Sorry, I meant add the builddep to your Pillow easyconfig, since that is where the linking is done!
Alan On Fri, 19 Oct 2018 at 10:25, Alan O'Cais <[email protected]<mailto:[email protected]>> wrote: Hi Jakob, It is always possible to shadow the LiBTIFF at GCCcore with another LibTIFF in the intel toolchain (so that you only use the intel toolchain version when you need to). That this is not an issue for other people though makes me wonder if something else is not the source of the problem. A bit of googling tells me that this may actually be a bug in the gold linker https://bugzilla.redhat.com/show_bug.cgi?id=1458003 . Does your site config ignore binutils as a dep? If you add a build dep on binutils 2.31.1 maybe the bug goes away...try adding builddependencies = [('binutils', '2.31.1', '', True)] to your LibTIFF easyconfig. Kind regards, Alan On Fri, 19 Oct 2018 at 09:33, Jakob Schiøtz <[email protected]<mailto:[email protected]>> wrote: Hi all, I wonder how this can be resolved. If --enable-ld-version-script is used when compiling LibTIFF, it cannot be used in the Intel toolchain. If it is compiled without this option, it breaks the rest of the OS (or at least important programs). The “real” solution would of course be never to use LD_LIBRARY_PATH to find libraries, but to compile the path into the executable (see the numerous “why LD_LIBRARY_PATH is considered evil” pages). But that would require a complete revamp of EasyBuild, and may not even be possible on some architectures. I guess that on the short term, problematic libraries like LibTIFF should be moved back to the foss and intel toolchains, instead of the more basic GCCcore toolchain, if the same version cannot play nice with both chains. Should this be done? It might break something if there are other GCCcore builds that rely on it. Best regards Jakob > On 18 Oct 2018, at 17:17, Benjamin Evans > <[email protected]<mailto:[email protected]>> wrote: > > Jakob, > > We saw that without the versions included several RHEL/centOS 7-provided > softwares would break. See > https://lists.ugent.be/wws/arc/easybuild/2017-05/msg00081.html as the fist > time this was discussed as far as I know. > > Cheers, > Ben > > > On Thu, Oct 18, 2018 at 10:10 AM Jakob Schiøtz > <[email protected]<mailto:[email protected]>> wrote: > Thanks, > > It is undoubtedly the same problem, in this case it is CentOS 7.4 not CentOS > 6. > > Is there a reason that --enable-ld-version-script was added to the LibTIFF > build? It seems to break compiling with Intel toolchains, maybe it should be > removed, maybe the build should again be split in a foss and an intel version. > > /Jakob > > > On 18 Oct 2018, at 14:55, Miguel Costa > > <[email protected]<mailto:[email protected]>> wrote: > > > > Dear Jakob, > > > > issue https://github.com/easybuilders/easybuild-easyconfigs/issues/6953 may > > be relevant. > > > > In that case, building LibTIFF without --enable-ld-version-script solved > > the problem. > > > > Miguel > > > > On Thu, Oct 18, 2018 at 7:17 PM Jakob Schiøtz > > <[email protected]<mailto:[email protected]>> wrote: > > Hi, > > > > I am trying to make easyconfigs for scikit-image and Pillow with > > intel/2018b. For previous versions, the foss and intel easyconfigs are > > identical (a part from the toolchain), so I just copied the foss version > > and tried it. > > > > Compiling Pillow fails with this error: > > > > icc -shared > > -L/home/modules/software/icc/2018.3.222-GCC-7.3.0-2.30/lib/intel64 > > -L/home/modules/software/imkl/2018.3.222-iimpi-2018b/lib [ ... lots of -L > > elided ... ] -ljpeg -lz -ltiff -lpython3.6m -o > > build/lib.linux-x86_64-3.6/PIL/_imaging.cpython-36m-x86_64-linux-gnu.so<http://imaging.cpython-36m-x86_64-linux-gnu.so> > > > > /home/niflheim/schiotz/easybuild_experimental/sandybridge/software/LibTIFF/4.0.9-GCCcore-7.3.0/lib/libtiff.so:(*IND*+0x0): > > multiple definition of `_end' > > > > /home/niflheim/schiotz/easybuild_experimental/sandybridge/software/LibTIFF/4.0.9-GCCcore-7.3.0/lib/libtiff.so:(*IND*+0x0): > > multiple definition of `_edata' > > > > /home/niflheim/schiotz/easybuild_experimental/sandybridge/software/LibTIFF/4.0.9-GCCcore-7.3.0/lib/libtiff.so:(*IND*+0x0): > > multiple definition of `__bss_start' > > error: command 'icc' failed with exit status 1 > > > > It looks like something is wrong with the LibTIFF installation, which was > > built as a prerequisite. I cannot help noticing that with the 2018b > > toolchains it has been moved to the GCCcore-7.3.0 toolchain instead of > > intel/foss 2017b for the previous versions. Could that have any influence > > on this problem? > > > > And can anyone suggest a solution? > > > > Best regards > > > > Jakob > > > > -- > > Jakob Schiøtz, professor, Ph.D. > > Department of Physics > > Technical University of Denmark > > DK-2800 Kongens Lyngby, Denmark > > http://www.fysik.dtu.dk/~schiotz/ > > > > > > > > -- > Jakob Schiøtz, professor, Ph.D. > Department of Physics > Technical University of Denmark > DK-2800 Kongens Lyngby, Denmark > http://www.fysik.dtu.dk/~schiotz/ > > > -- Jakob Schiøtz, professor, Ph.D. Department of Physics Technical University of Denmark DK-2800 Kongens Lyngby, Denmark http://www.fysik.dtu.dk/~schiotz/ -- 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. 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