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Error message during installation "OSError: [Errno 9] Bad file descriptor" #1467
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Is this because of the homebrew Python? There is no need to use homebrew to install yet another Python to drive spack. You can use the default python3 that comes with macOS. |
Thank you, I will try to uninstall homebrew Python and use the system-wide install. |
Not sure you need to uninstall homebrew. after running |
On one of the systems where this error message appears, some other problems result when having system-wide python3 found first in the $PATH variable, and after running source setup.sh that sets SPACK_PYTHON is set to The new error happens at the concretization phase. The example below is from x86_64 + Sonoma; similar results happen on arm64/M1 + Sonoma. This issue does not happen on M2 + Ventura OS X.
Attempted to install clingo-bootstrap :
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Solution to the problem found.
Final search path in ~/.bashrc is set up as following:
After starting a new bash shell, and running
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Do you want to add something to the documentation (Known issues for this) and then close the issue? Please note that we should not modify |
Hopefully, the issue could be closed; I'd only wait for the confirmation from a stakeholder that was inquiring about the issue that the solution worked on their system. The note to clear the ~/.spack directory ahead of new spack-stack installation might be a generally helpful troubleshooting tool, and I wonder if adding this as a solution for other occasions could be useful. This resolves conflicts after several installations at different times may cause buildup of different "default" configurations. It was certainly the case with my system, due to earlier OS upgrades (but with the user's directory ~/.spack remaining and carrying some older specs set as default) and different installation attempts of spack-stack and its versions. As to the changes suggested for ~/.bashrc - it was not given as a separate step, but it was one of the last steps for system preparation ahead of spack-stack install on MacOS. When the packages are installed using brew/HOMEBREW, it also suggests adding certains LDFLAGS or CPPFLAGS, or addition of the search path to a $PATH variable. Xcode or xcode-select tools do need to be installed on the system ahead of spack-stack, and setting the shell variables such as export SYSROOT=$(xcode-select -p) help to find the right paths and configurations when xcode or xcode-select tools need to be used, and as a diagnostic tool to troubleshoot issues... They could be set manually in a shell as well, not necessary added to .bashrc... |
Describe the bug
Numerous error messages of the same type are reported during installation of the spack-stack on MacOS (and possibly other machines, yet to confirm). This does not seem to affect installation of the packages however.
An example of the error:
Installation logs are writtedn in verbose mode, and too large to attach,
they are available from the GoogleDrive:
log.install.Darwin.001.txt
log.install.Darwin.002.txt
To Reproduce
Steps to reproduce the behavior:
Full MacOS installation directions are given in a GoogleDoc document
Expected behavior
No errors should be reported
System:
What system(s) are you running the code on?
MacOS, but has been reported on other systems
Additional context
Add any other context about the problem here.
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