Hi Kenneth, Kenneth Hoste <[email protected]> writes:
> Dear Loris, > > On 02/04/2019 17:04, Loris Bennett wrote: >> Dear Kenneth, >> >> OK, thanks for clarifying that point. >> >> One thing that surprised me in the context of trying to create a >> extension-only easyconfig was that, if I forget to include the primary >> program, such as Python 2.7.15, as a dependency, then the primary >> program itself, e.g. Python, will be installed as well as the >> extensions. This only made itself apparent to me when I loaded the >> extensions module and found that the primary program module was then, >> due to the conflict, automatically unloaded. > > EasyBuild is not doing that automatically trying to be smart of something, > you're somehow telling it to do that... > >> Or is this only the case >> if I also (!) mistakenly have >> >> source_urls = ['http://www.python.org/ftp/%(namelower)s/%(version)s/'] >> sources = [SOURCE_TGZ] > > That's likely the reason, but then you should still be using 'Python' as a > software name, otherwise you shouldn't see the behavior you're describing. > > Easyconfigs using the 'Bundle' easyblock should not specify any top-level > 'sources'. > We even prevent this in the central easyconfigs repository (the tests will > trip > over it), but it's not hard blocked in EasyBuild itself, so if you want to > shoot > yourself in the foot, you can. ;) OK, I have removed the 'sources', but am still now hitting a different foot. The Python packages seem to be installed OK, but the sanity check fails for two modules. However, if I load the corresponding Python version and set PYTHONPATH by hand, I can import the modules which cause the failure of the sanity check: $ module add Python/2.7.15-foss-2018b $ export PYTHONPATH=/trinity/shared/easybuild/software/Python/2.7.15-foss-2018b-zedat_extras/lib/python2.7/site-packages/ $ python Python 2.7.15 (default, Jan 18 2019, 10:12:12) [GCC 7.3.0] on linux2 Type "help", "copyright", "credits" or "license" for more information. >>> import dill >>> import nonconformist In the log from the build I have == 2019-04-04 10:43:44,756 build_log.py:162 ERROR EasyBuild crashed with an error (at easybuild/software/EasyBuild/3.8.1/lib/python2.7/site-packages/vsc_base-2.8.3-py2.7.egg/vsc/utils/exceptions.py:124 in __init__): Sanity check failed: extensions sanity check failed for 2 extensions: dill, nonconformist failing sanity check for 'dill' extension: command "/trinity/shared/easybuild/software/Python/2.7.15-foss-2018b/bin/python -c "import dill"" failed; output: Traceback (most recent call last): File "<string>", line 1, in <module> ImportError: No module named dill, failing sanity check for 'nonconformist' extension: command "/trinity/shared/easybuild/software/Python/2.7.15-foss-2018b/bin/python -c "import nonconformist"" failed; output: Traceback (most recent call last): File "<string>", line 1, in <module> ImportError: No module named nonconformist, (at easybuild/software/EasyBuild/3.8.1/lib/python2.7/site-packages/easybuild_framework-3.8.1-py2.7.egg/easybuild/framework/easyblock.py:2369 in _sanity_check_step) == 2019-04-04 10:43:44,756 easyblock.py:2870 WARNING build failed (first 300 chars): Sanity check failed: extensions sanity check failed for 2 extensions: dill, nonconformist failing sanity check for 'dill' extension: command "/trinity/shared/easybuild/software/Python/2.7.15-foss-2018b/bin/python -c "import dill"" failed; output: Traceback (most recent call last): File "<string>", The package directory looks like this: $ ll /trinity/shared/easybuild/software/Python/2.7.15-foss-2018b-zedat_extras/lib/python2.7/site-packages/ total 1024 drwxr-xr-x 4 build staff 46 Apr 4 10:15 dill-0.2.9-py2.7.egg -rw-r--r-- 1 build staff 592 Apr 4 10:43 easy-install.pth drwxr-xr-x 2 build staff 291 Apr 4 10:16 nonconformist -rw-r--r-- 1 build staff 829 Apr 4 10:16 nonconformist-2.1.0-py2.7.egg-info drwxr-xr-x 4 build staff 47 Apr 4 10:19 numpy-1.14.5-py2.7-linux-x86_64.egg drwxr-xr-x 4 build staff 48 Apr 4 10:43 pandas-0.24.2-py2.7-linux-x86_64.egg -rw-r--r-- 1 build staff 8246 Apr 4 10:35 scikit_learn-0.19.1-py2.7.egg-info drwxr-xr-x 4 build staff 47 Apr 4 10:32 scipy-1.1.0-py2.7-linux-x86_64.egg -rw-r--r-- 1 build staff 1011322 Apr 4 10:16 setuptools-39.1.0-py2.7.egg -rw-r--r-- 1 build staff 30 Apr 4 10:16 setuptools.pth -rw-r--r-- 1 build staff 2307 Apr 4 10:15 site.py -rw-r--r-- 1 build staff 1841 Apr 4 10:15 site.pyc drwxr-xr-x 27 build staff 4096 Apr 4 10:35 sklearn Any ideas what I am doing wrong this time? Cheers, Loris -- Dr. Loris Bennett (Mr.) ZEDAT, Freie Universität Berlin Email [email protected]
