> On 2 Nov 2018, at 01:37, Matthew Knepley <knepley@gmail.com> wrote:
>
> Well crap. h5py failed, and it does not look like a simple env fix. It is complaining about an SSL certificate. Is there
> a way to point to something that uses HTTP?
Hmmph, this is very odd. Because that failed checking the certificate for a host it had previously downloaded from (and passed the certificate checks).
This failed at a state late enough in the game that we can try building "in place" in the virtualenv:
$ . firedrake/bin/activate
$ cd firedrake/src/h5py
$ export CC=mpicc
# I assume you got PETSc to build hdf5
$ export HDF5_DIR=$PETSC_DIR/$PETSC_ARCH
$ export HDF5_MPI=ON
$ pip install .
(firedrake) firedrake:/PETSc3/fem/firedrake/src/h5py$ pip install .
Processing /PETSc3/fem/firedrake/src/h5py
Complete output from command python setup.py egg_info:
Download error on https://pypi.org/simple/pkgconfig/: [SSL: CERTIFICATE_VERIFY_FAILED] certificate verify failed (_ssl.c:833) -- Some packages may not be found!
Couldn't find index page for 'pkgconfig' (maybe misspelled?)
Download error on https://pypi.org/simple/: [SSL: CERTIFICATE_VERIFY_FAILED] certificate verify failed (_ssl.c:833) -- Some packages may not be found!
No local packages or working download links found for pkgconfig
Traceback (most recent call last):
File "<string>", line 1, in <module>
File "/private/var/folders/hk/tc1pd0g57l78rpt0lttc1sfh0000gn/T/pip-req-build-vy7d9wuj/setup.py", line 168, in <module>
cmdclass = CMDCLASS,
File "/PETSc3/fem/firedrake/lib/python3.6/site-packages/setuptools/__init__.py", line 139, in setup
_install_setup_requires(attrs)
File "/PETSc3/fem/firedrake/lib/python3.6/site-packages/setuptools/__init__.py", line 134, in _install_setup_requires
dist.fetch_build_eggs(dist.setup_requires)
File "/PETSc3/fem/firedrake/lib/python3.6/site-packages/setuptools/dist.py", line 514, in fetch_build_eggs
replace_conflicting=True,
File "/PETSc3/fem/firedrake/lib/python3.6/site-packages/pkg_resources/__init__.py", line 777, in resolve
replace_conflicting=replace_conflicting
File "/PETSc3/fem/firedrake/lib/python3.6/site-packages/pkg_resources/__init__.py", line 1060, in best_match
return self.obtain(req, installer)
File "/PETSc3/fem/firedrake/lib/python3.6/site-packages/pkg_resources/__init__.py", line 1072, in obtain
return installer(requirement)
File "/PETSc3/fem/firedrake/lib/python3.6/site-packages/setuptools/dist.py", line 581, in fetch_build_egg
return cmd.easy_install(req)
File "/PETSc3/fem/firedrake/lib/python3.6/site-packages/setuptools/command/easy_install.py", line 670, in easy_install
raise DistutilsError(msg)
distutils.errors.DistutilsError: Could not find suitable distribution for Requirement.parse('pkgconfig')
----------------------------------------
Command "python setup.py egg_info" failed with error code 1 in /private/var/folders/hk/tc1pd0g57l78rpt0lttc1sfh0000gn/T/pip-req-build-vy7d9wuj/
but I messed it up initially using
pip install h5py
which succeeds with
(firedrake) 1firedrake:/PETSc3/fem/firedrake/src/h5py$ pip install h5py
Collecting h5py
100% |████████████████████████████████| 6.1MB 677kB/s
Requirement already satisfied: six in /PETSc3/fem/firedrake/lib/python3.6/site-packages (from h5py) (1.11.0)
Requirement already satisfied: numpy>=1.7 in /PETSc3/fem/firedrake/lib/python3.6/site-packages (from h5py) (1.15.3)
Installing collected packages: h5py
Successfully installed h5py-2.8.0
Lawrence