ci: include duration to aws container

refactor: install container dependencies from source

.github/workflows/aws-container.yml

@@ -34,6 +34,7 @@ jobs:
         aws-secret-access-key: ${{ secrets.AWS_SECRET_ACCESS_KEY }}
         aws-region: ${{ secrets.AWS_REGION_NAME }}
         role-to-assume: github-actions-role
+        role-duration-seconds: 7200
 
     - name: Login to Amazon ECR
       id: login-ecr

Dockerfile

@@ -1,4 +1,4 @@
-FROM ubuntu:20.04
+FROM python:3.9-slim-buster
 
 LABEL Tyler Sutterley "[email protected]"
 
@@ -7,47 +7,301 @@ ENV DEBIAN_FRONTEND="noninteractive" TZ="America/Los_Angeles"
 RUN useradd --create-home --shell /bin/bash pytmd
 
 RUN apt-get update -y && \
-    apt-get install -y \
-        openmpi-bin \
-        mpi-default-bin \
-        openmpi-doc \
-        libopenmpi-dev \
-        python3-dev \
-        python3-pip \
-        gdal-bin \
-        libgdal-dev \
-        libproj-dev \
-        proj-data \
-        proj-bin \
-        libgeos-dev \
-        libhdf5-openmpi-dev \
-        libnetcdf-dev \
-        git && \
+    apt-get install -y --no-install-recommends \
+        autoconf \
+        automake \
+        build-essential \
+        ca-certificates \
+        cmake \
+        git \
+        libboost-dev \
+        libexpat1-dev \
+        libldap2-dev \
+        libtool \
+        liburiparser-dev \
+        libxml2-dev  \
+        pkg-config \
+        wget \
+        unzip && \
     apt-get clean
 
+WORKDIR /tmp
+
+ENV JOBS 2
+
+ENV CFLAGS="-fPIC"
+ENV ZLIB_VERSION=1.2.11
+RUN wget -q http://zlib.net/zlib-${ZLIB_VERSION}.tar.gz && \
+    tar -xzf zlib-${ZLIB_VERSION}.tar.gz && \
+    cd zlib-${ZLIB_VERSION} && \
+    ./configure --prefix=/usr/local && \
+    make --quiet --jobs=${JOBS} && \
+    make --quiet install && \
+    cd contrib/minizip && \
+    autoreconf -fvi && \
+    ./configure --quiet --prefix=/usr/local/ && \
+    make --quiet --jobs=${JOBS} && \
+    make --quiet install && \
+    make clean
+
+ENV CFLAGS="-fPIC"
+ENV SZIP_SHORT_VERSION=2.1.1
+ENV SZIP_VERSION=2.1.1
+RUN wget -q https://support.hdfgroup.org/ftp/lib-external/szip/${SZIP_SHORT_VERSION}/src/szip-${SZIP_VERSION}.tar.gz && \
+    tar -xzf szip-${SZIP_VERSION}.tar.gz && \
+    cd szip-${SZIP_VERSION} && \
+    ./configure --quiet --prefix=/usr/local && \
+    make --quiet --jobs=${JOBS} && \
+    make --quiet install && \
+    make clean
+
+ENV OPENSSL_SHORT_VERSION=1.1.1
+ENV OPENSSL_VERSION=1.1.1k
+RUN wget -q https://www.openssl.org/source/openssl-${OPENSSL_VERSION}.tar.gz && \
+    tar -xzf openssl-${OPENSSL_VERSION}.tar.gz && \
+    cd openssl-${OPENSSL_VERSION} && \
+    ./config shared --prefix=/usr/local && \
+    make --quiet --jobs=${JOBS} && \
+    make --quiet install && \
+    make clean
+
+ENV CURL_VERSION=7.77.0
+RUN wget -q https://curl.haxx.se/download/curl-${CURL_VERSION}.tar.gz && \
+    tar -xzf curl-${CURL_VERSION}.tar.gz && \
+    cd curl-${CURL_VERSION} && \
+    ./configure --quiet \
+        --enable-versioned-symbols \
+        --enable-openssl-auto-load-config \
+        --with-openssl \
+        --with-zlib=/usr/local \
+        --prefix=/usr/local && \
+    make --quiet --jobs=${JOBS} && \
+    make --quiet install && \
+    make clean
+
+ENV XZ_VERSION=5.2.5
+RUN wget -q https://tukaani.org/xz/xz-${XZ_VERSION}.tar.gz && \
+    tar -xzf xz-${XZ_VERSION}.tar.gz && \
+    cd xz-${XZ_VERSION} && \
+    ./configure --quiet --prefix=/usr/local && \
+    make --quiet --jobs=${JOBS} && \
+    make --quiet install && \
+    make clean
+
+ENV OPENMPI_SHORT_VERSION=v4.1
+ENV OPENMPI_VERSION=4.1.1
+RUN wget -q https://download.open-mpi.org/release/open-mpi/${OPENMPI_SHORT_VERSION}/openmpi-${OPENMPI_VERSION}.tar.gz && \
+    tar -xzf openmpi-${OPENMPI_VERSION}.tar.gz && \
+    cd openmpi-${OPENMPI_VERSION} && \
+    ./configure --quiet --prefix=/usr/local && \
+    make all install && \
+    make clean
+
+ENV SQLITE_VERSION=3350500
+ENV SQLITE_YEAR 2021
+RUN wget -q https://sqlite.org/${SQLITE_YEAR}/sqlite-autoconf-${SQLITE_VERSION}.tar.gz && \
+    tar -xzf sqlite-autoconf-${SQLITE_VERSION}.tar.gz && \
+    cd sqlite-autoconf-${SQLITE_VERSION} && \
+    ./configure --quiet --prefix=/usr/local && \
+    make --quiet --jobs=${JOBS} && \
+    make --quiet install && \
+    make clean
+
+ENV LIBJPEG_SHORT_VERSION=9d
+ENV LIBJPEG_VERSION=v9d
+RUN wget -q http://ijg.org/files/jpegsrc.${LIBJPEG_VERSION}.tar.gz && \
+    tar -xzf jpegsrc.${LIBJPEG_VERSION}.tar.gz && \
+    cd jpeg-${LIBJPEG_SHORT_VERSION} && \
+    ./configure --quiet --prefix=/usr/local && \
+    make --quiet --jobs=${JOBS} && \
+    make --quiet install && \
+    make clean
+
+ENV ZLIBLIB="/usr/local/lib"
+ENV ZLIBINC="/usr/local/include"
+ENV CPPFLAGS="-I/usr/local/include"
+ENV LDFLAGS="-L/usr/local/lib"
+ENV LD_LIBRARY_PATH="${ZLIBLIB}:${LD_LIBRARY_PATH}"
+ENV CFLAGS="-Wall -O -funroll-loops -malign-loops=2 -malign-functions=2"
+ENV LIBPNG_VERSION=1.6.37
+RUN wget -q https://download.sourceforge.net/libpng/libpng-${LIBPNG_VERSION}.tar.gz && \
+    tar -xzf libpng-${LIBPNG_VERSION}.tar.gz && \
+    cd libpng-${LIBPNG_VERSION} && \
+    ./configure --quiet --prefix=/usr/local && \
+    make --quiet --jobs=${JOBS} && \
+    make --quiet install && \
+    make clean
+
+ENV LIBTIFF_VERSION=4.2.0
+RUN wget -q https://download.osgeo.org/libtiff/tiff-${LIBTIFF_VERSION}.tar.gz && \
+    tar -xzf tiff-${LIBTIFF_VERSION}.tar.gz && \
+    cd tiff-${LIBTIFF_VERSION} && \
+    ./configure --quiet --prefix=/usr/local \
+        --with-jpeg-include-dir=/usr/local/include \
+        --with-jpeg-lib-dir=/usr/local/lib && \
+    make --quiet --jobs=${JOBS} && \
+    make --quiet install && \
+    make clean
+
+ENV LIBKML_VERSION=1.3.0
+RUN wget -q https://github.com/libkml/libkml/archive/${LIBKML_VERSION}.tar.gz && \
+    tar -xzf ${LIBKML_VERSION}.tar.gz && \
+    cd libkml-${LIBKML_VERSION} && \
+    mkdir build && \
+    cd build && \
+    cmake \
+        -DZLIB_INCLUDE_DIR=/usr/local/include \
+        -DMINIZIP_LIBRARY=/usr/local/lib \
+        -DMINIZIP_INCLUDE_DIR=/usr/local/lib \
+        -DCMAKE_BUILD_TYPE=Release \
+        -DCMAKE_INSTALL_PREFIX=/usr/local/ .. && \
+    make --quiet --jobs=${JOBS} && \
+    make --quiet install && \
+    make clean
+
+ENV CC=mpicc
+ENV HDF5_VERSION=1.10.5
+RUN wget -q https://support.hdfgroup.org/ftp/HDF5/current/src/hdf5-${HDF5_VERSION}.tar.gz && \
+    tar -xzf hdf5-${HDF5_VERSION}.tar.gz && \
+    cd hdf5-${HDF5_VERSION} && \
+    ./configure --quiet \
+        --enable-parallel \
+        --enable-hl \
+        --enable-shared \
+        --prefix=/usr/local \
+        --with-zlib=/usr/local \
+        --with-szlib=/usr/local && \
+    make --quiet --jobs=${JOBS} && \
+    make --quiet install && \
+    make clean
+
+ENV CC=mpicc
+ENV CPPFLAGS="-I/usr/local/include"
+ENV LDFLAGS="-L/usr/local/lib -lhdf5_hl -lhdf5 -lz -lm -lcurl"
+ENV NETCDF_VERSION=4.7.4
+RUN wget -q ftp://ftp.unidata.ucar.edu/pub/netcdf/netcdf-c-${NETCDF_VERSION}.tar.gz && \
+    tar -xzf netcdf-c-${NETCDF_VERSION}.tar.gz && \
+    cd netcdf-c-${NETCDF_VERSION} && \
+    ./configure --quiet \
+        --enable-shared \
+        --enable-parallel-tests \
+        --enable-netcdf-4 \
+        --enable-nczarr \
+        --prefix=/usr/local && \
+    make --quiet --jobs=${JOBS} && \
+    make --quiet install && \
+    make clean
+
+ENV GEOS_VERSION=3.9.1
+RUN wget -q https://download.osgeo.org/geos/geos-${GEOS_VERSION}.tar.bz2 && \
+    tar -xjf geos-${GEOS_VERSION}.tar.bz2 && \
+    cd geos-${GEOS_VERSION} && \
+    ./configure --quiet --prefix=/usr/local && \
+    make --quiet --jobs=${JOBS} && \
+    make --quiet install && \
+    make clean
+
+ENV PROJ_VERSION=7.2.1
+ENV PROJ_DATUMGRID_VERSION=1.8
+ENV PROJ_NETWORK ON
+ENV SQLITE3_CFLAGS="-I/usr/local/include"
+ENV SQLITE3_LIBS="-L/usr/local/lib -lsqlite3"
+RUN wget -q https://download.osgeo.org/proj/proj-${PROJ_VERSION}.tar.gz && \
+    wget -q http://download.osgeo.org/proj/proj-datumgrid-${PROJ_DATUMGRID_VERSION}.zip && \
+    tar -xzf proj-${PROJ_VERSION}.tar.gz && \
+    unzip proj-datumgrid-${PROJ_DATUMGRID_VERSION}.zip -d proj-${PROJ_VERSION}/data/ && \
+    cd proj-${PROJ_VERSION} && \
+    mkdir build && \
+    cd build && \
+    cmake \
+        -DSQLITE3_INCLUDE_DIR=/usr/local/include/ \
+        -DSQLITE3_LIBRARY=/usr/local/lib/libsqlite3.so \
+        -DTIFF_INCLUDE_DIR=/usr/local/include \
+        -DTIFF_LIBRARY_RELEASE=/usr/local/lib/libtiff.so \
+        -DCURL_INCLUDE_DIR=/usr/local/include/ \
+        -DCURL_LIBRARY=/usr/local/lib/libcurl.so \
+        -DPYTHON_EXECUTABLE=/usr/local/bin/python3 \
+        -DCMAKE_BUILD_TYPE=Release \
+        -DCMAKE_INSTALL_PREFIX=/usr/local/ .. && \
+    cmake --build . && \
+    make --quiet --jobs=${JOBS} && \
+    make --quiet install && \
+    make clean
+
+ENV CC=mpicc
+ENV CPPFLAGS="-I/usr/local/include"
+ENV LDFLAGS="-L/usr/local/lib"
+ENV LIBKML_CFLAGS="/usr/local/include"
+ENV LIBKML_LIB="/usr/local/lib"
+ENV HDF5_CFLAGS="--enable-parallel --enable-hl --enable-shared"
+ENV HDF5_INCLUDE="/usr/local/include"
+ENV HDF5_LIBS="/usr/local/lib"
+ENV GDAL_VERSION=3.3.0
+RUN wget -q https://download.osgeo.org/gdal/CURRENT/gdal-${GDAL_VERSION}.tar.gz && \
+    tar -xzf gdal-${GDAL_VERSION}.tar.gz && \
+    cd gdal-${GDAL_VERSION} && \
+    ./configure --quiet \
+        --disable-debug \
+        --disable-static \
+        --with-hdf5=/usr/local \
+        --with-netcdf=/usr/local \
+        --with-curl=/usr/local/bin/curl-config \
+        --with-crypto=/usr/local \
+        --with-geos=/usr/local/bin/geos-config \
+        --with-geotiff \
+        --with-hide-internal-symbols=yes \
+        --with-libkml=/usr/local \
+        --with-libkml-inc=/usr/local/include \
+        --with-libkml-lib=/usr/local/lib \
+        --with-liblzma=/usr/local \
+        --with-libtiff=/usr/local \
+        --with-libz=/usr/local \
+        --with-jpeg=/usr/local \
+        --with-openjpeg \
+        --with-png=/usr/local \
+        --with-proj=/usr/local \
+        --with-sqlite3=/usr/local \
+        --with-proj=/usr/local \
+        --with-rename-internal-libgeotiff-symbols=yes \
+        --with-rename-internal-libtiff-symbols=yes \
+        --with-threads=yes \
+        --without-hdf4 \
+        --without-idb \
+        --without-jpeg12 \
+        --without-perl \
+        --without-python \
+        --prefix=/usr/local && \
+    make --quiet --jobs=${JOBS} && \
+    make --quiet install && \
+    make clean
+
+RUN ldconfig
+
+RUN rm -rf /tmp/*
+
 WORKDIR /home/pytmd
 
 ENV MPICC=mpicc
 ENV CC=mpicc
 ENV HDF5_MPI="ON"
 
 RUN pip3 install --no-cache-dir --no-binary=h5py,cartopy \
-        setuptools_scm \
+        cartopy \
+        gdal \
+        h5py \
+        lxml \
+        matplotlib \
         mpi4py \
+        netCDF4 \
         numpy \
-        scipy \
-        lxml \
+        pandas \
         pyproj \
         python-dateutil \
         pyyaml \
-        pandas \
         scikit-learn \
-        matplotlib \
-        gdal \
-        netCDF4 \
-        zarr \
-        h5py \
-        cartopy && \
+        scipy \
+        setuptools_scm \
+        zarr && \
     pip3 install --no-cache-dir --no-deps git+https://github.com/tsutterley/read-ICESat-2.git && \
     pip3 install --no-cache-dir --no-deps git+https://github.com/tsutterley/read-ATM1b-QFIT-binary.git