{"id":270,"date":"2021-02-27T15:59:06","date_gmt":"2021-02-27T15:59:06","guid":{"rendered":"http:\/\/www.martin-rdz.de\/?p=270"},"modified":"2021-12-23T10:36:01","modified_gmt":"2021-12-23T10:36:01","slug":"flexpart-10-into-a-docker-container","status":"publish","type":"post","link":"http:\/\/www.martin-rdz.de\/index.php\/2021\/02\/27\/flexpart-10-into-a-docker-container\/","title":{"rendered":"FLEXPART 10 into a Docker container"},"content":{"rendered":"

For a recent project<\/a>, I wanted to include the Lagrangian particle dispersion model FLEXPART (more<\/a> on that<\/a>) 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<\/a>. FLEXPART provides the actual input for the analysis part, so it seemed logical to also include that part.<\/p>\n

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

FROM ubuntu:18.04\r\n\r\n\r\nARG DEBIAN_FRONTEND=noninteractive\r\n\r\nRUN apt-get update && apt-get update && apt-get install -y \\\r\n  language-pack-en openssh-server vim software-properties-common \\\r\n  build-essential make gcc g++ zlib1g-dev git python3 python3-dev python3-pip \\\r\n  pandoc python3-setuptools imagemagick\\\r\n  gfortran autoconf libtool automake flex bison cmake git-core \\\r\n  libjpeg8-dev libfreetype6-dev libhdf5-serial-dev \\\r\n  libeccodes0 libeccodes-data libeccodes-dev \\\r\n  libnetcdf-c++4 libnetcdf-c++4-dev libnetcdff-dev \\\r\n  binutils  python3-numpy python3-mysqldb \\\r\n  python3-scipy python3-sphinx libedit-dev unzip curl wget\r\n  \r\n  \r\n# replaced 'libpng12-dev' by libpng-dev\r\nRUN add-apt-repository ppa:ubuntugis\/ppa \\\r\n  && apt-get update \\\r\n  && apt-get install -y libatlas-base-dev libpng-dev \\\r\n     libproj-dev libgdal-dev gdal-bin  \r\n\r\nRUN add-apt-repository 'deb http:\/\/security.ubuntu.com\/ubuntu xenial-security main' \\\r\n  && apt-get update \\\r\n  && apt-get install -y libjasper1 libjasper-dev libeccodes-tools libeccodes-dev\r\n\r\n#ENV HTTP https:\/\/confluence.ecmwf.int\/download\/attachments\/45757960\r\n#ENV ECCODES eccodes-2.9.2-Source\r\n\r\n#\r\n# Download, modify and compile flexpart 10\r\n#\r\nRUN mkdir flex_src && cd flex_src \\\r\n  && wget https:\/\/www.flexpart.eu\/downloads\/66 \\\r\n  && tar -xvf 66 \\\r\n  && rm 66 \\\r\n  && cd flexpart_v10.4_3d7eebf\/src \\\r\n  && cp makefile makefile_local \\\r\n  && sed -i '74 a INCPATH1 = \/usr\/include\\nINCPATH2 = \/usr\/include\\nLIBPATH1 = \/usr\/lib\\n F90 = gfortran' makefile_local \\\r\n  && sed -i 's\/LIBS = -lgrib_api_f90 -lgrib_api -lm -ljasper $(NCOPT)\/LIBS = -leccodes_f90 -leccodes -lm -ljasper $(NCOPT)\/' makefile_local \\\r\n  && make -f makefile_local\r\n\r\nENV PATH \/flex_src\/flexpart_v10.4_3d7eebf\/src\/:$PATH\r\n\r\n# pip install some more python libraries\r\n<\/pre>\n
The interesting part happens in L34-42. The source is downloaded and unpacked. Then the makefile<\/code>\u00a0 needs to be modified to find all libraries (which were installed with apt-get before). Sed<\/a> is of great use here. First a line is added to the makefile_local<\/code> and another line is searched and replaces. Finally make is executed to compile FLEXPART.<\/p>\n
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.<\/p>\n
Further reading:<\/h5>\n