Dear all, Just for documenting this publicly:
An alternative workaround is to simply set -DDEAL_II_LINKER_FLAGS="-w" on the command line. This also suppresses the warning (without disabling lapack and subsequently umfpack). It would still be nice if we could actually identify the main cause of this problem. :-D Best, Matthias On Thu, Jan 31, 2019, at 14:42 CST, Jean-Paul Pelteret <jppelte...@gmail.com> wrote: > Dear Zachary, > > Here’s the relevant part of the detailed.log file: > >> # DEAL_II_WITH_LAPACK set up with external dependencies >> # LAPACK_WITH_64BIT_BLAS_INDICES = OFF >> # LAPACK_LINKER_FLAGS = >> # LAPACK_LIBRARIES = >> /System/Library/Frameworks/Accelerate.framework;m > > > So I reckon that if you force deal.II to ignore LAPACK then the > warning should go away. As I said previously, you should be able to do > this by cleaning the build directory (at least removing > CMakeCache.txt), and configuring deal.II with the following settings > > cmake -DLAPACK_FOUND=false -DBLAS_FOUND=false … > > and then you’d need to rebuild and reinstall the library. Before you rebuild, > may first want to verify that “DEAL_II_WITH_LAPACK = OFF” in the detailed.log. > > I hope that this solves the issue. > > Best, > Jean-Paul > >> On 31 Jan 2019, at 20:56, Zachary Hardy <zach.ha...@tamu.edu> wrote: >> >> Attached are the requested files. >> >> Please let me know what you believe the best remedy would be! >> >> Zachary Hardy '18 >> ––––––––––––––––––––––––––––––––––––––––––– >> Texas A&M University >> B.S. Nuclear Engineering >> ––––––––––––––––––––––––––––––––––––––––––– >> ––––––––––––––––––––––––––––––––––––––––––– >> Cell: (682) 667-3646 >> School Email: zach.ha...@tamu.edu <mailto:zach.ha...@tamu.edu> >> Personal Email: zhardy1...@gmail.com <mailto:zhardy1...@gmail.com> >> >> -- >> >> >> On Thu, Jan 31, 2019 at 12:26 PM Jean-Paul Pelteret <jppelte...@gmail.com >> <mailto:jppelte...@gmail.com>> wrote: >> Hi Zachary, >> >> So it looks like maybe the “-framework Accelerate” is what’s being >> complained about, but I’m not sure. I also don’t have the latest >> MacOS, so I can’t inspect this myself. But what you could try to do >> is build deal.II without BLAS and LAPACK support, and this might >> prevent this from appearing on the link line. To do this I believe >> that you should pass the following flags to CMake: >> >> cmake -DLAPACK_FOUND=false -DBLAS_FOUND=false ... >> >> The two log are files are located in the directory in which you >> originally built deal.II. It would be great to see those, because >> then we can inspect which features have been auto detected during >> the initial configuration. >> >> Best, >> Jean-Paul >> >> >>> On 31 Jan 2019, at 18:58, Zachary Hardy <zach.ha...@tamu.edu >>> <mailto:zach.ha...@tamu.edu>> wrote: >>> >>> Hi Jean-Paul, >>> >>> Thanks for the response! >>> >>> I am running on MacOS 10.14.2, with Xcode 10.1. >>> >>> The verbose output is as follows: >>> /usr/local/Cellar/cmake/3.13.3/bin/cmake -E cmake_link_script >>> CMakeFiles/step-1.dir/link.txt --verbose=1 >>> /Library/Developer/CommandLineTools/usr/bin/c++ >>> -Wl,-search_paths_first -Wl,-headerpad_max_install_names -g -ggdb >>> CMakeFiles/step-1.dir/step-1.cc.o -o step-1 >>> /Users/ZachHardy/codes/dealii-9.0.1-installed/lib/libdeal_II.g.9.0.1.dylib >>> -framework Accelerate -lm -lc /usr/lib/libz.dylib >>> >>> Where are the deal.II configuration logs you mentioned located? I am a bit >>> new, so I am unsure. >>> >>> Zachary Hardy '18 >>> ––––––––––––––––––––––––––––––––––––––––––– >>> Texas A&M University >>> B.S. Nuclear Engineering >>> ––––––––––––––––––––––––––––––––––––––––––– >>> ––––––––––––––––––––––––––––––––––––––––––– >>> Cell: (682) 667-3646 >>> School Email: zach.ha...@tamu.edu <mailto:zach.ha...@tamu.edu> >>> Personal Email: zhardy1...@gmail.com <mailto:zhardy1...@gmail.com> >>> >>> -- >>> >>> >>> On Wed, Jan 30, 2019 at 11:57 PM Jean-Paul Pelteret <jppelte...@gmail.com >>> <mailto:jppelte...@gmail.com>> wrote: >>> Dear Zachary, >>> >>> I googled this problem and it seems that, dependent on what version >>> of Xcode and MacOS you’re running, there might be one of two >>> solutions. Here’s a similar post on the Apple forums that outlines >>> the two possibilities >>> <https://urldefense.proofpoint.com/v2/url?u=https-3A__forums.developer.apple.com_thread_97850&d=DwMFaQ&c=ODFT-G5SujMiGrKuoJJjVg&r=nizQCYyKabiLGJAOrCZANoq162AR9hpPweEmKQxyveY&m=HOJxNpKM99ijPmOpK6-HFYTTFEkzqyo61wVwWKj8Zks&s=xLb6bS-ywf-0No8b_e_wOiyTH8KQYRLhGrNuzb9alyY&e=>. >>> The >>> first possible solution (which may only work for older versions of >>> Xcode) to remove and reinstall the command line tools. The second >>> would be that the link line generated by CMake is causing the >>> issue. >>> >>> This is the selected solution from the Apple forum post >>> <https://urldefense.proofpoint.com/v2/url?u=https-3A__forums.developer.apple.com_thread_97850&d=DwMFaQ&c=ODFT-G5SujMiGrKuoJJjVg&r=nizQCYyKabiLGJAOrCZANoq162AR9hpPweEmKQxyveY&m=HOJxNpKM99ijPmOpK6-HFYTTFEkzqyo61wVwWKj8Zks&s=xLb6bS-ywf-0No8b_e_wOiyTH8KQYRLhGrNuzb9alyY&e=>: >>>> You have to link directly to the library and not rely on -isysroot or >>>> -frameworks in your makefile. you need to link like -L /path/to/lib >>>> libstuff.dylib >>> and something that we’d likely have to implement on our side. >>> >>> Can you please provide the deal.II configuration logs >>> (detailed.log, summary.log), tell us more about your system setup >>> (MacOS and Xcode version), and also provide the verbose output when >>> building one of the tutorial programs (you can get this using “make >>> VERBOSE=1”). I hope that this might be sufficient information to >>> help solve this issue. >>> >>> Best, >>> Jean-Paul >>> >>>> On 31 Jan 2019, at 03:34, Zachary Hardy <zach.ha...@tamu.edu >>>> <mailto:zach.ha...@tamu.edu>> wrote: >>>> >>>> When I compile the examples, I receive about 12 warning messages >>>> about linking stating that the text-based stub files and library >>>> files are not in sync, all from within >>>> `/System/Library/Framework/Accelerate.framework.' Everything ends >>>> up working in the end, but I can't seem to remedy this issue to >>>> get rid of the warning messages. Has anyone seen this before, and >>>> if so, what steps can be taken to resolve this issue? Below is an >>>> example of the warning messages. >>>> >>>> ld: warning: text-based stub file >>>> /System/Library/Frameworks//Accelerate.framework/Accelerate.tbd >>>> and library file >>>> /System/Library/Frameworks//Accelerate.framework/Accelerate are >>>> out of sync. Falling back to library file for linking. >>>> >>>> -- >>>> The deal.II project is located at http://www.dealii.org/ >>>> <https://urldefense.proofpoint.com/v2/url?u=http-3A__www.dealii.org_&d=DwMFaQ&c=ODFT-G5SujMiGrKuoJJjVg&r=nizQCYyKabiLGJAOrCZANoq162AR9hpPweEmKQxyveY&m=HOJxNpKM99ijPmOpK6-HFYTTFEkzqyo61wVwWKj8Zks&s=5CLsR_qvHDVn8MkbjQR3Ry6D2PVS_ccQ3TN2JoRmSdw&e=> >>>> For mailing list/forum options, see >>>> https://groups.google.com/d/forum/dealii?hl=en >>>> <https://urldefense.proofpoint.com/v2/url?u=https-3A__groups.google.com_d_forum_dealii-3Fhl-3Den&d=DwMFaQ&c=ODFT-G5SujMiGrKuoJJjVg&r=nizQCYyKabiLGJAOrCZANoq162AR9hpPweEmKQxyveY&m=HOJxNpKM99ijPmOpK6-HFYTTFEkzqyo61wVwWKj8Zks&s=4GletThGMFcMh-5VKjDf3FuSJeL97ax-NI1GftOceak&e=> >>>> --- >>>> 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 >>>> <mailto:dealii+unsubscr...@googlegroups.com>. >>>> For more options, visit https://groups.google.com/d/optout >>>> <https://urldefense.proofpoint.com/v2/url?u=https-3A__groups.google.com_d_optout&d=DwMFaQ&c=ODFT-G5SujMiGrKuoJJjVg&r=nizQCYyKabiLGJAOrCZANoq162AR9hpPweEmKQxyveY&m=HOJxNpKM99ijPmOpK6-HFYTTFEkzqyo61wVwWKj8Zks&s=EXMkMx6p0xktYXh8QpOjHbqsPApS5Hez2DNst3IxZpo&e=>. >>> >>> >>> -- >>> The deal.II project is located at http://www.dealii.org/ >>> <https://urldefense.proofpoint.com/v2/url?u=http-3A__www.dealii.org_&d=DwMFaQ&c=ODFT-G5SujMiGrKuoJJjVg&r=nizQCYyKabiLGJAOrCZANoq162AR9hpPweEmKQxyveY&m=HOJxNpKM99ijPmOpK6-HFYTTFEkzqyo61wVwWKj8Zks&s=5CLsR_qvHDVn8MkbjQR3Ry6D2PVS_ccQ3TN2JoRmSdw&e=> >>> For mailing list/forum options, see >>> https://groups.google.com/d/forum/dealii?hl=en >>> <https://urldefense.proofpoint.com/v2/url?u=https-3A__groups.google.com_d_forum_dealii-3Fhl-3Den&d=DwMFaQ&c=ODFT-G5SujMiGrKuoJJjVg&r=nizQCYyKabiLGJAOrCZANoq162AR9hpPweEmKQxyveY&m=HOJxNpKM99ijPmOpK6-HFYTTFEkzqyo61wVwWKj8Zks&s=4GletThGMFcMh-5VKjDf3FuSJeL97ax-NI1GftOceak&e=> >>> --- >>> 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 >>> <mailto:dealii+unsubscr...@googlegroups.com>. >>> For more options, visit https://groups.google.com/d/optout >>> <https://urldefense.proofpoint.com/v2/url?u=https-3A__groups.google.com_d_optout&d=DwMFaQ&c=ODFT-G5SujMiGrKuoJJjVg&r=nizQCYyKabiLGJAOrCZANoq162AR9hpPweEmKQxyveY&m=HOJxNpKM99ijPmOpK6-HFYTTFEkzqyo61wVwWKj8Zks&s=EXMkMx6p0xktYXh8QpOjHbqsPApS5Hez2DNst3IxZpo&e=>. >>> >>> -- >>> The deal.II project is located at http://www.dealii.org/ >>> <https://urldefense.proofpoint.com/v2/url?u=http-3A__www.dealii.org_&d=DwMFaQ&c=ODFT-G5SujMiGrKuoJJjVg&r=nizQCYyKabiLGJAOrCZANoq162AR9hpPweEmKQxyveY&m=V-Yhc-ja4iWXgMCdCloI-gan8IrqzRU-LYcAPMLZQl4&s=xtdoYLBaydpu31rtarMy_d5aJjLuHQhxokgl2CkyytU&e=> >>> For mailing list/forum options, see >>> https://groups.google.com/d/forum/dealii?hl=en >>> <https://urldefense.proofpoint.com/v2/url?u=https-3A__groups.google.com_d_forum_dealii-3Fhl-3Den&d=DwMFaQ&c=ODFT-G5SujMiGrKuoJJjVg&r=nizQCYyKabiLGJAOrCZANoq162AR9hpPweEmKQxyveY&m=V-Yhc-ja4iWXgMCdCloI-gan8IrqzRU-LYcAPMLZQl4&s=CMFxy0dBnny9m4AVOD1pELiRdVlqRzXlkjP8xpcIjGU&e=> >>> --- >>> 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 >>> <mailto:dealii+unsubscr...@googlegroups.com>. >>> For more options, visit https://groups.google.com/d/optout >>> <https://urldefense.proofpoint.com/v2/url?u=https-3A__groups.google.com_d_optout&d=DwMFaQ&c=ODFT-G5SujMiGrKuoJJjVg&r=nizQCYyKabiLGJAOrCZANoq162AR9hpPweEmKQxyveY&m=V-Yhc-ja4iWXgMCdCloI-gan8IrqzRU-LYcAPMLZQl4&s=g3Ksw3NPyuXHDPgehCuUxZisa0OP6P4zRyQEGScKxJk&e=>. >> >> >> -- >> The deal.II project is located at http://www.dealii.org/ >> <https://urldefense.proofpoint.com/v2/url?u=http-3A__www.dealii.org_&d=DwMFaQ&c=ODFT-G5SujMiGrKuoJJjVg&r=nizQCYyKabiLGJAOrCZANoq162AR9hpPweEmKQxyveY&m=V-Yhc-ja4iWXgMCdCloI-gan8IrqzRU-LYcAPMLZQl4&s=xtdoYLBaydpu31rtarMy_d5aJjLuHQhxokgl2CkyytU&e=> >> For mailing list/forum options, see >> https://groups.google.com/d/forum/dealii?hl=en >> <https://urldefense.proofpoint.com/v2/url?u=https-3A__groups.google.com_d_forum_dealii-3Fhl-3Den&d=DwMFaQ&c=ODFT-G5SujMiGrKuoJJjVg&r=nizQCYyKabiLGJAOrCZANoq162AR9hpPweEmKQxyveY&m=V-Yhc-ja4iWXgMCdCloI-gan8IrqzRU-LYcAPMLZQl4&s=CMFxy0dBnny9m4AVOD1pELiRdVlqRzXlkjP8xpcIjGU&e=> >> --- >> You received this message because you are 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