Unable to refresh spack module

[Vinayak Vijay]

Hello,

In order to upgrade the version of dealii, i reinstalled the latest version of spack. I have been able to also install dealii using spack. However, when i use the command "spack module tcl refresh", i get the following error.

==> Error: Cannot use invalid module set default.    Valid module set names are []

If i just ignore this and perform "make run" of my code i get the following error:

[ 14%] Linking CXX executable main
/usr/bin/ld.gold: error: cannot find -lhdf5-shared
collect2: error: ld returned 1 exit status
make[3]: *** [CMakeFiles/main.dir/build.make:292: main] Error 1
make[2]: *** [CMakeFiles/Makefile2:90: CMakeFiles/main.dir/all] Error 2
make[1]: *** [CMakeFiles/Makefile2:123: CMakeFiles/run.dir/rule] Error 2
make: *** [Makefile:137: run] Error 2

I think these two errors are linked. Can someone point out what i should do now?

Note: I was able to perfectly run dealii v9.3 befor this reinstallation. 

Thanks,

Vinayak

[陈敏]

Hi, Vinayak Vijay

I think installing dealii-9.4 with hdf5 using spack maybe some bug, you can turn off the hdf5 by spack install dea...@9.4.0~hdf5.

Best

Chen

Vinayak Vijay <vinay...@gmail.com> 于2023年5月12日周五 17:23写道：

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[Daniel Arndt]

Yes, our HDF5 integration only works well with a raw install (like a system package manager provides) that doesn't expose CMake files.
https://github.com/dealii/dealii/pull/15199 offers a workaround for that issue but otherwise, it's best to just use the system installation obtainable through

apt-get install libhdf5-dev

or the like and let spack know about it.

Best,

Daniel

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[Vinayak Vijay]

Hi,

Thank you for your reply. I will try it. Can you tell me how can I let spack know about the package that is installed through system installation?

Also, can you help me with the other error that I get when I try to refresh the modules?

==> Error: Cannot use invalid module set default.    Valid module set names are []

Thanks again for your help.

Vinayak 

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[Daniel Arndt]

> Can you tell me how can I let spack know about the package that is installed through system installation?

Have a look at https://spack.readthedocs.io/en/latest/build_settings.html#external-packages.

I don't know about the other spack issue.

Best,

Daniel

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