From b26a66f656e5d0cdf21063168c5e7185a8915004 Mon Sep 17 00:00:00 2001 From: Miguel Dias Costa Date: Thu, 29 Oct 2020 11:04:53 +0800 Subject: [PATCH] update release notes for EasyBuild v4.3.1 --- docs/Release_notes.rst | 192 ++++++++++++++++++++++++++++++++++++++++- 1 file changed, 188 insertions(+), 4 deletions(-) diff --git a/docs/Release_notes.rst b/docs/Release_notes.rst index 5efd9df8..1d87cc0b 100644 --- a/docs/Release_notes.rst +++ b/docs/Release_notes.rst @@ -3,12 +3,196 @@ EasyBuild release notes ======================= -The latest version of EasyBuild provides support for building and installing **2,059** different software packages, -including 31 different (compiler) toolchains. It contains 224 software-specific easyblocks and 37 generic easyblocks, -alongside 10,384 easyconfig files. +The latest version of EasyBuild provides support for building and installing **2,134** different software packages, +including 31 different (compiler) toolchains. It contains 225 software-specific easyblocks and 37 generic easyblocks, +alongside 10,794 easyconfig files. .. note:: See also the :ref:`concise overview of major changes in EasyBuild v4.0 `. +.. _release_notes_eb431: + +EasyBuild v4.3.1 (October 29th 2020) +------------------------------------ + +bugfix/update release + +**framework** + +* various enhancements, including: + + * further GCC toolchain fixes for aarch64 (`#3433 `_) + * take into account ``--include-easyblocks-from-pr`` when uploading test reports (`#3446 `_) + * add path to pkg-config files in sysroot to ``$PKG_CONFIG_PATH`` when ``--sysroot`` is specified (`#3451 `_) + * add support for NVHPC compiler + toolchain (based on PGI) (`#3454 `_) + * check for _VERSION and _PREFIX Cray environment variables with both software and module name (`#3460 `_) + * allow including easyblocks from multiple PRs (`#3480 `_, `#3481 `_) + +* various bug fixes, including: + + * avoid ``UnicodeDecodeError`` in ``apply_regex_substitutions`` when patching files that include non-UTF-8 characters (`#3450 `_) + * avoid appending lib stubs pattern to RPATH filter over and over again (`#3452 `_) + * fix missing string template on error for incorrect extension ``sources`` value (`#3461 `_) + * fix compatibility with Python 3.9 by renaming fancy root logger (`#3465 `_) + * also remove empty checksums list specified in easyconfig file when using ``--inject-checksums`` (`#3466 `_) + * avoid confusing error log message when determining impi version while trying to define value for ``%(mpi_cmd_prefix)s`` template (`#3474 `_) + * unset ``$LD_LIBRARY_PATH`` when checking for OS dependencies with ``rpm`` & co (`#3477 `_) + * don't change directory in ``download_repo`` function in ``tools.github`` (`#3486 `_) + * take ``source_urls``, ``checksums``, ``patches`` into account when extension source is specified via ``sources`` (`#3487 `_) + +* other changes: + + * consider ``$EB_INSTALLPYTHON`` in ``eb`` command to specify ``python`` command to use for running EasyBuild (`#3428 `_) + * use only the sub folder name for ``createSubmoduleDeps`` script (`#3464 `_) + +**easyblocks** + +* 2 new software-specific easyblocks: + + * CFDEMcoupling (`#1439 `_), NVHPC (`#2190 `_) + +* minor enhancements, including: + + * support having PyQt5 installed as part of Qt5 in QScintilla easyblock (`#2040 `_) + * update TensorFlow easyblock to put Bazel build files in build directory + avoid unnecessary runtime patching (`#2166 `_) + * update CBLAS easyblock for toolchains that include imkl (`#2175 `_) + * add workaround for duplicate prefix path in Eigen CMake config (`#2176 `_) + * enable ``CTEST_OUTPUT_ON_FAILURE`` for CMakeMake test step (`#2181 `_) + * add XLA build support to TensorFlow easyblock (`#2182 `_) + * also consider libfabric dep (``--with-ofi``) when setting default OpenMPI configure options (`#2184 `_) + * make easyblock for installing CMake aware of ``--sysroot`` (`#2187 `_) + * make OpenBLAS respect the parallelism set by easybuild (`#2191 `_) + * handle option of building Michigan State University CCT3 & CCSD3A methods in GAMESS_US easyblock (`#2194 `_) + * add support to RubyGem easyblock for installing zipped gems (`#2203 `_) + * update ScaLAPACK easyblock to support installation with CMake for recent versions (>= v2.1.0) (`#2205 `_) + * update Score-P easyblock to add support for NVHPC toolchain (`#2206 `_) + +* various bug fixes, including: + + * add ``torch/lib`` subdirectory in Python lib dir to ``$LD_LIBRARY_PATH`` for PyTorch installations (`#2183 `_) + * update MUMmer easyblock to use ``apply_regex_substitutions`` and ``copy_file`` functions (`#2185 `_) + * configure OpenMPI 4.x with ``--without-verbs`` when using UCX (`#2188 `_) + * take into account that zlib may be listed in ``--filter-deps`` in custom easyblock for XML R package (`#2189 `_) + * add sanity check commands to Clang easyblock and print warning for missing ncurses (`#2193 `_) + * enhance OpenFOAM easyblock to add symlinks for libraries to ensure ``mpi`` versions have preference over ``dummy`` versions (`#2196 `_) + * leverage installed OpenSSL/BoringSSL when cURL is used as a dependency for TensorFlow (`#2197 `_) + * add ``-ffree-line-length-none`` to gfortran flags in Siesta easyblock (`#2204 `_) + * respect ``--disable-mpi-tests`` in Siesta easyblock (`#2207 `_) + +* other changes, including: + + * set ``$EB_INSTALLPYTHON`` in module generated for EasyBuild rather than setting ``$EB_PYTHON``, to allow overriding Python command to be used for running EasyBuild with ``$EB_PYTHON`` (`#2109 `_) + * remove unused custom easyblock for DIRAC (`#2192 `_, `#2198 `_) + +**easyconfigs** + +* added easyconfigs for 2 new toolchains: + + * fosscuda/2020a (`#11424 `_) and intelcuda/2020a (`#11425 `_) + +* added example easyconfig files for 75 new software packages: + + * Bsoft (`#6551 `_, `#11537 `_), causallift (`#11436 `_), CAVIAR (`#11158 `_), CCfits (`#11505 `_), Cereal (`#11506 `_), + CFDEMcoupling (`#6465 `_), Check (`#11295 `_), chewBBACA (`#11418 `_), COMSOL (`#11513 `_), CUDAcore (`#11295 `_), Dalton (`#5808 `_), + DIRAC (`#11414 `_), ESMValTool (`#6329 `_), eSpeak-NG (`#11236 `_), ExifTool (`#11521 `_), FabIO (`#11517 `_), festival (`#11236 `_), + fetchMG (`#11283 `_), FHI-aims (`#11198 `_), Flexbar (`#11305 `_), FRUIT (`#6613 `_), FRUIT_processor (`#6631 `_), Gaussian (`#4247 `_), + GBprocesS (`#11512 `_), GDRCopy (`#11295 `_), Genome_Profiler (`#6066 `_), groff (`#11200 `_), ILAMB (`#11309 `_), kedro (`#11436 `_), + leidenalg (`#11407 `_), libav (`#6194 `_), libmo_unpack (`#6329 `_), libobjcryst (`#11321 `_), makeinfo (`#11368 `_), + mauveAligner (`#11395 `_), MBROLA (`#11236 `_), MDSplus-Java (`#10705 `_), MDSplus-Python (`#10705 `_), MyCC (`#11283 `_), + nanomax-analysis-utils (`#11517 `_), Nek5000 (`#6408 `_), NVHPC (`#11391 `_), OPERA-MS (`#11410 `_), ORFfinder (`#7031 `_), + phonemizer (`#11236 `_), Pingouin (`#11280 `_), Pint (`#11151 `_), pydantic (`#11151 `_), pyobjcryst (`#11321 `_), PyOpenCL (`#11517 `_), + pyspoa (`#11438 `_), QtPy (`#11517 `_), Qtconsole (`#11517 `_), rasterio (`#11468 `_), rasterstats (`#11468 `_), ReMatCh (`#6067 `_), + Ruby-Tk (`#6613 `_), SBCL (`#11413 `_), scikit-uplift (`#11432 `_), SDL (`#6202 `_), SDL2 (`#6203 `_), SDL2_image (`#6203 `_), + SDL_image (`#6202 `_), SeqKit (`#11538 `_), silx (`#11517 `_), SiNVICT (`#11404 `_), sonic (`#11236 `_), speech_tools (`#11236 `_), + Statistics-R (`#11274 `_), SUMO (`#11435 `_), tidybayes (`#11335 `_), treatSens (`#11431 `_), tsne (`#11283 `_), wandb (`#11450 `_), + WisecondorX (`#11399 `_) + +* added additional easyconfigs for various supported software packages, including: + + * ABINIT 9.2.1, ASE 3.20.1, Autotools 20200321, Bazel 3.6.0, Biopython 1.78, CCL 1.12, CMake 3.18.4, CUDA 11.0.2, + cURL 7.72.0, deepdiff 5.0.2, fmt 7.0.3, GATK 4.1.8.1, GLib 2.66.1, GROMACS 2020.3, GTK+ 3.24.23, git 2.28.0, + HMMER 3.3.1, Horovod 0.20.3, ICU 67.1, IPython 7.18.1, ichorCNA 0.3.2, JupyterHub 1.1.0, JupyterLab 2.2.8, + LLVM 11.0.0, libarchive 3.4.3, libcircle 0.3, libevent 2.1.12, libfabric 1.11.0, libglvnd 1.3.2, libunwind 1.4.0, + libxcb 1.13, MAFFT 7.471, MDSplus 7.96.12, MEGAHIT 1.2.9, MMseqs2 11-e1a1c, Mako 1.1.3, Mesa 20.2.1, Meson 0.55.3, + medaka 1.1.3, mpifileutils 0.10.1, NASM 2.15.05, NSPR 4.29, NSS 3.57, Ninja 1.10.1, nettle 3.6, nglview 2.7.7, + nodejs 12.19.0, OpenImageIO 2.1.12.0, OpenRefine 3.4.1, OpenSSL 1.1.1h, PCRE2 10.35, PSI4 1.3.2, Pango 1.47.0, + PyGEOS 0.8, PyOpenGL 3.1.5, PyQt5 5.15.1, PyQtGraph 0.11.0, PyRETIS 2.5.0, Python 3.8.6, pandas 1.1.2, + phonopy 2.7.1, picard 2.22.1, pixman 0.40.0, protobuf 3.13.0, pyEGA3 3.4.0, pytest 6.0.1, ReFrame 3.2. re2c 2.0.3, + SAMtools 1.11, SCons 4.0.1, SQLite 3.33.0, Spyder 4.1.5, Subversion 1.14.0, sbt 1.3.13, spglib-python 1.16.0, + spoa 4.0.0, TINKER 8.8.1, TRIQS 3.0.0, Taiyaki 5.1.0, TensorFlow 2.3.1, Tkinter 2.7.18 + 3.8.6, torchvision 0.7.0, + UCX 1.9.0, V8 3.2.0, VirtualGL 2.6.2, vsc mympirun 5.2.0 X11 20201008, XGBoost 1.2.0, + XZ 5.2.5, Xerces-C++ 3.2.3, xarray 0.16.1, ZeroMQ 4.3.3, zstd 1.4.5 + +* minor enhancements, including: + + * use more EasyBuild installed dependencies for TensorFlow 2.2.0 (`#11224 `_) + * add additional extensions to R 4.0.0 easyconfig (`#11340 `_, `#11430 `_, `#11487 `_) + * add additional extensions to Bioconductor 3.11 bundle (`#11341 `_, `#11488 `_) + * make libtirpc easier to use as replacement of rpc in glibc (for RHEL8) (`#11355 `_) + * add libevent, libfabric and PMIx dependencies to OpenMPI 4.0.3 (for foss/2020a & iomkl/2020a) (`#11387 `_, `#11568 `_) + * build LibTIFF with ``-fPIC`` (`#11527 `_) + * update Java/1.8 wrapper to also support aarch64 (`#11545 `_) + +* various bug fixes, including: + + * add Python 3 as build dep for Xvfb 1.20.8 easyconfigs (`#10745 `_) + * patch out bug in collective primitive in TensorFlow 2.2.0 (`#11175 `_) + * add missing groff build dependency for Perl (provides nroff tool requires to install man pages) (`#11200 `_) + * add pocl dependency to GDAL easyconfig using fosscuda/2019b toolchain to make sure it builds on POWER (`#11273 `_) + * add libtirpc as a build dep for HDF to fix installation on RHEL8 (`#11279 `_) + * fix build problems with make 4.2.1 on RHEL8 (`#11282 `_, `#11371 `_) + * change ``$LIBS`` in Ghostscript 9.27 easyconfig to include location of zlib library to link with (`#11291 `_) + * remove ``--no-dist-info`` configuration option for SIP in recent PyQt5 easyconfigs (`#11307 `_) + * make sure correct zlib is used in recent Ghostscript easyconfigs (`#11319 `_) + * remove GLog and GFlags from PyTorch 1.2.0 (`#11327 `_), 1.3.1 (`#11325 `_), 1.4.0 (`#11322 `_) and 1.6.0 (`#11323 `_) + * use PyTorch easyblock for PyTorch 1.3.1 (`#11325 `_) + * add missing git build dependency for OpenImageIO 2.0.12 (`#11328 `_) + * fix HDF 4.2.14 easyconfigs for RHEL8 (`#11330 `_) + * add patch to fix installation of LAMMPS 7Aug2019 on AMD Epyc systems (`#11334 `_) + * fix dependency on Bowtie of v0.x in seq2HLA easyconfigs (`#11339 `_) + * fix installation of Hadoop v2.10.0 on RHEL8 (`#11358 `_) + * add patch to fix installation of Sailfish v0.10.1 on RHEL8 (`#11364 `_) + * add patch to fix installation of FuSeq v1.1.2 on RHEL8 (`#11365 `_) + * fix installation of Qt5 5.14.1 on top of zlib provided by Gentoo + stick to Python 2 as build dep (`#11385 `_, `#11386 `_) + * add patch for LAME configure script to make it check for correct ncurses symbol (`#11388 `_) + * add protobuf-python as a dependency and corresponding sanity check to PyTorch 1.6 (`#11390 `_) + * fix Multiwfn 3.6 installation on RHEL8 (`#11402 `_) + * fix OpenFOAM 2.3.1 installation with intel/2019b on RHEL8 (`#11409 `_) + * fix broken worker easyconfigs (`#11412 `_) + * add ncurses runtime dependency to Clang easyconfigs (`#11415 `_, `#11416 `_, `#11419 `_, `#11472 `_) + * fix installation of Bioconductor 3.11 bundle on aarch64 (`#11417 `_) + * add patch to libunwind fixing a failure on POWER (`#11421 `_) + * fix infinite loop build bug on ppc64le for R 4.0.0 (`#11428 `_) + * fix compilation of Qt5 v5.12.3 and v5.13.1 on Ubuntu 20.04 (`#11434 `_) + * fix PyVCF easyconfig, only supports Python 2 (`#11437 `_) + * add patches to fix miscomputation (on POWER) and performance issues for OpenBLAS (`#11443 `_, `#11444 `_, `#11445 `_) + * add missing DB dependency (required for DB_File) to easyconfigs for Perl (`#11451 `_, `#11452 `_) + * fix dbarts extension in R v4.0.0 easyconfigs for non-x86_64 (`#11453 `_) + * use Homebrew source mirror to auto-download sources for DB v18.1.25 and v18.1.32 (`#11454 `_) + * add missing UnZip dependency for Python 3.8.2 (`#11458 `_) + * add support for building OpenBLAS on ARM TSV110 with GCC 8.3 (`#11464 `_) + * allow Kent_tools to build when MySQL installed at the OS level (`#11471 `_) + * add missing ``moduleclass`` to easyconfigs for: + + * Arlequin 3.5.2.2 (`#11473 `_), MEGAHIT 1.2.8 (`#11474 `_) and 1.2.9 (`#11475 `_), PyCUDA 2019.1.2 (`#11476 `_) + + * fix source for SQLite 3.31.1 (`#11483 `_) + * fix installation of worker 1.6.11 with intel/2019b on RHEL 8.2 (`#11498 `_) + * fix checksum in NAMD 2.12 easyconfigs + add source URL (`#11515 `_) + * add BLAS/LAPACK check to GPAW patch adding EasyBuild configuration files (`#11523 `_) + * backport fixes for Score-P v6.0 (`#11540 `_) + * add XZ build dep to easyconfigs for libarchive v3.4.0 and v3.4.2 (`#11561 `_) + * add patch for OpenMPI 3.1.4 adding device parameters for ConnectX-6 (`#11575 `_) + +* other changes: + + * update README on constructing source file for MATLAB (`#6341 `_) + * remove easyconfigs for Taiyaki that depend on PyTorch 1.3.1, since latest version still requires PyTorch 1.2.0 (`#11301 `_) + * make CI error messages less confusing ("is" -> "should be") (`#11314 `_) + * remove extensions from R-bundle-Bioconductor 3.11 easyconfigs that are also included in R 4.0.0 (`#11429 `_) + * cache M4 source tarball to avoid test failures because of download problems (`#11469 `_) + * rename jupyterhub to JupyterHub (`#11571 `_) + + .. _release_notes_eb430: EasyBuild v4.3.0 (September 13th 2020) @@ -111,7 +295,7 @@ feature release * solve issue where pybind11 picks up on the system Python instead of one provided by a module (`#2158 `_) * fix Qt5 easyblock to support installation on Arm/aarch64 (requires platform to be ``linux-g++``) (`#2160 `_) * fix OpenFOAM easyblock to support installation on Arm/aarch64 systems (`#2162 `_) - * explicitely enable/disable CUDA options in PyTorch easyblock + fix download check in sanity check + fix for disabling of *NNPACK on POWER systems (`#2164 `_) + * explicitly enable/disable CUDA options in PyTorch easyblock + fix download check in sanity check + fix for disabling of *NNPACK on POWER systems (`#2164 `_) * fix sanity check in Mathematica easyblock for 11.x versions older than 11.3 (`#2168 `_) * unset ``$COLUMNS`` if it is set to ``0`` before running Perl's configure script (`#2169 `_)