Ok - this is not clang from apple. So I guess it needs that extra 'xcode-select --install'
I don't think gcc from brew needed this. [And I don't remember if I checked clang from brew] Satish On Mon, 16 Oct 2017, Kong, Fande wrote: > On Mon, Oct 16, 2017 at 12:07 PM, Satish Balay <ba...@mcs.anl.gov> wrote: > > > BTW: Which clang are you using? > > > > mpicc -show > > > > > > mpicc -show > > clang -Wl,-commons,use_dylibs > -I/opt/moose/mpich/mpich-3.2/clang-opt/include > -L/opt/moose/mpich/mpich-3.2/clang-opt/lib -lmpi -lpmpi > > > > > mpicc --version > > > > mpicc -v > > mpicc for MPICH version 3.2 > clang version 3.9.0 (tags/RELEASE_390/final) > Target: x86_64-apple-darwin16.7.0 > Thread model: posix > InstalledDir: /opt/moose/llvm-3.9.0/bin > clang-3.9: warning: argument unused during compilation: '-I > /opt/moose/mpich/mpich-3.2/clang-opt/include' > > > I guess because we are using a customize installation of clang. > > > Fande, > > > > > > Satish > > > > On Mon, 16 Oct 2017, Satish Balay wrote: > > > > > Thats weird. > > > > > > From what I can recall - some tools (like pgi compilers) need this - > > > but the xcode compilers do not. > > > > > > Basically xcode clang can pick up includes from the xcode specific > > > location - but other tools look for includes in /usr/incldue > > > > > > And 'xcode-select --install' adds the /usr/include etc links. > > > > > > Satish > > > > > > > > > On Mon, 16 Oct 2017, Kong, Fande wrote: > > > > > > > Now it is working. It turns out I need to do something like > > "xcode-select > > > > --install" after upgrading OS, and of course we need to agree the > > license. > > > > > > > > > > > > Fande, > > > > > > > > On Mon, Oct 16, 2017 at 10:58 AM, Richard Tran Mills <rtmi...@anl.gov> > > > > wrote: > > > > > > > > > Fande, > > > > > > > > > > Did you remember to agree to the XCode license after your upgrade, > > if you > > > > > did an XCode upgrade? You have to do the license agreement again, > > otherwise > > > > > the compilers don't work at all. Apologies if this seems like a > > silly thing > > > > > to ask, but this has caused me a few minutes of confusion before. > > > > > > > > > > --Richard > > > > > > > > > > On Mon, Oct 16, 2017 at 9:52 AM, Jed Brown <j...@jedbrown.org> wrote: > > > > > > > > > >> "Kong, Fande" <fande.k...@inl.gov> writes: > > > > >> > > > > >> > Hi All, > > > > >> > > > > > >> > I just upgraded MAC OS, and also updated all other related > > packages. > > > > >> Now > > > > >> > I can not configure PETSc-master any more. > > > > >> > > > > >> Your compiler paths are broken. > > > > >> > > > > >> /var/folders/6q/y12qpzw12dg5qx5x96dd5_bhtzr4_y/T/petsc- > > > > >> mFgio7/config.setCompilers/conftest.c:3:10: fatal error: > > 'stdlib.h' file > > > > >> not found > > > > >> #include <stdlib.h> > > > > >> ^ > > > > >> 1 error generated. > > > > >> > > > > > > > > > > > > > > > > > > > > > > > > >