docs/source/tuto_network_calibration/Dockerfile

   1 FROM debian:11.1-slim
   2
   3 RUN printf '%s\n' \
   4     "deb    [check-valid-until=no, trusted=yes] http://snapshot.debian.org/archive/debian/20211101T024700Z/ bullseye main contrib non-free" \
   5     "deb-src [check-valid-until=no, trusted=yes] http://snapshot.debian.org/archive/debian/20211101T024700Z/ bullseye main contrib non-free" \
   6     "deb     [check-valid-until=no, trusted=yes] http://snapshot.debian.org/archive/debian/20211101T024700Z/ bullseye-updates main contrib non-free" \
   7     "deb-src [check-valid-until=no, trusted=yes] http://snapshot.debian.org/archive/debian/20211101T024700Z/ bullseye-updates main contrib non-free" > /etc/apt/sources.list \
   8 && \
   9     apt-get -o Acquire::Check-Valid-Until=false update \
  10 && \
  11     apt-get install -y --no-install-recommends \
  12 # R
  13     r-base-core \
  14     r-cran-ggplot2 \
  15     r-cran-dplyr \
  16     r-cran-irkernel \
  17     r-cran-quantreg \
  18 # simgrid dependencies
  19     g++ \
  20     gcc \
  21     git \
  22     valgrind \
  23     gfortran \
  24     libboost-dev \
  25     libboost-all-dev \
  26     libeigen3-dev \
  27     cmake \
  28     dpkg-dev \
  29 # misc tools
  30     curl \
  31 # python
  32     python3-dev \
  33     python3-pip \
  34     python3-setuptools \
  35     python3-pandas \
  36     python3-matplotlib \
  37 # jupyterlab dependencies
  38     libffi-dev \
  39     pandoc \
  40 && \
  41     apt-get clean \
  42     && rm -rf /var/lib/apt/lists/*
  43
  44 # pycewise
  45 RUN pip install --no-cache-dir --no-dependencies \
  46     pycewise==0.1.4 \
  47     plotnine==0.8.0 \
  48     patsy==0.5.2 \
  49     mizani==0.7.3 \
  50     palettable==3.3.0 \
  51     scipy==1.7.2 \
  52     statsmodels==0.13.0 \
  53     descartes==1.1.0
  54
  55 # R package not available at debian's cran
  56 RUN R -e "install.packages('remotes', dependencies=TRUE, repos='http://cran.rstudio.com/')" && \
  57     R -e "require(remotes); install_version('Ckmeans.1d.dp','4.3.3', dependencies=TRUE, repos='http://cran.rstudio.com/')"
  58
  59 # python jupyterlab packages
  60 RUN pip install --no-cache-dir --upgrade pip && \
  61     pip install --no-cache-dir \
  62     jupyterlab==3.2.3 \
  63     papermill==2.3.3 \
  64     ipywidgets==7.6.5
  65
  66 # simgrid
  67 RUN mkdir -p /source && cd /source && git clone --depth=1 https://framagit.org/simgrid/simgrid.git simgrid.git && \
  68     cd simgrid.git && \
  69     cmake -DCMAKE_INSTALL_PREFIX=/usr/ -Denable_documentation=OFF -Denable_smpi=ON -Denable_compile_optimizations=ON . && \
  70     make -j4 install
  71
  72 # platform-calibration
  73 RUN cd /source && git clone --depth=1 https://framagit.org/simgrid/platform-calibration.git && \
  74     cd platform-calibration && \
  75     git checkout 899f044658246fb86f24e4efc96489df546ad3d3 && \
  76     cd src/calibration && \
  77     sed -i -e 's/#define NB_RUNS .*/#define NB_RUNS 1/g' calibrate.c && \
  78     make CC=smpicc
  79
  80 # get old calibration data for dahu cluster
  81 RUN curl -s -L -o /source/simgrid.git/docs/source/tuto_network_calibration/grenoble_2018-08-29_1808878.zip \
  82     https://github.com/Ezibenroc/calibration_analysis/raw/4837a5d841380ab3dfdbfbc919eab485c08890e9/dahu/mpi/grenoble_2018-08-29_1808878.zip
  83
  84 # tuto_network_calibration compilation
  85 RUN cd /source/simgrid.git/docs/source/tuto_network_calibration && \
  86     cmake . && \
  87     make
  88
  89 # prepare files for execution
  90 RUN cd /source/simgrid.git/docs/source/tuto_network_calibration && \
  91     cp grenoble_2018-08-29_1808878.zip /tmp/ && \
  92     cd /tmp/ && unzip grenoble_2018-08-29_1808878.zip && \
  93     sed -i 1d exp.csv
  94
  95 WORKDIR /source/simgrid.git/docs/source/tuto_network_calibration/
  96 ENTRYPOINT ["jupyter", "lab", "--ip=0.0.0.0", "--allow-root"]