Dear David, Okay, I think I've tracked down the source of the problem. A while back, I installed a binary version of gcc/gfortran from http://hpc.sourceforge.net. This has always worked fine for me, but it seems to have put a bunch of this "/Users/admin/build8" stuff in various subdirectories of /usr/local. (I'm guessing that this was the build folder on the machine of the person who distributed the binaries.) I'm not sure why this hasn't caused issues for me in the past, but obviously it's doing so now. Anyway, I'll go ahead and remove those and try again, but I suspect that will resolve the problem. Thanks again, Ari

On Aug 1, 2019, at 10:36 AM, Ari Stern <stern@wustl.edu> wrote:

Dear David,

Thanks for the response! I also noticed this "/Users/admin" line, which is very strange, since I don't have a "/Users/admin" folder on my computer at all, hence the "directory not found" error.

I searched the firedrake folder for this using grep and found the following matches:

Binary file firedrake/lib/python3.7/site-packages/sympy/strategies/tests/__pycache__/test_rl.cpython-37.pyc matches firedrake/lib/python3.7/site-packages/petsc/lib/libnetcdf.la:dependency_libs=' -L/usr/local/opt/libevent/lib -L/usr/local/Cellar/open-mpi/4.0.1_1/lib -L/usr/local/lib/gcc/x86_64-apple-darwin17.5.0/8.1.0 -L/usr/local/lib -L/Users/admin/build8/x86_64-apple-darwin17.5.0/libstdc++-v3/src -L/Users/admin/build8/x86_64-apple-darwin17.5.0/libstdc++-v3/src/.libs -L/Users/admin/build8/x86_64-apple-darwin17.5.0/libstdc++-v3/libsupc++/.libs -L/Users/astern/Downloads/firedrake/lib/python3.7/site-packages/petsc/lib /Users/astern/Downloads/firedrake/lib/python3.7/site-packages/petsc/lib/libpnetcdf.la -lmpi_usempif08 -lmpi_usempi_ignore_tkr -lmpi_mpifh -lmpi /usr/local/lib/libgfortran.la /usr/local/lib/libquadmath.la /Users/astern/Downloads/firedrake/lib/python3.7/site-packages/petsc/lib/libhdf5_fortran.la /Users/astern/Downloads/firedrake/lib/python3.7/site-packages/petsc/lib/libhdf5_hl.la /Users/astern/Downloads/firedrake/lib/python3.7/site-packages/petsc/lib/libhdf5.la -lz /usr/local/lib/libstdc++.la -lm -ldl' firedrake/lib/python3.7/site-packages/petsc/lib/libpnetcdf.la:dependency_libs=' -L/usr/local/opt/libevent/lib -L/usr/local/Cellar/open-mpi/4.0.1_1/lib -L/usr/local/lib/gcc/x86_64-apple-darwin17.5.0/8.1.0 -L/usr/local/lib -L/Users/admin/build8/x86_64-apple-darwin17.5.0/libstdc++-v3/src -L/Users/admin/build8/x86_64-apple-darwin17.5.0/libstdc++-v3/src/.libs -L/Users/admin/build8/x86_64-apple-darwin17.5.0/libstdc++-v3/libsupc++/.libs /usr/local/lib/libstdc++.la -ldl -lmpi_usempif08 -lmpi_usempi_ignore_tkr -lmpi_mpifh -lmpi /usr/local/lib/libgfortran.la -lz /usr/local/lib/libquadmath.la -lm'

I'll try running "brew doctor" to see if it resolves this.

Thanks again, Ari

...

On Aug 1, 2019, at 10:05 AM, Ham, David A <david.ham@imperial.ac.uk> wrote:

Dear Ari,

The line which is failing for you is:

libtool: link: mpicc -dynamiclib -o .libs/libspatialindex.4.dylib -Wl,-force_load,src/spatialindex/.libs/liblibrary.a -Wl,-force_load,src/storagemanager/.libs/libstoragemanager.a -Wl,-force_load,src/rtree/.libs/librtree.a -Wl,-force_load,src/mvrtree/.libs/libmvrtree.a -Wl,-force_load,src/tprtree/.libs/libtprtree.a -Wl,-force_load,src/tools/.libs/libtools.a /usr/local/lib/libstdc++.dylib -L/Users/admin/build8/x86_64-apple-darwin17.5.0/libstdc++-v3/src -L/Users/admin/build8/x86_64-apple-darwin17.5.0/libstdc++-v3/src/.libs -L/Users/admin/build8/x86_64-apple-darwin17.5.0/libstdc++-v3/libsupc++/.libs -lm -lpthread -install_name /Users/astern/Downloads/firedrake/lib/libspatialindex.4.dylib -compatibility_version 5 -current_version 5.2 -Wl,-single_module

This immediately spews forth the following warnings:

ld: warning: directory not found for option '-L/Users/admin/build8/x86_64-apple-darwin17.5.0/libstdc++-v3/src' ld: warning: directory not found for option '-L/Users/admin/build8/x86_64-apple-darwin17.5.0/libstdc++-v3/src/.libs' ld: warning: directory not found for option '-L/Users/admin/build8/x86_64-apple-darwin17.5.0/libstdc++-v3/libsupc++/.libs'

... and then you get failures to link.

In contrast, the corresponding line from my install log (also on Mojave) is:

libtool: link: mpicc -dynamiclib -o .libs/libspatialindex.4.dylib -Wl,-force_load,src/spatialindex/.libs/liblibrary.a -Wl,-force_load,src/storagemanager/.libs/libstoragemanager.a -Wl,-force_load,src/rtree/.libs/librtree.a -Wl,-force_load,src/mvrtree/.libs/libmvrtree.a -Wl,-force_load,src/tprtree/.libs/libtprtree.a -Wl,-force_load,src/tools/.libs/libtools.a -lstdc++ -lpthread -install_name /Users/dham/src/firedrake-complex/lib/libspatialindex.4.dylib -compatibility_version 5 -current_version 5.2 -Wl,-single_module libtool: link: mpicc -dynamiclib -o .libs/libspatialindex_c.4.dylib -Wl,-force_load,src/capi/.libs/libsidxc.a ./.libs/libspatialindex.dylib -lstdc++ -lpthread -install_name /Users/dham/src/firedrake-complex/lib/libspatialindex_c.4.dylib -compatibility_version 5 -current_version 5.2 -Wl,-single_module

It therefore appears that the issue is that you have traces in your environment of another libstdc++ which was built in /Users/admin. The build system for libspatialindex is picking this up and failing as a result. It's not immediately obvious to me how your other libstdc++ is leaking into your environment, but that's the think which needs hunting down. Sometimes running "brew doctor" helps in these circumstances as it can find instances where the homebrew versions of things have been overwritten or are otherwise not being used.

Regards,

David

On 31/07/2019, 16:42, "firedrake-bounces@imperial.ac.uk on behalf of Stern, Ari" <firedrake-bounces@imperial.ac.uk on behalf of stern@wustl.edu> wrote:

Hi all,

I've been attempting to install Firedrake using the standard install script, but the installation throws an error when attempting to compile/link libspatialindex. The firedrake-install.log is attached.

A couple pieces of pertinent info: 1. I'm running macOS Mojave 10.14.5 with Homebrew Python 3. 2. Although I have a miniconda installation on my system, I did a "conda deactivate" before running the install script, so nothing from miniconda (except the conda binary itself) is in my path.

Cheers, Ari