On Fri, Nov 2, 2018 at 1:36 PM Lawrence Mitchell <wence@gmx.li> wrote:
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"
Okay, we get farther. I had to set PYTHONPATH in order to see the configuration file: (firedrake) :/PETSc3/fem$ export PYTHONPATH=$PWD/firedrake/src/firedrake (firedrake) :/PETSc3/fem$ python -c "import firedrake_configuration; print(firedrake_configuration.get_config())" {'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': []} (firedrake) :/PETSc3/fem$ firedrake_update -bash: firedrake_update: command not found (firedrake) 127:/PETSc3/fem$ firedrake-update Running /PETSc3/fem/firedrake/bin/firedrake-update The PYTHONPATH environment variable is set. This is probably an error. If you really want to use your own Python packages, please run again with the --honour-pythonpath option. Update log saved in firedrake-update.log (firedrake) 1:/PETSc3/fem$ firedrake-update --honour-pythonpath Running /PETSc3/fem/firedrake/bin/firedrake-update --honour-pythonpath Updating the git repository for firedrake Creating firedrake-update script. Running ../bin/firedrake-update --no-update-script --honour-pythonpath Xcode and homebrew installation disabled. Proceeding on the rash assumption that packaged dependencies are in place. Finding dependencies of PyOP2 Finding dependencies of firedrake Updating the git repository for petsc4py Updating the git repository for COFFEE Updating the git repository for ufl Updating the git repository for fiat Updating the git repository for FInAT Updating the git repository for tsfc Updating the git repository for PyOP2 Updating the git repository for firedrake Installing pip dependencies for COFFEE Installing pip dependencies for ufl No dependencies found. Skipping. Installing pip dependencies for fiat No dependencies found. Skipping. Installing pip dependencies for FInAT Installing pip dependencies for tsfc Installing pip dependencies for PyOP2 Installing pip dependencies for firedrake Installing h5py Updating the git repository for h5py No need to rebuild h5py Installing libspatialindex Cloning libspatialindex Successfully cloned repository libspatialindex Checking out branch master Successfully checked out branch master Traceback (most recent call last): File "../bin/firedrake-update", line 1207, in <module> build_and_install_libspatialindex() File "../bin/firedrake-update", line 808, in build_and_install_libspatialindex check_call(["./autogen.sh"]) File "../bin/firedrake-update", line 435, in check_call log.debug(subprocess.check_output(arguments, stderr=subprocess.STDOUT, env=env).decode()) File "/Users/knepley/MacSoftware/lib/python3.6/subprocess.py", line 336, in check_output **kwargs).stdout File "/Users/knepley/MacSoftware/lib/python3.6/subprocess.py", line 418, in run output=stdout, stderr=stderr) subprocess.CalledProcessError: Command '['./autogen.sh']' returned non-zero exit status 1. Update log saved in firedrake-update.log Here is the log. Thanks, Matt Cheers,
Lawrence
-- What most experimenters take for granted before they begin their experiments is infinitely more interesting than any results to which their experiments lead. -- Norbert Wiener https://www.cse.buffalo.edu/~knepley/ <http://www.cse.buffalo.edu/~knepley/>