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Dockerfile
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#-----------------------------------------------------------------------------
# start by building the basic container
#-----------------------------------------------------------------------------
FROM ubuntu:22.04
MAINTAINER Steven Smith <[email protected]>
# Non interactive mode
ENV DEBIAN_FRONTEND noninteractive
RUN apt-get update && \
ln -fs /usr/share/zoneinfo/America/New_York /etc/localtime && \
apt-get install -y tzdata && \
dpkg-reconfigure --frontend noninteractive tzdata && \
apt-get install -y \
build-essential \
wget \
curl \
libcurl4 \
git \
gfortran \
libopenblas-dev \
liblapack-dev \
openmpi-bin \
libopenmpi-dev \
libhdf5-openmpi-dev \
libhdf5-openmpi-103 \
python3 \
python3-pip \
python3-venv \
tcl-dev \
tk-dev \
cmake \
libxml2 \
libxml2-dev
RUN mkdir -p /home/parflow
#-----------------------------------------------------------------------------
# Set environment vars
#-----------------------------------------------------------------------------
ENV PARFLOW_DIR /usr/opt/parflow
ENV PARFLOW_DEP_DIR /usr/opt/parflow
ENV PATH $PATH:$PARFLOW_DIR/bin
#-----------------------------------------------------------------------------
# Build libraries
#-----------------------------------------------------------------------------
#
# HDF5
# New version does not work with NetCDF; use Ubunuto supplied version
# https://support.hdfgroup.org/ftp/HDF5/releases/hdf5-1.12/hdf5-1.12.2/src/hdf5-1.12.2.tar.bz2
#
# WORKDIR /home/parflow
# RUN wget -q https://support.hdfgroup.org/ftp/HDF5/releases/hdf5-1.8/hdf5-1.8.21/src/hdf5-1.8.21.tar.gz && \
# tar -xf hdf5-1.8.21.tar.gz && \
# cd hdf5-1.8.21 && \
# CC=mpicc ./configure \
# --prefix=$PARFLOW_DIR \
# --enable-parallel && \
# make && make install && \
# cd .. && \
# rm -fr hdf5-1.8.21 hdf5-1.8.21.tar.gz
#
# NetCDF
#
WORKDIR /home/parflow
run wget -q https://github.com/Unidata/netcdf-c/archive/v4.9.0.tar.gz && \
tar -xf v4.9.0.tar.gz && \
cd netcdf-c-4.9.0 && \
CC=mpicc CPPFLAGS=-I/usr/include/hdf5/openmpi LDFLAGS=-L/usr/lib/x86_64-linux-gnu/hdf5/openmpi ./configure --prefix=${PARFLOW_DIR} && \
make && \
make install && \
cd .. && \
rm -fr netcdf-c-4.9.0 v4.9.0.tar.gz
#
# NetCDF Fortran
#
WORKDIR /home/parflow
run wget -q https://github.com/Unidata/netcdf-fortran/archive/v4.5.4.tar.gz && \
tar -xf v4.5.4.tar.gz && \
cd netcdf-fortran-4.5.4 && \
CC=mpicc FC=mpifort CPPFLAGS=-I${PARFLOW_DIR}/include LDFLAGS=-L${PARFLOW_DIR}/lib ./configure --prefix=${PARFLOW_DIR} && \
make && \
make install && \
cd .. && \
rm -fr netcdf-fortran-4.5.4 v4.5.4.tar.gz
#
# SILO
#
WORKDIR /home/parflow
RUN wget -q https://github.com/LLNL/Silo/archive/refs/tags/4.10.2.tar.gz && \
tar -xf 4.10.2.tar.gz && \
cd Silo-4.10.2 && \
./configure --prefix=$PARFLOW_DIR --disable-silex --disable-hzip --disable-fpzip && \
make install && \
cd .. && \
rm -fr Silo-4.10.2 4.10.2.tar.gz
#
# Hypre
#
WORKDIR /home/parflow
RUN wget -q https://github.com/hypre-space/hypre/archive/v2.26.0.tar.gz && \
tar xf v2.26.0.tar.gz && \
cd hypre-2.26.0/src && \
./configure --prefix=$PARFLOW_DIR && \
make install && \
cd ../.. && \
rm -fr hypre-2.18.2 v2.18.2.tar.gz
#-----------------------------------------------------------------------------
# Parflow configure and build
#-----------------------------------------------------------------------------
ENV PARFLOW_MPIEXEC_EXTRA_FLAGS "--mca mpi_yield_when_idle 1 --oversubscribe --allow-run-as-root"
# Disable HWLOC warnings from showing up, confusing messages, this has been fixed in later OpenMPI versions
ENV HWLOC_HIDE_ERRORS "2"
WORKDIR /home/parflow
RUN git clone -b master --single-branch https://github.com/parflow/parflow.git parflow
RUN mkdir -p build && \
cd build && \
cmake ../parflow \
-DPARFLOW_AMPS_LAYER=mpi1 \
-DPARFLOW_AMPS_SEQUENTIAL_IO=TRUE \
-DHYPRE_ROOT=$PARFLOW_DIR \
-DSILO_ROOT=$PARFLOW_DIR \
-DPARFLOW_ENABLE_HDF5=TRUE \
-DPARFLOW_ENABLE_NETCDF=TRUE \
-DPARFLOW_ENABLE_TIMING=TRUE \
-DPARFLOW_HAVE_CLM=TRUE \
-DPARFLOW_ENABLE_PYTHON=TRUE \
-DPARFLOW_PYTHON_VIRTUAL_ENV=ON \
-DCURL_LIBRARY=/usr/lib/x86_64-linux-gnu/libcurl.so.4 \
-DCMAKE_INSTALL_PREFIX=$PARFLOW_DIR && \
make install && \
cd .. && \
rm -fr parflow build
WORKDIR /data
ENTRYPOINT ["pfrun"]