Merge pull request easybuilders#23365 from sassy-crick/20250709151442_new_pr_LavaVu199

{devel,vis}[foss/2023b] LavaVu v1.9.9, Underworld v2.16.4

Author: Crivella

easybuild/easyconfigs/l/LavaVu/LavaVu-1.9.9-foss-2023b-egl.eb

@@ -0,0 +1,82 @@
+# Thanks to Mikael Öhman, Alexandre Strube and Alex Domingo for helping with
+# the Python problem
+# Author: J. Saßmannshausen (Imperial College London / UK)
+# Use this version for any GUI installations you want to do
+
+easyblock = 'PythonBundle'
+
+name = 'LavaVu'
+version = '1.9.9'
+versionsuffix = '-egl'
+
+homepage = 'https://lavavu.github.io/Documentation/'
+description = """
+A lightweight scientific visualisation tool with a python interface for fast
+and flexible visual analysis.
+
+LavaVu provides access to OpenGL powered 3D rendering of point, line, surface
+and volume data with minimal setup and an interface focused on simple mapping
+of values to visual properties while abstracting all the intricacies of OpenGL.
+A scientific visualisation tool with a python interface for fast and flexible
+visual analysis.
+"""
+citing = """
+[1] Stegman, D.R., Moresi, L., Turnbull, R., Giordani, J., Sunter, P., Lo, A.
+and S. Quenette
+gLucifer: Next Generation Visualization Framework for High performance
+computational geodynamics, 2008, Visual Geosciences
+http://dx.doi.org/10.1007/s10069-008-0010-2
+[2] Ruijters, Daniel & ter Haar Romeny, Bart & Suetens, Paul. (2008).
+Efficient GPU-Based Texture Interpolation using Uniform B-Splines.
+J. Graphics Tools. 13. 61-69.
+http://dx.doi.org/10.1080/2151237X.2008.10129269
+
+Zenodo: https://doi.org/10.5281/zenodo.2585376
+"""
+
+toolchain = {'name': 'foss', 'version': '2023b'}
+
+builddependencies = [
+    ('SWIG', '4.1.1'),
+]
+
+dependencies = [
+    ('Python', '3.11.5'),
+    ('SciPy-bundle', '2023.11'),
+    ('Python-bundle-PyPI', '2023.10'),
+    ('X11', '20231019'),
+    ('FFmpeg', '6.0'),
+    ('libglvnd', '1.7.0'),
+    ('aiohttp', '3.9.5'),
+    ('jupyter-server-proxy', '4.1.2'),
+    ('matplotlib', '3.8.2'),
+    ('Mesa', '23.1.9'),
+]
+
+# We need to run a post-install command, and that way it hopefully makes it
+# easier to maintain. Thanks to Davide Grassano for helping out here.
+_lavavu_dir = '%(installdir)s/lib/python%(pyshortver)s/site-packages/lavavu'
+_lavavu_postinstall_cmd = ' && '.join([
+    f'rm -f {_lavavu_dir}/osmesa/LavaVuPython.py',
+    f'cp -f {_lavavu_dir}/LavaVuPython.py {_lavavu_dir}/osmesa/',
+    f'cd {_lavavu_dir}/osmesa/',
+    'sed -i "9,11d" LavaVuPython.py',
+    'sed -i "s/    import _LavaVuPython/import _LavaVuPython/" LavaVuPython.py',
+    'cd -',
+])
+
+exts_list = [
+    ('numpy_quaternion', '2024.0.9', {
+        'modulename': 'quaternion',
+        'checksums': ['de0125055bb2fed019c1afe8fe5a9844739a46196a1ee8838fa6b6b2a149aaad'],
+    }),
+    ('lavavu', version, {
+        # Possible choices: EGL, OSMESA or X11
+        'prebuildopts': 'export LV_EGL=1 && ',
+        # The original symlink leads to problems, so we are doing this dance to get that fixed:
+        'postinstallcmds': [_lavavu_postinstall_cmd],
+        'checksums': ['7e31c0d18b8bff3690101df3b12d883c2fdfdada3d88b15b082559b77d7c416d'],
+    }),
+]
+
+moduleclass = 'vis'

easybuild/easyconfigs/u/Underworld/Underworld-2.16.4-foss-2023b-egl.eb

@@ -0,0 +1,84 @@
+# Author: J. Saßmannshausen (Imperial College London/UK)
+
+easyblock = 'PythonBundle'
+
+name = 'Underworld'
+version = '2.16.4'
+versionsuffix = '-egl'
+
+homepage = 'https://www.underworldcode.'
+description = """
+Underworld is a Python API (Application Programming Interface) which provides
+functionality for the modelling of geodynamics processes, and is designed to
+work (almost) seamlessly across PC, cloud and HPC infrastructure. Primarily
+the API consists of a set of Python classes from which numerical geodynamics
+models may be constructed. The API also provides the tools required for inline
+analysis and data management. For scalability across multiprocessor platforms,
+MPI (Message Passing Interface) is leveraged, and for performant operation all
+heavy computations are executed within a statically typed layer.
+Note: This version does not come with badlands.
+"""
+
+citing = """
+Mansour, J., Giordani, J., Moresi, L., Beucher, R., Kaluza, O., Velic, M.,
+Farrington, R., Quenette, S., Beall, A., 2020, Underworld2:
+Python Geodynamics Modelling for Desktop, HPC and Cloud,
+Journal of Open Source Software, 5(47), 1797,
+https://doi.org/10.21105/joss.01797
+
+Beucher et al., (2019). UWGeodynamics: A teaching and research tool for
+numerical geodynamic modelling.
+Journal of Open Source Software, 4(36), 1136,
+https://doi.org/10.21105/joss.01136
+
+Zenodo: https://doi.org/10.5281/zenodo.1436039
+"""
+
+toolchain = {'name': 'foss', 'version': '2023b'}
+
+builddependencies = [
+    ('CMake', '3.27.6'),
+    ('Ninja', '1.11.1'),
+    ('SWIG', '4.1.1'),
+    ('pkgconf', '2.0.3'),
+    ('Xvfb', '21.1.9'),  # for virtual display during tests
+    ('hatchling', '1.18.0'),
+    ('pytest', '8.2.2'),  # required for testing, must be after hatchling to work
+]
+
+dependencies = [
+    ('Python', '3.11.5'),
+    ('SciPy-bundle', '2023.11'),
+    ('Python-bundle-PyPI', '2023.10'),
+    ('PETSc', '3.22.5'),
+    ('HDF5', '1.14.3'),
+    ('libxml2', '2.11.5'),
+    ('LavaVu', '1.9.9', '-egl'),  # more suited for graphical installations
+    ('h5py', '3.11.0'),
+    ('mpi4py', '3.1.5'),
+    ('Pint', '0.24'),
+]
+
+exts_list = [
+    ('nbmake', '1.5.5', {
+        'checksums': ['239dc868ea13a7c049746e2aba2c229bd0f6cdbc6bfa1d22f4c88638aa4c5f5c'],
+    }),
+    ('underworld', version, {
+        'patches': ['Underworld-2.16.4_ninja-job.patch'],
+        'preinstallopts': "export UNDERWORLD_BUILD_PARALLEL=%(parallel)s && ",
+        'source_urls': ['https://github.com/underworldcode/underworld2/archive'],
+        'sources': ['v%(version)s.tar.gz'],
+        'checksums': [
+            {'v2.16.4.tar.gz': '70b2ccadc4917b82cf64819956acf2a0c8b69fcb3117188e801ef435da2c2f28'},
+            {'Underworld-2.16.4_ninja-job.patch': 'e2bc7ce830b55ed88ff0ac58373b3b973e86a38f01809f54968ce4794c10bc1a'},
+        ],
+        'testinstall': True,
+        'runtest': 'xvfb-run pytest -vvv docs/pytests/tests.py '
+                   'docs/pytests/test_examples.py docs/pytests/test_user_guide.py '
+
+    }),
+]
+
+postinstallcmds = ['cp -R docs %(installdir)s/']
+
+moduleclass = 'geo'

easybuild/easyconfigs/u/Underworld/Underworld-2.16.4_ninja-job.patch

@@ -0,0 +1,25 @@
+Without that patch, Ninja is taken over the node and uses every available core
+The patch is using the UNDERWORLD_BUILD_PARALLEL variable, so set, else it is falling back to
+use 4 cores. The UNDERWORLD_BUILD_PARALLEL is either set in the EasyConfig file, or comes from 
+an environment variable. The latter is what Kenneth Hoste suggested so it can be used upstream
+as well 
+Author: J. Saßmannshausen (Imperial College London/UK)
+diff --git a/underworld2-2.16.4.orig/setup.py b/underworld2-2.16.4/setup.py
+index 4c09b49..43c259b 100755
+--- a/underworld2-2.16.4.orig/setup.py
++++ b/underworld2-2.16.4/setup.py
+@@ -221,7 +221,13 @@ class BuildExtension(build_ext):
+             ['cmake', '-S', ext.source_dir, '-B', build_folder] + configure_args
+ 
+         # 2. Compose CMake build command
+-        build_command = ['cmake', '--build', build_folder] + build_args
++        env_var = 'UNDERWORLD_BUILD_PARALLEL'
++        if env_var in os.environ:
++            number_cpus = os.environ['UNDERWORLD_BUILD_PARALLEL']
++        else:
++            number_cpus = '4'
++
++        build_command = ['cmake', '--build', build_folder, '-j', str(number_cpus)] + build_args
+ 
+         # 3. Compose CMake install command
+         install_command = ['cmake', '--install', build_folder]