{astro,lib}[foss/2023b] EveryBeam v0.6.1, WSClean v3.5, DP3 v6.2 #21765

casparvl · 2024-10-29T22:00:52Z

(created using eb --new-pr)

Duplicates a patch from {lib}[foss/2023b] EveryBeam v0.5.2, v0.5.8, including patch to install python bindings and add metadata #21655 (whichever gets merged last will have to sync-with-develop)

Created this PR because Rapthor needs a newer WSClean, which then in turn needs a newer EveryBeam. Currently testing a rapthor pipeline to confirm that this combination works - then I'll mark this ready for review.

Edit: confirmed to work with Rapthor, so I'd like to get this reviewed and merged :) Note that this requires breaking the one-dep-per-toolchain policy. I'm reasonably sure that these tools are typically used in combination in such pipelines though. Plus: it's the only way to make that particular pipeline work in Rapthor - I believe we find that good enough reason. I'll add exceptions for these CI checks.

…023b.eb

github-actions · 2024-11-07T13:17:30Z

Updated software `DP3-6.2-foss-2023b.eb`

Diff against DP3-6.0-foss-2023b.eb

easybuild/easyconfigs/d/DP3/DP3-6.0-foss-2023b.eb

diff --git a/easybuild/easyconfigs/d/DP3/DP3-6.0-foss-2023b.eb b/easybuild/easyconfigs/d/DP3/DP3-6.2-foss-2023b.eb
index 8373cc5f8b..95c28fff22 100644
--- a/easybuild/easyconfigs/d/DP3/DP3-6.0-foss-2023b.eb
+++ b/easybuild/easyconfigs/d/DP3/DP3-6.2-foss-2023b.eb
@@ -1,7 +1,7 @@
 easyblock = 'CMakeMake'
 
 name = 'DP3'
-version = '6.0'
+version = '6.2'
 
 homepage = 'https://dp3.readthedocs.io/'
 description = "DP3: streaming processing pipeline for radio interferometric data."
@@ -22,11 +22,11 @@ sources = [
         }
     },
 ]
-patches = ['DP3-6.0_fix-for-xsimd-error-on-neoverse-v1.patch']
+patches = ['DP3-6.2_fix-for-xsimd-error-on-neoverse-v1.patch']
 checksums = [
     None,  # checksum for git clone source is non-deterministic
-    # DP3-6.0_fix-for-xsimd-error-on-neoverse-v1.patch
-    '7f5069388846c9c715013d5a3a267a6d8e266520445a6427e63e9d52d3046c9d',
+    # DP3-6.2_fix-for-xsimd-error-on-neoverse-v1.patch
+    '51209661ee657151d94778916d4f295b9d767f6bbd13720fc5054a2a24f740dc',
 ]
 
 builddependencies = [
@@ -40,7 +40,7 @@ dependencies = [
     ('GSL', '2.7'),
     ('HDF5', '1.14.3'),
     ('Python', '3.11.5'),
-    ('EveryBeam', '0.5.2'),
+    ('EveryBeam', '0.6.1'),
     ('Armadillo', '12.8.0'),
     ('AOFlagger', '3.4.0'),
     ('IDG', '1.2.0'),

Diff against DP3-6.0-foss-2022a.eb

easybuild/easyconfigs/d/DP3/DP3-6.0-foss-2022a.eb

diff --git a/easybuild/easyconfigs/d/DP3/DP3-6.0-foss-2022a.eb b/easybuild/easyconfigs/d/DP3/DP3-6.2-foss-2023b.eb
index c18f4974ac..95c28fff22 100644
--- a/easybuild/easyconfigs/d/DP3/DP3-6.0-foss-2022a.eb
+++ b/easybuild/easyconfigs/d/DP3/DP3-6.2-foss-2023b.eb
@@ -1,51 +1,57 @@
 easyblock = 'CMakeMake'
 
 name = 'DP3'
-version = '6.0'
+version = '6.2'
+
 homepage = 'https://dp3.readthedocs.io/'
-description = """DP3: streaming processing pipeline for radio interferometric data."""
-
-toolchain = {'name': 'foss', 'version': '2022a'}
-
-sources = [{
-    'filename': '%(name)s-v%(version)s.tar.gz',
-    'git_config': {
-        'url': 'https://git.astron.nl/RD',
-        'repo_name': '%(name)s',
-        'tag': 'v%(version)s',
-        'clone_into': '%(name)s',
-        'recursive': True,
+description = "DP3: streaming processing pipeline for radio interferometric data."
+
+toolchain = {'name': 'foss', 'version': '2023b'}
+
+sources = [
+    {
+        'filename': '%(name)s-v%(version)s.tar.gz',
+        # Repo uses git submodules, which are not included in the release tarballs.
+        # Thus, we let EasyBuild download directly from the git repository.
+        'git_config': {
+            'url': 'https://git.astron.nl/RD',
+            'repo_name': '%(name)s',
+            'tag': 'v%(version)s',
+            'clone_into': '%(name)s',
+            'recursive': True
+        }
     },
-}]
-checksums = [None]
+]
+patches = ['DP3-6.2_fix-for-xsimd-error-on-neoverse-v1.patch']
+checksums = [
+    None,  # checksum for git clone source is non-deterministic
+    # DP3-6.2_fix-for-xsimd-error-on-neoverse-v1.patch
+    '51209661ee657151d94778916d4f295b9d767f6bbd13720fc5054a2a24f740dc',
+]
 
 builddependencies = [
-    ('CMake', '3.24.3'),
+    ('CMake', '3.27.6'),
 ]
-
 dependencies = [
     ('casacore', '3.5.0'),
-    ('Boost', '1.79.0'),
-    ('CFITSIO', '4.2.0'),
+    ('Boost', '1.83.0'),
+    ('CFITSIO', '4.3.1'),
     ('WCSLIB', '7.11'),
     ('GSL', '2.7'),
-    ('HDF5', '1.12.2'),
-    ('Python', '3.10.4'),
-    ('EveryBeam', '0.5.2'),
-    ('Armadillo', '11.4.3'),
-    ('AOFlagger', '3.4.0')
+    ('HDF5', '1.14.3'),
+    ('Python', '3.11.5'),
+    ('EveryBeam', '0.6.1'),
+    ('Armadillo', '12.8.0'),
+    ('AOFlagger', '3.4.0'),
+    ('IDG', '1.2.0'),
 ]
 
-# Without this, the wrong (system) python is picked up by cmake
-# in cases where the system python is newer than the one used in these EasyConfigs
-# See PR # 19119
-configopts = '-DPython3_EXECUTABLE=$EBROOTPYTHON/bin/python '
 
 sanity_check_paths = {
-    'files': ['include/include/dp3/base/DP3.h', 'bin/DP3'],
+    'files': ['include/include/%(namelower)s/base/%(name)s.h', 'bin/%(name)s'],
     'dirs': ['bin'],
 }
 
-sanity_check_commands = [('DP3', '--version')]
+sanity_check_commands = [('%(name)s', '--version')]
 
 moduleclass = 'astro'

Updated software `EveryBeam-0.6.1-foss-2023b.eb`

Diff against EveryBeam-0.5.2-foss-2023b.eb

easybuild/easyconfigs/e/EveryBeam/EveryBeam-0.5.2-foss-2023b.eb

diff --git a/easybuild/easyconfigs/e/EveryBeam/EveryBeam-0.5.2-foss-2023b.eb b/easybuild/easyconfigs/e/EveryBeam/EveryBeam-0.6.1-foss-2023b.eb
index bec1bf004e..3dfbb81de6 100644
--- a/easybuild/easyconfigs/e/EveryBeam/EveryBeam-0.5.2-foss-2023b.eb
+++ b/easybuild/easyconfigs/e/EveryBeam/EveryBeam-0.6.1-foss-2023b.eb
@@ -1,7 +1,7 @@
 easyblock = 'CMakeMake'
 
 name = 'EveryBeam'
-version = '0.5.2'
+version = "0.6.1"
 
 homepage = 'https://everybeam.readthedocs.io/'
 description = """Library that provides the antenna response pattern for several instruments,
@@ -23,7 +23,13 @@ sources = [
         }
     },
 ]
-checksums = [None]
+patches = [
+    'EveryBeam-0.5.4_python_metadata.patch'
+]
+checksums = [
+    None,  # checksum for git clone source is non-deterministic
+    '63c42e85d1b63cbf5887d10ec158be9b69e2c63cf3b209e9c1944f46c01810ac'  # EveryBeam-0.5.4_python_metadata.patch
+]
 
 builddependencies = [
     ('CMake', '3.27.6'),
@@ -40,10 +46,25 @@ dependencies = [
     ('libxml2', '2.11.5'),
 ]
 
+configopts = "-DBUILD_WITH_PYTHON=ON "
+
+# Note: we need to create a dir %(builddir)s/EveryBeam/everybeam for the pip install to complete successfully
+postinstallcmds = [
+    "mkdir -p %(builddir)s/EveryBeam/everybeam && pip install %(builddir)s/EveryBeam --prefix=%(installdir)s"
+]
+
+modextravars = {'EVERYBEAM_DATADIR': '%(installdir)s/share/everybeam'}
+modextrapaths = {'PYTHONPATH': 'lib/python%(pyshortver)s/site-packages'}
 
 sanity_check_paths = {
     'files': ['include/%(name)s/beamformer.h', 'lib/libeverybeam.%s' % SHLIB_EXT],
     'dirs': [],
 }
 
+# Check if Python support was built correctly, and can be found by pip
+sanity_check_commands = [
+    'python3 -c "import everybeam"',
+    'pip list | grep everybeam'
+]
+
 moduleclass = 'lib'

Diff against EveryBeam-0.5.2-foss-2022a.eb

easybuild/easyconfigs/e/EveryBeam/EveryBeam-0.5.2-foss-2022a.eb

diff --git a/easybuild/easyconfigs/e/EveryBeam/EveryBeam-0.5.2-foss-2022a.eb b/easybuild/easyconfigs/e/EveryBeam/EveryBeam-0.6.1-foss-2023b.eb
index b61f0c8616..3dfbb81de6 100644
--- a/easybuild/easyconfigs/e/EveryBeam/EveryBeam-0.5.2-foss-2022a.eb
+++ b/easybuild/easyconfigs/e/EveryBeam/EveryBeam-0.6.1-foss-2023b.eb
@@ -1,49 +1,70 @@
 easyblock = 'CMakeMake'
 
 name = 'EveryBeam'
-version = '0.5.2'
+version = "0.6.1"
+
 homepage = 'https://everybeam.readthedocs.io/'
 description = """Library that provides the antenna response pattern for several instruments,
 such as LOFAR (and LOBES), SKA (OSKAR), MWA, JVLA, etc."""
 
-toolchain = {'name': 'foss', 'version': '2022a'}
+toolchain = {'name': 'foss', 'version': '2023b'}
 
-sources = [{
-    'filename': '%(name)s-v%(version)s.tar.gz',
-    'git_config': {
-        'url': 'https://git.astron.nl/RD',
-        'repo_name': '%(name)s',
-        'tag': 'v%(version)s',
-        'clone_into': '%(name)s',
-        'recursive': True,
+sources = [
+    {
+        'filename': '%(name)s-v%(version)s.tar.gz',
+        # Repo uses git submodules, which are not included in the release tarballs.
+        # Thus, we let EasyBuild download directly from the git repository.
+        'git_config': {
+            'url': 'https://git.astron.nl/RD',
+            'repo_name': '%(name)s',
+            'tag': 'v%(version)s',
+            'clone_into': '%(name)s',
+            'recursive': True
+        }
     },
-}]
-checksums = [None]
+]
+patches = [
+    'EveryBeam-0.5.4_python_metadata.patch'
+]
+checksums = [
+    None,  # checksum for git clone source is non-deterministic
+    '63c42e85d1b63cbf5887d10ec158be9b69e2c63cf3b209e9c1944f46c01810ac'  # EveryBeam-0.5.4_python_metadata.patch
+]
 
 builddependencies = [
-    ('CMake', '3.24.3'),
-    ('wget', '1.21.3'),
+    ('CMake', '3.27.6'),
+    ('wget', '1.21.4'),
 ]
-
 dependencies = [
     ('casacore', '3.5.0'),
-    ('Boost', '1.79.0'),
-    ('CFITSIO', '4.2.0'),
+    ('Boost', '1.83.0'),
+    ('CFITSIO', '4.3.1'),
     ('WCSLIB', '7.11'),
     ('GSL', '2.7'),
-    ('HDF5', '1.12.2'),
-    ('Python', '3.10.4'),
-    ('libxml2', '2.9.13'),
+    ('HDF5', '1.14.3'),
+    ('Python', '3.11.5'),
+    ('libxml2', '2.11.5'),
 ]
 
-# Without this, the wrong (system) python is picked up by cmake
-# in cases where the system python is newer than the one used in these EasyConfigs
-# See PR # 19119
-configopts = '-DPython3_EXECUTABLE=$EBROOTPYTHON/bin/python '
+configopts = "-DBUILD_WITH_PYTHON=ON "
+
+# Note: we need to create a dir %(builddir)s/EveryBeam/everybeam for the pip install to complete successfully
+postinstallcmds = [
+    "mkdir -p %(builddir)s/EveryBeam/everybeam && pip install %(builddir)s/EveryBeam --prefix=%(installdir)s"
+]
+
+modextravars = {'EVERYBEAM_DATADIR': '%(installdir)s/share/everybeam'}
+modextrapaths = {'PYTHONPATH': 'lib/python%(pyshortver)s/site-packages'}
 
 sanity_check_paths = {
-    'files': ['include/EveryBeam/beamformer.h', 'lib/libeverybeam.so'],
+    'files': ['include/%(name)s/beamformer.h', 'lib/libeverybeam.%s' % SHLIB_EXT],
     'dirs': [],
 }
 
+# Check if Python support was built correctly, and can be found by pip
+sanity_check_commands = [
+    'python3 -c "import everybeam"',
+    'pip list | grep everybeam'
+]
+
 moduleclass = 'lib'

Updated software `WSClean-3.5-foss-2023b.eb`

Diff against WSClean-3.4-foss-2023b.eb

easybuild/easyconfigs/w/WSClean/WSClean-3.4-foss-2023b.eb

diff --git a/easybuild/easyconfigs/w/WSClean/WSClean-3.4-foss-2023b.eb b/easybuild/easyconfigs/w/WSClean/WSClean-3.5-foss-2023b.eb
index b1bdea0de2..55a951838a 100644
--- a/easybuild/easyconfigs/w/WSClean/WSClean-3.4-foss-2023b.eb
+++ b/easybuild/easyconfigs/w/WSClean/WSClean-3.5-foss-2023b.eb
@@ -1,7 +1,7 @@
 easyblock = 'CMakeMake'
 
 name = 'WSClean'
-version = '3.4'
+version = "3.5"
 
 homepage = 'https://wsclean.readthedocs.io/'
 description = """WSClean (w-stacking clean) is a fast generic widefield imager.
@@ -10,21 +10,29 @@ multi-frequency deconvolution."""
 
 toolchain = {'name': 'foss', 'version': '2023b'}
 
+# Regular source tarballs don't include the git submodules. Check https://gitlab.com/aroffringa/wsclean/-/packages/
+# for the right path to a tarball that does contain it
 sources = [
     {
-        'source_urls': ['https://gitlab.com/aroffringa/%(namelower)s/-/package_files/97237455/'],
+        'source_urls': ['https://gitlab.com/aroffringa/%(namelower)s/-/package_files/140629243/'],
         'filename': '%(namelower)s-v%(version)s.tar.bz2',
         'download_filename': 'download'
     },
 ]
-checksums = ['b43d8ca490ccf34dd22aae6c5ca88a5dcb3cff0526835d3f97fa6d239745e641']
+patches = ['WSClean-3.5_cmake-fixes-python-and-boost.patch']
+checksums = [
+    {'wsclean-v3.5.tar.bz2': 'ba1863945b6341398409d9fee0ab9ff202c4cb1216a102d0d91a92b45103ec95'},
+    {'WSClean-3.5_cmake-fixes-python-and-boost.patch':
+     '21cd5a9b3e94bab4ebe7d16cd24995a16726f290a432a50b407005d45144e3c7'},
+]
 
 builddependencies = [
     ('CMake', '3.27.6'),
 ]
+
 dependencies = [
     ('casacore', '3.5.0'),
-    ('EveryBeam', '0.5.2'),
+    ('EveryBeam', '0.6.1'),
     ('Boost', '1.83.0'),
     ('CFITSIO', '4.3.1'),
     ('GSL', '2.7'),

Diff against WSClean-3.4-foss-2022a.eb

easybuild/easyconfigs/w/WSClean/WSClean-3.4-foss-2022a.eb

diff --git a/easybuild/easyconfigs/w/WSClean/WSClean-3.4-foss-2022a.eb b/easybuild/easyconfigs/w/WSClean/WSClean-3.5-foss-2023b.eb
index e3bdcb0089..55a951838a 100644
--- a/easybuild/easyconfigs/w/WSClean/WSClean-3.4-foss-2022a.eb
+++ b/easybuild/easyconfigs/w/WSClean/WSClean-3.5-foss-2023b.eb
@@ -1,46 +1,52 @@
 easyblock = 'CMakeMake'
 
 name = 'WSClean'
-version = '3.4'
+version = "3.5"
 
 homepage = 'https://wsclean.readthedocs.io/'
 description = """WSClean (w-stacking clean) is a fast generic widefield imager.
 It implements several gridding algorithms and offers fully-automated multi-scale
 multi-frequency deconvolution."""
 
-toolchain = {'name': 'foss', 'version': '2022a'}
+toolchain = {'name': 'foss', 'version': '2023b'}
 
-sources = [{
-    'source_urls': ['https://gitlab.com/aroffringa/wsclean/-/package_files/97237455/'],
-    'filename': '%(namelower)s-v%(version)s.tar.bz2',
-    'download_filename': 'download'  # endpoint for source tarball is not versioned
-}]
-checksums = ['b43d8ca490ccf34dd22aae6c5ca88a5dcb3cff0526835d3f97fa6d239745e641']
+# Regular source tarballs don't include the git submodules. Check https://gitlab.com/aroffringa/wsclean/-/packages/
+# for the right path to a tarball that does contain it
+sources = [
+    {
+        'source_urls': ['https://gitlab.com/aroffringa/%(namelower)s/-/package_files/140629243/'],
+        'filename': '%(namelower)s-v%(version)s.tar.bz2',
+        'download_filename': 'download'
+    },
+]
+patches = ['WSClean-3.5_cmake-fixes-python-and-boost.patch']
+checksums = [
+    {'wsclean-v3.5.tar.bz2': 'ba1863945b6341398409d9fee0ab9ff202c4cb1216a102d0d91a92b45103ec95'},
+    {'WSClean-3.5_cmake-fixes-python-and-boost.patch':
+     '21cd5a9b3e94bab4ebe7d16cd24995a16726f290a432a50b407005d45144e3c7'},
+]
 
 builddependencies = [
-    ('CMake', '3.24.3'),
+    ('CMake', '3.27.6'),
 ]
 
 dependencies = [
     ('casacore', '3.5.0'),
-    ('EveryBeam', '0.5.2'),
-    ('Boost', '1.79.0'),
-    ('CFITSIO', '4.2.0'),
+    ('EveryBeam', '0.6.1'),
+    ('Boost', '1.83.0'),
+    ('CFITSIO', '4.3.1'),
     ('GSL', '2.7'),
-    ('HDF5', '1.12.2'),
-    ('Python', '3.10.4'),
+    ('HDF5', '1.14.3'),
+    ('Python', '3.11.5'),
+    ('IDG', '1.2.0'),
 ]
 
-# Without this, the wrong (system) python is picked up by cmake
-# in cases where the system python is newer than the one used in these EasyConfigs
-# See PR # 19119
-configopts = '-DPython3_EXECUTABLE=$EBROOTPYTHON/bin/python '
 
 sanity_check_paths = {
-    'files': ['include/wscleaninterface.h', 'bin/wsclean'],
+    'files': ['include/wscleaninterface.h', 'bin/%(namelower)s'],
     'dirs': ['bin'],
 }
 
-sanity_check_commands = [('wsclean', '--version')]
+sanity_check_commands = [('%(namelower)s', '--version')]
 
 moduleclass = 'astro'

casparvl · 2024-11-11T15:13:25Z

@boegelbot please test @ generoso

boegelbot · 2024-11-11T15:25:11Z

@casparvl: Request for testing this PR well received on login1

PR test command 'EB_PR=21765 EB_ARGS= EB_CONTAINER= EB_REPO=easybuild-easyconfigs /opt/software/slurm/bin/sbatch --job-name test_PR_21765 --ntasks=4 ~/boegelbot/eb_from_pr_upload_generoso.sh' executed!

exit code: 0
output:

Submitted batch job 14687

Test results coming soon (I hope)...

- notification for comment with ID 2468410804 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 · 2024-11-11T15:26:02Z

Test report by @boegelbot
FAILED
Build succeeded for 0 out of 3 (3 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/1073c9803bdd26b65fb0b1504958456a for a full test report.

casparvl · 2024-11-11T15:40:42Z

@boegelbot please test @ generoso

boegelbot · 2024-11-11T15:45:11Z

@casparvl: Request for testing this PR well received on login1

PR test command 'EB_PR=21765 EB_ARGS= EB_CONTAINER= EB_REPO=easybuild-easyconfigs /opt/software/slurm/bin/sbatch --job-name test_PR_21765 --ntasks=4 ~/boegelbot/eb_from_pr_upload_generoso.sh' executed!

exit code: 0
output:

Submitted batch job 14688

Test results coming soon (I hope)...

- notification for comment with ID 2468471070 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).

casparvl · 2024-11-11T15:49:11Z

@boegelbot please test @ jsc-zen3

boegelbot · 2024-11-11T15:50:09Z

@casparvl: 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=21765 EB_ARGS= EB_CONTAINER= EB_REPO=easybuild-easyconfigs EB_BRANCH=develop /opt/software/slurm/bin/sbatch --job-name test_PR_21765 --ntasks=8 ~/boegelbot/eb_from_pr_upload_jsc-zen3.sh' executed!

exit code: 0
output:

Submitted batch job 5250

Test results coming soon (I hope)...

- notification for comment with ID 2468489307 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 · 2024-11-11T15:56:48Z

Test report by @boegelbot
FAILED
Build succeeded for 2 out of 3 (3 easyconfigs in total)
jsczen3c1.int.jsc-zen3.fz-juelich.de - Linux Rocky Linux 9.4, x86_64, AMD EPYC-Milan Processor (zen3), Python 3.9.18
See https://gist.github.com/boegelbot/a5146e9b2d00df8b0ae23ba46b9868db for a full test report.

boegelbot · 2024-11-11T15:57:38Z

Test report by @boegelbot
FAILED
Build succeeded for 2 out of 3 (3 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/61d59a291628d22716c8a00a0bac0548 for a full test report.

casparvl · 2024-11-11T16:25:01Z

Test report by @casparvl
SUCCESS
Build succeeded for 3 out of 3 (3 easyconfigs in total)
tcn1.local.snellius.surf.nl - Linux RHEL 9.4, x86_64, AMD EPYC 7H12 64-Core Processor, Python 3.9.18
See https://gist.github.com/casparvl/234697d2cd9bffe5306ba59df8e39210 for a full test report.

casparvl · 2024-11-11T16:27:02Z

@boegelbot please test @ generoso

boegelbot · 2024-11-11T16:30:08Z

@casparvl: Request for testing this PR well received on login1

PR test command 'EB_PR=21765 EB_ARGS= EB_CONTAINER= EB_REPO=easybuild-easyconfigs /opt/software/slurm/bin/sbatch --job-name test_PR_21765 --ntasks=4 ~/boegelbot/eb_from_pr_upload_generoso.sh' executed!

exit code: 0
output:

Submitted batch job 14690

Test results coming soon (I hope)...

- notification for comment with ID 2468572755 processed

Message to humans: this is just bookkeeping information for me,
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boegelbot · 2024-11-11T16:50:33Z

Test report by @boegelbot
SUCCESS
Build succeeded for 3 out of 3 (3 easyconfigs in total)
cns2 - 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/819ad8ccb1905ecfb148a750adba3bf2 for a full test report.

casparvl · 2024-11-19T10:43:12Z

@boegelbot please test @ jsc-zen3

boegelbot · 2025-01-22T15:40:08Z

@casparvl: 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=21765 EB_ARGS= EB_CONTAINER= EB_REPO=easybuild-easyconfigs EB_BRANCH=develop /opt/software/slurm/bin/sbatch --job-name test_PR_21765 --ntasks=8 ~/boegelbot/eb_from_pr_upload_jsc-zen3.sh' executed!

exit code: 0
output:

Submitted batch job 5570

Test results coming soon (I hope)...

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Message to humans: this is just bookkeeping information for me,
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boegelbot · 2025-01-22T15:52:09Z

Test report by @boegelbot
SUCCESS
Build succeeded for 3 out of 3 (3 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/8086fd35c5f37b2f826756c6bdfab90c for a full test report.

casparvl · 2025-01-22T16:26:23Z

Test report by @casparvl
SUCCESS
Build succeeded for 3 out of 3 (3 easyconfigs in total)
tcn1.local.snellius.surf.nl - Linux RHEL 9.4, x86_64, AMD EPYC 7H12 64-Core Processor, Python 3.9.18
See https://gist.github.com/casparvl/304bc9d315a9bc7dc1cd0f8d68ff8b01 for a full test report.

boegel

lgtm

casparvl · 2025-01-22T17:04:56Z

FYI, also plenty of succesful builds in EESSI/software-layer#877

boegel · 2025-01-22T17:19:59Z

Test report by @boegel
FAILED
Build succeeded for 1 out of 6 (3 easyconfigs in total)
node3107.skitty.os - Linux RHEL 9.4, x86_64, Intel(R) Xeon(R) Gold 6140 CPU @ 2.30GHz (skylake_avx512), Python 3.9.18
See https://gist.github.com/boegel/7856a34c996bae9fa169e203432961f0 for a full test report.

boegel · 2025-01-22T18:17:40Z

@casparvl wget --retry-connrefused ftp://anonymous@ftp.astron.nl/outgoing/Measures/WSRT_Measures.ztar fails because FTP is blocked on our system.

Is there any way we can avoid relying on ftp://?

Also, it would be great if we didn't rely on on-the-fly downloading durign the installation itself, so this file could be added to sources instead, and then copied when needed (that would make it OK-ish to have it downloaded over FTP, since then it'll be cached)

casparvl · 2025-01-22T20:11:26Z

Wait, where does this get downloaded?

casparvl · 2025-01-22T20:18:17Z

Ah, found it, in one of the deps https://github.com/easybuilders/easybuild-easyconfigs/blob/develop/easybuild/easyconfigs/c/casacore/casacore-3.5.0-foss-2023b.eb

The official instructions say to get it from the FTP server, I have no idea if it would be available in any other way https://github.com/casacore/casacore?tab=readme-ov-file#obtaining-measures-data

Can the source step download from FTP? If so, we can definitely do that (would be better, also because then things like --fetch work properly). But then: how do we get this tarball to be extracted in desired location (%(installdir)s/data if I read the casacore easyconfig right)?

Edit: I guess maybe I can do:

extract_cmd = 'tar xfvz %s --one-top-level=%(installdir)s/data

or something?

casparvl · 2025-01-22T20:50:42Z

Fixed in #22201

easybuild/easyconfigs/e/EveryBeam/EveryBeam-0.6.1-foss-2023b.eb

test/easyconfigs/easyconfigs.py

easybuild/easyconfigs/e/EveryBeam/EveryBeam-0.6.1-foss-2023b.eb

easybuild/easyconfigs/e/EveryBeam/EveryBeam-0.5.4_python_metadata.patch

Co-authored-by: Bob Dröge <b.e.droge@rug.nl>

bedroge · 2025-02-06T15:58:34Z

Test report by @bedroge
SUCCESS
Build succeeded for 3 out of 3 (3 easyconfigs in total)
interactive1 - Linux Rocky Linux 8.10, x86_64, AMD EPYC-Milan Processor (zen3), Python 3.6.8
See https://gist.github.com/bedroge/2b30318d27ee524db05318988e83ddae for a full test report.

bedroge · 2025-02-06T16:36:26Z

Test report by @bedroge
Using easyblocks from PR(s) easybuilders/easybuild-easyblocks#3463
FAILED
Build succeeded for 4 out of 5 (3 easyconfigs in total)
bob-Latitude-5300 - Linux Ubuntu 24.04.1 LTS (Noble Numbat), x86_64, Intel(R) Core(TM) i7-8665U CPU @ 1.90GHz, Python 3.12.3
See https://gist.github.com/bedroge/c2469aa66a2a2330874f371c92680f45 for a full test report.

It's picking up Python libraries from the OS. Verified locally that this can be solved by including the change from https://gitlab.com/aroffringa/wsclean/-/commit/46e7d797c9184d67b90b26a38877f91cd07b8e16, and by using the updated CMakeMake easyblock from easybuilders/easybuild-easyblocks#3463.

…7c9184d67b90b26a38877f91cd07b8e16

…_python_fix Add patch that fixes cmake warning related to boost and python

bedroge · 2025-02-06T19:07:54Z

@boegelbot please test @ jsc-zen3

boegelbot · 2025-02-06T19:10:09Z

@bedroge: 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=21765 EB_ARGS= EB_CONTAINER= EB_REPO=easybuild-easyconfigs EB_BRANCH=develop /opt/software/slurm/bin/sbatch --job-name test_PR_21765 --ntasks=8 ~/boegelbot/eb_from_pr_upload_jsc-zen3.sh' executed!

exit code: 0
output:

Submitted batch job 5676

Test results coming soon (I hope)...

- notification for comment with ID 2640760861 processed

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bedroge · 2025-02-06T19:20:26Z

Test report by @bedroge
Using easyblocks from PR(s) easybuilders/easybuild-easyblocks#3463
SUCCESS
Build succeeded for 3 out of 3 (3 easyconfigs in total)
bob-Latitude-5300 - Linux Ubuntu 24.04.1 LTS (Noble Numbat), x86_64, Intel(R) Core(TM) i7-8665U CPU @ 1.90GHz, Python 3.12.3
See https://gist.github.com/bedroge/02e5742a96da2cefdd4e7baeab0eb3d9 for a full test report.

boegelbot · 2025-02-06T19:22:30Z

Test report by @boegelbot
SUCCESS
Build succeeded for 3 out of 3 (3 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/f4ec313686da6cff50bfb3226c165e92 for a full test report.

bedroge · 2025-02-06T19:33:55Z

Test report by @bedroge
SUCCESS
Build succeeded for 3 out of 3 (3 easyconfigs in total)
interactive1 - Linux Rocky Linux 8.10, x86_64, AMD EPYC-Milan Processor (zen3), Python 3.6.8
See https://gist.github.com/bedroge/2f94d8790b9d357f76399f625f0eebd6 for a full test report.

bedroge

Looks good to me!

bedroge · 2025-02-06T20:05:19Z

Going in, thanks @casparvl!

adding easyconfigs: EveryBeam-0.6.1-foss-2023b.eb, WSClean-3.5-foss-2…

08ae511

…023b.eb

casparvl added the update label Oct 29, 2024

casparvl marked this pull request as draft October 29, 2024 22:02

casparvl changed the title ~~{astro,lib}[foss/2023b] EveryBeam v0.6.1, WSClean v3.5~~ {astro,lib}[foss/2023b] EveryBeam v0.6.1, WSClean v3.5, DP3 v6.2 Nov 4, 2024

casparl added 4 commits November 4, 2024 16:12

add DP3 as it also depends on EveryBeam

178870b

update patch

0054564

update patch checksum description

975cb97

Add EVERYBEAM_DATADIR environment variable

c3b3019

Add EVERYBEAM_DATADIR environment variable

88ba2ab

casparvl marked this pull request as ready for review November 11, 2024 15:13

Caspar van Leeuwen added 3 commits November 11, 2024 16:33

Make exception for 2nd EveryBeam dependency in 2023b

d7f9d7b

Add checksum for source

7f938fc

Add patch to this PR as well

c573ccd

Fixed checksum to correct version (3.5)

0c8f1dd

Fix CI issue

f8ecb4f

casparvl mentioned this pull request Jan 22, 2025

{2023.06}[foss/2023b] DP3 v6.2, EveryBeam v0.6.1, WSClean v3.5 EESSI/software-layer#877

Merged

1 task

boegel previously approved these changes Jan 22, 2025

View reviewed changes

casparvl mentioned this pull request Jan 23, 2025

move download of data files to source step for Casacore v3.5.0 #22201

Merged

casparvl requested a review from boegel January 31, 2025 13:49

bedroge requested changes Feb 6, 2025

View reviewed changes

Fix my English thanks to Bob :)

2bb10ad

Co-authored-by: Bob Dröge <b.e.droge@rug.nl>

casparvl dismissed boegel’s stale review via 2bb10ad February 6, 2025 14:20

bedroge and others added 3 commits February 6, 2025 19:56

add patch from https://gitlab.com/aroffringa/wsclean/-/commit/46e7d79…

a4fb6d2

…7c9184d67b90b26a38877f91cd07b8e16

use cmake patch for python and boost warnings

8c51818

Merge pull request #9 from bedroge/20241029230044_new_pr_EveryBeam061…

aef874a

…_python_fix Add patch that fixes cmake warning related to boost and python

bedroge approved these changes Feb 6, 2025

View reviewed changes

bedroge added this to the release after 4.9.4 milestone Feb 6, 2025

bedroge merged commit c7e4bfe into easybuilders:develop Feb 6, 2025
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{astro,lib}[foss/2023b] EveryBeam v0.6.1, WSClean v3.5, DP3 v6.2 #21765

{astro,lib}[foss/2023b] EveryBeam v0.6.1, WSClean v3.5, DP3 v6.2 #21765

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{astro,lib}[foss/2023b] EveryBeam v0.6.1, WSClean v3.5, DP3 v6.2 #21765

{astro,lib}[foss/2023b] EveryBeam v0.6.1, WSClean v3.5, DP3 v6.2 #21765

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Updated software DP3-6.2-foss-2023b.eb

Updated software EveryBeam-0.6.1-foss-2023b.eb

Updated software WSClean-3.5-foss-2023b.eb

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Updated software `DP3-6.2-foss-2023b.eb`

Updated software `EveryBeam-0.6.1-foss-2023b.eb`

Updated software `WSClean-3.5-foss-2023b.eb`

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