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@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@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@imperial.ac.uk https://mailman.ic.ac.uk/mailman/listinfo/firedrake
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@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@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@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@imperial.ac.uk https://mailman.ic.ac.uk/mailman/listinfo/firedrake
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@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@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@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@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@imperial.ac.uk https://mailman.ic.ac.uk/mailman/listinfo/firedrake
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@imperial.ac.uk <firedrake-bounces@imperial.ac.uk> de la part de David Ham <David.Ham@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@imperial.ac.uk<mailto:David.Ham@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@imperial.ac.uk<mailto:David.Ham@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@gmail.com<mailto:jychang48@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@imperial.ac.uk<mailto:lawrence.mitchell@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@imperial.ac.uk<mailto:firedrake@imperial.ac.uk> https://mailman.ic.ac.uk/mailman/listinfo/firedrake
On 26/11/15 12:12, Floriane Gidel [RPG] wrote:
Moreover, Onno gets stalled as well at his macbook pro at:
...
*******************************************************************************
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'?
*******************************************************************************
Well, can you run and compile code using mpif90? Cheers, Lawrence
I’m getting the same thing — firedrake now doesn’t install due to “mpif90” not working: TESTING: checkFortranCompiler from config.setCompilers(/private/var/folders/zn/46_9pn0x2k32_z59z6fw5j2w0000gn/T/pip-AO07XK-build/config/BuildSystem/config/setCompilers.py:919) ******************************************************************************* UNABLE to CONFIGURE with GIVEN OPTIONS (see configure.log for details): ------------------------------------------------------------------------------- Fortran compiler you provided with --with-fc=/usr/local/bin/mpif90 does not work. Cannot compile FC with /usr/local/bin/mpif90. ******************************************************************************* Traceback (most recent call last): File "<string>", line 1, in <module> File "/var/folders/zn/46_9pn0x2k32_z59z6fw5j2w0000gn/T/pip-AO07XK-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/zn/46_9pn0x2k32_z59z6fw5j2w0000gn/T/pip-AO07XK-build/setup.py", line 218, in run config(prefix, self.dry_run) File "/var/folders/zn/46_9pn0x2k32_z59z6fw5j2w0000gn/T/pip-AO07XK-build/setup.py", line 148, in config if status != 0: raise RuntimeError(status) RuntimeError: 256 On 26 Nov 2015, at 12:15 p.m., Lawrence Mitchell <lawrence.mitchell@imperial.ac.uk<mailto:lawrence.mitchell@imperial.ac.uk>> wrote: On 26/11/15 12:12, Floriane Gidel [RPG] wrote: Moreover, Onno gets stalled as well at his macbook pro at: ... ******************************************************************************* 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'? ******************************************************************************* Well, can you run and compile code using mpif90? Cheers, Lawrence _______________________________________________ firedrake mailing list firedrake@imperial.ac.uk<mailto:firedrake@imperial.ac.uk> https://mailman.ic.ac.uk/mailman/listinfo/firedrake Prof. Beth Wingate b.wingate@exeter.ac.uk<mailto:b.wingate@exeter.ac.uk> “The world is but a canvas to the imagination.” - Thoreau
That is what I got yesterday, but Floriane Gidel went past it on her mac laptop. Computer IT staff and I could not figure out what it was. We tried anaconda (worked with Floriane), but not with me. He thought my mpif90 was probably slightly older: so reloading Xcode an option? Updating the OS? ________________________________ From: firedrake-bounces@imperial.ac.uk <firedrake-bounces@imperial.ac.uk> on behalf of Wingate, Beth <B.Wingate@exeter.ac.uk> Sent: Friday, November 27, 2015 3:41 PM To: firedrake@imperial.ac.uk Subject: Re: [firedrake] FD on mac I'm getting the same thing - firedrake now doesn't install due to "mpif90" not working: TESTING: checkFortranCompiler from config.setCompilers(/private/var/folders/zn/46_9pn0x2k32_z59z6fw5j2w0000gn/T/pip-AO07XK-build/config/BuildSystem/config/setCompilers.py:919) ******************************************************************************* UNABLE to CONFIGURE with GIVEN OPTIONS (see configure.log for details): ------------------------------------------------------------------------------- Fortran compiler you provided with --with-fc=/usr/local/bin/mpif90 does not work. Cannot compile FC with /usr/local/bin/mpif90. ******************************************************************************* Traceback (most recent call last): File "<string>", line 1, in <module> File "/var/folders/zn/46_9pn0x2k32_z59z6fw5j2w0000gn/T/pip-AO07XK-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/zn/46_9pn0x2k32_z59z6fw5j2w0000gn/T/pip-AO07XK-build/setup.py", line 218, in run config(prefix, self.dry_run) File "/var/folders/zn/46_9pn0x2k32_z59z6fw5j2w0000gn/T/pip-AO07XK-build/setup.py", line 148, in config if status != 0: raise RuntimeError(status) RuntimeError: 256 On 26 Nov 2015, at 12:15 p.m., Lawrence Mitchell <lawrence.mitchell@imperial.ac.uk<mailto:lawrence.mitchell@imperial.ac.uk>> wrote: On 26/11/15 12:12, Floriane Gidel [RPG] wrote: Moreover, Onno gets stalled as well at his macbook pro at: ... ******************************************************************************* 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'? ******************************************************************************* Well, can you run and compile code using mpif90? Cheers, Lawrence _______________________________________________ firedrake mailing list firedrake@imperial.ac.uk<mailto:firedrake@imperial.ac.uk> https://mailman.ic.ac.uk/mailman/listinfo/firedrake Prof. Beth Wingate b.wingate@exeter.ac.uk<mailto:b.wingate@exeter.ac.uk> "The world is but a canvas to the imagination." - Thoreau
On 27 Nov 2015, at 15:44, Onno Bokhove <O.Bokhove@leeds.ac.uk> wrote:
That is what I got yesterday, but Floriane Gidel went past it on her mac laptop. Computer IT staff and I could not figure out what it was. We tried anaconda (worked with Floriane), but not with me. He thought my mpif90 was probably slightly older: so reloading Xcode an option? Updating the OS?
Hopefully not!
From: firedrake-bounces@imperial.ac.uk <firedrake-bounces@imperial.ac.uk> on behalf of Wingate, Beth <B.Wingate@exeter.ac.uk> Sent: Friday, November 27, 2015 3:41 PM To: firedrake@imperial.ac.uk Subject: Re: [firedrake] FD on mac
I’m getting the same thing — firedrake now doesn’t install due to “mpif90” not working:
TESTING: checkFortranCompiler from config.setCompilers(/private/var/folders/zn/46_9pn0x2k32_z59z6fw5j2w0000gn/T/pip-AO07XK-build/config/BuildSystem/config/setCompilers.py:919) ******************************************************************************* UNABLE to CONFIGURE with GIVEN OPTIONS (see configure.log for details): ------------------------------------------------------------------------------- Fortran compiler you provided with --with-fc=/usr/local/bin/mpif90 does not work. Cannot compile FC with /usr/local/bin/mpif90. *******************************************************************************
If you try to compile the following simple Fortran hello world code with mpif90, what happens? $ cat > hello.f90 << EOF program main use mph implicit none write(*, *)'Hello world' end program EOF $ mpif90 hello.f90 -o hello $ ./hello Cheers, Lawrence
Hi all, I also had the mpif90 error on my El Capitan Macbook, but worked around it by rebuilding the openmpi with the latest brew gcc compilers (GCC 5.2.0). It seems the default configuration provided by Homebrew is built with Apple's compilers (and thus has no wrapper for the mpif90). I put these in my ~/.profile: export HOMEBREW_CC=gcc-5 export HOMEBREW_CXX=g++-5 export FC=gfortran-5 and rebuilt openmpi via: brew reinstall openmpi --build-from-source Firedrake installs successfully, but now I am running into a spatialindex related problem whenever I try to import the firedrake module: python -c 'from firedrake import *' Traceback (most recent call last): File "<string>", line 1, in <module> File "/Users/justin/Software/firedrake/src/firedrake/firedrake/__init__.py", line 31, in <module> from firedrake.assemble import * File "/Users/justin/Software/firedrake/src/firedrake/firedrake/assemble.py", line 10, in <module> from firedrake import assemble_expressions File "/Users/justin/Software/firedrake/src/firedrake/firedrake/assemble_expressions.py", line 17, in <module> from firedrake import function File "/Users/justin/Software/firedrake/src/firedrake/firedrake/function.py", line 14, in <module> from firedrake import functionspace File "/Users/justin/Software/firedrake/src/firedrake/firedrake/functionspace.py", line 17, in <module> import firedrake.mesh as mesh_t File "/Users/justin/Software/firedrake/src/firedrake/firedrake/mesh.py", line 16, in <module> import firedrake.spatialindex as spatialindex ImportError: dlopen(/Users/justin/Software/firedrake/src/firedrake/firedrake/spatialindex.so, 2): Symbol not found: __ZN5Tools11PropertySet11setPropertyENSt7__cxx1112basic_stringIcSt11char_traitsIcESaIcEEERKNS_7VariantE Referenced from: /Users/justin/Software/firedrake/src/firedrake/firedrake/spatialindex.so Expected in: flat namespace in /Users/justin/Software/firedrake/src/firedrake/firedrake/spatialindex.so Looks like something went awry with spatialindex. Anyone else having this problem? Thanks, Justin On Fri, Nov 27, 2015 at 11:26 AM, Lawrence Mitchell < lawrence.mitchell@imperial.ac.uk> wrote:
On 27 Nov 2015, at 15:44, Onno Bokhove <O.Bokhove@leeds.ac.uk> wrote:
That is what I got yesterday, but Floriane Gidel went past it on her mac laptop. Computer IT staff and I could not figure out what it was. We tried anaconda (worked with Floriane), but not with me. He thought my mpif90 was probably slightly older: so reloading Xcode an option? Updating the OS?
Hopefully not!
From: firedrake-bounces@imperial.ac.uk <firedrake-bounces@imperial.ac.uk> on behalf of Wingate, Beth <B.Wingate@exeter.ac.uk> Sent: Friday, November 27, 2015 3:41 PM To: firedrake@imperial.ac.uk Subject: Re: [firedrake] FD on mac
I’m getting the same thing — firedrake now doesn’t install due to “mpif90” not working:
TESTING: checkFortranCompiler from config.setCompilers(/private/var/folders/zn/46_9pn0x2k32_z59z6fw5j2w0000gn/T/pip-AO07XK-build/config/BuildSystem/config/setCompilers.py:919)
*******************************************************************************
UNABLE to CONFIGURE with GIVEN OPTIONS (see
configure.log for details):
-------------------------------------------------------------------------------
Fortran compiler you provided with --with-fc=/usr/local/bin/mpif90
does not work.
Cannot compile FC with /usr/local/bin/mpif90.
*******************************************************************************
If you try to compile the following simple Fortran hello world code with mpif90, what happens?
$ cat > hello.f90 << EOF program main use mph implicit none write(*, *)'Hello world' end program EOF $ mpif90 hello.f90 -o hello $ ./hello
Cheers,
Lawrence
_______________________________________________ firedrake mailing list firedrake@imperial.ac.uk https://mailman.ic.ac.uk/mailman/listinfo/firedrake
With respect to the libspatialindex problem: Yes, see https://github.com/firedrakeproject/firedrake/issues/640 I suggest you to try rebuilding libspatialindex from source (you can do that with homebrew) using the same compiler as you used to build firedrake. On 28/11/15 07:11, Justin Chang wrote:
Hi all,
I also had the mpif90 error on my El Capitan Macbook, but worked around it by rebuilding the openmpi with the latest brew gcc compilers (GCC 5.2.0). It seems the default configuration provided by Homebrew is built with Apple's compilers (and thus has no wrapper for the mpif90). I put these in my ~/.profile:
export HOMEBREW_CC=gcc-5 export HOMEBREW_CXX=g++-5 export FC=gfortran-5
and rebuilt openmpi via:
brew reinstall openmpi --build-from-source
Firedrake installs successfully, but now I am running into a spatialindex related problem whenever I try to import the firedrake module:
python -c 'from firedrake import *'
Traceback (most recent call last):
File "<string>", line 1, in <module>
File "/Users/justin/Software/firedrake/src/firedrake/firedrake/__init__.py", line 31, in <module>
from firedrake.assemble import *
File "/Users/justin/Software/firedrake/src/firedrake/firedrake/assemble.py", line 10, in <module>
from firedrake import assemble_expressions
File "/Users/justin/Software/firedrake/src/firedrake/firedrake/assemble_expressions.py", line 17, in <module>
from firedrake import function
File "/Users/justin/Software/firedrake/src/firedrake/firedrake/function.py", line 14, in <module>
from firedrake import functionspace
File "/Users/justin/Software/firedrake/src/firedrake/firedrake/functionspace.py", line 17, in <module>
import firedrake.mesh as mesh_t
File "/Users/justin/Software/firedrake/src/firedrake/firedrake/mesh.py", line 16, in <module>
import firedrake.spatialindex as spatialindex
ImportError: dlopen(/Users/justin/Software/firedrake/src/firedrake/firedrake/spatialindex.so, 2): Symbol not found: __ZN5Tools11PropertySet11setPropertyENSt7__cxx1112basic_stringIcSt11char_traitsIcESaIcEEERKNS_7VariantE
Referenced from: /Users/justin/Software/firedrake/src/firedrake/firedrake/spatialindex.so
Expected in: flat namespace
in /Users/justin/Software/firedrake/src/firedrake/firedrake/spatialindex.so
Looks like something went awry with spatialindex. Anyone else having this problem?
Thanks, Justin
On Fri, Nov 27, 2015 at 11:26 AM, Lawrence Mitchell <lawrence.mitchell@imperial.ac.uk <mailto:lawrence.mitchell@imperial.ac.uk>> wrote:
> On 27 Nov 2015, at 15:44, Onno Bokhove <O.Bokhove@leeds.ac.uk <mailto:O.Bokhove@leeds.ac.uk>> wrote: > > That is what I got yesterday, but Floriane Gidel went past it on her mac laptop. > Computer IT staff and I could not figure out what it was. > We tried anaconda (worked with Floriane), but not with me. > He thought my mpif90 was probably slightly older: so reloading Xcode an option? > Updating the OS?
Hopefully not!
> From: firedrake-bounces@imperial.ac.uk <mailto:firedrake-bounces@imperial.ac.uk> <firedrake-bounces@imperial.ac.uk <mailto:firedrake-bounces@imperial.ac.uk>> on behalf of Wingate, Beth <B.Wingate@exeter.ac.uk <mailto:B.Wingate@exeter.ac.uk>> > Sent: Friday, November 27, 2015 3:41 PM > To: firedrake@imperial.ac.uk <mailto:firedrake@imperial.ac.uk> > Subject: Re: [firedrake] FD on mac > > I’m getting the same thing — firedrake now doesn’t install due to “mpif90” not working: > > TESTING: checkFortranCompiler from config.setCompilers(/private/var/folders/zn/46_9pn0x2k32_z59z6fw5j2w0000gn/T/pip-AO07XK-build/config/BuildSystem/config/setCompilers.py:919) > ******************************************************************************* > UNABLE to CONFIGURE with GIVEN OPTIONS (see configure.log for details): > ------------------------------------------------------------------------------- > Fortran compiler you provided with --with-fc=/usr/local/bin/mpif90 does not work. > Cannot compile FC with /usr/local/bin/mpif90. > *******************************************************************************
If you try to compile the following simple Fortran hello world code with mpif90, what happens?
$ cat > hello.f90 << EOF program main use mph implicit none write(*, *)'Hello world' end program EOF $ mpif90 hello.f90 -o hello $ ./hello
Cheers,
Lawrence
_______________________________________________ firedrake mailing list firedrake@imperial.ac.uk <mailto:firedrake@imperial.ac.uk> https://mailman.ic.ac.uk/mailman/listinfo/firedrake
_______________________________________________ firedrake mailing list firedrake@imperial.ac.uk https://mailman.ic.ac.uk/mailman/listinfo/firedrake
Ah right, didn't think about that. Got it, thanks! On Sat, Nov 28, 2015 at 3:35 AM, Miklós Homolya <m.homolya14@imperial.ac.uk> wrote:
With respect to the libspatialindex problem:
Yes, see https://github.com/firedrakeproject/firedrake/issues/640
I suggest you to try rebuilding libspatialindex from source (you can do that with homebrew) using the same compiler as you used to build firedrake.
On 28/11/15 07:11, Justin Chang wrote:
Hi all,
I also had the mpif90 error on my El Capitan Macbook, but worked around it by rebuilding the openmpi with the latest brew gcc compilers (GCC 5.2.0). It seems the default configuration provided by Homebrew is built with Apple's compilers (and thus has no wrapper for the mpif90). I put these in my ~/.profile:
export HOMEBREW_CC=gcc-5 export HOMEBREW_CXX=g++-5 export FC=gfortran-5
and rebuilt openmpi via:
brew reinstall openmpi --build-from-source
Firedrake installs successfully, but now I am running into a spatialindex related problem whenever I try to import the firedrake module:
python -c 'from firedrake import *'
Traceback (most recent call last):
File "<string>", line 1, in <module>
File "/Users/justin/Software/firedrake/src/firedrake/firedrake/__init__.py", line 31, in <module>
from firedrake.assemble import *
File "/Users/justin/Software/firedrake/src/firedrake/firedrake/assemble.py", line 10, in <module>
from firedrake import assemble_expressions
File "/Users/justin/Software/firedrake/src/firedrake/firedrake/assemble_expressions.py", line 17, in <module>
from firedrake import function
File "/Users/justin/Software/firedrake/src/firedrake/firedrake/function.py", line 14, in <module>
from firedrake import functionspace
File "/Users/justin/Software/firedrake/src/firedrake/firedrake/functionspace.py", line 17, in <module>
import firedrake.mesh as mesh_t
File "/Users/justin/Software/firedrake/src/firedrake/firedrake/mesh.py", line 16, in <module>
import firedrake.spatialindex as spatialindex
ImportError: dlopen(/Users/justin/Software/firedrake/src/firedrake/firedrake/spatialindex.so, 2): Symbol not found: __ZN5Tools11PropertySet11setPropertyENSt7__cxx1112basic_stringIcSt11char_traitsIcESaIcEEERKNS_7VariantE
Referenced from: /Users/justin/Software/firedrake/src/firedrake/firedrake/spatialindex.so
Expected in: flat namespace
in /Users/justin/Software/firedrake/src/firedrake/firedrake/spatialindex.so
Looks like something went awry with spatialindex. Anyone else having this problem?
Thanks, Justin
On Fri, Nov 27, 2015 at 11:26 AM, Lawrence Mitchell < <lawrence.mitchell@imperial.ac.uk>lawrence.mitchell@imperial.ac.uk> wrote:
On 27 Nov 2015, at 15:44, Onno Bokhove < <O.Bokhove@leeds.ac.uk> O.Bokhove@leeds.ac.uk> wrote:
That is what I got yesterday, but Floriane Gidel went past it on her mac laptop. Computer IT staff and I could not figure out what it was. We tried anaconda (worked with Floriane), but not with me. He thought my mpif90 was probably slightly older: so reloading Xcode an option? Updating the OS?
Hopefully not!
From: firedrake-bounces@imperial.ac.uk < firedrake-bounces@imperial.ac.uk> on behalf of Wingate, Beth < B.Wingate@exeter.ac.uk> Sent: Friday, November 27, 2015 3:41 PM To: firedrake@imperial.ac.uk Subject: Re: [firedrake] FD on mac
I’m getting the same thing — firedrake now doesn’t install due to “mpif90” not working:
TESTING: checkFortranCompiler from config.setCompilers(/private/var/folders/zn/46_9pn0x2k32_z59z6fw5j2w0000gn/T/pip-AO07XK-build/config/BuildSystem/config/setCompilers.py:919)
*******************************************************************************
UNABLE to CONFIGURE with GIVEN OPTIONS (see
configure.log for details):
-------------------------------------------------------------------------------
Fortran compiler you provided with --with-fc=/usr/local/bin/mpif90
does not work.
Cannot compile FC with /usr/local/bin/mpif90.
*******************************************************************************
If you try to compile the following simple Fortran hello world code with mpif90, what happens?
$ cat > hello.f90 << EOF program main use mph implicit none write(*, *)'Hello world' end program EOF $ mpif90 hello.f90 -o hello $ ./hello
Cheers,
Lawrence
_______________________________________________ firedrake mailing list firedrake@imperial.ac.uk https://mailman.ic.ac.uk/mailman/listinfo/firedrake
_______________________________________________ firedrake mailing listfiredrake@imperial.ac.ukhttps://mailman.ic.ac.uk/mailman/listinfo/firedrake
_______________________________________________ firedrake mailing list firedrake@imperial.ac.uk https://mailman.ic.ac.uk/mailman/listinfo/firedrake
Please let me know if that fixes your problem. On 28/11/15 20:08, Justin Chang wrote:
Ah right, didn't think about that. Got it, thanks!
On Sat, Nov 28, 2015 at 3:35 AM, Miklós Homolya <m.homolya14@imperial.ac.uk <mailto:m.homolya14@imperial.ac.uk>> wrote:
With respect to the libspatialindex problem:
Yes, see https://github.com/firedrakeproject/firedrake/issues/640
I suggest you to try rebuilding libspatialindex from source (you can do that with homebrew) using the same compiler as you used to build firedrake.
On 28/11/15 07:11, Justin Chang wrote:
Hi all,
I also had the mpif90 error on my El Capitan Macbook, but worked around it by rebuilding the openmpi with the latest brew gcc compilers (GCC 5.2.0). It seems the default configuration provided by Homebrew is built with Apple's compilers (and thus has no wrapper for the mpif90). I put these in my ~/.profile:
export HOMEBREW_CC=gcc-5 export HOMEBREW_CXX=g++-5 export FC=gfortran-5
and rebuilt openmpi via:
brew reinstall openmpi --build-from-source
Firedrake installs successfully, but now I am running into a spatialindex related problem whenever I try to import the firedrake module:
python -c 'from firedrake import *'
Traceback (most recent call last):
File "<string>", line 1, in <module>
File "/Users/justin/Software/firedrake/src/firedrake/firedrake/__init__.py", line 31, in <module>
from firedrake.assemble import *
File "/Users/justin/Software/firedrake/src/firedrake/firedrake/assemble.py", line 10, in <module>
from firedrake import assemble_expressions
File "/Users/justin/Software/firedrake/src/firedrake/firedrake/assemble_expressions.py", line 17, in <module>
from firedrake import function
File "/Users/justin/Software/firedrake/src/firedrake/firedrake/function.py", line 14, in <module>
from firedrake import functionspace
File "/Users/justin/Software/firedrake/src/firedrake/firedrake/functionspace.py", line 17, in <module>
import firedrake.mesh as mesh_t
File "/Users/justin/Software/firedrake/src/firedrake/firedrake/mesh.py", line 16, in <module>
import firedrake.spatialindex as spatialindex
ImportError: dlopen(/Users/justin/Software/firedrake/src/firedrake/firedrake/spatialindex.so, 2): Symbol not found: __ZN5Tools11PropertySet11setPropertyENSt7__cxx1112basic_stringIcSt11char_traitsIcESaIcEEERKNS_7VariantE
Referenced from: /Users/justin/Software/firedrake/src/firedrake/firedrake/spatialindex.so
Expected in: flat namespace
in /Users/justin/Software/firedrake/src/firedrake/firedrake/spatialindex.so
Looks like something went awry with spatialindex. Anyone else having this problem?
Thanks, Justin
On Fri, Nov 27, 2015 at 11:26 AM, Lawrence Mitchell <lawrence.mitchell@imperial.ac.uk <mailto:lawrence.mitchell@imperial.ac.uk>> wrote:
> On 27 Nov 2015, at 15:44, Onno Bokhove <O.Bokhove@leeds.ac.uk <mailto:O.Bokhove@leeds.ac.uk>> wrote: > > That is what I got yesterday, but Floriane Gidel went past it on her mac laptop. > Computer IT staff and I could not figure out what it was. > We tried anaconda (worked with Floriane), but not with me. > He thought my mpif90 was probably slightly older: so reloading Xcode an option? > Updating the OS?
Hopefully not!
> From: firedrake-bounces@imperial.ac.uk <mailto:firedrake-bounces@imperial.ac.uk> <firedrake-bounces@imperial.ac.uk <mailto:firedrake-bounces@imperial.ac.uk>> on behalf of Wingate, Beth <B.Wingate@exeter.ac.uk <mailto:B.Wingate@exeter.ac.uk>> > Sent: Friday, November 27, 2015 3:41 PM > To: firedrake@imperial.ac.uk <mailto:firedrake@imperial.ac.uk> > Subject: Re: [firedrake] FD on mac > > I’m getting the same thing — firedrake now doesn’t install due to “mpif90” not working: > > TESTING: checkFortranCompiler from config.setCompilers(/private/var/folders/zn/46_9pn0x2k32_z59z6fw5j2w0000gn/T/pip-AO07XK-build/config/BuildSystem/config/setCompilers.py:919) > ******************************************************************************* > UNABLE to CONFIGURE with GIVEN OPTIONS (see configure.log for details): > ------------------------------------------------------------------------------- > Fortran compiler you provided with --with-fc=/usr/local/bin/mpif90 does not work. > Cannot compile FC with /usr/local/bin/mpif90. > *******************************************************************************
If you try to compile the following simple Fortran hello world code with mpif90, what happens?
$ cat > hello.f90 << EOF program main use mph implicit none write(*, *)'Hello world' end program EOF $ mpif90 hello.f90 -o hello $ ./hello
Cheers,
Lawrence
_______________________________________________ firedrake mailing list firedrake@imperial.ac.uk <mailto:firedrake@imperial.ac.uk> https://mailman.ic.ac.uk/mailman/listinfo/firedrake
_______________________________________________ firedrake mailing list firedrake@imperial.ac.uk <mailto:firedrake@imperial.ac.uk> https://mailman.ic.ac.uk/mailman/listinfo/firedrake
_______________________________________________ firedrake mailing list firedrake@imperial.ac.uk <mailto:firedrake@imperial.ac.uk> https://mailman.ic.ac.uk/mailman/listinfo/firedrake
_______________________________________________ firedrake mailing list firedrake@imperial.ac.uk https://mailman.ic.ac.uk/mailman/listinfo/firedrake
Miklos, Yes my error has been resolved by recompiling spatialindex with the same homebrew compilers as was used for firedrake Thanks Justin On Mon, Nov 30, 2015 at 3:29 AM, Miklós Homolya <m.homolya14@imperial.ac.uk> wrote:
Please let me know if that fixes your problem.
On 28/11/15 20:08, Justin Chang wrote:
Ah right, didn't think about that. Got it, thanks!
On Sat, Nov 28, 2015 at 3:35 AM, Miklós Homolya < m.homolya14@imperial.ac.uk> wrote:
With respect to the libspatialindex problem:
Yes, see https://github.com/firedrakeproject/firedrake/issues/640
I suggest you to try rebuilding libspatialindex from source (you can do that with homebrew) using the same compiler as you used to build firedrake.
On 28/11/15 07:11, Justin Chang wrote:
Hi all,
I also had the mpif90 error on my El Capitan Macbook, but worked around it by rebuilding the openmpi with the latest brew gcc compilers (GCC 5.2.0). It seems the default configuration provided by Homebrew is built with Apple's compilers (and thus has no wrapper for the mpif90). I put these in my ~/.profile:
export HOMEBREW_CC=gcc-5 export HOMEBREW_CXX=g++-5 export FC=gfortran-5
and rebuilt openmpi via:
brew reinstall openmpi --build-from-source
Firedrake installs successfully, but now I am running into a spatialindex related problem whenever I try to import the firedrake module:
python -c 'from firedrake import *'
Traceback (most recent call last):
File "<string>", line 1, in <module>
File "/Users/justin/Software/firedrake/src/firedrake/firedrake/__init__.py", line 31, in <module>
from firedrake.assemble import *
File "/Users/justin/Software/firedrake/src/firedrake/firedrake/assemble.py", line 10, in <module>
from firedrake import assemble_expressions
File "/Users/justin/Software/firedrake/src/firedrake/firedrake/assemble_expressions.py", line 17, in <module>
from firedrake import function
File "/Users/justin/Software/firedrake/src/firedrake/firedrake/function.py", line 14, in <module>
from firedrake import functionspace
File "/Users/justin/Software/firedrake/src/firedrake/firedrake/functionspace.py", line 17, in <module>
import firedrake.mesh as mesh_t
File "/Users/justin/Software/firedrake/src/firedrake/firedrake/mesh.py", line 16, in <module>
import firedrake.spatialindex as spatialindex
ImportError: dlopen(/Users/justin/Software/firedrake/src/firedrake/firedrake/spatialindex.so, 2): Symbol not found: __ZN5Tools11PropertySet11setPropertyENSt7__cxx1112basic_stringIcSt11char_traitsIcESaIcEEERKNS_7VariantE
Referenced from: /Users/justin/Software/firedrake/src/firedrake/firedrake/spatialindex.so
Expected in: flat namespace
in /Users/justin/Software/firedrake/src/firedrake/firedrake/spatialindex.so
Looks like something went awry with spatialindex. Anyone else having this problem?
Thanks, Justin
On Fri, Nov 27, 2015 at 11:26 AM, Lawrence Mitchell < <lawrence.mitchell@imperial.ac.uk>lawrence.mitchell@imperial.ac.uk> wrote:
On 27 Nov 2015, at 15:44, Onno Bokhove <O.Bokhove@leeds.ac.uk> wrote:
That is what I got yesterday, but Floriane Gidel went past it on her mac laptop. Computer IT staff and I could not figure out what it was. We tried anaconda (worked with Floriane), but not with me. He thought my mpif90 was probably slightly older: so reloading Xcode an option? Updating the OS?
Hopefully not!
From: firedrake-bounces@imperial.ac.uk < firedrake-bounces@imperial.ac.uk> on behalf of Wingate, Beth < <B.Wingate@exeter.ac.uk>B.Wingate@exeter.ac.uk> Sent: Friday, November 27, 2015 3:41 PM To: firedrake@imperial.ac.uk Subject: Re: [firedrake] FD on mac
I’m getting the same thing — firedrake now doesn’t install due to “mpif90” not working:
TESTING: checkFortranCompiler from config.setCompilers(/private/var/folders/zn/46_9pn0x2k32_z59z6fw5j2w0000gn/T/pip-AO07XK-build/config/BuildSystem/config/setCompilers.py:919)
*******************************************************************************
UNABLE to CONFIGURE with GIVEN OPTIONS (see
configure.log for details):
-------------------------------------------------------------------------------
Fortran compiler you provided with --with-fc=/usr/local/bin/mpif90
does not work.
Cannot compile FC with /usr/local/bin/mpif90.
*******************************************************************************
If you try to compile the following simple Fortran hello world code with mpif90, what happens?
$ cat > hello.f90 << EOF program main use mph implicit none write(*, *)'Hello world' end program EOF $ mpif90 hello.f90 -o hello $ ./hello
Cheers,
Lawrence
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Tried: 1) Updating .profile as suggested by Justin 2) Reinstalled home-brew after uninstalling it. 3) But the hello.world fortran code still crashes. 4) Hence, same error message holds. ******************************************************************************* UNABLE to CONFIGURE with GIVEN OPTIONS (see configure.log for details): ------------------------------------------------------------------------------- Fortran compiler you provided with --with-fc=/usr/local/bin/mpif90 does not work. Cannot compile FC with /usr/local/bin/mpif90. ******************************************************************************* ... ---------------------------------------- Command "//anaconda/bin/python -c "import setuptools, tokenize;__file__='/var/folders/c0/rzc18gxj0619yv1l5zqlbrssh33xh5/T/pip-TL5bgv-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-YcsuFy-record/install-record.txt --single-version-externally-managed --compile" failed with error code 1 in /var/folders/c0/rzc18gxj0619yv1l5zqlbrssh33xh5/T/pip-TL5bgv-build Any suggestions? ________________________________ From: firedrake-bounces@imperial.ac.uk <firedrake-bounces@imperial.ac.uk> on behalf of Justin Chang <jychang48@gmail.com> Sent: Monday, November 30, 2015 3:53 PM To: Firedrake Project Subject: Re: [firedrake] FD on mac Miklos, Yes my error has been resolved by recompiling spatialindex with the same homebrew compilers as was used for firedrake Thanks Justin On Mon, Nov 30, 2015 at 3:29 AM, Miklós Homolya <m.homolya14@imperial.ac.uk<mailto:m.homolya14@imperial.ac.uk>> wrote: Please let me know if that fixes your problem. On 28/11/15 20:08, Justin Chang wrote: Ah right, didn't think about that. Got it, thanks! On Sat, Nov 28, 2015 at 3:35 AM, Miklós Homolya <m.homolya14@imperial.ac.uk<mailto:m.homolya14@imperial.ac.uk>> wrote: With respect to the libspatialindex problem: Yes, see https://github.com/firedrakeproject/firedrake/issues/640 I suggest you to try rebuilding libspatialindex from source (you can do that with homebrew) using the same compiler as you used to build firedrake. On 28/11/15 07:11, Justin Chang wrote: Hi all, I also had the mpif90 error on my El Capitan Macbook, but worked around it by rebuilding the openmpi with the latest brew gcc compilers (GCC 5.2.0). It seems the default configuration provided by Homebrew is built with Apple's compilers (and thus has no wrapper for the mpif90). I put these in my ~/.profile: export HOMEBREW_CC=gcc-5 export HOMEBREW_CXX=g++-5 export FC=gfortran-5 and rebuilt openmpi via: brew reinstall openmpi --build-from-source Firedrake installs successfully, but now I am running into a spatialindex related problem whenever I try to import the firedrake module: python -c 'from firedrake import *' Traceback (most recent call last): File "<string>", line 1, in <module> File "/Users/justin/Software/firedrake/src/firedrake/firedrake/__init__.py", line 31, in <module> from firedrake.assemble import * File "/Users/justin/Software/firedrake/src/firedrake/firedrake/assemble.py", line 10, in <module> from firedrake import assemble_expressions File "/Users/justin/Software/firedrake/src/firedrake/firedrake/assemble_expressions.py", line 17, in <module> from firedrake import function File "/Users/justin/Software/firedrake/src/firedrake/firedrake/function.py", line 14, in <module> from firedrake import functionspace File "/Users/justin/Software/firedrake/src/firedrake/firedrake/functionspace.py", line 17, in <module> import firedrake.mesh as mesh_t File "/Users/justin/Software/firedrake/src/firedrake/firedrake/mesh.py", line 16, in <module> import firedrake.spatialindex as spatialindex ImportError: dlopen(/Users/justin/Software/firedrake/src/firedrake/firedrake/spatialindex.so, 2): Symbol not found: __ZN5Tools11PropertySet11setPropertyENSt7__cxx1112basic_stringIcSt11char_traitsIcESaIcEEERKNS_7VariantE Referenced from: /Users/justin/Software/firedrake/src/firedrake/firedrake/spatialindex.so Expected in: flat namespace in /Users/justin/Software/firedrake/src/firedrake/firedrake/spatialindex.so Looks like something went awry with spatialindex. Anyone else having this problem? Thanks, Justin On Fri, Nov 27, 2015 at 11:26 AM, Lawrence Mitchell <<mailto:lawrence.mitchell@imperial.ac.uk>lawrence.mitchell@imperial.ac.uk<mailto:lawrence.mitchell@imperial.ac.uk>> wrote:
On 27 Nov 2015, at 15:44, Onno Bokhove <O.Bokhove@leeds.ac.uk<mailto:O.Bokhove@leeds.ac.uk>> wrote:
That is what I got yesterday, but Floriane Gidel went past it on her mac laptop. Computer IT staff and I could not figure out what it was. We tried anaconda (worked with Floriane), but not with me. He thought my mpif90 was probably slightly older: so reloading Xcode an option? Updating the OS?
Hopefully not!
From: firedrake-bounces@imperial.ac.uk<mailto:firedrake-bounces@imperial.ac.uk> <firedrake-bounces@imperial.ac.uk<mailto:firedrake-bounces@imperial.ac.uk>> on behalf of Wingate, Beth <<mailto:B.Wingate@exeter.ac.uk>B.Wingate@exeter.ac.uk<mailto:B.Wingate@exeter.ac.uk>> Sent: Friday, November 27, 2015 3:41 PM To: firedrake@imperial.ac.uk<mailto:firedrake@imperial.ac.uk> Subject: Re: [firedrake] FD on mac
I'm getting the same thing - firedrake now doesn't install due to "mpif90" not working:
TESTING: checkFortranCompiler from config.setCompilers(/private/var/folders/zn/46_9pn0x2k32_z59z6fw5j2w0000gn/T/pip-AO07XK-build/config/BuildSystem/config/setCompilers.py:919) ******************************************************************************* UNABLE to CONFIGURE with GIVEN OPTIONS (see configure.log for details): ------------------------------------------------------------------------------- Fortran compiler you provided with --with-fc=/usr/local/bin/mpif90 does not work. Cannot compile FC with /usr/local/bin/mpif90. *******************************************************************************
If you try to compile the following simple Fortran hello world code with mpif90, what happens? $ cat > hello.f90 << EOF program main use mph implicit none write(*, *)'Hello world' end program EOF $ mpif90 hello.f90 -o hello $ ./hello Cheers, Lawrence _______________________________________________ firedrake mailing list firedrake@imperial.ac.uk<mailto:firedrake@imperial.ac.uk> https://mailman.ic.ac.uk/mailman/listinfo/firedrake _______________________________________________ firedrake mailing list firedrake@imperial.ac.uk<mailto:firedrake@imperial.ac.uk> https://mailman.ic.ac.uk/mailman/listinfo/firedrake _______________________________________________ firedrake mailing list firedrake@imperial.ac.uk<mailto:firedrake@imperial.ac.uk> https://mailman.ic.ac.uk/mailman/listinfo/firedrake _______________________________________________ firedrake mailing list firedrake@imperial.ac.uk<mailto:firedrake@imperial.ac.uk> https://mailman.ic.ac.uk/mailman/listinfo/firedrake _______________________________________________ firedrake mailing list firedrake@imperial.ac.uk<mailto:firedrake@imperial.ac.uk> https://mailman.ic.ac.uk/mailman/listinfo/firedrake
On 30/11/15 16:05, Onno Bokhove wrote:
1) Updating .profile as suggested by Justin
2) Reinstalled home-brew after uninstalling it.
3) But the hello.world fortran code still crashes.
Can you be more specific? This description covers a multitude of sins. Lawrence
On 26/11/15 12:12, Floriane Gidel [RPG] wrote:
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.
You mean, the machine actually rebooted?
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)
Yes, this is why the description says to pass --no-deps (you've asserted that petsc is already installed and the correct version). I'm confused as to your other errors. Lawrence
participants (7)
-
David Ham
-
Floriane Gidel [RPG]
-
Justin Chang
-
Lawrence Mitchell
-
Miklós Homolya
-
Onno Bokhove
-
Wingate, Beth