Hi Alan,thanks for the explanations. I wasn't expecting the result of --module-only to be different depending on whether the actual installation of the software was already present or not. So that was the problem apparently. But you are right that it works properly when I do it again now.
I had to recreate the module because I forgot to change something in the easybuild configuration (module-depends-on=True). At the same time, I wanted to introduce architecture-specific builds for the different node types in our cluster that share the same module path on the login nodes. So it seems like the software was not built for this architecture yet, thus missing the installation dir and then the --module-only created modulefiles without the environment variables in them.
All solved now though, thanks again! Best, Maik Am 11.06.2018 um 12:57 schrieb Alan O'Cais:
(EB version 3.6.0) On Mon, 11 Jun 2018 at 12:56, Alan O'Cais <[email protected]<mailto:[email protected]>> wrote: I just tested using '--module-only' on our (existing) installation and it set the envvars correctly. Are you sure you have the right idea about what --module-only does? If you use --module-only and --force on a blank slate you will get module files you describe since that skips the sanity check (which would've failed because the installation doesn't actually exist). Alan On Mon, 11 Jun 2018 at 12:37, Alan O'Cais <[email protected]<mailto:[email protected]>> wrote: Hi Maik, Can you explain that a little more? Why are you using '--module-only', are you re-using the CentOS 6 installation and creating a new module tree somewhere else? The guesses (I think) lead to the envvars being set in the module only if the something exists in the target, maybe send a debug log to see if these guesses are getting things wrong. It'll also be interesting to see what is being checked in the sanity check step that this passes but still generates an empty module. Alan On Mon, 11 Jun 2018 at 12:11, Maik Schmidt <[email protected]<mailto:[email protected]>> wrote: Hm, could this be related to having used --module-only? I found this: https://github.com/easybuilders/easybuild-framework/issues/1877 but the environment variables in GCCcore are not mentioned there. So I guess this should have worked? Best, Maik Am 11.06.2018 um 10:41 schrieb Maik Schmidt:Hi all, we're finally upgrading from RHEL6 to 7 and so I wanted to do fresh builds of most of our software using EasyBuild. Now, when trying to use the TensorFlow that I have built using the foss-toolchain, I got the error: ImportError: /usr/lib64/libstdc++.so.6: version `GLIBCXX_3.4.21' not found (required by /sw/installed/TensorFlow/1.8.0-foss-2018a-Python-3.6.4/lib/python3.6/site-packages/tensorflow/python/_pywrap_tensorflow_internal.so) Apparently, it still uses the libstdc++.so from /usr instead of the one from the GCCcore module. I have looked at the module file, and to my surprise, I did not see it setting any environment variables like LD_LIBRARY_PATH at all. This cannot be intentional, right? It does not even set things like PATH or MANPATH, so a: $ module load GCC $ which gcc /usr/bin/gcc still points to /usr, too. I've seen that in the gcc easyblock, there is the function "make_module_req_guess" that looks like it is supposed to handle those environment variables, but apparently, thoses "guesses" are not used anywhere. At least it doesn't end up in the module file for me... What am I missing here? Is this a bug? Best, Maik-- Maik Schmidt HPC Services Technische Universität Dresden Zentrum für Informationsdienste und Hochleistungsrechnen (ZIH) Willers-Bau A116 D-01062 Dresden Telefon: +49 351 463-32836 -- Dr. Alan O'Cais E-CAM Software Manager Juelich Supercomputing Centre Forschungszentrum Juelich GmbH 52425 Juelich, Germany Phone: +49 2461 61 5213 Fax: +49 2461 61 6656 E-mail: [email protected]<mailto:[email protected]> WWW: http://www.fz-juelich.de/ias/jsc/EN -- Dr. Alan O'Cais E-CAM Software Manager Juelich Supercomputing Centre Forschungszentrum Juelich GmbH 52425 Juelich, Germany Phone: +49 2461 61 5213 Fax: +49 2461 61 6656 E-mail: [email protected]<mailto:[email protected]> WWW: http://www.fz-juelich.de/ias/jsc/EN -- Dr. Alan O'Cais E-CAM Software Manager Juelich Supercomputing Centre Forschungszentrum Juelich GmbH 52425 Juelich, Germany Phone: +49 2461 61 5213 Fax: +49 2461 61 6656 E-mail: [email protected]<mailto:[email protected]> WWW: http://www.fz-juelich.de/ias/jsc/EN ------------------------------------------------------------------------------------------------ ------------------------------------------------------------------------------------------------ Forschungszentrum Juelich GmbH 52425 Juelich Sitz der Gesellschaft: Juelich Eingetragen im Handelsregister des Amtsgerichts Dueren Nr. HR B 3498 Vorsitzender des Aufsichtsrats: MinDir Dr. Karl Eugen Huthmacher Geschaeftsfuehrung: Prof. Dr.-Ing. Wolfgang Marquardt (Vorsitzender), Karsten Beneke (stellv. Vorsitzender), Prof. Dr.-Ing. Harald Bolt, Prof. Dr. Sebastian M. Schmidt ------------------------------------------------------------------------------------------------ ------------------------------------------------------------------------------------------------
-- Maik Schmidt HPC Services Technische Universität Dresden Zentrum für Informationsdienste und Hochleistungsrechnen (ZIH) Willers-Bau A116 D-01062 Dresden Telefon: +49 351 463-32836
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