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Compiling codes

To compile, open a terminal in the upper most directory, where src and thirdparty folders are located, and run:

make -j

To test the compilation, run:

make test

Once everything compiled successfully, to clean the temporary files, type:

make clean

The above command can be run inside most of the subfolders, wherever a makefile or Makefile is present. The libraries, those with a makefile, will be compiled before the apps that contain Makefiles.

Compilation requires gnu (Linux) make, cmake, a c++ compiler with -std=c++11 support and MPI. The compilation is tested using g++ (version 5+) (default) and using intel-2018 compilers.

For the modules which have thirdparty/foamx3m as dependancy, you if you have any other OpenFOAM you have on your machine, need to temporarily deactivate your OpenFOAM installation when compiling this code to avoid conflict between the foam3m provided here and your openfoam instalation. Additionally, you need to install foam3m dependancies, this can be done in Ubuntu by running:
sudo apt install mpi-default-dev flex libscotch-dev

Tests and demos

To test the codes type:

make test

This should copy a series of input files/scripts in a test folder and run a series of relatively quick test cases (see README.md files in subdirectories).

Technical notes for code developers

GNU Makefile scripts are used primarily for code compilation and running quick tests by code developers.

Automatic tests are written using input files for C++ codes, new C++ executables testing internals of the codes and Python scripts. All these can be run using make test command, which uses script/testApp bash script.

All scripts, either for testing or production, which need mathematical calculations or plotting and are not performance critical are developed using Python. We use Python 3, shich should be available as python3 command. In Ubuntu (18.04-20.04) this can be installed by typing in a terminal:
sudo apt install python3

Bash/Shell scripts are used to run Makefile and Python scripts, either for testing or in production to simplify the run of openfoam solvers.

The initbash is an independent bash script containing utility macros, which together with bashrc (that contain installation variabls), is required for running of the compiled applications.

Aims

These scripts has been released as a separate module, to help the code developers with script re-use,and simplification of workflow for code compilation, testing, deployment and release.

Caution

The scripts here use recursive make. These change and delete files on your system: the top directory where files are changed, generated or deleted is called msRoot which, by default, points to two directories upper to the location of these script themselves. So, if you consider using these scripts for building your applications, make sure these are wrapped inside two (sub-)sub-folders, dedicated to source codes. Here is what the directory structure should looks like:

  • apps/ -------------------- msRoot directory

    • src/ ----------------- -- source codes

      • script/ ---------- -- ** this module, build & install
      • include/ --------- -- ** C++ utility codes
      • bench/ ----------- -- ** test/example data
      • ...
      • ...

    • thirdparty/ ---------- -- others' source codes

      • foamx3m ---------- -- ** a minified openfoam
      • svplot ---------- -- ** a modified former svg_plot
      • zlib
      • libtiff
      • ...

    • bench/ --------------- -- large input files, too large for src/

    • test/ ---------------- -- test folder (auto copied from bench/)

    • bin/ ----------------- -- executables folder (auto crea/deleted)

    • lib/ ----------------- -- library files (auto crea/deleted)

    • share/ --------------- -- configuration files (auto crea/deleted)

    • build/ --------------- -- temporary files (auto crea/deleted)

    • ...

As shown above, this script folder is typically located in src (which holds regularly changed source codes as subdirectories). The less frequently changed source code are placed a directory called thirdparty. A bench folder is also sometimes included holding temporary/client data, as shown above. A .git directory is kept outside the msRoot directory and is used to test and release varius modules of the code, which it ends up in the msRoot directory in the modules published using git. The build, bin,lib, test and share folders are auto-generated and should not be used to store any user data as they are removed by make distclean command.

Makefile.in usage

In Makefiles, define variables tsts together with USE_msTEST=1 and srcs with USE_msMAKE=1 and include the Makefile.in file.
If not defined, srcs will be set to all .cpp files. Example Makefiles can be found in libvoxel (single source.cpp apps) or pnextract (multiple source.cpp files).