Dear group,
We are reinstalling the ET_2019_10 version following the CactusTutorial.ipynb and keep running into issues when installing the prerequisites. Our system is macOS Catalina with Xcode and Macports installed successfully. When we use the commend: sudo port -N install pkgconfig gcc9 openmpi-gcc9 fftw-3 gsl jpeg zlib hdf5 +fortran +gfortran openssl subversion ld64 We get the following errors:
---> Computing dependencies for pkgconfig ---> Cleaning pkgconfig ---> Computing dependencies for gcc9 ---> Cleaning gcc9 ---> Computing dependencies for openmpi-gcc9 ---> Configuring openmpi-gcc9 Error: Failed to configure openmpi-gcc9, consult /opt/local/var/macports/build/_opt_local_var_macports_sources_rsync.macports.org_macports_release_tarballs_ports_science_openmpi/openmpi-gcc9/work/build/config.log Error: Failed to configure openmpi-gcc9: configure failure: command execution failed Error: See /opt/local/var/macports/logs/_opt_local_var_macports_sources_rsync.macports.org_macports_release_tarballs_ports_science_openmpi/openmpi-gcc9/main.log for details. Error: Follow https://guide.macports.org/#project.tickets to report a bug. Error: Processing of port openmpi-gcc9 failed
We are wondering if anyone have ran into similar issues and could give us a hint about how to fix this.
Thank you very much, Shanshan
Hello Shanshan,
we have had issues with OpenMPI and MacPorts in the past (see eg https://bitbucket.org/einsteintoolkit/tickets/issues/2290/failure-to-compile...) though usually with OpenMPI preventing us from building and not so much it itself not building.
Not usually building OpenMPI.
It worked for me a couple of weeks ago (on a freshly installed Catalina system), though this may have changed since.
Can you include (or check) the file
/opt/local/var/macports/logs/_opt_local_var_macports_sources_rsync.macports.org_macports_release_tarballs_ports_science_openmpi/openmpi-gcc9/main.log
mentioned in the error message?
Yours, Roland
Dear group,
We are reinstalling the ET_2019_10 version following the CactusTutorial.ipynb and keep running into issues when installing the prerequisites. Our system is macOS Catalina with Xcode and Macports installed successfully. When we use the commend: sudo port -N install pkgconfig gcc9 openmpi-gcc9 fftw-3 gsl jpeg zlib hdf5 +fortran +gfortran openssl subversion ld64 We get the following errors:
---> Computing dependencies for pkgconfig ---> Cleaning pkgconfig ---> Computing dependencies for gcc9 ---> Cleaning gcc9 ---> Computing dependencies for openmpi-gcc9 ---> Configuring openmpi-gcc9 Error: Failed to configure openmpi-gcc9, consult /opt/local/var/macports/build/_opt_local_var_macports_sources_rsync.macports.org_macports_release_tarballs_ports_science_openmpi/openmpi-gcc9/work/build/config.log Error: Failed to configure openmpi-gcc9: configure failure: command execution failed Error: See /opt/local/var/macports/logs/_opt_local_var_macports_sources_rsync.macports.org_macports_release_tarballs_ports_science_openmpi/openmpi-gcc9/main.log for details. Error: Follow https://guide.macports.org/#project.tickets to report a bug. Error: Processing of port openmpi-gcc9 failed
We are wondering if anyone have ran into similar issues and could give us a hint about how to fix this.
Thank you very much, Shanshan
Hi Roland,
Thanks for your quick reply. I’ve attached the log file and also noticed this error message right at the failing point in the log file:
:info:configure configure: error: ptrdiff_t type is not available, this is required by C99 standard. Cannot continue
Any ideas about this ‘ptrdiff_t type’?
Sincerely, Shanshan
On May 26, 2020, at 1:04 PM, Roland Haas <rhaas@illinois.edumailto:rhaas@illinois.edu> wrote:
/opt/local/var/macports/logs/_opt_local_var_macports_sources_rsync.macports.org_macports_release_tarballs_ports_science_openmpi/openmpi-gcc9/main.log
Hello Shanshan,
Thanks for your quick reply. I’ve attached the log file and also noticed this error message right at the failing point in the log file:
:info:configure configure: error: ptrdiff_t type is not available, this is required by C99 standard. Cannot continue
Any ideas about this ‘ptrdiff_t type’?
Not really. I can only guess. This could be a bug in OpenMPI's configure script. To get ptrdiff_t one usually has to include stddef.h or some other stdXXX.h header file.
You may also want to check if your environment has any CFLAGS, CXXFLAGS or similar variables installed (visible in the output of "env").
Note that MacPorts tends to have a complex interaction with any other package management system (eg HomeBrew, Fink, Anaconda, ...) and if you have one of those installed then there may be very strange effects.
Yours, Roland
Hi Roland,
I updated Catalina and removed Anaconda, not sure which step helped but the openmpi issue was solved.
Thanks a lot for your advice!
Best, Shanshan
On May 26, 2020, at 1:38 PM, Roland Haas rhaas@illinois.edu wrote:
Hello Shanshan,
Thanks for your quick reply. I’ve attached the log file and also noticed this error message right at the failing point in the log file:
:info:configure configure: error: ptrdiff_t type is not available, this is required by C99 standard. Cannot continue
Any ideas about this ‘ptrdiff_t type’?
Not really. I can only guess. This could be a bug in OpenMPI's configure script. To get ptrdiff_t one usually has to include stddef.h or some other stdXXX.h header file.
You may also want to check if your environment has any CFLAGS, CXXFLAGS or similar variables installed (visible in the output of "env").
Note that MacPorts tends to have a complex interaction with any other package management system (eg HomeBrew, Fink, Anaconda, ...) and if you have one of those installed then there may be very strange effects.
Yours, Roland
-- My email is as private as my paper mail. I therefore support encrypting and signing email messages. Get my PGP key from http://pgp.mit.edu .
Hello Shanshan,
I updated Catalina and removed Anaconda, not sure which step helped but the openmpi issue was solved.
Glad to have been able to help.
Yours, Roland
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