> 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"
(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
Cheers,
Lawrence