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Merge pull request #292 from openworm/development
v0.9 Dockerfile release!
2 parents 5c0b60e + 53faeb3 commit 6a56948

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‎.dockerignore‎

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.git
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.github
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.DS_Store
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.gitignore
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.openworm.yml
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output

‎.gitignore‎

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.DS_Store
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output/C2*
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/rebuild.sh
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/output/siminfo.py
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/output/wor*

‎Dockerfile‎

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FROM ubuntu:16.04
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MAINTAINER David Lung "[email protected]"
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LABEL maintainer="David Lung ([email protected]); Padraig Gleeson ([email protected])"
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ARG INTEL_SDK_VERSION=2017_7.0.0.2511_x64
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COPY ./silent-intel-sdk.cfg /tmp/silent-intel-sdk.cfg
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#COPY ./silent-intel-sdk.cfg /tmp/silent-intel-sdk.cfg
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ARG USR=ow
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ENV USER=$USR
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RUN apt-get update && \
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apt-get upgrade -y && \
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apt-get dist-upgrade -y
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RUN mkdir -p /etc/sudoers.d && \
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export uid=1000 gid=1000 && \
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mkdir -p /home/$USER && \
@@ -34,39 +30,23 @@ ENV DEBIAN_FRONTEND noninteractive # TODO: change
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#RUN useradd -ms /bin/bash $USER
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################################################################################
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######## Update/install essential libraries
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RUN apt-get update && apt-get install -y --no-install-recommends apt-utils \
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wget \
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nano \
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htop \
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build-essential \
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make \
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git \
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automake \
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autoconf \
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g++ \
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rpm \
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libtool \
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libncurses5-dev \
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zlib1g-dev \
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bison \
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flex \
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lsb-core \
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sudo \
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xorg \
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openbox \
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x11-xserver-utils \
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wget nano htop build-essential make git automake autoconf \
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g++ rpm libtool libncurses5-dev zlib1g-dev bison flex lsb-core \
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sudo xorg openbox x11-xserver-utils \
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libxext-dev libncurses-dev python-dev mercurial \
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freeglut3-dev libglu1-mesa-dev libglew-dev python-dev python-pip python-lxml python-numpy python-scipy python-tk \
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kmod dkms \
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linux-source linux-headers-generic \
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kmod dkms linux-source linux-headers-generic \
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maven openjdk-8-jdk \
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python-setuptools python-yaml libnuma1 \
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openmpi-bin libopenmpi-dev \
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openmpi-bin libopenmpi-dev \
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libgl1-mesa-glx libgl1-mesa-dri libfreetype6-dev \
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libpng12-dev libxft-dev python-matplotlib xubuntu-desktop ffmpeg xvfb tmux
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#RUN sudo pip install --upgrade matplotlib
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#RUN sudo pip install --upgrade pip
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#RUN sudo apt-get install nvidia-opencl-dev
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RUN sudo usermod -a -G video $USER
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ENV HOME /home/$USER
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WORKDIR $HOME
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################################################################################
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######## Install NEURON simulator
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RUN mkdir neuron && \
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cd neuron && \
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git clone https://github.com/nrnhines/iv.git && \
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cd src/nrnpython && \
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sudo python setup.py install
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RUN mkdir intel-opencl-tmp && \
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cd intel-opencl-tmp && \
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mkdir intel-opencl && \
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wget http://registrationcenter-download.intel.com/akdlm/irc_nas/11396/SRB5.0_linux64.zip && \
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unzip SRB5.0_linux64.zip && \
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tar -C intel-opencl -Jxf intel-opencl-r5.0-63503.x86_64.tar.xz && \
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tar -C intel-opencl -Jxf intel-opencl-devel-r5.0-63503.x86_64.tar.xz && \
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tar -C intel-opencl -Jxf intel-opencl-cpu-r5.0-63503.x86_64.tar.xz && \
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sudo cp -R intel-opencl/* / && \
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sudo ldconfig && \
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cd .. && \
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sudo rm -r intel-opencl-tmp
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RUN wget http://registrationcenter-download.intel.com/akdlm/irc_nas/vcp/11705/intel_sdk_for_opencl_$INTEL_SDK_VERSION.tgz && \
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tar xvf intel_sdk_for_opencl_$INTEL_SDK_VERSION.tgz && \
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cd intel_sdk_for_opencl_$INTEL_SDK_VERSION && \
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sudo ./install.sh --silent /tmp/silent-intel-sdk.cfg && \
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cd $HOME && \
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rm intel_sdk_for_opencl_$INTEL_SDK_VERSION.tgz && \
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sudo rm /tmp/silent-intel-sdk.cfg
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################################################################################
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######## Install pyNeuroML for handling NeuroML network model
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RUN git clone https://github.com/NeuroML/pyNeuroML.git && \
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cd pyNeuroML && \
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git checkout ow-0.8a && \
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git checkout ow-0.9 && \
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sudo python setup.py install
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################################################################################
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######## Install PyOpenWorm
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RUN pip install pyparsing==2.0.3 Jinja2==2.11.1 configparser==4.0.2 GitPython==3.0.7 gitdb2==2.0.6
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RUN git clone https://github.com/openworm/PyOpenWorm.git && \
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cd PyOpenWorm && \
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git checkout 7ff1266 && \
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git checkout ow-0.9 && \
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sudo apt-get install -y python-cffi && \
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sudo python setup.py install && \
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pow clone https://github.com/openworm/OpenWormData.git
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################################################################################
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######## Install c302 for building neuronal network models
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RUN git clone https://github.com/openworm/c302.git && \
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cd c302 && \
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git checkout ow-0.9 && \
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sudo python setup.py install
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RUN git clone https://github.com/openworm/CElegansNeuroML.git && \
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cd CElegansNeuroML && \
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# Pointing this at a recent commit that adds python 3 support!
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# https://github.com/openworm/CElegansNeuroML/commit/c8b13642d79335bb8157431b83624e33d50a166e
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git checkout c8b1364
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################################################################################
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######## Install Sibernetic for the worm body model
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RUN git clone https://github.com/openworm/sibernetic.git && \
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cd sibernetic && \
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# fixed to a specific commit in development branch:
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# https://github.com/openworm/sibernetic/commit/3eb9914db040fff852cba76ef8f4f39d0bed3294
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git checkout 3eb9914 && \
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make clean && make all
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# fixed to a specific branch
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git checkout ow-0.9
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RUN cp c302/pyopenworm.conf sibernetic/ # Temp step until PyOpenWorm can be run from any dir...
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################################################################################
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######## Set some paths//environment variables
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ENV JNML_HOME=$HOME/jNeuroML
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ENV PATH=$PATH:$JNML_HOME
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ENV CPU=x86_64
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ENV PATH=$PATH:$IV/$CPU/bin:$N/$CPU/bin
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ENV NEURON_HOME=$N/$CPU
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ENV C302_HOME=$HOME/CElegansNeuroML/CElegans/pythonScripts/c302
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ENV C302_HOME=$HOME/c302/c302
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ENV SIBERNETIC_HOME=$HOME/sibernetic
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ENV PYTHONPATH=$PYTHONPATH:$C302_HOME:$SIBERNETIC_HOME
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ENV PYTHONPATH=$PYTHONPATH:$HOME/c302:$SIBERNETIC_HOME
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# Not working with --chown=$USER:$USER
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COPY ./master_openworm.py $HOME/master_openworm.py
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RUN sudo chown $USER:$USER $HOME/master_openworm.py
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################################################################################
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######## Install Intel OpenCL libraries needed for Sibernetic
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RUN mkdir intel-opencl-tmp && \
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cd intel-opencl-tmp && \
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mkdir intel-opencl && \
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wget http://registrationcenter-download.intel.com/akdlm/irc_nas/11396/SRB5.0_linux64.zip && \
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unzip SRB5.0_linux64.zip && \
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tar -C intel-opencl -Jxf intel-opencl-r5.0-63503.x86_64.tar.xz && \
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tar -C intel-opencl -Jxf intel-opencl-devel-r5.0-63503.x86_64.tar.xz && \
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tar -C intel-opencl -Jxf intel-opencl-cpu-r5.0-63503.x86_64.tar.xz && \
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sudo cp -R intel-opencl/* / && \
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sudo ldconfig && \
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cd .. && \
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sudo rm -r intel-opencl-tmp
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RUN sudo cp -R /opt/intel/opencl/include/CL /usr/include/ && \
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sudo apt install -y ocl-icd-opencl-dev
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#sudo ln -s /opt/intel/opencl/libOpenCL.so.1 /usr/lib/libOpenCL.so
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################################################################################
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######## Build Sibernetic
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RUN cd sibernetic && \
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make clean && make all
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# intel i5, hd 5500, linux 4.15.0-39-generic
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# ./Release/Sibernetic -f worm -no_g device=CPU 190ms
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# ./Release/Sibernetic -f worm -no_g device=GPU 150ms (initialization takes some time)
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# Intel(R) Xeon(R) CPU E5-1650 v4 @ 3.60GHz, linux 4.4.0-139-generic
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# ./Release/Sibernetic -f worm -no_g device=CPU 60ms
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#
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# after installing the nvidia driver used in host:
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## wget http://us.download.nvidia.com/tesla/390.30/nvidia-diag-driver-local-repo-ubuntu1604-390.30_1.0-1_amd64.deb
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## sudo dpkg -i nvidia-diag-driver-local-repo-ubuntu1604-390.30_1.0-1_amd64.deb
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## sudo apt-key add /var/nvidia-diag-driver-local-repo-390.30/7fa2af80.pub
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## sudo apt-get update
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## sudo apt-get install -y cuda-drivers
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# ./Release/Sibernetic -f worm -no_g device=GPU 37ms

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