Installing v2.2.2 from source: Syntax error in building h5py dependency

Hello everyone

I am install pylith 2.2.2 on a standalone computer. Everything seems ok expect when building h5py a syntaxError occur in the file on line 281 seemingly associated with *_ unpacking. How do I go around this?

If i disable h5py, everything runs to completion but pylith doesn’t install because it finds error when checking for h5py dependency files

Below is the error

cd h5py-2.9.0 &&
python configure --hdf5=/home/dmanu-ma/pylith &&
CC=mpicc CPPFLAGS="-I/home/dmanu-ma/pylith/include -I/home/dmanu-ma/pylith/include " LDFLAGS="-L/home/dmanu-ma/pylith/lib -L/home/dmanu-ma/pylith/lib64 -L/home/dmanu-ma/pylith/lib -L/home/dmanu-ma/pylith/lib64 " CFLAGS="-g -O2" CXXFLAGS="-g -O2 -DMPICH_IGNORE_CXX_SEEK" FCFLAGS="" python build &&
python install --prefix=/home/dmanu-ma/pylith &&
touch /home/dmanu-ma/build/installed_h5py
File “build/bdist.linux-x86_64/egg/pkgconfig/”, line 281
flags = _query(packages, *os_opts, *_build_options(option, static=static))
SyntaxError: invalid syntax

zip_safe flag not set; analyzing archive contents…

Installed /home/dmanu-ma/build/h5py-2.9.0/.eggs/pkgconfig-1.5.5-py2.7.egg
Searching for Cython>=0.23
Reading Links for Cython
Best match: Cython 3.0.0a9
Processing Cython-3.0.0a9-cp27-cp27m-manylinux1_x86_64.whl
Installing Cython-3.0.0a9-cp27-cp27m-manylinux1_x86_64.whl to /home/dmanu-ma/build/h5py-2.9.0/.eggs

Installed /home/dmanu-ma/build/h5py-2.9.0/.eggs/Cython-3.0.0a9-py2.7-linux-x86_64.egg
running configure
Autodetection skipped [invalid syntax (, line 281)]

                   Summary of the h5py configuration

Path to HDF5: '/home/dmanu-ma/pylith'
HDF5 Version: '1.8.4'
 MPI Enabled: False

Rebuild Required: True

running build

copying h5py/tests/hl/test_vds/ → build/lib.linux-x86_64-2.7/h5py/tests/hl/test_vds
running build_ext
Autodetection skipped [invalid syntax (, line 281)]

                   Summary of the h5py configuration

Path to HDF5: '/home/dmanu-ma/pylith'
HDF5 Version: '1.8.4'
 MPI Enabled: False

Rebuild Required: True

Executing api_gen rebuild of defs
Executing cythonize()
Traceback (most recent call last):
File “”, line 168, in
cmdclass = CMDCLASS,
File “build/bdist.linux-x86_64/egg/setuptools/”, line 129, in setup
File “/home/dmanu-ma/pylith/lib/python2.7/distutils/”, line 151, in setup
File “/home/dmanu-ma/pylith/lib/python2.7/distutils/”, line 953, in run_commands
File “/home/dmanu-ma/pylith/lib/python2.7/distutils/”, line 972, in run_command
File “/home/dmanu-ma/pylith/lib/python2.7/distutils/command/”, line 127, in run
File “/home/dmanu-ma/pylith/lib/python2.7/distutils/”, line 326, in run_command
File “/home/dmanu-ma/pylith/lib/python2.7/distutils/”, line 972, in run_command
File “/home/dmanu-ma/build/h5py-2.9.0/”, line 202, in run
self.extensions = cythonize(self._make_extensions(config),
File “/home/dmanu-ma/build/h5py-2.9.0/”, line 80, in _make_extensions
import pkgconfig
File “build/bdist.linux-x86_64/egg/pkgconfig/”, line 1, in
File “/home/dmanu-ma/build/h5py-2.9.0/.eggs/pkgconfig-1.5.5-py2.7.egg/pkgconfig/”, line 281
flags = _query(packages, *os_opts, *_build_options(option, static=static))
SyntaxError: invalid syntax
make[2]: *** [Makefile:1227: h5py] Error 1
make[2]: Leaving directory ‘/home/dmanu-ma/build’
make[1]: *** [Makefile:1238: installed_h5py] Error 2
make[1]: Leaving directory ‘/home/dmanu-ma/build’
make: *** [Makefile:1436: installed_pylith] Error 2

My guess is that the cython version being installed is incompatible with this version of h5py. Try using Cython version 0.29.24 available from Index of /~buildbot/deps.

In this is not a cluster, I recommend using the PyLith binary.

Dear Baagaard,

Thanks for the comment, I used an order version of the pkgconfig file and manage to install pylith.

Yes this is not a cluster but a 6 core, 12 threads computer, I was hoping that installing from source would allow me to run pylith using the multiprocessors. Does that not work?

You can use multiple cores and processors with the binary. Just use the --nodes=NUM_PROCESSES command line argument.

The primary reason for building from source on a cluster is to make use of the MPI installed on the cluster that takes advantage of the interconnect hardware like infiniband.

This site does not let me attach config.log (it says I am a new user and I can only make 3 reply).
I have continued with my compilation, I have advanced but I still have errors. After compiling netcdf it passes numpy, then to cython and here I have the error with h5py:

writing build/bdist.macosx-10.13-intel/egg/EGG-INFO/native_libs.txt
creating dist
creating ‘dist/Cython-0.29.16-py2.7-macosx-10.13-intel.egg’ and adding ‘build/bdist.macosx-10.13-intel/egg’ to it
removing ‘build/bdist.macosx-10.13-intel/egg’ (and everything under it)
Processing Cython-0.29.16-py2.7-macosx-10.13-intel.egg
creating /Users/cyclo/pylith_222_1/lib/python2.7/site-packages/Cython-0.29.16-py2.7-macosx-10.13-intel.egg
Extracting Cython-0.29.16-py2.7-macosx-10.13-intel.egg to /Users/cyclo/pylith_222_1/lib/python2.7/site-packages
Adding Cython 0.29.16 to easy-install.pth file
Installing cython script to /Users/cyclo/pylith_222_1/bin
Installing cygdb script to /Users/cyclo/pylith_222_1/bin
Installing cythonize script to /Users/cyclo/pylith_222_1/bin

Installed /Users/cyclo/pylith_222_1/lib/python2.7/site-packages/Cython-0.29.16-py2.7-macosx-10.13-intel.egg
Processing dependencies for Cython==0.29.16
Finished processing dependencies for Cython==0.29.16
/Users/cyclo/Pylith222_1/src/pylith/pylith-installer-2.2.2-1/bin/ “/opt/local/bin/curl -L -O -o” h5py-2.9.0.tar.gz Index of /~buildbot/deps
Found local copy of h5py-2.9.0.tar.gz.
/usr/bin/tar -zxf h5py-2.9.0.tar.gz
cd h5py-2.9.0 &&
python configure --hdf5=/Users/cyclo/pylith_222_1 &&
CC=mpicc CPPFLAGS="-I/Users/cyclo/pylith_222_1/include -I/Users/cyclo/pylith_222_1/include " LDFLAGS="-L/Users/cyclo/pylith_222_1/lib -L/Users/cyclo/pylith_222_1/lib64 -L/Users/cyclo/pylith_222_1/lib -L/Users/cyclo/pylith_222_1/lib64 " CFLAGS="-g -O2" CXXFLAGS="-g -O2 -DMPICH_IGNORE_CXX_SEEK" FCFLAGS="-g -O2" python build &&
python install --prefix=/Users/cyclo/pylith_222_1 &&
touch /Users/cyclo/Pylith222_1/installed_h5py
Couldn’t find index page for ‘pkgconfig’ (maybe misspelled?)
No local packages or download links found for pkgconfig
Traceback (most recent call last):
File “”, line 168, in
cmdclass = CMDCLASS,
File “/System/Library/Frameworks/Python.framework/Versions/2.7/lib/python2.7/distutils/”, line 111, in setup
_setup_distribution = dist = klass(attrs)
File “/System/Library/Frameworks/Python.framework/Versions/2.7/Extras/lib/python/setuptools/”, line 268, in init
File “/System/Library/Frameworks/Python.framework/Versions/2.7/Extras/lib/python/setuptools/”, line 313, in fetch_build_eggs
File “/System/Library/Frameworks/Python.framework/Versions/2.7/Extras/lib/python/pkg_resources/”, line 843, in resolve
dist = best[req.key] = env.best_match(req, ws, installer)
File “/System/Library/Frameworks/Python.framework/Versions/2.7/Extras/lib/python/pkg_resources/”, line 1088, in best_match
return self.obtain(req, installer)
File “/System/Library/Frameworks/Python.framework/Versions/2.7/Extras/lib/python/pkg_resources/”, line 1100, in obtain
return installer(requirement)
File “/System/Library/Frameworks/Python.framework/Versions/2.7/Extras/lib/python/setuptools/”, line 380, in fetch_build_egg
return cmd.easy_install(req)
File “/System/Library/Frameworks/Python.framework/Versions/2.7/Extras/lib/python/setuptools/command/”, line 632, in easy_install
raise DistutilsError(msg)
distutils.errors.DistutilsError: Could not find suitable distribution for Requirement.parse(‘pkgconfig’)
make[2]: *** [h5py] Error 1
make[1]: *** [installed_h5py] Error 2
make: *** [installed_pylith] Error 2

What am I missing?

Please try version 2.2.2-2 of the PyLith installer. I have it working on Linux (tested on CentOS 7, Ubuntu 20.04) and macOS (BigSur). You can download the tarball (temporary location) at
Release Installer version 0 for PyLith v2.2.2 · geodynamics/pylith_installer · GitHub.

Documentation (raw Markdown, temporary): pylith_installer/ at releases/v2.2 · geodynamics/pylith_installer · GitHub

Note: I will make a new release once I have the Docker development container built. The new release will include online documentation with detailed, up-to-date instructions. I will post all of the information for the v2.2.2-2 installer release once it is available (should be mid-December).

See docs/configs for examples of which Linux packages to install (Ubuntu 20.04 packages).

Important: For development do NOT use the configure arguments listed in the docs/configs files. Instead, use the ones listed in devenv/