pyprecice 2.1.0.1rc2

Python language bindings for the preCICE coupling library

Python language bindings for the C++ library preCICE

This package provides python language bindings for the C++ library preCICE. Note that the first three digits of the version number of the bindings indicate the preCICE version that the bindings support. The last digit represents the version of the bindings. Example: v2.0.0.1 and v2.0.0.2 of the bindings represent versions 1 and 2 of the bindings that are compatible with preCICE v2.0.0.

Required dependencies

preCICE: Refer to the preCICE wiki for information on building and installation.

MPI: mpi4py requires MPI to be installed on your system.

Installing the package

We recommend using pip3 (version 19.0 or newer) for the sake of simplicity. You can check your pip3 version via pip3 --version. To update pip3, use the following line:

$ pip3 install --upgrade pip

Using pip3

preCICE system installs

For system installs of preCICE, installation works out of the box. There are different ways how pip can be used to install pyprecice. pip will fetch cython and other build-time dependencies, compile the bindings and finally install the package pyprecice.

• (recommended) install pyprecice from PyPI

  $ pip3 install --user pyprecice
  

• provide the link to this repository to pip (replace <branch> with the branch you want to use, preferably master or develop)

  $ pip3 install --user https://github.com/precice/python-bindings/archive/<branch>.zip
  

• if you already cloned this repository, execute the following command from this directory:

  $ pip3 install --user .
  

  note the dot at the end of the line

preCICE at custom location (setting PATHS)

If preCICE (the C++ library) was installed in a custom prefix, or only built but not installed at all, you have to extend the following environment variables:

• LIBRARY_PATH, LD_LIBRARY_PATH to the library location, or $prefix/lib
• CPATH either to the src directory or the $prefix/include

The precice wiki provides more informaiton on linking preCICE.

Using setup.py

preCICE system installs

In this directory, execute:

$ python3 setup.py install --user

preCICE at custom location (setting PATHS)

see above. Then run

$ python3 setup.py install --user

preCICE at custom location (explicit include path, library path)

1. Install cython and other dependencies via pip3

   $ pip3 install --user setuptools wheel cython packaging numpy
   

2. Open terminal in this folder.
3. Build the bindings

   $ python3 setup.py build_ext --include-dirs=$PRECICE_ROOT/src --library-dirs=$PRECICE_ROOT/build/last
   

Options:

• --include-dirs=, default: '' Path to the headers of preCICE, point to the sources $PRECICE_ROOT/src, or the your custom install prefix $prefix/include.

NOTES:

• If you have built preCICE using CMake, you can pass the path to the CMake binary directory using --library-dirs.
• It is recommended to use preCICE as a shared library here.

4. Install the bindings

   $ python3 setup.py install --user
   

5. Clean-up optional

   $ python3 setup.py clean --all
   

Test the installation

Update LD_LIBRARY_PATH such that python can find precice.so

$ export LD_LIBRARY_PATH=$LD_LIBRARY_PATH:$PRECICE_ROOT/build/last

Run the following to test the installation:

$ python3 -c "import precice"

Unit tests

1. Clean-up mandatory (because we must not link against the real precice.so, but we use a mocked version)

   $ python3 setup.py clean --all
   

2. Set CPLUS_INCLUDE_PATH (we cannot use build_ext and the --include-dirs option here)

   $ export CPLUS_INCLUDE_PATH=$CPLUS_INCLUDE_PATH:$PRECICE_ROOT/src
   

3. Run tests with

   $ python3 setup.py test
   

Usage

You can find the documentation of the implemented interface in the file precice.pyx. For an example of how pyprecice can be used please refer to the 1D elastic tube example.

Note The python package that is installed is called pyprecice. It provides the python module precice that can be use in your code via import precice, for example.

Troubleshooting & miscellaneous

preCICE is not found

The following error shows up during installation, if preCICE is not found:

  /tmp/pip-install-d_fjyo1h/pyprecice/precice.cpp:643:10: fatal error: precice/SolverInterface.hpp: No such file or directory
    643 | #include "precice/SolverInterface.hpp"
        |          ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~
  compilation terminated.
  error: command 'x86_64-linux-gnu-gcc' failed with exit status 1
  ----------------------------------------
  ERROR: Failed building wheel for pyprecice
Failed to build pyprecice
ERROR: Could not build wheels for pyprecice which use PEP 517 and cannot be installed directly

There are two possible reasons, why preCICE is not found:

1. preCICE is not installed. Please download and install the C++ library preCICE. See above.
2. preCICE is installed, but cannot be found. Please make sure that preCICE can be found during the installation process. See our wiki page on linking to preCICE and the instructions above.

Version of Cython is too old

In case the compilation fails with shared_ptr.pxd not found messages, check if you use the latest version of Cython.

Version of pip3 is too old

If you see the following error

error: option --single-version-externally-managed not recognized

your version of pip might be too old. Please update pip and try again. One possible way for updating pip is to run the following commands:

wget -q https://bootstrap.pypa.io/get-pip.py -O get-pip.py && python3 get-pip.py

Be aware that python3 get-pip.py might require root privileges.

Check your version of pip via pip3 --version. For version 8.1.1 and 9.0.1 we know that this problem occurs. Remark: you get versions 8.1.1 of pip if you use sudo apt install python3-pip on Ubuntu 16.04 (pip version 9.0.1 on Ubuntu 18.04)

Build-time dependencies (Cython, numpy...) defined in pyproject.toml are not installed automatically

If you see the following error

Collecting pyprecice
  Using cached https://files.pythonhosted.org/packages/a6/fb/66f78168394afa2adca62ecd9079a98e741fbf3c6a96845719641ea27912/pyprecice-2.0.0.1.tar.gz
    Complete output from command python setup.py egg_info:
    Traceback (most recent call last):
      File "<string>", line 1, in <module>
      File "/tmp/pip-build-ebyoc0sq/pyprecice/setup.py", line 7, in <module>
        from Cython.Distutils.extension import Extension
    ModuleNotFoundError: No module named 'Cython'

your pip might be too old and therefore it does not use the information from pyproject.toml. You can update your pip via

pip3 install --upgrade pip

then try to install pyprecice, again.

Python.h missing

$ python3 -m pip install pyprecice
Collecting pyprecice
...
  /tmp/pip-build-7rj4_h93/pyprecice/precice.cpp:25:20: fatal error: Python.h: No such file or directory
  compilation terminated.
  error: command 'x86_64-linux-gnu-gcc' failed with exit status 1

  ----------------------------------------
  Failed building wheel for pyprecice 

Please try to install python3-dev. E.g. via apt install python3-dev. Please make sure that you use the correct version (e.g. python3.5-dev or python3.6-dev). You can check your version via python3 --version.

libprecice.so is not found at runtime

$ python3 -c "import precice"
Traceback (most recent call last):
  File "<stdin>", line 1, in <module>
ImportError: libprecice.so.2: cannot open shared object file: No such file or directory

Make sure that your LD_LIBRARY_PATH includes the directory that contains libprecice.so. The actual path depends on how you installed preCICE. Example: If preCICE was installed using sudo make install and you did not define a CMAKE_INSTALL_PREFIX the library path is /usr/local/lib. This means you have to export LD_LIBRARY_PATH=/usr/local/lib:$LD_LIBRARY_PATH.

I'm using preCICE < 2.0.0, but there is no matching version of the bindings. What can I do?

If you want to use the old experimental python bindings (released with preCICE version < 2.0.0), please refer to the corresponding preCICE version. Example: for preCICE v1.6.1 there are three different versions of the python bindings: precice_future, precice and PySolverInterface. Installation instructions can be found in the corresponding README files.

Installing the python bindings for Python 2.7.17

Note that the instructions in this section are outdated and refer to the deprecated python bindings. Until we have updated information on the installation procedure for the python bindings under this use-case, we will keep these instructions, since they might still be very useful (Originally contributed by huangq1234553 to the precice wiki in precice/precice/wiki:8bb74b7.)

show details

This guide provides steps to install python bindings for precice-1.6.1 for a conda environment Python 2.7.17 on the CoolMUC. Note that preCICE no longer supports Python 2 after v1.4.0. Hence, some modifications to the python setup code was necessary. Most steps are similar if not identical to the basic guide without petsc or python above. This guide assumes that the Eigen dependencies have already been installed.

Load the prerequisite libraries:

module load gcc/7
module unload mpi.intel
module load mpi.intel/2018_gcc
module load cmake/3.12.1

At the time of this writing module load boost/1.68.0 is no longer available. Instead boost 1.65.1 was installed per the boost and yaml-cpp guide above.

In order to have the right python dependencies, a packaged conda environment was transferred to SuperMUC. The following dependencies were installed:

• numpy
• mpi4py

With the python environment active, we have to feed the right python file directories to the cmake command. Note that -DPYTHON_LIBRARY expects a python shared library. You can likely modify the version to fit what is required.

mkdir build && cd build
cmake -DBUILD_SHARED_LIBS=ON -DPRECICE_PETScMapping=OFF -DPRECICE_PythonActions=ON -DCMAKE_INSTALL_PREFIX=/path/to/precice -DCMAKE_BUILD_TYPE=Debug .. -DPYTHON_INCLUDE_DIR=$(python -c "from distutils.sysconfig import get_python_inc; print(get_python_inc())")  -DPYTHON_LIBRARY=$(python -c "import distutils.sysconfig as sysconfig; print(sysconfig.get_config_var('LIBDIR')+'/libpython2.7.so')") -DNumPy_INCLUDE_DIR=$(python -c "import numpy; print(numpy.get_include())")
make -j 12
make install

After installing, make sure you add the preCICE installation paths to your .bashrc, so that other programs can find it:

export PRECICE_ROOT="path/to/precice_install"
export PKG_CONFIG_PATH="path/to/precice_install/lib/pkgconfig:${PKG_CONFIG_PATH}"
export CPLUS_INCLUDE_PATH="path/to/precice_install/include:${CPLUS_INCLUDE_PATH}"
export LD_LIBRARY_PATH="path/to/precice_install/lib:${LD_LIBRARY_PATH}"

Then, navigate to the python_future bindings script.

cd /path/to/precice/src/precice/bindings/python_future

Append the following to the head of the file to allow Python2 to run Python3 code. Note that importing unicode_literals from future will cause errors in setuptools methods as string literals in code are interpreted as unicode with this import.

from __future__ import (absolute_import, division,
                        print_function)
from builtins import (
         bytes, dict, int, list, object, range, str,
         ascii, chr, hex, input, next, oct, open,
         pow, round, super,
         filter, map, zip)

Modify mpicompiler_default = "mpic++" to mpicompiler_default = "mpicxx" in line 100. Run the setup file using the default Python 2.7.17.

python setup.py install --user

Contributors

• Benjamin Rüth
• Ishaan Desai
• Saumitra Vinay Joshi contributed first working prototype in 3db9c9 on precice/precice
• Frédéric Simonis
• Florian Lindner
• Benjamin Uekermann
• Gerasimos Chourdakis