From 9c3d5c48694db1018d50aa85acad434f47e5ed0b Mon Sep 17 00:00:00 2001 From: "Suren A. Chilingaryan" Date: Thu, 13 Dec 2018 00:05:49 +0100 Subject: Initial import --- biomedisa/Dockerfile | 49 +++++++++++++++++++++++++++++++ biomedisa/Makefile | 48 ++++++++++++++++++++++++++++++ biomedisa/docker-entrypoint.sh | 16 ++++++++++ biomedisa/run-queues.sh | 9 ++++++ biomedisa/supervisor/supervisord-cpu.conf | 27 +++++++++++++++++ biomedisa/supervisor/supervisord-gpu.conf | 32 ++++++++++++++++++++ biomedisa/tests/test.sh | 4 +++ 7 files changed, 185 insertions(+) create mode 100644 biomedisa/Dockerfile create mode 100644 biomedisa/Makefile create mode 100755 biomedisa/docker-entrypoint.sh create mode 100755 biomedisa/run-queues.sh create mode 100644 biomedisa/supervisor/supervisord-cpu.conf create mode 100644 biomedisa/supervisor/supervisord-gpu.conf create mode 100755 biomedisa/tests/test.sh (limited to 'biomedisa') diff --git a/biomedisa/Dockerfile b/biomedisa/Dockerfile new file mode 100644 index 0000000..6666be7 --- /dev/null +++ b/biomedisa/Dockerfile @@ -0,0 +1,49 @@ +#FROM nvidia/cuda:10.0-cudnn7-devel-ubuntu18.04 +FROM nvidia/cuda:9.0-cudnn7-devel-ubuntu16.04 +MAINTAINER Suren A. Chilingaryan + +# 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 new file mode 100644 index 0000000..c14b89e --- /dev/null +++ b/biomedisa/Makefile @@ -0,0 +1,48 @@ +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 new file mode 100755 index 0000000..a0f9cba --- /dev/null +++ b/biomedisa/docker-entrypoint.sh @@ -0,0 +1,16 @@ +#! /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 new file mode 100755 index 0000000..a531b3b --- /dev/null +++ b/biomedisa/run-queues.sh @@ -0,0 +1,9 @@ +#!/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 new file mode 100644 index 0000000..c942d7d --- /dev/null +++ b/biomedisa/supervisor/supervisord-cpu.conf @@ -0,0 +1,27 @@ +[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 new file mode 100644 index 0000000..94323d5 --- /dev/null +++ b/biomedisa/supervisor/supervisord-gpu.conf @@ -0,0 +1,32 @@ +[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 new file mode 100755 index 0000000..cf16ce1 --- /dev/null +++ b/biomedisa/tests/test.sh @@ -0,0 +1,4 @@ +#! /bin/bash + +python -c 'import tensorflow; print(tensorflow.__version__)' +python -c 'import keras; print(keras.__version__)' -- cgit v1.2.1