SciPy Numpy Extension fails to build when LC_ALL=POSIX

[dithwick]

Tried to build SciPy-bundle-2020.11-intel-2020b.eb on CentOS 8.3 where LC_ALL=POSIX and got the following error message:

== installing...
== taking care of extensions...
== installing extension numpy 1.19.4 (1/8)...
==      configuring...
ERROR: Traceback (most recent call last):
  File "/scrtp/avon/eb/software/EasyBuild/4.3.4/lib/python3.6/site-packages/easybuild/main.py", line 117, in build_and_install_software
    (ec_res['success'], app_log, err) = build_and_install_one(ec, init_env)
  File "/scrtp/avon/eb/software/EasyBuild/4.3.4/lib/python3.6/site-packages/easybuild/framework/easyblock.py", line 3404, in build_and_install_one
    result = app.run_all_steps(run_test_cases=run_test_cases)
  File "/scrtp/avon/eb/software/EasyBuild/4.3.4/lib/python3.6/site-packages/easybuild/framework/easyblock.py", line 3303, in run_all_steps
    self.run_step(step_name, step_methods)
  File "/scrtp/avon/eb/software/EasyBuild/4.3.4/lib/python3.6/site-packages/easybuild/framework/easyblock.py", line 3158, in run_step
    step_method(self)()
  File "/scrtp/avon/eb/software/EasyBuild/4.3.4/lib/python3.6/site-packages/easybuild/easyblocks/generic/pythonbundle.py", line 128, in extensions_step
    super(PythonBundle, self).extensions_step(*args, **kwargs)
  File "/scrtp/avon/eb/software/EasyBuild/4.3.4/lib/python3.6/site-packages/easybuild/framework/easyblock.py", line 2352, in extensions_step
    txt = ext.run()
  File "/scrtp/avon/eb/software/EasyBuild/4.3.4/lib/python3.6/site-packages/easybuild/easyblocks/n/numpy.py", line 314, in run
    super(EB_numpy, self).run()
  File "/scrtp/avon/eb/software/EasyBuild/4.3.4/lib/python3.6/site-packages/easybuild/easyblocks/generic/pythonpackage.py", line 722, in run
    step_method(self)()
  File "/scrtp/avon/eb/software/EasyBuild/4.3.4/lib/python3.6/site-packages/easybuild/easyblocks/n/numpy.py", line 145, in configure_step
    if patch_wl_regex.search(open(patch, 'r').read()):
  File "/usr/lib64/python3.6/encodings/ascii.py", line 26, in decode
    return codecs.ascii_decode(input, self.errors)[0]
UnicodeDecodeError: 'ascii' codec can't decode byte 0xc3 in position 142: ordinal not in range(128)

Running again with LC_ALL= and it builds/installs fine. This is similar to issue #2279 which was fixed with easybuilders/easybuild-framework#3565.

[dithwick]

Just had a similar issue with TensorFlow-2.4.1-fosscuda-2020b.eb

== taking care of extensions...
ERROR: Traceback (most recent call last):
  File "/scrtp/avon/eb/software/EasyBuild/4.3.4/lib/python3.6/site-packages/easybuild/main.py", line 117, in build_and_install_software
    (ec_res['success'], app_log, err) = build_and_install_one(ec, init_env)
  File "/scrtp/avon/eb/software/EasyBuild/4.3.4/lib/python3.6/site-packages/easybuild/framework/easyblock.py", line 3404, in build_and_install_one
    result = app.run_all_steps(run_test_cases=run_test_cases)
  File "/scrtp/avon/eb/software/EasyBuild/4.3.4/lib/python3.6/site-packages/easybuild/framework/easyblock.py", line 3303, in run_all_steps
    self.run_step(step_name, step_methods)
  File "/scrtp/avon/eb/software/EasyBuild/4.3.4/lib/python3.6/site-packages/easybuild/framework/easyblock.py", line 3158, in run_step
    step_method(self)()
  File "/scrtp/avon/eb/software/EasyBuild/4.3.4/lib/python3.6/site-packages/easybuild/easyblocks/generic/pythonbundle.py", line 128, in extensions_step
    super(PythonBundle, self).extensions_step(*args, **kwargs)
  File "/scrtp/avon/eb/software/EasyBuild/4.3.4/lib/python3.6/site-packages/easybuild/framework/easyblock.py", line 2242, in extensions_step
    fake_mod_data = self.load_fake_module(purge=True, extra_modules=build_dep_mods)
  File "/scrtp/avon/eb/software/EasyBuild/4.3.4/lib/python3.6/site-packages/easybuild/framework/easyblock.py", line 1555, in load_fake_module
    fake_mod_path = self.make_module_step(fake=True)
  File "/scrtp/avon/eb/software/EasyBuild/4.3.4/lib/python3.6/site-packages/easybuild/framework/easyblock.py", line 2958, in make_module_step
    txt += self.make_module_dep()
  File "/scrtp/avon/eb/software/EasyBuild/4.3.4/lib/python3.6/site-packages/easybuild/framework/easyblock.py", line 1179, in make_module_dep
    full_mod_subdir, all_deps)
  File "/scrtp/avon/eb/software/EasyBuild/4.3.4/lib/python3.6/site-packages/easybuild/tools/modules.py", line 1108, in path_to_top_of_module_tree
    modpath_exts = dict([(k, v) for k, v in self.modpath_extensions_for(deps).items() if v])
  File "/scrtp/avon/eb/software/EasyBuild/4.3.4/lib/python3.6/site-packages/easybuild/tools/modules.py", line 1040, in modpath_extensions_for
    modtxt = self.read_module_file(mod_name)
  File "/scrtp/avon/eb/software/EasyBuild/4.3.4/lib/python3.6/site-packages/easybuild/tools/modules.py", line 970, in read_module_file
    modfilepath = self.modulefile_path(mod_name)
  File "/scrtp/avon/eb/software/EasyBuild/4.3.4/lib/python3.6/site-packages/easybuild/tools/modules.py", line 735, in modulefile_path
    modpath = self.get_value_from_modulefile(mod_name, modpath_re)
  File "/scrtp/avon/eb/software/EasyBuild/4.3.4/lib/python3.6/site-packages/easybuild/tools/modules.py", line 713, in get_value_from_modulefile
    if self.exist([mod_name], skip_avail=True)[0]:
  File "/scrtp/avon/eb/software/EasyBuild/4.3.4/lib/python3.6/site-packages/easybuild/tools/modules.py", line 615, in exist
    mod_exists = mod_exists_via_show(mod_name)
  File "/scrtp/avon/eb/software/EasyBuild/4.3.4/lib/python3.6/site-packages/easybuild/tools/modules.py", line 551, in mod_exists_via_show
    stderr = self.show(mod_name)
  File "/scrtp/avon/eb/software/EasyBuild/4.3.4/lib/python3.6/site-packages/easybuild/tools/modules.py", line 698, in show
    ans = self.run_module('show', mod_name, check_output=False, return_stderr=True)
  File "/scrtp/avon/eb/software/EasyBuild/4.3.4/lib/python3.6/site-packages/easybuild/tools/modules.py", line 811, in run_module
    (stdout, stderr) = proc.communicate()
  File "/usr/lib64/python3.6/subprocess.py", line 863, in communicate
    stdout, stderr = self._communicate(input, endtime, timeout)
  File "/usr/lib64/python3.6/subprocess.py", line 1578, in _communicate
    self.stderr.errors)
  File "/usr/lib64/python3.6/subprocess.py", line 760, in _translate_newlines
    data = data.decode(encoding, errors)
UnicodeDecodeError: 'ascii' codec can't decode byte 0xe2 in position 565: ordinal not in range(128)

[dithwick]

This has been fixed with PR #2395.

[boegel]

@dithwick The fix for the numpy easyblock can't have fixed the problem you ran into with TensorFlow, right?

[dithwick]

@boegel yes that's correct the problem persists after the fix to numpy. I've opened a separate issue #2396 for the TensorFlow problem.

[smoors]

fixed via #2395