Merge pull request #28 from elephant-track/dev

ELEPHANT server v0.5.3

Dockerfile

@@ -1,4 +1,4 @@
-FROM pytorch/pytorch:1.10.0-cuda11.3-cudnn8-runtime
+FROM nvidia/cuda:11.3.1-runtime-ubuntu20.04
 # Modified from https://github.com/tiangolo/uwsgi-nginx-flask-docker (Apache license)
 
 LABEL maintainer="Ko Sugawara <[email protected]>"
@@ -13,19 +13,30 @@ RUN set -x \
     ca-certificates \
     curl \
     gnupg \
-    gosu && \
+    gosu \
+    gettext-base && \
     apt-get clean && \
     rm -rf /var/lib/apt/lists/*
 
+ENV PATH /opt/conda/bin:$PATH
+SHELL ["/bin/bash", "-c"]
+
 # Install Python modules
 COPY ./environment.yml /tmp/environment.yml
 RUN sed -i '/.\/elephant-core/d' /tmp/environment.yml \
-    && conda install -c conda-forge -y mamba \
+    && curl -OL https://repo.continuum.io/miniconda/Miniconda3-py37_4.11.0-Linux-x86_64.sh \
+    && bash Miniconda3-py37_4.11.0-Linux-x86_64.sh -bfp /opt/conda \
+    && rm Miniconda3-py37_4.11.0-Linux-x86_64.sh \
+    && . /opt/conda/etc/profile.d/conda.sh \
+    && conda init \
+    && echo "conda activate base" >> ~/.bashrc \
+    && conda install -c conda-forge -y mamba=0.19.1 \
     && mamba clean -qafy \
     && mamba env update -f /tmp/environment.yml \
     && mamba clean -qafy \
     && rm -rf /tmp/elephant-core \
     && rm /tmp/environment.yml
+RUN mamba install jupyter
 
 # Install and set up RabbbitMQ
 COPY docker/install-rabbitmq.sh /tmp/install-rabbitmq.sh
@@ -38,16 +49,15 @@ COPY docker/rabbitmq.sh /rabbitmq.sh
 RUN chmod +x /rabbitmq.sh
 
 # Set up nginx
-COPY docker/nginx.conf /etc/nginx/nginx.conf
+COPY docker/nginx.conf.template /etc/nginx/nginx.conf.template
 EXPOSE 80 443
 RUN groupadd -r nginx && useradd -r -g nginx nginx
 # forward request and error logs to docker log collector
 RUN ln -sf /dev/stdout /var/log/nginx/access.log \
     && ln -sf /dev/stderr /var/log/nginx/error.log
 
-RUN pip install memory_profiler line_profiler
-RUN mamba install jupyter
-RUN pip install --no-deps stardist==0.8.3 csbdeep==0.7.2 numba==0.56.0 llvmlite==0.39.0 natsort==8.1.0
+# RUN pip install memory_profiler line_profiler
+# RUN pip install --no-deps stardist==0.8.3 csbdeep==0.7.2 numba==0.56.0 llvmlite==0.39.0 natsort==8.1.0
 
 # Copy the base uWSGI ini file to enable default dynamic uwsgi process number
 COPY docker/uwsgi.ini /etc/uwsgi/uwsgi.ini
@@ -77,7 +87,6 @@ ENTRYPOINT ["/entrypoint.sh"]
 COPY ./elephant-core /tmp/elephant-core
 RUN pip install -U /tmp/elephant-core && rm -rf /tmp/elephant-core
 
-
 # Run the start script provided by the parent image tiangolo/uwsgi-nginx.
 # It will check for an /app/prestart.sh script (e.g. for migrations)
 # And then will start Supervisor, which in turn will start Nginx and uWSGI

Dockerfile-test

@@ -1,4 +1,4 @@
-FROM elephant-server:0.5.2
+FROM elephant-server:0.5.3
 
 LABEL maintainer="Ko Sugawara <[email protected]>"
 

Makefile

@@ -5,13 +5,19 @@ help:
 
 ELEPHANT_GPU?=all
 ELEPHANT_WORKSPACE?=${PWD}/workspace
-ELEPHANT_IMAGE_NAME?=elephant-server:0.5.2
+ELEPHANT_IMAGE_NAME?=elephant-server:0.5.3
 ELEPHANT_NVIDIA_GID?=$$(ls -n /dev/nvidia0 2>/dev/null | awk '{print $$4}')
 ELEPHANT_DOCKER?=docker
 ELEPHANT_RABBITMQ_NODENAME?=rabbit@localhost
 ELEPHANT_RABBITMQ_NODE_PORT?=5672
+ELEPHANT_RABBITMQ_MANAGEMENT_PORT?=15672
+ELEPHANT_RABBITMQ_USER?=user
+ELEPHANT_RABBITMQ_PASSWORD?=user
+ELEPHANT_RABBITMQ_PID_FILE?=/var/lib/rabbitmq/mnesia/rabbitmq.pid
 ELEPHANT_REDIS_PORT?=6379
-ELEPHANT_BATCH_ID?=
+ELEPHANT_HTTP_PORT?=8080
+ELEPHANT_NOTEBOOK_PORT?=8888
+ELEPHANT_BATCH_ID?=0
 
 rebuild:
 	@IMAGEID=$$($(ELEPHANT_DOCKER) images -q $(ELEPHANT_IMAGE_NAME)); \
@@ -42,9 +48,22 @@ warmup:
 	fi
 
 launch: warmup
-	$(ELEPHANT_DOCKER) run -it --rm $(GPU_ARG) --shm-size=8g -v $(ELEPHANT_WORKSPACE):/workspace -p 8080:80 -p 5672:5672 \
-	-e LOCAL_UID=$(shell id -u) -e LOCAL_GID=$(shell id -g) -e NVIDIA_GID=$(ELEPHANT_NVIDIA_GID) \
-	-e RABBITMQ_NODENAME=$(ELEPHANT_RABBITMQ_NODENAME) -e RABBITMQ_NODE_PORT=$(ELEPHANT_RABBITMQ_NODE_PORT) -e ELEPHANT_REDIS_PORT=$(ELEPHANT_REDIS_PORT) \
+	$(ELEPHANT_DOCKER) run -it --rm $(GPU_ARG) --shm-size=8g -v $(ELEPHANT_WORKSPACE):/workspace \
+	-p $(ELEPHANT_HTTP_PORT):$(ELEPHANT_HTTP_PORT) \
+	-p $(ELEPHANT_RABBITMQ_NODE_PORT):$(ELEPHANT_RABBITMQ_NODE_PORT) \
+	-p $(ELEPHANT_RABBITMQ_MANAGEMENT_PORT):$(ELEPHANT_RABBITMQ_MANAGEMENT_PORT) \
+	-e LOCAL_UID=$(shell id -u) \
+	-e LOCAL_GID=$(shell id -g) \
+	-e NVIDIA_GID=$(ELEPHANT_NVIDIA_GID) \
+	-e RABBITMQ_NODENAME=$(ELEPHANT_RABBITMQ_NODENAME) \
+	-e RABBITMQ_NODE_PORT=$(ELEPHANT_RABBITMQ_NODE_PORT) \
+	-e RABBITMQ_MANAGEMENT_PORT=$(ELEPHANT_RABBITMQ_MANAGEMENT_PORT) \
+	-e RABBITMQ_USER=$(ELEPHANT_RABBITMQ_USER) \
+	-e RABBITMQ_PASSWORD=$(ELEPHANT_RABBITMQ_PASSWORD) \
+	-e RABBITMQ_PID_FILE=$(ELEPHANT_RABBITMQ_PID_FILE) \
+	-e ELEPHANT_REDIS_PORT=$(ELEPHANT_REDIS_PORT) \
+	-e ELEPHANT_HTTP_PORT=$(ELEPHANT_HTTP_PORT) \
+	-e ELEPHANT_BATCH_ID=$(ELEPHANT_BATCH_ID) \
 	$(ELEPHANT_IMAGE_NAME)
 
 bash: warmup
@@ -59,7 +78,7 @@ bashroot: warmup
 notebook: warmup
 	$(ELEPHANT_DOCKER) run -it --rm $(GPU_ARG) --shm-size=8g -v $(ELEPHANT_WORKSPACE):/workspace \
 	-e LOCAL_UID=$(shell id -u) -e LOCAL_GID=$(shell id -g) -e AS_LOCAL_USER=1 -e NVIDIA_GID=$(ELEPHANT_NVIDIA_GID) \
-	--network host -p 8888:8888 $(ELEPHANT_IMAGE_NAME) jupyter notebook --no-browser --notebook-dir=/workspace
+	--network host -p $(ELEPHANT_NOTEBOOK_PORT):$(ELEPHANT_NOTEBOOK_PORT) $(ELEPHANT_IMAGE_NAME) jupyter notebook --no-browser --port=$(ELEPHANT_NOTEBOOK_PORT) --notebook-dir=/workspace
 
 test:
 	$(ELEPHANT_DOCKER) build -t $(ELEPHANT_IMAGE_NAME)-test -f Dockerfile-test . && $(ELEPHANT_DOCKER) image prune -f 
@@ -72,23 +91,61 @@ apptainer-init:
 	apptainer run --fakeroot --bind $(HOME):/root elephant.sif
 
 apptainer-launch:
-	apptainer instance start --nv --bind $(HOME),$(HOME)/.elephant_binds/var/lib:/var/lib,$(HOME)/.elephant_binds/var/log:/var/log,$(HOME)/.elephant_binds/var/run:/var/run,$(HOME)/.elephant_binds/etc/nginx:/etc/nginx,$(ELEPHANT_WORKSPACE):/workspace elephant.sif elephant$(ELEPHANT_BATCH_ID)
+	apptainer instance start --nv \
+	--bind \
+	$(HOME),\
+	$(HOME)/.elephant_binds/var/lib:/var/lib,\
+	$(HOME)/.elephant_binds/var/log:/var/log,\
+	$(HOME)/.elephant_binds/var/run:/var/run,\
+	$(HOME)/.elephant_binds/etc/nginx:/etc/nginx,\
+	$(ELEPHANT_WORKSPACE):/workspace \
+	elephant.sif elephant$(ELEPHANT_BATCH_ID)
 	if [ $(ELEPHANT_GPU) = all ]; then \
-		apptainer exec --env RABBITMQ_NODENAME=$(ELEPHANT_RABBITMQ_NODENAME),RABBITMQ_NODE_PORT=$(ELEPHANT_RABBITMQ_NODE_PORT),ELEPHANT_REDIS_PORT=$(ELEPHANT_REDIS_PORT) instance://elephant$(ELEPHANT_BATCH_ID) /start.sh; \
+		apptainer exec \
+		--env RABBITMQ_NODENAME=$(ELEPHANT_RABBITMQ_NODENAME) \
+		--env RABBITMQ_NODE_PORT=$(ELEPHANT_RABBITMQ_NODE_PORT) \
+		--env RABBITMQ_MANAGEMENT_PORT=$(ELEPHANT_RABBITMQ_MANAGEMENT_PORT) \
+		--env RABBITMQ_USER=$(ELEPHANT_RABBITMQ_USER) \
+		--env RABBITMQ_PASSWORD=$(ELEPHANT_RABBITMQ_PASSWORD) \
+		--env RABBITMQ_PID_FILE=$(ELEPHANT_RABBITMQ_PID_FILE) \
+		--env ELEPHANT_REDIS_PORT=$(ELEPHANT_REDIS_PORT) \
+		--env ELEPHANT_HTTP_PORT=$(ELEPHANT_HTTP_PORT) \
+		--env ELEPHANT_BATCH_ID=$(ELEPHANT_BATCH_ID) \
+		instance://elephant$(ELEPHANT_BATCH_ID) /start.sh; \
 	else \
-		apptainer exec --env CUDA_VISIBLE_DEVICES=$(ELEPHANT_GPU),RABBITMQ_NODENAME=$(ELEPHANT_RABBITMQ_NODENAME),RABBITMQ_NODE_PORT=$(ELEPHANT_RABBITMQ_NODE_PORT),ELEPHANT_REDIS_PORT=$(ELEPHANT_REDIS_PORT) instance://elephant$(ELEPHANT_BATCH_ID) /start.sh; \
+		apptainer exec \
+		--env CUDA_VISIBLE_DEVICES=$(ELEPHANT_GPU) \
+		--env RABBITMQ_NODENAME=$(ELEPHANT_RABBITMQ_NODENAME) \
+		--env RABBITMQ_NODE_PORT=$(ELEPHANT_RABBITMQ_NODE_PORT) \
+		--env RABBITMQ_MANAGEMENT_PORT=$(ELEPHANT_RABBITMQ_MANAGEMENT_PORT) \
+		--env RABBITMQ_USER=$(ELEPHANT_RABBITMQ_USER) \
+		--env RABBITMQ_PASSWORD=$(ELEPHANT_RABBITMQ_PASSWORD) \
+		--env RABBITMQ_PID_FILE=$(ELEPHANT_RABBITMQ_PID_FILE) \
+		--env ELEPHANT_REDIS_PORT=$(ELEPHANT_REDIS_PORT) \
+		--env ELEPHANT_HTTP_PORT=$(ELEPHANT_HTTP_PORT) \
+		--env ELEPHANT_BATCH_ID=$(ELEPHANT_BATCH_ID) \
+		instance://elephant$(ELEPHANT_BATCH_ID) /start.sh; \
 	fi
 
 apptainer-shell:
 	if [ $(ELEPHANT_GPU) = all ]; then \
-		apptainer shell --fakeroot --nv --env RABBITMQ_NODENAME=$(ELEPHANT_RABBITMQ_NODENAME) --bind $(HOME),$(HOME)/.elephant_binds/var/lib:/var/lib,$(HOME)/.elephant_binds/var/log:/var/log,$(HOME)/.elephant_binds/var/run:/var/run,$(HOME)/.elephant_binds/etc/nginx:/etc/nginx elephant.sif; \
+		apptainer shell --fakeroot --nv \
+		--bind $(HOME) \
+		--bind $(HOME)/.elephant_binds/var/lib:/var/lib \
+		--bind $(HOME)/.elephant_binds/var/log:/var/log \
+		--bind $(HOME)/.elephant_binds/var/run:/var/run \
+		--bind $(HOME)/.elephant_binds/etc/nginx:/etc/nginx \
+		elephant.sif; \
 	else \
-		apptainer shell --fakeroot --nv --env CUDA_VISIBLE_DEVICES=$(ELEPHANT_GPU) --bind $(HOME),$(HOME)/.elephant_binds/var/lib:/var/lib,$(HOME)/.elephant_binds/var/log:/var/log,$(HOME)/.elephant_binds/var/run:/var/run,$(HOME)/.elephant_binds/etc/nginx:/etc/nginx elephant.sif; \
+		apptainer shell --fakeroot --nv \
+		--env CUDA_VISIBLE_DEVICES=$(ELEPHANT_GPU) \
+		--bind $(HOME) \
+		--bind $(HOME)/.elephant_binds/var/lib:/var/lib \
+		--bind $(HOME)/.elephant_binds/var/log:/var/log \
+		--bind $(HOME)/.elephant_binds/var/run:/var/run \
+		--bind $(HOME)/.elephant_binds/etc/nginx:/etc/nginx \
+		elephant.sif; \
 	fi
 
-apptainer-create-rabbitmq-user:
-	apptainer exec --fakeroot --env RABBITMQ_NODENAME=$(ELEPHANT_RABBITMQ_NODENAME) --bind $(HOME),$(HOME)/.elephant_binds/var/lib:/var/lib,$(HOME)/.elephant_binds/var/log:/var/log,$(HOME)/.elephant_binds/var/run:/var/run elephant.sif docker/create_rabbitmq_user.sh
-
-
 apptainer-stop:
-	apptainer instance stop elephant
+	apptainer instance stop elephant$(ELEPHANT_BATCH_ID)

docker/nginx.conf → docker/nginx.conf.template

@@ -23,7 +23,7 @@ http {
     client_max_body_size 0;
 
     server {
-        listen 80;
+        listen ${ELEPHANT_HTTP_PORT};
         location / {
             try_files $uri @app;
         }

docker/rabbitmq.sh

@@ -7,9 +7,15 @@ rabbitmqctl add_user $RABBITMQ_USER $RABBITMQ_PASSWORD 2>/dev/null ; \
 rabbitmqctl set_user_tags $RABBITMQ_USER administrator ; \
 rabbitmqctl set_permissions -p / $RABBITMQ_USER  ".*" ".*" ".*" ; \
 echo "*** User '$RABBITMQ_USER' with password '$RABBITMQ_PASSWORD' completed. ***" ; \
-echo "*** Log in the WebUI at port 5672 (example: http:/localhost:5672) ***") &
+echo "*** RabbitMQ server is working at $RABBITMQ_NODENAME:$RABBITMQ_NODE_PORT ***"; \
+echo "*** Log in the WebUI at port $RABBITMQ_MANAGEMENT_PORT (example: http://localhost:$RABBITMQ_MANAGEMENT_PORT) ***") &
+
+# enable rabbitmq_management
+rabbitmq-plugins enable rabbitmq_management
+
+echo "management.tcp.port = $RABBITMQ_MANAGEMENT_PORT" > /etc/rabbitmq/rabbitmq.conf
 
 # $@ is used to pass arguments to the rabbitmq-server command.
 # For example if you use it like this: docker run -d rabbitmq arg1 arg2,
 # it will be as you run in the container rabbitmq-server arg1 arg2 
-/etc/init.d/rabbitmq-server $@
+rabbitmq-server $@

docker/setup-rabbitmq.sh

@@ -0,0 +1,14 @@
+#!/usr/bin/env bash
+/etc/init.d/rabbitmq-server start
+rabbitmqctl add_user $RABBITMQ_USER $RABBITMQ_PASSWORD 2>/dev/null
+rabbitmqctl set_user_tags $RABBITMQ_USER administrator
+rabbitmqctl set_permissions -p / $RABBITMQ_USER  ".*" ".*" ".*"
+/etc/init.d/rabbitmq-server stop
+echo "*** User '$RABBITMQ_USER' with password '$RABBITMQ_PASSWORD' completed. ***"
+echo "*** RabbitMQ server is working at $RABBITMQ_NODENAME:$RABBITMQ_NODE_PORT ***"
+echo "*** Log in the WebUI at port $RABBITMQ_MANAGEMENT_PORT (example: http://localhost:$RABBITMQ_MANAGEMENT_PORT) ***"
+
+# enable rabbitmq_management
+rabbitmq-plugins enable rabbitmq_management
+
+echo "management.tcp.port = $RABBITMQ_MANAGEMENT_PORT" > /etc/rabbitmq/rabbitmq.conf

docker/supervisord.conf

@@ -15,7 +15,7 @@ killasgroup=true
 priority=700
 
 [program:nginx]
-command=/usr/sbin/nginx
+command=/bin/bash -c "envsubst '$$ELEPHANT_HTTP_PORT'< /etc/nginx/nginx.conf.template > /etc/nginx/nginx.conf && /usr/sbin/nginx"
 stdout_logfile=/dev/stdout
 stdout_logfile_maxbytes=0
 stderr_logfile=/dev/stderr
@@ -33,7 +33,7 @@ stderr_logfile_maxbytes=0
 priority=600
 
 [program:rabbitmq-server]
-command=/usr/bin/pidproxy /var/lib/rabbitmq/mnesia/rabbitmq.pid /bin/bash -c "/rabbitmq.sh"
+command=/usr/bin/pidproxy %(ENV_RABBITMQ_PID_FILE)s /bin/bash -c "/rabbitmq.sh"
 stdout_logfile=/dev/stdout
 stdout_logfile_maxbytes=0
 stderr_logfile=/dev/stderr

elephant-core/elephant/version.py

@@ -24,4 +24,4 @@
 # ==============================================================================
 """Version definition."""
 
-__version__ = "0.5.2"
+__version__ = "0.5.3"

elephant.def

@@ -1,5 +1,5 @@
 Bootstrap: docker
-From: pytorch/pytorch:1.10.0-cuda11.3-cudnn8-runtime
+From: nvidia/cuda:11.3.1-runtime-ubuntu20.04
 
 %files
     ./docker /docker
@@ -15,8 +15,14 @@ From: pytorch/pytorch:1.10.0-cuda11.3-cudnn8-runtime
     export PYTHONPATH=/app
     export MKL_THREADING_LAYER=GNU
     export GRPC_POLL_STRATEGY=epoll1
+    export PATH=/opt/conda/bin:$PATH
+    export RABBITMQ_USER=user
+    export RABBITMQ_PASSWORD=user
+    export RABBITMQ_MANAGEMENT_PORT=15672
+    export RABBITMQ_PID_FILE=/var/lib/rabbitmq/mnesia/rabbitmq.pid
+    export ElEPHANT_HTTP_PORT=8080
 
-%post
+%post -c /bin/bash
     # Install requirements
     set -x \
     && apt-get update \
@@ -26,33 +32,43 @@ From: pytorch/pytorch:1.10.0-cuda11.3-cudnn8-runtime
     supervisor \
     ca-certificates \
     curl \
-    gnupg && \
+    gnupg \
+    gosu \
+    gettext-base && \
     apt-get clean && \
     rm -rf /var/lib/apt/lists/*
 
     # Install Python modules
     sed -i 's/.\/elephant-core/\/src\/elephant-core/g' /src/environment.yml \
-    && conda install -c conda-forge -y mamba \
+    && curl -OL https://repo.continuum.io/miniconda/Miniconda3-py37_4.11.0-Linux-x86_64.sh \
+    && bash Miniconda3-py37_4.11.0-Linux-x86_64.sh -bfp /opt/conda \
+    && rm Miniconda3-py37_4.11.0-Linux-x86_64.sh \
+    && . /opt/conda/etc/profile.d/conda.sh \
+    && conda init \
+    && echo "conda activate base" >> ~/.bashrc \
+    && conda install -c conda-forge -y mamba==0.19.1 \
+    && mamba clean -qafy \
     && mamba env update -f /src/environment.yml \
     && mamba clean -qafy \
     && rm -rf /src/elephant-core \
     && rm /src/environment.yml
 
     # Install and set up RabbbitMQ
     chmod +x /docker/install-rabbitmq.sh && /docker/install-rabbitmq.sh
+    echo "rabbitmq-server \$@" > /rabbitmq.sh
+    chmod +x /rabbitmq.sh
     cp /docker/rabbitmq-env.conf /etc/rabbitmq/rabbitmq-env.conf
+    export RABBITMQ_USER=user
+    export RABBITMQ_PASSWORD=user
+    export RABBITMQ_MANAGEMENT_PORT=15672
+    cp /docker/setup-rabbitmq.sh /setup-rabbitmq.sh
+    chmod +x /setup-rabbitmq.sh
 
-    RABBITMQ_USER=user && RABBITMQ_PASSWORD=user
-    /etc/init.d/rabbitmq-server start
-    rabbitmqctl add_user $RABBITMQ_USER $RABBITMQ_PASSWORD 2>/dev/null
-    rabbitmqctl set_user_tags $RABBITMQ_USER administrator
-    rabbitmqctl set_permissions -p / $RABBITMQ_USER ".*" ".*" ".*"
-    /etc/init.d/rabbitmq-server stop
+    /setup-rabbitmq.sh
 
     # Set up nginx
-    cp /docker/nginx.conf /etc/nginx/nginx.conf
-    groupadd nginx && useradd -g nginx nginx
-    sed -i 's/listen 80/listen 8080/g' /etc/nginx/nginx.conf
+    cp /docker/nginx.conf.template /etc/nginx/nginx.conf.template
+    groupadd -r nginx && useradd -r -g nginx nginx
 
     # forward request and error logs to docker log collector
     ln -sf /dev/stdout /var/log/nginx/access.log && \
@@ -64,7 +80,6 @@ From: pytorch/pytorch:1.10.0-cuda11.3-cudnn8-runtime
 
     # Custom Supervisord config
     cp /docker/supervisord.conf /etc/supervisor/conf.d/supervisord.conf
-    sed -i 's#/usr/bin/pidproxy /var/lib/rabbitmq/mnesia/rabbitmq.pid /bin/bash -c "/rabbitmq.sh"#rabbitmq-server#g' /etc/supervisor/conf.d/supervisord.conf
     sed -i '/user=user/d' /etc/supervisor/conf.d/supervisord.conf
     sed -i '/group=user/d' /etc/supervisor/conf.d/supervisord.conf
 
@@ -84,6 +99,8 @@ From: pytorch/pytorch:1.10.0-cuda11.3-cudnn8-runtime
     mkdir -p $HOME/.elephant_binds/etc
     cp -a /etc/nginx $HOME/.elephant_binds/etc/
     cp -a /etc/rabbitmq $HOME/.elephant_binds/etc/
+    chown -R $(id -u):$(id -g) $HOME/.elephant_binds
+
 
 %labels
     Author Ko Sugawara <[email protected]>
@@ -92,7 +109,7 @@ From: pytorch/pytorch:1.10.0-cuda11.3-cudnn8-runtime
     This is a container to run ELEPHANt server.
     Usage:
     apptainer build --fakeroot elephant.sif elephant.def
-    apptainer run --bind $HOME elephant.sif
+    apptainer run --fakeroot --bind $HOME:/root elephant.sif
     apptainer instance start --nv --bind $HOME,$HOME/.elephant_binds/var/lib:/var/lib,$HOME/.elephant_binds/var/log:/var/log,$HOME/.elephant_binds/var/run:/var/run,$HOME/.elephant_binds/etc/nginx:/etc/nginx,$HOME/.elephant_binds/etc/rabbitmq:/etc/rabbitmq,$ELEPHANT_WORKSPACE:/workspace elephant.sif elephant
     apptainer exec instance://elephant python /opt/elephant/script/dataset_generator.py --uint16 /workspace/datasets/elephant-demo/elephant-demo.h5 /workspace/datasets/elephant-demo
     SINGULARITYENV_CUDA_VISIBLE_DEVICES=0 apptainer exec instance://elephant /start.sh

elephant_server.ipynb

@@ -39,7 +39,7 @@
       },
       "outputs": [],
       "source": [
-        "%env ELEPHANT_SERVER_VERSION = v0.5.2"
+        "%env ELEPHANT_SERVER_VERSION = v0.5.3"
       ]
     },
     {
@@ -380,4 +380,4 @@
   },
   "nbformat": 4,
   "nbformat_minor": 0
-}
+}