Update spack packages #332

victorapm · 2026-01-21T13:50:46Z

Update hypre to v3.1.0 (MGR improvements, particularly for thermal simulations)
Remove internal scotch package and rely on upstream one (from spack-packages) by @bmhan12
Update spack-packages commit to 21st Jan 2026
Update uberenv to latest develop
Update spack to v1.1.0
Update silo to v4.1.2 (preferable version by spack-packages)
Update hdf5 to v1.14.6 (preferable version by spack-packages)
Update rocky linux clang Dockerfile to use gcc-13 headers (required by GPU-enabled builds of hypre)

bmhan12 · 2026-01-21T21:33:09Z

.uberenv_config.json

 "spack_configs_path": "scripts/spack_configs",
 "spack_packages_path": "scripts/spack_packages/packages",
-"spack_packages_commit": "a75a7f75182ffc7a51c6ca7f0fec4bf9b2705be8"
+"spack_packages_commit": "cfa8d650480c409de2d568cf1355bf7e509f4c1c" // (Jan 21st 2026)


You'll need to update the uberenv submodule as well.
There is a bug in the current uberenv that locks the spack_packages commit being used.
More details in this uberenv PR: llnl/uberenv#152

Thanks for the heads up, Brian! Saved some time!

No problem! I have a branch here (https://github.com/GEOS-DEV/thirdPartyLibs/tree/feature/han12/spack_updates) that is testing out Spack 1.1.0 . Hopefully the other changes might be useful!

Oh nice, yes those do look useful and more comprehensive than this branch. Are you close to finishing it? Maybe we can put all together

Feel free to integrate the parts that work into your PR!
Last I checked, I was running into compilation errors when building GEOS related to newer hypre API changes.

Also, I think json is particular about comments, so C-style // comments may not work.

That's a bummer, wish uberenv could understand jsonc
I fixed the hypre API changes here: GEOS-DEV/GEOS#3939
I'll go ahead and merge your stuff into this PR

…retization error (compiler mixing error)

…/mgr-thermal

bmhan12

Thanks @victorapm!
Just have some comments related to cleanup/clarity.

EDIT: For reference, related PR GEOS-DEV/GEOS#3939

bmhan12 · 2026-01-23T15:47:22Z

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

-# Run uberenv
-# Have to create install directory first for uberenv
-# -k flag is to ignore SSL errors


We should preserve comments like these for future reference.

Good catch, restored

bmhan12 · 2026-01-23T15:54:06Z

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

+     scl enable gcc-toolset-13 ' \
+     export CXXFLAGS="--gcc-toolchain=/opt/rh/gcc-toolset-13/root/usr" && \
+     export CFLAGS="--gcc-toolchain=/opt/rh/gcc-toolset-13/root/usr" && \


There looks to be 3 methods to pass the specific toolchain to clang here and elsewhere:

Creating a bash wrapper script that invokes clang with --gcc-toolchain and setting those paths for the llvm external dependency inside docker/rocky-spack.yaml.

Setting CFLAGS and CXXFLAGS here with --gcc-toolchain

Specifying --gcc-toolchain through cxxflags/cflags under the spack toolchain inside docker/rocky-spack.yaml.

Are these all necessary? Is there any redundancy or methods that didn't end up working here?

We should only need the first one. I had tried the other two solutions, but couldn't make it work. I cleaned up the stuff that I didn't need anymore in the code

bmhan12 · 2026-01-23T15:57:38Z

docker/tpl-ubuntu-clang-cuda.Dockerfile

     ./scripts/uberenv/uberenv.py \
       --spec "+cuda~uncrustify~openmp~pygeosx cuda_arch=70 %clang-10  ^cuda@11.8.0+allow-unsupported-compilers ^caliper~gotcha~sampler~libunwind~libdw~papi" \
-       --spack-env-file=${SRC_DIR}/docker/spack.yaml \
+       --spack-env-file=${SRC_DIR}/docker/ubuntu20-spack.yaml \


Maybe rename this file as ubuntu20-clang-cuda.yaml, spack-cuda.yaml, etc. ?
To indicate that this is now cuda-specific/config-specific.

Renamed to docker/ubuntu20-clang-cuda-spack.yaml

bmhan12 · 2026-01-23T16:03:35Z

docker/ubuntu20-clang-cuda-spack.yaml

+  - ../versions.yaml
+
+  # Ubuntu 20.04 clang/cuda image only has clang/llvm 10.x available.
+  # Keep this environment llvm10-only to avoid concretizer conflicts with llvm@15.


Just curious - was spack failing to concretize and/or was it trying to use llvm@15?

I think here spack has hitting concretization issues because the environment could see multiple llvm externals and spack would either treat %llvm deps ambiguous (multiple external satisfies) and/or concretize into constraints that pulled in llvm@15 even though the image is clang/llvm 10.

spack passes clang-cuda build by not building hypre (false positive)

bmhan12 · 2026-01-23T16:24:49Z

Hm, looks like the clang-cuda configuration is passing, but spack does so by not building hypre:

Here's the geosx concretization from the CI run(https://github.com/GEOS-DEV/thirdPartyLibs/actions/runs/21274976099) :

geosx@develop+addr2line+caliper+cuda~docs~grpc~hypre~ipo+mathpresso~openmp~petsc~pygeosx~rocm+scotch+shared+trilinos~uncrustify+vtk build_system=cmake build_type=Release cuda_arch:=70 cuda_stack_size=0 dev_path=/tmp/thirdPartyLibs generator=make lai=trilinos platform=linux os=ubuntu20.04 target=x86_64 %fortran=gcc@9.4.0 %c,cxx=clang@10.0.0

That would explain why the associated CI job is failing inside GEOS with error: ENABLE_HYPRE is ON but HYPRE_DIR isn't defined. (https://github.com/GEOS-DEV/GEOS/actions/runs/21278342687/job/61285289879?pr=3939)

victorapm · 2026-01-23T16:36:46Z

Thanks for catching this! Trying to force lai=hypre in 5765cc6. Let's see...

Update hypre

1dec15d

victorapm mentioned this pull request Jan 21, 2026

perf: Improve MGR recipes for thermal GEOS-DEV/GEOS#3939

Open

victorapm added 3 commits January 21, 2026 07:52

Update hypre to 89b60a212f06bcc4d30a59f3961bcd8a937415f3

88abae4

Remove build_system=cmake until we upgrade spack

74a8a9a

Bump spack/packages commit

a21470f

bmhan12 reviewed Jan 21, 2026

View reviewed changes

bmhan12 and others added 23 commits January 21, 2026 13:44

Update uberenv for spack packages commit checkout fix

324d295

Update spack packages commit

bfa9542

Remove custom scotch recipe in favor of upstream spack

3dfbc37

Try spack 1.1.0 - remove gcc-runtime as an external which causes conc…

93b008d

…retization error (compiler mixing error)

Try toss 4 cray

282180e

Use +pic variant instead of extra flags for hypre

b8cafa1

Bump uberenv

0b62ba8

Merge branch 'feature/han12/spack_updates' into feature/paludettomag1…

ccc60de

…/mgr-thermal

Change versions/default location

f6b2759

Right way of fixing it

96b31fb

Add spack_packages as well

b07b893

Fixing llvm issue

fcda68c

Fixing more issues

6044b34

Fixing more issues

fc10e69

Adding separate spack file for ubuntu 20

105df5c

More

eabd909

Pinning openmpi

9facbda

Bumping silo version

71c7ff3

Bumping HDF5 version

d2305db

Rocky 8 to use gcc-13 headers

35f250d

Forcing clang-17 to pick gcc 13 headers

cda9675

Trying again

01e15eb

Simplify

3264c4a

victorapm changed the title ~~WIP - Update hypre~~ Update spack packages Jan 23, 2026

victorapm requested review from bmhan12 and rrsettgast January 23, 2026 04:19

Tweak

c22a848

bmhan12 previously approved these changes Jan 23, 2026

View reviewed changes

bmhan12 self-requested a review January 23, 2026 16:18

Review

83aaafc

Forcing lai=hypre

5765cc6

Update spack packages #332

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Update spack packages #332

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