{phys}[foss/2023a] HOOMD-blue v4.9.1 WIP

[sassy-crick]

(created using eb --new-pr)

See also here for some of the encountered problems.

[github-actions]

Updated software HOOMD-blue-4.9.1-foss-2023a.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.eb
index f576061ecc..20197c06e4 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.eb
@@ -1,32 +1,42 @@
+# LLVM included, needs to be version 16.x as newer versions have a different API
+# Author: J. Sassmannshausenb (Imperial College London/UK)
+
 easyblock = 'CMakeMake'
 
 name = 'HOOMD-blue'
-version = "4.0.1"
+version = "4.9.1"
 
 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."""
 
-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': '3b611c177414c2b9c1da1c7dd54d149406875fda37f92fcf24ce34ebf416a30b'},
+]
 
 builddependencies = [
-    ('CMake', '3.24.3'),
-    ('pybind11', '2.9.2'),
+    ('CMake', '3.26.3'),
+    ('pybind11', '2.11.1'),
+    ('Ninja', '1.11.1'),
 ]
 
 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),
+    ('LLVM', '16.0.6'),
+    ('Clang', '16.0.6'),
 ]
 
 _copts = [
@@ -36,8 +46,9 @@ _copts = [
     '-DBUILD_METAL=ON',
     '-DENABLE_TBB=ON',
     '-DBUILD_TESTING=ON',
-    '-DPYTHON_EXECUTABLE=$EBROOTPYTHON/bin/python',
+    '-DENABLE_LLVM=ON',
 ]
+
 configopts = ' '.join(_copts)
 
 postinstallcmds = [
@@ -52,9 +63,10 @@ sanity_check_paths = {
     'dirs': ['lib/cmake'],
 }
 
-sanity_check_commands = [
-    "python -c 'import hoomd'",
-]
+# This causes a segfault but seems to work when done manually
+# sanity_check_commands = [
+#     "python -c 'import hoomd'",
+# ]
 
 modextrapaths = {'PYTHONPATH': ''}
 

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.eb
index ab46959e6c..20197c06e4 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.eb
@@ -1,53 +1,61 @@
+# LLVM included, needs to be version 16.x as newer versions have a different API
+# Author: J. Sassmannshausenb (Imperial College London/UK)
+
 easyblock = 'CMakeMake'
 
 name = 'HOOMD-blue'
-version = "4.0.1"
-versionsuffix = '-CUDA-%(cudaver)s'
+version = "4.9.1"
 
-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."""
 
-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': '3b611c177414c2b9c1da1c7dd54d149406875fda37f92fcf24ce34ebf416a30b'},
+]
 
 builddependencies = [
-    ('CMake', '3.24.3'),
-    ('pybind11', '2.9.2'),
+    ('CMake', '3.26.3'),
+    ('pybind11', '2.11.1'),
+    ('Ninja', '1.11.1'),
 ]
 
 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),
+    ('LLVM', '16.0.6'),
+    ('Clang', '16.0.6'),
 ]
 
 _copts = [
-    '-DENABLE_GPU=ON',
-    '-DHOOMD_GPU_PLATFORM=CUDA',
+    '-DENABLE_GPU=OFF',
     '-DENABLE_MPI=ON',
     '-DBUILD_MD=ON',
     '-DBUILD_METAL=ON',
     '-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 = {
@@ -55,9 +63,10 @@ sanity_check_paths = {
     'dirs': ['lib/cmake'],
 }
 
-sanity_check_commands = [
-    "python -c 'import hoomd'",
-]
+# This causes a segfault but seems to work when done manually
+# sanity_check_commands = [
+#     "python -c 'import hoomd'",
+# ]
 
 modextrapaths = {'PYTHONPATH': ''}
 

[sassy-crick]

@boegelbot: please test @ generoso

[boegelbot]

@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)...

- 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]

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]

@boegelbot: please test @ generoso

[boegelbot]

@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)...

- 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]

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]

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