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optimizers / homebrew-fenics

Building FEniCS on OSX with Homebrew and Pip.
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brew install dolfin #12

Open francispoulin opened 8 years ago

francispoulin commented 8 years ago

Thanks a lot for merging this, I think that has helped a lot in me trying to install it.

I tried following the README and received the following message, see below. When I type python and try import dolfin I get that there is no module named doflin so I guess the installation didn't work for me.

I did unlink python before, thinking that would help. Maybe not?

$ brew install dolfin --without-trilinos ==> Installing dolfin from optimizers/fenics ==> Using Homebrew-provided fortran compiler. This may be changed by setting the FC environment variable. ==> Downloading https://bitbucket.org/fenics-project/dolfin/downloads/dolfin-1.6.0.tar.gz Already downloaded: /Library/Caches/Homebrew/dolfin-1.6.0.tar.gz ==> cmake .. -DCMAKE_INSTALL_PREFIX=/usr/local/Cellar/dolfin/1.6.0 -DBUILD_SHARED_LIBS:BOOL=ON -DDOLFIN_ENABLE_PYTHON:BOOL=ON -DDOLFIN_INSTALL_PYTHON_MODULE_DIR=/usr/local/Cellar/dolf ==> make ==> make install Warning: optimizers/fenics/dolfin dependency gcc was built with a different C++ standard library (libstdc++ from clang). This may cause problems at runtime. Traceback (most recent call last): File "", line 1, in AttributeError: 'module' object has no attribute 'getusersitepackages' Traceback (most recent call last): File "", line 1, in AttributeError: 'module' object has no attribute 'getusersitepackages' ==> Caveats Do not source dolfin.conf, as the DYLIB settings conflict with Homebrew.

Python modules have been installed and Homebrew's site-packages is not in your Python sys.path, so you will not be able to import the modules this formula installed. If you plan to develop with these modules, please run: mkdir -p echo 'import site; site.addsitedir("/usr/local/lib/python2.7/site-packages")' >> homebrew.pth ==> Summary 🍺 /usr/local/Cellar/dolfin/1.6.0: 755 files, 26.0M, built in 8 minutes 21 seconds

dpo commented 8 years ago

It looks like the build went through! There's just something up with your PYTHONPATH. Does it contain /usr/local/lib/python2.7/site-packages? If not, try

export PYTHONPATH=/usr/local/lib/python2.7/site-packages:$PYTHONPATH
dpo commented 8 years ago

ps: there's no need to say --without-trilinos any more (unless you don't need Trilinos support).

francispoulin commented 8 years ago

Thanks.

I added the path to python.

$ echo $PYTHONPATH /usr/local/lib/python2.7/site-packages:/Users/fpoulin/software/firedrake/firedrake-bench:/Users/fpoulin/software/pyro2:/Users/fpoulin/software/SPINSpy:/Users/fpoulin/software/clawpack-5.2.2:

But now it can't seem to find numpy.

$ python Python 2.7.10 (default, Jul 14 2015, 19:46:27) [GCC 4.2.1 Compatible Apple LLVM 6.0 (clang-600.0.39)] on darwin Type "help", "copyright", "credits" or "license" for more information.

import numpy Traceback (most recent call last): File "", line 1, in File "/usr/local/lib/python2.7/site-packages/numpy/init.py", line 180, in File "/usr/local/lib/python2.7/site-packages/numpy/add_newdocs.py", line 13, in File "/usr/local/lib/python2.7/site-packages/numpy/lib/init.py", line 8, in File "/usr/local/lib/python2.7/site-packages/numpy/lib/type_check.py", line 11, in File "/usr/local/lib/python2.7/site-packages/numpy/core/init.py", line 14, in ImportError: cannot import name multiarray

$ brew install dolfin ==> Installing dolfin from optimizers/fenics dolfin: Unsatisfied dependency: numpy Homebrew does not provide Python dependencies; install with: pip install numpy trilinos: Unsatisfied dependency: numpy Homebrew does not provide Python dependencies; install with: pip install numpy fiat: Unsatisfied dependency: numpy Homebrew does not provide Python dependencies; install with: pip install numpy ufl: Unsatisfied dependency: numpy Homebrew does not provide Python dependencies; install with: pip install numpy ffc: Unsatisfied dependency: numpy Homebrew does not provide Python dependencies; install with: pip install numpy instant: Unsatisfied dependency: numpy Homebrew does not provide Python dependencies; install with: pip install numpy Error: Unsatisfied requirements failed this build. (fenics) Francis-Poulins-MacBook-Pro:Re__plots_matt fpoulin$ echo $PYTHONPATH /usr/local/lib/python2.7/site-packages:/Users/fpoulin/software/firedrake/firedrake-bench:/Users/fpoulin/software/pyro2:/Users/fpoulin/software/SPINSpy:/Users/fpoulin/software/clawpack

I tried installing numpy using pip in both the fenics environment. If I import numpy in regular environment there is no problem. But when I import it in virtualenv

$ python Python 2.7.10 (default, Jul 14 2015, 19:46:27) [GCC 4.2.1 Compatible Apple LLVM 6.0 (clang-600.0.39)] on darwin Type "help", "copyright", "credits" or "license" for more information.

import numpy Traceback (most recent call last): File "", line 1, in File "/usr/local/lib/python2.7/site-packages/numpy/init.py", line 180, in File "/usr/local/lib/python2.7/site-packages/numpy/add_newdocs.py", line 13, in File "/usr/local/lib/python2.7/site-packages/numpy/lib/init.py", line 8, in File "/usr/local/lib/python2.7/site-packages/numpy/lib/type_check.py", line 11, in File "/usr/local/lib/python2.7/site-packages/numpy/core/init.py", line 14, in ImportError: cannot import name multiarray

I think this is a problem with system python vs homebrew python. Should I uninstall homebrew python?

dpo commented 8 years ago

Is 2.7.10 system Python for you? I assume that you created the virtual environment with that version of Python and ran the brew commands from inside the virtual env?

It's best to only run pip from inside the virtual env, so everything is in there, including numpy.

francispoulin commented 8 years ago

Yes, my system python is 2.7.10 and I did try and install everything from the virtualenv.

Problem: when I update pip normally, it gives me 8.0.3, the latest (and presumably greatest).

\ try and update pip, fail ** (fenics) Francis-Poulins-MacBook-Pro:Re__plots_matt fpoulin$ pip install --upgrade pip Collecting pip Using cached pip-8.0.3-py2.py3-none-any.whl Installing collected packages: pip Found existing installation: pip 8.0.2 Not uninstalling pip at /usr/local/lib/python2.7/site-packages, outside environment /Users/fpoulin/.virtualenvs/fenics Successfully installed pip-8.0.2 You are using pip version 8.0.2, however version 8.0.3 is available. You should consider upgrading via the 'pip install --upgrade pip' command.

When I do it from virtualenv it won't upgrade it. I'm not sure if that is a big problem in itself but it might help to show why I can't find numpy when I use the fenics generated version of python.

\ try and update numpy, failed **

(fenics) Francis-Poulins-MacBook-Pro:Re__plots_matt fpoulin$ pip install --upgrade numpy Requirement already up-to-date: numpy in /usr/local/lib/python2.7/site-packages You are using pip version 8.0.2, however version 8.0.3 is available. You should consider upgrading via the 'pip install --upgrade pip' command.

\ try and load numpy in virtual python, fail **

(fenics) Francis-Poulins-MacBook-Pro:Re__plots_matt fpoulin$ python Python 2.7.10 (default, Jul 14 2015, 19:46:27) [GCC 4.2.1 Compatible Apple LLVM 6.0 (clang-600.0.39)] on darwin Type "help", "copyright", "credits" or "license" for more information.

import numpy Traceback (most recent call last): File "", line 1, in File "/usr/local/lib/python2.7/site-packages/numpy/init.py", line 180, in File "/usr/local/lib/python2.7/site-packages/numpy/add_newdocs.py", line 13, in File "/usr/local/lib/python2.7/site-packages/numpy/lib/init.py", line 8, in File "/usr/local/lib/python2.7/site-packages/numpy/lib/type_check.py", line 11, in File "/usr/local/lib/python2.7/site-packages/numpy/core/init.py", line 14, in ImportError: cannot import name multiarray exit()

(fenics) Francis-Poulins-MacBook-Pro:Re__plots_matt fpoulin$ echo $PYTHONPATH /usr/local/lib/python2.7/site-packages:/Users/fpoulin/software/firedrake/firedrake-bench:/Users/fpoulin/software/pyro2:/Users/fpoulin/software/SPINSpy:/Users/fpoulin/software/clawpack-5.2.2:

My python path is as follows:

print(sys.path) ['', '/usr/local/lib/python2.7/site-packages', '/Users/fpoulin/software/firedrake/firedrake-bench', '/Users/fpoulin/software/pyro2', '/Users/fpoulin/software/SPINSpy', '/Users/fpoulin/software/clawpack-5.2.2', '/Users/fpoulin/Downloads/Re__plots_matt', '/Users/fpoulin/.virtualenvs/fenics/lib/python27.zip', '/Users/fpoulin/.virtualenvs/fenics/lib/python2.7', '/Users/fpoulin/.virtualenvs/fenics/lib/python2.7/plat-darwin', '/Users/fpoulin/.virtualenvs/fenics/lib/python2.7/plat-mac', '/Users/fpoulin/.virtualenvs/fenics/lib/python2.7/plat-mac/lib-scriptpackages', '/Users/fpoulin/.virtualenvs/fenics/Extras/lib/python', '/Users/fpoulin/.virtualenvs/fenics/lib/python2.7/lib-tk', '/Users/fpoulin/.virtualenvs/fenics/lib/python2.7/lib-old', '/Users/fpoulin/.virtualenvs/fenics/lib/python2.7/lib-dynload', '/System/Library/Frameworks/Python.framework/Versions/2.7/lib/python2.7', '/System/Library/Frameworks/Python.framework/Versions/2.7/lib/python2.7/plat-darwin', '/System/Library/Frameworks/Python.framework/Versions/2.7/lib/python2.7/lib-tk', '/System/Library/Frameworks/Python.framework/Versions/2.7/lib/python2.7/plat-mac', '/System/Library/Frameworks/Python.framework/Versions/2.7/lib/python2.7/plat-mac/lib-scriptpackages', '/Users/fpoulin/.virtualenvs/fenics/lib/python2.7/site-packages']

Any ideas what I can do?

dpo commented 8 years ago

The PYTHONPATH seems to be mixed up. Here's how I have it:

$ echo $PYTHONPATH   # outside of the virtualenv
/usr/local/lib/python2.7/site-packages:
$ workon fenics-from-scratch
(fenics-from-scratch)$ echo $PYTHONPATH  # inside the virtualenv
/Users/dpo/.virtualenvs/fenics-from-scratch/lib/python2.7/site-packages:/usr/local/lib/python2.7/site-packages:

It's not a good idea to install Python packages in the system dirs. You might have another numpy and/or another pip lying around?!

francispoulin commented 8 years ago

Thank you. I think I'm nearly there, hopefully.

I removed everything from my pythonpath except for the system pythonpath and that seemed to work, I think. There were some warnings, as you can see below.

Good news: now I have the right pip and numpy!

Bad news: I can't import dolfin.

I think it's because it's not in my pythonpath. Should this have been set automatically or do I need to set it?

(fenics) am-laptop24:~ fpoulin$ echo $PYTHONPATH /Library/Python/2.7/site-packages

Below I have copied the results from my install dolfin and also what happens when I install dolfin.

$ brew install dolfin ==> Installing dolfin from optimizers/fenics ==> Installing dependencies for optimizers/fenics/dolfin: homebrew/science/trilinos ==> Installing optimizers/fenics/dolfin dependency: homebrew/science/trilinos ==> Downloading https://homebrew.bintray.com/bottles-science/trilinos-12.4.2_1.yosemite.bottle.tar.gz Already downloaded: /Library/Caches/Homebrew/trilinos-12.4.2_1.yosemite.bottle.tar.gz ==> Pouring trilinos-12.4.2_1.yosemite.bottle.tar.gz Traceback (most recent call last): File "", line 1, in AttributeError: 'module' object has no attribute 'getusersitepackages' Traceback (most recent call last): File "", line 1, in AttributeError: 'module' object has no attribute 'getusersitepackages' ==> Caveats The following Trilinos packages were disabled due to compile errors: FEI, Pike, Piro, SEACAS, STK, Stokhos, Zoltan2, Amesos2

On Linuxbrew install with:
  --with-openblas

Python modules have been installed and Homebrew's site-packages is not in your Python sys.path, so you will not be able to import the modules this formula installed. If you plan to develop with these modules, please run: mkdir -p echo 'import site; site.addsitedir("/usr/local/lib/python2.7/site-packages")' >> homebrew.pth ==> Summary 🍺 /usr/local/Cellar/trilinos/12.4.2_1: 5,593 files, 212.4M ==> Installing optimizers/fenics/dolfin ==> Using Homebrew-provided fortran compiler. This may be changed by setting the FC environment variable. ==> Downloading https://bitbucket.org/fenics-project/dolfin/downloads/dolfin-1.6.0.tar.gz Already downloaded: /Library/Caches/Homebrew/dolfin-1.6.0.tar.gz ==> cmake .. -DCMAKE_INSTALL_PREFIX=/usr/local/Cellar/dolfin/1.6.0 -DBUILD_SHARED_LIBS:BOOL=ON -DDOLFIN_ENABLE_PYTHON:BOOL=ON -DDOLFIN_INSTALL_PYTHON_MODULE_DIR=/usr/local/Cellar/dolfin/1.6.0/lib/p ==> make ==> make install Warning: optimizers/fenics/dolfin dependency gcc was built with a different C++ standard library (libstdc++ from clang). This may cause problems at runtime. Traceback (most recent call last): File "", line 1, in AttributeError: 'module' object has no attribute 'getusersitepackages' Traceback (most recent call last): File "", line 1, in AttributeError: 'module' object has no attribute 'getusersitepackages' ==> Caveats Do not source dolfin.conf, as the DYLIB settings conflict with Homebrew.

Python modules have been installed and Homebrew's site-packages is not in your Python sys.path, so you will not be able to import the modules this formula installed. If you plan to develop with these modules, please run: mkdir -p echo 'import site; site.addsitedir("/usr/local/lib/python2.7/site-packages")' >> homebrew.pth ==> Summary 🍺 /usr/local/Cellar/dolfin/1.6.0: 755 files, 26.0M, built in 8 minutes 16 seconds (fenics) am-laptop24:~ fpoulin$ python Python 2.7.10 (default, Jul 14 2015, 19:46:27) [GCC 4.2.1 Compatible Apple LLVM 6.0 (clang-600.0.39)] on darwin Type "help", "copyright", "credits" or "license" for more information.

import numpy import dolfin Traceback (most recent call last): File "", line 1, in ImportError: No module named dolfin

dpo commented 8 years ago

It's again because /usr/local/lib/python2.7/site-packages isn't on your PYTHONPATH. That's where Homebrew installs Python modules, even if they're built against system Python. Make sure that when you're in the virtual environment, your PYTHONPATH contains the virtualenv's path, and the Homebrew path, in that order.

dpo commented 8 years ago

ps: I suspect the messages AttributeError: 'module' object has no attribute 'getusersitepackages' from Homebrew are due to your PYTHONPATH not containing /usr/local/lib/python2.7/site-packages.

francispoulin commented 8 years ago

Thank you, and sorry for not fixing the path sooner. I will try it again with the revised path. But before I do, should I have my homebrew python unlinked or can I have it installed? I remember before I needed it unlinked, and I have it that way now, but not sure if that is still the case. It seems to me that if fenics is going to use homebrew libraries it might want to use homebrew python, but I thought I'd check.

dpo commented 8 years ago

It's ok to have it linked as long as you're working in the virtual environment. While in the virtual environment, python will always refer to the Python used to create the virtual environment. If that was system Python, there won't be any confusion.

francispoulin commented 8 years ago

But I should not have it linked before I go into the virtual environment?

dpo commented 8 years ago

You'll find out quickly. I'm not sure.

francispoulin commented 8 years ago

Thanks. I installed python with homebrew and dolfin seemed to install nicely.

I was able to import dolfin and that worked! At long last. But when I try running an example that runs with the fenics app, I get a problem. I seem to have the wrong version of swig?

python linear_wave.py Incompatible swig versions detected. UFC swig version is not the same as extension module swig version: '3.0.8' != '3.0.5' Traceback (most recent call last): File "linear_wave.py", line 42, in V0 = FunctionSpace(mesh, 'CG', p, constrained_domain=PeriodicBoundary()) File "/usr/local/lib/python2.7/site-packages/dolfin/functions/functionspace.py", line 468, in init FunctionSpaceBase.init(self, mesh, element, constrained_domain) File "/usr/local/lib/python2.7/site-packages/dolfin/functions/functionspace.py", line 153, in init ufc_element, ufc_dofmap = jit(self._ufl_element, mpi_comm=mesh.mpi_comm()) File "/usr/local/lib/python2.7/site-packages/dolfin/compilemodules/jit.py", line 64, in mpi_jit return local_jit(_args, _kwargs) File "/usr/local/lib/python2.7/site-packages/dolfin/compilemodules/jit.py", line 128, in jit return form_compiler.jit(form, parameters=p) File "/usr/local/lib/python2.7/site-packages/ffc/jitcompiler.py", line 72, in jit return jit_element(ufl_object, parameters) File "/usr/local/lib/python2.7/site-packages/ffc/jitcompiler.py", line 180, in jit_element compiled_form, module, prefix = jit_form(form, parameters) File "/usr/local/lib/python2.7/site-packages/ffc/jitcompiler.py", line 158, in jit_form check_swig_version(module) File "/usr/local/lib/python2.7/site-packages/ffc/jitcompiler.py", line 83, in check_swig_version (ufc.swigversion, compiled_module.swigversion)) File "", line 1, in File "/usr/local/lib/python2.7/site-packages/ufl/log.py", line 151, in error raise self._exception_type(self._format_raw(message)) Exception: Incompatible swig versions detected. UFC swig version is not the same as extension module swig version: '3.0.8' != '3.0.5'

dpo commented 8 years ago

Do you have another swig than the one installed when installing dolfin? Hombrew's swig is version 3.0.8. I'm not sure where 3.0.5 comes from?!

francispoulin commented 8 years ago

No, I don't think so.

When I do which swig it points me to /usr/local/bin/swig.

What version of swig should be installed?

I tried another example and it failed for another reason.

Should I remove dolfin and its dependencies and try again

(fenics) Francis-Poulins-MacBook-Pro:python fpoulin$ python demo_mixed-poisson.py Calling FFC just-in-time (JIT) compiler, this may take some time. Calling FFC just-in-time (JIT) compiler, this may take some time. In instant.import_module_directly: Failed to import module 'dolfin_compile_code_c8b988ab6016262c9eebd6dc8482b98c0cf05c33' from '/Users/fpoulin/.instant/cache'; ImportError:dlopen(/Users/fpoulin/.instant/cache/dolfin_compile_code_c8b988ab6016262c9eebd6dc8482b98c0cf05c33/_dolfin_compile_code_c8b988ab6016262c9eebd6dc8482b98c0cf05c33.so, 2): Library not loaded: libboost_filesystem.dylib Referenced from: /Users/fpoulin/.instant/cache/dolfin_compile_code_c8b988ab6016262c9eebd6dc8482b98c0cf05c33/_dolfin_compile_code_c8b988ab6016262c9eebd6dc8482b98c0cf05c33.so Reason: image not found; Failed to import module found in cache. Modulename: 'dolfin_compile_code_c8b988ab6016262c9eebd6dc8482b98c0cf05c33'; Path: '/Users/fpoulin/.instant/cache'; ImportError:dlopen(/Users/fpoulin/.instant/cache/dolfin_compile_code_c8b988ab6016262c9eebd6dc8482b98c0cf05c33/_dolfin_compile_code_c8b988ab6016262c9eebd6dc8482b98c0cf05c33.so, 2): Library not loaded: libboost_filesystem.dylib Referenced from: /Users/fpoulin/.instant/cache/dolfin_compile_code_c8b988ab6016262c9eebd6dc8482b98c0cf05c33/_dolfin_compile_code_c8b988ab6016262c9eebd6dc8482b98c0cf05c33.so Reason: image not found; Traceback (most recent call last): File "demo_mixed-poisson.py", line 59, in f = Expression("10exp(-(pow(x[0] - 0.5, 2) + pow(x[1] - 0.5, 2)) / 0.02)") File "/usr/local/lib/python2.7/site-packages/dolfin/functions/expression.py", line 602, in new mpi_comm=mpi_comm) File "/usr/local/lib/python2.7/site-packages/dolfin/compilemodules/expressions.py", line 217, in compile_expressions mpi_comm=mpi_comm) File "/usr/local/lib/python2.7/site-packages/dolfin/compilemodules/expressions.py", line 145, in compile_expression_code mpi_comm=mpi_comm) File "/usr/local/lib/python2.7/site-packages/dolfin/compilemodules/jit.py", line 64, in mpi_jit return local_jit(_args, _kwargs) File "/usr/local/lib/python2.7/site-packages/dolfin/compilemodules/compilemodule.py", line 411, in compile_extension_module compiled_module = instant.import_module(module_name) File "/usr/local/lib/python2.7/site-packages/instant/cache.py", line 171, in import_module return check_disk_cache(modulename, cache_dir, moduleids) File "/usr/local/lib/python2.7/site-packages/instant/cache.py", line 139, in check_disk_cache module = import_and_cache_module(path, modulename, moduleids) File "/usr/local/lib/python2.7/site-packages/instant/cache.py", line 87, in import_and_cache_module instant_assert(module is not None, "Failed to import module found in cache. Modulename: '%s';\nPath: '%s';\n%s:%s;" % (modulename, path, type(e).name, e)) File "/usr/local/lib/python2.7/site-packages/instant/output.py", line 91, in instant_assert raise AssertionError(text) AssertionError: Failed to import module found in cache. Modulename: 'dolfin_compile_code_c8b988ab6016262c9eebd6dc8482b98c0cf05c33'; Path: '/Users/fpoulin/.instant/cache'; ImportError:dlopen(/Users/fpoulin/.instant/cache/dolfin_compile_code_c8b988ab6016262c9eebd6dc8482b98c0cf05c33/_dolfin_compile_code_c8b988ab6016262c9eebd6dc8482b98c0cf05c33.so, 2): Library not loaded: libboost_filesystem.dylib Referenced from: /Users/fpoulin/.instant/cache/dolfin_compile_code_c8b988ab6016262c9eebd6dc8482b98c0cf05c33/_dolfin_compile_code_c8b988ab6016262c9eebd6dc8482b98c0cf05c33.so Reason: image not found;

dpo commented 8 years ago

That's an issue with boost. Something odd is going on. Please post the output of brew doctor and brew missing.

francispoulin commented 8 years ago

Sure thing. Brew missing says nothing but brew doctor says the following.

If you think this is because I'm not using system python I can always try it with that and see if things work any better. Not sure if that would help though.

(fenics) Francis-Poulins-MacBook-Pro:python fpoulin$ brew doctor Please note that these warnings are just used to help the Homebrew maintainers with debugging if you file an issue. If everything you use Homebrew for is working fine: please don't worry and just ignore them. Thanks!

Warning: "config" scripts exist outside your system or Homebrew directories. ./configure scripts often look for *-config scripts to determine if software packages are installed, and what additional flags to use when compiling and linking.

Having additional scripts in your path can confuse software installed via Homebrew if the config script overrides a system or Homebrew provided script of the same name. We found the following "config" scripts: /Users/fpoulin/.virtualenvs/fenics/bin/python-config Traceback (most recent call last): File "", line 1, in AttributeError: 'module' object has no attribute 'getusersitepackages'

Warning: Your default Python does not recognize the Homebrew site-packages directory as a special site-packages directory, which means that .pth files will not be followed. This means you will not be able to import some modules after installing them with Homebrew, like wxpython. To fix this for the current user, you can run:

mkdir -p echo 'import site; site.addsitedir("/usr/local/lib/python2.7/site-packages")' >> /homebrew.pth (fenics) Francis-Poulins-MacBook-Pro:python fpoulin$ brew missing

dpo commented 8 years ago

When you are in the virtual env, what is your PYTHONPATH?

francispoulin commented 8 years ago

I set it to what you had suggested,

/usr/local/lib/python2.7/site-packages

As a result it can find dolfin, numpy, ...

dpo commented 8 years ago

But that's only right outside of the virtualenv. In the virtualenv, the virtualenv's Python path should appear in there too. I'm very confused. See https://github.com/optimizers/homebrew-fenics/issues/12#issuecomment-190885638.

francispoulin commented 8 years ago

Not sure why it wasn't adjusted. Maybe it's because I set PYTHONPATH in my bashrc file. I don't append to it.

export PYTHONPATH=/usr/local/lib/python2.7/site-packages

Maybe a bad idea. Would this mess things up?

Also, I tried setting PYTHONPATH to what I think it should be and in the virtual environment it didn't help.

PYTHONPATH=/Users/fpoulin/.virtualenvs/fenics/lib/python2.7/site-packages:/usr/local/lib/python2.7/site-packages

dpo commented 8 years ago

Is /usr/local/lib on your LD_LIBRARY_PATH?

francispoulin commented 8 years ago

Actually, no. It was blank. I just set it to /usr/local/lib. Should I now redo the installation of dolfin?

dpo commented 8 years ago

Give it a try first. Does it work?

francispoulin commented 8 years ago

No, sorry.

I redid the dolfin install and it has a concern with a module that I don't understand.

$ brew install dolfin ==> Installing dolfin from optimizers/fenics ==> Using Homebrew-provided fortran compiler. This may be changed by setting the FC environment variable. ==> Downloading https://bitbucket.org/fenics-project/dolfin/downloads/dolfin-1.6.0.tar.gz Already downloaded: /Library/Caches/Homebrew/dolfin-1.6.0.tar.gz ==> cmake .. -DCMAKE_INSTALL_PREFIX=/usr/local/Cellar/dolfin/1.6.0 -DBUILD_SHARED_LIBS:BOOL=ON -DDOLFIN_ENABLE_PYTHON:BOOL=ON ==> make ==> make install Warning: optimizers/fenics/dolfin dependency gcc was built with a different C++ standard library (libstdc++ from clang). This may cause problems at runtime. Traceback (most recent call last): File "", line 1, in AttributeError: 'module' object has no attribute 'getusersitepackages' Traceback (most recent call last): File "", line 1, in AttributeError: 'module' object has no attribute 'getusersitepackages' ==> Caveats Do not source dolfin.conf, as the DYLIB settings conflict with Homebrew. ==> Summary 🍺 /usr/local/Cellar/dolfin/1.6.0: 800 files, 34.4M, built in 10 minutes 37 seconds (fenics) am-laptop24:~ fpoulin$ brew doctor

When I try the same example I get library problems:

$ python demo_mixed-poisson.py In instant.import_module_directly: Failed to import module 'dolfin_compile_code_c8b988ab6016262c9eebd6dc8482b98c0cf05c33' from '/Users/fpoulin/.instant/cache'; ImportError:dlopen(/Users/fpoulin/.instant/cache/dolfin_compile_code_c8b988ab6016262c9eebd6dc8482b98c0cf05c33/_dolfin_compile_code_c8b988ab6016262c9eebd6dc8482b98c0cf05c33.so, 2): Library not loaded: libboost_filesystem.dylib Referenced from: /Users/fpoulin/.instant/cache/dolfin_compile_code_c8b988ab6016262c9eebd6dc8482b98c0cf05c33/_dolfin_compile_code_c8b988ab6016262c9eebd6dc8482b98c0cf05c33.so Reason: image not found; Failed to import module found in cache. Modulename: 'dolfin_compile_code_c8b988ab6016262c9eebd6dc8482b98c0cf05c33'; Path: '/Users/fpoulin/.instant/cache'; ImportError:dlopen(/Users/fpoulin/.instant/cache/dolfin_compile_code_c8b988ab6016262c9eebd6dc8482b98c0cf05c33/_dolfin_compile_code_c8b988ab6016262c9eebd6dc8482b98c0cf05c33.so, 2): Library not loaded: libboost_filesystem.dylib Referenced from: /Users/fpoulin/.instant/cache/dolfin_compile_code_c8b988ab6016262c9eebd6dc8482b98c0cf05c33/_dolfin_compile_code_c8b988ab6016262c9eebd6dc8482b98c0cf05c33.so Reason: image not found; Traceback (most recent call last): File "demo_mixed-poisson.py", line 59, in f = Expression("10exp(-(pow(x[0] - 0.5, 2) + pow(x[1] - 0.5, 2)) / 0.02)") File "/usr/local/lib/python2.7/site-packages/dolfin/functions/expression.py", line 602, in new mpi_comm=mpi_comm) File "/usr/local/lib/python2.7/site-packages/dolfin/compilemodules/expressions.py", line 217, in compile_expressions mpi_comm=mpi_comm) File "/usr/local/lib/python2.7/site-packages/dolfin/compilemodules/expressions.py", line 145, in compile_expression_code mpi_comm=mpi_comm) File "/usr/local/lib/python2.7/site-packages/dolfin/compilemodules/jit.py", line 64, in mpi_jit return local_jit(_args, _kwargs) File "/usr/local/lib/python2.7/site-packages/dolfin/compilemodules/compilemodule.py", line 411, in compile_extension_module compiled_module = instant.import_module(module_name) File "/usr/local/lib/python2.7/site-packages/instant/cache.py", line 171, in import_module return check_disk_cache(modulename, cache_dir, moduleids) File "/usr/local/lib/python2.7/site-packages/instant/cache.py", line 139, in check_disk_cache module = import_and_cache_module(path, modulename, moduleids) File "/usr/local/lib/python2.7/site-packages/instant/cache.py", line 87, in import_and_cache_module instant_assert(module is not None, "Failed to import module found in cache. Modulename: '%s';\nPath: '%s';\n%s:%s;" % (modulename, path, type(e).name, e)) File "/usr/local/lib/python2.7/site-packages/instant/output.py", line 91, in instant_assert raise AssertionError(text) AssertionError: Failed to import module found in cache. Modulename: 'dolfin_compile_code_c8b988ab6016262c9eebd6dc8482b98c0cf05c33'; Path: '/Users/fpoulin/.instant/cache'; ImportError:dlopen(/Users/fpoulin/.instant/cache/dolfin_compile_code_c8b988ab6016262c9eebd6dc8482b98c0cf05c33/_dolfin_compile_code_c8b988ab6016262c9eebd6dc8482b98c0cf05c33.so, 2): Library not loaded: libboost_filesystem.dylib Referenced from: /Users/fpoulin/.instant/cache/dolfin_compile_code_c8b988ab6016262c9eebd6dc8482b98c0cf05c33/_dolfin_compile_code_c8b988ab6016262c9eebd6dc8482b98c0cf05c33.so Reason: image not found;

This happens regardless of how LD_LIBRARY_PATH is set. Can you make any sense of this?

dpo commented 8 years ago

Ok, so if you look at ls $(brew --prefix boost)/lib, do you have libboost_filesystem-mt but not libboost_filesystem?

dpo commented 8 years ago

As a sanity check, could you try instant-clean and re-run the demo? You might have old stuff lying around the instant cache.

francispoulin commented 8 years ago

Thanks again.

Some good news. I tried instant-clean and that allowed the demo to go much further,

(fenics) am-laptop24:python fpoulin$ python demo_mixed-poisson.py Calling FFC just-in-time (JIT) compiler, this may take some time. Calling FFC just-in-time (JIT) compiler, this may take some time. Calling FFC just-in-time (JIT) compiler, this may take some time. Calling DOLFIN just-in-time (JIT) compiler, this may take some time. In instant.recompile: The module did not compile with command 'make VERBOSE=1', see '/Users/fpoulin/.instant/error/dolfin_compile_code_c8b988ab6016262c9eebd6dc8482b98c0cf05c33/compile.log' Traceback (most recent call last): File "demo_mixed-poisson.py", line 59, in f = Expression("10_exp(-(pow(x[0] - 0.5, 2) + pow(x[1] - 0.5, 2)) / 0.02)") File "/usr/local/lib/python2.7/site-packages/dolfin/functions/expression.py", line 602, in new mpi_comm=mpi_comm) File "/usr/local/lib/python2.7/site-packages/dolfin/compilemodules/expressions.py", line 217, in compile_expressions mpi_comm=mpi_comm) File "/usr/local/lib/python2.7/site-packages/dolfin/compilemodules/expressions.py", line 145, in compile_expression_code mpi_comm=mpi_comm) File "/usr/local/lib/python2.7/site-packages/dolfin/compilemodules/jit.py", line 64, in mpi_jit return local_jit(_args, _kwargs) File "/usr/local/lib/python2.7/site-packages/dolfin/compilemodules/compilemodule.py", line 458, in compile_extension_module _instant_kwargs) File "/usr/local/lib/python2.7/site-packages/instant/build.py", line 563, in build_module recompile(modulename, module_path, new_compilation_checksum, build_system) File "/usr/local/lib/python2.7/site-packages/instant/build.py", line 165, in recompile instant_error(msg % (cmd, compile_log_filename_dest)) File "/usr/local/lib/python2.7/site-packages/instant/output.py", line 85, in instant_error raise RuntimeError(text) RuntimeError: In instant.recompile: The module did not compile with command 'make VERBOSE=1', see '/Users/fpoulin/.instant/error/dolfin_compile_code_c8b988ab6016262c9eebd6dc8482b98c0cf05c33/compile.log'

I checked the filesystem and have

libboost_filesystem-mt.a/.dylib

and the only thing with libboost and filesystem.

Is there something that I should install?

dpo commented 8 years ago

RuntimeError: In instant.recompile: The module did not compile with command 'make VERBOSE=1', see '/Users/fpoulin/.instant/error/dolfin_compile_code_c8b988ab6016262c9eebd6dc8482b98c0cf05c33/compile.log'

The error's in that log file, hopefully.

I checked the filesystem and have libboost_filesystem-mt.a/.dylib and the only thing with libboost and filesystem. Is there something that I should install?

No, cleaning the instant cache resolved that apparently.

francispoulin commented 8 years ago

Great. I looked at the file and see a lot of stuff I don't understand.

Maybe a header problem?

One thing I noticed is that there is a version of swig in /usr/local/opt/swig/bin/swig, which is what it finds. I thought this was installed by Xcode,maybe?

But when I do which swig, it points to /usr/local/bin/swig.

(fenics) am-laptop24:python fpoulin$ more /Users/fpoulin/.instant/error/dolfin_compile_code_c8b988ab6016262c9eebd6dc8482b98c0cf05c33/compile.log -- The C compiler identification is AppleClang 7.0.2.7000181 -- The CXX compiler identification is AppleClang 7.0.2.7000181 -- Check for working C compiler: /Applications/Xcode.app/Contents/Developer/Toolchains/XcodeDefault.xctoolchain/usr/bin/cc -- Check for working C compiler: /Applications/Xcode.app/Contents/Developer/Toolchains/XcodeDefault.xctoolchain/usr/bin/cc -- works -- Detecting C compiler ABI info -- Detecting C compiler ABI info - done -- Detecting C compile features -- Detecting C compile features - done -- Check for working CXX compiler: /Applications/Xcode.app/Contents/Developer/Toolchains/XcodeDefault.xctoolchain/usr/bin/c++ -- Check for working CXX compiler: /Applications/Xcode.app/Contents/Developer/Toolchains/XcodeDefault.xctoolchain/usr/bin/c++ -- works -- Detecting CXX compiler ABI info -- Detecting CXX compiler ABI info - done -- Detecting CXX compile features -- Detecting CXX compile features - done -- Found SWIG: /usr/local/opt/swig/bin/swig (found version "3.0.8") -- Configuring done -- Generating done CMake Warning: Manually-specified variables were not used by the project:

DEBUG

-- Build files have been written to: /private/var/folders/nl/wfwj3nps2wx8m6jx9bh_gslc0000gn/T/tmp66UdKS2016-3-2-14-18_instant_03d12e83a6b5aa9b239a298463abdcc634c8d453/dolfin_compile_code_c8b988ab6016262c9eebd6dc8482b98c0cf05c33 /usr/local/Cellar/cmake/3.4.3/bin/cmake -H/private/var/folders/nl/wfwj3nps2wx8m6jx9bh_gslc0000gn/T/tmp66UdKS2016-3-2-14-18_instant_03d12e83a6b5aa9b239a298463abdcc634c8d453/dolfin_compile_code_c8b988ab6016262c9eebd6dc8482b98c0cf05c33 -B/private/var/folders/nl/wfwj3nps2wx8m6jx9bh_gslc0000gn/T/tmp66UdKS2016-3-2-14-18_instant_03d12e83a6b5aa9b239a298463abdcc634c8d453/dolfin_compile_code_c8b988ab6016262c9eebd6dc8482b98c0cf05c33 --check-build-system CMakeFiles/Makefile.cmake 0 /usr/local/Cellar/cmake/3.4.3/bin/cmake -E cmake_progress_start /private/var/folders/nl/wfwj3nps2wx8m6jx9bh_gslc0000gn/T/tmp66UdKS2016-3-2-14-18_instant_03d12e83a6b5aa9b239a298463abdcc634c8d453/dolfin_compile_code_c8b988ab6016262c9eebd6dc8482b98c0cf05c33/CMakeFiles 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-fastinit -fastunpack -fastquery -nobuildnone -DDOLFIN_VERSION="1.6.0" -DNDEBUG -DDOLFIN_SIZE_T=8 -DDOLFIN_LA_INDEX_SIZE=4 -DHAS_HDF5 -DHAS_SLEPC -DHAS_PETSC -DENABLE_PETSC_TAO -DHAS_UMFPACK -DHAS_CHOLMOD -DHAS_PASTIX -DHAS_SCOTCH -DHAS_PARMETIS -DHAS_ZLIB -DHAS_CPPUNIT -DHAS_MPI -DHAS_QT4 -DHAS_VTK -DHAS_QVTK -DHAS_PETSC4PY -DHAS_SLEPC4PY -DNUMPY_VERSION_MAJOR=1 -DNUMPY_VERSION_MINOR=10 -DNUMPY_VERSION_MICRO=4 -DNPY_NO_DEPRECATED_API=NPY_1_10_API_VERSION -c++ -fcompact -O -I. -small -outdir /private/var/folders/nl/wfwj3nps2wx8m6jx9bh_gslc0000gn/T/tmp66UdKS2016-3-2-14-18_instant_03d12e83a6b5aa9b239a298463abdcc634c8d453/dolfin_compile_code_c8b988ab6016262c9eebd6dc8482b98c0cf05c33 -c++ -I/usr/local/Cellar/dolfin/1.6.0/include -I/usr/local/Cellar/ffc/1.6.0/include -I/usr/local/Cellar/slepc/3.6.2_1/real/include -I/usr/local/opt/suite-sparse/include -I/usr/local/include -I/usr/include -I/usr/local/Cellar/cppunit/1.13.2/include -I/usr/local/Cellar/open-mpi/1.10.2/include -I/usr/local/include/eigen3 -I/usr/local/Cellar/hdf5/1.8.16_1/include -I/usr/local/Cellar/petsc/3.6.3_3/real/include -I/usr/local/opt/hypre/include -I/usr/local/opt/mumps/libexec/include -I/usr/local/opt/sundials/include -I/usr/local/Cellar/superlu43/4.3_1/include/superlu -I/usr/local/opt/superlu_dist/include/superlu_dist -I/usr/local/opt/parmetis/include -I/usr/local/opt/metis/include -I/usr/local/opt/netcdf/include -I/usr/local/opt/hdf5/include -I/usr/local/opt/fftw/include -I/usr/local/opt/hwloc/include -I/opt/X11/include -I/usr/local/Cellar/qt/4.8.7_2/include -I/usr/local/Cellar/qt/4.8.7_2/lib/QtCore.framework -I/usr/local/Cellar/vtk/7.0.0/include/vtk-7.0 -I/System/Library/Frameworks/Python.framework/Versions/2.7/include/python2.7 -I/usr/include/libxml2 -I/private/var/folders/nl/wfwj3nps2wx8m6jx9bh_gslc0000gn/T/tmp66UdKS2016-3-2-14-18_instant_03d12e83a6b5aa9b239a298463abdcc634c8d453/dolfin_compile_code_c8b988ab6016262c9eebd6dc8482b98c0cf05c33/. -I/Users/fpoulin/.virtualenvs/fenics/lib/python2.7/site-packages/numpy/core/include -I/Users/fpoulin/.virtualenvs/fenics/lib/python2.7/site-packages/petsc4py/include -I/Users/fpoulin/.virtualenvs/fenics/lib/python2.7/site-packages/slepc4py/include -I/private/var/folders/nl/wfwj3nps2wx8m6jx9bh_gslc0000gn/T/tmp66UdKS2016-3-2-14-18_instant_03d12e83a6b5aa9b239a298463abdcc634c8d453/dolfin_compile_code_c8b988ab6016262c9eebd6dc8482b98c0cf05c33 -o /private/var/folders/nl/wfwj3nps2wx8m6jx9bh_gslc0000gn/T/tmp66UdKS2016-3-2-14-18_instant_03d12e83a6b5aa9b239a298463abdcc634c8d453/dolfin_compile_code_c8b988ab6016262c9eebd6dc8482b98c0cf05c33/dolfin_compile_code_c8b988ab6016262c9eebd6dc8482b98c0cf05c33PYTHON_wrap.cxx /private/var/folders/nl/wfwj3nps2wx8m6jx9bh_gslc0000gn/T/tmp66UdKS2016-3-2-14-18_instant_03d12e83a6b5aa9b239a298463abdcc634c8d453/dolfin_compile_code_c8b988ab6016262c9eebd6dc8482b98c0cf05c33/dolfin_compile_code_c8b988ab6016262c9eebd6dc8482b98c0cf05c33.i /usr/local/Cellar/dolfin/1.6.0/include/dolfin/la/LinearAlgebraObject.h:36: Warning 520: Derived class 'LinearAlgebraObject' of 'dolfin::Variable' is not similarly marked as a smart pointer. /usr/local/Cellar/dolfin/1.6.0/include/dolfin/function/Function.h:63: Warning 402: Base class 'Hierarchical< Function >' is incomplete. /usr/local/Cellar/dolfin/1.6.0/include/dolfin/swig/function/pre.i:219: Warning 402: Only forward declaration 'Hierarchical< Function >' was found. /usr/local/Cellar/dolfin/1.6.0/include/dolfin/function/Function.h:64: Warning 520: Derived class 'Function' of 'dolfin::GenericFunction' is not similarly marked as a smart pointer. /usr/local/Cellar/dolfin/1.6.0/include/dolfin/function/Function.h:64: Warning 520: Derived class 'Function' of 'ufc::function' is not similarly marked as a smart pointer. /usr/local/Cellar/dolfin/1.6.0/include/dolfin/function/Function.h:64: Warning 520: Derived class 'Function' of 'dolfin::Variable' is not similarly marked as a smart pointer. /usr/local/Cellar/dolfin/1.6.0/include/dolfin/function/FunctionSpace.h:53: Warning 402: Base class 'Hierarchical< FunctionSpace >' is incomplete. /usr/local/Cellar/dolfin/1.6.0/include/dolfin/swig/function/pre.i:218: Warning 402: Only forward declaration 'Hierarchical< FunctionSpace >' was found. /usr/local/Cellar/dolfin/1.6.0/include/dolfin/function/FunctionSpace.h:54: Warning 520: Derived class 'FunctionSpace' of 'dolfin::Variable' is not similarly marked as a smart pointer. /private/var/folders/nl/wfwj3nps2wx8m6jx9bh_gslc0000gn/T/tmp66UdKS2016-3-2-14-18_instant_03d12e83a6b5aa9b239a298463abdcc634c8d453/dolfin_compile_code_c8b988ab6016262c9eebd6dc8482b98c0cf05c33/dolfin_compile_code_c8b988ab6016262c9eebd6dc8482b98c0cf05c33.i:170: Warning 315: Nothing known about 'std::cos'. /private/var/folders/nl/wfwj3nps2wx8m6jx9bh_gslc0000gn/T/tmp66UdKS2016-3-2-14-18_instant_03d12e83a6b5aa9b239a298463abdcc634c8d453/dolfin_compile_code_c8b988ab6016262c9eebd6dc8482b98c0cf05c33/dolfin_compile_code_c8b988ab6016262c9eebd6dc8482b98c0cf05c33.i:171: Warning 315: Nothing known about 'std::sin'. /private/var/folders/nl/wfwj3nps2wx8m6jx9bh_gslc0000gn/T/tmp66UdKS2016-3-2-14-18_instant_03d12e83a6b5aa9b239a298463abdcc634c8d453/dolfin_compile_code_c8b988ab6016262c9eebd6dc8482b98c0cf05c33/dolfin_compile_code_c8b988ab6016262c9eebd6dc8482b98c0cf05c33.i:172: Warning 315: Nothing known about 'std::tan'. /private/var/folders/nl/wfwj3nps2wx8m6jx9bh_gslc0000gn/T/tmp66UdKS2016-3-2-14-18_instant_03d12e83a6b5aa9b239a298463abdcc634c8d453/dolfin_compile_code_c8b988ab6016262c9eebd6dc8482b98c0cf05c33/dolfin_compile_code_c8b988ab6016262c9eebd6dc8482b98c0cf05c33.i:173: Warning 315: Nothing known about 'std::acos'. /private/var/folders/nl/wfwj3nps2wx8m6jx9bh_gslc0000gn/T/tmp66UdKS2016-3-2-14-18_instant_03d12e83a6b5aa9b239a298463abdcc634c8d453/dolfin_compile_code_c8b988ab6016262c9eebd6dc8482b98c0cf05c33/dolfin_compile_code_c8b988ab6016262c9eebd6dc8482b98c0cf05c33.i:174: Warning 315: Nothing known about 'std::asin'. /private/var/folders/nl/wfwj3nps2wx8m6jx9bh_gslc0000gn/T/tmp66UdKS2016-3-2-14-18_instant_03d12e83a6b5aa9b239a298463abdcc634c8d453/dolfin_compile_code_c8b988ab6016262c9eebd6dc8482b98c0cf05c33/dolfin_compile_code_c8b988ab6016262c9eebd6dc8482b98c0cf05c33.i:175: Warning 315: Nothing known about 'std::atan'. /private/var/folders/nl/wfwj3nps2wx8m6jx9bh_gslc0000gn/T/tmp66UdKS2016-3-2-14-18_instant_03d12e83a6b5aa9b239a298463abdcc634c8d453/dolfin_compile_code_c8b988ab6016262c9eebd6dc8482b98c0cf05c33/dolfin_compile_code_c8b988ab6016262c9eebd6dc8482b98c0cf05c33.i:176: Warning 315: Nothing known about 'std::atan2'. /private/var/folders/nl/wfwj3nps2wx8m6jx9bh_gslc0000gn/T/tmp66UdKS2016-3-2-14-18_instant_03d12e83a6b5aa9b239a298463abdcc634c8d453/dolfin_compile_code_c8b988ab6016262c9eebd6dc8482b98c0cf05c33/dolfin_compile_code_c8b988ab6016262c9eebd6dc8482b98c0cf05c33.i:177: Warning 315: Nothing known about 'std::cosh'. /private/var/folders/nl/wfwj3nps2wx8m6jx9bh_gslc0000gn/T/tmp66UdKS2016-3-2-14-18_instant_03d12e83a6b5aa9b239a298463abdcc634c8d453/dolfin_compile_code_c8b988ab6016262c9eebd6dc8482b98c0cf05c33/dolfin_compile_code_c8b988ab6016262c9eebd6dc8482b98c0cf05c33.i:178: Warning 315: Nothing known about 'std::sinh'. /private/var/folders/nl/wfwj3nps2wx8m6jx9bh_gslc0000gn/T/tmp66UdKS2016-3-2-14-18_instant_03d12e83a6b5aa9b239a298463abdcc634c8d453/dolfin_compile_code_c8b988ab6016262c9eebd6dc8482b98c0cf05c33/dolfin_compile_code_c8b988ab6016262c9eebd6dc8482b98c0cf05c33.i:179: Warning 315: Nothing known about 'std::tanh'. /private/var/folders/nl/wfwj3nps2wx8m6jx9bh_gslc0000gn/T/tmp66UdKS2016-3-2-14-18_instant_03d12e83a6b5aa9b239a298463abdcc634c8d453/dolfin_compile_code_c8b988ab6016262c9eebd6dc8482b98c0cf05c33/dolfin_compile_code_c8b988ab6016262c9eebd6dc8482b98c0cf05c33.i:180: Warning 315: Nothing known about 'std::exp'. /private/var/folders/nl/wfwj3nps2wx8m6jx9bh_gslc0000gn/T/tmp66UdKS2016-3-2-14-18_instant_03d12e83a6b5aa9b239a298463abdcc634c8d453/dolfin_compile_code_c8b988ab6016262c9eebd6dc8482b98c0cf05c33/dolfin_compile_code_c8b988ab6016262c9eebd6dc8482b98c0cf05c33.i:181: Warning 315: Nothing known about 'std::frexp'. /private/var/folders/nl/wfwj3nps2wx8m6jx9bh_gslc0000gn/T/tmp66UdKS2016-3-2-14-18_instant_03d12e83a6b5aa9b239a298463abdcc634c8d453/dolfin_compile_code_c8b988ab6016262c9eebd6dc8482b98c0cf05c33/dolfin_compile_code_c8b988ab6016262c9eebd6dc8482b98c0cf05c33.i:182: Warning 315: Nothing known about 'std::ldexp'. /private/var/folders/nl/wfwj3nps2wx8m6jx9bh_gslc0000gn/T/tmp66UdKS2016-3-2-14-18_instant_03d12e83a6b5aa9b239a298463abdcc634c8d453/dolfin_compile_code_c8b988ab6016262c9eebd6dc8482b98c0cf05c33/dolfin_compile_code_c8b988ab6016262c9eebd6dc8482b98c0cf05c33.i:183: Warning 315: Nothing known about 'std::log'. /private/var/folders/nl/wfwj3nps2wx8m6jx9bh_gslc0000gn/T/tmp66UdKS2016-3-2-14-18_instant_03d12e83a6b5aa9b239a298463abdcc634c8d453/dolfin_compile_code_c8b988ab6016262c9eebd6dc8482b98c0cf05c33/dolfin_compile_code_c8b988ab6016262c9eebd6dc8482b98c0cf05c33.i:184: Warning 315: Nothing known about 'std::log10'. /private/var/folders/nl/wfwj3nps2wx8m6jx9bh_gslc0000gn/T/tmp66UdKS2016-3-2-14-18_instant_03d12e83a6b5aa9b239a298463abdcc634c8d453/dolfin_compile_code_c8b988ab6016262c9eebd6dc8482b98c0cf05c33/dolfin_compile_code_c8b988ab6016262c9eebd6dc8482b98c0cf05c33.i:185: Warning 315: Nothing known about 'std::modf'. /private/var/folders/nl/wfwj3nps2wx8m6jx9bh_gslc0000gn/T/tmp66UdKS2016-3-2-14-18_instant_03d12e83a6b5aa9b239a298463abdcc634c8d453/dolfin_compile_code_c8b988ab6016262c9eebd6dc8482b98c0cf05c33/dolfin_compile_code_c8b988ab6016262c9eebd6dc8482b98c0cf05c33.i:186: Warning 315: Nothing known about 'std::pow'. /private/var/folders/nl/wfwj3nps2wx8m6jx9bh_gslc0000gn/T/tmp66UdKS2016-3-2-14-18_instant_03d12e83a6b5aa9b239a298463abdcc634c8d453/dolfin_compile_code_c8b988ab6016262c9eebd6dc8482b98c0cf05c33/dolfin_compile_code_c8b988ab6016262c9eebd6dc8482b98c0cf05c33.i:187: Warning 315: Nothing known about 'std::sqrt'. /private/var/folders/nl/wfwj3nps2wx8m6jx9bh_gslc0000gn/T/tmp66UdKS2016-3-2-14-18_instant_03d12e83a6b5aa9b239a298463abdcc634c8d453/dolfin_compile_code_c8b988ab6016262c9eebd6dc8482b98c0cf05c33/dolfin_compile_code_c8b988ab6016262c9eebd6dc8482b98c0cf05c33.i:188: Warning 315: Nothing known about 'std::ceil'. /private/var/folders/nl/wfwj3nps2wx8m6jx9bh_gslc0000gn/T/tmp66UdKS2016-3-2-14-18_instant_03d12e83a6b5aa9b239a298463abdcc634c8d453/dolfin_compile_code_c8b988ab6016262c9eebd6dc8482b98c0cf05c33/dolfin_compile_code_c8b988ab6016262c9eebd6dc8482b98c0cf05c33.i:189: Warning 315: Nothing known about 'std::fabs'. /private/var/folders/nl/wfwj3nps2wx8m6jx9bh_gslc0000gn/T/tmp66UdKS2016-3-2-14-18_instant_03d12e83a6b5aa9b239a298463abdcc634c8d453/dolfin_compile_code_c8b988ab6016262c9eebd6dc8482b98c0cf05c33/dolfin_compile_code_c8b988ab6016262c9eebd6dc8482b98c0cf05c33.i:190: Warning 315: Nothing known about 'std::floor'. /private/var/folders/nl/wfwj3nps2wx8m6jx9bh_gslc0000gn/T/tmp66UdKS2016-3-2-14-18_instant_03d12e83a6b5aa9b239a298463abdcc634c8d453/dolfin_compile_code_c8b988ab6016262c9eebd6dc8482b98c0cf05c33/dolfin_compile_code_c8b988ab6016262c9eebd6dc8482b98c0cf05c33.i:191: Warning 315: Nothing known about 'std::fmod'. /private/var/folders/nl/wfwj3nps2wx8m6jx9bh_gslc0000gn/T/tmp66UdKS2016-3-2-14-18_instant_03d12e83a6b5aa9b239a298463abdcc634c8d453/dolfin_compile_code_c8b988ab6016262c9eebd6dc8482b98c0cf05c33/dolfin_compile_code_c8b988ab6016262c9eebd6dc8482b98c0cf05c33.i:192: Warning 315: Nothing known about 'std::max'. /private/var/folders/nl/wfwj3nps2wx8m6jx9bh_gslc0000gn/T/tmp66UdKS2016-3-2-14-18_instant_03d12e83a6b5aa9b239a298463abdcc634c8d453/dolfin_compile_code_c8b988ab6016262c9eebd6dc8482b98c0cf05c33/dolfin_compile_code_c8b988ab6016262c9eebd6dc8482b98c0cf05c33.i:193: Warning 315: Nothing known about 'std::min'. cd /private/var/folders/nl/wfwj3nps2wx8m6jx9bh_gslc0000gn/T/tmp66UdKS2016-3-2-14-18_instant_03d12e83a6b5aa9b239a298463abdcc634c8d453/dolfin_compile_code_c8b988ab6016262c9eebd6dc8482b98c0cf05c33 && /usr/local/Cellar/cmake/3.4.3/bin/cmake -E cmake_depends "Unix Makefiles" 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/private/var/folders/nl/wfwj3nps2wx8m6jx9bh_gslc0000gn/T/tmp66UdKS2016-3-2-14-18_instant_03d12e83a6b5aa9b239a298463abdcc634c8d453/dolfin_compile_code_c8b988ab6016262c9eebd6dc8482b98c0cf05c33/CMakeFiles/_dolfin_compile_code_c8b988ab6016262c9eebd6dc8482b98c0cf05c33.dir/DependInfo.cmake --color= Dependee "/private/var/folders/nl/wfwj3nps2wx8m6jx9bh_gslc0000gn/T/tmp66UdKS2016-3-2-14-18_instant_03d12e83a6b5aa9b239a298463abdcc634c8d453/dolfin_compile_code_c8b988ab6016262c9eebd6dc8482b98c0cf05c33/CMakeFiles/_dolfin_compile_code_c8b988ab6016262c9eebd6dc8482b98c0cf05c33.dir/DependInfo.cmake" is newer than depender "/private/var/folders/nl/wfwj3nps2wx8m6jx9bh_gslc0000gn/T/tmp66UdKS2016-3-2-14-18_instant_03d12e83a6b5aa9b239a298463abdcc634c8d453/dolfin_compile_code_c8b988ab6016262c9eebd6dc8482b98c0cf05c33/CMakeFiles/_dolfin_compile_code_c8b988ab6016262c9eebd6dc8482b98c0cf05c33.dir/depend.internal". 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/usr/local/Cellar/vtk/7.0.0/lib/libvtkFiltersSources-7.0.1.dylib /usr/local/Cellar/vtk/7.0.0/lib/libvtkFiltersGeneral-7.0.1.dylib /usr/local/Cellar/vtk/7.0.0/lib/libvtkFiltersCore-7.0.1.dylib /usr/local/Cellar/vtk/7.0.0/lib/libvtkCommonExecutionModel-7.0.1.dylib /usr/local/Cellar/vtk/7.0.0/lib/libvtkCommonComputationalGeometry-7.0.1.dylib /usr/local/Cellar/vtk/7.0.0/lib/libvtkCommonDataModel-7.0.1.dylib /usr/local/Cellar/vtk/7.0.0/lib/libvtkCommonMisc-7.0.1.dylib /usr/local/Cellar/vtk/7.0.0/lib/libvtkCommonTransforms-7.0.1.dylib /usr/local/Cellar/vtk/7.0.0/lib/libvtkCommonMath-7.0.1.dylib /usr/local/Cellar/vtk/7.0.0/lib/libvtkCommonSystem-7.0.1.dylib /usr/local/Cellar/vtk/7.0.0/lib/libvtkCommonCore-7.0.1.dylib /usr/local/Cellar/vtk/7.0.0/lib/libvtksys-7.0.1.dylib /usr/local/Cellar/vtk/7.0.0/lib/libvtkfreetype-7.0.1.dylib /usr/lib/libz.dylib -framework ApplicationServices -framework CoreServices -Wl,-rpath,/usr/local/Cellar/dolfin/1.6.0/lib ld: file not found: /System/Library/Frameworks/CoreServices.framework/Versions/A/Frameworks/SharedFileList.framework/Versions/A/SharedFileList for architecture x86_64 clang: error: linker command failed with exit code 1 (use -v to see invocation) make[2]: * [_dolfin_compile_code_c8b988ab6016262c9eebd6dc8482b98c0cf05c33.so] Error 1 make[1]: * [CMakeFiles/_dolfin_compile_code_c8b988ab6016262c9eebd6dc8482b98c0cf05c33.dir/all] Error 2 make: *\ [all] Error 2

dpo commented 8 years ago

Here's the error message:

ld: file not found: /System/Library/Frameworks/CoreServices.framework/Versions/A/Frameworks/SharedFileList.framework/Versions/A/SharedFileList for architecture x86_64

I'm not sure where that comes from but I notice that your Xcode uses the MacOSX10.11.sdk SDK while you're on 10.10. Without really knowing what the issue is, what I could suggest is to brew edit dolfin and insert

-DCMAKE_OSX_DEPLOYMENT_TARGET:STRING=10.10

between lines 59 and 60, and brew reinstall dolfin.

francispoulin commented 8 years ago

Strange. I am running OS 10.10 and xcode is 7.2.1. If you are using 10.10 I'd be curious to know what xcode you are running.

I did the reinstall and instant-clean but came up with the same error, the tail is copied below.

ld: file not found: /System/Library/Frameworks/CoreServices.framework/Versions/A/Frameworks/SharedFileList.framework/Versions/A/SharedFileList for architecture x86_64 clang: error: linker command failed with exit code 1 (use -v to see invocation) make[2]: * [_dolfin_compile_code_c8b988ab6016262c9eebd6dc8482b98c0cf05c33.so] Error 1 make[1]: * [CMakeFiles/_dolfin_compile_code_c8b988ab6016262c9eebd6dc8482b98c0cf05c33.dir/all] Error 2 make: *\ [all] Error 2

Can find right version of xcode if you think that would help.

dpo commented 8 years ago

I'm not running 10.10 but I'll give it a go on a 10.10 machine asap. Either some dependency did something wrong, or there's an issue with Xcode.

francispoulin commented 8 years ago

If you know that it works on 10.11 I can upgrade to that. But it would be nice if it worked on 10.10.

dpo commented 8 years ago

Ok I have it working on a fresh 10.10 system with system Python. I'll send you instructions soon and we'll see if it works for you too.

dpo commented 8 years ago

Could you let me know if this works for you? https://gist.github.com/6a370d9f6e57dcb78224 @lukeolson

If anything breaks, try brew uninstall -f $(brew deps --recursive dolfin) to wipe all dependencies and start over. You might have to pip uninstall previously-installed deps, such as ply, petsc4py, etc.

dpo commented 8 years ago

Actually, it builds fine but I get the same SharedFileList error as you do. I wonder if that's a bug in Xcode.

francispoulin commented 8 years ago

I started from scratch, using system Python this time, and I'm getting an error, see below.

If you think it's an Xcode problem I am happy to contact the developers of Xcode, but it'd be nice to have a simple test case to show them.

==> cmake .. -DCMAKE_INSTALL_PREFIX=/usr/local/Cellar/dolfin/1.6.0 -DBUILD_SHARED_LIBS:BOOL=ON -DDOLFIN_ENABLE_PYTHON:BOOL=ON -DDOLFIN_INSTALL_PYTHON_MODULE_DIR=/usr/local/Cellar/dolfin/1.6. Last 15 lines from /Users/fpoulin/Library/Logs/Homebrew/dolfin/01.cmake:

CMake Error at /Applications/CMake 2.8-10.app/Contents/share/cmake-2.8/Modules/Platform/Darwin.cmake:190 (message): CMAKE_OSX_DEPLOYMENT_TARGET is '10.10' but CMAKE_OSX_SYSROOT:

""

is not set to a MacOSX SDK with a recognized version. Either set CMAKE_OSX_SYSROOT to a valid SDK or set CMAKE_OSX_DEPLOYMENT_TARGET to empty. Call Stack (most recent call first): /Applications/CMake 2.8-10.app/Contents/share/cmake-2.8/Modules/CMakeSystemSpecificInformation.cmake:36 (include) CMakeLists.txt:9 (project)

-- Configuring incomplete, errors occurred!

dpo commented 8 years ago

In my case CMAKE_OSX_DEPLOYMENT_TARGET is 10.10 and CMAKE_OSX_SYSROOT points to the MacOSX10.11.sdk, and I get the failure from the log file you posted. Something else is going on. On 10.9, it works fine.

francispoulin commented 8 years ago

Do you think it is worth while trying either of these two options?

either set CMAKE_OSX_SYSROOT to a valid SDK or set CMAKE_OSX_DEPLOYMENT_TARGET to empty.

dpo commented 8 years ago

It's worth a try. You can directly modify the Homebrew formula with brew edit dolfin.

francispoulin commented 8 years ago

I trying to set CMAKE_OSX_SYSROOT and added this line

francispoulin commented 8 years ago 
                -DCMAKE_OSX_SYSROOT=/Developer/SDKs/MacOSX10.6.sdk/

since I looked in the folder and saw there was 10.5 and 10.6.

Francis-Poulins-MacBook-Pro:~ fpoulin$ ls /Developer/SDKs/ MacOSX10.5.sdk MacOSX10.6.sdk

But it gives me an error that the DEPLOYMENT_TARGET should be 10.6 or lower. Could it be that these two options are using a different convention?

CMake Error at /Applications/CMake 2.8-10.app/Contents/share/cmake-2.8/Modules/Platform/Darwin.cmake:198 (message): CMAKE_OSX_DEPLOYMENT_TARGET (10.10) is greater than CMAKE_OSX_SYSROOT SDK:

/Developer/SDKs/MacOSX10.6.sdk

Please set CMAKE_OSX_DEPLOYMENT_TARGET to 10.6 or lower.

dpo commented 8 years ago

I think it should be something like /Applications/Xcode.app/Contents/Developer/Platforms/MacOSX.platform/Developer/SDKs/...

dpo commented 8 years ago

ps: you don't seem to be using Homebrew cmake. Perhaps that's another issue.

francispoulin commented 8 years ago

Thanks.

If you tell me how to change cmake I'm happy to do that. I tried it with only changing the path above and get a bit further, but still errors. Maybe changing my cmake would help?

==> cmake .. -DCMAKE_INSTALL_PREFIX=/usr/local/Cellar/dolfin/1.6.0 -DCMAKE_OSX_SYSROOT=/Applications/Xcode.app/Contents/Developer/Platforms/MacOSX.platform/Developer/SDKs/MacOSX10.11.sdk -DB Last 15 lines from /Users/fpoulin/Library/Logs/Homebrew/dolfin/01.cmake: -- Looking for Q_WS_QWS -- Looking for Q_WS_QWS - not found -- Looking for Q_WS_MAC -- Looking for Q_WS_MAC - found -- Looking for QT_MAC_USE_COCOA -- Looking for QT_MAC_USE_COCOA - found -- Found Qt4: /usr/local/bin/qmake (found version "4.8.7") CMake Error at /usr/local/Cellar/vtk/7.0.0/lib/cmake/vtk-7.0/VTKTargets.cmake:1393 (message): This file relies on consumers using CMake 2.8.12 or greater. Call Stack (most recent call first): /usr/local/lib/cmake/vtk-7.0/VTKConfig.cmake:68 (include) CMakeLists.txt:602 (find_package)

-- Configuring incomplete, errors occurred!

francispoulin commented 8 years ago

I did a couple of things: 1) I installed cmake with hombrew. 2) I changed my path so that /usr/local/bin is before /usr/local now make is taking a lot longer. A good sign. Will let you know what happens.

francispoulin commented 8 years ago

I went through all the tests and all of them look good, except for ffc.

I copy the first part below but gcc compilation fails for every of the 227 elements.

Verifying evaluate_basis and evaluate_basis_derivatives for elements

Verifying element 1 of 227: <CG1 on a <Domain built from <interval cell in 1D> with label None>> GCC compilation failed.

Verifying element 2 of 227: <CG2 on a <Domain built from <interval cell in 1D> with label None>> GCC compilation failed.

dpo commented 8 years ago

Why is it using gcc?