{phys}[foss/2023a] HOOMD-blue v4.9.1 by sassy-crick · Pull Request #22013 · easybuilders/easybuild-easyconfigs

sassy-crick · 2024-12-11T20:43:01Z

(created using eb --new-pr)

See also here for some of the encountered problems.

Requires:

PR {compiler}[GCCcore/12.3.0] Clang v16.0.6 w/ shared #22327

…-blue-4.9.1.patch

github-actions · 2024-12-11T20:43:30Z

Updated software `HOOMD-blue-4.9.1-foss-2023a-llvm.eb`

Diff against HOOMD-blue-4.0.1-foss-2022a.eb

easybuild/easyconfigs/h/HOOMD-blue/HOOMD-blue-4.0.1-foss-2022a.eb

diff --git a/easybuild/easyconfigs/h/HOOMD-blue/HOOMD-blue-4.0.1-foss-2022a.eb b/easybuild/easyconfigs/h/HOOMD-blue/HOOMD-blue-4.9.1-foss-2023a-llvm.eb
index f576061ecc..c3c0bc3d60 100644
--- a/easybuild/easyconfigs/h/HOOMD-blue/HOOMD-blue-4.0.1-foss-2022a.eb
+++ b/easybuild/easyconfigs/h/HOOMD-blue/HOOMD-blue-4.9.1-foss-2023a-llvm.eb
@@ -1,43 +1,56 @@
+# LLVM included, needs to be version 16.x as newer versions have a different API
+# See: https://github.com/easybuilders/easybuild-easyconfigs/issues/21960
+# Author: J. Sassmannshausen (Imperial College London/UK)
+
 easyblock = 'CMakeMake'
 
 name = 'HOOMD-blue'
-version = "4.0.1"
+version = "4.9.1"
+versionsuffix = '-llvm'
 
 homepage = "https://bitbucket.org/glotzer/hoomd-blue"
 description = """HOOMD-blue is a general-purpose particle simulation
 toolkit, implementing molecular dynamics and hard particle Monte Carlo
-optimized for fast execution on both GPUs and CPUs."""
+optimized for fast execution on both GPUs and CPUs.
+This version contains the LLVM environment.
+"""
 
-toolchain = {'name': 'foss', 'version': '2022a'}
+toolchain = {'name': 'foss', 'version': '2023a'}
 toolchainopts = {'usempi': True}
 
 github_account = 'glotzerlab'
 source_urls = [GITHUB_LOWER_RELEASE]
 sources = ['hoomd-%(version)s.tar.gz']
-checksums = ['b63dd8debb96f9c530983bd54ecbafa8fd07e017ded3ea64604cfb1f41a644b8']
+patches = ['%(name)s-%(version)s.patch']
+checksums = [
+    {'hoomd-4.9.1.tar.gz': 'b48ff3d44fef56ddf95c64b462b5d7f670bfc7a76b47223207edd3e7438e52bd'},
+    {'HOOMD-blue-4.9.1.patch': '185584a621fb02a554fb2c383b0d7c8bbb7e1251298fc58529b22b8ce7212854'},
+]
 
 builddependencies = [
-    ('CMake', '3.24.3'),
-    ('pybind11', '2.9.2'),
+    ('CMake', '3.26.3'),
+    ('pybind11', '2.11.1'),
 ]
 
 dependencies = [
-    ('Python', '3.10.4'),
-    ('SciPy-bundle', '2022.05'),
-    ('tbb', '2021.5.0'),
+    ('Python', '3.11.3'),
+    ('SciPy-bundle', '2023.07'),
+    ('tbb', '2021.11.0'),
     ('Eigen', '3.4.0'),
     ('Cereal', '1.3.2', '', SYSTEM),
+    ('Clang', '16.0.6', '-shared'),
 ]
 
 _copts = [
     '-DENABLE_GPU=OFF',
     '-DENABLE_MPI=ON',
     '-DBUILD_MD=ON',
-    '-DBUILD_METAL=ON',
+    '-DBUILD_METAL=OFF',
     '-DENABLE_TBB=ON',
     '-DBUILD_TESTING=ON',
-    '-DPYTHON_EXECUTABLE=$EBROOTPYTHON/bin/python',
+    '-DENABLE_LLVM=ON',
 ]
+
 configopts = ' '.join(_copts)
 
 postinstallcmds = [

Diff against HOOMD-blue-4.0.1-foss-2022a-CUDA-11.7.0.eb

easybuild/easyconfigs/h/HOOMD-blue/HOOMD-blue-4.0.1-foss-2022a-CUDA-11.7.0.eb

diff --git a/easybuild/easyconfigs/h/HOOMD-blue/HOOMD-blue-4.0.1-foss-2022a-CUDA-11.7.0.eb b/easybuild/easyconfigs/h/HOOMD-blue/HOOMD-blue-4.9.1-foss-2023a-llvm.eb
index ab46959e6c..c3c0bc3d60 100644
--- a/easybuild/easyconfigs/h/HOOMD-blue/HOOMD-blue-4.0.1-foss-2022a-CUDA-11.7.0.eb
+++ b/easybuild/easyconfigs/h/HOOMD-blue/HOOMD-blue-4.9.1-foss-2023a-llvm.eb
@@ -1,53 +1,63 @@
+# LLVM included, needs to be version 16.x as newer versions have a different API
+# See: https://github.com/easybuilders/easybuild-easyconfigs/issues/21960
+# Author: J. Sassmannshausen (Imperial College London/UK)
+
 easyblock = 'CMakeMake'
 
 name = 'HOOMD-blue'
-version = "4.0.1"
-versionsuffix = '-CUDA-%(cudaver)s'
+version = "4.9.1"
+versionsuffix = '-llvm'
 
-homepage = "https://glotzerlab.engin.umich.edu/hoomd-blue/"
+homepage = "https://bitbucket.org/glotzer/hoomd-blue"
 description = """HOOMD-blue is a general-purpose particle simulation
 toolkit, implementing molecular dynamics and hard particle Monte Carlo
-optimized for fast execution on both GPUs and CPUs."""
+optimized for fast execution on both GPUs and CPUs.
+This version contains the LLVM environment.
+"""
 
-toolchain = {'name': 'foss', 'version': '2022a'}
+toolchain = {'name': 'foss', 'version': '2023a'}
 toolchainopts = {'usempi': True}
 
 github_account = 'glotzerlab'
 source_urls = [GITHUB_LOWER_RELEASE]
 sources = ['hoomd-%(version)s.tar.gz']
-checksums = ['b63dd8debb96f9c530983bd54ecbafa8fd07e017ded3ea64604cfb1f41a644b8']
+patches = ['%(name)s-%(version)s.patch']
+checksums = [
+    {'hoomd-4.9.1.tar.gz': 'b48ff3d44fef56ddf95c64b462b5d7f670bfc7a76b47223207edd3e7438e52bd'},
+    {'HOOMD-blue-4.9.1.patch': '185584a621fb02a554fb2c383b0d7c8bbb7e1251298fc58529b22b8ce7212854'},
+]
 
 builddependencies = [
-    ('CMake', '3.24.3'),
-    ('pybind11', '2.9.2'),
+    ('CMake', '3.26.3'),
+    ('pybind11', '2.11.1'),
 ]
 
 dependencies = [
-    ('CUDA', '11.7.0', '', SYSTEM),
-    ('UCX-CUDA', '1.12.1', versionsuffix),
-    ('Python', '3.10.4'),
-    ('SciPy-bundle', '2022.05'),
-    ('tbb', '2021.5.0'),
+    ('Python', '3.11.3'),
+    ('SciPy-bundle', '2023.07'),
+    ('tbb', '2021.11.0'),
     ('Eigen', '3.4.0'),
     ('Cereal', '1.3.2', '', SYSTEM),
+    ('Clang', '16.0.6', '-shared'),
 ]
 
 _copts = [
-    '-DENABLE_GPU=ON',
-    '-DHOOMD_GPU_PLATFORM=CUDA',
+    '-DENABLE_GPU=OFF',
     '-DENABLE_MPI=ON',
     '-DBUILD_MD=ON',
-    '-DBUILD_METAL=ON',
+    '-DBUILD_METAL=OFF',
     '-DENABLE_TBB=ON',
     '-DBUILD_TESTING=ON',
-    '-DPYTHON_EXECUTABLE=$EBROOTPYTHON/bin/python',
+    '-DENABLE_LLVM=ON',
 ]
+
 configopts = ' '.join(_copts)
 
 postinstallcmds = [
     'ln -s hoomd/include %(installdir)s/include',
 ]
 
+pretestopts = "OMPI_MCA_rmaps_base_oversubscribe=1 "
 runtest = 'test'
 
 sanity_check_paths = {

sassy-crick · 2024-12-11T21:15:03Z

@boegelbot: please test @ generoso

boegelbot · 2024-12-11T21:20:06Z

@sassy-crick: Request for testing this PR well received on login1

PR test command 'EB_PR=22013 EB_ARGS= EB_CONTAINER= EB_REPO=easybuild-easyconfigs /opt/software/slurm/bin/sbatch --job-name test_PR_22013 --ntasks=4 ~/boegelbot/eb_from_pr_upload_generoso.sh' executed!

exit code: 0
output:

Submitted batch job 14853

Test results coming soon (I hope)...

Details

- notification for comment with ID 2537207234 processed

Message to humans: this is just bookkeeping information for me,
it is of no use to you (unless you think I have a bug, which I don't).

boegelbot · 2024-12-11T21:50:13Z

Test report by @boegelbot
FAILED
Build succeeded for 0 out of 1 (1 easyconfigs in total)
cns1 - Linux Rocky Linux 8.9, x86_64, Intel(R) Xeon(R) CPU E5-2667 v3 @ 3.20GHz (haswell), Python 3.6.8
See https://gist.github.com/boegelbot/dd9e619c6b887aac5fcafd685663ac9f for a full test report.

sassy-crick · 2024-12-11T23:14:53Z

@boegelbot: please test @ generoso

boegelbot · 2024-12-11T23:15:09Z

@sassy-crick: Request for testing this PR well received on login1

PR test command 'EB_PR=22013 EB_ARGS= EB_CONTAINER= EB_REPO=easybuild-easyconfigs /opt/software/slurm/bin/sbatch --job-name test_PR_22013 --ntasks=4 ~/boegelbot/eb_from_pr_upload_generoso.sh' executed!

exit code: 0
output:

Submitted batch job 14854

Test results coming soon (I hope)...

Details

- notification for comment with ID 2537393806 processed

Message to humans: this is just bookkeeping information for me,
it is of no use to you (unless you think I have a bug, which I don't).

boegelbot · 2024-12-11T23:44:52Z

Test report by @boegelbot
SUCCESS
Build succeeded for 1 out of 1 (1 easyconfigs in total)
cns1 - Linux Rocky Linux 8.9, x86_64, Intel(R) Xeon(R) CPU E5-2667 v3 @ 3.20GHz (haswell), Python 3.6.8
See https://gist.github.com/boegelbot/7c6593ff07edea528e376dcfb5129c78 for a full test report.

sassy-crick · 2024-12-11T23:50:34Z

Something seems to be odd here: the test jobs are all working yet the python -c 'import hoomd' causes a segfault.

boegel · 2025-02-12T17:13:19Z

+    ('Eigen', '3.4.0'),
+    ('Cereal', '1.3.2', '', SYSTEM),
+    ('LLVM', '16.0.6'),
+    ('Clang', '16.0.6'),


Clang dependency will no longer be required with an LLVM built with easybuilders/easybuild-easyblocks#3373

That might be true for newer versions but I am stuck with the 16.0.6 version and I need Clang. So in the end, the way forward was to use the Clang included LLVM but build Clang with shared libraries. Then it was very easy.

And just to add: I actually just have tried it, rebuild LLVM-16.0.6 with the EasyBlock you mentioned, removed Clang and that configuration fails right at the beginning.
So I guess here we are stuck with the PR as it is, unless somebody shows me a better way of doing it. :-)

I've tried quite a lot of things and it simply isn't possible to build HOOMD-blue with the existing statical libarary Clang 16.0.6
Once the _jit...so python library is linked with all libraries it needs it fails with

== FAILED: Installation ended unsuccessfully: Sanity check failed: sanity check command python -c 'import hoomd' failed with exit code -6 (output: : CommandLine Error: Option 'scalarize-variable-insert-extract' registered more than once!

That comes from LLVM somewhere, and it just isn't possible to get rid of with that build. It do need a shared library Clang build.

…d with shared libs

Old file deleted

sassy-crick · 2025-04-17T08:37:57Z

Test report by @sassy-crick
SUCCESS
Build succeeded for 1 out of 1 (1 easyconfigs in total)
hp - Linux Debian GNU/Linux 12, x86_64, 11th Gen Intel(R) Core(TM) i7-1185G7 @ 3.00GHz, Python 3.11.2
See https://gist.github.com/sassy-crick/5c5177b55a715f18d394bccdd8ba3fc9 for a full test report.

…asyconfigs into 20241211204258_new_pr_HOOMD-blue491

Crivella · 2025-07-01T11:35:14Z

@boegelbot please test @ jsc-zen3

boegelbot · 2025-07-01T11:40:11Z

@Crivella: Request for testing this PR well received on jsczen3l1.int.jsc-zen3.fz-juelich.de

PR test command 'if [[ develop != 'develop' ]]; then EB_BRANCH=develop ./easybuild_develop.sh 2> /dev/null 1>&2; EB_PREFIX=/home/boegelbot/easybuild/develop source init_env_easybuild_develop.sh; fi; EB_PR=22013 EB_ARGS= EB_CONTAINER= EB_REPO=easybuild-easyconfigs EB_BRANCH=develop /opt/software/slurm/bin/sbatch --job-name test_PR_22013 --ntasks=8 ~/boegelbot/eb_from_pr_upload_jsc-zen3.sh' executed!

exit code: 0
output:

Submitted batch job 7058

Test results coming soon (I hope)...

Details

- notification for comment with ID 3023565454 processed

Message to humans: this is just bookkeeping information for me,
it is of no use to you (unless you think I have a bug, which I don't).

Crivella · 2025-07-01T11:42:38Z

Test report by @Crivella
SUCCESS
Build succeeded for 2 out of 2 (1 easyconfigs in total)
crivella-desktop - Linux Ubuntu 22.04.5 LTS (Jammy Jellyfish), x86_64, 13th Gen Intel(R) Core(TM) i9-13900K (skylake), Python 3.11.13
See https://gist.github.com/Crivella/beafd80f78c52b73d77531ba60f9fe1c for a full test report.

Crivella · 2025-07-01T11:49:23Z

For the CI we might need an exception in

easybuild-easyconfigs/test/easyconfigs/easyconfigs.py

Lines 362 to 365 in 1853c80

    
           def check_dep_vars(self, gen, dep, dep_vars): 
        
               """Check whether available variants of a particular dependency are acceptable or not.""" 
        
               # short-circuit in case there's only one dependency variant, or none at all

boegelbot · 2025-07-01T11:52:22Z

Test report by @boegelbot
SUCCESS
Build succeeded for 1 out of 1 (1 easyconfigs in total)
jsczen3c1.int.jsc-zen3.fz-juelich.de - Linux Rocky Linux 9.5, x86_64, AMD EPYC-Milan Processor (zen3), Python 3.9.21
See https://gist.github.com/boegelbot/31ea89fbea3b0e661d8691b0279427fc for a full test report.

…asyconfigs into 20241211204258_new_pr_HOOMD-blue491

Crivella

LGTM

Crivella · 2025-10-13T12:11:53Z

Going in, thanks @sassy-crick!

adding easyconfigs: HOOMD-blue-4.9.1-foss-2023a.eb and patches: HOOMD…

05b90f4

…-blue-4.9.1.patch

sassy-crick added the update label Dec 11, 2024

Python sanity check removed as it segfaults

c45eb93

sassy-crick changed the title ~~{phys}[foss/2023a] HOOMD-blue v4.9.1~~ {phys}[foss/2023a] HOOMD-blue v4.9.1 WIP Dec 13, 2024

sassy-crick mentioned this pull request Feb 1, 2025

Builddir 114 GB when compiling Rust-1.70.0-GCCcore-12.3.0.eb inside Rocky-8.9 container #22247

Closed

boegel reviewed Feb 12, 2025

View reviewed changes

sassy and others added 2 commits February 18, 2025 09:44

LLVM removed, fallback to clang-provided LLVM, clang needs to be buil…

8a4fffe

…d with shared libs

Delete easybuild/easyconfigs/h/HOOMD-blue/HOOMD-blue-4.9.1-foss-2023a.eb

cd33233

Old file deleted

sassy-crick changed the title ~~{phys}[foss/2023a] HOOMD-blue v4.9.1 WIP~~ {phys}[foss/2023a] HOOMD-blue v4.9.1 Feb 18, 2025

sassy-crick added the EasyBuild-5.0 EasyBuild 5.0 label Feb 18, 2025

gkaf89 mentioned this pull request Feb 25, 2025

{phys}[foss/2023b] HOOMD-blue v5.1.0 w/ CUDA 12.6.0 #22387

Open

Ninja removed as not needed

1ff8c71

Jorg Sassmannshausen and others added 2 commits April 17, 2025 09:41

Merge branch 'develop' of https://github.com/easybuilders/easybuild-e…

05567cb

…asyconfigs into 20241211204258_new_pr_HOOMD-blue491

Merge branch 'develop' of https://github.com/easybuilders/easybuild-e…

d4593f8

…asyconfigs into 20241211204258_new_pr_HOOMD-blue491

Crivella reviewed Jul 1, 2025

View reviewed changes

Comment thread easybuild/easyconfigs/h/HOOMD-blue/HOOMD-blue-4.9.1-foss-2023a-llvm.eb

sassy-crick added the 2023a label Aug 18, 2025

Crivella and others added 2 commits October 13, 2025 12:13

Merge branch 'develop' of https://github.com/easybuilders/easybuild-e…

1bb915e

…asyconfigs into 20241211204258_new_pr_HOOMD-blue491

Add exception to CI for HOOMD-blue with specific Clang

1ca3d9f

Crivella added this to the next release (5.2.0?) milestone Oct 13, 2025

Crivella approved these changes Oct 13, 2025

View reviewed changes

Crivella merged commit f22ee3a into easybuilders:develop Oct 13, 2025
5 checks passed

sassy-crick deleted the 20241211204258_new_pr_HOOMD-blue491 branch December 9, 2025 11:06

Conversation

sassy-crick commented Dec 11, 2024 • edited by akesandgren Loading Uh oh! There was an error while loading. Please reload this page.

Uh oh!

Uh oh!

github-actions Bot commented Dec 11, 2024 • edited Loading Uh oh! There was an error while loading. Please reload this page.

Uh oh!

Updated software HOOMD-blue-4.9.1-foss-2023a-llvm.eb

Uh oh!

sassy-crick commented Dec 11, 2024

Uh oh!

boegelbot commented Dec 11, 2024

Uh oh!

boegelbot commented Dec 11, 2024

Uh oh!

sassy-crick commented Dec 11, 2024

Uh oh!

boegelbot commented Dec 11, 2024

Uh oh!

boegelbot commented Dec 11, 2024

Uh oh!

sassy-crick commented Dec 11, 2024

Uh oh!

boegel Feb 12, 2025

Choose a reason for hiding this comment

Uh oh!

sassy-crick Feb 18, 2025

Choose a reason for hiding this comment

Uh oh!

sassy-crick Jun 11, 2025

Choose a reason for hiding this comment

Uh oh!

akesandgren Jun 27, 2025 • edited Loading Uh oh! There was an error while loading. Please reload this page.

Uh oh!

Choose a reason for hiding this comment

Uh oh!

sassy-crick commented Apr 17, 2025

Uh oh!

Crivella commented Jul 1, 2025

Uh oh!

Uh oh!

boegelbot commented Jul 1, 2025

Uh oh!

Crivella commented Jul 1, 2025

Uh oh!

Crivella commented Jul 1, 2025 • edited Loading Uh oh! There was an error while loading. Please reload this page.

Uh oh!

Uh oh!

boegelbot commented Jul 1, 2025

Uh oh!

Crivella left a comment

Choose a reason for hiding this comment

Uh oh!

Crivella commented Oct 13, 2025

Uh oh!

Uh oh!

Reviewers

Assignees

Labels

Projects

Milestone

Development

Uh oh!

5 participants

sassy-crick commented Dec 11, 2024 •

edited by akesandgren

Loading

github-actions Bot commented Dec 11, 2024 •

edited

Loading

Updated software `HOOMD-blue-4.9.1-foss-2023a-llvm.eb`

akesandgren Jun 27, 2025 •

edited

Loading

Crivella commented Jul 1, 2025 •

edited

Loading