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Dependencies

This version features more dependencies than the original one, but most are relatively easy do get (meaning, by using pip).

The main dependency is the sparse matrix direct solver MUMPS. For this package, you have to install MUMPS along with MPI (or OpenMPI).

You may be able to find MUMPS in your OS's package system (if it has one), but if you don't, or just prefer to compile yourself, you can find a CMake fork at This repo which makes it straightforward to install (although it requires a CMake build with minimum version of 3.13).

Other dependencies are Python packages, you may get them with pip:

pip install typing pathlib matplotlib sympy numpy pyvtk scipy cython mpi4py pymumps numexpr

Be aware that you may need to point to MPI's and MUMPS's include and binary files to be able to install mpi4pyand pymumps. If you installed them using Linuxbrew, for example, then they will be at:

/home/linuxbrew/.linuxbrew/opt/brewsci-mumps/lib
/home/linuxbrew/.linuxbrew/opt/brewsci-mumps/include
/home/linuxbrew/.linuxbrew/opt/openmpi/lib
/home/linuxbrew/.linuxbrew/opt/openmpi/include
/home/linuxbrew/.linuxbrew/opt/openmpi/bin

If you compiled the source and installed it without specifying install location, you can find it at the build folder's install_manifest.txt.

Add the last one to your PATH with:

export PATH="/home/linuxbrew/.linuxbrew/opt/openmpi/bin:$PATH"

And then run, in this order:

pip install mpi4py --global-option="build_ext" \
  --global-option="-I/home/linuxbrew/.linuxbrew/opt/openmpi/include" \
  --global-option="-L/home/linuxbrew/.linuxbrew/opt/openmpi/lib"
pip install pymumps --global-option="build_ext" \
  --global-option="-I/home/linuxbrew/.linuxbrew/opt/brewsci-mumps/include" \
  --global-option="-L/home/linuxbrew/.linuxbrew/opt/brewsci-mumps/lib"

It is a good idea to keep OpenMPI's bin folder in your path to run ToPy, especially because you need mpiexec in order to run MUMPS in parallel. To do that, I recommend using a virtual environment and include them in its activate file. For example:

python3 -m venv ~/venv-topy
gedit ~/venv-topy/bin/activate

And then add:

PATH="/home/linuxbrew/.linuxbrew/opt/openmpi/bin:$PATH"

After the function deactivate (). You can then enter the virtual environment with source ~/venv-topy/bin/activate and leave it with deactivate.

Installing ToPy

CD into the 'topy' directory (where 'setup.py' is located) and in a terminal ('cmd' on Windows), type:

python setup.py install

The command above is the one to use if you are using a virtual environment too. If you want to install locally, type:

python setup.py install --user

You may require Administrator rights on Windows, depending on your setup.

If there aren't any errors, then ToPy is installed. Congratulations!

Getting started

See https://github.com/williamhunter/topy/wiki/Tutorials

First run of ToPy

The original ToPy created all element matrices on the first run and stored them for future use. This version introduces the possibility to use material properties such as Young's modulus and thermal conductivity, so now the element required by the TPD file will be generated with each execution.