Hi all, I’ve seen a similar problem building Gusto on Archer. In that case I was able to fix it by pointing the HDF5_DIR and NETCDF4_DIR environment variables at the petsc directory e.g. export HDF5_DIR=/path/to/firedrake/lib/python3.7/site-packages/petsc export NETCDF4_DIR=/path/to/firedrake/lib/python3.7/site-packages/petsc This might work for OS X too? Regards, Dave
On 26 Sep 2018, at 20:16, Lawrence Mitchell <wence@gmx.li> wrote:
On 26 Sep 2018, at 20:10, Yamazaki, Hiroe <h.yamazaki@imperial.ac.uk> wrote:
Hi all,
The problem is solved by doing
brew install hdf5 brew install netcdf
Although this fixed things, I don't think it is a safe solution, because now netcdf4 is linked against a different hdf5 library to the one installed by petsc (and used by h5py).
then inside the Firedrake virtualenv,
pip install netcdf4 python3 ~/firedrake/bin/firedrake-update --install gusto
Now I pass all the tests on gusto, but still get thousands of warnings. Most of them are:
/Users/hiroe/firedrake/src/ufl/ufl/corealg/multifunction.py:31: DeprecationWarning: inspect.getargspec() is deprecated, use inspect.signature() or inspect.getfullargspec() insp = getargspec(function)
/Users/hiroe/firedrake/src/COFFEE/coffee/visitor.py:47: DeprecationWarning: inspect.getargspec() is deprecated, use inspect.signature() or inspect.getfullargspec() argspec = inspect.getargspec(meth)
I attached the full error message. Do you know how to get rid of these?
This is presumably because your python is so new and shiny (3.7.x). We will have to update COFFEE and UFL to fix them for modern python. These warnings are harmless, but annoying!
Lawrence _______________________________________________ firedrake mailing list firedrake@imperial.ac.uk https://mailman.ic.ac.uk/mailman/listinfo/firedrake