[firedrake] FD on mac

[David Ham]

On Thu, 26 Nov 2015 at 13:12 Floriane Gidel [RPG] <mmfg at leeds.ac.uk> wrote:

>
> Dear all,
>
>
> Onno and I still have problem when trying to update/install Firedrake on
> our mac, at different stages. Here are the errors we get:
>
>
> I first tried to update FD, but the command to update petsc4py (pip
> install -U --no-deps git+
> https://bitbucket.org/mapdes/petsc4py.git@firedrake#egg=petsc4py) was
> taking all the application memory of the computer, and the computer just
> crashed in the end.
>
>
> So I tried to re-install Firedrake from scratch, but I still have an issue
> when trying to install petsc4py:
>
>
> - when installing Petsc, it installs version 3.7.0; I get the following
> message :
>
>
> Installing collected packages: petsc
>
>   Found existing installation: petsc 3.6.2
>
>     Uninstalling petsc-3.6.2:
>
>       Successfully uninstalled petsc-3.6.2
>
>   Running setup.py install for petsc
>
> Successfully installed petsc-3.7.0.dev0
>
> - when I then try to install petsc4py, I've got an error saying that the
> version of petsc needed must be lower than 3.7.0 :
>
> Collecting petsc<3.7,>=3.6 (from petsc4py)
>
>   Could not find a version that satisfies the requirement petsc<3.7,>=3.6
> (from petsc4py) (from versions: )
>
>   Some externally hosted files were ignored as access to them may be
> unreliable (use --allow-external petsc to allow).
>
> No matching distribution found for petsc<3.7,>=3.6 (from petsc4py)
>
>
This error is usually a symptom of failing to pass --no-deps to the
petsc4py build (it's a bug in upstream petsc4py really but --no-deps is
usually an adequate work around).

Regards,

David


> I tried to allow external petsc by adding the option '--allow-external
> petsc', but I then have a fatal error  :
>
> fatal error: too many errors emitted, stopping now [-ferror-limit=]
>
>     1 warning and 20 errors generated.
>
>     error: command '/usr/local/bin/mpicc' failed with exit status 1
>
> and this comment:
>
> Command "/Users/mmfg/anaconda/bin/python -c "import setuptools,
> tokenize;__file__='/private/tmp/pip-build-8fgPi3/petsc4py/setup.py';exec(compile(getattr(tokenize,
> 'open', open)(__file__).read().replace('\r\n', '\n'), __file__, 'exec'))"
> install --record /tmp/pip-u2WItt-record/install-record.txt
> --single-version-externally-managed --compile" failed with error code 1 in
> /private/tmp/pip-build-8fgPi3/petsc4py
>
> I have also tried to install FD using your script, but I get error as well
> :
>
> Creating firedrake virtualenv.
>
> Traceback (most recent call last):
>
>   File "firedrake-install", line 527, in <module>
>
>     virtualenv.create_environment("firedrake", site_packages=True)
>
>   File "/Users/mmfg/.local/lib/python2.7/site-packages/virtualenv.py",
> line 1004, in create_environment
>
>     install_wheel(to_install, py_executable, search_dirs)
>
>   File "/Users/mmfg/.local/lib/python2.7/site-packages/virtualenv.py",
> line 969, in install_wheel
>
>     'PIP_NO_INDEX': '1'
>
>   File "/Users/mmfg/.local/lib/python2.7/site-packages/virtualenv.py",
> line 910, in call_subprocess
>
>     % (cmd_desc, proc.returncode))
>
> OSError: Command /Users/mmfg/anaconda/bin/firedrake/bin/python -c "import
> sys, pip; sys...d\"] + sys.argv[1:]))" setuptools pip wheel failed with
> error code 1
>
> Moreover, Onno gets stalled as well at his macbook pro at:
>
>
> campus-10-41-94-68:werk amtob$ PETSC_CONFIGURE_OPTIONS="--download-ctetgen
> --download-triangle --download-chaco --download-hdf5" \
>
> >   pip install https://bitbucket.org/mapdes/petsc/get/firedrake.tar.bz2
>
> Collecting https://bitbucket.org/mapdes/petsc/get/firedrake.tar.bz2
>
>   Downloading https://bitbucket.org/mapdes/petsc/get/firedrake.tar.bz2
> (12.1MB)
>
>     100% |████████████████████████████████| 12.1MB 40kB/s
>
> Installing collected packages: petsc
>
>   Running setup.py install for petsc
>
>     Complete output from command /usr/local/opt/python/bin/python2.7 -c
> "import setuptools,
> tokenize;__file__='/var/folders/c0/rzc18gxj0619yv1l5zqlbrssh33xh5/T/pip-5zNG1S-build/setup.py';exec(compile(getattr(tokenize,
> 'open', open)(__file__).read().replace('\r\n', '\n'), __file__, 'exec'))"
> install --record
> /var/folders/c0/rzc18gxj0619yv1l5zqlbrssh33xh5/T/pip-I6eRXQ-record/install-record.txt
> --single-version-externally-managed --compile:
>
>     running install
>
>     PETSc: configure
>
>     configure options:
>
>         --prefix=/usr/local/lib/python2.7/site-packages/petsc
>
>         PETSC_ARCH=arch-python-macosx-10.9-x86_64
>
>         --with-shared-libraries=1
>
>         --with-debugging=0
>
>         --with-c2html=0
>
>         --with-cc=/usr/local/bin/mpicc
>
>         --with-cxx=/usr/local/bin/mpicxx
>
>         --with-fc=/usr/local/bin/mpif90
>
>         --download-ctetgen
>
>         --download-triangle
>
>         --download-chaco
>
>         --download-hdf5
>
>
> ===============================================================================
>
>                  Configuring PETSc to compile on your system
>
>
> ===============================================================================
>
>     TESTING: configureExternalPackagesDir from
> config.framework(/private/var/folders/c0/rzc18gxj0619yv1l5zqlbrssh33xh5/T/pip-5zNG1S-build/config/BuildSystem/config/framework.py:833)
>
>     TESTING: configureDebuggers from
> config.utilities.debuggers(/private/var/folders/c0/rzc18gxj0619yv1l5zqlbrssh33xh5/T/pip-5zNG1S-build/config/BuildSystem/config/utilities/debuggers.py:22)
>
>     TESTING: configureGit from
> config.sourceControl(/private/var/folders/c0/rzc18gxj0619yv1l5zqlbrssh33xh5/T/pip-5zNG1S-build/config/BuildSystem/config/sourceControl.py:24)
>
>     TESTING: configureCLanguage from
> PETSc.options.languages(/private/var/folders/c0/rzc18gxj0619yv1l5zqlbrssh33xh5/T/pip-5zNG1S-build/config/PETSc/options/languages.py:27)
>
>     TESTING: configureDirectories from
> PETSc.options.petscdir(/private/var/folders/c0/rzc18gxj0619yv1l5zqlbrssh33xh5/T/pip-5zNG1S-build/config/PETSc/options/petscdir.py:23)
>
>     TESTING: configureInstallationMethod from
> PETSc.options.petscclone(/private/var/folders/c0/rzc18gxj0619yv1l5zqlbrssh33xh5/T/pip-5zNG1S-build/config/PETSc/options/petscclone.py:20)
>
>     TESTING: getDatafilespath from
> PETSc.options.dataFilesPath(/private/var/folders/c0/rzc18gxj0619yv1l5zqlbrssh33xh5/T/pip-5zNG1S-build/config/PETSc/options/dataFilesPath.py:29)
>
>     TESTING: configureArchitecture from
> PETSc.options.arch(/private/var/folders/c0/rzc18gxj0619yv1l5zqlbrssh33xh5/T/pip-5zNG1S-build/config/PETSc/options/arch.py:25)
>
>     TESTING: setInstallDir from
> PETSc.options.installDir(/private/var/folders/c0/rzc18gxj0619yv1l5zqlbrssh33xh5/T/pip-5zNG1S-build/config/PETSc/options/installDir.py:35)
>
>     TESTING: saveReconfigure from
> PETSc.options.installDir(/private/var/folders/c0/rzc18gxj0619yv1l5zqlbrssh33xh5/T/pip-5zNG1S-build/config/PETSc/options/installDir.py:74)
>
>     TESTING: cleanInstallDir from
> PETSc.options.installDir(/private/var/folders/c0/rzc18gxj0619yv1l5zqlbrssh33xh5/T/pip-5zNG1S-build/config/PETSc/options/installDir.py:67)
>
>     TESTING: configureInstallDir from
> PETSc.options.installDir(/private/var/folders/c0/rzc18gxj0619yv1l5zqlbrssh33xh5/T/pip-5zNG1S-build/config/PETSc/options/installDir.py:51)
>
>     TESTING: restoreReconfigure from
> PETSc.options.installDir(/private/var/folders/c0/rzc18gxj0619yv1l5zqlbrssh33xh5/T/pip-5zNG1S-build/config/PETSc/options/installDir.py:87)
>
>     TESTING: setExternalPackagesDir from
> PETSc.options.externalpackagesdir(/private/var/folders/c0/rzc18gxj0619yv1l5zqlbrssh33xh5/T/pip-5zNG1S-build/config/PETSc/options/externalpackagesdir.py:15)
>
>     TESTING: cleanExternalpackagesDir from
> PETSc.options.externalpackagesdir(/private/var/folders/c0/rzc18gxj0619yv1l5zqlbrssh33xh5/T/pip-5zNG1S-build/config/PETSc/options/externalpackagesdir.py:22)
>
>     TESTING: printEnvVariables from
> config.setCompilers(/private/var/folders/c0/rzc18gxj0619yv1l5zqlbrssh33xh5/T/pip-5zNG1S-build/config/BuildSystem/config/setCompilers.py:1572)
>
>     TESTING: resetEnvCompilers from
> config.setCompilers(/private/var/folders/c0/rzc18gxj0619yv1l5zqlbrssh33xh5/T/pip-5zNG1S-build/config/BuildSystem/config/setCompilers.py:1579)
>
>     TESTING: checkEnvCompilers from
> config.setCompilers(/private/var/folders/c0/rzc18gxj0619yv1l5zqlbrssh33xh5/T/pip-5zNG1S-build/config/BuildSystem/config/setCompilers.py:1609)
>
>     TESTING: checkMPICompilerOverride from
> config.setCompilers(/private/var/folders/c0/rzc18gxj0619yv1l5zqlbrssh33xh5/T/pip-5zNG1S-build/config/BuildSystem/config/setCompilers.py:1544)
>
>     TESTING: requireMpiLdPath from
> config.setCompilers(/private/var/folders/c0/rzc18gxj0619yv1l5zqlbrssh33xh5/T/pip-5zNG1S-build/config/BuildSystem/config/setCompilers.py:1563)
>
>     TESTING: checkVendor from
> config.setCompilers(/private/var/folders/c0/rzc18gxj0619yv1l5zqlbrssh33xh5/T/pip-5zNG1S-build/config/BuildSystem/config/setCompilers.py:402)
>
>     TESTING: checkInitialFlags from
> config.setCompilers(/private/var/folders/c0/rzc18gxj0619yv1l5zqlbrssh33xh5/T/pip-5zNG1S-build/config/BuildSystem/config/setCompilers.py:412)
>
>     TESTING: checkCCompiler from
> config.setCompilers(/private/var/folders/c0/rzc18gxj0619yv1l5zqlbrssh33xh5/T/pip-5zNG1S-build/config/BuildSystem/config/setCompilers.py:538)
>
>     TESTING: checkCPreprocessor from
> config.setCompilers(/private/var/folders/c0/rzc18gxj0619yv1l5zqlbrssh33xh5/T/pip-5zNG1S-build/config/BuildSystem/config/setCompilers.py:571)
>
>     TESTING: checkCUDACompiler from
> config.setCompilers(/private/var/folders/c0/rzc18gxj0619yv1l5zqlbrssh33xh5/T/pip-5zNG1S-build/config/BuildSystem/config/setCompilers.py:612)
>
>     TESTING: checkCUDAPreprocessor from
> config.setCompilers(/private/var/folders/c0/rzc18gxj0619yv1l5zqlbrssh33xh5/T/pip-5zNG1S-build/config/BuildSystem/config/setCompilers.py:652)
>
>     TESTING: checkCxxCompiler from
> config.setCompilers(/private/var/folders/c0/rzc18gxj0619yv1l5zqlbrssh33xh5/T/pip-5zNG1S-build/config/BuildSystem/config/setCompilers.py:764)
>
>     TESTING: checkCxxPreprocessor from
> config.setCompilers(/private/var/folders/c0/rzc18gxj0619yv1l5zqlbrssh33xh5/T/pip-5zNG1S-build/config/BuildSystem/config/setCompilers.py:802)
>
>     TESTING: checkFortranCompiler from
> config.setCompilers(/private/var/folders/c0/rzc18gxj0619yv1l5zqlbrssh33xh5/T/pip-5zNG1S-build/config/BuildSystem/config/setCompilers.py:919)
>
>
> *******************************************************************************
>
>                         UNABLE to EXECUTE BINARIES for ./configure
>
>
> -------------------------------------------------------------------------------
>
>     Cannot run executables created with FC. If this machine uses a batch
> system
>
>     to submit jobs you will need to configure using ./configure with the
> additional option  --with-batch.
>
>      Otherwise there is problem with the compilers. Can you compile and
> run code with your compiler '/usr/local/bin/mpif90'?
>
>
> *******************************************************************************
>
>
>
>     Traceback (most recent call last):
>
>       File "<string>", line 1, in <module>
>
>       File
> "/var/folders/c0/rzc18gxj0619yv1l5zqlbrssh33xh5/T/pip-5zNG1S-build/setup.py",
> line 302, in <module>
>
>         **metadata)
>
>       File
> "/usr/local/Cellar/python/2.7.10_2/Frameworks/Python.framework/Versions/2.7/lib/python2.7/distutils/core.py",
> line 151, in setup
>
>         dist.run_commands()
>
>       File
> "/usr/local/Cellar/python/2.7.10_2/Frameworks/Python.framework/Versions/2.7/lib/python2.7/distutils/dist.py",
> line 953, in run_commands
>
>         self.run_command(cmd)
>
>       File
> "/usr/local/Cellar/python/2.7.10_2/Frameworks/Python.framework/Versions/2.7/lib/python2.7/distutils/dist.py",
> line 972, in run_command
>
>         cmd_obj.run()
>
>       File
> "/var/folders/c0/rzc18gxj0619yv1l5zqlbrssh33xh5/T/pip-5zNG1S-build/setup.py",
> line 218, in run
>
>         config(prefix, self.dry_run)
>
>       File
> "/var/folders/c0/rzc18gxj0619yv1l5zqlbrssh33xh5/T/pip-5zNG1S-build/setup.py",
> line 148, in config
>
>         if status != 0: raise RuntimeError(status)
>
>     RuntimeError: 256
>
>
>
>     ----------------------------------------
>
> Command "/usr/local/opt/python/bin/python2.7 -c "import setuptools,
> tokenize;__file__='/var/folders/c0/rzc18gxj0619yv1l5zqlbrssh33xh5/T/pip-5zNG1S-build/setup.py';exec(compile(getattr(tokenize,
> 'open', open)(__file__).read().replace('\r\n', '\n'), __file__, 'exec'))"
> install --record
> /var/folders/c0/rzc18gxj0619yv1l5zqlbrssh33xh5/T/pip-I6eRXQ-record/install-record.txt
> --single-version-externally-managed --compile" failed with error code 1 in
> /var/folders/c0/rzc18gxj0619yv1l5zqlbrssh33xh5/T/pip-5zNG1S-build
>
>
> Best regards,
> Floriane
>
> ------------------------------
> *De :* firedrake-bounces at imperial.ac.uk <firedrake-bounces at imperial.ac.uk>
> de la part de David Ham <David.Ham at imperial.ac.uk>
> *Envoyé :* mercredi 25 novembre 2015 12:03
> *À :* firedrake
> *Objet :* Re: [firedrake] FD on mac
>
> Hi all,
>
> It turns out that this is a problem in PETSc caused by a "fix" to a
> different OSX problem. We have reverted the offending commit on the
> firedrake/petsc fork so hopefully updating now should fix the issue. Please
> scream immediately if it does not.
>
> Regards,
>
> David
>
> On Tue, 24 Nov 2015 at 22:23 David Ham <David.Ham at imperial.ac.uk> wrote:
>
>> Reproduced. Very odd, it seems petsc4py is currently borked. I don't
>> understand where this library location is coming from. It certainly isn't
>> where the petsc python module reports the python being installed.
>>
>> On Tue, 24 Nov 2015 at 22:06 David Ham <David.Ham at imperial.ac.uk> wrote:
>>
>>> OK. I'm doing a scratch rebuild to see if I can reproduce this.
>>>
>>> David
>>>
>>> On Tue, 24 Nov 2015 at 21:33 Justin Chang <jychang48 at gmail.com> wrote:
>>>
>>>> Hi all,
>>>>
>>>> Just wanted to say that I am also now having these exact same issues as
>>>> others after updating Firedrake on my mac.
>>>>
>>>> Thanks,
>>>> Justin
>>>>
>>>> On Tue, Nov 24, 2015 at 6:11 AM, Lawrence Mitchell <
>>>> lawrence.mitchell at imperial.ac.uk> wrote:
>>>>
>>>>>
>>>>> On 23/11/15 16:52, Wingate, Beth wrote:
>>>>> >     module = imp.load_module(fullname, fo, fn, stuff)
>>>>> > ImportError:
>>>>> >
>>>>> dlopen(/Users/wingate/firedrake/lib/python2.7/site-packages/petsc4py/lib/PETSc.so,
>>>>> > 2): Library not loaded:
>>>>> >
>>>>> /private/var/folders/rw/1wgmdvd50sv7bb1dksy4y_l00000gq/T/pip-DOH6bI-build/arch-python-macosx-10.11-x86_64/lib/libpetsc.3.06.dylib
>>>>> >   Referenced from:
>>>>> >
>>>>> /Users/wingate/firedrake/lib/python2.7/site-packages/petsc4py/lib/PETSc.so
>>>>> >   Reason: image not found
>>>>>
>>>>>
>>>>> Hmph, petsc4py has linked against the temporary location of libpetsc
>>>>> (which appeared via pip presumably), rather than its final location.
>>>>>
>>>>> It is not immediately obvious to me why this would be the case.  I do
>>>>> not think it is likely anything wrong with your build setup though.
>>>>>
>>>>> Lawrence
>>>>>
>>>>>
>>>>> _______________________________________________
>>>>> firedrake mailing list
>>>>> firedrake at imperial.ac.uk
>>>>> https://mailman.ic.ac.uk/mailman/listinfo/firedrake
>>>>>
>>>>>
>>>>
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