On 2 Nov 2018, at 17:27, Matthew Knepley <knepley@gmail.com> wrote:
On Fri, Nov 2, 2018 at 1:20 PM Lawrence Mitchell <wence@gmx.li> wrote:
On 2 Nov 2018, at 17:16, Matthew Knepley <knepley@gmail.com> wrote:
I went on to
cd src/h5py pip install .
and it that worked
(firedrake) :/PETSc3/fem/firedrake$ pushd src/h5py/ /PETSc3/fem/firedrake/src/h5py /PETSc3/fem/firedrake /PETSc3/fem (firedrake) firedrake:/PETSc3/fem/firedrake/src/h5py$ pip install . Processing /PETSc3/fem/firedrake/src/h5py Requirement already satisfied: numpy>=1.7 in
/lib/python3.6/site-packages (from h5py==2.8.0.post0) (1.15.3)
Requirement already satisfied: six in /PETSc3/fem/firedrake/lib/python3.6/site-packages (from h5py==2.8.0.post0) (1.11.0) Installing collected packages: h5py Found existing installation: h5py 2.8.0 Uninstalling h5py-2.8.0: Successfully uninstalled h5py-2.8.0 Running setup.py install for h5py ... done Successfully installed h5py-2.8.0.post0
Great!
How do I restart the whole Firedrake now?
This is unsupported, but I think it should work:
$ cp firedrake-install firedrake/bin/firedrake-update $ chmod u+x firedrake/bin/firedrake-update $ . firedrake/bin/activate $ rm -rf firedrake/src/libspatialindex $ firedrake-update
I get
(firedrake) :/PETSc3/fem$ cp firedrake-install firedrake/bin/firedrake-update (firedrake) :/PETSc3/fem$ chmod u+x firedrake/bin/firedrake-update (firedrake) :/PETSc3/fem$ rm -rf firedrake/src/libspatialindex (firedrake) :/PETSc3/fem$ firedrake-update Running /PETSc3/fem/firedrake/bin/firedrake-update Traceback (most recent call last): File "/PETSc3/fem/firedrake/bin/firedrake-update", line 277, in <module> import firedrake_configuration ModuleNotFoundError: No module named 'firedrake_configuration'
Ah, ok, we have to do this manually then. First: $ cat > firedrake/src/firedrake/firedrake_configuration/configuration.json <<EOF {"options": {"package_manager": false, "minimal_petsc": false, "mpicc": "mpicc", "mpicxx": "mpicxx", "mpif90": "mpif90", "disable_ssh": false, "honour_petsc_dir": true, "show_petsc_configure_options": false, "slepc": false, "slope": false, "packages": [], "honour_pythonpath": false, "petsc_int_type": "int32", "cache_dir": "/PETSc3/fem/firedrake/.cache"}, "environment": {}, "additions": []} EOF This makes the configuration file firedrake-install would have done. Now let's pretend we installed the firedrake_configuration module: $ cat > firedrake/lib/python3.6/site-packages/firedrake.egg-link << EOF /PETSc3/fem/firedrake/src/firedrake . EOF Now try doing: $ python -c "import firedrake_configuration; print(firedrake_configuration.get_config())" If that works, try again with "firedrake-update" Cheers, Lawrence