tweak release notes for EasyBuild v4.9.0

smoors · Dec 30, 2023 · 7b7b847 · 7b7b847
1 parent 6ecc41e
commit 7b7b847
Showing 1 changed file with 45 additions and 78 deletions.
diff --git a/RELEASE_NOTES b/RELEASE_NOTES
@@ -13,120 +13,87 @@ v4.9.0 (30 December 2023)
 feature release
 
 - added easyconfigs for foss/2023b (#19449) and intel/2023b (#19450) common toolchains
-- added example easyconfig files for 48 new software packages:
+- added example easyconfig files for 77 new software packages:
   - AICSImageIO (#19315), ANTIC (#19203), BiasAdjustCXX (#19341), BOPTEST (#19295), BRiAl (#19208), castor (#19176),
-    CellBender (#19296), cliquer (#19210), CPMD (#19387), cppyy (#19204), CUDD (#19208), datalad (#18675), Demystify
-    (#17990), dftd4 (#19223), dialog (#17696), DIA-NN (#19454), dynesty (#19091), ebGSEA (#19447), ECL (#44), eclib
-    (#19209), epct (#19298), EUKulele (#19217), FACE (#14840), fastml (#19357), forbear (#14840), fplll (#19371), fpylll
-    (#19371), ftfy (#19353), Gdspy (#19458), GFF3-toolkit (#19071), giac (#19323), GMP-ECM (#19323), HepMC (#19139),
-    hic-straw (#19309), HPCC (#18892), iced (#19309), IML (#19201), iperf (#19259), jedi (#19269), jedi-language-server
-    (#19269), jupyter-rsession-proxy (#19311), lcalc (#19329), libaed2 (#14840), LoopTools (#19397), m4ri (#19208), m4rie
-    (#19208), MDI (#19417), mdust (#19106), MitoHiFi (#19263), MPFI (#19323), multicharge (#19221), OMERO.insight (#19337),
-    OMERO.py (#19338), PFFT (#19255), primecount (#19370), primecountpy (#19370), PyAV (#19359), pycubescd (#19302), pylipid
-    (#19428), PySINDy (#19306), pythermalcomfort (#19285), PyTorchVideo (#19359), R-bundle-CRAN (#19170), Restrander
-    (#19232), scikit-lego (#19064), scrublet (#19215), SEACells (#18724), simanneal (#19347), Simstrat (#14840), solo
-    (#19216), SPEI (#19441), SUPPA (#19181), SYMMETRICA (#19328), Triton (#19381), vaeda (#19214), VSCode (#19418), waLBerla
-    (#18932)
+    CellBender (#19296), cliquer (#19210, #19323), CPMD (#19387), cppyy (#19204), CUDD (#19208), datalad (#18675),
+    Demystify (#17990), dftd4 (#19223), dialog (#17696), DIA-NN (#19454), dynesty (#19091), ebGSEA (#19447),
+    ECL (#19211), eclib (#19209), epct (#19298), EUKulele (#19217), FACE (#14840), fastml (#19357), forbear (#14840),
+    fplll (#19371), fpylll (#19371), ftfy (#19353), Gdspy (#19458), GFF3-toolkit (#19071), giac (#19323), GMP-ECM (#19323),
+    HepMC (#19139), hic-straw (#19309), HPCC (#18892), iced (#19309), IML (#19201), iperf (#19259), jedi (#19269),
+    jedi-language-server (#19269), jupyter-rsession-proxy (#19311), lcalc (#19329), libaed2 (#14840),
+    LoopTools (#19397), m4ri (#19208), m4rie (#19208), MDI (#19417), mdust (#19106), MitoHiFi (#19263), MPFI (#19323),
+    multicharge (#19221), OMERO.insight (#19337), OMERO.py (#19338), PFFT (#19255), primecount (#19370),
+    primecountpy (#19370), PyAV (#19359), pycubescd (#19302), pylipid (#19428), PySINDy (#19306),
+    pythermalcomfort (#19285), PyTorchVideo (#19359), R-bundle-CRAN (#19170), Restrander (#19232), scikit-lego (#19064),
+    scrublet (#19215), SEACells (#18724), simanneal (#19347), Simstrat (#14840), solo (#19216), SPEI (#19441),
+    SUPPA (#19181, #19275), SYMMETRICA (#19328), Triton (#19381), vaeda (#19214), VSCode (#19418), waLBerla (#18932)
 - added additional easyconfigs for various supported software packages, including:
-  - 4ti2 1.6.9, AICSImageIO 4.14.0, ALL 0.9.2, ANTIC 0.2.5, ANTs 2.5.0, Arriba 2.4.0, Arrow 14.0.1, ATK 2.38.0, at-spi2-atk
-    2.38.0, at-spi2-core 2.50.0, Autoconf-archive 2023.02.20, awscli 2.15.2, BAGEL 1.2.2, bcbio-gff 0.7.0, BeautifulSoup
-    4.12.2, BiasAdjustCXX 1.9.1, Blender 3.6.5, Blender 4.0.1, Boost 1.83.0, BOPTEST 0.3.0, boto3 1.28.70, Bracken 2.9,
-    BRiAl 1.2.12, BUStools 0.43.1, cairo 1.18.0, cairomm 1.16.2, CASTEP 23.1, castor 1.7.11, Catch2 2.13.9, Catch2 2.13.9,
-    Catch2 2.13.9, CCL 1.12.2, cddlib 0.94m, cdo-bindings 1.6.0, CellBender 0.2.2, CellRanger 7.2.0, CESM-deps 2, cimfomfa
-    22.273, Clang 13.0.1, cliquer 1.21, CoCoALib 0.99818, COMSOL 6.2.0.290, Coreutils 9.1, CP2K 2023.1, CPLEX 22.1.1, CPMD
-    4.3, cppyy 3.0.0, cryptography 41.0.5, ctffind 4.1.14, CubeLib 4.8.2, CubeWriter 4.8.2, CUDA 12.3.0, CUDD 3.0.0, CVXPY
-    1.3.0, CWIPI 0.12.0, cysignals 1.11.2, datalad 0.18.4, DBus 1.15.8, DeepLabCut 2.2.0.6, Demystify 0.0.17, DFT-D3 3.2.0,
-    dftd4 3.4.0, dialog 1.3, DIA-NN 1.8.1, dynesty 2.1.3, e3nn 0.3.3, E-ANTIC 1.3.0, ebGSEA 0.1.0, ECL 23.9.9, eclib
-    20230424, elfutils 0.190, epct 3.2.0, EUKulele 2.0.6, f90wrap 0.2.11, FACE 1.1.1, fastml 2.3, FastQC 0.12.1, Ferret
-    7.6.0, FFLAS-FFPACK 2.5.0, FFmpeg 6.0, ffnvcodec 12.1.14.0, FFTW.MPI 3.3.10, FLINT 2.9.0, flit 3.9.0, flook 0.8.1, FLTK
-    1.3.8, forbear 1.2.0, fplll 5.4.5, FPM 1.15.1, fpylll 0.5.9, freeglut 3.4.0, FriBidi 1.0.13, ftfy 6.1.1, futile 1.8.3,
-    gap 4.12.2, Gdk-Pixbuf 2.42.8, Gdspy 1.6.13, GFF3-toolkit 2.1.0, gflags 2.2.2, giac 1.9.0, git-lfs 3.4.0, GitPython
-    3.1.40, Givaro 4.2.0, GLib 2.78.1, glog 0.6.0, GMP-ECM 7.0.5, GObject-Introspection 1.78.1, gperftools 2.13, GPyTorch
-    1.10, Graphene 1.10.8, graphite2 1.3.14, GROMACS 2023.3, HarfBuzz 8.2.2, hatchling 1.18.0, HepMC 2.06.11, HiC-Pro 3.1.0,
-    hic-straw 1.3.1, hifiasm 0.19.7, Horovod 0.28.1, HPCC 1.5.0, HPL 2.3, hypothesis 6.90.0, iced 0.5.10, ICU 74.1, imageio
-    2.33.1, IMB 2021.3, imkl 2023.1.0, imkl 2024.0.0, imkl-FFTW 2023.2.0, imkl-FFTW 2024.0.0, IML 1.0.5, impi 2021.11.0,
-    intel-compilers 2024.0.0, iperf 2.1.9, iperf 3.15, IPython 8.17.2, ISA-L 2.30.0, ITK 5.3.0, JasPer 4.0.0, jedi 0.18.1,
-    jedi 0.19.1, jedi-language-server 0.39.0, json-fortran 8.3.0, jupyter-rsession-proxy 2.1.0, Kent_tools 457, kim-api
-    2.3.0, KyotoCabinet 1.2.80, LAME 3.100, lcalc 2.0.5, LHAPDF 6.5.4, libaed2 1.3.0, libepoxy 1.5.10, libfdf 0.5.0, Libint
-    2.7.2, libjxl 0.8.2, libvori 220621, libxslt 1.1.38, libxsmm 1.17, LinBox 1.7.0, LittleCMS 2.15, LoopTools 2.15, lrslib
-    7.2, lxml 4.9.3, m4ri 20200125, m4rie 20200125, MACS2 2.2.9.1, magma 2.7.2, maturin 1.3.1, MCL 22.282, mctc-lib 0.3.1,
-    MDI 1.4.16, MDTraj 1.9.7, mdust 20150102, MEME 5.5.4, meson-python 0.15.0, Miniconda3 23.9.0, MitoHiFi 3.2, Mmg 5.7.2,
-    Molden 7.3, motif 2.3.8, MPFI 1.5.4, mrcfile 1.4.3, mstore 0.2.0, multicharge 0.2.0, nanoflann 1.5.0, nauty 2.8.6,
-    nettle 3.9.1, Nextflow 23.10.0, nglview 3.0.3, nodejs 20.9.0, Normaliz 3.10.1, NSPR 4.35, NSS 3.94, NVHPC 23.7, NWChem
-    7.2.2, Oases 20180312, OMERO.insight 5.8.3, OMERO.py 5.17.0, OpenFold 1.0.1, OpenMM 7.7.0, OSU-Micro-Benchmarks 7.2,
-    Pango 1.51.0, Parallel-Hashmap 1.36, parameterized 0.9.0, PARI-GP 2.7.6, PFFT 20181230, pFUnit 4.2.0, phonopy 2.20.0,
-    PICRUSt2 2.5.2, pigz 2.8, pixman 0.42.2, PLUMED 2.9.0, pmt 1.2.0, pmt 1.2.0, poetry 1.6.1, PostgreSQL 16.1, ppl 1.2,
-    pplpy 0.8.9, primecount 7.9, primecountpy 0.1.0, PyAV 10.0.0, pybind11 2.11.1, PyCairo 1.25.1, pycubescd 20220704,
-    PyGObject 3.46.0, pylipid 1.5.14, pypmt 1.2.0, pypmt 1.2.0, PyQt5 5.15.7, PySINDy 1.7.3, pytest 7.4.2,
-    pytest-flakefinder 1.1.0, pytest-xdist 3.3.1, pythermalcomfort 2.8.10, Python-bundle-PyPI 2023.10, python-isal 1.1.0,
-    python-louvain 0.16, python-xxhash 3.2.0, PyTorch 2.0.1, PyTorch 2.1.2, PyTorchVideo 0.1.5, R 4.3.2, RapidJSON 1.1.0,
-    RASPA2 2.0.47, R-bundle-CRAN 2023.12, re2c 3.1, ReaxFF 2.0, Restrander 20230713, RFdiffusion 1.1.0, SBCL 2.3.11,
-    ScaFaCoS 1.0.4, ScaLAPACK 2.2.0, SCENIC 1.3.0, scikit-build 0.17.6, scikit-image 0.22.0, scikit-lego 0.6.16,
-    SciPy-bundle 2023.11, SCopeLoomR 0.13.0_20220408, Score-P 8.1, scrublet 0.2.3, SDL2 2.28.5, SEACells 20230731,
-    segmentation-models-pytorch 0.3.3, setuptools-rust 1.8.0, Seurat 4.4.0, simanneal 0.5.0, SimpleITK 2.3.1, Simstrat 3.01,
-    Singular 4.3.2p10, solo 1.3, Spark 3.5.0, SPEI 0.3.5, STAR 2.7.11a, STAR-CCM+ 18.06.006, STAR-CCM+ 2302, STAR-CCM+ 2310,
-    strace 6.6, SuiteSparse 7.1.0, SUPPA 2.3, SYMMETRICA 2.0, tabix 0.2.6, tbb 2021.11.0, tensorflow-probability 0.19.0,
-    TOML-Fortran 0.4.1, topaz 0.2.5.20230926, TRAVIS-Analyzer 220729, Triton 1.1.1, UCX-CUDA 1.15.0, vaeda 0.0.30, VirSorter
-    1.0.6, VirSorter2 2.2.4, virtualenv 20.24.6, Voro++ 0.4.6, VSCode 1.85.0, VSEARCH 2.25.0, VTK 9.3.0, waLBerla 6.1, wandb
-    0.16.1, Wannier90 3.1.0, Wayland 1.22.0, XGBoost 2.0.2, XML-Compile 1.63, xprop 1.2.6, xproto 7.0.31, xtb 6.6.0, xtb
-    6.6.1, Xvfb 21.1.9, xxd 9.0.2112, xxHash 0.8.1, Z3 4.12.2
+  - ANTs 2.5.0, Arriba 2.4.0, Arrow 14.0.1, at-spi2-core 2.50.0, Autoconf-archive 2023.02.20, awscli 2.15.2,
+    Blender 3.6.5 + 4.0.1, Boost 1.83.0, boto3 1.28.70, Bracken 2.9, BUStools 0.43.1, cairo 1.18.0, cairomm 1.16.2,
+    CASTEP 23.1, cddlib 0.94m, cdo-bindings 1.6.0, CellRanger 7.2.0, CoCoALib 0.99818, COMSOL 6.2.0.290, Coreutils 9.1,
+    cryptography 41.0.5, CubeLib 4.8.2, CubeWriter 4.8.2,  CUDA 12.3.0, CVXPY 1.3.0, cysignals 1.11.2, DBus 1.15.8,
+    dftd4 3.4.0, E-ANTIC 1.3.0, elfutils 0.190, f90wrap 0.2.11, FastQC 0.12.1, Ferret 7.6.0, FFLAS-FFPACK 2.5.0,
+    ffnvcodec 12.1.14.0, FPM 1.15.1, FriBidi 1.0.13, gap 4.12.2, git-lfs 3.4.0, GitPython 3.1.40, Givaro 4.2.0,
+    GLib 2.78.1, glog 0.6.0, GObject-Introspection 1.78.1, gperftools 2.13, GPyTorch 1.10, GROMACS 2023.3,
+    HarfBuzz 8.2.2, HiC-Pro 3.1.0, hifiasm 0.19.7, hypothesis 6.90.0, ICU 74.1, imageio 2.33.1, imkl 2024.0.0,
+    impi 2021.11.0, intel-compilers 2024.0.0, IPython 8.17.2, ITK 5.3.0, Kent_tools 457, KyotoCabinet 1.2.80,
+    LHAPDF 6.5.4, libfdf 0.5.0, libjxl 0.8.2, LinBox 1.7.0, lrslib 7.2, lxml 4.9.3, magma 2.7.2, maturin 1.3.1,
+    MEME 5.5.4, meson-python 0.15.0, Miniconda3 23.9.0, Mmg 5.7.2, Molden 7.3, mrcfile 1.4.3, nanoflann 1.5.0,
+    nauty 2.8.6, Nextflow 23.10.0, nodejs 20.9.0, Normaliz 3.10.1, NSS 3.94, NWChem 7.2.2, Oases 20180312, Pango 1.51.0,
+    Parallel-Hashmap 1.36, parameterized 0.9.0, phonopy 2.20.0, pigz 2.8, pmt 1.2.0, poetry 1.6.1, PostgreSQL 16.1,
+    pplpy 0.8.9, PyCairo 1.25.1, pypmt 1.2.0, PyQt5 5.15.7, pytest 7.4.2, pytest-xdist 3.3.1,
+    Python-bundle-PyPI 2023.10, PyTorch 2.1.2, R 4.3.2, RASPA2 2.0.47, SBCL 2.3.11, SCENIC 1.3.0, scikit-image 0.22.0,
+    SciPy-bundle 2023.11, SDL2 2.28.5, setuptools-rust 1.8.0, Seurat 4.4.0, SimpleITK 2.3.1, Singular 4.3.2p10,
+    Spark 3.5.0, STAR 2.7.11a, STAR-CCM+ 2310, strace 6.6, SuiteSparse 7.1.0, tbb 2021.11.0, TOML-Fortran 0.4.1,
+    TRAVIS-Analyzer 220729, UCX-CUDA 1.15.0, VirSorter 1.0.6, virtualenv 20.24.6, VSEARCH 2.25.0, VTK 9.3.0,
+    wandb 0.16.1, XGBoost 2.0.2, xprop 1.2.6, xtb 6.6.1, Xvfb 21.1.9, xxd 9.0.2112
 - minor enhancements, including:
   - add sanity check commands for recent GDB versions (#19102)
   - add aarch64 and ppc64le checksums to NVHPC 23.7 (#19249)
-  - add missing description to patch file for flook v0.8.1 (#19293)
-  - remove Boost build dependency from pybind11 2.11.1 (#19327)
   - allow Python version of Z3 to be used as a dependency (#19354)
 - various bug fixes, including:
   - use `CargoPythonBundle` generic easyblock for timm to install required Rust packages in a controlled way (#18332)
-  - Add alternate checksum for OpenImageIO v2.4.14.0 (#19090)
+  - add alternate checksum for OpenImageIO v2.4.14.0 (#19090)
   - only set flag `--enable-asmjit` for PLUMED when installing on `x86_64` (#19110)
   - ensure right Python version is used in DP3, WSClean and dependencies by specifying `-DPython3_EXECUTABLE` CMake option (#19119)
   - add patch to work around potential crash in PyTorch 1.13.1 caused by GCC 12 compiler bug (#19133)
-  - add patch to fix detection of newer Intel CPUs in OpenBLAS 0.3.20-0.3.23 (#19141)
+  - add patch to fix detection of newer Intel CPUs in OpenBLAS 0.3.20 through 0.3.23 (#19141)
   - remove outdated `--disable-docs` configure option from FriBidi-1.0.12 (#19147)
   - add libiconv dependency to gettext 0.22 (#19155)
   - fix OpenBLAS 0.3.20+ on newer Intel CPUs (#19159)
   - only use ScaFaCos as dependency for LAMMPS 23Jun2022 on `x86_64` (#19164)
   - add patch to fix regression in GCC 12.x on AVX512 systems (#19180)
   - add pkgconf build dependency to libGLU (#19186)
-  - Sidestep some build issues with CUDA-Samples 12.1 (#19189)
-  - make Pillow easyconfigs aware of sysroot template (#19226)
+  - sidestep some build issues with CUDA-Samples 12.1 (#19189)
+  - make Pillow easyconfigs aware of sysroot template (#19226, #19267)
   - fix possible error/crash in NCCL on x86 due to cpuid (#19231)
   - reduce timestep to fix sanity check commands in LAMMPS 23Jun2022 (#19246)
   - add patch for GCC 12.x to fix miscompiling C++ code causing double-free in case of exceptions (#19253)
   - replace format tag with explicit extension name in Optuna v3.0.3 (#19256)
   - enhance easyconfigs for gnuplot 5.4.x to make sure that Lua dependency is always used (#19261)
-  - patch Pillow's setup.py rather than hardcoding system paths in `$CPATH` and `$LIBRARY_PATH` (#19267)
   - patch setup.py for grpcio extension in TensorFlow 2.13.0 easyconfigs to take into account alternate sysroot (#19268)
   - avoid indirect dependency on old CMake version built with GCCcore/10.2.0 via Catch2 build dependency using system toolchain in recent pybind11 easyconfigs (#19270)
-  - fix link creation and sanity check for SUPPA (#19275)
   - use existing patch in pybind11 2.6.2 and 2.7.1 to fix failing test due to extra whitespace (#19279)
-  - `json-fortran` creates Fortran modules, so must be at compiler level (#19283)
+  - change toolchain in `json-fortran` easyconfigs to `GCC`, since it includes Fortran modules (#19283)
   - remove Unicode character in description of SMRT-Link easyconfigs (#19312)
   - don't use `%(namelower)s` template in extension name in IPython v8.14.0 easyconfig (#19330)
-  - add patch to fix [cz]asums in OpenBLAS 0.3.24 (#19331)
-  - Fix failing tokenizers with `CargoPythonPackage` easyblock (#19333)
-  - define $GTKDOCIZE as 'echo' before generating configure script for new HarfBuzz versions (#19339)
+  - add patch to fix `[cz]asums` in OpenBLAS 0.3.24 (#19331)
+  - fix failing tokenizers with `CargoPythonPackage` easyblock (#19333)
+  - define `$GTKDOCIZE` as '`echo`' before generating configure script for new HarfBuzz versions (#19339)
   - fix PAPI test step hanging on some systems (#19372)
   - compile LERC test binary in `postinstallcmds` to fix sanity check error when RPATH linking is enabled (#19386)
-  - move kim-api/2.3.0-GCCcore-12.3.0 to GCC (#19399)
-  - move kim-api/2.3.0-GCCcore-12.2.0 to GCC (#19401)
-  - move kim-api/2.3.0-GCCcore-11.3.0 to GCC (#19402)
-  - move kim-api/2.3.0-GCCcore-11.2.0 to GCC (#19403)
-  - move kim-api/2.2.1-GCCcore-10.3.0 to GCC (#19404)
-  - move kim-api/2.2.1-GCCcore-10.2.0 to GCC (#19405)
+  - use `GCC` toolchain in `kim-api`, since it includes Fortran modules (#19399, #19401, #19402, #19403, #19404, #19405)
   - fix wrong handling of floats in z3-solver (#19414)
-  - Fix numpy build on Sapphire Rapids CPUs in SciPy-bundle-2023.07-gfbf-2023a (#19419)
-  - Fix numpy build on Sapphire Rapids CPUs in SciPy-bundle-2023.11-gfbf-2023.09 (#19425)
+  - Fix numpy build on Sapphire Rapids CPUs in SciPy-bundle-2023.07-gfbf-2023a (#19419, #19425)
   - allow ITK legacy code and Python wrappers in ITK v5.2.1 (#19431)
-  - link to xxHash library from EB in python-xxhash-3.2.0-GCCcore-12.2.0.eb (#19432)
+  - link to xxHash library provided via EasyBuild in python-xxhash v3.2.0 (#19432)
   - include MPFR 4.1.0 patch in MPFR 4.2.0 easyconfigs to fix failing tsprintf test with glibc >= 2.37 (#19438)
   - skip `Test::Sys::Info` test that expects `/etc/fstab` in Perl-bundle-CPAN (#19440)
   - exclude `cdp*` CUDA samples that fail to build on aarch64 in CUDA-Samples v12.1 (#19451)
 - other changes:
   - let SuiteSparse easyblock set `CMAKE_OPTIONS` for SuiteSparse v7.1.0 (#19177)
-  - Use `LooseVersion` from easybuilt.tools (#19376)
-  - Python louvain 0.15 foss 2021b (#19427)
+  - add versionsuffix `-param` to easyconfig for ReaxFF 2.0 (#19307)
+  - use `LooseVersion` from `easybuild.tools` (#19376)
 
 
 v4.8.2 (29 October 2023)