Re: [deal.II] install problems with clang@12.0.0 and Xcode12.0 from spack

[Jean-Paul Pelteret]

Hi Alexander, I am, unfortunately, marginally acquainted with the problem that you’re facing. I’m not 100% sure, but I believe that this is an upstream problem that has to do with how these packages are configured for Apple systems. I too noticed that within a couple of update cycles SuiteSparse, for example, went from linking fine, to not specifying any path (only a library name) when linked, to linking with an @rpath placeholder. Here is a silent update that offered some mitigation for the problem with SuiteSparse, which probably (?) was released after the Mac package was built: https://github.com/DrTimothyAldenDavis/SuiteSparse/commit/f900df09d2ee3f7ecfd9243b69e181d80f720790#diff-d1c5d2f7b51daaca451f6322f8cd89adR59 This is a super annoying problem. So what can you do about it? Well, possibly the quickest solution to your problem lies with a tool called “install_name_tool”, which allows you to modify the paths of the libraries that an executable is linked against. I’ve attached a script that I wrote for myself a while ago because, well, I faced the same issue. If you modify it appropriately, you can at least use it to build your executable and modify the locations of the linked libraries before you get to run the program. It’s not a great solution, and you definitely shouldn’t have to go this route, but maybe it would at least help you get going while we (or the dependency maintainers) get to fixing the core issue. Jean-Paul -- The deal.II project is located at http://www.dealii.org/ For mailing list/forum options, see https://groups.google.com/d/forum/dealii?hl=en --- You received this message because you are subscribed to the Google Groups "deal.II User Group" group. To unsubscribe from this group and stop receiving emails from it, send an email to dealii+unsubscr...@googlegroups.com. To view this discussion on the web visit https://groups.google.com/d/msgid/dealii/6F98B2EB-127D-4CB3-8A93-828FC1255324%40gmail.com.

build_install.sh
Description: Binary data

On 30 Sep 2020, at 11:16, 'Alexander Greiner' via deal.II User Group <dealii@googlegroups.com> wrote: Dear all, I would like to share a bit more information what I found out (as a beginner) that might be helpful. I used otool -L and otool -l to check out the .dylib files. I attached the results for libdeal_II.9.2.0.dylib and libdeal_II.g.9.2.0.dylib.  Here I could find out that libraries from the suite-sparse package are not linked correctly. Although the rpath is correct, the load command is missing an @rpath (see e.g. libumfpack.5.dylib). This problem exists also in other dependent libraries like libmuelu from trilinos where libraries from suite-sparse are not linked properly. I furthermore attached the output of otool -L and otool -l  applied to the step-40 executable. Here occurs the same problem with suite-sparse again, and additionally, there are no rpathsset such it cannot find the libmuelu-adapters.13.dylib for example (among all others from the trilinos package). Hope that helps to clarify my issues! Thank's! Alex Alexander Greiner schrieb am Mittwoch, 30. September 2020 um 10:20:00 UTC+2: Hi Praveen, I've (hopefully) done what you suggested and attached the outputs again. It has definitely changed something, but I'm still running into the same error. Might it be possible that during installation also not spack's Cmake version was used resulting in missing links in dylib-files? Regards Alex Praveen C schrieb am Mittwoch, 30. September 2020 um 05:44:36 UTC+2: I notice that you are using cmake from /opt/local/bin, but spack would have installed its own cmake. Could you try using cmake from spack to compile and then run the example ? best praveen On 29-Sep-2020, at 7:35 PM, 'Alexander Greiner' via deal.II User Group <dea...@googlegroups.com> wrote: Hi Luca, I ran step-40 and the output of Cmake log file from the CMakeFiles Folder is attached. Additionally, the output of make -d if that is what you meant.  Thanks!  Alex --  The deal.II project is located at http://www.dealii.org/ For mailing list/forum options, see https://groups.google.com/d/forum/dealii?hl=en ---  You received this message because you are subscribed to the Google Groups "deal.II User Group" group. To unsubscribe from this group and stop receiving emails from it, send an email to dealii+unsubscr...@googlegroups.com. To view this discussion on the web visit https://groups.google.com/d/msgid/dealii/1f813aa4-acaf-4839-aa00-9151de231756n%40googlegroups.com. <otool_l_step_40.txt><otool_l_libdeal_II_g_9_2_0_dylib.txt><otool_l_libdeal_II_9_2_0_dylib.txt><otool-L_libdeal_II_g_9_2_0_dylib.txt><otool-L_step_40.txt><otool-L_libdeal_II_9_2_0_dylib.txt> -- The deal.II project is located at http://www.dealii.org/ For mailing list/forum options, see https://groups.google.com/d/forum/dealii?hl=en --- You received this message because you are subscribed to the Google Groups "deal.II User Group" group. To unsubscribe from this group and stop receiving emails from it, send an email to dealii+unsubscr...@googlegroups.com. To view this discussion on the web visit https://groups.google.com/d/msgid/dealii/6F98B2EB-127D-4CB3-8A93-828FC1255324%40gmail.com.