refactor: Complete spack migration & move versions to geos package.py.

[CusiniM]

1. Force the definition of the versions of all tpls in the geosx package.py. This should ensure that we don't need to specify the commit in all environments and it should make updating a version easier. I would argue that the only library for which we may want to track a commit instead of a release is hypre. It seems that we can't specify a commit in the package.py, however, we could modify hypre's package.py by doing something like this

2. Update uncrustify.

3. Remove mirrors and old cmake-base tpls installation workflow

Once this PR is merged, we should be able to move everything to the geos repo and completely get rid of this repository. I think the tpls built can be set up as independent CI jobs conditionals to changes to the spack env files. And we can probably do something clever to avoid rebuilding all tpls when only one of them is updated.

[victorapm]

Another idea: let's just point to hypre@master. Only drawback is that is a moving target...

PS: if we are removing all the tarballs, do we want to keep CMakeLists.txt?

[CusiniM]

Another idea: let's just point to hypre@master. Only drawback is that is a moving target...

The thing is that, for Hypre, sometimes we may want commits that are not on master. I also don't know whether that can be specified in the package.py or not. We could try. It's true that ideally we want to control when updates occur.

PS: if we are removing all the tarballs, do we want to keep CMakeLists.txt?
no, I got rid of it.

[CusiniM]

There is one job that fails while building caliper. First of all, I do not understand why but I have also noticed that it's trying to build caliper 2.11 even though the version specified in the geos package is 2.12. I do not understand where it's picking up that version.

[bmhan12]

There is one job that fails while building caliper. First of all, I do not understand why but I have also noticed that it's trying to build caliper 2.11 even though the version specified in the geos package is 2.12. I do not understand where it's picking up that version.

Looking at the job log, for some reason, spack concretizes the spec as:
geosx@develop%clang@17.0.6 cflags=-pthread cxxflags=-pthread +addr2line~caliper+cuda~docs+hypre~ipo+mathpresso~openmp~petsc~pygeosx+scotch+shared+trilinos~uncrustify+vtk build_system=cmake build_type=Release
(note the ~caliper).

For whatever reason, spack isn't picking the expected +caliper default.
From the log, that means it is not respecting geos's specified caliper dependency (version, variants we want), and is instead building caliper as part of hypre's dependency.
I would try explicitly adding +caliper to the spec that is passed to uberenv, see if that gets spack to build geos with the right version of caliper:

thirdPartyLibs/docker/tpl-rockylinux-clang-cuda-12.Dockerfile

Line 74 in e4eb2d6

--spec "%clang@17.0.6+cuda~uncrustify~openmp~pygeosx cuda_arch=70 ^cuda@12.6.3+allow-unsupported-compilers ^caliper~gotcha~sampler~libunwind~libdw~papi" \

---

Alternatively, the error from the log when building caliper 2.11 is the following:
../../libcaliper.so.2.11.0: undefined reference to std::filesystem::__cxx11::path::parent_path() const

This post suggests adding -lstdc++fs to fix it:
https://stackoverflow.com/questions/53852684/stdfilesystem-link-error-on-ubuntu-18-10

Looks like that can be done in two ways through spack:

1. Adding ldflags to the compiler section of the spack.yaml (example here: https://github.com/LLNL/UMT/blob/69648a82c524963ee2a8d1c4f0c7bdfde9548260/spack/environment/cray/spack.yaml#L25)
2. Require caliper in the packages section to be build with the appropriate ldflags (example here: https://github.com/LLNL/axom/blob/4d8e328928a4182eb0032a6df28d81bc942dec73/scripts/spack/configs/toss_4_x86_64_ib_cray/spack.yaml#L575-L577)

[victorapm]

It's probably time to re-evaluate if we want the unified memory option in hypre:

thirdPartyLibs/scripts/spack_packages/packages/geosx/package.py

Line 163 in 7b798e3

depends_on("hypre +cuda+superlu-dist+mixedint+mpi+umpire+unified-memory~shared cflags='-fPIC' cxxflags='-fPIC'", when='+cuda')

The reason to keep it would be to allow over-subscription of GPU RAM, but that generally leads to poor performance