[firedrake] FD on mac
Floriane Gidel [RPG]
mmfg at leeds.ac.uk
Thu Nov 26 12:12:16 GMT 2015
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)
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>
Envoye : mercredi 25 novembre 2015 12:03
A : 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<mailto: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<mailto: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<mailto: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<mailto: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
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