Dear Zhibo, I guess that this could be fixed in Candi (? ping Uwe, Timo). As of the El Capitan release (I think), its not possible to use DYLD_LIBRARY_PATH anymore if SIP (System Integrity Protection) is enabled. For an immediate solution I would suggest trying to use install_name_tool to add the full path of (or an @rpath to) these problematic libraries. Here’s a link to a StackOverflow post <https://stackoverflow.com/a/33992190> that has more details. I hope that using this tool to direct to the location of the linked in library will resolve the issue.
Best, Jean-Paul > On 22 Aug 2018, at 21:30, Zhibo Luo <[email protected]> wrote: > > > Hi all, > > I recently update my MacOs system to latest macOS High Sierra (10.13.6) and > crash my dealii. so I decide to reinstall dealii through candi script. The > installation works fine except some warnings. The problem is that when I cd > to step-1, cmake and make command get passed, however, when I make run, error > comes: > > [ 66%] Built target step-1 > [100%] Run step-1 with Debug configuration > dyld: Library not loaded: libsuperlu_dist.5.dylib > Referenced from: > /Users/zhiboluo/deal.ii-candi/deal.II-v9.0.0/examples/step-1/./step-1 > Reason: image not found > make[3]: *** [CMakeFiles/run] Abort trap: 6 > make[2]: *** [CMakeFiles/run.dir/all] Error 2 > make[1]: *** [CMakeFiles/run.dir/rule] Error 2 > > I found similar issue here: > https://groups.google.com/forum/#!searchin/dealii/dyld$3A$20Library$20not$20loaded$20%7Csort:date/dealii/fIXfMnaFdEc/zgHjkY3_CAAJ > > <https://groups.google.com/forum/#!searchin/dealii/dyld$3A$20Library$20not$20loaded$20%7Csort:date/dealii/fIXfMnaFdEc/zgHjkY3_CAAJ> > > And I tried the suggested method by export > DYLD_LIBRARY_PATH=$DYLD_LIBRARY_PATH:~/deal.ii-candi/superlu_dist_5.1.2/lib, > but it doesn't work for me. > > I used otool command to output the link libraries: > > zhiboluo$ otool -L step-1 > step-1: > > /Users/zhiboluo/deal.ii-candi/deal.II-v9.0.0/lib/libdeal_II.g.9.0.0.dylib > (compatibility version 9.0.0, current version 9.0.0) > /Users/zhiboluo/deal.ii-candi/p4est-2.0/DEBUG/lib/libp4est-2.0.dylib > (compatibility version 0.0.0, current version 0.0.0) > /Users/zhiboluo/deal.ii-candi/p4est-2.0/DEBUG/lib/libsc-2.0.dylib > (compatibility version 0.0.0, current version 0.0.0) > /usr/lib/libz.1.dylib (compatibility version 1.0.0, current version > 1.2.11) > @rpath/libmuelu-adapters.12.dylib (compatibility version 12.0.0, > current version 12.10.1) > @rpath/libmuelu-interface.12.dylib (compatibility version 12.0.0, > current version 12.10.1) > @rpath/libmuelu.12.dylib (compatibility version 12.0.0, current version > 12.10.1) > @rpath/libteko.12.dylib (compatibility version 12.0.0, current version > 12.10.1) > @rpath/libstratimikos.12.dylib (compatibility version 12.0.0, current > version 12.10.1) > @rpath/libstratimikosbelos.12.dylib (compatibility version 12.0.0, > current version 12.10.1) > @rpath/libstratimikosaztecoo.12.dylib (compatibility version 12.0.0, > current version 12.10.1) > @rpath/libstratimikosamesos.12.dylib (compatibility version 12.0.0, > current version 12.10.1) > @rpath/libstratimikosml.12.dylib (compatibility version 12.0.0, current > version 12.10.1) > @rpath/libstratimikosifpack.12.dylib (compatibility version 12.0.0, > current version 12.10.1) > @rpath/libifpack2-adapters.12.dylib (compatibility version 12.0.0, > current version 12.10.1) > @rpath/libifpack2.12.dylib (compatibility version 12.0.0, current > version 12.10.1) > @rpath/libanasazitpetra.12.dylib (compatibility version 12.0.0, current > version 12.10.1) > @rpath/libModeLaplace.12.dylib (compatibility version 12.0.0, current > version 12.10.1) > @rpath/libanasaziepetra.12.dylib (compatibility version 12.0.0, current > version 12.10.1) > @rpath/libanasazi.12.dylib (compatibility version 12.0.0, current > version 12.10.1) > @rpath/libamesos2.12.dylib (compatibility version 12.0.0, current > version 12.10.1) > @rpath/libbelostpetra.12.dylib (compatibility version 12.0.0, current > version 12.10.1) > @rpath/libbelosepetra.12.dylib (compatibility version 12.0.0, current > version 12.10.1) > @rpath/libbelos.12.dylib (compatibility version 12.0.0, current version > 12.10.1) > @rpath/libml.12.dylib (compatibility version 12.0.0, current version > 12.10.1) > @rpath/libifpack.12.dylib (compatibility version 12.0.0, current > version 12.10.1) > @rpath/libzoltan2.12.dylib (compatibility version 12.0.0, current > version 12.10.1) > @rpath/libpamgen_extras.12.dylib (compatibility version 12.0.0, current > version 12.10.1) > @rpath/libpamgen.12.dylib (compatibility version 12.0.0, current > version 12.10.1) > @rpath/libamesos.12.dylib (compatibility version 12.0.0, current > version 12.10.1) > @rpath/libgaleri-xpetra.12.dylib (compatibility version 12.0.0, current > version 12.10.1) > @rpath/libgaleri-epetra.12.dylib (compatibility version 12.0.0, current > version 12.10.1) > @rpath/libaztecoo.12.dylib (compatibility version 12.0.0, current > version 12.10.1) > @rpath/libisorropia.12.dylib (compatibility version 12.0.0, current > version 12.10.1) > @rpath/libxpetra-sup.12.dylib (compatibility version 12.0.0, current > version 12.10.1) > @rpath/libxpetra.12.dylib (compatibility version 12.0.0, current > version 12.10.1) > @rpath/libthyratpetra.12.dylib (compatibility version 12.0.0, current > version 12.10.1) > @rpath/libthyraepetraext.12.dylib (compatibility version 12.0.0, > current version 12.10.1) > @rpath/libthyraepetra.12.dylib (compatibility version 12.0.0, current > version 12.10.1) > @rpath/libthyracore.12.dylib (compatibility version 12.0.0, current > version 12.10.1) > @rpath/libepetraext.12.dylib (compatibility version 12.0.0, current > version 12.10.1) > @rpath/libtpetraext.12.dylib (compatibility version 12.0.0, current > version 12.10.1) > @rpath/libtpetrainout.12.dylib (compatibility version 12.0.0, current > version 12.10.1) > @rpath/libtpetra.12.dylib (compatibility version 12.0.0, current > version 12.10.1) > @rpath/libkokkostsqr.12.dylib (compatibility version 12.0.0, current > version 12.10.1) > @rpath/libtpetrakernels.12.dylib (compatibility version 12.0.0, current > version 12.10.1) > @rpath/libtpetraclassiclinalg.12.dylib (compatibility version 12.0.0, > current version 12.10.1) > @rpath/libtpetraclassicnodeapi.12.dylib (compatibility version 12.0.0, > current version 12.10.1) > @rpath/libtpetraclassic.12.dylib (compatibility version 12.0.0, current > version 12.10.1) > @rpath/libtriutils.12.dylib (compatibility version 12.0.0, current > version 12.10.1) > @rpath/libzoltan.12.dylib (compatibility version 12.0.0, current > version 12.10.1) > @rpath/libepetra.12.dylib (compatibility version 12.0.0, current > version 12.10.1) > @rpath/libsacado.12.dylib (compatibility version 12.0.0, current > version 12.10.1) > @rpath/librtop.12.dylib (compatibility version 12.0.0, current version > 12.10.1) > @rpath/libteuchoskokkoscomm.12.dylib (compatibility version 12.0.0, > current version 12.10.1) > @rpath/libteuchoskokkoscompat.12.dylib (compatibility version 12.0.0, > current version 12.10.1) > @rpath/libteuchosremainder.12.dylib (compatibility version 12.0.0, > current version 12.10.1) > @rpath/libteuchosnumerics.12.dylib (compatibility version 12.0.0, > current version 12.10.1) > @rpath/libteuchoscomm.12.dylib (compatibility version 12.0.0, current > version 12.10.1) > @rpath/libteuchosparameterlist.12.dylib (compatibility version 12.0.0, > current version 12.10.1) > @rpath/libteuchoscore.12.dylib (compatibility version 12.0.0, current > version 12.10.1) > @rpath/libkokkosalgorithms.12.dylib (compatibility version 12.0.0, > current version 12.10.1) > @rpath/libkokkoscontainers.12.dylib (compatibility version 12.0.0, > current version 12.10.1) > @rpath/libkokkoscore.12.dylib (compatibility version 12.0.0, current > version 12.10.1) > libsuperlu_dist.5.dylib (compatibility version 5.0.0, current version > 5.1.0) > /usr/lib/libSystem.B.dylib (compatibility version 1.0.0, current > version 1252.50.4) > /Users/zhiboluo/deal.ii-candi/hdf5-1.10.1/lib/libhdf5_hl.100.dylib > (compatibility version 101.0.0, current version 101.1.0) > /Users/zhiboluo/deal.ii-candi/hdf5-1.10.1/lib/libhdf5.101.dylib > (compatibility version 102.0.0, current version 102.0.0) > libTKBO.11.dylib (compatibility version 11.0.0, current version 11.0.0) > libTKBool.11.dylib (compatibility version 11.0.0, current version > 11.0.0) > libTKBRep.11.dylib (compatibility version 11.0.0, current version > 11.0.0) > libTKernel.11.dylib (compatibility version 11.0.0, current version > 11.0.0) > libTKFeat.11.dylib (compatibility version 11.0.0, current version > 11.0.0) > libTKFillet.11.dylib (compatibility version 11.0.0, current version > 11.0.0) > libTKG2d.11.dylib (compatibility version 11.0.0, current version 11.0.0) > libTKG3d.11.dylib (compatibility version 11.0.0, current version 11.0.0) > libTKGeomAlgo.11.dylib (compatibility version 11.0.0, current version > 11.0.0) > libTKGeomBase.11.dylib (compatibility version 11.0.0, current version > 11.0.0) > libTKHLR.11.dylib (compatibility version 11.0.0, current version 11.0.0) > libTKIGES.11.dylib (compatibility version 11.0.0, current version > 11.0.0) > libTKMath.11.dylib (compatibility version 11.0.0, current version > 11.0.0) > libTKMesh.11.dylib (compatibility version 11.0.0, current version > 11.0.0) > libTKOffset.11.dylib (compatibility version 11.0.0, current version > 11.0.0) > libTKPrim.11.dylib (compatibility version 11.0.0, current version > 11.0.0) > libTKShHealing.11.dylib (compatibility version 11.0.0, current version > 11.0.0) > libTKSTEP.11.dylib (compatibility version 11.0.0, current version > 11.0.0) > libTKSTEPAttr.11.dylib (compatibility version 11.0.0, current version > 11.0.0) > libTKSTEPBase.11.dylib (compatibility version 11.0.0, current version > 11.0.0) > libTKSTEP209.11.dylib (compatibility version 11.0.0, current version > 11.0.0) > libTKSTL.11.dylib (compatibility version 11.0.0, current version 11.0.0) > libTKTopAlgo.11.dylib (compatibility version 11.0.0, current version > 11.0.0) > libTKXSBase.11.dylib (compatibility version 11.0.0, current version > 11.0.0) > /System/Library/Frameworks/Accelerate.framework/Versions/A/Accelerate > (compatibility version 1.0.0, current version 4.0.0) > /usr/local/opt/open-mpi/lib/libmpi_usempif08.40.dylib (compatibility > version 51.0.0, current version 51.1.0) > /usr/local/opt/open-mpi/lib/libmpi_usempi_ignore_tkr.40.dylib > (compatibility version 51.0.0, current version 51.1.0) > /usr/local/opt/open-mpi/lib/libmpi_mpifh.40.dylib (compatibility > version 51.0.0, current version 51.1.0) > /usr/local/opt/open-mpi/lib/libmpi.40.dylib (compatibility version > 51.0.0, current version 51.1.0) > /Users/zhiboluo/deal.ii-candi/slepc-3.7.3/lib/libslepc.3.7.dylib > (compatibility version 3.7.0, current version 3.7.3) > /Users/zhiboluo/deal.ii-candi/petsc-3.7.6/lib/libpetsc.3.7.dylib > (compatibility version 3.7.0, current version 3.7.6) > libparmetis.dylib (compatibility version 0.0.0, current version 0.0.0) > libmetis.dylib (compatibility version 0.0.0, current version 0.0.0) > > /System/Library/Frameworks/Accelerate.framework/Versions/A/Frameworks/vecLib.framework/Versions/A/libLAPACK.dylib > (compatibility version 1.0.0, current version 1.0.0) > > /System/Library/Frameworks/Accelerate.framework/Versions/A/Frameworks/vecLib.framework/Versions/A/libBLAS.dylib > (compatibility version 1.0.0, current version 1.0.0) > /usr/local/opt/openssl/lib/libssl.1.0.0.dylib (compatibility version > 1.0.0, current version 1.0.0) > /usr/local/opt/openssl/lib/libcrypto.1.0.0.dylib (compatibility version > 1.0.0, current version 1.0.0) > /usr/local/lib/gcc/8/libgcc_s.1.dylib (compatibility version 1.0.0, > current version 1.0.0) > /usr/lib/libc++.1.dylib (compatibility version 1.0.0, current version > 400.9.0) > @rpath/libLTO.dylib (compatibility version 1.0.0, current version > 3902.0.39) > > I found that some other libraries path (like p4est, slepc, and petsc) are set > correctly. However, the library path of superlu_dist, parmetis, and oce are > not set correctly. The generated object try to find "libsuperlu_dist.5.dylib" > in the current path, but actually this library is installed in > /Users/zhiboluo/deal.ii-candi/superlu_dist_5.1.2/lib. Then I copy these > libraries to current folder, "make run" works! But I don't want to copy these > libraries everytime I go to compile another project. > > Any suggestions to solve this dynamic library link problems? > > Thanks~ > > > > > -- > The deal.II project is located at http://www.dealii.org/ > <http://www.dealii.org/> > For mailing list/forum options, see > https://groups.google.com/d/forum/dealii?hl=en > <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 [email protected] > <mailto:[email protected]>. > For more options, visit https://groups.google.com/d/optout > <https://groups.google.com/d/optout>. -- 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. 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