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FLEXPART 10 into a Docker container

By on Saturday, February 27, 2021

For a recent project, I wanted to include the Lagrangian particle dispersion model FLEXPART (more on that) into an easy-to-deploy project. The analysis part of that project runs on python, but uses some nifty geography libraries, which in turn require C and Fortran libraries. So, I already put this part into a docker container. FLEXPART provides the actual input for the analysis part, so it seemed logical to also include that part.

Not too long ago version 10 came available, also including netCDF output. However, with added dependencies, compiling the source became a bit more complicated. Let’s have a look at the Dockerfile:

FROM ubuntu:18.04


ARG DEBIAN_FRONTEND=noninteractive

RUN apt-get update && apt-get update && apt-get install -y \
  language-pack-en openssh-server vim software-properties-common \
  build-essential make gcc g++ zlib1g-dev git python3 python3-dev python3-pip \
  pandoc python3-setuptools imagemagick\
  gfortran autoconf libtool automake flex bison cmake git-core \
  libjpeg8-dev libfreetype6-dev libhdf5-serial-dev \
  libeccodes0 libeccodes-data libeccodes-dev \
  libnetcdf-c++4 libnetcdf-c++4-dev libnetcdff-dev \
  binutils  python3-numpy python3-mysqldb \
  python3-scipy python3-sphinx libedit-dev unzip curl wget
  
  
# replaced 'libpng12-dev' by libpng-dev
RUN add-apt-repository ppa:ubuntugis/ppa \
  && apt-get update \
  && apt-get install -y libatlas-base-dev libpng-dev \
     libproj-dev libgdal-dev gdal-bin  

RUN add-apt-repository 'deb http://security.ubuntu.com/ubuntu xenial-security main' \
  && apt-get update \
  && apt-get install -y libjasper1 libjasper-dev libeccodes-tools libeccodes-dev

#ENV HTTP https://confluence.ecmwf.int/download/attachments/45757960
#ENV ECCODES eccodes-2.9.2-Source

#
# Download, modify and compile flexpart 10
#
RUN mkdir flex_src && cd flex_src \
  && wget https://www.flexpart.eu/downloads/66 \
  && tar -xvf 66 \
  && rm 66 \
  && cd flexpart_v10.4_3d7eebf/src \
  && cp makefile makefile_local \
  && sed -i '74 a INCPATH1 = /usr/include\nINCPATH2 = /usr/include\nLIBPATH1 = /usr/lib\n F90 = gfortran' makefile_local \
  && sed -i 's/LIBS = -lgrib_api_f90 -lgrib_api -lm -ljasper $(NCOPT)/LIBS = -leccodes_f90 -leccodes -lm -ljasper $(NCOPT)/' makefile_local \
  && make -f makefile_local

ENV PATH /flex_src/flexpart_v10.4_3d7eebf/src/:$PATH

# pip install some more python libraries

The interesting part happens in L34-42. The source is downloaded and unpacked. Then the makefile  needs to be modified to find all libraries (which were installed with apt-get before). Sed is of great use here. First a line is added to the makefile_local and another line is searched and replaces. Finally make is executed to compile FLEXPART.

Now the container can be ran and FLEXPART be executed from within. At least for my application with a couple of thousand particles being simulated, performance is sufficient and a small penalty is outweigh by the ease of deployment.

Further reading:
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