Elmer Failed To Brew on OSX 10.13.6

[NGeorgescu]

Hi,

I am having issues installing Elmer via homebrew. Here is the most recent attempt of mine:

$ brew install elmer --with-elmergui --HEAD --with-elmerice
==> Installing elmer from elmercsc/elmerfem
==> Installing dependencies for elmercsc/elmerfem/elmer: cmake, openblas, veclibfort, hypre, qt5
==> Installing elmercsc/elmerfem/elmer dependency: cmake
==> Downloading https://homebrew.bintray.com/bottles/cmake-3.12.0.high_sierra.bottle.tar.g
######################################################################## 100.0%
==> Pouring cmake-3.12.0.high_sierra.bottle.tar.gz
==> Caveats
Emacs Lisp files have been installed to:
/usr/local/share/emacs/site-lisp/cmake
==> Summary
🍺 /usr/local/Cellar/cmake/3.12.0: 2,415 files, 33.6MB
==> Installing elmercsc/elmerfem/elmer dependency: openblas
==> Downloading https://homebrew.bintray.com/bottles/openblas-0.3.2.high_sierra.bottle.tar
######################################################################## 100.0%
==> Pouring openblas-0.3.2.high_sierra.bottle.tar.gz
==> Caveats
This formula is keg-only, which means it was not symlinked into /usr/local,
because macOS provides BLAS and LAPACK in the Accelerate framework.

For compilers to find this software you may need to set:
LDFLAGS: -L/usr/local/opt/openblas/lib
CPPFLAGS: -I/usr/local/opt/openblas/include
For pkg-config to find this software you may need to set:
PKG_CONFIG_PATH: /usr/local/opt/openblas/lib/pkgconfig

==> Summary
🍺 /usr/local/Cellar/openblas/0.3.2: 21 files, 117.6MB
==> Installing elmercsc/elmerfem/elmer dependency: veclibfort
==> Downloading https://homebrew.bintray.com/bottles/veclibfort-0.4.2_6.high_sierra.bottle
######################################################################## 100.0%
==> Pouring veclibfort-0.4.2_6.high_sierra.bottle.tar.gz
🍺 /usr/local/Cellar/veclibfort/0.4.2_6: 8 files, 85.6KB
==> Installing elmercsc/elmerfem/elmer dependency: hypre
==> Downloading https://homebrew.bintray.com/bottles/hypre-2.11.2_3.high_sierra.bottle.tar
######################################################################## 100.0%
==> Pouring hypre-2.11.2_3.high_sierra.bottle.tar.gz
🍺 /usr/local/Cellar/hypre/2.11.2_3: 50 files, 4.5MB
==> Installing elmercsc/elmerfem/elmer dependency: qt5
==> Downloading https://homebrew.bintray.com/bottles/qt-5.11.1.high_sierra.bottle.tar.gz
######################################################################## 100.0%
==> Pouring qt-5.11.1.high_sierra.bottle.tar.gz
==> Caveats
We agreed to the Qt open source license for you.
If this is unacceptable you should uninstall.

This formula is keg-only, which means it was not symlinked into /usr/local,
because Qt 5 has CMake issues when linked.

If you need to have this software first in your PATH run:
echo 'export PATH="/usr/local/opt/qt/bin:$PATH"' >> ~/.bash_profile

For compilers to find this software you may need to set:
LDFLAGS: -L/usr/local/opt/qt/lib
CPPFLAGS: -I/usr/local/opt/qt/include
For pkg-config to find this software you may need to set:
PKG_CONFIG_PATH: /usr/local/opt/qt/lib/pkgconfig

==> Summary
🍺 /usr/local/Cellar/qt/5.11.1: 9,492 files, 303.9MB
==> Installing elmercsc/elmerfem/elmer --HEAD --with-elmerice --with-elmergui
==> Cloning https://github.com/ElmerCSC/elmerfem.git
Cloning into '/Users/nsg/Library/Caches/Homebrew/elmer--git'...
remote: Counting objects: 8458, done.
remote: Compressing objects: 100% (5568/5568), done.
remote: Total 8458 (delta 3048), reused 6576 (delta 2532), pack-reused 0
Receiving objects: 100% (8458/8458), 50.81 MiB | 3.33 MiB/s, done.
Resolving deltas: 100% (3048/3048), done.
Checking out files: 100% (9262/9262), done.
==> Checking out branch devel
Already on 'devel'
Your branch is up to date with 'origin/devel'.
==> cmake ../ -DCMAKE_INSTALL_PREFIX=/usr/local/Cellar/elmer/HEAD-f4f9b8a -DWITH_Hypre:BOOL=TRUE -DWITH_ElmerIce:BOOL=TRUE -DWITH_Mump
==> make
Last 15 lines from /Users/nsg/Library/Logs/Homebrew/elmer/02.make:
/usr/local/Cellar/cmake/3.12.0/bin/cmake -E touch fem/src/CMakeFiles/elmersolver.dir/DiffuseConvectiveGeneralAnisotropic.F90.o.provides.build
/usr/local/Cellar/cmake/3.12.0/bin/cmake -E touch fem/src/CMakeFiles/elmersolver.dir/ParticleUtils.F90.o.provides.build
/usr/local/Cellar/cmake/3.12.0/bin/cmake -E cmake_copy_f90_mod fmodules/zirka.mod fem/src/CMakeFiles/elmersolver.dir/zirka.mod.stamp GNU
/usr/local/Cellar/cmake/3.12.0/bin/cmake -E cmake_copy_f90_mod fmodules/zirkautils.mod fem/src/CMakeFiles/elmersolver.dir/zirkautils.mod.stamp GNU
/usr/local/Cellar/cmake/3.12.0/bin/cmake -E touch fem/src/CMakeFiles/elmersolver.dir/ZirkaHysteresis.F90.o.provides.build
/usr/local/Cellar/cmake/3.12.0/bin/cmake -E cmake_copy_f90_mod fmodules/radiationfactorglobals.mod fem/src/CMakeFiles/elmersolver.dir/radiationfactorglobals.mod.stamp GNU
/usr/local/Cellar/cmake/3.12.0/bin/cmake -E touch fem/src/CMakeFiles/elmersolver.dir/RadiationFactors.F90.o.provides.build
[ 70%] Linking Fortran shared library libelmersolver.dylib
cd /tmp/elmer-20180803-95581-kaow32/build/fem/src && /usr/local/Cellar/cmake/3.12.0/bin/cmake -E cmake_link_script CMakeFiles/elmersolver.dir/link.txt --verbose=1
/usr/local/bin/gfortran -O3 -DNDEBUG -O3 -dynamiclib -Wl,-headerpad_max_install_names -Wl,-flat_namespace -Wl,-commons,use_dylibs -o libelmersolver.dylib -install_name @rpath/libelmersolver.dylib CMakeFiles/elmersolver.dir/AddrFunc.F90.o CMakeFiles/elmersolver.dir/NavierStokes.F90.o CMakeFiles/elmersolver.dir/NavierStokesGeneral.F90.o CMakeFiles/elmersolver.dir/NavierStokesCylindrical.F90.o CMakeFiles/elmersolver.dir/Lists.F90.o CMakeFiles/elmersolver.dir/DiffuseConvectiveAnisotropic.F90.o CMakeFiles/elmersolver.dir/LoadMod.F90.o CMakeFiles/elmersolver.dir/DiffuseConvectiveGeneralAnisotropic.F90.o CMakeFiles/elmersolver.dir/PElementMaps.F90.o CMakeFiles/elmersolver.dir/PElementBase.F90.o CMakeFiles/elmersolver.dir/ElementDescription.F90.o CMakeFiles/elmersolver.dir/Integration.F90.o CMakeFiles/elmersolver.dir/ListMatrixArray.F90.o CMakeFiles/elmersolver.dir/ModelDescription.F90.o CMakeFiles/elmersolver.dir/GeneralUtils.F90.o CMakeFiles/elmersolver.dir/Stress.F90.o CMakeFiles/elmersolver.dir/StressGeneral.F90.o CMakeFiles/elmersolver.dir/LinearAlgebra.F90.o CMakeFiles/elmersolver.dir/CoordinateSystems.F90.o CMakeFiles/elmersolver.dir/ListMatrix.F90.o CMakeFiles/elmersolver.dir/CRSMatrix.F90.o CMakeFiles/elmersolver.dir/BandMatrix.F90.o CMakeFiles/elmersolver.dir/BandwidthOptimize.F90.o CMakeFiles/elmersolver.dir/BlockSolve.F90.o CMakeFiles/elmersolver.dir/MaterialModels.F90.o CMakeFiles/elmersolver.dir/DirectSolve.F90.o CMakeFiles/elmersolver.dir/IterSolve.F90.o CMakeFiles/elmersolver.dir/IterativeMethods.F90.o CMakeFiles/elmersolver.dir/TimeIntegrate.F90.o CMakeFiles/elmersolver.dir/Types.F90.o CMakeFiles/elmersolver.dir/SolveBand.F90.o CMakeFiles/elmersolver.dir/ElementUtils.F90.o CMakeFiles/elmersolver.dir/Radiation.F90.o CMakeFiles/elmersolver.dir/fft.c.o CMakeFiles/elmersolver.dir/Load.c.o CMakeFiles/elmersolver.dir/Differentials.F90.o CMakeFiles/elmersolver.dir/FreeSurface.F90.o CMakeFiles/elmersolver.dir/Maxwell.F90.o CMakeFiles/elmersolver.dir/MaxwellAxiS.F90.o CMakeFiles/elmersolver.dir/MaxwellGeneral.F90.o CMakeFiles/elmersolver.dir/Walls.F90.o CMakeFiles/elmersolver.dir/SolverUtils.F90.o CMakeFiles/elmersolver.dir/SolveSBand.F90.o CMakeFiles/elmersolver.dir/CPUTime.c.o CMakeFiles/elmersolver.dir/Interpolation.F90.o CMakeFiles/elmersolver.dir/MainUtils.F90.o CMakeFiles/elmersolver.dir/Adaptive.F90.o CMakeFiles/elmersolver.dir/EigenSolve.F90.o CMakeFiles/elmersolver.dir/HashTable.F90.o CMakeFiles/elmersolver.dir/MeshUtils.F90.o CMakeFiles/elmersolver.dir/SParIterGlobals.F90.o CMakeFiles/elmersolver.dir/SParIterComm.F90.o CMakeFiles/elmersolver.dir/SParIterPrecond.F90.o CMakeFiles/elmersolver.dir/SParIterSolver.F90.o CMakeFiles/elmersolver.dir/Messages.F90.o CMakeFiles/elmersolver.dir/Multigrid.F90.o CMakeFiles/elmersolver.dir/Smoothers.F90.o CMakeFiles/elmersolver.dir/ClusteringMethods.F90.o CMakeFiles/elmersolver.dir/ParallelUtils.F90.o CMakeFiles/elmersolver.dir/ParallelEigenSolve.F90.o CMakeFiles/elmersolver.dir/solve_cmplx.F90.o CMakeFiles/elmersolver.dir/solve_real.F90.o CMakeFiles/elmersolver.dir/MGPrec.F90.o CMakeFiles/elmersolver.dir/DefUtils.F90.o CMakeFiles/elmersolver.dir/LUDecomposition.F90.o CMakeFiles/elmersolver.dir/RadiationFactors.F90.o CMakeFiles/elmersolver.dir/f_stubs.c.o CMakeFiles/elmersolver.dir/ExchangeCorrelations.F90.o CMakeFiles/elmersolver.dir/SolveHypre.c.o CMakeFiles/elmersolver.dir/SolverActivate_x.F90.o CMakeFiles/elmersolver.dir/SolveTrilinos.cxx.o CMakeFiles/elmersolver.dir/SolveSuperLU.c.o CMakeFiles/elmersolver.dir/iso_varying_string.F90.o CMakeFiles/elmersolver.dir/umf4_f77wrapper.c.o CMakeFiles/elmersolver.dir/VankaCreate.F90.o CMakeFiles/elmersolver.dir/ParticleUtils.F90.o CMakeFiles/elmersolver.dir/Feti.F90.o CMakeFiles/elmersolver.dir/cholmod.c.o CMakeFiles/elmersolver.dir/InterpolateMeshToMesh.F90.o CMakeFiles/elmersolver.dir/InterpVarToVar.F90.o CMakeFiles/elmersolver.dir/LinearForms.F90.o CMakeFiles/elmersolver.dir/H1Basis.F90.o CMakeFiles/elmersolver.dir/CircuitUtils.F90.o CMakeFiles/elmersolver.dir/BackwardError.F90.o CMakeFiles/elmersolver.dir/ElmerSolver.F90.o CMakeFiles/elmersolver.dir/MagnetoDynamicsUtils.F90.o CMakeFiles/elmersolver.dir/ComponentUtils.F90.o CMakeFiles/elmersolver.dir/ZirkaHysteresis.F90.o -Wl,-rpath,/tmp/elmer-20180803-95581-kaow32/build/matc/src -Wl,-rpath,/tmp/elmer-20180803-95581-kaow32/build/fhutiter/src -Wl,-rpath,/tmp/elmer-20180803-95581-kaow32/build/mathlibs/src/parpack -Wl,-rpath,/tmp/elmer-20180803-95581-kaow32/build/mathlibs/src/arpack ../../matc/src/libmatc.dylib ../../umfpack/src/umfpack/libumfpack.a ../../umfpack/src/amd/libamd.a ../../fhutiter/src/libfhuti.dylib binio/libbinio.a /usr/local/opt/openblas/lib/libopenblas.dylib -lpthread /usr/local/opt/openblas/lib/libopenblas.dylib -lpthread /usr/local/lib/libdmumps.dylib /usr/local/lib/libmumps_common.dylib /usr/local/lib/libpord.dylib /usr/local/lib/libscalapack.dylib /usr/local/lib/libHYPRE.a ../../mathlibs/src/parpack/libparpack.dylib /usr/local/lib/libmpi_usempif08.dylib /usr/local/lib/libmpi_usempi_ignore_tkr.dylib /usr/local/lib/libmpi_mpifh.dylib /usr/local/lib/libmpi.dylib -lm ../../mathlibs/src/arpack/libarpack.dylib /usr/local/opt/openblas/lib/libopenblas.dylib -lpthread -lc++
ld: file not found: /usr/local/opt/openblas/lib/libopenblasp-r0.3.0.dev.dylib for architecture x86_64
collect2: error: ld returned 1 exit status
make[2]: *** [fem/src/libelmersolver.dylib] Error 1
make[1]: *** [fem/src/CMakeFiles/elmersolver.dir/all] Error 2
make: *** [all] Error 2

If reporting this issue please do so at (not Homebrew/brew or Homebrew/core):
https://github.com/elmercsc/homebrew-elmerfem/issues

These open issues may also help:
Elmer build error on 10.11.6 #6
Umfpack problem while compiling Elmer with homebrew #2
Elmer failed to build on OS 10.12.6 #8
Unable to install elmer on Mac by using brew #1
Elmer failed to build on OS 10.12.1 #5

Let me know if any more information is pertinent. Any help is appreciated.

Thanks in advance.

[NGeorgescu]

Ok Update for anyone running into this issue: I have installed it with $ brew install elmer --with-elmergui --HEAD --with-elmerice --without-mumps and it seemed to build ok. I can open it and get a GUI, but I have not tried solving any models with it. I will try to do so and update with the results.

[undeadinu]

I tried to install elmer with the command,

$ brew install elmer --with-elmergui --HEAD --with-elmerice --without-mumps

but it returned this error,

==> Installing elmer from elmercsc/elmerfem
==> Cloning https://github.com/ElmerCSC/elmerfem.git
Cloning into '/Users/<username>/Library/Caches/Homebrew/elmer--git'...
Checking out files: 100% (9506/9506), done.
==> Checking out branch devel
Already on 'devel'
Your branch is up to date with 'origin/devel'.
Submodule 'contrib/Zoltan_v3.83' (https://github.com/ElmerCSC/Zoltan) registered for path 'contrib/Zoltan_v3.83'
Cloning into '/Users/<username>/Library/Caches/Homebrew/elmer--git/contrib/Zoltan_v3.83'...
Submodule path 'contrib/Zoltan_v3.83': checked out 'ab98b531972b55eb9af6035e06806284cc19be46'
/Users/<username>/Library/Caches/Homebrew/elmer--git/contrib/Zoltan_v3.83
==> cmake ../ -DCMAKE_INSTALL_PREFIX=/usr/local/Cellar/elmer/HEAD-dc0f1be -DWITH_Hypre:BOOL=TRUE -DWITH_ElmerIc
==> make
Last 15 lines from /Users/<username>/Library/Logs/Homebrew/elmer/02.make:
/usr/local/Cellar/cmake/3.13.3/bin/cmake -E touch fem/src/CMakeFiles/elmersolver.dir/SolverUtils.F90.o.provides.build
[ 68%] Building Fortran object fem/src/CMakeFiles/elmersolver.dir/Adaptive.F90.o
cd /tmp/elmer-20190126-35722-ozq6zk/build/fem/src && /usr/local/bin/gfortran -DCONTIG=,CONTIGUOUS -DHAVE_EXECUTECOMMANDLINE -DUSE_ARPACK -DUSE_ISO_C_BINDINGS -Delmersolver_EXPORTS -I/usr/local/Cellar/open-mpi/4.0.0/include -I/usr/local/Cellar/open-mpi/4.0.0/lib -I/usr/local/include -I/tmp/elmer-20190126-35722-ozq6zk/build -I/tmp/elmer-20190126-35722-ozq6zk/build/fem/src -I/tmp/elmer-20190126-35722-ozq6zk/fhutiter/src -I/tmp/elmer-20190126-35722-ozq6zk/build/fem/src/binio -I/tmp/elmer-20190126-35722-ozq6zk/build/fhutiter/src  -O3 -DNDEBUG -O3 -J../../fmodules -fPIC   -c /tmp/elmer-20190126-35722-ozq6zk/fem/src/Adaptive.F90 -o CMakeFiles/elmersolver.dir/Adaptive.F90.o
/usr/local/Cellar/cmake/3.13.3/bin/cmake -E cmake_copy_f90_mod fmodules/adaptive.mod fem/src/CMakeFiles/elmersolver.dir/adaptive.mod.stamp GNU
/usr/local/Cellar/cmake/3.13.3/bin/cmake -E touch fem/src/CMakeFiles/elmersolver.dir/Adaptive.F90.o.provides.build
[ 68%] Building Fortran object fem/src/CMakeFiles/elmersolver.dir/DefUtils.F90.o
cd /tmp/elmer-20190126-35722-ozq6zk/build/fem/src && /usr/local/bin/gfortran -DCONTIG=,CONTIGUOUS -DHAVE_EXECUTECOMMANDLINE -DUSE_ARPACK -DUSE_ISO_C_BINDINGS -Delmersolver_EXPORTS -I/usr/local/Cellar/open-mpi/4.0.0/include -I/usr/local/Cellar/open-mpi/4.0.0/lib -I/usr/local/include -I/tmp/elmer-20190126-35722-ozq6zk/build -I/tmp/elmer-20190126-35722-ozq6zk/build/fem/src -I/tmp/elmer-20190126-35722-ozq6zk/fhutiter/src -I/tmp/elmer-20190126-35722-ozq6zk/build/fem/src/binio -I/tmp/elmer-20190126-35722-ozq6zk/build/fhutiter/src  -O3 -DNDEBUG -O3 -J../../fmodules -fPIC   -c /tmp/elmer-20190126-35722-ozq6zk/fem/src/DefUtils.F90 -o CMakeFiles/elmersolver.dir/DefUtils.F90.o
/tmp/elmer-20190126-35722-ozq6zk/fem/src/DefUtils.F90:3221:11:

     SOL => x % Values
           1
Error: Assignment to contiguous pointer from non-contiguous target at (1)
make[2]: *** [fem/src/CMakeFiles/elmersolver.dir/DefUtils.F90.o] Error 1
make[1]: *** [fem/src/CMakeFiles/elmersolver.dir/all] Error 2
make: *** [all] Error 2

If reporting this issue please do so at (not Homebrew/brew or Homebrew/core):
https://github.com/elmercsc/homebrew-elmerfem/issues

These open issues may also help:
Unable to install elmer on Mac by using brew https://github.com/ElmerCSC/homebrew-elmerfem/issues/1
Elmer build error on 10.11.6 https://github.com/ElmerCSC/homebrew-elmerfem/issues/6
Umfpack problem while compiling Elmer with homebrew https://github.com/ElmerCSC/homebrew-elmerfem/issues/2
Elmer Failed To Brew on OSX 10.13.6 https://github.com/ElmerCSC/homebrew-elmerfem/issues/12
Elmer failed to build on OS 10.12.6 https://github.com/ElmerCSC/homebrew-elmerfem/issues/8
Elmer failed to build on OS 10.12.1 https://github.com/ElmerCSC/homebrew-elmerfem/issues/5

How can I fix it?

[NGeorgescu]

Hmm I made it work another time with:

brew install dpo/openblas/mumps
brew tap ElmerCSC/elmerfem
brew install elmer --with-elmergui --HEAD --with-elmerice

If that doesn't work make sure mumps and elmer are uninstalled with brew (use --ignore-dependencies if you're given a hard time at all.

[undeadinu]

Thank you for replying. I tried that commands with any combination of options, but cmake process does not complete. There's a possibility that my Homebrew environment variables should be change. I'm not sure.

$ brew install elmer --ignore-dependencies

==> Installing elmer from elmercsc/elmerfem
==> Downloading https://github.com/ElmerCSC/elmerfem/archive/release-8.2.tar.gz
==> Downloading from https://codeload.github.com/ElmerCSC/elmerfem/tar.gz/release-8.2
######################################################################## 100.0%
==> cmake ../ -DCMAKE_INSTALL_PREFIX=/usr/local/Cellar/elmer/8.2 -DWITH_Hypre:BOOL=TRUE -DWITH_Mumps:BOOL=TRUE -DWITH_MPI:BOOL=TRUE -DBLAS_LIBRARIES:STRING=/usr/local/opt/ope
Last 15 lines from /Users/<username>/Library/Logs/Homebrew/elmer/01.cmake:
../
-DCMAKE_INSTALL_PREFIX=/usr/local/Cellar/elmer/8.2
-DWITH_Hypre:BOOL=TRUE
-DWITH_Mumps:BOOL=TRUE
-DWITH_MPI:BOOL=TRUE
-DBLAS_LIBRARIES:STRING=/usr/local/opt/openblas/lib/libopenblas.dylib;-lpthread
-DLAPACK_LIBRARIES:STRING=/usr/local/opt/openblas/lib/libopenblas.dylib;-lpthread
-DCMAKE_C_FLAGS_RELEASE=-DNDEBUG
-DCMAKE_CXX_FLAGS_RELEASE=-DNDEBUG
-DCMAKE_INSTALL_PREFIX=/usr/local/Cellar/elmer/8.2
-DCMAKE_BUILD_TYPE=Release
-DCMAKE_FIND_FRAMEWORK=LAST
-DCMAKE_VERBOSE_MAKEFILE=ON
-Wno-dev


If reporting this issue please do so at (not Homebrew/brew or Homebrew/core):
https://github.com/elmercsc/homebrew-elmerfem/issues

These open issues may also help:
Elmer Failed To Brew on OSX 10.13.6 https://github.com/ElmerCSC/homebrew-elmerfem/issues/12
Unable to install elmer on Mac by using brew https://github.com/ElmerCSC/homebrew-elmerfem/issues/1
Elmer build error on 10.11.6 https://github.com/ElmerCSC/homebrew-elmerfem/issues/6
Umfpack problem while compiling Elmer with homebrew https://github.com/ElmerCSC/homebrew-elmerfem/issues/2
Elmer failed to build on OS 10.12.6 https://github.com/ElmerCSC/homebrew-elmerfem/issues/8
Elmer failed to build on OS 10.12.1 https://github.com/ElmerCSC/homebrew-elmerfem/issues/5

[NGeorgescu]

See if the dylib exists ls /usr/local/opt/openblas/lib/

If not locate it and run an ln -s ... command to make a symbolic link and try again.