Containerization support

2d_cnn/deploy_config.sh

@@ -0,0 +1,5 @@
+#!/bin/bash
+
+srcdir=$(dirname ${BASH_SOURCE[0]})
+config_file=$1
+cp "${srcdir}/config.yaml" $(pwd)/"${config_file}"

2d_cnn/deploy_local_2D_container.sh

@@ -0,0 +1,23 @@
+#!/bin/bash
+
+srcdir=$(dirname ${BASH_SOURCE[0]})
+config_file=$1
+export CUDA_VISIBLE_DEVICES=
+for i in $(seq 1 1 $(nvidia-smi --list-gpus | wc -l))
+do
+   if [ $i -eq 1 ]
+   then
+      export CUDA_VISIBLE_DEVICES=$(expr $i - 1)
+   else
+      export CUDA_VISIBLE_DEVICES=$CUDA_VISIBLE_DEVICES,$(expr $i - 1)
+   fi
+done
+echo $CUDA_VISIBLE_DEVICES
+
+snakemake \
+    --snakefile "${srcdir}/snakefile.py" \
+    --config config="${config_file}" \
+    --forceall \
+    --printshellcmds \
+    --cores $(nvidia-smi --list-gpus | wc -l) \
+    --resources gpu=$(nvidia-smi --list-gpus | wc -l)

3d_cnn/deploy_config.sh

@@ -0,0 +1,5 @@
+#!/bin/bash
+
+srcdir=$(dirname ${BASH_SOURCE[0]})
+config_file=$1
+cp "${srcdir}/config.yaml" $(pwd)/"${config_file}"

3d_cnn/deploy_local_3D_container.sh

@@ -0,0 +1,24 @@
+#!/bin/bash
+
+export srcdir="$( cd "$(dirname "$0")" >/dev/null 2>&1 ; pwd -P )"
+config_file=$1
+export CUDA_VISIBLE_DEVICES=
+for i in $(seq 1 1 $(nvidia-smi --list-gpus | wc -l))
+do
+   if [ $i -eq 1 ]
+   then
+      export CUDA_VISIBLE_DEVICES=$(expr $i - 1)
+   else
+      export CUDA_VISIBLE_DEVICES=$CUDA_VISIBLE_DEVICES,$(expr $i - 1)
+   fi
+done
+echo $CUDA_VISIBLE_DEVICES
+export PYTHONPATH=${srcdir}/src
+echo PYTHONPATH=$PYTHONPATH
+
+snakemake \
+    --snakefile "${srcdir}/snakefile" \
+    --config config="${config_file}" gpu=$CUDA_VISIBLE_DEVICES \
+    --printshellcmds \
+    --cores $(nvidia-smi --list-gpus | wc -l) \
+    --resources gpu=$(nvidia-smi --list-gpus | wc -l)

3d_cnn/environment.yaml

@@ -1,25 +1,28 @@
 name: 3d-unet
 channels:
+  - pytorch
   - bioconda
-  - anaconda
   - conda-forge
+  - anaconda
   - default
 dependencies:
   - python=3.7
   - jupyter
   - imageio
-  - pytorch
-  - torchvision
   - scikit-learn
   - scikit-image
   - scipy
   - numpy
-  - tensorboardX
   - tqdm
   - pandas
   - pyaml
   - pip
-  - pip:
-      - h5py==2.10.0
-      - mrcfile==1.1.2
-      - monai
+  - h5py==2.10.0
+  - mrcfile==1.1.2
+  - monai
+  - pytorch==1.12.1
+  - torchvision==0.13.1
+  - cudatoolkit=11.6
+  - tensorboardx
+  - crc32c
+  - snakemake==5.13.0

Dockerfile-2d_cnn

@@ -0,0 +1,33 @@
+FROM nvidia/cuda:10.0-devel-ubuntu18.04
+
+COPY DeePiCt /app/DeePiCt
+COPY deploy_local_2D_container.sh /app/DeePiCt/2d_cnn
+WORKDIR /app/DeePiCt
+
+# Install necessary packages
+RUN echo 'debconf debconf/frontend select Noninteractive' | debconf-set-selections && \
+    apt-get update -y && apt-get install -y dialog apt-utils && \
+    apt-get install -y build-essential git wget software-properties-common && \
+    apt-get update && rm -rf /var/lib/apt/lists/*
+
+# Install miniconda
+ENV PATH="/usr/local/miniconda3/bin:${PATH}"
+ARG PATH="/usr/local/miniconda3/bin:${PATH}"
+RUN cd /tmp  \
+    && wget \
+    https://repo.anaconda.com/miniconda/Miniconda3-latest-Linux-x86_64.sh -O Miniconda3.sh\
+    && bash Miniconda3.sh -b -p /usr/local/miniconda3 \
+    && rm -f Miniconda3.sh
+
+
+# Create environment
+RUN conda init bash && \
+    conda install -c conda-forge mamba --yes && \
+    mamba env create -f /app/DeePiCt/2d_cnn/envs/keras-env.yaml
+
+RUN cd 2d_cnn && \
+    ln -s deploy_local_2D_container.sh deepict2D && \
+    ln -s deploy_config.sh deepict2D_config
+
+ENV PATH="${PATH}:/app/DeePiCt/2d_cnn"
+ARG PATH="${PATH}:/app/DeePiCt/2d_cnn"

Dockerfile-3d_cnn

@@ -0,0 +1,35 @@
+FROM nvidia/cuda:11.6.2-devel-ubuntu20.04
+
+COPY DeePiCt /app/DeePiCt
+COPY environment.yaml /app/DeePiCt/3d_cnn
+COPY deploy_config.sh /app/DeePiCt/3d_cnn
+COPY deploy_local_3D_container.sh /app/DeePiCt/3d_cnn
+WORKDIR /app/DeePiCt
+
+# Install necessary packages
+RUN echo 'debconf debconf/frontend select Noninteractive' | debconf-set-selections && \
+    apt-get update -y && apt-get install -y dialog apt-utils && \
+    apt-get install -y build-essential git wget software-properties-common && \
+    apt-get update && rm -rf /var/lib/apt/lists/*
+
+# Install miniconda
+ENV PATH="/usr/local/miniconda3/bin:${PATH}"
+ARG PATH="/usr/local/miniconda3/bin:${PATH}"
+RUN cd /tmp  \
+    && wget \
+    https://repo.anaconda.com/miniconda/Miniconda3-latest-Linux-x86_64.sh -O Miniconda3.sh\
+    && bash Miniconda3.sh -b -p /usr/local/miniconda3 \
+    && rm -f Miniconda3.sh
+
+
+# Create environment
+RUN conda init bash && \
+    conda install -c conda-forge mamba --yes && \
+    mamba env create -f /app/DeePiCt/3d_cnn/environment.yaml
+
+RUN cd 3d_cnn && \
+    ln -s deploy_local_3D_container.sh deepict3D && \
+    ln -s deploy_config.sh deepict3D_config
+
+ENV PATH="${PATH}:/app/DeePiCt/3d_cnn"
+ARG PATH="${PATH}:/app/DeePiCt/3d_cnn"