Bluebrain CoreNeuron on Backend.AI

Author: hephaex

vendor/bluebrain/Dockerfile

@@ -0,0 +1,105 @@
+FROM nvcr.io/hpc/pgi-compilers:ce
+
+ENV PYTHONUNBUFFERED=1 \
+    LD_LIBRARY_PATH=/usr/local/cuda/lib64/stubs:/usr/local/cuda/lib64:/usr/local/nvidia/lib64:/usr/local/lib:$LD_LIBRARY_PATH \
+    PATH=/usr/local/nvidia/bin:/usr/local/cuda/bin:/usr/local/sbin:/usr/local/bin:/usr/sbin:/usr/bin:/sbin:/bin:$PATH \
+    LANG=C.UTF-8
+
+ENV CC=mpicc
+ENV CXX=mpicxx
+
+RUN apt-get update -y && \
+    apt-get install -y \
+    	gcc g++ make \
+	gfortran \
+	git \
+	python3 python3-pip \
+        xz-utils \
+        wget curl git-core \
+        vim-tiny bzip2 zip unzip \
+        libssl-dev \
+        libmpdec2 \
+        proj-bin libproj-dev \
+        libgeos-dev libgeos++-dev \
+        mime-support \
+	mpich \
+	bison \
+	flex \
+        libssl-dev && \
+    apt-get clean && \
+    rm -rf /var/lib/apt/lists/
+	
+WORKDIR /tmp
+RUN wget https://github.com/Kitware/CMake/releases/download/v3.15.4/cmake-3.15.4.tar.gz && \
+    tar xvf cmake-3.15.4.tar.gz  && \
+    cd cmake-3.15.4/ && \
+    ./configure && \
+    make -j${nproc} && \
+    make install && \
+    rm /tmp/cmake-3.15.4.tar.gz
+
+# python alternative support
+RUN update-alternatives --install /usr/bin/python python /usr/bin/python3 2
+
+WORKDIR /opt
+RUN git clone https://github.com/BlueBrain/mod2c.git && \
+    cd mod2c && \
+    mkdir build && cd build && \
+    cmake .. \
+      -DCMAKE_C_FLAGS:STRING="-O2" \
+      -DCMAKE_CXX_FLAGS:STRING="-O2" \
+      -DCOMPILE_LIBRARY_TYPE=STATIC \
+      -DCUDA_HOST_COMPILER=`which gcc` \
+      -DCUDA_PROPAGATE_HOST_FLAGS=OFF \
+      -DENABLE_SELECTIVE_GPU_PROFILING=ON \
+      -DENABLE_OPENACC=ON \
+    && \
+    make -j${nproc} && \
+    make install
+
+WORKDIR /opt
+RUN git clone --recursive https://github.com/BlueBrain/CoreNeuron.git && \
+    cd CoreNeuron && \
+    mkdir build && \
+    cd build && \
+    cmake .. && \
+    make -j${nproc} && \
+    make install 
+    
+RUN curl https://bootstrap.pypa.io/get-pip.py | python3 && \
+    python3 -m pip install --no-cache-dir -U setuptools && \
+    python3 -m pip install --no-cache-dir h5py && \
+    python3 -m pip install --no-cache-dir Cython && \
+    python3 -m pip install --no-cache-dir matplotlib bokeh && \
+    python3 -m pip install --no-cache-dir versioneer==0.17 && \
+    python3 -m pip install --no-cache-dir pyproj Cartopy==0.16 && \
+    python3 -m pip install --no-cache-dir pandas && \
+    python3 -m pip install --no-cache-dir seaborn && \
+    python3 -m pip install --no-cache-dir pillow && \
+    python3 -m pip install --no-cache-dir networkx cvxpy && \
+    python3 -m pip install --no-cache-dir scikit-learn scikit-image && \
+    python3 -m pip install --no-cache-dir pygments && \
+    python3 -m pip install --no-cache-dir ipython && \
+    python3 -m pip install --no-cache-dir jupyter && \
+    python3 -m pip install --no-cache-dir jupyterlab && \
+    rm -rf /root/.cache && \
+    rm -f /tmp/*.whl
+
+# Backend.AI specifics
+LABEL ai.backend.kernelspec="1" \
+      ai.backend.envs.corecount="OPENBLAS_NUM_THREADS,OMP_NUM_THREADS,NPROC" \
+      ai.backend.features="batch query uid-match user-input" \
+      ai.backend.base-distro="ubuntu16.04" \
+      ai.backend.resource.min.cpu="1" \
+      ai.backend.resource.min.mem="1g" \
+      ai.backend.resource.min.cuda.device=1 \
+      ai.backend.resource.min.cuda.shares=0.1 \
+      ai.backend.runtime-type="python" \
+      ai.backend.runtime-path="/usr/local/bin/python3" \
+      ai.backend.service-ports="ipython:pty:3000,jupyter:http:8080,jupyterlab:http:8090"
+
+COPY policy.yml /etc/backend.ai/jail/policy.yml
+
+WORKDIR /home/work
+# vim: ft=dockerfile
+

vendor/bluebrain/policy.yml

@@ -0,0 +1,27 @@
+whitelist_paths:
+  OP_OPEN: ["*"]
+  OP_ACCESS: ["*"]
+  OP_EXEC: ["*"]
+  OP_STAT: ["*"]
+  OP_CHMOD: ["/home/work/*", "/tmp/*"]
+exec_allowance: -1
+fork_allowance: -1
+max_child_procs: 32
+extra_envs: []
+preserved_env_keys: [
+  "HOME", "PATH", "LANG",
+  "USER", "SHELL", "TERM",
+  "LD_LIBRARY_PATH",
+  "LD_PRELOAD",
+  # Python-specific
+  "PYTHONPATH",
+  "PYTHONUNBUFFERED",
+  "MPLCONFIGDIR",
+  "OPENBLAS_NUM_THREADS",
+]
+
+diff_to_default: true
+
+# Following syscalls are blindly allowed.
+# IMPORTANT: ptrace MUST NOT be included!
+allowed_syscalls: