Initial import

7 files changed, 185 insertions, 0 deletions

diff --git a/biomedisa/Dockerfile b/biomedisa/Dockerfile
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+#FROM nvidia/cuda:10.0-cudnn7-devel-ubuntu18.04
+FROM nvidia/cuda:9.0-cudnn7-devel-ubuntu16.04
+MAINTAINER Suren A. Chilingaryan <csa@suren.me>
+
+# Install Devel & Python
+RUN apt-get update -qq \
+ && apt-get install --no-install-recommends -y \
+    git pkg-config netcat supervisor \
+    telnet iputils-ping dnsutils \
+    python python-dev python-pip python-setuptools python-virtualenv python-wheel python-numpy python-scipy python-h5py python-yaml python-pydot python-matplotlib libopenblas-base
+
+# Install Keras + Tensor Flow
+ARG TENSORFLOW_VERSION=1.12.0
+ARG TENSORFLOW_DEVICE=gpu
+ARG TENSORFLOW_APPEND=_gpu
+
+ARG KERAS_VERSION=2.2.4
+ENV KERAS_BACKEND=tensorflow
+
+RUN pip --no-cache-dir install \
+    https://storage.googleapis.com/tensorflow/linux/${TENSORFLOW_DEVICE}/tensorflow${TENSORFLOW_APPEND}-${TENSORFLOW_VERSION}-cp27-none-linux_x86_64.whl
+
+RUN pip --no-cache-dir install --no-dependencies \
+    git+https://github.com/fchollet/keras.git@${KERAS_VERSION}
+
+ADD tests/ /root/tests
+
+# install dependencies from debian packages
+RUN apt-get install --no-install-recommends -y \
+    mc \
+    libsm6 libxrender-dev \
+    openmpi-bin openmpi-doc libopenmpi-dev \
+    python-gdcm python-mysqldb
+
+# upgrade pip
+RUN pip --no-cache-dir install --upgrade pip
+
+# install dependencies from python packages
+RUN pip --no-cache-dir install \
+    setuptools==39.1.0 numpy==1.14.5 tifffile==0.14.0 SimpleParse==2.1.1 redis==2.10.6 rq==0.12 \
+    scipy weave scikit-image opencv-python h5py pydicom Pillow django mpi4py pycuda
+
+COPY supervisor/*.conf /etc/
+COPY *-entrypoint.sh /
+COPY run-*.sh /
+ENTRYPOINT ["/docker-entrypoint.sh"]
+
+ENV BIOMEDISA_DEVICE=${TENSORFLOW_DEVICE}
+CMD /usr/bin/supervisord -c /etc/supervisord-${BIOMEDISA_DEVICE}.conf
diff --git a/biomedisa/Makefile b/biomedisa/Makefile
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+++ b/biomedisa/Makefile
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+all: build
+#install: push
+
+.PHONY: rebuild build push start stop restart bash
+
+build: Dockerfile
+	docker build --tag chsa/biomedisa:latest .
+
+rebuild: Dockerfile
+	docker build --no-cache --tag chsa/biomedisa:latest .
+
+#push: build
+#	docker push chsa/biomedisa:latest
+
+start: build
+	@if [ `docker ps | grep adei-mysql | wc -l` -eq 0 ]; then \
+	    if [ `docker ps -a | grep adei-mysql | wc -l` -eq 0 ]; then \
+		docker run --name adei-mysql -p 53306:3306/tcp  -e MYSQL_ROOT_PASSWORD="adei" -e MYSQL_DATABASE="adei" -e MYSQL_USER="adei" -e MYSQL_PASSWORD="adei" -d mysql:5.7 ;\
+	    else \
+		docker start adei-mysql ;\
+	    fi ;\
+	fi ;\
+	if [ `docker ps | grep chsa/adei | wc -l` -eq 0 ]; then \
+	    if [ `docker ps -a | grep adei-full | wc -l` -gt 0 ]; then \
+		echo "Removing the stalled copy..." ;\
+		docker rm adei-full ;\
+	    fi ;\
+	    docker run -p 8000:80 --name adei-full --link adei-mysql:adei-mysql -e ADEI_PORTS=8000 -t -d chsa/adei:latest ;\
+	else \
+	    echo "Already running..." ;\
+	fi
+
+stop:
+	@if [ `docker ps | grep adei-full | wc -l` -gt 0 ]; then \
+	    docker stop adei-full ;\
+	    docker rm adei-full ;\
+	fi
+
+stop_mysql: stop
+	docker stop adei-mysql
+
+restart:
+	make stop
+	make start
+
+bash: build
+	docker run --runtime=nvidia -it chsa/biomedisa /bin/bash
+#	docker exec -it chsa/biomedisa /bin/bash
diff --git a/biomedisa/docker-entrypoint.sh b/biomedisa/docker-entrypoint.sh
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+++ b/biomedisa/docker-entrypoint.sh
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+#! /bin/bash
+
+set -e
+
+export PYTHONPATH=/biomedisa:${PYTHONPATH}
+export DJANGO_SETTINGS_MODULE=biomedisa.settings
+
+if ! whoami &> /dev/null; then
+  if [ -w /etc/passwd ]; then
+      echo "${USER_NAME:-default}:x:$(id -u):0:${USER_NAME:-default} user:${HOME}:/sbin/nologin" >> /etc/passwd
+  fi
+fi
+
+cd "/biomedisa"
+echo "Running: $@"
+exec "$@"
diff --git a/biomedisa/run-queues.sh b/biomedisa/run-queues.sh
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+++ b/biomedisa/run-queues.sh
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+#!/bin/bash
+
+# start background workers
+rq worker -u http://redis rq worker first_queue &
+rq worker -u http://redis rq worker slices &
+rq worker -u http://redis rq worker acwe &
+rq worker -u http://redis rq worker cleanup &
+rq worker -u http://redis rq worker share_notification &
+rq worker -u http://redis rq worker stop_job &
diff --git a/biomedisa/supervisor/supervisord-cpu.conf b/biomedisa/supervisor/supervisord-cpu.conf
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+++ b/biomedisa/supervisor/supervisord-cpu.conf
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+[supervisord]
+nodaemon=true
+
+[program:slices]
+command=rq worker -u http://redis rq worker slices
+autorestart=true
+exitcodes=0
+
+[program:acwe]
+command=rq worker -u http://redis rq worker acwe
+autorestart=true
+exitcodes=0
+
+[program:cleanup]
+command=rq worker -u http://redis rq worker cleanup
+autorestart=true
+exitcodes=0
+
+[program:share_notification]
+command=rq worker -u http://redis rq worker share_notification
+autorestart=true
+exitcodes=0
+
+[program:stop_job]
+command=rq worker -u http://redis rq worker stop_job
+autorestart=true
+exitcodes=0
diff --git a/biomedisa/supervisor/supervisord-gpu.conf b/biomedisa/supervisor/supervisord-gpu.conf
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+++ b/biomedisa/supervisor/supervisord-gpu.conf
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+[supervisord]
+nodaemon=true
+
+[program:first]
+command=rq worker -u http://redis rq worker first_queue
+autorestart=true
+exitcodes=0
+
+[program:slices]
+command=rq worker -u http://redis rq worker slices
+autorestart=true
+exitcodes=0
+
+[program:acwe]
+command=rq worker -u http://redis rq worker acwe
+autorestart=true
+exitcodes=0
+
+[program:cleanup]
+command=rq worker -u http://redis rq worker cleanup
+autorestart=true
+exitcodes=0
+
+[program:share_notification]
+command=rq worker -u http://redis rq worker share_notification
+autorestart=true
+exitcodes=0
+
+[program:stop_job]
+command=rq worker -u http://redis rq worker stop_job
+autorestart=true
+exitcodes=0
diff --git a/biomedisa/tests/test.sh b/biomedisa/tests/test.sh
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+++ b/biomedisa/tests/test.sh
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+#! /bin/bash
+
+python -c 'import tensorflow; print(tensorflow.__version__)'
+python -c 'import keras; print(keras.__version__)'