Python fails to install in OpenSuse 15.1

[kserradell]

Python fails to install with this error

== 2020-02-12 15:59:50,754 build_log.py:169 ERROR EasyBuild crashed with an error (at easybuild/opensuse-leap/15.1/x86_64/software/EasyBuild/4.1.1/lib/python2.7/site-packages/easybuild/base/exceptions.py:124 in __init__): cmd " ulimit -s unlimited &&   /shared/earth/easybuild/opensuse-leap/15.1/x86_64/software/Python/2.7.16-GCCcore-8.3.0/bin/python setup.py build " exited with exit code 1 and output:
Could not find platform dependent libraries <exec_prefix>
Consider setting $PYTHONHOME to <prefix>[:<exec_prefix>]
Traceback (most recent call last):
  File "setup.py", line 9, in <module>
    import setuptools
  File "/tmp/eb-build/Python/2.7.16/GCCcore-8.3.0/setuptools/setuptools-41.2.0/setuptools/__init__.py", line 5, in <module>
    import functools
  File "/shared/earth/easybuild/opensuse-leap/15.1/x86_64/software/Python/2.7.16-GCCcore-8.3.0/lib/python2.7/functools.py", line 10, in <module>
    from _functools import partial, reduce
ImportError: No module named _functools
 (at easybuild/opensuse-leap/15.1/x86_64/software/EasyBuild/4.1.1/lib/python2.7/site-packages/easybuild/tools/run.py:529 in parse_cmd_output)

The error is related to this bug.

Workaround from @boegel and @omula

installopts = " && cd %(installdir)s && ln -s ../../lib64/python2.7/lib-dynload lib/python2.7/lib-dynload"

[boegel]

@kserradell Should be fixed with #1966, please test (you can download the updated easyblock from the PR, and use eb --include-easyblocks python.py to use it).

[kserradell]

@boegel Of course. I'll try to do it today or tomorrow.

[kserradell]

@boegel The installation crashes...

eadmin@bscearth408:~> eb Python-2.7.15-GCCcore-8.3.0.eb --include-easyblocks python.py
== temporary log file in case of crash /tmp/eb-UOdSDa/easybuild-8hazZX.log
== processing EasyBuild easyconfig /home/eadmin/Python-2.7.15-GCCcore-8.3.0.eb
== building and installing Python/2.7.15-GCCcore-8.3.0...
== fetching files...
== creating build dir, resetting environment...
== unpacking...
== patching...
== preparing...
== configuring...
== building...
== testing...
== installing...
== taking care of extensions...
== installing extension setuptools 41.2.0 (1/79)...
== installing extension pip 19.2.3 (2/79)...
== installing extension wheel 0.33.6 (3/79)...
== installing extension nose 1.3.7 (4/79)...
== installing extension blist 1.3.6 (5/79)...
== installing extension paycheck 1.0.2 (6/79)...
== installing extension pbr 5.4.3 (7/79)...
== installing extension Cython 0.29.13 (8/79)...
== installing extension six 1.12.0 (9/79)...
== installing extension setuptools_scm 3.3.3 (10/79)...
== installing extension python-dateutil 2.8.0 (11/79)...
== installing extension deap 1.3.0 (12/79)...
== installing extension decorator 4.4.0 (13/79)...
== installing extension liac-arff 2.4.0 (14/79)...
== installing extension pycrypto 2.6.1 (15/79)...
== installing extension ecdsa 0.13.2 (16/79)...
== installing extension enum34 1.1.6 (17/79)...
== installing extension ipaddress 1.0.22 (18/79)...
== installing extension asn1crypto 0.24.0 (19/79)...
== installing extension idna 2.8 (20/79)...
== installing extension pycparser 2.19 (21/79)...
== installing extension cffi 1.12.3 (22/79)...
== installing extension cryptography 2.7 (23/79)...
== installing extension pyasn1 0.4.7 (24/79)...
== installing extension PyNaCl 1.3.0 (25/79)...
== installing extension bcrypt 3.1.7 (26/79)...
== installing extension paramiko 2.6.0 (27/79)...
== installing extension pyparsing 2.4.2 (28/79)...
== installing extension netifaces 0.10.9 (29/79)...
== installing extension netaddr 0.7.19 (30/79)...
== installing extension funcsigs 1.0.2 (31/79)...
== installing extension mock 3.0.5 (32/79)...
== installing extension pytz 2019.2 (33/79)...
== installing extension bitstring 3.1.6 (34/79)...
== installing extension virtualenv 16.7.5 (35/79)...
== installing extension docopt 0.6.2 (36/79)...
== installing extension joblib 0.13.2 (37/79)...
== installing extension chardet 3.0.4 (38/79)...
== installing extension certifi 2019.9.11 (39/79)...
== installing extension urllib3 1.25.3 (40/79)...
== installing extension requests 2.22.0 (41/79)...
== installing extension xlrd 1.2.0 (42/79)...
== installing extension py_expression_eval 0.3.9 (43/79)...
== installing extension tabulate 0.8.3 (44/79)...
== installing extension ujson 1.35 (45/79)...
== installing extension atomicwrites 1.3.0 (46/79)...
== installing extension py 1.8.0 (47/79)...
== installing extension scandir 1.10.0 (48/79)...
== installing extension pathlib2 2.3.4 (49/79)...
== installing extension zipp 0.6.0 (50/79)...
== installing extension configparser 4.0.2 (51/79)...
== installing extension contextlib2 0.5.5 (52/79)...
== installing extension importlib_metadata 0.22 (53/79)...
== installing extension pluggy 0.13.0 (54/79)...
== installing extension more-itertools 5.0.0 (55/79)...
== installing extension attrs 19.1.0 (56/79)...
== installing extension wcwidth 0.1.7 (57/79)...
== installing extension pytest 4.6.5 (58/79)...
== installing extension MarkupSafe 1.1.1 (59/79)...
== installing extension Jinja2 2.10.1 (60/79)...
== installing extension packaging 19.1 (61/79)...
== installing extension sphinxcontrib-websupport 1.1.2 (62/79)...
== installing extension Pygments 2.4.2 (63/79)...
== installing extension imagesize 1.1.0 (64/79)...
== installing extension docutils 0.15.2 (65/79)...
== installing extension snowballstemmer 1.9.1 (66/79)...
== installing extension Babel 2.7.0 (67/79)...
== installing extension alabaster 0.7.12 (68/79)...
== installing extension typing 3.7.4.1 (69/79)...
== installing extension Sphinx 1.8.5 (70/79)...
== installing extension Click 7.0 (71/79)...
== installing extension psutil 5.6.3 (72/79)...
== installing extension future 0.17.1 (73/79)...
== installing extension singledispatch 3.4.0.3 (74/79)...
== installing extension networkx 2.2 (75/79)...
== installing extension saga-python 0.60.1 (76/79)...
== installing extension pydotplus 2.0.2 (77/79)...
== installing extension xxhash 1.4.3 (78/79)...
== installing extension openpyxl 3.0.3 (79/79)...
== FAILED: Installation ended unsuccessfully (build directory: /tmp/eb-build/Python/2.7.15/GCCcore-8.3.0): build failed (first 300 chars): cmd " pip install --prefix=/shared/earth/easybuild/opensuse-leap/15.1/x86_64/software/Python/2.7.15-GCCcore-8.3.0  --no-deps  --ignore-installed  --no-build-isolation  ." exited with exit code 1 and output:
DEPRECATION: Python 2.7 will reach the end of its life on January 1st, 2020. Please upgrade y (took 17 min 48 sec)
== Results of the build can be found in the log file(s) /tmp/eb-UOdSDa/easybuild-Python-2.7.15-20200219.171500.vPlkt.log
ERROR: Build of /home/eadmin/Python-2.7.15-GCCcore-8.3.0.eb failed (err: 'build failed (first 300 chars): cmd " pip install --prefix=/shared/earth/easybuild/opensuse-leap/15.1/x86_64/software/Python/2.7.15-GCCcore-8.3.0  --no-deps  --ignore-installed  --no-build-isolation  ." exited with exit code 1 and output:\nDEPRECATION: Python 2.7 will reach the end of its life on January 1st, 2020. Please upgrade y')

easybuild-Python-2.7.15-20200219.171500.vPlkt.log

[boegel]

@kserradell I had to fix some import issues that I overlooked in #1966, did you fix those yourself too, or are you using the wrong python.py?

Also, it looks like a different issue now...

Processing /tmp/eb-build/Python/2.7.15/GCCcore-8.3.0/openpyxl/openpyxl-3.0.3
    ERROR: Command errored out with exit status 1:
     command: /shared/earth/easybuild/opensuse-leap/15.1/x86_64/software/Python/2.7.15-GCCcore-8.3.0/bin/python -c 'import sys, setuptools, tokenize; sys.argv[0] = '"'"'/tmp/eb-UOdSDa/pip-req-build-wcUysv/setup.py'"'"'; __file__='"'"'/tmp/eb-UOdSDa/pip-req-build-wcUysv/setup.py'"'"';f=getattr(tokenize, '"'"'open'"'"', open)(__file__);code=f.read().replace('"'"'\r\n'"'"', '"'"'\n'"'"');f.close();exec(compile(code, __file__, '"'"'exec'"'"'))' egg_info --egg-base pip-egg-info
         cwd: /tmp/eb-UOdSDa/pip-req-build-wcUysv/
    Complete output (5 lines):
    Traceback (most recent call last):
      File "<string>", line 1, in <module>
      File "/tmp/eb-UOdSDa/pip-req-build-wcUysv/setup.py", line 28, in <module>
        from importlib.util import module_from_spec, spec_from_file_location
    ImportError: No module named util
    ----------------------------------------
ERROR: Command errored out with exit status 1: python setup.py egg_info Check the logs for full command output.

Do you have an importlib/util.* in your Python installation (/shared/earth/easybuild/opensuse-leap/15.1/x86_64/software/Python/2.7.15-GCCcore-8.3.0)?

[boegel]

@kserradell Any updates on the last issue?

[boegel]

re-opening, #1966 is only a partial fix for the issues reported by @kserradell ...

[kserradell]

Sorry @boegel for my late reply. I'm quite busy in the office with all this mess with the virus. I'll try to take a look as soon as possible.

[boegel]

I was able to install both Python-2.7.18-GCCcore-11.2.0.eb and Python-3.9.6-GCCcore-11.2.0.eb in an openSUSE 15.3 container image using current develop (so somewhere in between EasyBuild v4.5.3 and whatever version is released after that), so this should be good to close...