macOS Sonoma fails installing PETSc #3392
Replies: 9 comments 20 replies
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Attached is the firedrake-install.log: In addition: fberon@MacBook[~]% which python3 |
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Please can you also share From looking at your logs you are failing to build bison, which I have not encountered before. I notice that |
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Done, but not tried to python3 firedrake-install yet. brew doctor lists a number of 'Warning: Unbrewed...' Is this to worry about? No unliked things anymore. brew is up to date. |
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Do you mean, for instance, I have to DELETE these files: 690 Warning: Unbrewed '.la' files were found in /usr/local/lib. ?? |
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If that is what homebrew suggests then yes. |
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Latest log files included. I'm giving up... |
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But: I :-( |
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Oh, I see, I'm sure I |
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Is it working? I think |
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Latest logs, look better, but there's still are errors in there... configure.log Compiled using: Doctor says: Sorry... |
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You've hit issues with libsupermesh and rtree. @JDBetteridge was working on this recently. How old is the |
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You are hitting the issue that I documented here https://github.com/firedrakeproject/libsupermesh/blob/master/CMakeLists.txt#L161 I legitimately have no idea how to test for C++11 strings on a Mac. There is no canonical way to test anyway, my method works on Linux by querying the strings in the shared object (not ideal). Can you try in your activated virtual environment: cd $VIRTUAL_ENV/src/libsupermesh/build
$VIRTUAL_ENV/src/petsc/default/bin/cmake .. \
-DBUILD_SHARED_LIBS=ON \
-DMAKE_CXX_FLAGS="-D_GLIBCXX_USE_CXX11_ABI=0"
-DCMAKE_INSTALL_PREFIX=$VIRTUAL_ENV \
-DMPI_C_COMPILER=$VIRTUAL_ENV/bin/mpicc \
-DMPI_CXX_COMPILER=$VIRTUAL_ENV/bin/mpicxx \
-DMPI_Fortran_COMPILER=$VIRTUAL_ENV/bin/mpif90 \
-DCMAKE_Fortran_COMPILER=$VIRTUAL_ENV/bin/mpif90 \
-DMPIEXEC_EXECUTABLE=$VIRTUAL_ENV/bin/mpiexec
make
make install
firedrake-update |
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I'm using the one provided here: https://www.firedrakeproject.org/download.html ? |
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You don't need to download anything new. Activate the virtual environment from you previous failed install and then run those commands. |
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This what I got up to the first error (ther was one before saying that cmake was not available in /Users/fberon/firedrake/src/petsc/default/bin/, so I sudo ln -s /usr/local/bin/cmake /Users/fberon/firedrake/src/petsc/default/bin/cmake): (firedrake) fberon@MacBook[~/firedrake/src/libsupermesh/build]% -DCMAKE_INSTALL_PREFIX=$VIRTUAL_ENV \
Use execute_process() instead. -- Git revision: 84becef14eb117defa49354116c04aa180471a07-- MPI_Fortran_COMPILER=/Users/fberon/firedrake/src/petsc/default/bin/mpif90
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I think a backslash is missing from the cmake instruction so it's getting run as two instructions rather than one. |
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Sorry again. I added \ and when got make (which doesn't exist in /Users/fberon/firedrake/src/petsc/default/bin/ so I sudo ln -s /usr/local/bin/cmake /Users/fberon/firedrake/src/petsc/default/bin/cmake) it run until here: [ 47%] Linking CXX executable test_element_intersector |
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Let's try a different approach. Can you see if your "command line tools" are fully up-to-date. You can update them by: Basically the problem that you are currently experiencing is that there is still something slightly wrong with the C++ compiler on your machine. It doesn't seem to support a new-ish type of string. Hopefully if you update command line tools the error will go away and you can run I am surprised that you are hitting this issue. I don't think any of our other MacOS users have run into this. |
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What headache. I upgraded to Xcode 15.2 beta and the corresponding command line tools. However: fberon@MacBook[/]% brew doctor Warning: A newer Command Line Tools release is available. If that doesn't show you any updates, run: Alternatively, manually download them from: |
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I did the above and got this: |
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@JDBetteridge I'm stumped. Do you have any further ideas? |
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My installation gets interrupted when attempting to install PETSc. Hope somebody can get me some hint? Thank you in advance. -Francisco
Running firedrake-install
Installing command line tools...
Checking brew doctor...
Installing required packages via homebrew...
Required package 'gcc' is already installed via Homebrew.
Required package 'autoconf' is already installed via Homebrew.
Required package 'make' is already installed via Homebrew.
Required package 'automake' is already installed via Homebrew.
Required package 'cmake' is already installed via Homebrew.
Required package 'libtool' is already installed via Homebrew.
Required package 'boost' is already installed via Homebrew.
Creating firedrake venv in '/Users/fberon/firedrake'.
BLAS config is {'BLAS': '/Users/fberon/firedrake/src/petsc/default', 'OPENBLAS': '/Users/fberon/firedrake/src/petsc/default', 'LDFLAGS': '-L/usr/local/opt/gcc/lib/gcc/11'}
Configuration saved to /Users/fberon/firedrake/.configuration.json
Cloning firedrake
Failed to clone firedrake using ssh, falling back to https.
Successfully cloned repository firedrake.
Checking out branch master
Successfully checked out branch master
Updating submodules.
Successfully updated submodules.
Creating firedrake-update script.
Cloning the dependencies of firedrake
Cloning ufl
Failed to clone ufl using ssh, falling back to https.
Successfully cloned repository ufl.
Checking out branch master
...
Cloning the dependencies of PyOP2
Cloning loopy
Failed to clone loopy using ssh, falling back to https.
Successfully cloned repository loopy.
Checking out branch main
Successfully checked out branch main
Updating submodules.
Successfully updated submodules.
Installing petsc/
Depending on your platform, PETSc may take an hour or more to build!
Traceback (most recent call last):
File "/Users/fberon/firedrake-install", line 1865, in
install("petsc/")
File "/Users/fberon/firedrake-install", line 1055, in install
build_and_install_petsc()
File "/Users/fberon/firedrake-install", line 1167, in build_and_install_petsc
check_call([python, "./configure", "PETSC_DIR={}".format(petsc_dir), "PETSC_ARCH={}".format(petsc_arch)] + petsc_options)
File "/Users/fberon/firedrake-install", line 668, in check_call
log.debug(subprocess.check_output(arguments, stderr=subprocess.STDOUT, env=os.environ).decode())
File "/usr/local/Cellar/python@3.9/3.9.12/Frameworks/Python.framework/Versions/3.9/lib/python3.9/subprocess.py", line 424, in check_output
return run(*popenargs, stdout=PIPE, timeout=timeout, check=True,
File "/usr/local/Cellar/python@3.9/3.9.12/Frameworks/Python.framework/Versions/3.9/lib/python3.9/subprocess.py", line 528, in run
raise CalledProcessError(retcode, process.args,
subprocess.CalledProcessError: Command '['/Users/fberon/firedrake/bin/python', './configure', 'PETSC_DIR=/Users/fberon/firedrake/src/petsc', 'PETSC_ARCH=default', '--with-debugging=0', '--download-netcdf', '--download-metis', '--download-scalapack', '--with-x=0', '--download-suitesparse', '--download-pastix', '--download-hwloc', '--CFLAGS=-Wno-implicit-function-declaration', '--LDFLAGS=-Wl,-ld_classic', '--download-mumps', '--download-hwloc-configure-arguments=--disable-opencl', '--with-shared-libraries=1', '--download-openblas', '--download-bison', '--with-c2html=0', '--download-ptscotch', '--with-zlib', '--download-mpich-device=ch3:sock', '--download-pnetcdf', '--download-mpich', '--download-mpich-configure-arguments=--disable-opencl', '--download-hypre', '--with-fortran-bindings=0', '--download-chaco', '--download-superlu_dist', "--download-openblas-make-options='USE_THREAD=0 USE_LOCKING=1 USE_OPENMP=0'", '--download-hdf5']' returned non-zero exit status 1.
Install log saved in /Users/fberon/firedrake-install.log
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