packages/cryoem-services /install/cryoem-services
-COPY packages/ccpem-pipeliner /install/ccpem-pipeliner
-RUN source "/conda/etc/profile.d/conda.sh" && conda activate /install/pythonenv && pip install -e /install/cryoem-services && pip install -e /install/ccpem-pipeliner
-
-# Add cryolo files
-RUN mkdir -p /dls_sw/apps/EM/crYOLO/phosaurus_models
-COPY cryolo_models/* /dls_sw/apps/EM/crYOLO/phosaurus_models
-
-# Change permissions
-RUN chown -R "${userid}":"${groupid}" install && chown -R "${userid}":"${groupid}" /dls_sw
-
-ENV PATH="/install/pythonenv/bin:${PATH}"
-
+RUN source "/conda/etc/profile.d/conda.sh" && conda activate /install/pythonenv && pip install /install/cryoem-services
+RUN chown -R "${userid}":"${groupid}" install
+ENV PATH=/install/pythonenv/bin:${PATH}
+
+# Install MotionCor2 executable
+COPY --chown="${userid}":"${groupid}" packages/motioncor-1.4.0 /MotionCor2/1.4.0
+WORKDIR /MotionCor2/1.4.0
+RUN rm MotionCor2 && ln -s MotionCor2_1.4.0_Cuda102 MotionCor2
+ENV PATH=/MotionCor2/1.4.0:${PATH}
+RUN chmod +x /MotionCor2/1.4.0
diff --git a/Dockerfiles/motioncor_relion b/Dockerfiles/motioncor_relion
@@ -0,0 +1,42 @@
+# This Dockerfile is used for Relion's own motion correction and Relion postprocessing
+# First stage builds relion
+FROM rockylinux:8 AS relion-build
+
+# Get required build packages and libraries
+RUN yum install gcc gcc-c++ cmake openmpi -y
+RUN yum install fftw-devel libtiff-devel libpng-devel libjpeg-devel zlib-devel -y
+
+# Build Relion - need to be on the ver4.0 tag
+RUN mkdir -p /install/relion4.0
+COPY packages/relion_fork /install/relion_src
+RUN mkdir /install/relion_src/build
+
+RUN cmake -DCMAKE_INSTALL_PREFIX=/install/relion4.0 -DCMAKE_C_COMPILER=/usr/bin/gcc -DCMAKE_CXX_COMPILER=/usr/bin/g++ -DMPI_C_COMPILER=/usr/lib64/openmpi/bin/mpicc -DMPI_CXX_COMPILER=/usr/lib64/openmpi/bin/mpicxx -DMPI_C_LIBRARIES=/usr/lib64/openmpi/lib/libmpi.so -DMPI_CXX_LIBRARIES=/usr/lib64/openmpi/lib/libmpi.so -DGUI=OFF -DALTCPU=ON -DDoublePrec_CPU=OFF -DFORCE_OWN_FFTW=ON -DAMDFFTW=ON -B/install/relion_src/build -S/install/relion_src
+RUN make --directory=/install/relion_src/build/ install
+
+
+# Second stage combines the Relion build with a python environment
+FROM rockylinux:9
+
+# Create EM user
+ARG groupid
+ARG userid
+ARG groupname
+RUN groupadd -r -g "${groupid}" "${groupname}" && useradd -r -M "${groupname}" -u "${userid}" -g "${groupname}"
+
+# Install libraries for Relion
+RUN yum install openmpi fftw-devel libtiff-devel libpng-devel libjpeg-devel python3.11 zlib-devel -y
+
+# Copy Relion
+RUN mkdir -p /install/relion4.0
+COPY --from=relion-build /install/relion4.0 /install/relion4.0
+ENV PATH="/install/relion4.0/bin:${PATH}"
+RUN chown -R "${userid}":"${groupid}" install
+
+# Make the python virtual environment and install cryoem-services
+ENV VIRTUAL_ENV=/venv
+RUN python3.11 -m venv $VIRTUAL_ENV
+ENV PATH="$VIRTUAL_ENV/bin:$PATH"
+COPY --chown="${userid}":"${groupid}" packages/cryoem-services ./cryoem-services
+RUN python3.11 -m pip install --upgrade pip && python3.11 -m pip install ./cryoem-services
+
diff --git a/Dockerfiles/motioncorr b/Dockerfiles/motioncorr
diff --git a/Dockerfiles/tomo_align b/Dockerfiles/tomo_align
@@ -1,17 +1,32 @@
-FROM cryoem-services:gpu
+# This Dockerfile is used for GPU AreTomo2 processing
+FROM nvidia/cuda:12.4.1-runtime-rockylinux8
 
+# Create EM user
 ARG groupid
 ARG userid
+ARG groupname
+RUN groupadd -r -g "${groupid}" "${groupname}" && useradd -r -M "${groupname}" -u "${userid}" -g "${groupname}"
+
+# Set up conda environment
+RUN curl -L -O "https://github.com/conda-forge/miniforge/releases/latest/download/Mambaforge-$(uname)-$(uname -m).sh"
+RUN bash Mambaforge-$(uname)-$(uname -m).sh -b -p "conda"
+
+RUN source "/conda/etc/profile.d/conda.sh" && source "/conda/etc/profile.d/mamba.sh" && mamba create -c conda-forge -p /install/pythonenv python=3.10 pip libtiff=4.4.0 --override-channels -y
+RUN chmod -R a+x /install/pythonenv/bin
+
+# Install cryoem-services
+RUN mkdir /install/cryoem-services
+COPY packages/cryoem-services /install/cryoem-services
+RUN source "/conda/etc/profile.d/conda.sh" && conda activate /install/pythonenv && pip install /install/cryoem-services
+RUN chown -R "${userid}":"${groupid}" install
+ENV PATH=/install/pythonenv/bin:${PATH}
 
 # Install IMOD
 COPY --chown="${userid}":"${groupid}" packages/imod-4.11.1 /IMOD/4.11.1
-WORKDIR /IMOD/4.11.1
 ENV PATH=/IMOD/4.11.1/IMOD/bin/realbin:${PATH}
 RUN chmod +x /IMOD/4.11.1
 
 # Install AreTomo
-COPY --chown="${userid}":"${groupid}" packages/aretomo-1.3.0 /AreTomo/1.3.0
-WORKDIR /AreTomo/1.3.0
-RUN rm AreTomo && ln -s AreTomo_1.3.0_Cuda102_09292022 AreTomo
-ENV PATH=/AreTomo/1.3.0:${PATH}
-RUN chmod +x /AreTomo/1.3.0
+COPY --chown="${userid}":"${groupid}" packages/AreTomo2 /AreTomo2
+ENV PATH=/AreTomo2:${PATH}
+RUN chmod +x /AreTomo2