From 65f1a2586dadb4b7e40e34ca6689838ca22c7ddc Mon Sep 17 00:00:00 2001 From: tanmoy1989 Date: Mon, 29 Jul 2024 11:16:02 +0100 Subject: [PATCH 01/85] adding easyconfigs: ASE-3.23.0-gfbf-2023b.eb --- .../a/ASE/ASE-3.23.0-gfbf-2023b.eb | 48 +++++++++++++++++++ 1 file changed, 48 insertions(+) create mode 100644 easybuild/easyconfigs/a/ASE/ASE-3.23.0-gfbf-2023b.eb diff --git a/easybuild/easyconfigs/a/ASE/ASE-3.23.0-gfbf-2023b.eb b/easybuild/easyconfigs/a/ASE/ASE-3.23.0-gfbf-2023b.eb new file mode 100644 index 000000000000..07ad1ecc5553 --- /dev/null +++ b/easybuild/easyconfigs/a/ASE/ASE-3.23.0-gfbf-2023b.eb @@ -0,0 +1,48 @@ +easyblock = 'PythonBundle' + +name = 'ASE' +version = '3.23.0' + +homepage = 'https://wiki.fysik.dtu.dk/ase' +description = """ASE is a python package providing an open source Atomic Simulation Environment + in the Python scripting language. + +From version 3.20.1 we also include the ase-ext package, it contains optional reimplementations +in C of functions in ASE. ASE uses it automatically when installed.""" + +toolchain = {'name': 'gfbf', 'version': '2023b'} + +dependencies = [ + ('Python', '3.11.5'), + ('Python-bundle-PyPI', '2023.10'), + ('SciPy-bundle', '2023.11'), + ('Flask', '3.0.0'), + ('matplotlib', '3.8.2'), + ('Tkinter', '%(pyver)s'), # Needed by GUI of ASE + ('spglib-python', '2.5.0'), # optional +] + +use_pip = True +sanity_pip_check = True + +exts_list = [ + ('pytest-mock', '3.14.0', { + 'checksums': ['2719255a1efeceadbc056d6bf3df3d1c5015530fb40cf347c0f9afac88410bd0'], + }), + ('ase', version, { + 'checksums': ['91a2aa31d89bd90b0efdfe4a7e84264f32828b2abfc9f38e65e041ad76fec8ae'], + }), + ('ase-ext', '20.9.0', { + 'checksums': ['a348b0e42cf9fdd11f04b3df002b0bf150002c8df2698ff08d3c8fc7a1223aed'], + }), +] + +sanity_check_paths = { + 'files': ['bin/ase'], + 'dirs': ['lib/python%(pyshortver)s/site-packages'], +} + +# make sure Tkinter is available, otherwise 'ase gui' will not work +sanity_check_commands = ["python -c 'import tkinter' "] + +moduleclass = 'chem' From a9a54ba6c29c6194bc2787c09bb0950a0c148d7c Mon Sep 17 00:00:00 2001 From: Stefan Wolfsheimer Date: Thu, 12 Sep 2024 16:30:22 +0200 Subject: [PATCH 02/85] Added binaries to Wannier90 module --- .../easyconfigs/w/Wannier90/Wannier90-3.1.0-foss-2023a.eb | 5 +++-- 1 file changed, 3 insertions(+), 2 deletions(-) diff --git a/easybuild/easyconfigs/w/Wannier90/Wannier90-3.1.0-foss-2023a.eb b/easybuild/easyconfigs/w/Wannier90/Wannier90-3.1.0-foss-2023a.eb index 9807690b35c3..f8fe7f68bbf2 100644 --- a/easybuild/easyconfigs/w/Wannier90/Wannier90-3.1.0-foss-2023a.eb +++ b/easybuild/easyconfigs/w/Wannier90/Wannier90-3.1.0-foss-2023a.eb @@ -25,10 +25,11 @@ buildopts = 'all F90=$F90 MPIF90=$MPIF90 FCOPTS="$FFLAGS -fallow-argument-mismat buildopts += 'LIBDIR="$LAPACK_LIB_DIR" LIBS="$LIBLAPACK" ' buildopts += 'COMMS=mpi' -files_to_copy = [(['wannier90.x', 'postw90.x'], 'bin'), (['libwannier.a'], 'lib')] +local_executables = ['wannier90.x', 'postw90.x', 'w90chk2chk.x', 'w90spn2spn.x'] +files_to_copy = [(local_executables, 'bin'), (['libwannier.a'], 'lib')] sanity_check_paths = { - 'files': ['bin/wannier90.x', 'bin/postw90.x', 'lib/libwannier.a'], + 'files': ['bin/%s' % x for x in local_executables] + ['lib/libwannier.a'], 'dirs': [] } From 3a8ed87051ae429a8307c67f3021d614cdaac65b Mon Sep 17 00:00:00 2001 From: Ake Sandgren Date: Wed, 2 Oct 2024 14:42:38 +0200 Subject: [PATCH 03/85] GTDB-Tk v2.4.0 should use skani and not FastANI --- .../g/GTDB-Tk/GTDB-Tk-2.4.0-foss-2023a.eb | 2 +- .../s/skani/skani-0.2.2-GCCcore-12.3.0.eb | 481 ++++++++++++++++++ 2 files changed, 482 insertions(+), 1 deletion(-) create mode 100644 easybuild/easyconfigs/s/skani/skani-0.2.2-GCCcore-12.3.0.eb diff --git a/easybuild/easyconfigs/g/GTDB-Tk/GTDB-Tk-2.4.0-foss-2023a.eb b/easybuild/easyconfigs/g/GTDB-Tk/GTDB-Tk-2.4.0-foss-2023a.eb index 271be65a5ddb..a8f48c5966b0 100644 --- a/easybuild/easyconfigs/g/GTDB-Tk/GTDB-Tk-2.4.0-foss-2023a.eb +++ b/easybuild/easyconfigs/g/GTDB-Tk/GTDB-Tk-2.4.0-foss-2023a.eb @@ -19,7 +19,7 @@ dependencies = [ ('prodigal', '2.6.3'), ('HMMER', '3.4'), ('pplacer', '1.1.alpha19', '', SYSTEM), - ('FastANI', '1.34'), + ('skani', '0.2.2'), ('FastTree', '2.1.11'), ('Mash', '2.3'), ('tqdm', '4.66.1'), diff --git a/easybuild/easyconfigs/s/skani/skani-0.2.2-GCCcore-12.3.0.eb b/easybuild/easyconfigs/s/skani/skani-0.2.2-GCCcore-12.3.0.eb new file mode 100644 index 000000000000..889947f5c2c6 --- /dev/null +++ b/easybuild/easyconfigs/s/skani/skani-0.2.2-GCCcore-12.3.0.eb @@ -0,0 +1,481 @@ +easyblock = 'Cargo' + +name = 'skani' +version = '0.2.2' + +homepage = 'https://github.com/bluenote-1577/skani' +description = "skani - accurate, fast nucleotide identity calculation for MAGs, genomes, and databases" + +toolchain = {'name': 'GCCcore', 'version': '12.3.0'} + +github_account = 'bluenote-1577' +source_urls = [GITHUB_SOURCE] +sources = ['v%(version)s.tar.gz'] +checksums = [ + {'v0.2.2.tar.gz': 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{'windows_x86_64_msvc-0.48.5.tar.gz': 'ed94fce61571a4006852b7389a063ab983c02eb1bb37b47f8272ce92d06d9538'}, + {'xz2-0.1.7.tar.gz': '388c44dc09d76f1536602ead6d325eb532f5c122f17782bd57fb47baeeb767e2'}, +] + +builddependencies = [ + ('binutils', '2.40'), + ('Rust', '1.75.0'), +] + +dependencies = [ + ('bzip2', '1.0.8'), + ('XZ', '5.4.2'), +] + +# Since we do the download of partitions, remove the download part from skani +prebuildopts = """sed -i -e 's/^partitions = {/#&/' -e 's/^#partitions = ".*/partitions = "0.2.4"/' Cargo.toml && """ + +crates = [ + ('adler', '1.0.2'), + ('aho-corasick', '1.1.2'), + ('anyhow', '1.0.75'), + ('approx', '0.5.1'), + ('assert_cmd', '1.0.8'), + ('atty', '0.2.14'), + ('autocfg', '0.1.8'), + ('autocfg', '1.1.0'), + ('bincode', '1.3.3'), + ('bio', '1.4.0'), + ('bio-types', '1.0.1'), + ('bit-set', '0.5.3'), + ('bit-vec', '0.5.1'), + ('bit-vec', '0.6.3'), + ('bitflags', '1.3.2'), + ('bitflags', '2.4.0'), + ('bstr', '0.2.17'), + ('buffer-redux', '1.0.0'), + ('bv', '0.11.1'), + ('bytecount', '0.6.4'), + ('bytemuck', '1.14.0'), + ('byteorder', '1.5.0'), + ('bzip2', '0.4.4'), + ('bzip2-sys', '0.1.11+1.0.8'), + ('cc', '1.0.83'), + ('cfg-if', '0.1.10'), + ('cfg-if', '1.0.0'), + ('clap', '3.2.25'), + ('clap_lex', '0.2.4'), + ('cloudabi', '0.0.3'), + ('crc32fast', '1.3.2'), + ('crossbeam-deque', '0.8.3'), + ('crossbeam-epoch', '0.9.15'), + ('crossbeam-utils', '0.8.16'), + ('csv', '1.3.0'), + ('csv-core', '0.1.11'), + ('custom_derive', '0.1.7'), + ('dashmap', '5.5.3'), + ('derive-new', '0.5.9'), + ('difference', '2.0.0'), + ('difflib', '0.4.0'), + ('doc-comment', '0.3.3'), + ('editdistancek', '1.0.2'), + ('either', '1.9.0'), + ('enum-map', '1.1.1'), + ('enum-map-derive', '0.6.0'), + ('equivalent', '1.0.1'), + ('errno', '0.3.5'), + ('fastrand', '1.9.0'), + ('fastrand', '2.0.1'), + ('feature-probe', '0.1.1'), + ('fixedbitset', '0.4.2'), + ('flate2', '1.0.27'), + ('float-cmp', '0.8.0'), + ('fnv', '1.0.7'), + ('fuchsia-cprng', '0.1.1'), + ('futures', '0.3.28'), + ('futures-channel', '0.3.28'), + ('futures-core', '0.3.28'), + ('futures-executor', '0.3.28'), + ('futures-io', '0.3.28'), + ('futures-sink', '0.3.28'), + ('futures-task', '0.3.28'), + ('futures-util', '0.3.28'), + ('fxhash', '0.2.1'), + ('gbdt', '0.1.1'), + ('gcollections', '1.5.0'), + ('getrandom', '0.2.10'), + ('getset', '0.1.2'), + ('hashbrown', '0.12.3'), + ('hashbrown', '0.14.1'), + ('heck', '0.4.1'), + ('hermit-abi', '0.1.19'), + ('indexed', '0.1.1'), + ('indexmap', '1.9.3'), + ('indexmap', '2.0.2'), + ('instant', '0.1.12'), + ('intervallum', '1.4.0'), + ('itertools', '0.10.5'), + ('itertools', '0.11.0'), + ('itertools-num', '0.1.3'), + ('itoa', '1.0.9'), + ('lazy_static', '1.4.0'), + ('libc', '0.2.149'), + ('libm', '0.2.8'), + ('linux-raw-sys', '0.4.10'), + ('lock_api', '0.4.10'), + ('log', '0.4.20'), + ('lzma-sys', '0.1.20'), + ('matrixmultiply', '0.3.8'), + ('memchr', '2.6.4'), + ('memoffset', '0.9.0'), + ('miniz_oxide', '0.7.1'), + ('multimap', '0.8.3'), + ('nalgebra', '0.29.0'), + ('nalgebra-macros', '0.1.0'), + ('ndarray', '0.15.6'), + ('needletail', '0.5.1'), + ('newtype_derive', '0.1.6'), + ('normalize-line-endings', '0.3.0'), + ('num-complex', '0.4.4'), + ('num-integer', '0.1.45'), + ('num-rational', '0.4.1'), + ('num-traits', '0.2.17'), + ('once_cell', '1.18.0'), + ('ordered-float', '3.9.1'), + ('os_str_bytes', '6.5.1'), + ('parking_lot', '0.12.1'), + ('parking_lot_core', '0.9.8'), + ('partitions', '0.2.4'), + ('paste', '1.0.14'), + ('petgraph', '0.6.4'), + ('pin-project-lite', '0.2.13'), + ('pin-utils', '0.1.0'), + ('pkg-config', '0.3.27'), + ('ppv-lite86', '0.2.17'), + ('predicates', '1.0.8'), + ('predicates', '2.1.5'), + ('predicates-core', '1.0.6'), + ('predicates-tree', '1.0.9'), + ('proc-macro-error', '1.0.4'), + ('proc-macro-error-attr', '1.0.4'), + ('proc-macro2', '0.2.3'), + ('proc-macro2', '1.0.69'), + ('proptest', '0.8.7'), + ('quick-error', '1.2.3'), + ('quote', '0.4.2'), + ('quote', '1.0.33'), + ('rand', '0.5.6'), + ('rand', '0.6.5'), + ('rand', '0.8.5'), + ('rand_chacha', '0.1.1'), + ('rand_chacha', '0.3.1'), + ('rand_core', '0.3.1'), + ('rand_core', '0.4.2'), + ('rand_core', '0.6.4'), + ('rand_distr', '0.4.3'), + ('rand_hc', '0.1.0'), + ('rand_isaac', '0.1.1'), + ('rand_jitter', '0.1.4'), + ('rand_os', '0.1.3'), + ('rand_pcg', '0.1.2'), + ('rand_xorshift', '0.1.1'), + ('rawpointer', '0.2.1'), + ('rayon', '1.8.0'), + ('rayon-core', '1.12.0'), + ('rdrand', '0.4.0'), + ('redox_syscall', '0.1.57'), + ('redox_syscall', '0.3.5'), + ('reflection', '0.1.3'), + ('reflection_derive', '0.1.1'), + ('regex', '1.10.0'), + ('regex-automata', '0.1.10'), + ('regex-automata', '0.4.1'), + ('regex-syntax', '0.6.29'), + ('regex-syntax', '0.8.0'), + ('rust-lapper', '1.1.0'), + ('rustc_version', '0.1.7'), + ('rustix', '0.38.18'), + ('rustversion', '1.0.14'), + ('rusty-fork', '0.2.2'), + ('ryu', '1.0.15'), + ('safe_arch', '0.7.1'), + ('safemem', '0.3.3'), + ('scopeguard', '1.2.0'), + ('semver', '0.1.20'), + ('serde', '1.0.188'), + ('serde_derive', '1.0.188'), + ('serde_derive_internals', '0.21.0'), + ('serde_json', '1.0.107'), + ('serial_test', '0.10.0'), + ('serial_test_derive', '0.10.0'), + ('simba', '0.6.0'), + ('simple-logging', '2.0.2'), + ('slab', '0.4.9'), + ('smallvec', '1.11.1'), + ('statrs', '0.16.0'), + ('strsim', '0.10.0'), + ('strum', '0.25.0'), + ('strum_macros', '0.25.2'), + ('syn', '0.12.15'), + ('syn', '1.0.109'), + ('syn', '2.0.38'), + ('tempfile', '3.8.0'), + ('termcolor', '1.3.0'), + ('termtree', '0.4.1'), + ('textwrap', '0.16.0'), + ('thiserror', '1.0.49'), + ('thiserror-impl', '1.0.49'), + ('thread-id', '3.3.0'), + ('tikv-jemalloc-sys', '0.5.4+5.3.0-patched'), + ('tikv-jemallocator', '0.5.4'), + ('trees', '0.2.1'), + ('trilean', '1.1.0'), + ('triple_accel', '0.4.0'), + ('tsv', '0.1.1'), + ('typenum', '1.17.0'), + ('unicode-ident', '1.0.12'), + ('unicode-xid', '0.1.0'), + ('vec_map', '0.8.2'), + ('version_check', '0.9.4'), + ('wait-timeout', '0.2.0'), + ('wasi', '0.11.0+wasi-snapshot-preview1'), + ('wide', '0.7.12'), + ('winapi', '0.3.9'), + ('winapi-i686-pc-windows-gnu', '0.4.0'), + ('winapi-util', '0.1.6'), + ('winapi-x86_64-pc-windows-gnu', '0.4.0'), + ('windows-sys', '0.48.0'), + ('windows-targets', '0.48.5'), + ('windows_aarch64_gnullvm', '0.48.5'), + ('windows_aarch64_msvc', '0.48.5'), + ('windows_i686_gnu', '0.48.5'), + ('windows_i686_msvc', '0.48.5'), + ('windows_x86_64_gnu', '0.48.5'), + ('windows_x86_64_gnullvm', '0.48.5'), + ('windows_x86_64_msvc', '0.48.5'), + ('xz2', '0.1.7'), +] + +sanity_check_paths = { + 'files': ['bin/skani'], + 'dirs': [], +} + +sanity_check_commands = [ + 'skani --help', +] + + +moduleclass = 'bio' From 175e9afacf7679916d2306bd6c25f2a3ab21bedd Mon Sep 17 00:00:00 2001 From: Sebastian Achilles Date: Sat, 5 Oct 2024 10:45:03 +0200 Subject: [PATCH 04/85] add patch to SciPy-bundle 2024.05 that fixes test failure on aarch64 --- .../SciPy-bundle-2024.05-gfbf-2024a.eb | 3 ++ .../scipy-1.13.1_TestLinprogIPSparse.patch | 30 +++++++++++++++++++ 2 files changed, 33 insertions(+) create mode 100644 easybuild/easyconfigs/s/SciPy-bundle/scipy-1.13.1_TestLinprogIPSparse.patch diff --git a/easybuild/easyconfigs/s/SciPy-bundle/SciPy-bundle-2024.05-gfbf-2024a.eb b/easybuild/easyconfigs/s/SciPy-bundle/SciPy-bundle-2024.05-gfbf-2024a.eb index 2abab977addb..5584d888f308 100644 --- a/easybuild/easyconfigs/s/SciPy-bundle/SciPy-bundle-2024.05-gfbf-2024a.eb +++ b/easybuild/easyconfigs/s/SciPy-bundle/SciPy-bundle-2024.05-gfbf-2024a.eb @@ -64,12 +64,15 @@ exts_list = [ 'patches': [ 'scipy-1.11.1_disable-tests.patch', 'scipy-1.11.1_xfail-aarch64_test_maxiter_worsening.patch', + 'scipy-1.13.1_TestLinprogIPSparse.patch', ], 'checksums': [ {'scipy-1.13.1.tar.gz': '095a87a0312b08dfd6a6155cbbd310a8c51800fc931b8c0b84003014b874ed3c'}, {'scipy-1.11.1_disable-tests.patch': '906bfb03397d94882ccdc1b93bc2c8e854e0e060c2d107c83042992394e6a4af'}, {'scipy-1.11.1_xfail-aarch64_test_maxiter_worsening.patch': '918c8e6fa8215d459126f267764c961bde729ea4a116c7f6287cddfdc58ffcea'}, + {'scipy-1.13.1_TestLinprogIPSparse.patch': + '7213c2690b76c69f7e7103529cea3fa2098c05fbea556f04325fab9ca8c065f5'}, ], }), ('numexpr', '2.10.0', { diff --git a/easybuild/easyconfigs/s/SciPy-bundle/scipy-1.13.1_TestLinprogIPSparse.patch b/easybuild/easyconfigs/s/SciPy-bundle/scipy-1.13.1_TestLinprogIPSparse.patch new file mode 100644 index 000000000000..1b0573190866 --- /dev/null +++ b/easybuild/easyconfigs/s/SciPy-bundle/scipy-1.13.1_TestLinprogIPSparse.patch @@ -0,0 +1,30 @@ +disable problematic tests +TestLinprogIPSparse::test_bug_6139 + TestLinprogIPSparsePresolve::test_bug_6139 fail on Grace Hopper aarch64 +author: Sebastian Achilles (Juelich Supercomputing Centre) + +diff --git a/scipy/optimize/tests/test_linprog.py b/scipy/optimize/tests/test_linprog.py +index 49a0f8de5..8ffbb0b47 100644 +--- a/scipy/optimize/tests/test_linprog.py ++++ b/scipy/optimize/tests/test_linprog.py +@@ -1977,6 +1977,10 @@ if has_umfpack: + class TestLinprogIPSparse(LinprogIPTests): + options = {"sparse": True, "cholesky": False, "sym_pos": False} + ++ @pytest.mark.skipif( ++ platform.machine() == 'aarch64', ++ reason="Fails on aarch64" ++ ) + @pytest.mark.xfail_on_32bit("This test is sensitive to machine epsilon level " + "perturbations in linear system solution in " + "_linprog_ip._sym_solve.") +@@ -2027,6 +2031,10 @@ class TestLinprogIPSparse(LinprogIPTests): + class TestLinprogIPSparsePresolve(LinprogIPTests): + options = {"sparse": True, "_sparse_presolve": True} + ++ @pytest.mark.skipif( ++ platform.machine() == 'aarch64', ++ reason="Fails on aarch64" ++ ) + @pytest.mark.xfail_on_32bit("This test is sensitive to machine epsilon level " + "perturbations in linear system solution in " + "_linprog_ip._sym_solve.") From fa639e1ee4076f9837834212790f68157929897f Mon Sep 17 00:00:00 2001 From: maxim-masterov Date: Sat, 5 Oct 2024 20:25:36 +0200 Subject: [PATCH 05/85] Add HPX and dependencies --- .../gperftools-2.16-GCCcore-13.3.0.eb | 37 ++++++++++++++++ .../h/HDF5/HDF5-1.14.5-gompi-2024a.eb | 27 ++++++++++++ .../h/HPX/HPX-1.10.0-foss-2024a.eb | 44 +++++++++++++++++++ 3 files changed, 108 insertions(+) create mode 100644 easybuild/easyconfigs/g/gperftools/gperftools-2.16-GCCcore-13.3.0.eb create mode 100644 easybuild/easyconfigs/h/HDF5/HDF5-1.14.5-gompi-2024a.eb create mode 100644 easybuild/easyconfigs/h/HPX/HPX-1.10.0-foss-2024a.eb diff --git a/easybuild/easyconfigs/g/gperftools/gperftools-2.16-GCCcore-13.3.0.eb b/easybuild/easyconfigs/g/gperftools/gperftools-2.16-GCCcore-13.3.0.eb new file mode 100644 index 000000000000..b142fbdb34d8 --- /dev/null +++ b/easybuild/easyconfigs/g/gperftools/gperftools-2.16-GCCcore-13.3.0.eb @@ -0,0 +1,37 @@ +easyblock = 'ConfigureMake' + +name = 'gperftools' +version = '2.16' + +homepage = 'https://github.com/gperftools/gperftools' +description = """ +gperftools is a collection of a high-performance multi-threaded malloc() +implementation, plus some pretty nifty performance analysis tools. +Includes TCMalloc, heap-checker, heap-profiler and cpu-profiler. +""" + +toolchain = {'name': 'GCCcore', 'version': '13.3.0'} + +source_urls = [GITHUB_SOURCE] +sources = [SOURCE_TAR_GZ] +checksums = ['737be182b4e42f5c7f595da2a7aa59ce0489a73d336d0d16847f2aa52d5221b4'] + +builddependencies = [ + ('Autotools', '20231222'), + ('binutils', '2.42'), +] +dependencies = [ + ('libunwind', '1.8.1'), +] + +preconfigopts = "autoreconf -f -i && " +configopts = '--enable-libunwind' + +github_account = '%(name)s' + +sanity_check_paths = { + 'files': ['bin/pprof', 'lib/libprofiler.a', 'lib/libprofiler.so', 'lib/libtcmalloc.a', 'lib/libtcmalloc.so'], + 'dirs': ['include'], +} + +moduleclass = 'tools' diff --git a/easybuild/easyconfigs/h/HDF5/HDF5-1.14.5-gompi-2024a.eb b/easybuild/easyconfigs/h/HDF5/HDF5-1.14.5-gompi-2024a.eb new file mode 100644 index 000000000000..591719629241 --- /dev/null +++ b/easybuild/easyconfigs/h/HDF5/HDF5-1.14.5-gompi-2024a.eb @@ -0,0 +1,27 @@ +name = 'HDF5' +# Note: Odd minor releases are only RCs and should not be used. +version = '1.14.5' + +homepage = 'https://portal.hdfgroup.org/display/support' +description = """HDF5 is a data model, library, and file format for storing and managing data. + It supports an unlimited variety of datatypes, and is designed for flexible + and efficient I/O and for high volume and complex data.""" + +toolchain = {'name': 'gompi', 'version': '2024a'} +toolchainopts = {'pic': True, 'usempi': True} + +source_urls = ['https://github.com/HDFGroup/hdf5/archive'] +sources = ['hdf5_%(version)s.tar.gz'] +checksums = ['c83996dc79080a34e7b5244a1d5ea076abfd642ec12d7c25388e2fdd81d26350'] + +dependencies = [ + ('zlib', '1.3.1'), + ('Szip', '2.1.1'), +] + +postinstallcmds = [ + 'sed -i -r "s, -I[^[:space:]]+H5FDsubfiling , -I%(installdir)s/include ,g" %(installdir)s/bin/h5c++', + 'sed -i -r "s, -I[^[:space:]]+H5FDsubfiling , -I%(installdir)s/include ,g" %(installdir)s/bin/h5pcc', +] + +moduleclass = 'data' diff --git a/easybuild/easyconfigs/h/HPX/HPX-1.10.0-foss-2024a.eb b/easybuild/easyconfigs/h/HPX/HPX-1.10.0-foss-2024a.eb new file mode 100644 index 000000000000..493d4a7743f9 --- /dev/null +++ b/easybuild/easyconfigs/h/HPX/HPX-1.10.0-foss-2024a.eb @@ -0,0 +1,44 @@ +# # +# Author: Benjamin Czaja (benjamin.czaja@surf.nl) +# Institute: SURF(sara) +# +# # +easyblock = 'CMakeMake' + +name = 'HPX' +version = '1.10.0' + +homepage = 'http://stellar-group.org/libraries/hpx/' +description = """HPX (High Performance ParalleX) is a general purpose C++ runtime system + for parallel and distributed applications of any scale.""" + +toolchain = {'name': 'foss', 'version': '2024a'} +toolchainopts = {'pic': True} + +source_urls = ['https://github.com/STEllAR-GROUP/%(namelower)s/archive'] +sources = ['v%(version)s.tar.gz'] + +builddependencies = [ + ('CMake', '3.29.3'), + ('Ninja', '1.12.1'), + ('pkgconf', '2.2.0'), +] +dependencies = [ + ('HDF5', '1.14.5'), + ('Boost', '1.85.0'), + ('hwloc', '2.10.0'), + ('gperftools', '2.12'), +] + +configopts = "-DCMAKE_CXX_COMPILER=g++ -DCMAKE_BUILD_TYPE=Release -DHPX_WITH_MALLOC=tcmalloc -DHPX_WITH_HWLOC=TRUE -DHPX_WITH_GOOGLE_PERFTOOLS=TRUE -DHPX_WITH_NETWORKING=TRUE -DHPX_WITH_PARCELPORT_TCP=FALSE -DHPX_WITH_PARCELPORT_MPI=TRUE -DHPX_WITH_TESTS=FALSE -DHPX_WITH_EXAMPLES=TRUE -DHPX_WITH_FETCH_ASIO=TRUE " + +bin_lib_subdirs = ['lib/%(namelower)s/'] + +sanity_check_paths = { + 'files': [], + 'dirs': ['bin', 'lib'], +} + +modextrapaths = {'LD_LIBRARY_PATH': ['lib/%(namelower)s']} + +moduleclass = 'math' From 2f81b66fe30db90a2736dcaf446cbdbf2a259131 Mon Sep 17 00:00:00 2001 From: maxim-masterov Date: Mon, 7 Oct 2024 12:35:31 +0200 Subject: [PATCH 06/85] Add HPX --- easybuild/easyconfigs/h/HPX/HPX-1.10.0-foss-2024a.eb | 4 ++-- 1 file changed, 2 insertions(+), 2 deletions(-) diff --git a/easybuild/easyconfigs/h/HPX/HPX-1.10.0-foss-2024a.eb b/easybuild/easyconfigs/h/HPX/HPX-1.10.0-foss-2024a.eb index 493d4a7743f9..301f804cc827 100644 --- a/easybuild/easyconfigs/h/HPX/HPX-1.10.0-foss-2024a.eb +++ b/easybuild/easyconfigs/h/HPX/HPX-1.10.0-foss-2024a.eb @@ -3,7 +3,7 @@ # Institute: SURF(sara) # # # -easyblock = 'CMakeMake' +easyblock = 'CMakeNinja' name = 'HPX' version = '1.10.0' @@ -27,7 +27,7 @@ dependencies = [ ('HDF5', '1.14.5'), ('Boost', '1.85.0'), ('hwloc', '2.10.0'), - ('gperftools', '2.12'), + ('gperftools', '2.16'), ] configopts = "-DCMAKE_CXX_COMPILER=g++ -DCMAKE_BUILD_TYPE=Release -DHPX_WITH_MALLOC=tcmalloc -DHPX_WITH_HWLOC=TRUE -DHPX_WITH_GOOGLE_PERFTOOLS=TRUE -DHPX_WITH_NETWORKING=TRUE -DHPX_WITH_PARCELPORT_TCP=FALSE -DHPX_WITH_PARCELPORT_MPI=TRUE -DHPX_WITH_TESTS=FALSE -DHPX_WITH_EXAMPLES=TRUE -DHPX_WITH_FETCH_ASIO=TRUE " From 60a35617dd841278c8b749711246b954150a6a7c Mon Sep 17 00:00:00 2001 From: maxim-masterov Date: Wed, 9 Oct 2024 18:45:11 +0200 Subject: [PATCH 07/85] Fix style --- .../easyconfigs/h/HPX/HPX-1.10.0-foss-2024a.eb | 14 +++++++++++++- 1 file changed, 13 insertions(+), 1 deletion(-) diff --git a/easybuild/easyconfigs/h/HPX/HPX-1.10.0-foss-2024a.eb b/easybuild/easyconfigs/h/HPX/HPX-1.10.0-foss-2024a.eb index 301f804cc827..2674dfe85080 100644 --- a/easybuild/easyconfigs/h/HPX/HPX-1.10.0-foss-2024a.eb +++ b/easybuild/easyconfigs/h/HPX/HPX-1.10.0-foss-2024a.eb @@ -30,7 +30,19 @@ dependencies = [ ('gperftools', '2.16'), ] -configopts = "-DCMAKE_CXX_COMPILER=g++ -DCMAKE_BUILD_TYPE=Release -DHPX_WITH_MALLOC=tcmalloc -DHPX_WITH_HWLOC=TRUE -DHPX_WITH_GOOGLE_PERFTOOLS=TRUE -DHPX_WITH_NETWORKING=TRUE -DHPX_WITH_PARCELPORT_TCP=FALSE -DHPX_WITH_PARCELPORT_MPI=TRUE -DHPX_WITH_TESTS=FALSE -DHPX_WITH_EXAMPLES=TRUE -DHPX_WITH_FETCH_ASIO=TRUE " +configopts = '-DCMAKE_CXX_COMPILER=g++ ' +configopts += '-DCMAKE_BUILD_TYPE=Release ' +configopts += '-DHPX_WITH_MALLOC=tcmalloc ' +configopts += '-DHPX_WITH_HWLOC=TRUE ' +configopts += '-DHPX_WITH_GOOGLE_PERFTOOLS=TRUE ' +configopts += '-DHPX_WITH_NETWORKING=TRUE ' +configopts += '-DHPX_WITH_PARCELPORT_TCP=FALSE ' +configopts += '-DHPX_WITH_PARCELPORT_MPI=TRUE ' +configopts += '-DHPX_WITH_TESTS=FALSE ' +configopts += '-DHPX_WITH_EXAMPLES=TRUE ' +# configopts += '-DHPX_WITH_MAX_CPU_COUNT=128' #this should be handled by a hook for the system +# configopts += '-DHPX_WITH_MAX_CPU_COUNT=' + os.cpu_count() +configopts += '-DHPX_WITH_FETCH_ASIO=TRUE ' bin_lib_subdirs = ['lib/%(namelower)s/'] From 00c9a50b45d1cd570060051e9f273ac6f12633b3 Mon Sep 17 00:00:00 2001 From: maxim-masterov Date: Wed, 9 Oct 2024 18:49:06 +0200 Subject: [PATCH 08/85] Add checksum --- easybuild/easyconfigs/h/HPX/HPX-1.10.0-foss-2024a.eb | 3 +++ 1 file changed, 3 insertions(+) diff --git a/easybuild/easyconfigs/h/HPX/HPX-1.10.0-foss-2024a.eb b/easybuild/easyconfigs/h/HPX/HPX-1.10.0-foss-2024a.eb index 2674dfe85080..9e1c986fa71b 100644 --- a/easybuild/easyconfigs/h/HPX/HPX-1.10.0-foss-2024a.eb +++ b/easybuild/easyconfigs/h/HPX/HPX-1.10.0-foss-2024a.eb @@ -17,6 +17,7 @@ toolchainopts = {'pic': True} source_urls = ['https://github.com/STEllAR-GROUP/%(namelower)s/archive'] sources = ['v%(version)s.tar.gz'] +checksums = ['5720ed7d2460fa0b57bd8cb74fa4f70593fe8675463897678160340526ec3c19'] builddependencies = [ ('CMake', '3.29.3'), @@ -30,6 +31,8 @@ dependencies = [ ('gperftools', '2.16'), ] +build_type = 'Release' + configopts = '-DCMAKE_CXX_COMPILER=g++ ' configopts += '-DCMAKE_BUILD_TYPE=Release ' configopts += '-DHPX_WITH_MALLOC=tcmalloc ' From 7b7bf5cafc50d26ccfc91590ee1d5d2fb26f367d Mon Sep 17 00:00:00 2001 From: maximm Date: Tue, 15 Oct 2024 11:21:48 +0200 Subject: [PATCH 09/85] adding easyconfigs: MCR-R2024b.eb --- easybuild/easyconfigs/m/MCR/MCR-R2024b.eb | 17 +++++++++++++++++ 1 file changed, 17 insertions(+) create mode 100644 easybuild/easyconfigs/m/MCR/MCR-R2024b.eb diff --git a/easybuild/easyconfigs/m/MCR/MCR-R2024b.eb b/easybuild/easyconfigs/m/MCR/MCR-R2024b.eb new file mode 100644 index 000000000000..17ad8df12f62 --- /dev/null +++ b/easybuild/easyconfigs/m/MCR/MCR-R2024b.eb @@ -0,0 +1,17 @@ +name = 'MCR' +version = 'R2024b' # runtime version 24.2 +local_update = '0' + +homepage = 'https://www.mathworks.com/products/compiler/mcr/' +description = """The MATLAB Runtime is a standalone set of shared libraries + that enables the execution of compiled MATLAB applications + or components on computers that do not have MATLAB installed.""" + +toolchain = SYSTEM + +source_urls = ['https://ssd.mathworks.com/supportfiles/downloads/%%(version)s/Release/%s/deployment_files/' + 'installer/complete/glnxa64/' % local_update] +sources = ['MATLAB_Runtime_%(version)s_glnxa64.zip'] +checksums = ['c46f4b55747aa4a8c03c1ece5bd5360c4dbb2ca402608fbd44688ba55f9b7a54'] + +moduleclass = 'math' From 96675c98ef08d9444cfeece3117078147ea76fd5 Mon Sep 17 00:00:00 2001 From: Leonard Nielsen Date: Tue, 15 Oct 2024 19:26:36 +0000 Subject: [PATCH 10/85] adding easyconfigs: modin-0.32.0-foss-2024a.eb --- .../m/modin/modin-0.32.0-foss-2024a.eb | 45 +++++++++++++++++++ 1 file changed, 45 insertions(+) create mode 100644 easybuild/easyconfigs/m/modin/modin-0.32.0-foss-2024a.eb diff --git a/easybuild/easyconfigs/m/modin/modin-0.32.0-foss-2024a.eb b/easybuild/easyconfigs/m/modin/modin-0.32.0-foss-2024a.eb new file mode 100644 index 000000000000..3a8709cbcfbd --- /dev/null +++ b/easybuild/easyconfigs/m/modin/modin-0.32.0-foss-2024a.eb @@ -0,0 +1,45 @@ +easyblock = 'PythonBundle' + +name = 'modin' +version = '0.32.0' + +homepage = 'https://github.com/libvips/pyvips' +description = """This module wraps the libvips image processing library. +libvips is a demand-driven, horizontally threaded image processing library.""" + +toolchain = {'name': 'foss', 'version': '2024a'} + +builddependencies = [ + ('Cython', '3.0.10'), +] + +dependencies = [ + ('Python', '3.12.3'), + ('Python-bundle-PyPI', '2024.06'), + ('SciPy-bundle', '2024.05'), + ('dask', '2024.9.1'), + ('OpenMPI', '5.0.3'), + ('Ray-project', '2.37.0'), + ('Arrow', '17.0.0'), + ('mpi4py', '4.0.1') +] + +download_dep_fail = True +use_pip = True + +exts_list = [ + (name, version, { + 'checksums': ['9f68557add5e92617d006eb98bfd93d298e7d4d9932a0cd48a5e38ee4f30a134'], + }), + ('unidist', '0.7.1', { + 'source_tmpl': '%(namelower)s-%(version)s-cp312-cp312-manylinux_2_17_%(arch)s.manylinux2014_%(arch)s.whl', + 'use_pip_extras': 'mpi', + 'checksums': ['1433753726d8be0e484ca53f75d501afa8c4d94acf9c45a0970949411b4b41e0'], + }), +] + +sanity_check_commands = ['python -c "import modin"'] + +sanity_pip_check = True + +moduleclass = 'tools' From 5b122322f014bc2a659b261c1f1f63781579b068 Mon Sep 17 00:00:00 2001 From: Leonard Nielsen Date: Tue, 15 Oct 2024 19:32:20 +0000 Subject: [PATCH 11/85] updated description and link --- easybuild/easyconfigs/m/modin/modin-0.32.0-foss-2024a.eb | 5 ++--- 1 file changed, 2 insertions(+), 3 deletions(-) diff --git a/easybuild/easyconfigs/m/modin/modin-0.32.0-foss-2024a.eb b/easybuild/easyconfigs/m/modin/modin-0.32.0-foss-2024a.eb index 3a8709cbcfbd..02ac1a152351 100644 --- a/easybuild/easyconfigs/m/modin/modin-0.32.0-foss-2024a.eb +++ b/easybuild/easyconfigs/m/modin/modin-0.32.0-foss-2024a.eb @@ -3,9 +3,8 @@ easyblock = 'PythonBundle' name = 'modin' version = '0.32.0' -homepage = 'https://github.com/libvips/pyvips' -description = """This module wraps the libvips image processing library. -libvips is a demand-driven, horizontally threaded image processing library.""" +homepage = 'https://github.com/modin-project/modin' +description = """Modin uses Ray, Dask or Unidist to provide an effortless way to speed up your pandas notebooks, scripts, and libraries. """ toolchain = {'name': 'foss', 'version': '2024a'} From df0f3a4b0756716d072bfed484466a00218eb514 Mon Sep 17 00:00:00 2001 From: =?UTF-8?q?Mikael=20=C3=96hman?= Date: Thu, 17 Oct 2024 11:17:40 +0200 Subject: [PATCH 12/85] Update easybuild/easyconfigs/m/modin/modin-0.32.0-foss-2024a.eb --- easybuild/easyconfigs/m/modin/modin-0.32.0-foss-2024a.eb | 3 ++- 1 file changed, 2 insertions(+), 1 deletion(-) diff --git a/easybuild/easyconfigs/m/modin/modin-0.32.0-foss-2024a.eb b/easybuild/easyconfigs/m/modin/modin-0.32.0-foss-2024a.eb index 02ac1a152351..268f59942f6c 100644 --- a/easybuild/easyconfigs/m/modin/modin-0.32.0-foss-2024a.eb +++ b/easybuild/easyconfigs/m/modin/modin-0.32.0-foss-2024a.eb @@ -4,7 +4,8 @@ name = 'modin' version = '0.32.0' homepage = 'https://github.com/modin-project/modin' -description = """Modin uses Ray, Dask or Unidist to provide an effortless way to speed up your pandas notebooks, scripts, and libraries. """ +description = """Modin uses Ray, Dask or Unidist to provide an effortless way to speed up your pandas notebooks, +scripts, and libraries. """ toolchain = {'name': 'foss', 'version': '2024a'} From 37217fb461038262f9146e47cfae5eda56d7fe1b Mon Sep 17 00:00:00 2001 From: Leonard Nielsen <55690238+lcniel@users.noreply.github.com> Date: Thu, 17 Oct 2024 13:09:00 +0200 Subject: [PATCH 13/85] Update modin-0.32.0-foss-2024a.eb --- easybuild/easyconfigs/m/modin/modin-0.32.0-foss-2024a.eb | 2 -- 1 file changed, 2 deletions(-) diff --git a/easybuild/easyconfigs/m/modin/modin-0.32.0-foss-2024a.eb b/easybuild/easyconfigs/m/modin/modin-0.32.0-foss-2024a.eb index 268f59942f6c..ce7cb19ce0d7 100644 --- a/easybuild/easyconfigs/m/modin/modin-0.32.0-foss-2024a.eb +++ b/easybuild/easyconfigs/m/modin/modin-0.32.0-foss-2024a.eb @@ -38,8 +38,6 @@ exts_list = [ }), ] -sanity_check_commands = ['python -c "import modin"'] - sanity_pip_check = True moduleclass = 'tools' From 0840096cc02a7f811d260229a74166539172381f Mon Sep 17 00:00:00 2001 From: Leonard Nielsen Date: Thu, 17 Oct 2024 14:38:25 +0000 Subject: [PATCH 14/85] enable some tests --- .../m/modin/modin-0.32.0-foss-2024a.eb | 27 ++++++++++++++----- .../modin-0.32.0_fix-pytest-config.patch | 20 ++++++++++++++ 2 files changed, 40 insertions(+), 7 deletions(-) create mode 100644 easybuild/easyconfigs/m/modin/modin-0.32.0_fix-pytest-config.patch diff --git a/easybuild/easyconfigs/m/modin/modin-0.32.0-foss-2024a.eb b/easybuild/easyconfigs/m/modin/modin-0.32.0-foss-2024a.eb index ce7cb19ce0d7..636679481037 100644 --- a/easybuild/easyconfigs/m/modin/modin-0.32.0-foss-2024a.eb +++ b/easybuild/easyconfigs/m/modin/modin-0.32.0-foss-2024a.eb @@ -11,6 +11,9 @@ toolchain = {'name': 'foss', 'version': '2024a'} builddependencies = [ ('Cython', '3.0.10'), + # Needed for tests + ('boto3', '1.35.36'), + ('s3fs', '2024.9.0'), ] dependencies = [ @@ -24,17 +27,27 @@ dependencies = [ ('mpi4py', '4.0.1') ] -download_dep_fail = True use_pip = True +local_pytest_cmd = 'pytest modin/tests/pandas --ignore=modin/tests/pandas/test_io.py --ignore=modin/tests/pandas/integrations/test_lazy_import.py' + exts_list = [ - (name, version, { - 'checksums': ['9f68557add5e92617d006eb98bfd93d298e7d4d9932a0cd48a5e38ee4f30a134'], - }), ('unidist', '0.7.1', { - 'source_tmpl': '%(namelower)s-%(version)s-cp312-cp312-manylinux_2_17_%(arch)s.manylinux2014_%(arch)s.whl', - 'use_pip_extras': 'mpi', - 'checksums': ['1433753726d8be0e484ca53f75d501afa8c4d94acf9c45a0970949411b4b41e0'], + 'source_tmpl': '%(version)s.tar.gz', + 'source_urls': ['https://github.com/modin-project/%(name)s/archive/refs/tags/'], + 'checksums': ['9bae91f0bbc33af3b55948990f69400ee819dfda9c635286e6917aebd7f24791'], + }), + (name, version, { + 'patches': ['modin-0.32.0_fix-pytest-config.patch'], + 'runtest': 'MODIN_BACKEND=unidist UNIDIST_BACKEND=mpi %(local_pytest_cmd)s && MODIN_BACKEND=ray %(local_pytest_cmd)s && MODIN_BACKEND=dask %(local_pytest_cmd)s' % {'local_pytest_cmd': local_pytest_cmd}, + 'source_tmpl': '%(version)s.tar.gz', + 'source_urls': ['https://github.com/modin-project/%(name)s/archive/refs/tags'], + 'testinstall': True, + 'checksums': [ + {'0.32.0.tar.gz': 'f2ef11f384a7d47eb6680a2f6f4bbc3404fa6290163d36384032daff3837b063'}, + {'modin-0.32.0_fix-pytest-config.patch': + 'c49bd5c072a87321760c7c5eebc957f4f6962763a3526a500fe6330cf3f2b765'}, + ], }), ] diff --git a/easybuild/easyconfigs/m/modin/modin-0.32.0_fix-pytest-config.patch b/easybuild/easyconfigs/m/modin/modin-0.32.0_fix-pytest-config.patch new file mode 100644 index 000000000000..990e053d3284 --- /dev/null +++ b/easybuild/easyconfigs/m/modin/modin-0.32.0_fix-pytest-config.patch @@ -0,0 +1,20 @@ +Removes unnecessary options for pytest that induce additional dependencies. + +--- 0.32.0/foss-2024a/modin/modin-0.32.0/setup.cfg.orig 2024-10-17 15:56:55.245266649 +0200 ++++ 0.32.0/foss-2024a/modin/modin-0.32.0/setup.cfg 2024-10-17 15:57:34.748841878 +0200 +@@ -11,15 +11,6 @@ + tag_prefix = + parentdir_prefix = modin- + +-[tool:pytest] +-addopts = --cov-config=setup.cfg --cov=modin --cov-append --cov-report= -m "not exclude_by_default" +-xfail_strict=true +-markers = +- exclude_in_sanity +- exclude_by_default +-filterwarnings = +- error:.*defaulting to pandas.*:UserWarning +- + [isort] + profile = black + From 646ab3444003de3d36b3039e25f930f5c05a245d Mon Sep 17 00:00:00 2001 From: Leonard Nielsen Date: Thu, 17 Oct 2024 15:17:29 +0000 Subject: [PATCH 15/85] checksums --- easybuild/easyconfigs/m/modin/modin-0.32.0-foss-2024a.eb | 2 +- 1 file changed, 1 insertion(+), 1 deletion(-) diff --git a/easybuild/easyconfigs/m/modin/modin-0.32.0-foss-2024a.eb b/easybuild/easyconfigs/m/modin/modin-0.32.0-foss-2024a.eb index 636679481037..209a10272577 100644 --- a/easybuild/easyconfigs/m/modin/modin-0.32.0-foss-2024a.eb +++ b/easybuild/easyconfigs/m/modin/modin-0.32.0-foss-2024a.eb @@ -39,7 +39,7 @@ exts_list = [ }), (name, version, { 'patches': ['modin-0.32.0_fix-pytest-config.patch'], - 'runtest': 'MODIN_BACKEND=unidist UNIDIST_BACKEND=mpi %(local_pytest_cmd)s && MODIN_BACKEND=ray %(local_pytest_cmd)s && MODIN_BACKEND=dask %(local_pytest_cmd)s' % {'local_pytest_cmd': local_pytest_cmd}, + 'runtest': "MODIN_BACKEND=unidist UNIDIST_BACKEND=mpi pytest modin/tests/pandas --ignore=modin/tests/pandas/test_io.py --ignore=modin/tests/pandas/integrations/test_lazy_import.py && MODIN_BACKEND=ray pytest modin/tests/pandas --ignore=modin/tests/pandas/test_io.py --ignore=modin/tests/pandas/integrations/test_lazy_import.py && MODIN_BACKEND=dask pytest modin/tests/pandas --ignore=modin/tests/pandas/test_io.py --ignore=modin/tests/pandas/integrations/test_lazy_import.py", 'source_tmpl': '%(version)s.tar.gz', 'source_urls': ['https://github.com/modin-project/%(name)s/archive/refs/tags'], 'testinstall': True, From fc5c77d1b2fbe4a2357f2bfed5d53860c8b040fe Mon Sep 17 00:00:00 2001 From: Leonard Nielsen Date: Thu, 17 Oct 2024 17:09:41 +0000 Subject: [PATCH 16/85] test suite --- .../easyconfigs/m/modin/modin-0.32.0-foss-2024a.eb | 11 ++++++++--- 1 file changed, 8 insertions(+), 3 deletions(-) diff --git a/easybuild/easyconfigs/m/modin/modin-0.32.0-foss-2024a.eb b/easybuild/easyconfigs/m/modin/modin-0.32.0-foss-2024a.eb index 209a10272577..098027eecd66 100644 --- a/easybuild/easyconfigs/m/modin/modin-0.32.0-foss-2024a.eb +++ b/easybuild/easyconfigs/m/modin/modin-0.32.0-foss-2024a.eb @@ -29,17 +29,22 @@ dependencies = [ use_pip = True -local_pytest_cmd = 'pytest modin/tests/pandas --ignore=modin/tests/pandas/test_io.py --ignore=modin/tests/pandas/integrations/test_lazy_import.py' - exts_list = [ ('unidist', '0.7.1', { 'source_tmpl': '%(version)s.tar.gz', 'source_urls': ['https://github.com/modin-project/%(name)s/archive/refs/tags/'], 'checksums': ['9bae91f0bbc33af3b55948990f69400ee819dfda9c635286e6917aebd7f24791'], }), + # Cannot test for Ray due to unix socket issue (name, version, { 'patches': ['modin-0.32.0_fix-pytest-config.patch'], - 'runtest': "MODIN_BACKEND=unidist UNIDIST_BACKEND=mpi pytest modin/tests/pandas --ignore=modin/tests/pandas/test_io.py --ignore=modin/tests/pandas/integrations/test_lazy_import.py && MODIN_BACKEND=ray pytest modin/tests/pandas --ignore=modin/tests/pandas/test_io.py --ignore=modin/tests/pandas/integrations/test_lazy_import.py && MODIN_BACKEND=dask pytest modin/tests/pandas --ignore=modin/tests/pandas/test_io.py --ignore=modin/tests/pandas/integrations/test_lazy_import.py", + 'runtest': ( + "MODIN_BACKEND=unidist UNIDIST_BACKEND=mpi pytest modin/tests/pandas " + " --ignore=modin/tests/pandas/test_io.py " + "--ignore=modin/tests/pandas/integrations/test_lazy_import.py &&" + " MODIN_BACKEND=dask pytest modin/tests/pandas --ignore=modin/tests/pandas/test_io.py" + " --ignore=modin/tests/pandas/integrations/test_lazy_import.py" + ), 'source_tmpl': '%(version)s.tar.gz', 'source_urls': ['https://github.com/modin-project/%(name)s/archive/refs/tags'], 'testinstall': True, From da0530e5da3054612f0378e6cbdfd545b92c489d Mon Sep 17 00:00:00 2001 From: Leonard Nielsen Date: Thu, 17 Oct 2024 17:37:29 +0000 Subject: [PATCH 17/85] test suite --- easybuild/easyconfigs/m/modin/modin-0.32.0-foss-2024a.eb | 4 ++-- 1 file changed, 2 insertions(+), 2 deletions(-) diff --git a/easybuild/easyconfigs/m/modin/modin-0.32.0-foss-2024a.eb b/easybuild/easyconfigs/m/modin/modin-0.32.0-foss-2024a.eb index 098027eecd66..57ceac35c950 100644 --- a/easybuild/easyconfigs/m/modin/modin-0.32.0-foss-2024a.eb +++ b/easybuild/easyconfigs/m/modin/modin-0.32.0-foss-2024a.eb @@ -39,10 +39,10 @@ exts_list = [ (name, version, { 'patches': ['modin-0.32.0_fix-pytest-config.patch'], 'runtest': ( - "MODIN_BACKEND=unidist UNIDIST_BACKEND=mpi pytest modin/tests/pandas " + "MODIN_ENGINE=unidist UNIDIST_ENGINE=mpi pytest modin/tests/pandas " " --ignore=modin/tests/pandas/test_io.py " "--ignore=modin/tests/pandas/integrations/test_lazy_import.py &&" - " MODIN_BACKEND=dask pytest modin/tests/pandas --ignore=modin/tests/pandas/test_io.py" + " MODIN_ENGINE=dask pytest modin/tests/pandas --ignore=modin/tests/pandas/test_io.py" " --ignore=modin/tests/pandas/integrations/test_lazy_import.py" ), 'source_tmpl': '%(version)s.tar.gz', From e6198a162675109a4532b01707645fdd52f19958 Mon Sep 17 00:00:00 2001 From: Leonard Nielsen Date: Thu, 17 Oct 2024 20:09:03 +0000 Subject: [PATCH 18/85] cut down on test suite --- easybuild/easyconfigs/m/modin/modin-0.32.0-foss-2024a.eb | 7 ++----- 1 file changed, 2 insertions(+), 5 deletions(-) diff --git a/easybuild/easyconfigs/m/modin/modin-0.32.0-foss-2024a.eb b/easybuild/easyconfigs/m/modin/modin-0.32.0-foss-2024a.eb index 57ceac35c950..b08f03c09751 100644 --- a/easybuild/easyconfigs/m/modin/modin-0.32.0-foss-2024a.eb +++ b/easybuild/easyconfigs/m/modin/modin-0.32.0-foss-2024a.eb @@ -39,11 +39,8 @@ exts_list = [ (name, version, { 'patches': ['modin-0.32.0_fix-pytest-config.patch'], 'runtest': ( - "MODIN_ENGINE=unidist UNIDIST_ENGINE=mpi pytest modin/tests/pandas " - " --ignore=modin/tests/pandas/test_io.py " - "--ignore=modin/tests/pandas/integrations/test_lazy_import.py &&" - " MODIN_ENGINE=dask pytest modin/tests/pandas --ignore=modin/tests/pandas/test_io.py" - " --ignore=modin/tests/pandas/integrations/test_lazy_import.py" + "MODIN_ENGINE=unidist UNIDIST_ENGINE=mpi pytest modin/tests/pandas/test_general.py &&" + " MODIN_ENGINE=dask pytest modin/tests/pandas/test_general.py" ), 'source_tmpl': '%(version)s.tar.gz', 'source_urls': ['https://github.com/modin-project/%(name)s/archive/refs/tags'], From d31ae4f9f1d0d6b3be1eddab4a9120bc43db2510 Mon Sep 17 00:00:00 2001 From: Leonard Nielsen Date: Thu, 17 Oct 2024 20:26:47 +0000 Subject: [PATCH 19/85] cut down on test suite --- easybuild/easyconfigs/m/modin/modin-0.32.0-foss-2024a.eb | 4 ++-- 1 file changed, 2 insertions(+), 2 deletions(-) diff --git a/easybuild/easyconfigs/m/modin/modin-0.32.0-foss-2024a.eb b/easybuild/easyconfigs/m/modin/modin-0.32.0-foss-2024a.eb index b08f03c09751..5d6a7971f535 100644 --- a/easybuild/easyconfigs/m/modin/modin-0.32.0-foss-2024a.eb +++ b/easybuild/easyconfigs/m/modin/modin-0.32.0-foss-2024a.eb @@ -39,8 +39,8 @@ exts_list = [ (name, version, { 'patches': ['modin-0.32.0_fix-pytest-config.patch'], 'runtest': ( - "MODIN_ENGINE=unidist UNIDIST_ENGINE=mpi pytest modin/tests/pandas/test_general.py &&" - " MODIN_ENGINE=dask pytest modin/tests/pandas/test_general.py" + "MODIN_ENGINE=unidist UNIDIST_ENGINE=mpi pytest modin/tests/pandas/test_reshape.py &&" + " MODIN_ENGINE=dask pytest modin/tests/pandas/test_reshape.py" ), 'source_tmpl': '%(version)s.tar.gz', 'source_urls': ['https://github.com/modin-project/%(name)s/archive/refs/tags'], From 88ec16cd3e4fa8f0631d13d17ac684022461d24b Mon Sep 17 00:00:00 2001 From: Leonard Nielsen Date: Thu, 17 Oct 2024 20:36:33 +0000 Subject: [PATCH 20/85] cut down on test suite --- easybuild/easyconfigs/m/modin/modin-0.32.0-foss-2024a.eb | 3 +-- 1 file changed, 1 insertion(+), 2 deletions(-) diff --git a/easybuild/easyconfigs/m/modin/modin-0.32.0-foss-2024a.eb b/easybuild/easyconfigs/m/modin/modin-0.32.0-foss-2024a.eb index 5d6a7971f535..5bc7ac030db9 100644 --- a/easybuild/easyconfigs/m/modin/modin-0.32.0-foss-2024a.eb +++ b/easybuild/easyconfigs/m/modin/modin-0.32.0-foss-2024a.eb @@ -39,8 +39,7 @@ exts_list = [ (name, version, { 'patches': ['modin-0.32.0_fix-pytest-config.patch'], 'runtest': ( - "MODIN_ENGINE=unidist UNIDIST_ENGINE=mpi pytest modin/tests/pandas/test_reshape.py &&" - " MODIN_ENGINE=dask pytest modin/tests/pandas/test_reshape.py" + "MODIN_ENGINE=dask pytest modin/tests/pandas/test_reshape.py" ), 'source_tmpl': '%(version)s.tar.gz', 'source_urls': ['https://github.com/modin-project/%(name)s/archive/refs/tags'], From 3296c1bf546577e954fb69734a4241ff2499981d Mon Sep 17 00:00:00 2001 From: Leonard Nielsen Date: Thu, 17 Oct 2024 20:48:45 +0000 Subject: [PATCH 21/85] removed unidist due to non-functionality --- easybuild/easyconfigs/m/modin/modin-0.32.0-foss-2024a.eb | 7 ++----- 1 file changed, 2 insertions(+), 5 deletions(-) diff --git a/easybuild/easyconfigs/m/modin/modin-0.32.0-foss-2024a.eb b/easybuild/easyconfigs/m/modin/modin-0.32.0-foss-2024a.eb index 5bc7ac030db9..69879efa8ab5 100644 --- a/easybuild/easyconfigs/m/modin/modin-0.32.0-foss-2024a.eb +++ b/easybuild/easyconfigs/m/modin/modin-0.32.0-foss-2024a.eb @@ -30,15 +30,12 @@ dependencies = [ use_pip = True exts_list = [ - ('unidist', '0.7.1', { - 'source_tmpl': '%(version)s.tar.gz', - 'source_urls': ['https://github.com/modin-project/%(name)s/archive/refs/tags/'], - 'checksums': ['9bae91f0bbc33af3b55948990f69400ee819dfda9c635286e6917aebd7f24791'], - }), + # modin has another backend, "unidist", for MPI, but it seems broken currently. # Cannot test for Ray due to unix socket issue (name, version, { 'patches': ['modin-0.32.0_fix-pytest-config.patch'], 'runtest': ( + "MODIN_ENGINE=ray pytest modin/tests/pandas/test_reshape.py &&" "MODIN_ENGINE=dask pytest modin/tests/pandas/test_reshape.py" ), 'source_tmpl': '%(version)s.tar.gz', From 54574e3a6c8174df50ae12d4d54c03ddbf10bb5f Mon Sep 17 00:00:00 2001 From: Leonard Nielsen Date: Thu, 17 Oct 2024 20:56:59 +0000 Subject: [PATCH 22/85] confirmed ray non-functional tests --- easybuild/easyconfigs/m/modin/modin-0.32.0-foss-2024a.eb | 5 ++--- 1 file changed, 2 insertions(+), 3 deletions(-) diff --git a/easybuild/easyconfigs/m/modin/modin-0.32.0-foss-2024a.eb b/easybuild/easyconfigs/m/modin/modin-0.32.0-foss-2024a.eb index 69879efa8ab5..128dd0aae8c3 100644 --- a/easybuild/easyconfigs/m/modin/modin-0.32.0-foss-2024a.eb +++ b/easybuild/easyconfigs/m/modin/modin-0.32.0-foss-2024a.eb @@ -31,12 +31,11 @@ use_pip = True exts_list = [ # modin has another backend, "unidist", for MPI, but it seems broken currently. - # Cannot test for Ray due to unix socket issue + # Also cannot test for Ray in general due to unix socket issue, need to specify short tmpdir path (name, version, { 'patches': ['modin-0.32.0_fix-pytest-config.patch'], 'runtest': ( - "MODIN_ENGINE=ray pytest modin/tests/pandas/test_reshape.py &&" - "MODIN_ENGINE=dask pytest modin/tests/pandas/test_reshape.py" + "MODIN_ENGINE=dask pytest modin/tests/pandas/test_general.py" ), 'source_tmpl': '%(version)s.tar.gz', 'source_urls': ['https://github.com/modin-project/%(name)s/archive/refs/tags'], From 9eef90ae526237506465911e6a099c83ecb52663 Mon Sep 17 00:00:00 2001 From: Leonard Nielsen Date: Thu, 17 Oct 2024 21:14:01 +0000 Subject: [PATCH 23/85] removed mpi4py dep --- easybuild/easyconfigs/m/modin/modin-0.32.0-foss-2024a.eb | 1 - 1 file changed, 1 deletion(-) diff --git a/easybuild/easyconfigs/m/modin/modin-0.32.0-foss-2024a.eb b/easybuild/easyconfigs/m/modin/modin-0.32.0-foss-2024a.eb index 128dd0aae8c3..388c781b8b56 100644 --- a/easybuild/easyconfigs/m/modin/modin-0.32.0-foss-2024a.eb +++ b/easybuild/easyconfigs/m/modin/modin-0.32.0-foss-2024a.eb @@ -24,7 +24,6 @@ dependencies = [ ('OpenMPI', '5.0.3'), ('Ray-project', '2.37.0'), ('Arrow', '17.0.0'), - ('mpi4py', '4.0.1') ] use_pip = True From 0918cffb46ca1737e35fd0aef08c41a072aef306 Mon Sep 17 00:00:00 2001 From: Leonard Nielsen Date: Fri, 18 Oct 2024 12:20:22 +0000 Subject: [PATCH 24/85] added unidist problem info --- easybuild/easyconfigs/m/modin/modin-0.32.0-foss-2024a.eb | 1 + 1 file changed, 1 insertion(+) diff --git a/easybuild/easyconfigs/m/modin/modin-0.32.0-foss-2024a.eb b/easybuild/easyconfigs/m/modin/modin-0.32.0-foss-2024a.eb index 388c781b8b56..5ed0e424dfdb 100644 --- a/easybuild/easyconfigs/m/modin/modin-0.32.0-foss-2024a.eb +++ b/easybuild/easyconfigs/m/modin/modin-0.32.0-foss-2024a.eb @@ -30,6 +30,7 @@ use_pip = True exts_list = [ # modin has another backend, "unidist", for MPI, but it seems broken currently. + # The unidist backend will just fire up all cores as if initializing but not actually advance. # Also cannot test for Ray in general due to unix socket issue, need to specify short tmpdir path (name, version, { 'patches': ['modin-0.32.0_fix-pytest-config.patch'], From 654c9a6a38c657899d7ebc59ae3b1e5f097a5f18 Mon Sep 17 00:00:00 2001 From: Sam Moors Date: Sat, 19 Oct 2024 13:23:08 +0200 Subject: [PATCH 25/85] Update gperftools-2.16-GCCcore-13.3.0.eb --- .../g/gperftools/gperftools-2.16-GCCcore-13.3.0.eb | 8 ++++---- 1 file changed, 4 insertions(+), 4 deletions(-) diff --git a/easybuild/easyconfigs/g/gperftools/gperftools-2.16-GCCcore-13.3.0.eb b/easybuild/easyconfigs/g/gperftools/gperftools-2.16-GCCcore-13.3.0.eb index b142fbdb34d8..115b3754cfff 100644 --- a/easybuild/easyconfigs/g/gperftools/gperftools-2.16-GCCcore-13.3.0.eb +++ b/easybuild/easyconfigs/g/gperftools/gperftools-2.16-GCCcore-13.3.0.eb @@ -12,6 +12,7 @@ Includes TCMalloc, heap-checker, heap-profiler and cpu-profiler. toolchain = {'name': 'GCCcore', 'version': '13.3.0'} +github_account = '%(name)s' source_urls = [GITHUB_SOURCE] sources = [SOURCE_TAR_GZ] checksums = ['737be182b4e42f5c7f595da2a7aa59ce0489a73d336d0d16847f2aa52d5221b4'] @@ -27,10 +28,9 @@ dependencies = [ preconfigopts = "autoreconf -f -i && " configopts = '--enable-libunwind' -github_account = '%(name)s' - -sanity_check_paths = { - 'files': ['bin/pprof', 'lib/libprofiler.a', 'lib/libprofiler.so', 'lib/libtcmalloc.a', 'lib/libtcmalloc.so'], +sanity_check_paths = { + 'files': ['bin/pprof', 'lib/libprofiler.a', 'lib/libprofiler.%s' % SHLIB_EXT, + 'lib/libtcmalloc.a', 'lib/libtcmalloc.%s' % SHLIB_EXT], 'dirs': ['include'], } From 11638b4b9cdeea4990cae51191be295f5cf21251 Mon Sep 17 00:00:00 2001 From: Sam Moors Date: Sat, 19 Oct 2024 14:09:12 +0200 Subject: [PATCH 26/85] remove trailing whitespace --- .../easyconfigs/g/gperftools/gperftools-2.16-GCCcore-13.3.0.eb | 2 +- 1 file changed, 1 insertion(+), 1 deletion(-) diff --git a/easybuild/easyconfigs/g/gperftools/gperftools-2.16-GCCcore-13.3.0.eb b/easybuild/easyconfigs/g/gperftools/gperftools-2.16-GCCcore-13.3.0.eb index 115b3754cfff..1a31ffabd1b6 100644 --- a/easybuild/easyconfigs/g/gperftools/gperftools-2.16-GCCcore-13.3.0.eb +++ b/easybuild/easyconfigs/g/gperftools/gperftools-2.16-GCCcore-13.3.0.eb @@ -28,7 +28,7 @@ dependencies = [ preconfigopts = "autoreconf -f -i && " configopts = '--enable-libunwind' -sanity_check_paths = { +sanity_check_paths = { 'files': ['bin/pprof', 'lib/libprofiler.a', 'lib/libprofiler.%s' % SHLIB_EXT, 'lib/libtcmalloc.a', 'lib/libtcmalloc.%s' % SHLIB_EXT], 'dirs': ['include'], From 932949489b4af84c0b8497917b737588b94da3e3 Mon Sep 17 00:00:00 2001 From: Sam Moors Date: Sat, 19 Oct 2024 14:44:09 +0200 Subject: [PATCH 27/85] don't use CMAKE_BUILD_TYPE=Release --- easybuild/easyconfigs/h/HPX/HPX-1.10.0-foss-2024a.eb | 1 - 1 file changed, 1 deletion(-) diff --git a/easybuild/easyconfigs/h/HPX/HPX-1.10.0-foss-2024a.eb b/easybuild/easyconfigs/h/HPX/HPX-1.10.0-foss-2024a.eb index 9e1c986fa71b..cc85303ac573 100644 --- a/easybuild/easyconfigs/h/HPX/HPX-1.10.0-foss-2024a.eb +++ b/easybuild/easyconfigs/h/HPX/HPX-1.10.0-foss-2024a.eb @@ -34,7 +34,6 @@ dependencies = [ build_type = 'Release' configopts = '-DCMAKE_CXX_COMPILER=g++ ' -configopts += '-DCMAKE_BUILD_TYPE=Release ' configopts += '-DHPX_WITH_MALLOC=tcmalloc ' configopts += '-DHPX_WITH_HWLOC=TRUE ' configopts += '-DHPX_WITH_GOOGLE_PERFTOOLS=TRUE ' From 9da9917445061757bc89d35af9b013973f437aa0 Mon Sep 17 00:00:00 2001 From: Maxim Date: Mon, 21 Oct 2024 12:52:55 +0200 Subject: [PATCH 28/85] Update easybuild/easyconfigs/h/HPX/HPX-1.10.0-foss-2024a.eb Co-authored-by: Sam Moors --- easybuild/easyconfigs/h/HPX/HPX-1.10.0-foss-2024a.eb | 2 -- 1 file changed, 2 deletions(-) diff --git a/easybuild/easyconfigs/h/HPX/HPX-1.10.0-foss-2024a.eb b/easybuild/easyconfigs/h/HPX/HPX-1.10.0-foss-2024a.eb index cc85303ac573..edc922f3056a 100644 --- a/easybuild/easyconfigs/h/HPX/HPX-1.10.0-foss-2024a.eb +++ b/easybuild/easyconfigs/h/HPX/HPX-1.10.0-foss-2024a.eb @@ -31,8 +31,6 @@ dependencies = [ ('gperftools', '2.16'), ] -build_type = 'Release' - configopts = '-DCMAKE_CXX_COMPILER=g++ ' configopts += '-DHPX_WITH_MALLOC=tcmalloc ' configopts += '-DHPX_WITH_HWLOC=TRUE ' From c52d81dc6bf47759f6c89de9b8b5c71608ea2286 Mon Sep 17 00:00:00 2001 From: WilleBell Date: Mon, 21 Oct 2024 15:20:03 +0200 Subject: [PATCH 29/85] adding easyconfigs: SciANN-0.7.0.1-foss-2022a.eb --- .../s/SciANN/SciANN-0.7.0.1-foss-2022a.eb | 39 +++++++++++++++++++ 1 file changed, 39 insertions(+) create mode 100644 easybuild/easyconfigs/s/SciANN/SciANN-0.7.0.1-foss-2022a.eb diff --git a/easybuild/easyconfigs/s/SciANN/SciANN-0.7.0.1-foss-2022a.eb b/easybuild/easyconfigs/s/SciANN/SciANN-0.7.0.1-foss-2022a.eb new file mode 100644 index 000000000000..0717fc8e997b --- /dev/null +++ b/easybuild/easyconfigs/s/SciANN/SciANN-0.7.0.1-foss-2022a.eb @@ -0,0 +1,39 @@ +easyblock = 'PythonBundle' + +name = 'SciANN' +version = '0.7.0.1' + +homepage = 'https://github.com/ehsanhaghighat/sciann' +description = """ +A Keras/Tensorflow wrapper for scientific computations and physics-informed deep learning +using artificial neural networks. +""" + +toolchain = {'name': 'foss', 'version': '2022a'} + +dependencies = [ + ('Python', '3.10.4'), + ('SciPy-bundle', '2022.05'), + ('PyYAML', '6.0'), + ('h5py', '3.7.0'), + ('scikit-learn', '1.1.2'), + ('TensorFlow', '2.11.0'), + ('pymatgen', '2023.3.10'), # for pybtex and latexcodec + ('matplotlib', '3.5.2'), + ('pygraphviz', '1.10'), +] + +use_pip = True +sanity_pip_check = True + +exts_list = [ + ('pydot', '2.0.0', { + 'checksums': ['60246af215123fa062f21cd791be67dda23a6f280df09f68919e637a1e4f3235'], + }), + (name, version, { + 'modulename': 'sciann', + 'checksums': ['7d7acf61346b4201628c5656e2c904e9a9c7cda78086e76d075b5c7bb90adf3c'], + }), +] + +moduleclass = 'ai' From 091cfe5dade66635aea58a3c4e9090c4600bedec Mon Sep 17 00:00:00 2001 From: Stefan Wolfsheimer Date: Mon, 21 Oct 2024 17:59:40 +0200 Subject: [PATCH 30/85] fix mpi include issue, see https://github.com/wannier-developers/wannier90/issues/521 --- .../w/Wannier90/Wannier90-3.1.0-foss-2023a.eb | 4 ++- .../w/Wannier90/Wannier90-3.1.0-foss-2024a.eb | 4 ++- .../Wannier90/Wannier90-3.1.0-gomkl-2023a.eb | 9 ++++--- .../Wannier90/Wannier90-3.1.0-intel-2023a.eb | 9 ++++--- .../Wannier90/Wannier90-3.1.0-intel-2024a.eb | 9 ++++--- .../Wannier90_3.1.0_fix_mpi_include.patch | 27 +++++++++++++++++++ 6 files changed, 51 insertions(+), 11 deletions(-) create mode 100644 easybuild/easyconfigs/w/Wannier90/Wannier90_3.1.0_fix_mpi_include.patch diff --git a/easybuild/easyconfigs/w/Wannier90/Wannier90-3.1.0-foss-2023a.eb b/easybuild/easyconfigs/w/Wannier90/Wannier90-3.1.0-foss-2023a.eb index f8fe7f68bbf2..57105d3bdb64 100644 --- a/easybuild/easyconfigs/w/Wannier90/Wannier90-3.1.0-foss-2023a.eb +++ b/easybuild/easyconfigs/w/Wannier90/Wannier90-3.1.0-foss-2023a.eb @@ -12,10 +12,12 @@ toolchainopts = {'usempi': True} github_account = 'wannier-developers' source_urls = [GITHUB_LOWER_SOURCE] sources = [{'download_filename': 'v%(version)s.tar.gz', 'filename': SOURCELOWER_TAR_GZ}] -patches = ['Wannier90_3x_ignore_makeinc.patch'] +patches = ['Wannier90_3x_ignore_makeinc.patch', + 'Wannier90_3.1.0_fix_mpi_include.patch'] checksums = [ '40651a9832eb93dec20a8360dd535262c261c34e13c41b6755fa6915c936b254', # wannier90-3.1.0.tar.gz '561c0d296e0e30b8bb303702cd6e41ded54c153d9b9e6cd9cab73858e5e2945e', # Wannier90_3x_ignore_makeinc.patch + 'dd7217d8bf12ac4161fd0b6504f7c085ebcc69b23ab2ac4abcf9251f34b8bc30', # Wannier90_3.1.0_fix_mpi_include.patch ] # The -fallow-argument-mismatch allows MPI communication calls to be diff --git a/easybuild/easyconfigs/w/Wannier90/Wannier90-3.1.0-foss-2024a.eb b/easybuild/easyconfigs/w/Wannier90/Wannier90-3.1.0-foss-2024a.eb index 3228ba164b9b..26e4b587a1f2 100644 --- a/easybuild/easyconfigs/w/Wannier90/Wannier90-3.1.0-foss-2024a.eb +++ b/easybuild/easyconfigs/w/Wannier90/Wannier90-3.1.0-foss-2024a.eb @@ -12,10 +12,12 @@ toolchainopts = {'usempi': True} github_account = 'wannier-developers' source_urls = [GITHUB_LOWER_SOURCE] sources = [{'download_filename': 'v%(version)s.tar.gz', 'filename': SOURCELOWER_TAR_GZ}] -patches = ['Wannier90_3x_ignore_makeinc.patch'] +patches = ['Wannier90_3x_ignore_makeinc.patch', + 'Wannier90_3.1.0_fix_mpi_include.patch'] checksums = [ '40651a9832eb93dec20a8360dd535262c261c34e13c41b6755fa6915c936b254', # wannier90-3.1.0.tar.gz '561c0d296e0e30b8bb303702cd6e41ded54c153d9b9e6cd9cab73858e5e2945e', # Wannier90_3x_ignore_makeinc.patch + 'dd7217d8bf12ac4161fd0b6504f7c085ebcc69b23ab2ac4abcf9251f34b8bc30', # Wannier90_3.1.0_fix_mpi_include.patch ] buildopts = 'all F90=$F90 MPIF90=$MPIF90 FCOPTS="$FFLAGS -fallow-argument-mismatch" LDOPTS="$FFLAGS" ' diff --git a/easybuild/easyconfigs/w/Wannier90/Wannier90-3.1.0-gomkl-2023a.eb b/easybuild/easyconfigs/w/Wannier90/Wannier90-3.1.0-gomkl-2023a.eb index 336ac8a3895a..a3e59ef46a97 100644 --- a/easybuild/easyconfigs/w/Wannier90/Wannier90-3.1.0-gomkl-2023a.eb +++ b/easybuild/easyconfigs/w/Wannier90/Wannier90-3.1.0-gomkl-2023a.eb @@ -12,10 +12,12 @@ toolchainopts = {'usempi': True} github_account = 'wannier-developers' source_urls = [GITHUB_LOWER_SOURCE] sources = [{'download_filename': 'v%(version)s.tar.gz', 'filename': SOURCELOWER_TAR_GZ}] -patches = ['Wannier90_3x_ignore_makeinc.patch'] +patches = ['Wannier90_3x_ignore_makeinc.patch', + 'Wannier90_3.1.0_fix_mpi_include.patch'] checksums = [ '40651a9832eb93dec20a8360dd535262c261c34e13c41b6755fa6915c936b254', # wannier90-3.1.0.tar.gz '561c0d296e0e30b8bb303702cd6e41ded54c153d9b9e6cd9cab73858e5e2945e', # Wannier90_3x_ignore_makeinc.patch + 'dd7217d8bf12ac4161fd0b6504f7c085ebcc69b23ab2ac4abcf9251f34b8bc30', # Wannier90_3.1.0_fix_mpi_include.patch ] # The -fallow-argument-mismatch allows MPI communication calls to be @@ -25,10 +27,11 @@ buildopts = 'all F90=$F90 MPIF90=$MPIF90 FCOPTS="$FFLAGS -fallow-argument-mismat buildopts += 'LIBDIR="$LAPACK_LIB_DIR" LIBS="$LIBLAPACK" ' buildopts += 'COMMS=mpi' -files_to_copy = [(['wannier90.x', 'postw90.x'], 'bin'), (['libwannier.a'], 'lib')] +local_executables = ['wannier90.x', 'postw90.x', 'w90chk2chk.x', 'w90spn2spn.x'] +files_to_copy = [(local_executables, 'bin'), (['libwannier.a'], 'lib')] sanity_check_paths = { - 'files': ['bin/wannier90.x', 'bin/postw90.x', 'lib/libwannier.a'], + 'files': ['bin/%s' % x for x in local_executables] + ['lib/libwannier.a'], 'dirs': [] } diff --git a/easybuild/easyconfigs/w/Wannier90/Wannier90-3.1.0-intel-2023a.eb b/easybuild/easyconfigs/w/Wannier90/Wannier90-3.1.0-intel-2023a.eb index cf2583687712..eb71d75290d0 100644 --- a/easybuild/easyconfigs/w/Wannier90/Wannier90-3.1.0-intel-2023a.eb +++ b/easybuild/easyconfigs/w/Wannier90/Wannier90-3.1.0-intel-2023a.eb @@ -12,20 +12,23 @@ toolchainopts = {'usempi': True} github_account = 'wannier-developers' source_urls = [GITHUB_LOWER_SOURCE] sources = [{'download_filename': 'v%(version)s.tar.gz', 'filename': SOURCELOWER_TAR_GZ}] -patches = ['Wannier90_3x_ignore_makeinc.patch'] +patches = ['Wannier90_3x_ignore_makeinc.patch', + 'Wannier90_3.1.0_fix_mpi_include.patch'] checksums = [ '40651a9832eb93dec20a8360dd535262c261c34e13c41b6755fa6915c936b254', # wannier90-3.1.0.tar.gz '561c0d296e0e30b8bb303702cd6e41ded54c153d9b9e6cd9cab73858e5e2945e', # Wannier90_3x_ignore_makeinc.patch + 'dd7217d8bf12ac4161fd0b6504f7c085ebcc69b23ab2ac4abcf9251f34b8bc30', # Wannier90_3.1.0_fix_mpi_include.patch ] buildopts = 'all F90=$F90 MPIF90=$MPIF90 FCOPTS="$FFLAGS" LDOPTS="$FFLAGS" ' buildopts += 'LIBDIR="$LAPACK_LIB_DIR" LIBS="$LIBLAPACK" ' buildopts += 'COMMS=mpi' -files_to_copy = [(['wannier90.x', 'postw90.x'], 'bin'), (['libwannier.a'], 'lib')] +local_executables = ['wannier90.x', 'postw90.x', 'w90chk2chk.x', 'w90spn2spn.x'] +files_to_copy = [(local_executables, 'bin'), (['libwannier.a'], 'lib')] sanity_check_paths = { - 'files': ['bin/wannier90.x', 'bin/postw90.x', 'lib/libwannier.a'], + 'files': ['bin/%s' % x for x in local_executables] + ['lib/libwannier.a'], 'dirs': [] } diff --git a/easybuild/easyconfigs/w/Wannier90/Wannier90-3.1.0-intel-2024a.eb b/easybuild/easyconfigs/w/Wannier90/Wannier90-3.1.0-intel-2024a.eb index dd30db79af6c..34d3457ccc48 100644 --- a/easybuild/easyconfigs/w/Wannier90/Wannier90-3.1.0-intel-2024a.eb +++ b/easybuild/easyconfigs/w/Wannier90/Wannier90-3.1.0-intel-2024a.eb @@ -12,20 +12,23 @@ toolchainopts = {'usempi': True} github_account = 'wannier-developers' source_urls = [GITHUB_LOWER_SOURCE] sources = [{'download_filename': 'v%(version)s.tar.gz', 'filename': SOURCELOWER_TAR_GZ}] -patches = ['Wannier90_3x_ignore_makeinc.patch'] +patches = ['Wannier90_3x_ignore_makeinc.patch', + 'Wannier90_3.1.0_fix_mpi_include.patch'] checksums = [ '40651a9832eb93dec20a8360dd535262c261c34e13c41b6755fa6915c936b254', # wannier90-3.1.0.tar.gz '561c0d296e0e30b8bb303702cd6e41ded54c153d9b9e6cd9cab73858e5e2945e', # Wannier90_3x_ignore_makeinc.patch + 'dd7217d8bf12ac4161fd0b6504f7c085ebcc69b23ab2ac4abcf9251f34b8bc30', # Wannier90_3.1.0_fix_mpi_include.patch ] buildopts = 'all F90=$F90 MPIF90=$MPIF90 FCOPTS="$FFLAGS" LDOPTS="$FFLAGS" ' buildopts += 'LIBDIR="$LAPACK_LIB_DIR" LIBS="$LIBLAPACK" ' buildopts += 'COMMS=mpi' -files_to_copy = [(['wannier90.x', 'postw90.x'], 'bin'), (['libwannier.a'], 'lib')] +local_executables = ['wannier90.x', 'postw90.x', 'w90chk2chk.x', 'w90spn2spn.x'] +files_to_copy = [(local_executables, 'bin'), (['libwannier.a'], 'lib')] sanity_check_paths = { - 'files': ['bin/wannier90.x', 'bin/postw90.x', 'lib/libwannier.a'], + 'files': ['bin/%s' % x for x in local_executables] + ['lib/libwannier.a'], 'dirs': [] } diff --git a/easybuild/easyconfigs/w/Wannier90/Wannier90_3.1.0_fix_mpi_include.patch b/easybuild/easyconfigs/w/Wannier90/Wannier90_3.1.0_fix_mpi_include.patch new file mode 100644 index 000000000000..fdc859c8a7f6 --- /dev/null +++ b/easybuild/easyconfigs/w/Wannier90/Wannier90_3.1.0_fix_mpi_include.patch @@ -0,0 +1,27 @@ +Use "use mpi" to load all required interfaces. +See https://github.com/wannier-developers/wannier90/issues/521 +Author: Stefan Wolfsheimer (SURF) + + +diff -ruN wannier90-3.1.0.orig/src/comms.F90 wannier90-3.1.0/src/comms.F90 +--- wannier90-3.1.0.orig/src/comms.F90 2020-03-05 19:41:10.000000000 +0100 ++++ wannier90-3.1.0/src/comms.F90 2024-10-21 17:01:00.542755184 +0200 +@@ -23,15 +23,13 @@ + + use w90_constants, only: dp + use w90_io, only: io_error +- ++#ifdef MPI ++ use mpi ++#endif + implicit none + + private + +-#ifdef MPI +- include 'mpif.h' +-#endif +- + logical, public, save :: on_root + !! Are we the root node + integer, public, save :: num_nodes From 61826702179fcba592e84e718a251a0a051bb19a Mon Sep 17 00:00:00 2001 From: maxim-masterov Date: Mon, 21 Oct 2024 18:48:54 +0200 Subject: [PATCH 31/85] Improve snaity check part --- .../h/HPX/HPX-1.10.0-foss-2024a.eb | 28 +++++++++++++++++-- 1 file changed, 25 insertions(+), 3 deletions(-) diff --git a/easybuild/easyconfigs/h/HPX/HPX-1.10.0-foss-2024a.eb b/easybuild/easyconfigs/h/HPX/HPX-1.10.0-foss-2024a.eb index edc922f3056a..07eeef3d4464 100644 --- a/easybuild/easyconfigs/h/HPX/HPX-1.10.0-foss-2024a.eb +++ b/easybuild/easyconfigs/h/HPX/HPX-1.10.0-foss-2024a.eb @@ -46,11 +46,33 @@ configopts += '-DHPX_WITH_FETCH_ASIO=TRUE ' bin_lib_subdirs = ['lib/%(namelower)s/'] +local_lib_names = [ + 'libhpx_accumulator.%s' % SHLIB_EXT, + 'libhpx_cancelable_action.%s' % SHLIB_EXT, + 'libhpx_component_storage.%s' % SHLIB_EXT, + 'libhpx_core.%s' % SHLIB_EXT, + 'libhpx_iostreams.%s' % SHLIB_EXT, + 'libhpx_jacobi.%s' % SHLIB_EXT, + 'libhpx_nqueen.%s' % SHLIB_EXT, + 'libhpx_partitioned_vector.%s' % SHLIB_EXT, + 'libhpx_process.%s' % SHLIB_EXT, + 'libhpx_random_mem_access.%s' % SHLIB_EXT, + 'libhpx_simple_central_tuplespace.%s' % SHLIB_EXT, + 'libhpx.%s' % SHLIB_EXT, + 'libhpx_startup_shutdown.%s' % SHLIB_EXT, + 'libhpx_template_accumulator.%s' % SHLIB_EXT, + 'libhpx_template_function_accumulator.%s' % SHLIB_EXT, + 'libhpx_throttle.%s' % SHLIB_EXT, + 'libhpx_unordered.%s' % SHLIB_EXT, +] + sanity_check_paths = { - 'files': [], - 'dirs': ['bin', 'lib'], + 'files': ['lib/%s' % l for l in local_lib_names] + + ['include/asio.hpp', 'include/hpx/hpx.hpp'] + + ['bin/hpxcxx', 'bin/hpxrun.py'], + 'dirs': ['bin', 'lib'] + bin_lib_subdirs, } -modextrapaths = {'LD_LIBRARY_PATH': ['lib/%(namelower)s']} +modextrapaths = {'LD_LIBRARY_PATH': bin_lib_subdirs} moduleclass = 'math' From e2784cac2a4cb2d92bbe9de57181e958c2550065 Mon Sep 17 00:00:00 2001 From: Leonard Nielsen Date: Mon, 21 Oct 2024 20:54:23 +0000 Subject: [PATCH 32/85] try adding unidist again --- .../easyconfigs/m/modin/modin-0.32.0-foss-2024a.eb | 11 ++++++----- 1 file changed, 6 insertions(+), 5 deletions(-) diff --git a/easybuild/easyconfigs/m/modin/modin-0.32.0-foss-2024a.eb b/easybuild/easyconfigs/m/modin/modin-0.32.0-foss-2024a.eb index 5ed0e424dfdb..68d20abb1379 100644 --- a/easybuild/easyconfigs/m/modin/modin-0.32.0-foss-2024a.eb +++ b/easybuild/easyconfigs/m/modin/modin-0.32.0-foss-2024a.eb @@ -29,14 +29,15 @@ dependencies = [ use_pip = True exts_list = [ - # modin has another backend, "unidist", for MPI, but it seems broken currently. - # The unidist backend will just fire up all cores as if initializing but not actually advance. - # Also cannot test for Ray in general due to unix socket issue, need to specify short tmpdir path + ('unidist', '0.7.2', { + 'checksums': ['6386e1ad5143fe132b9f96e232fe85fc39830ed2886515440e4ba1473255e4a0'], + }), (name, version, { 'patches': ['modin-0.32.0_fix-pytest-config.patch'], 'runtest': ( - "MODIN_ENGINE=dask pytest modin/tests/pandas/test_general.py" - ), + "MODIN_ENGINE=unidist UNIDIST_ENGINE=mpi pytest modin/tests/pandas/test_general.py " + "MODIN_ENGINE=dask pytest modin/tests/pandas/test_general.py" + ), 'source_tmpl': '%(version)s.tar.gz', 'source_urls': ['https://github.com/modin-project/%(name)s/archive/refs/tags'], 'testinstall': True, From e26dbceba35823e7d8a1382802575f8f52a8c59e Mon Sep 17 00:00:00 2001 From: Leonard Nielsen Date: Mon, 21 Oct 2024 20:59:07 +0000 Subject: [PATCH 33/85] fix a typo --- easybuild/easyconfigs/m/modin/modin-0.32.0-foss-2024a.eb | 2 +- 1 file changed, 1 insertion(+), 1 deletion(-) diff --git a/easybuild/easyconfigs/m/modin/modin-0.32.0-foss-2024a.eb b/easybuild/easyconfigs/m/modin/modin-0.32.0-foss-2024a.eb index 68d20abb1379..d9239113e25d 100644 --- a/easybuild/easyconfigs/m/modin/modin-0.32.0-foss-2024a.eb +++ b/easybuild/easyconfigs/m/modin/modin-0.32.0-foss-2024a.eb @@ -35,7 +35,7 @@ exts_list = [ (name, version, { 'patches': ['modin-0.32.0_fix-pytest-config.patch'], 'runtest': ( - "MODIN_ENGINE=unidist UNIDIST_ENGINE=mpi pytest modin/tests/pandas/test_general.py " + "MODIN_ENGINE=unidist UNIDIST_ENGINE=mpi pytest modin/tests/pandas/test_general.py && " "MODIN_ENGINE=dask pytest modin/tests/pandas/test_general.py" ), 'source_tmpl': '%(version)s.tar.gz', From f0f4e2433f6d48b23aab70c4dbdf79c785479df1 Mon Sep 17 00:00:00 2001 From: maxim-masterov Date: Mon, 21 Oct 2024 23:00:18 +0200 Subject: [PATCH 34/85] Fix stile --- easybuild/easyconfigs/h/HPX/HPX-1.10.0-foss-2024a.eb | 2 +- 1 file changed, 1 insertion(+), 1 deletion(-) diff --git a/easybuild/easyconfigs/h/HPX/HPX-1.10.0-foss-2024a.eb b/easybuild/easyconfigs/h/HPX/HPX-1.10.0-foss-2024a.eb index 07eeef3d4464..110ca403b7cd 100644 --- a/easybuild/easyconfigs/h/HPX/HPX-1.10.0-foss-2024a.eb +++ b/easybuild/easyconfigs/h/HPX/HPX-1.10.0-foss-2024a.eb @@ -67,7 +67,7 @@ local_lib_names = [ ] sanity_check_paths = { - 'files': ['lib/%s' % l for l in local_lib_names] + + 'files': ['lib/%s' % lib for lib in local_lib_names] + ['include/asio.hpp', 'include/hpx/hpx.hpp'] + ['bin/hpxcxx', 'bin/hpxrun.py'], 'dirs': ['bin', 'lib'] + bin_lib_subdirs, From 065333017730480123859eda539cf51741639d92 Mon Sep 17 00:00:00 2001 From: Leonard Nielsen Date: Tue, 22 Oct 2024 10:20:07 +0000 Subject: [PATCH 35/85] fix unidist test? --- easybuild/easyconfigs/m/modin/modin-0.32.0-foss-2024a.eb | 9 ++++++--- 1 file changed, 6 insertions(+), 3 deletions(-) diff --git a/easybuild/easyconfigs/m/modin/modin-0.32.0-foss-2024a.eb b/easybuild/easyconfigs/m/modin/modin-0.32.0-foss-2024a.eb index d9239113e25d..3d6ce8d2958e 100644 --- a/easybuild/easyconfigs/m/modin/modin-0.32.0-foss-2024a.eb +++ b/easybuild/easyconfigs/m/modin/modin-0.32.0-foss-2024a.eb @@ -32,12 +32,15 @@ exts_list = [ ('unidist', '0.7.2', { 'checksums': ['6386e1ad5143fe132b9f96e232fe85fc39830ed2886515440e4ba1473255e4a0'], }), + # The oversubscription is done in their own CI as well. + # Ray has limitations on unix socket path length, so it is not tested here. (name, version, { 'patches': ['modin-0.32.0_fix-pytest-config.patch'], 'runtest': ( - "MODIN_ENGINE=unidist UNIDIST_ENGINE=mpi pytest modin/tests/pandas/test_general.py && " - "MODIN_ENGINE=dask pytest modin/tests/pandas/test_general.py" - ), + "MODIN_ENGINE=unidist UNIDIST_ENGINE=mpi " + "mpiexec -n=1 --map-by :OVERSUBSCRIBE pytest modin/tests/pandas/test_general.py &&" + "MODIN_ENGINE=dask pytest modin/tests/pandas/test_general.py" + ), 'source_tmpl': '%(version)s.tar.gz', 'source_urls': ['https://github.com/modin-project/%(name)s/archive/refs/tags'], 'testinstall': True, From dc8710c4bd7512f1a5cfca39d2be596181db23bd Mon Sep 17 00:00:00 2001 From: Stefan Wolfsheimer Date: Tue, 22 Oct 2024 17:23:11 +0200 Subject: [PATCH 36/85] adding easyconfigs: GSL-2.8-GCC-13.3.0.eb --- .../easyconfigs/g/GSL/GSL-2.8-GCC-13.3.0.eb | 25 +++++++++++++++++++ 1 file changed, 25 insertions(+) create mode 100644 easybuild/easyconfigs/g/GSL/GSL-2.8-GCC-13.3.0.eb diff --git a/easybuild/easyconfigs/g/GSL/GSL-2.8-GCC-13.3.0.eb b/easybuild/easyconfigs/g/GSL/GSL-2.8-GCC-13.3.0.eb new file mode 100644 index 000000000000..251304ed936a --- /dev/null +++ b/easybuild/easyconfigs/g/GSL/GSL-2.8-GCC-13.3.0.eb @@ -0,0 +1,25 @@ +easyblock = 'ConfigureMake' + +name = 'GSL' +version = '2.8' + +homepage = 'https://www.gnu.org/software/gsl/' +description = """The GNU Scientific Library (GSL) is a numerical library for C and C++ programmers. + The library provides a wide range of mathematical routines such as random number generators, special functions + and least-squares fitting.""" + +toolchain = {'name': 'GCC', 'version': '13.3.0'} +toolchainopts = {'unroll': True, 'pic': True} + +source_urls = [GNU_SOURCE] +sources = [SOURCELOWER_TAR_GZ] +checksums = ['6a99eeed15632c6354895b1dd542ed5a855c0f15d9ad1326c6fe2b2c9e423190'] + +sanity_check_paths = { + 'files': ['bin/%s' % x for x in ['gsl-config', 'gsl-histogram', 'gsl-randist']] + + ['include/gsl/gsl_types.h'] + + ['lib/lib%s.%s' % (x, SHLIB_EXT) for x in ['gsl', 'gslcblas']], + 'dirs': [], +} + +moduleclass = 'numlib' From 42bf4d53f732286a61ead16586802156ca68546e Mon Sep 17 00:00:00 2001 From: Stefan Wolfsheimer Date: Tue, 22 Oct 2024 18:39:40 +0200 Subject: [PATCH 37/85] adding easyconfigs: libepoxy-1.5.10-GCCcore-13.3.0.eb --- .../libepoxy-1.5.10-GCCcore-13.3.0.eb | 37 +++++++++++++++++++ 1 file changed, 37 insertions(+) create mode 100644 easybuild/easyconfigs/l/libepoxy/libepoxy-1.5.10-GCCcore-13.3.0.eb diff --git a/easybuild/easyconfigs/l/libepoxy/libepoxy-1.5.10-GCCcore-13.3.0.eb b/easybuild/easyconfigs/l/libepoxy/libepoxy-1.5.10-GCCcore-13.3.0.eb new file mode 100644 index 000000000000..bca992c268a1 --- /dev/null +++ b/easybuild/easyconfigs/l/libepoxy/libepoxy-1.5.10-GCCcore-13.3.0.eb @@ -0,0 +1,37 @@ +easyblock = 'MesonNinja' + +name = 'libepoxy' +version = '1.5.10' + +homepage = 'https://github.com/anholt/libepoxy' +description = "Epoxy is a library for handling OpenGL function pointer management for you" + +toolchain = {'name': 'GCCcore', 'version': '13.3.0'} + +github_account = 'anholt' +source_urls = [GITHUB_LOWER_SOURCE] +sources = ['%(version)s.tar.gz'] +checksums = ['a7ced37f4102b745ac86d6a70a9da399cc139ff168ba6b8002b4d8d43c900c15'] + +builddependencies = [ + ('binutils', '2.42'), + ('Meson', '1.4.0'), + ('Ninja', '1.12.1'), + ('pkgconf', '2.2.0'), +] + +dependencies = [ + ('X11', '20240607'), + ('Mesa', '24.1.3'), +] + +configopts = '-Degl=yes --libdir %(installdir)s/lib ' + +sanity_check_paths = { + 'files': ['include/epoxy/%s.h' % x for x in ['common', 'egl_generated', 'egl', 'gl_generated', + 'gl', 'glx_generated', 'glx']] + + ['lib/libepoxy.%s' % SHLIB_EXT], + 'dirs': ['lib'] +} + +moduleclass = 'lib' From ae174c2c5fde948cafceeb097850fb4d68e7814c Mon Sep 17 00:00:00 2001 From: Stefan Wolfsheimer Date: Wed, 23 Oct 2024 00:06:57 +0200 Subject: [PATCH 38/85] GTK3-3.24.42-GCCcore-13.3.0.eb --- .../g/GTK3/GTK3-3.24.42-GCCcore-13.3.0.eb | 72 +++++++++++++++++++ 1 file changed, 72 insertions(+) create mode 100644 easybuild/easyconfigs/g/GTK3/GTK3-3.24.42-GCCcore-13.3.0.eb diff --git a/easybuild/easyconfigs/g/GTK3/GTK3-3.24.42-GCCcore-13.3.0.eb b/easybuild/easyconfigs/g/GTK3/GTK3-3.24.42-GCCcore-13.3.0.eb new file mode 100644 index 000000000000..2df9a346d4a2 --- /dev/null +++ b/easybuild/easyconfigs/g/GTK3/GTK3-3.24.42-GCCcore-13.3.0.eb @@ -0,0 +1,72 @@ +easyblock = 'Bundle' + +name = 'GTK3' +version = '3.24.42' + +homepage = 'https://developer.gnome.org/gtk3/stable/' +description = """GTK+ is the primary library used to construct user interfaces in GNOME. It + provides all the user interface controls, or widgets, used in a common + graphical application. Its object-oriented API allows you to construct + user interfaces without dealing with the low-level details of drawing and + device interaction. +""" + +toolchain = {'name': 'GCCcore', 'version': '13.3.0'} + +builddependencies = [ + ('binutils', '2.42'), + ('Autotools', '20231222'), + ('Meson', '1.4.0'), + ('Ninja', '1.12.1'), + ('pkgconf', '2.2.0'), + ('GObject-Introspection', '1.80.1'), +] + +dependencies = [ + ('ATK', '2.38.0'), + ('at-spi2-atk', '2.38.0'), + ('cairo', '1.18.0'), + ('Gdk-Pixbuf', '2.42.11'), + ('GLib', '2.80.4'), + ('Pango', '1.54.0'), + ('libepoxy', '1.5.10'), + ('X11', '20240607'), + ('FriBidi', '1.0.15'), + ('Wayland', '1.23.0'), +] + +default_easyblock = 'MesonNinja' + +default_component_specs = { + 'sources': [SOURCELOWER_TAR_XZ], + 'start_dir': '%(namelower)s-%(version)s', +} + +components = [ + ('GTK+', version, { + 'source_urls': [FTPGNOME_SOURCE], + 'checksums': ['50f89f615092d4dd01bbd759719f8bd380e5f149f6fd78a94725e2de112377e2'], + }), + ('hicolor-icon-theme', '0.18', { + 'easyblock': 'MesonNinja', + 'source_urls': ['https://icon-theme.freedesktop.org/releases/'], + 'checksums': ['db0e50a80aa3bf64bb45cbca5cf9f75efd9348cf2ac690b907435238c3cf81d7'], + }), + ('adwaita-icon-theme', '47.0', { + 'source_urls': ['https://ftp.gnome.org/pub/GNOME/sources/%(namelower)s/%(version_major)s'], + 'checksums': ['ad088a22958cb8469e41d9f1bba0efb27e586a2102213cd89cc26db2e002bdfe'], + }), +] + +postinstallcmds = ['gtk-update-icon-cache'] + +sanity_check_paths = { + 'files': ['bin/%s' % x for x in ['gtk3-demo', 'gtk3-demo-application', 'gtk3-icon-browser', 'gtk3-widget-factory', + 'gtk-builder-tool', 'gtk-launch', 'gtk-query-immodules-3.0', 'gtk-query-settings', + 'gtk-update-icon-cache']] + + ['lib/%s-%%(version_major)s.%s' % (x, SHLIB_EXT) for x in ['libgailutil', 'libgdk', 'libgtk']], + 'dirs': ['include/%s-%%(version_major)s.0' % x for x in ['gail', 'gtk']] + + ['share/icons/hicolor', 'share/icons/Adwaita'], +} + +moduleclass = 'vis' From 5890289f3584a0618432f93dd30da777bc23363b Mon Sep 17 00:00:00 2001 From: WilleBell Date: Wed, 23 Oct 2024 15:47:05 +0200 Subject: [PATCH 39/85] adding easyconfigs: Dask-ML-2024.4.4-foss-2023a.eb --- .../d/Dask-ML/Dask-ML-2024.4.4-foss-2023a.eb | 54 +++++++++++++++++++ 1 file changed, 54 insertions(+) create mode 100644 easybuild/easyconfigs/d/Dask-ML/Dask-ML-2024.4.4-foss-2023a.eb diff --git a/easybuild/easyconfigs/d/Dask-ML/Dask-ML-2024.4.4-foss-2023a.eb b/easybuild/easyconfigs/d/Dask-ML/Dask-ML-2024.4.4-foss-2023a.eb new file mode 100644 index 000000000000..9ff4d7c1b9c4 --- /dev/null +++ b/easybuild/easyconfigs/d/Dask-ML/Dask-ML-2024.4.4-foss-2023a.eb @@ -0,0 +1,54 @@ +easyblock = 'PythonBundle' + +name = 'Dask-ML' +version = '2024.4.4' + +homepage = 'http://ml.dask.org/' +description = """ +Dask-ML provides scalable machine learning in Python using Dask alongside popular machine +learning libraries like Scikit-Learn, XGBoost, and others. +""" + +toolchain = {'name': 'foss', 'version': '2023a'} + +builddependencies = [('hatchling', '1.18.0')] + +dependencies = [ + ('Python', '3.11.3'), + ('scikit-learn', '1.3.1'), + ('dask', '2023.9.2'), + ('numba', '0.58.1'), + ('SciPy-bundle', '2023.07'), +] + +use_pip = True +sanity_pip_check = True + +exts_list = [ + ('setuptools-scm', '8.1.0', { + 'sources': ['setuptools_scm-%(version)s.tar.gz'], + 'checksums': ['42dea1b65771cba93b7a515d65a65d8246e560768a66b9106a592c8e7f26c8a7'], + }), # sparse needs setuptools-scm>=8 + ('sparse', '0.15.4', { + 'checksums': ['d4b1c57d24ff0f64f2fd5b5a95b49b7fb84ed207a26d7d58ce2764dcc5c72b84'], + }), + ('dask-glm', '0.3.2', { + 'checksums': ['c947a566866698a01d79978ae73233cb5e838ad5ead6085143582c5e930b9a4a'], + }), + ('distributed', '2023.9.2', { + 'checksums': ['b76b43be6a297c6cc6dc4eac7f5a05a8c6834aaf025ed37395d1d830448d540e'], + }), + ('multipledispatch', '1.0.0', { + 'checksums': ['5c839915465c68206c3e9c473357908216c28383b425361e5d144594bf85a7e0'], + }), + ('packaging', '24.1', { + 'checksums': ['026ed72c8ed3fcce5bf8950572258698927fd1dbda10a5e981cdf0ac37f4f002'], + }), + (name, version, { + 'modulename': 'dask_ml', + 'sources': ['dask_ml-%(version)s.tar.gz'], + 'checksums': ['7956910a49e1e31944280fdb311adf245da11ef410d67deb7a05c67c7d0c4498'], + }), +] + +moduleclass = 'ai' From 45aadd9b6883717fc743de39792960fa99b80f73 Mon Sep 17 00:00:00 2001 From: maximm Date: Thu, 24 Oct 2024 11:41:40 +0200 Subject: [PATCH 40/85] adding easyconfigs: ReFrame-4.6.3-GCCcore-13.3.0.eb --- .../r/ReFrame/ReFrame-4.6.3-GCCcore-13.3.0.eb | 76 +++++++++++++++++++ 1 file changed, 76 insertions(+) create mode 100644 easybuild/easyconfigs/r/ReFrame/ReFrame-4.6.3-GCCcore-13.3.0.eb diff --git a/easybuild/easyconfigs/r/ReFrame/ReFrame-4.6.3-GCCcore-13.3.0.eb b/easybuild/easyconfigs/r/ReFrame/ReFrame-4.6.3-GCCcore-13.3.0.eb new file mode 100644 index 000000000000..6541b14b799e --- /dev/null +++ b/easybuild/easyconfigs/r/ReFrame/ReFrame-4.6.3-GCCcore-13.3.0.eb @@ -0,0 +1,76 @@ +easyblock = 'PythonBundle' + +name = 'ReFrame' +version = '4.6.3' + +homepage = 'https://github.com/reframe-hpc/reframe' +description = '''ReFrame is a framework for writing regression tests for HPC systems.''' + +toolchain = {'name': 'GCCcore', 'version': '13.3.0'} + +builddependencies = [ + ('binutils', '2.42'), + ('cURL', '8.7.1'), # Used by ReFrame to download pip in the bootstrap +] + +# Note that for ReFrame's CPU autodetect to work +# the system also needs to provide (new enough versions of) these dependencies +dependencies = [ + ('Python', '3.12.3'), + ('libxslt', '1.1.42'), # Required by lxml, which is installed by ReFrame's bootstrap installer + ('libxml2', '2.12.7'), # Required by lxml, which is installed by ReFrame's bootstrap installer +] + +use_pip = True + +exts_list = [ + # ReFrame's bootstrap script is intended to run with zero dependencies. It downloads all python deps for ReFrame + # into a %(installdir)/external directory. ReFrame's main executable (reframe) adds this dir to python's sys.path + # so that ReFrame (and only ReFrame) will find & use all of these dependencies. + # In EasyBuild, we should adhere to this installation method because a) it is how ReFrame is meant to be used and + # b) it isolates all of ReFrame dependencies from any other python code you run. Thus, there is no chance that + # a test will pick up on any python deps from ReFrame itself. + # For this to work, we need to disable download_dep_fail and sanity_pip_check, as both are _expected_ to fail + # for this setup. + ('reframe', version, { + # Deps are downloaded to %(installdir)/external, which won't polute the PYTHONPATH, so is ok + 'download_dep_fail': False, + # ReFrame uses its custom sys.path to find necessary packages, they are not on PYTYHONPATH + # Thus, the regular pip sanity check is expected to fail, even if ReFrame would run just fine + 'sanity_pip_check': False, + # Set modulename to False, as to skip the sanity_check-step from extension.py (python -c "import reframe") + # This step would fail, since the regular python interpreter wouldn't find the additional packages in + # %(installdir)/external. That's fine, as ReFrame should never be imported directly, only through the + # reframe command. + 'modulename': False, + 'preinstallopts': "export PATH=%(installdir)s/bin:$PATH && " + "./bootstrap.sh +docs +pygelf && cp -r external %(installdir)s && ", + 'source_tmpl': 'v%(version)s.tar.gz', + 'source_urls': ['https://github.com/reframe-hpc/reframe/archive/'], + 'checksums': ['0f335e588d21a26d76beb011bc86baf80ba633d875512ecd564d0aeb320fcf2c'], + }), +] + +postinstallcmds = [ + "cp -a tools examples %(installdir)s", + "mkdir -p %(installdir)s/share && cp -a share/completions %(installdir)s/share/completions", + r"sed -i 's@/\(python[0-9.]*\)$@/\1 -S@g' %(installdir)s/bin/reframe", +] + +sanity_check_paths = { + 'files': ['bin/reframe', + 'share/completions/reframe.bash', + 'share/completions/reframe.fish', + 'share/completions/reframe.tcsh'], + 'dirs': ['external', 'lib', 'tools', 'examples'] +} + +sanity_check_commands = ['reframe -V'] + +# Since this is at the GCCcore toolchain level, make sure ReFrame is configured to purge modules before running +# any tests by default +modextravars = { + 'RFM_PURGE_ENVIRONMENT': '1', +} + +moduleclass = 'devel' From 563bfd8bdd1b3aa21d20665688e9bec5ad946cec Mon Sep 17 00:00:00 2001 From: maximm Date: Thu, 24 Oct 2024 13:34:55 +0200 Subject: [PATCH 41/85] adding easyconfigs: ncdu-1.20-GCC-13.3.0.eb --- .../n/ncdu/ncdu-1.20-GCC-13.3.0.eb | 27 +++++++++++++++++++ 1 file changed, 27 insertions(+) create mode 100644 easybuild/easyconfigs/n/ncdu/ncdu-1.20-GCC-13.3.0.eb diff --git a/easybuild/easyconfigs/n/ncdu/ncdu-1.20-GCC-13.3.0.eb b/easybuild/easyconfigs/n/ncdu/ncdu-1.20-GCC-13.3.0.eb new file mode 100644 index 000000000000..e8f91407acff --- /dev/null +++ b/easybuild/easyconfigs/n/ncdu/ncdu-1.20-GCC-13.3.0.eb @@ -0,0 +1,27 @@ +easyblock = 'ConfigureMake' + +name = 'ncdu' +version = '1.20' + +homepage = 'https://dev.yorhel.nl/ncdu' +description = """Ncdu is a disk usage analyzer with an ncurses interface. It is designed to find space hogs on a + remote server where you don't have an entire graphical setup available, but it is a useful tool even on regular + desktop systems. Ncdu aims to be fast, simple and easy to use, and should be able to run in any minimal POSIX-like + environment with ncurses installed.""" + +toolchain = {'name': 'GCC', 'version': '13.3.0'} + +source_urls = ['https://dev.yorhel.nl/download/'] +sources = [SOURCE_TAR_GZ] +checksums = ['5fe2bb841abe72374bb242dbb93293c4ae053078432d896a7481b2ff10be9572'] + +dependencies = [ + ('ncurses', '6.5'), +] + +sanity_check_paths = { + 'files': ['bin/%(name)s'], + 'dirs': [], +} + +moduleclass = 'tools' From c2c9d2aec78966c55b91776334d5f76915093502 Mon Sep 17 00:00:00 2001 From: WilleBell Date: Mon, 28 Oct 2024 10:34:57 +0100 Subject: [PATCH 42/85] pydot as dependency instead of extension --- easybuild/easyconfigs/s/SciANN/SciANN-0.7.0.1-foss-2022a.eb | 4 +--- 1 file changed, 1 insertion(+), 3 deletions(-) diff --git a/easybuild/easyconfigs/s/SciANN/SciANN-0.7.0.1-foss-2022a.eb b/easybuild/easyconfigs/s/SciANN/SciANN-0.7.0.1-foss-2022a.eb index 0717fc8e997b..9b14f9ce1be9 100644 --- a/easybuild/easyconfigs/s/SciANN/SciANN-0.7.0.1-foss-2022a.eb +++ b/easybuild/easyconfigs/s/SciANN/SciANN-0.7.0.1-foss-2022a.eb @@ -21,15 +21,13 @@ dependencies = [ ('pymatgen', '2023.3.10'), # for pybtex and latexcodec ('matplotlib', '3.5.2'), ('pygraphviz', '1.10'), + ('pydot', '1.4.2'), ] use_pip = True sanity_pip_check = True exts_list = [ - ('pydot', '2.0.0', { - 'checksums': ['60246af215123fa062f21cd791be67dda23a6f280df09f68919e637a1e4f3235'], - }), (name, version, { 'modulename': 'sciann', 'checksums': ['7d7acf61346b4201628c5656e2c904e9a9c7cda78086e76d075b5c7bb90adf3c'], From 86bc145a09cbd7ccc3d0ba96dda3b533a9dabe12 Mon Sep 17 00:00:00 2001 From: =?UTF-8?q?Jan=20Andr=C3=A9=20Reuter?= Date: Mon, 28 Oct 2024 17:01:54 +0100 Subject: [PATCH 43/85] Add Intel 2025.0.0 compilers MIME-Version: 1.0 Content-Type: text/plain; charset=UTF-8 Content-Transfer-Encoding: 8bit Signed-off-by: Jan André Reuter --- .../intel-compilers-2025.0.0.eb | 37 +++++++++++++++++++ 1 file changed, 37 insertions(+) create mode 100644 easybuild/easyconfigs/i/intel-compilers/intel-compilers-2025.0.0.eb diff --git a/easybuild/easyconfigs/i/intel-compilers/intel-compilers-2025.0.0.eb b/easybuild/easyconfigs/i/intel-compilers/intel-compilers-2025.0.0.eb new file mode 100644 index 000000000000..34a1074639e8 --- /dev/null +++ b/easybuild/easyconfigs/i/intel-compilers/intel-compilers-2025.0.0.eb @@ -0,0 +1,37 @@ +name = 'intel-compilers' +version = '2025.0.0' + +homepage = 'https://software.intel.com/content/www/us/en/develop/tools/oneapi/hpc-toolkit.html' +description = "Intel C, C++ & Fortran compilers" + +toolchain = SYSTEM + +# see https://software.intel.com/content/www/us/en/develop/articles/oneapi-standalone-components.html +sources = [ + { + 'source_urls': [ + 'https://registrationcenter-download.intel.com/akdlm/IRC_NAS/ac92f2bb-4818-4e53-a432-f8b34d502f23/' + ], + 'filename': 'intel-dpcpp-cpp-compiler-%(version)s.740_offline.sh', + }, + { + 'source_urls': [ + 'https://registrationcenter-download.intel.com/akdlm/IRC_NAS/69f79888-2d6c-4b20-999e-e99d72af68d4/' + ], + 'filename': 'intel-fortran-compiler-%(version)s.723_offline.sh', + }, +] +checksums = [ + {'intel-dpcpp-cpp-compiler-2025.0.0.740_offline.sh': + '04fadf63789acee731895e631db63f65a98b8279db3d0f48bdf0d81e6103bdd8'}, + {'intel-fortran-compiler-2025.0.0.723_offline.sh': + '2be6d607ce84f35921228595b118fbc516d28587cbc4e6dcf6b7219e5cd1a9a9'}, +] + +local_gccver = '14.2.0' +dependencies = [ + ('GCCcore', local_gccver), + ('binutils', '2.42', '', ('GCCcore', local_gccver)), +] + +moduleclass = 'compiler' From c796315c43a2a30ee2a06af4059d3553a044a342 Mon Sep 17 00:00:00 2001 From: vsc46128 Date: Mon, 28 Oct 2024 17:46:57 +0100 Subject: [PATCH 44/85] adding easyconfigs: tbl2asn-20230713-GCCcore-12.3.0.eb --- .../tbl2asn-20230713-GCCcore-12.3.0.eb | 88 +++++++++++++++++++ 1 file changed, 88 insertions(+) create mode 100644 easybuild/easyconfigs/t/tbl2asn/tbl2asn-20230713-GCCcore-12.3.0.eb diff --git a/easybuild/easyconfigs/t/tbl2asn/tbl2asn-20230713-GCCcore-12.3.0.eb b/easybuild/easyconfigs/t/tbl2asn/tbl2asn-20230713-GCCcore-12.3.0.eb new file mode 100644 index 000000000000..1e03c1f4e242 --- /dev/null +++ b/easybuild/easyconfigs/t/tbl2asn/tbl2asn-20230713-GCCcore-12.3.0.eb @@ -0,0 +1,88 @@ +# This file is an EasyBuild reciPY as per https://easybuilders.github.io/easybuild/ +# Author: Pablo Escobar Lopez +# sciCORE - University of Basel +# SIB Swiss Institute of Bioinformatics +# revised by Ariel Lozano + +easyblock = 'Bundle' + +name = 'tbl2asn' +version = '20230713' + +homepage = 'https://www.ncbi.nlm.nih.gov/genbank/tbl2asn2/' +description = """Tbl2asn is a command-line program that automates the creation of + sequence records for submission to GenBank""" + +toolchain = {'name': 'GCCcore', 'version': '12.3.0'} +builddependencies = [ + ('binutils', '2.40'), + ('patchelf', '0.18.0'), +] + +# libraries that are copied to installdir need to be patched to have an RPATH section +# when EasyBuild is configured to use RPATH linking (required to pass RPATH sanity check); + +default_easyblock = 'CmdCp' + +# It is not entirely clean how long NCBI keeps "older" versions. At April 29, 2022, we had six timestamps/versions, +# reporiting the same verion (tbl2asn --help -> 25.8) but 5 out of 6 (gunzipped) executables have different sha256 +# checksums. + +components = [ + ('libidn', '1.34', { + 'easyblock': 'ConfigureMake', + 'source_urls': [GNU_SOURCE], + 'sources': [SOURCELOWER_TAR_GZ], + 'start_dir': '%(namelower)s-%(version)s', + 'checksums': ['3719e2975f2fb28605df3479c380af2cf4ab4e919e1506527e4c7670afff6e3c'], + }), + (name, version, { + 'source_urls': ['https://ftp.ncbi.nih.gov/toolbox/ncbi_tools/converters/versions/%s/all/' % + (version[:4] + '-' + version[4:6] + '-' + version[6:])], + 'sources': [{'download_filename': 'tbl2asn.linux64.gz', + 'filename': '%(name)s-%(version)s%(versionsuffix)s.gz'}], + 'checksums': ['544c4a2a53f2121fd21c44778fc61980a701ce852ea0142979241c0465c38a0c'], + 'cmds_map': [('.*', "cp %(name)s-%(version)s%(versionsuffix)s tbl2asn")], + 'files_to_copy': [(['tbl2asn'], 'bin')], + }), +] + +postinstallcmds = [ + "if %(rpath_enabled)s; then " + " patchelf --force-rpath --set-rpath %(installdir)s/lib %(installdir)s/bin/tbl2asn;" + "fi", + "chmod +x %(installdir)s/bin/tbl2asn", +] + +sanity_check_paths = { + 'files': ['bin/tbl2asn', 'bin/idn', 'lib/libidn.%s' % SHLIB_EXT], + 'dirs': ['include'], +} + +sanity_check_commands = ['tbl2asn --help'] + +moduleclass = 'bio' + +# " for lib in $(ls %(installdir)s/lib/libidn.so*); do " +# " echo setting RPATH in $lib;" +# " patchelf --force-rpath --set-rpath %(installdir)s/lib/libidn.so.11 %(installdir)s/bin/tbl2asn" +# " done;" +# +# + +""" + " for lib in $(ls %(installdir)s/lib/libidn.so*); do " + " patchelf --force-rpath --set-rpath '$ORIGIN' $lib;" + " done;" + "fi", + + "if %(rpath_enabled)s; then " + " for lib in $(ls %(installdir)s/lib/libidn.so*); do " + " patchelf --force-rpath --set-rpath %(installdir)s/bin/tbl2asn $lib;" + " done;" + "fi", + + "if %(rpath_enabled)s; then " + " patchelf --force-rpath --set-rpath '$ORIGIN' %(installdir)s/lib/libidn.so.11;" + "fi", +""" \ No newline at end of file From 206e1526e91256577afbf6a661b8e2e9dfee3f69 Mon Sep 17 00:00:00 2001 From: vsc46128 Date: Mon, 28 Oct 2024 17:50:53 +0100 Subject: [PATCH 45/85] clean up config --- .../tbl2asn-20230713-GCCcore-12.3.0.eb | 26 +------------------ 1 file changed, 1 insertion(+), 25 deletions(-) diff --git a/easybuild/easyconfigs/t/tbl2asn/tbl2asn-20230713-GCCcore-12.3.0.eb b/easybuild/easyconfigs/t/tbl2asn/tbl2asn-20230713-GCCcore-12.3.0.eb index 1e03c1f4e242..68563984e257 100644 --- a/easybuild/easyconfigs/t/tbl2asn/tbl2asn-20230713-GCCcore-12.3.0.eb +++ b/easybuild/easyconfigs/t/tbl2asn/tbl2asn-20230713-GCCcore-12.3.0.eb @@ -61,28 +61,4 @@ sanity_check_paths = { sanity_check_commands = ['tbl2asn --help'] -moduleclass = 'bio' - -# " for lib in $(ls %(installdir)s/lib/libidn.so*); do " -# " echo setting RPATH in $lib;" -# " patchelf --force-rpath --set-rpath %(installdir)s/lib/libidn.so.11 %(installdir)s/bin/tbl2asn" -# " done;" -# -# - -""" - " for lib in $(ls %(installdir)s/lib/libidn.so*); do " - " patchelf --force-rpath --set-rpath '$ORIGIN' $lib;" - " done;" - "fi", - - "if %(rpath_enabled)s; then " - " for lib in $(ls %(installdir)s/lib/libidn.so*); do " - " patchelf --force-rpath --set-rpath %(installdir)s/bin/tbl2asn $lib;" - " done;" - "fi", - - "if %(rpath_enabled)s; then " - " patchelf --force-rpath --set-rpath '$ORIGIN' %(installdir)s/lib/libidn.so.11;" - "fi", -""" \ No newline at end of file +moduleclass = 'bio' \ No newline at end of file From 8bf310cc1a2901cebd5ddfd308dfc3626c375929 Mon Sep 17 00:00:00 2001 From: vsc46128 Date: Mon, 28 Oct 2024 18:19:49 +0100 Subject: [PATCH 46/85] add blank line to end of file --- .../easyconfigs/t/tbl2asn/tbl2asn-20230713-GCCcore-12.3.0.eb | 2 +- 1 file changed, 1 insertion(+), 1 deletion(-) diff --git a/easybuild/easyconfigs/t/tbl2asn/tbl2asn-20230713-GCCcore-12.3.0.eb b/easybuild/easyconfigs/t/tbl2asn/tbl2asn-20230713-GCCcore-12.3.0.eb index 68563984e257..dcf4c39e8d03 100644 --- a/easybuild/easyconfigs/t/tbl2asn/tbl2asn-20230713-GCCcore-12.3.0.eb +++ b/easybuild/easyconfigs/t/tbl2asn/tbl2asn-20230713-GCCcore-12.3.0.eb @@ -61,4 +61,4 @@ sanity_check_paths = { sanity_check_commands = ['tbl2asn --help'] -moduleclass = 'bio' \ No newline at end of file +moduleclass = 'bio' From 79caf6eec4c38c9507f4c05db9786e71558f91c1 Mon Sep 17 00:00:00 2001 From: Viktor Rehnberg Date: Tue, 29 Oct 2024 12:21:51 +0000 Subject: [PATCH 47/85] Build PyCUDA with OpenGL support --- .../p/PyCUDA/PyCUDA-2024.1-gfbf-2023a-CUDA-12.1.1.eb | 6 +++++- 1 file changed, 5 insertions(+), 1 deletion(-) diff --git a/easybuild/easyconfigs/p/PyCUDA/PyCUDA-2024.1-gfbf-2023a-CUDA-12.1.1.eb b/easybuild/easyconfigs/p/PyCUDA/PyCUDA-2024.1-gfbf-2023a-CUDA-12.1.1.eb index 0058b158c9e5..1706b5b8372d 100644 --- a/easybuild/easyconfigs/p/PyCUDA/PyCUDA-2024.1-gfbf-2023a-CUDA-12.1.1.eb +++ b/easybuild/easyconfigs/p/PyCUDA/PyCUDA-2024.1-gfbf-2023a-CUDA-12.1.1.eb @@ -14,6 +14,7 @@ dependencies = [ ('Python', '3.11.3'), ('SciPy-bundle', '2023.07'), ('Mako', '1.2.4'), + ('PyOpenGL', '3.1.7'), ] use_pip = True @@ -23,12 +24,15 @@ exts_list = [ 'checksums': ['80637873d206f6bcedf7cdb46ad93e868acb4ea2256db052dfcca872bdd0321f'], }), (name, version, { - 'preinstallopts': './configure.py --cuda-root="$EBROOTCUDA" && ', + 'preinstallopts': './configure.py --cuda-root="$EBROOTCUDA" --cuda-enable-gl && ', 'source_tmpl': '%(namelower)s-%(version)s.tar.gz', 'checksums': ['d50d23ff6371482cff7d4b953ef40ab81c9df038ecb614484f9fd5347327327e'], }), ] sanity_pip_check = True +sanity_check_commands = [ + 'python -c "import pycuda.gl"' +] moduleclass = 'lang' From de85cbb84e1f70c3cde0a627f217f74392935e26 Mon Sep 17 00:00:00 2001 From: Balazs Hajgato Date: Wed, 30 Oct 2024 10:50:00 +0100 Subject: [PATCH 48/85] OpenBLAS sequential with 64 bit interface --- .../OpenBLAS-0.3.27-GCC-13.2.0-seq-iface64.eb | 55 +++++++++++++++++++ 1 file changed, 55 insertions(+) create mode 100644 easybuild/easyconfigs/o/OpenBLAS/OpenBLAS-0.3.27-GCC-13.2.0-seq-iface64.eb diff --git a/easybuild/easyconfigs/o/OpenBLAS/OpenBLAS-0.3.27-GCC-13.2.0-seq-iface64.eb b/easybuild/easyconfigs/o/OpenBLAS/OpenBLAS-0.3.27-GCC-13.2.0-seq-iface64.eb new file mode 100644 index 000000000000..8b0c54b42482 --- /dev/null +++ b/easybuild/easyconfigs/o/OpenBLAS/OpenBLAS-0.3.27-GCC-13.2.0-seq-iface64.eb @@ -0,0 +1,55 @@ +name = 'OpenBLAS' +version = '0.3.27' +versionsuffix = '-seq-iface64' + +homepage = 'https://www.openblas.net/' +description = "OpenBLAS is an optimized BLAS library based on GotoBLAS2 1.13 BSD version." + +toolchain = {'name': 'GCC', 'version': '13.2.0'} + +source_urls = [ + # order matters, trying to download the large.tgz/timing.tgz LAPACK tarballs from GitHub causes trouble + 'https://www.netlib.org/lapack/timing/', + 'https://github.com/xianyi/OpenBLAS/archive/', +] +sources = ['v%(version)s.tar.gz'] +patches = [ + ('large.tgz', '.'), + ('timing.tgz', '.'), + 'OpenBLAS-0.3.15_workaround-gcc-miscompilation.patch', + 'OpenBLAS-0.3.21_fix-order-vectorization.patch', + 'OpenBLAS-0.3.26_lapack_qr_noninittest.patch', + 'OpenBLAS-0.3.27_fix_zscal.patch', + 'OpenBLAS-0.3.27_riscv-drop-static-fortran-flag.patch', +] +checksums = [ + {'v0.3.27.tar.gz': 'aa2d68b1564fe2b13bc292672608e9cdeeeb6dc34995512e65c3b10f4599e897'}, + {'large.tgz': 'f328d88b7fa97722f271d7d0cfea1c220e0f8e5ed5ff01d8ef1eb51d6f4243a1'}, + {'timing.tgz': '999c65f8ea8bd4eac7f1c7f3463d4946917afd20a997807300fe35d70122f3af'}, + {'OpenBLAS-0.3.15_workaround-gcc-miscompilation.patch': + 'e6b326fb8c4a8a6fd07741d9983c37a72c55c9ff9a4f74a80e1352ce5f975971'}, + {'OpenBLAS-0.3.21_fix-order-vectorization.patch': + '08af834e5d60441fd35c128758ed9c092ba6887c829e0471ecd489079539047d'}, + {'OpenBLAS-0.3.26_lapack_qr_noninittest.patch': '4781bf1d7b239374fd8069e15b4e2c0ef0e8efaa1a7d4c33557bd5b27e5de77c'}, + {'OpenBLAS-0.3.27_fix_zscal.patch': '9210d7b66538dabaddbe1bfceb16f8225708856f60876ca5561b19d3599f9fd1'}, + {'OpenBLAS-0.3.27_riscv-drop-static-fortran-flag.patch': + 'f374e41efffd592ab1c9034df9e7abf1045ed151f4fc0fd0da618ce9826f2d4b'}, +] + +builddependencies = [ + ('make', '4.4.1'), + # required by LAPACK test suite + ('Python', '3.11.5'), +] + +buildopts = "INTERFACE64=1 USE_OPENMP=0 USE_THREAD=0 USE_LOCKING=1 " +testopts = "INTERFACE64=1 USE_OPENMP=0 USE_THREAD=0 USE_LOCKING=1 " +installopts = "INTERFACE64=1 USE_OPENMP=0 USE_THREAD=0 USE_LOCKING=1 " + +run_lapack_tests = True +max_failing_lapack_tests_num_errors = 150 + +# extensive testing can be enabled by uncommenting the line below +# runtest = 'PATH=.:$PATH lapack-timing' + +moduleclass = 'numlib' From 85cb7520689f4da69fd77dc5149f6bd178bf69d6 Mon Sep 17 00:00:00 2001 From: WilleBell Date: Wed, 30 Oct 2024 11:52:03 +0100 Subject: [PATCH 49/85] remove setuptools-scm extension --- .../easyconfigs/d/Dask-ML/Dask-ML-2024.4.4-foss-2023a.eb | 6 ++---- 1 file changed, 2 insertions(+), 4 deletions(-) diff --git a/easybuild/easyconfigs/d/Dask-ML/Dask-ML-2024.4.4-foss-2023a.eb b/easybuild/easyconfigs/d/Dask-ML/Dask-ML-2024.4.4-foss-2023a.eb index 9ff4d7c1b9c4..fd593a4bb094 100644 --- a/easybuild/easyconfigs/d/Dask-ML/Dask-ML-2024.4.4-foss-2023a.eb +++ b/easybuild/easyconfigs/d/Dask-ML/Dask-ML-2024.4.4-foss-2023a.eb @@ -25,11 +25,9 @@ use_pip = True sanity_pip_check = True exts_list = [ - ('setuptools-scm', '8.1.0', { - 'sources': ['setuptools_scm-%(version)s.tar.gz'], - 'checksums': ['42dea1b65771cba93b7a515d65a65d8246e560768a66b9106a592c8e7f26c8a7'], - }), # sparse needs setuptools-scm>=8 ('sparse', '0.15.4', { + # replace use of 'version_file' (which requires setuptools-scm >= 8.0) with 'write_to' + 'preinstallopts': "sed -i 's/^version_file/write_to/' pyproject.toml && ", 'checksums': ['d4b1c57d24ff0f64f2fd5b5a95b49b7fb84ed207a26d7d58ce2764dcc5c72b84'], }), ('dask-glm', '0.3.2', { From 2f16e34b3ecaa491f50127ce4382db1969e6ca88 Mon Sep 17 00:00:00 2001 From: pecar Date: Wed, 30 Oct 2024 13:38:30 +0100 Subject: [PATCH 50/85] adding easyconfigs: BCFtools-1.21-GCC-13.3.0.eb, GSL-2.8-GCC-13.3.0.eb, HTSlib-1.21-GCC-13.3.0.eb, SAMtools-1.21-GCC-13.3.0.eb --- .../b/BCFtools/BCFtools-1.21-GCC-13.3.0.eb | 40 ++++++++++++++++++ .../easyconfigs/g/GSL/GSL-2.8-GCC-13.3.0.eb | 25 +++++++++++ .../h/HTSlib/HTSlib-1.21-GCC-13.3.0.eb | 41 +++++++++++++++++++ .../s/SAMtools/SAMtools-1.21-GCC-13.3.0.eb | 38 +++++++++++++++++ 4 files changed, 144 insertions(+) create mode 100644 easybuild/easyconfigs/b/BCFtools/BCFtools-1.21-GCC-13.3.0.eb create mode 100644 easybuild/easyconfigs/g/GSL/GSL-2.8-GCC-13.3.0.eb create mode 100644 easybuild/easyconfigs/h/HTSlib/HTSlib-1.21-GCC-13.3.0.eb create mode 100644 easybuild/easyconfigs/s/SAMtools/SAMtools-1.21-GCC-13.3.0.eb diff --git a/easybuild/easyconfigs/b/BCFtools/BCFtools-1.21-GCC-13.3.0.eb b/easybuild/easyconfigs/b/BCFtools/BCFtools-1.21-GCC-13.3.0.eb new file mode 100644 index 000000000000..ad508758ba5b --- /dev/null +++ b/easybuild/easyconfigs/b/BCFtools/BCFtools-1.21-GCC-13.3.0.eb @@ -0,0 +1,40 @@ +# This file is an EasyBuild reciPY as per https://github.com/easybuilders/easybuild +# +# Author: Jonas Demeulemeester +# The Francis Crick Insitute, London, UK +# Updated to 1.21 jpecar / EMBL + +easyblock = 'ConfigureMake' + +name = 'BCFtools' +version = '1.21' + +homepage = 'https://www.htslib.org/' +description = """Samtools is a suite of programs for interacting with high-throughput sequencing data. + BCFtools - Reading/writing BCF2/VCF/gVCF files and calling/filtering/summarising SNP and short indel sequence + variants""" + +toolchain = {'name': 'GCC', 'version': '13.3.0'} +toolchainopts = {'pic': True} + +source_urls = ['https://github.com/samtools/%(namelower)s/releases/download/%(version)s'] +sources = [SOURCELOWER_TAR_BZ2] +checksums = ['528a4cc1d3555368db75a700b22a3c95da893fd1827f6d304716dfd45ea4e282'] + +dependencies = [ + ('zlib', '1.3.1'), + ('HTSlib', '1.21'), + ('bzip2', '1.0.8'), + ('XZ', '5.4.5'), + ('GSL', '2.8'), +] + +configopts = "--with-htslib=$EBROOTHTSLIB --enable-libgsl" + + +sanity_check_paths = { + 'files': ['bin/%(namelower)s', 'bin/plot-vcfstats', 'bin/vcfutils.pl'], + 'dirs': ['libexec/%(namelower)s'], +} + +moduleclass = 'bio' diff --git a/easybuild/easyconfigs/g/GSL/GSL-2.8-GCC-13.3.0.eb b/easybuild/easyconfigs/g/GSL/GSL-2.8-GCC-13.3.0.eb new file mode 100644 index 000000000000..251304ed936a --- /dev/null +++ b/easybuild/easyconfigs/g/GSL/GSL-2.8-GCC-13.3.0.eb @@ -0,0 +1,25 @@ +easyblock = 'ConfigureMake' + +name = 'GSL' +version = '2.8' + +homepage = 'https://www.gnu.org/software/gsl/' +description = """The GNU Scientific Library (GSL) is a numerical library for C and C++ programmers. + The library provides a wide range of mathematical routines such as random number generators, special functions + and least-squares fitting.""" + +toolchain = {'name': 'GCC', 'version': '13.3.0'} +toolchainopts = {'unroll': True, 'pic': True} + +source_urls = [GNU_SOURCE] +sources = [SOURCELOWER_TAR_GZ] +checksums = ['6a99eeed15632c6354895b1dd542ed5a855c0f15d9ad1326c6fe2b2c9e423190'] + +sanity_check_paths = { + 'files': ['bin/%s' % x for x in ['gsl-config', 'gsl-histogram', 'gsl-randist']] + + ['include/gsl/gsl_types.h'] + + ['lib/lib%s.%s' % (x, SHLIB_EXT) for x in ['gsl', 'gslcblas']], + 'dirs': [], +} + +moduleclass = 'numlib' diff --git a/easybuild/easyconfigs/h/HTSlib/HTSlib-1.21-GCC-13.3.0.eb b/easybuild/easyconfigs/h/HTSlib/HTSlib-1.21-GCC-13.3.0.eb new file mode 100644 index 000000000000..2f35f9fa5a28 --- /dev/null +++ b/easybuild/easyconfigs/h/HTSlib/HTSlib-1.21-GCC-13.3.0.eb @@ -0,0 +1,41 @@ +# This file is an EasyBuild reciPY as per https://github.com/easybuilders/easybuild +# Author: Pablo Escobar Lopez +# Swiss Institute of Bioinformatics +# Biozentrum - University of Basel +# 1.4 modified by: +# Adam Huffman, Jonas Demeulemeester +# The Francis Crick Institute +# Updated to 1.14 +# J. Sassmannshausen /GSTT +# Updated to 1.21 jpecar EMBL + +easyblock = 'ConfigureMake' + +name = 'HTSlib' +version = '1.21' + +homepage = 'https://www.htslib.org/' +description = """A C library for reading/writing high-throughput sequencing data. + This package includes the utilities bgzip and tabix""" + +toolchain = {'name': 'GCC', 'version': '13.3.0'} + +source_urls = ['https://github.com/samtools/%(namelower)s/releases/download/%(version)s/'] +sources = [SOURCELOWER_TAR_BZ2] +checksums = ['84b510e735f4963641f26fd88c8abdee81ff4cb62168310ae716636aac0f1823'] + +# cURL added for S3 support +dependencies = [ + ('zlib', '1.3.1'), + ('bzip2', '1.0.8'), + ('XZ', '5.4.5'), + ('cURL', '8.7.1'), +] + + +sanity_check_paths = { + 'files': ['bin/bgzip', 'bin/tabix', 'lib/libhts.%s' % SHLIB_EXT], + 'dirs': [], +} + +moduleclass = 'bio' diff --git a/easybuild/easyconfigs/s/SAMtools/SAMtools-1.21-GCC-13.3.0.eb b/easybuild/easyconfigs/s/SAMtools/SAMtools-1.21-GCC-13.3.0.eb new file mode 100644 index 000000000000..775ce37b311e --- /dev/null +++ b/easybuild/easyconfigs/s/SAMtools/SAMtools-1.21-GCC-13.3.0.eb @@ -0,0 +1,38 @@ +# This is a contribution from DeepThought HPC Service, Flinders University, Adelaide, Australia +# Homepage: https://staff.flinders.edu.au/research/deep-thought +# +# Authors:: Robert Qiao +# License:: MIT +# +# Notes:: +# +# Updated to 1.14 and gcc-11.2.0 +# J. Sassmannshausen / GSTT +# Updated to 1.21 jpecar / EMBL + +name = 'SAMtools' +version = '1.21' + +homepage = 'https://www.htslib.org/' +description = """SAM Tools provide various utilities for manipulating alignments in the SAM format, + including sorting, merging, indexing and generating alignments in a per-position format.""" + +toolchain = {'name': 'GCC', 'version': '13.3.0'} +toolchainopts = {'pic': True} + +source_urls = ['https://github.com/%(namelower)s/%(namelower)s/releases/download/%(version)s'] +sources = [SOURCELOWER_TAR_BZ2] +checksums = ['05724b083a6b6f0305fcae5243a056cc36cf826309c3cb9347a6b89ee3fc5ada'] + +# The htslib component of SAMtools >= 1.4 uses zlib, bzip2 and lzma compression. +# The latter is currently provided by XZ. +dependencies = [ + ('ncurses', '6.5'), + ('zlib', '1.3.1'), + ('bzip2', '1.0.8'), + ('XZ', '5.4.5'), + ('cURL', '8.7.1'), +] + + +moduleclass = 'bio' From 9bcf061ae395e47018b751a8cc16bf8a7c0bd0a2 Mon Sep 17 00:00:00 2001 From: =?UTF-8?q?Mikael=20=C3=96hman?= Date: Fri, 1 Nov 2024 09:48:59 +0000 Subject: [PATCH 51/85] adding easyconfigs: networkx-3.4.2-gfbf-2024a.eb --- .../n/networkx/networkx-3.4.2-gfbf-2024a.eb | 24 +++++++++++++++++++ 1 file changed, 24 insertions(+) create mode 100644 easybuild/easyconfigs/n/networkx/networkx-3.4.2-gfbf-2024a.eb diff --git a/easybuild/easyconfigs/n/networkx/networkx-3.4.2-gfbf-2024a.eb b/easybuild/easyconfigs/n/networkx/networkx-3.4.2-gfbf-2024a.eb new file mode 100644 index 000000000000..9adfd4d52460 --- /dev/null +++ b/easybuild/easyconfigs/n/networkx/networkx-3.4.2-gfbf-2024a.eb @@ -0,0 +1,24 @@ +easyblock = 'PythonPackage' + +name = 'networkx' +version = '3.4.2' + +homepage = 'https://pypi.python.org/pypi/networkx' +description = """NetworkX is a Python package for the creation, manipulation, +and study of the structure, dynamics, and functions of complex networks.""" + +toolchain = {'name': 'gfbf', 'version': '2024a'} + +sources = [SOURCE_TAR_GZ] +checksums = ['307c3669428c5362aab27c8a1260aa8f47c4e91d3891f48be0141738d8d053e1'] + +dependencies = [ + ('Python', '3.12.3'), + ('SciPy-bundle', '2024.05'), # required for numpy, scipy, ... +] + +use_pip = True +download_dep_fail = True +sanity_pip_check = True + +moduleclass = 'tools' From 2865dbcf398ea2f0e8cda181f7048bfa84696d52 Mon Sep 17 00:00:00 2001 From: =?UTF-8?q?Mikael=20=C3=96hman?= Date: Fri, 1 Nov 2024 11:21:20 +0100 Subject: [PATCH 52/85] Change tagbot workflow to run on pull_request_target --- .github/workflows/tagbot.yml | 2 +- 1 file changed, 1 insertion(+), 1 deletion(-) diff --git a/.github/workflows/tagbot.yml b/.github/workflows/tagbot.yml index 1d382dae51d4..2b8c4e3ce1c8 100644 --- a/.github/workflows/tagbot.yml +++ b/.github/workflows/tagbot.yml @@ -1,5 +1,5 @@ name: Tagbot -on: [pull_request] +on: [pull_request_target] jobs: tagbot: From d2f33da9d7ddbdf1bb6396c906bd4a50a5a1a945 Mon Sep 17 00:00:00 2001 From: =?UTF-8?q?Mikael=20=C3=96hman?= Date: Fri, 1 Nov 2024 11:28:50 +0100 Subject: [PATCH 53/85] Add comments describing permissions on tagbot --- .github/workflows/tagbot.py | 4 ++++ .github/workflows/tagbot.yml | 4 ++-- 2 files changed, 6 insertions(+), 2 deletions(-) diff --git a/.github/workflows/tagbot.py b/.github/workflows/tagbot.py index 9c9710e9a466..649dd1dd8285 100644 --- a/.github/workflows/tagbot.py +++ b/.github/workflows/tagbot.py @@ -1,3 +1,7 @@ +# NOTE: In order to write comment and edit labels, this script requires workflows with write permissions. +# It should not use any untrusted third party code, or any code checked into the repository itself +# as that could indirectly grant PRs the ability to edit labels and comments on PRs. + import os import git import requests diff --git a/.github/workflows/tagbot.yml b/.github/workflows/tagbot.yml index 2b8c4e3ce1c8..74434f0d2c48 100644 --- a/.github/workflows/tagbot.yml +++ b/.github/workflows/tagbot.yml @@ -12,8 +12,8 @@ jobs: fetch-depth: 0 - run: | - # Make sure the script is unmodified - echo "8be2d295e8436ce557acc8a4d3b82a639913ae65de0d1a76871f21359b4e8d9f .github/workflows/tagbot.py"|sha256sum --check --status + # Make sure the script is unmodified as it runs with write permissions + echo "f525f362a99f13764791185da4d45959a632ef54e3b6b865461dabddb1b1df34 .github/workflows/tagbot.py"|sha256sum --check --status - name: set up Python uses: actions/setup-python@v5 From 2ac4ad42ab03137535f805e62cf886aee5216219 Mon Sep 17 00:00:00 2001 From: =?UTF-8?q?Mikael=20=C3=96hman?= Date: Fri, 1 Nov 2024 13:53:48 +0100 Subject: [PATCH 54/85] Try using conditional workflow based on if tagbot is modified. --- .github/workflows/tagbot.yml | 23 ++++++++++++++++++++--- 1 file changed, 20 insertions(+), 3 deletions(-) diff --git a/.github/workflows/tagbot.yml b/.github/workflows/tagbot.yml index 74434f0d2c48..a1b7f673e1ca 100644 --- a/.github/workflows/tagbot.yml +++ b/.github/workflows/tagbot.yml @@ -11,9 +11,25 @@ jobs: with: fetch-depth: 0 - - run: | - # Make sure the script is unmodified as it runs with write permissions - echo "f525f362a99f13764791185da4d45959a632ef54e3b6b865461dabddb1b1df34 .github/workflows/tagbot.py"|sha256sum --check --status + - name: Check if file has changed + run: | + if git diff --name-only origin/${{ github.event.pull_request.base.ref }}...HEAD | grep -q .github/workflows/tagbot.py; then + echo "tagbot_modified=true" >> $GITHUB_ENV + else + echo "tagbot_modified=false" >> $GITHUB_ENV + fi + + - name: Post warning comment + if: env.file_modified == 'true' + uses: actions/github-script@v7 + with: + script: | + github.rest.issues.createComment({ + issue_number: ${{ github.event.pull_request.number }}, + owner: context.repo.owner, + repo: context.repo.repo, + body: "⚠️ Warning: The tagbot.py file has been modified. Please review changes carefully." + }) - name: set up Python uses: actions/setup-python@v5 @@ -24,6 +40,7 @@ jobs: run: pip install gitpython requests - name: Tag and comment + if: env.tagbot_modified == 'false' env: GH_TOKEN: ${{ secrets.GITHUB_TOKEN }} run: python .github/workflows/tagbot.py From 3aed346a76bf91727ac1db30358eb4a4ef2b5973 Mon Sep 17 00:00:00 2001 From: =?UTF-8?q?Mikael=20=C3=96hman?= Date: Fri, 1 Nov 2024 20:26:34 +0100 Subject: [PATCH 55/85] Add debug printout temporarily --- .github/workflows/tagbot.py | 3 +++ 1 file changed, 3 insertions(+) diff --git a/.github/workflows/tagbot.py b/.github/workflows/tagbot.py index 649dd1dd8285..3c02574468c9 100644 --- a/.github/workflows/tagbot.py +++ b/.github/workflows/tagbot.py @@ -64,6 +64,9 @@ def pr_ecs(pr_diff): with open(event_path) as f: data = json.load(f) +print('env:', os.environ) +print('data:', data) + pr_number = data['pull_request']['number'] print("PR number:", pr_number) From 910b530d0d9039dddeb3f407f41694fd597c8e14 Mon Sep 17 00:00:00 2001 From: =?UTF-8?q?Mikael=20=C3=96hman?= Date: Fri, 1 Nov 2024 20:51:02 +0100 Subject: [PATCH 56/85] Add checkout of PR commit --- .github/workflows/tagbot.yml | 1 + 1 file changed, 1 insertion(+) diff --git a/.github/workflows/tagbot.yml b/.github/workflows/tagbot.yml index a1b7f673e1ca..dd0197456f59 100644 --- a/.github/workflows/tagbot.yml +++ b/.github/workflows/tagbot.yml @@ -9,6 +9,7 @@ jobs: steps: - uses: actions/checkout@v4 with: + ref: "${{ github.event.pull_request.merge_commit_sha }}" fetch-depth: 0 - name: Check if file has changed From 29232d7dd63da65f3bd56de7dc9b631821194daa Mon Sep 17 00:00:00 2001 From: =?UTF-8?q?Mikael=20=C3=96hman?= Date: Fri, 1 Nov 2024 21:17:38 +0100 Subject: [PATCH 57/85] Fix tagbot.py to use merge commit sha when diffing --- .github/workflows/tagbot.py | 10 +++------- 1 file changed, 3 insertions(+), 7 deletions(-) diff --git a/.github/workflows/tagbot.py b/.github/workflows/tagbot.py index 3c02574468c9..e5348382bf77 100644 --- a/.github/workflows/tagbot.py +++ b/.github/workflows/tagbot.py @@ -59,26 +59,22 @@ def pr_ecs(pr_diff): token = os.getenv("GH_TOKEN") repo = os.getenv("GITHUB_REPOSITORY") base_branch_name = os.getenv("GITHUB_BASE_REF") -pr_ref_name = os.getenv("GITHUB_REF_NAME") with open(event_path) as f: data = json.load(f) -print('env:', os.environ) -print('data:', data) - pr_number = data['pull_request']['number'] +merge_commit_sha = data['pull_request']['merge_commit_sha'] print("PR number:", pr_number) print("Repo:", repo) print("Base branch name:", base_branch_name) -print("PR ref:", pr_ref_name) +print("Merge commit ref:", ) gitrepo = git.Repo(".") - target_commit = gitrepo.commit('origin/' + base_branch_name) -pr_commit = gitrepo.commit('pull/' + pr_ref_name) +pr_commit = gitrepo.commit(merge_commit_sha) pr_diff = target_commit.diff(pr_commit) new_ecs, changed_ecs = pr_ecs(pr_diff) From 3572045db84852caef4e2a1ea007b3c3f9052cdc Mon Sep 17 00:00:00 2001 From: =?UTF-8?q?Mikael=20=C3=96hman?= Date: Fri, 1 Nov 2024 21:44:26 +0100 Subject: [PATCH 58/85] Fix typo --- .github/workflows/tagbot.yml | 2 +- 1 file changed, 1 insertion(+), 1 deletion(-) diff --git a/.github/workflows/tagbot.yml b/.github/workflows/tagbot.yml index dd0197456f59..e15a06ba6086 100644 --- a/.github/workflows/tagbot.yml +++ b/.github/workflows/tagbot.yml @@ -21,7 +21,7 @@ jobs: fi - name: Post warning comment - if: env.file_modified == 'true' + if: env.tagbot_modified == 'true' uses: actions/github-script@v7 with: script: | From 61d3f6e56bd9749b5942a33f6dc80868d0e27ee7 Mon Sep 17 00:00:00 2001 From: =?UTF-8?q?Mikael=20=C3=96hman?= Date: Fri, 1 Nov 2024 22:41:19 +0100 Subject: [PATCH 59/85] Fix missing printout in tagbot --- .github/workflows/tagbot.py | 2 +- 1 file changed, 1 insertion(+), 1 deletion(-) diff --git a/.github/workflows/tagbot.py b/.github/workflows/tagbot.py index e5348382bf77..5ab67361e922 100644 --- a/.github/workflows/tagbot.py +++ b/.github/workflows/tagbot.py @@ -69,7 +69,7 @@ def pr_ecs(pr_diff): print("PR number:", pr_number) print("Repo:", repo) print("Base branch name:", base_branch_name) -print("Merge commit ref:", ) +print("Merge commit ref:", merge_commit_sha) gitrepo = git.Repo(".") From 229223c423fec9750f7b32853fbe53980830eede Mon Sep 17 00:00:00 2001 From: =?UTF-8?q?Mikael=20=C3=96hman?= Date: Fri, 1 Nov 2024 23:05:46 +0100 Subject: [PATCH 60/85] Add additional label for workflow changes, to highlight for reviewers --- .github/workflows/tagbot.py | 9 ++++++++- 1 file changed, 8 insertions(+), 1 deletion(-) diff --git a/.github/workflows/tagbot.py b/.github/workflows/tagbot.py index 5ab67361e922..944571d8e459 100644 --- a/.github/workflows/tagbot.py +++ b/.github/workflows/tagbot.py @@ -78,9 +78,11 @@ def pr_ecs(pr_diff): pr_diff = target_commit.diff(pr_commit) new_ecs, changed_ecs = pr_ecs(pr_diff) +modified_workflow = any(item.a_path.startswith('.github/workflows/') for item in pr_diff) print("Changed ECs:", changed_ecs) print("Newly added ECs:", new_ecs) +print("Modified workflow:", modified_workflow) new_software = 0 updated_software = 0 @@ -125,9 +127,14 @@ def pr_ecs(pr_diff): print("Adjusting labels") current_labels = [label['name'] for label in data['pull_request']['labels']] +label_checks = [(changed_ecs, 'change'), + (new_software, 'new'), + (updated_software, 'update'), + (modified_workflow, 'workflow')] + labels_add = [] labels_del = [] -for condition, label in [(changed_ecs, 'change'), (new_software, 'new'), (updated_software, 'update')]: +for condition, label in label_checks: if condition and label not in current_labels: labels_add.append(label) elif not condition and label in current_labels: From 02bfe0a45564d81344b68e903d91831c1905e4e7 Mon Sep 17 00:00:00 2001 From: =?UTF-8?q?Mikael=20=C3=96hman?= Date: Sat, 2 Nov 2024 01:13:17 +0100 Subject: [PATCH 61/85] Rework yml, only run when no merge conflict, fix possible security hole --- .github/workflows/tagbot.py | 17 ++--------------- .github/workflows/tagbot.yml | 29 +++++++---------------------- 2 files changed, 9 insertions(+), 37 deletions(-) diff --git a/.github/workflows/tagbot.py b/.github/workflows/tagbot.py index 944571d8e459..51c181843879 100644 --- a/.github/workflows/tagbot.py +++ b/.github/workflows/tagbot.py @@ -6,7 +6,6 @@ import git import requests import json -import difflib from datetime import datetime from pathlib import Path @@ -31,17 +30,6 @@ def similar_easyconfigs(repo, new_file): return sort_by_added_date(repo, possible_neighbours) -def diff(old, new): - with open(old, 'r') as old_file, open(new, 'r') as new_file: - old_lines = list(old_file) - new_lines = list(new_file) - return ''.join(difflib.unified_diff( - old_lines, - new_lines, - fromfile=str(old), - tofile=str(new))) - - def pr_ecs(pr_diff): new_ecs = [] changed_ecs = [] @@ -67,11 +55,10 @@ def pr_ecs(pr_diff): merge_commit_sha = data['pull_request']['merge_commit_sha'] print("PR number:", pr_number) -print("Repo:", repo) print("Base branch name:", base_branch_name) print("Merge commit ref:", merge_commit_sha) -gitrepo = git.Repo(".") +gitrepo = git.Repo("pr") target_commit = gitrepo.commit('origin/' + base_branch_name) pr_commit = gitrepo.commit(merge_commit_sha) @@ -121,7 +108,7 @@ def pr_ecs(pr_diff): comment += f'Diff against {neighbour.name}\n\n' comment += f'[{neighbour}](https://github.com/{repo}/blob/{base_branch_name}/{neighbour})\n\n' comment += '```diff\n' - comment += diff(neighbour, new_file) + comment += gitrepo.git.diff(f'HEAD:{neighbour}', f'HEAD:{new_file}') comment += '```\n\n\n' print("Adjusting labels") diff --git a/.github/workflows/tagbot.yml b/.github/workflows/tagbot.yml index e15a06ba6086..9aaa8084e6af 100644 --- a/.github/workflows/tagbot.yml +++ b/.github/workflows/tagbot.yml @@ -3,35 +3,21 @@ on: [pull_request_target] jobs: tagbot: + if: github.event.pull_request.merge_commit_sha runs-on: ubuntu-24.04 permissions: pull-requests: write steps: - - uses: actions/checkout@v4 + - name: Checkout base branch for workflow scripts + uses: actions/checkout@v4 + + - name: Checkout PR for computing diff + uses: actions/checkout@v4 with: ref: "${{ github.event.pull_request.merge_commit_sha }}" + path: 'pr' fetch-depth: 0 - - name: Check if file has changed - run: | - if git diff --name-only origin/${{ github.event.pull_request.base.ref }}...HEAD | grep -q .github/workflows/tagbot.py; then - echo "tagbot_modified=true" >> $GITHUB_ENV - else - echo "tagbot_modified=false" >> $GITHUB_ENV - fi - - - name: Post warning comment - if: env.tagbot_modified == 'true' - uses: actions/github-script@v7 - with: - script: | - github.rest.issues.createComment({ - issue_number: ${{ github.event.pull_request.number }}, - owner: context.repo.owner, - repo: context.repo.repo, - body: "⚠️ Warning: The tagbot.py file has been modified. Please review changes carefully." - }) - - name: set up Python uses: actions/setup-python@v5 with: @@ -41,7 +27,6 @@ jobs: run: pip install gitpython requests - name: Tag and comment - if: env.tagbot_modified == 'false' env: GH_TOKEN: ${{ secrets.GITHUB_TOKEN }} run: python .github/workflows/tagbot.py From f8180eacaef082a134383ca5856fe094b7fdf8ad Mon Sep 17 00:00:00 2001 From: =?UTF-8?q?Mikael=20=C3=96hman?= Date: Sat, 2 Nov 2024 01:45:07 +0100 Subject: [PATCH 62/85] Add target commit sha for debuggin --- .github/workflows/tagbot.py | 1 + 1 file changed, 1 insertion(+) diff --git a/.github/workflows/tagbot.py b/.github/workflows/tagbot.py index 51c181843879..4d4defbaaf29 100644 --- a/.github/workflows/tagbot.py +++ b/.github/workflows/tagbot.py @@ -61,6 +61,7 @@ def pr_ecs(pr_diff): gitrepo = git.Repo("pr") target_commit = gitrepo.commit('origin/' + base_branch_name) +print("Target commit ref:", target_commit) pr_commit = gitrepo.commit(merge_commit_sha) pr_diff = target_commit.diff(pr_commit) From 8668891865975619ba074e290564a6f1fb078ecf Mon Sep 17 00:00:00 2001 From: =?UTF-8?q?Mikael=20=C3=96hman?= Date: Sat, 2 Nov 2024 01:50:48 +0100 Subject: [PATCH 63/85] Print out github event data for debugging --- .github/workflows/tagbot.py | 1 + 1 file changed, 1 insertion(+) diff --git a/.github/workflows/tagbot.py b/.github/workflows/tagbot.py index 4d4defbaaf29..ff77576bd090 100644 --- a/.github/workflows/tagbot.py +++ b/.github/workflows/tagbot.py @@ -51,6 +51,7 @@ def pr_ecs(pr_diff): with open(event_path) as f: data = json.load(f) +print(data) pr_number = data['pull_request']['number'] merge_commit_sha = data['pull_request']['merge_commit_sha'] From b2fb3c9417c6cad5e1628b57c8870935d5d32e40 Mon Sep 17 00:00:00 2001 From: =?UTF-8?q?Mikael=20=C3=96hman?= Date: Sun, 3 Nov 2024 21:11:05 +0100 Subject: [PATCH 64/85] Switch to manually attempting merge due to github race condition with pull_request_target --- .github/workflows/tagbot.py | 23 ++++++++++++----------- .github/workflows/tagbot.yml | 17 +++++++++++++++-- 2 files changed, 27 insertions(+), 13 deletions(-) diff --git a/.github/workflows/tagbot.py b/.github/workflows/tagbot.py index ff77576bd090..937b5b863138 100644 --- a/.github/workflows/tagbot.py +++ b/.github/workflows/tagbot.py @@ -15,8 +15,7 @@ def get_first_commit_date(repo, file_path): if commits: return commits[-1].committed_date else: - print(f"{file_path} has no commit info, putting it last") - return datetime.datetime.min + raise ValueError(f'{file_path} has no commit info, this should not happen') def sort_by_added_date(repo, file_paths): @@ -43,28 +42,30 @@ def pr_ecs(pr_diff): GITHUB_API_URL = 'https://api.github.com' -event_path = os.getenv("GITHUB_EVENT_PATH") -token = os.getenv("GH_TOKEN") -repo = os.getenv("GITHUB_REPOSITORY") -base_branch_name = os.getenv("GITHUB_BASE_REF") +event_path = os.getenv('GITHUB_EVENT_PATH') +token = os.getenv('GH_TOKEN') +repo = os.getenv('GITHUB_REPOSITORY') +base_branch_name = os.getenv('GITHUB_BASE_REF') with open(event_path) as f: data = json.load(f) print(data) pr_number = data['pull_request']['number'] -merge_commit_sha = data['pull_request']['merge_commit_sha'] +# Can't rely on merge_commit_sha for pull_request_target as it might be outdated +# merge_commit_sha = data['pull_request']['merge_commit_sha'] print("PR number:", pr_number) print("Base branch name:", base_branch_name) -print("Merge commit ref:", merge_commit_sha) -gitrepo = git.Repo("pr") +# Change into "pr" checkout directory to allow diffs and glob to work on the same content +os.chdir('pr') +gitrepo = git.Repo('.') target_commit = gitrepo.commit('origin/' + base_branch_name) print("Target commit ref:", target_commit) -pr_commit = gitrepo.commit(merge_commit_sha) -pr_diff = target_commit.diff(pr_commit) +merge_commit = gitrepo.head.commit +pr_diff = target_commit.diff(merge_commit) new_ecs, changed_ecs = pr_ecs(pr_diff) modified_workflow = any(item.a_path.startswith('.github/workflows/') for item in pr_diff) diff --git a/.github/workflows/tagbot.yml b/.github/workflows/tagbot.yml index 9aaa8084e6af..9001819d04f8 100644 --- a/.github/workflows/tagbot.yml +++ b/.github/workflows/tagbot.yml @@ -3,7 +3,8 @@ on: [pull_request_target] jobs: tagbot: - if: github.event.pull_request.merge_commit_sha + # Note: can't rely on github.event.pull_request.merge_commit_sha because pull_request_target + # does not wait github mergability check, and the value is outdated. runs-on: ubuntu-24.04 permissions: pull-requests: write @@ -14,9 +15,21 @@ jobs: - name: Checkout PR for computing diff uses: actions/checkout@v4 with: - ref: "${{ github.event.pull_request.merge_commit_sha }}" + ref: "${{ github.event.pull_request.head.sha }}" path: 'pr' fetch-depth: 0 + + - name: Attempt Merge + id: merge + run: | + git merge --no-commit --no-ff origin/${{ github.event.pull_request.base.ref }} + continue-on-error: true + + - name: Check merge result + if: steps.merge.outcome == 'failure' + run: | + echo "Merge conflict detected, failing job." + exit 1 - name: set up Python uses: actions/setup-python@v5 From 9772d1416c959c1a5ed2071791a50ffc04ec0689 Mon Sep 17 00:00:00 2001 From: =?UTF-8?q?Mikael=20=C3=96hman?= Date: Sun, 3 Nov 2024 21:31:18 +0100 Subject: [PATCH 65/85] Add concurrency to prevent conflicting tags/comments --- .github/workflows/tagbot.yml | 4 ++++ 1 file changed, 4 insertions(+) diff --git a/.github/workflows/tagbot.yml b/.github/workflows/tagbot.yml index 9001819d04f8..d47eb812c220 100644 --- a/.github/workflows/tagbot.yml +++ b/.github/workflows/tagbot.yml @@ -1,6 +1,10 @@ name: Tagbot on: [pull_request_target] +concurrency: + group: ${{ github.workflow }}-${{ github.ref }} + cancel-in-progress: true + jobs: tagbot: # Note: can't rely on github.event.pull_request.merge_commit_sha because pull_request_target From baaa8ba5b5e6b44556909e46f4123961074380be Mon Sep 17 00:00:00 2001 From: =?UTF-8?q?Mikael=20=C3=96hman?= Date: Sun, 3 Nov 2024 21:35:17 +0100 Subject: [PATCH 66/85] Remove unsused import --- .github/workflows/tagbot.py | 1 - 1 file changed, 1 deletion(-) diff --git a/.github/workflows/tagbot.py b/.github/workflows/tagbot.py index 937b5b863138..e16f10c2411f 100644 --- a/.github/workflows/tagbot.py +++ b/.github/workflows/tagbot.py @@ -6,7 +6,6 @@ import git import requests import json -from datetime import datetime from pathlib import Path From 58debaac6d668361d92296301a30425473a7c3b9 Mon Sep 17 00:00:00 2001 From: =?UTF-8?q?Mikael=20=C3=96hman?= Date: Sun, 3 Nov 2024 21:46:01 +0100 Subject: [PATCH 67/85] Add quotes around concurrency group --- .github/workflows/tagbot.yml | 2 +- 1 file changed, 1 insertion(+), 1 deletion(-) diff --git a/.github/workflows/tagbot.yml b/.github/workflows/tagbot.yml index d47eb812c220..7b7184e3415c 100644 --- a/.github/workflows/tagbot.yml +++ b/.github/workflows/tagbot.yml @@ -2,7 +2,7 @@ name: Tagbot on: [pull_request_target] concurrency: - group: ${{ github.workflow }}-${{ github.ref }} + group: "${{ github.workflow }}-${{ github.ref }}" cancel-in-progress: true jobs: From 16ac316aafebef4b6da77c366b7a1f317dc046b4 Mon Sep 17 00:00:00 2001 From: =?UTF-8?q?Mikael=20=C3=96hman?= Date: Sun, 3 Nov 2024 21:50:56 +0100 Subject: [PATCH 68/85] Fix indentation --- .github/workflows/tagbot.yml | 22 +++++++++++----------- 1 file changed, 11 insertions(+), 11 deletions(-) diff --git a/.github/workflows/tagbot.yml b/.github/workflows/tagbot.yml index 7b7184e3415c..c7b929a10daa 100644 --- a/.github/workflows/tagbot.yml +++ b/.github/workflows/tagbot.yml @@ -23,17 +23,17 @@ jobs: path: 'pr' fetch-depth: 0 - - name: Attempt Merge - id: merge - run: | - git merge --no-commit --no-ff origin/${{ github.event.pull_request.base.ref }} - continue-on-error: true - - - name: Check merge result - if: steps.merge.outcome == 'failure' - run: | - echo "Merge conflict detected, failing job." - exit 1 + - name: Attempt Merge + id: merge + run: | + git merge --no-commit --no-ff origin/${{ github.event.pull_request.base.ref }} + continue-on-error: true + + - name: Check merge result + if: steps.merge.outcome == 'failure' + run: | + echo "Merge conflict detected, failing job." + exit 1 - name: set up Python uses: actions/setup-python@v5 From b0f49b92cd5a0e306ef5f9924340a89d9e4c7c45 Mon Sep 17 00:00:00 2001 From: =?UTF-8?q?Mikael=20=C3=96hman?= Date: Sun, 3 Nov 2024 22:33:44 +0100 Subject: [PATCH 69/85] Make steps more explicit, perform merge in pr subdir --- .github/workflows/tagbot.yml | 5 +++-- 1 file changed, 3 insertions(+), 2 deletions(-) diff --git a/.github/workflows/tagbot.yml b/.github/workflows/tagbot.yml index c7b929a10daa..9aacbf0df08c 100644 --- a/.github/workflows/tagbot.yml +++ b/.github/workflows/tagbot.yml @@ -16,7 +16,7 @@ jobs: - name: Checkout base branch for workflow scripts uses: actions/checkout@v4 - - name: Checkout PR for computing diff + - name: Checkout PR for computing diff into "pr" subdirectory uses: actions/checkout@v4 with: ref: "${{ github.event.pull_request.head.sha }}" @@ -26,10 +26,11 @@ jobs: - name: Attempt Merge id: merge run: | + cd pr git merge --no-commit --no-ff origin/${{ github.event.pull_request.base.ref }} continue-on-error: true - - name: Check merge result + - name: Abort if merge failed if: steps.merge.outcome == 'failure' run: | echo "Merge conflict detected, failing job." From 51dd49e48c290a937e9ce72b7042a74c6c472e8e Mon Sep 17 00:00:00 2001 From: =?UTF-8?q?Mikael=20=C3=96hman?= Date: Sun, 3 Nov 2024 23:52:14 +0100 Subject: [PATCH 70/85] Add missing linebreak on code blocks --- .github/workflows/tagbot.py | 2 +- 1 file changed, 1 insertion(+), 1 deletion(-) diff --git a/.github/workflows/tagbot.py b/.github/workflows/tagbot.py index e16f10c2411f..a46ae810cfe3 100644 --- a/.github/workflows/tagbot.py +++ b/.github/workflows/tagbot.py @@ -111,7 +111,7 @@ def pr_ecs(pr_diff): comment += f'[{neighbour}](https://github.com/{repo}/blob/{base_branch_name}/{neighbour})\n\n' comment += '```diff\n' comment += gitrepo.git.diff(f'HEAD:{neighbour}', f'HEAD:{new_file}') - comment += '```\n\n\n' + comment += '\n```\n\n\n' print("Adjusting labels") current_labels = [label['name'] for label in data['pull_request']['labels']] From e9f42feb6da37054cbf16645f7f33337d51c7dc5 Mon Sep 17 00:00:00 2001 From: =?UTF-8?q?Mikael=20=C3=96hman?= Date: Sun, 3 Nov 2024 23:55:40 +0100 Subject: [PATCH 71/85] Make stdoutput nicer, display merge commit sha --- .github/workflows/tagbot.py | 6 ++++-- 1 file changed, 4 insertions(+), 2 deletions(-) diff --git a/.github/workflows/tagbot.py b/.github/workflows/tagbot.py index a46ae810cfe3..792f457c1978 100644 --- a/.github/workflows/tagbot.py +++ b/.github/workflows/tagbot.py @@ -64,13 +64,15 @@ def pr_ecs(pr_diff): target_commit = gitrepo.commit('origin/' + base_branch_name) print("Target commit ref:", target_commit) merge_commit = gitrepo.head.commit +print("Merge commit:", merge_commit) pr_diff = target_commit.diff(merge_commit) new_ecs, changed_ecs = pr_ecs(pr_diff) modified_workflow = any(item.a_path.startswith('.github/workflows/') for item in pr_diff) -print("Changed ECs:", changed_ecs) -print("Newly added ECs:", new_ecs) + +print("Changed ECs:", ', '.join(changed_ecs)) +print("Newly added ECs:", ', '.join(new_ecs)) print("Modified workflow:", modified_workflow) new_software = 0 From 40ca1dd72732a0257d3d9d3692f571dbd186a284 Mon Sep 17 00:00:00 2001 From: =?UTF-8?q?Mikael=20=C3=96hman?= Date: Mon, 4 Nov 2024 00:04:01 +0100 Subject: [PATCH 72/85] Add git name/email for temporary merge test --- .github/workflows/tagbot.yml | 7 +++++-- 1 file changed, 5 insertions(+), 2 deletions(-) diff --git a/.github/workflows/tagbot.yml b/.github/workflows/tagbot.yml index 9aacbf0df08c..e14752f1f860 100644 --- a/.github/workflows/tagbot.yml +++ b/.github/workflows/tagbot.yml @@ -9,6 +9,7 @@ jobs: tagbot: # Note: can't rely on github.event.pull_request.merge_commit_sha because pull_request_target # does not wait github mergability check, and the value is outdated. + # Instead we merge manually in a temporary subdir "pr" runs-on: ubuntu-24.04 permissions: pull-requests: write @@ -23,12 +24,14 @@ jobs: path: 'pr' fetch-depth: 0 - - name: Attempt Merge + - name: Attempt test merge id: merge run: | - cd pr + git config user.name "github-workflow" + git config user.email "github-workflow@github.com" git merge --no-commit --no-ff origin/${{ github.event.pull_request.base.ref }} continue-on-error: true + working-directory: pr - name: Abort if merge failed if: steps.merge.outcome == 'failure' From 4c021b4a719ae9fc961bc347f962c8243d17e4f3 Mon Sep 17 00:00:00 2001 From: =?UTF-8?q?Mikael=20=C3=96hman?= Date: Mon, 4 Nov 2024 00:14:30 +0100 Subject: [PATCH 73/85] Fix string conversion for printout --- .github/workflows/tagbot.py | 4 ++-- 1 file changed, 2 insertions(+), 2 deletions(-) diff --git a/.github/workflows/tagbot.py b/.github/workflows/tagbot.py index 792f457c1978..d9a16320aa5d 100644 --- a/.github/workflows/tagbot.py +++ b/.github/workflows/tagbot.py @@ -71,8 +71,8 @@ def pr_ecs(pr_diff): modified_workflow = any(item.a_path.startswith('.github/workflows/') for item in pr_diff) -print("Changed ECs:", ', '.join(changed_ecs)) -print("Newly added ECs:", ', '.join(new_ecs)) +print("Changed ECs:", ', '.join(str(p) for p in changed_ecs)) +print("Newly added ECs:", ', '.join(str(p) for p in new_ecs)) print("Modified workflow:", modified_workflow) new_software = 0 From 0318112770a7c65e9c085869936f8b9a3140886e Mon Sep 17 00:00:00 2001 From: =?UTF-8?q?Mikael=20=C3=96hman?= Date: Mon, 4 Nov 2024 02:01:05 +0100 Subject: [PATCH 74/85] Drop very verbose debug output of event data --- .github/workflows/tagbot.py | 1 - 1 file changed, 1 deletion(-) diff --git a/.github/workflows/tagbot.py b/.github/workflows/tagbot.py index d9a16320aa5d..26472f8bcbd3 100644 --- a/.github/workflows/tagbot.py +++ b/.github/workflows/tagbot.py @@ -49,7 +49,6 @@ def pr_ecs(pr_diff): with open(event_path) as f: data = json.load(f) -print(data) pr_number = data['pull_request']['number'] # Can't rely on merge_commit_sha for pull_request_target as it might be outdated # merge_commit_sha = data['pull_request']['merge_commit_sha'] From 3b69ab8fd9339e354d595ebe0cccb50666352bc4 Mon Sep 17 00:00:00 2001 From: =?UTF-8?q?Petr=20Kr=C3=A1l?= Date: Mon, 4 Nov 2024 11:35:33 +0100 Subject: [PATCH 75/85] adding easyconfigs: Stacks-2.68-foss-2023a.eb --- .../s/Stacks/Stacks-2.68-foss-2023a.eb | 29 +++++++++++++++++++ 1 file changed, 29 insertions(+) create mode 100644 easybuild/easyconfigs/s/Stacks/Stacks-2.68-foss-2023a.eb diff --git a/easybuild/easyconfigs/s/Stacks/Stacks-2.68-foss-2023a.eb b/easybuild/easyconfigs/s/Stacks/Stacks-2.68-foss-2023a.eb new file mode 100644 index 000000000000..f5c8c3b976d4 --- /dev/null +++ b/easybuild/easyconfigs/s/Stacks/Stacks-2.68-foss-2023a.eb @@ -0,0 +1,29 @@ +easyblock = 'ConfigureMake' + +name = 'Stacks' +version = '2.68' + +homepage = 'https://catchenlab.life.illinois.edu/stacks/' +description = """Stacks is a software pipeline for building loci from short-read sequences, such as those generated on + the Illumina platform. Stacks was developed to work with restriction enzyme-based data, such as RAD-seq, + for the purpose of building genetic maps and conducting population genomics and phylogeography. +""" + +toolchain = {'name': 'foss', 'version': '2023a'} + +source_urls = ['https://catchenlab.life.illinois.edu/stacks/source/'] +sources = [SOURCELOWER_TAR_GZ] +checksums = ['9dc51ea356d60eb4557b0b2d1a8854aafae492aed87f974e0249cc09aa5e7650'] + +dependencies = [ + ('zlib', '1.2.13'), +] + +sanity_check_paths = { + 'files': ['bin/clone_filter', 'bin/cstacks', 'bin/gstacks', 'bin/kmer_filter', 'bin/phasedstacks', + 'bin/populations', 'bin/process_radtags', 'bin/process_shortreads', 'bin/sstacks', + 'bin/tsv2bam', 'bin/ustacks'], + 'dirs': [], +} + +moduleclass = 'bio' From 3d955bff8243eddcd001344b23cef789e7f676c5 Mon Sep 17 00:00:00 2001 From: =?UTF-8?q?Petr=20Kr=C3=A1l?= Date: Mon, 4 Nov 2024 12:09:58 +0100 Subject: [PATCH 76/85] adding easyconfigs: mosdepth-0.3.9-GCC-12.3.0.eb, Nim-2.2.0-GCCcore-12.3.0.eb --- .../m/mosdepth/mosdepth-0.3.9-GCC-12.3.0.eb | 48 +++++++++++++++++++ .../n/Nim/Nim-2.2.0-GCCcore-12.3.0.eb | 17 +++++++ 2 files changed, 65 insertions(+) create mode 100644 easybuild/easyconfigs/m/mosdepth/mosdepth-0.3.9-GCC-12.3.0.eb create mode 100644 easybuild/easyconfigs/n/Nim/Nim-2.2.0-GCCcore-12.3.0.eb diff --git a/easybuild/easyconfigs/m/mosdepth/mosdepth-0.3.9-GCC-12.3.0.eb b/easybuild/easyconfigs/m/mosdepth/mosdepth-0.3.9-GCC-12.3.0.eb new file mode 100644 index 000000000000..8fcad4de92bd --- /dev/null +++ b/easybuild/easyconfigs/m/mosdepth/mosdepth-0.3.9-GCC-12.3.0.eb @@ -0,0 +1,48 @@ +easyblock = 'Binary' + +name = 'mosdepth' +version = '0.3.9' +local_hts_nim_ver = '0.3.25' + +homepage = 'https://github.com/brentp/mosdepth' +description = "Fast BAM/CRAM depth calculation for WGS, exome, or targeted sequencing" + +toolchain = {'name': 'GCC', 'version': '12.3.0'} + +sources = [ + { + 'source_urls': ['https://github.com/brentp/hts-nim/archive/'], + 'download_filename': 'v%s.tar.gz' % local_hts_nim_ver, + 'filename': 'hts-nim-%s.tar.gz' % local_hts_nim_ver, + }, + { + 'source_urls': ['https://github.com/brentp/mosdepth/archive/'], + 'download_filename': 'v%(version)s.tar.gz', + 'filename': SOURCE_TAR_GZ, + }, +] +checksums = [ + {'hts-nim-0.3.25.tar.gz': 'b13b9bb5aa567a69bf17547aadbbd39e37beb4f71a28f267b83dfea9ea4d05e8'}, + {'mosdepth-0.3.9.tar.gz': '9171ea9a6ddaccd0091db5b85fa9e6cb79516bbe005c47ffc8dcfe49c978eb69'}, +] + +dependencies = [ + ('Nim', '2.2.0'), + ('HTSlib', '1.18'), + ('PCRE', '8.45'), +] + +extract_sources = True + +install_cmd = "cd %(builddir)s/hts-nim-*/ && nimble install --nimbleDir:%(installdir)s --verbose -y && " +install_cmd += "cd ../mosdepth-*/ && " +install_cmd += "nimble install --nimbleDir:%(installdir)s --verbose -y" + +sanity_check_paths = { + 'files': ['bin/mosdepth'], + 'dirs': [], +} + +sanity_check_commands = ["mosdepth --help"] + +moduleclass = 'bio' diff --git a/easybuild/easyconfigs/n/Nim/Nim-2.2.0-GCCcore-12.3.0.eb b/easybuild/easyconfigs/n/Nim/Nim-2.2.0-GCCcore-12.3.0.eb new file mode 100644 index 000000000000..2214b1c94930 --- /dev/null +++ b/easybuild/easyconfigs/n/Nim/Nim-2.2.0-GCCcore-12.3.0.eb @@ -0,0 +1,17 @@ +name = 'Nim' +version = '2.2.0' + +homepage = 'https://nim-lang.org/' +description = "Nim is a systems and applications programming language." + +toolchain = {'name': 'GCCcore', 'version': '12.3.0'} + +source_urls = ['https://nim-lang.org/download/'] +sources = [SOURCELOWER_TAR_XZ] +checksums = ['ce9842849c9760e487ecdd1cdadf7c0f2844cafae605401c7c72ae257644893c'] + +builddependencies = [('binutils', '2.40')] + +dependencies = [('libreadline', '8.2')] + +moduleclass = 'lang' From cbb32e4b28f652c86f636f62f110e60b35ab6864 Mon Sep 17 00:00:00 2001 From: Alex Domingo Date: Mon, 4 Nov 2024 14:05:43 +0100 Subject: [PATCH 77/85] use upstream name for dask_ml extension in Dask-ML-2024.4.4-foss-2023a.eb --- .../easyconfigs/d/Dask-ML/Dask-ML-2024.4.4-foss-2023a.eb | 4 +--- 1 file changed, 1 insertion(+), 3 deletions(-) diff --git a/easybuild/easyconfigs/d/Dask-ML/Dask-ML-2024.4.4-foss-2023a.eb b/easybuild/easyconfigs/d/Dask-ML/Dask-ML-2024.4.4-foss-2023a.eb index fd593a4bb094..f4bdf4425aee 100644 --- a/easybuild/easyconfigs/d/Dask-ML/Dask-ML-2024.4.4-foss-2023a.eb +++ b/easybuild/easyconfigs/d/Dask-ML/Dask-ML-2024.4.4-foss-2023a.eb @@ -42,9 +42,7 @@ exts_list = [ ('packaging', '24.1', { 'checksums': ['026ed72c8ed3fcce5bf8950572258698927fd1dbda10a5e981cdf0ac37f4f002'], }), - (name, version, { - 'modulename': 'dask_ml', - 'sources': ['dask_ml-%(version)s.tar.gz'], + ('dask_ml', version, { 'checksums': ['7956910a49e1e31944280fdb311adf245da11ef410d67deb7a05c67c7d0c4498'], }), ] From 35c11c91b108a892372f64dc7b60392312f21cae Mon Sep 17 00:00:00 2001 From: Pavel Tomanek Date: Tue, 5 Nov 2024 14:45:57 +0100 Subject: [PATCH 78/85] adding easyconfigs: Porechop-0.2.4-20240119-GCCcore-12.3.0.eb --- .../Porechop-0.2.4-20240119-GCCcore-12.3.0.eb | 28 +++++++++++++++++++ 1 file changed, 28 insertions(+) create mode 100644 easybuild/easyconfigs/p/Porechop/Porechop-0.2.4-20240119-GCCcore-12.3.0.eb diff --git a/easybuild/easyconfigs/p/Porechop/Porechop-0.2.4-20240119-GCCcore-12.3.0.eb b/easybuild/easyconfigs/p/Porechop/Porechop-0.2.4-20240119-GCCcore-12.3.0.eb new file mode 100644 index 000000000000..e1dfa5d567c0 --- /dev/null +++ b/easybuild/easyconfigs/p/Porechop/Porechop-0.2.4-20240119-GCCcore-12.3.0.eb @@ -0,0 +1,28 @@ +easyblock = 'PythonPackage' + +name = 'Porechop' +version = '0.2.4-20240119' +local_commit = 'd2e77c6' + +homepage = 'https://github.com/dehui333/Porechop' +description = """Porechop is a tool for finding and removing adapters from Oxford Nanopore reads. + Adapters on the ends of reads are trimmed off, and when a read has an adapter in its middle, + it is treated as chimeric and chopped into separate reads. Porechop performs thorough alignments + to effectively find adapters, even at low sequence identity.""" + +toolchain = {'name': 'GCCcore', 'version': '12.3.0'} + +source_urls = ['https://github.com/dehui333/Porechop/archive/'] +sources = [{'download_filename': '%s.tar.gz' % local_commit, 'filename': SOURCE_TAR_GZ}] +checksums = ['6e5ff3a780fc2855b0101b4a6102437d9a0fc201e40ffabc44c0c67d7c9ad621'] + +builddependencies = [('binutils', '2.40')] +dependencies = [('Python', '3.11.3')] + +sanity_pip_check = True +use_pip = True +download_dep_fail = True + +sanity_check_commands = ['%(namelower)s -h'] + +moduleclass = 'bio' From d44547734a443238653d586db01553b1edf0f38c Mon Sep 17 00:00:00 2001 From: Balazs Hajgato Date: Tue, 5 Nov 2024 15:36:01 +0100 Subject: [PATCH 79/85] simplifying and add description --- .../o/OpenBLAS/OpenBLAS-0.3.27-GCC-13.2.0-seq-iface64.eb | 9 +++++++-- 1 file changed, 7 insertions(+), 2 deletions(-) diff --git a/easybuild/easyconfigs/o/OpenBLAS/OpenBLAS-0.3.27-GCC-13.2.0-seq-iface64.eb b/easybuild/easyconfigs/o/OpenBLAS/OpenBLAS-0.3.27-GCC-13.2.0-seq-iface64.eb index 8b0c54b42482..f205e063da91 100644 --- a/easybuild/easyconfigs/o/OpenBLAS/OpenBLAS-0.3.27-GCC-13.2.0-seq-iface64.eb +++ b/easybuild/easyconfigs/o/OpenBLAS/OpenBLAS-0.3.27-GCC-13.2.0-seq-iface64.eb @@ -42,9 +42,14 @@ builddependencies = [ ('Python', '3.11.5'), ] +# INTERFACE64=1 needs if you link OpenBLAS for fortran code compied with 64 bit integers (-i8) +# This would be in intel library naming convention ilp64 +# The USE_OPENMP=0 and USE_THREAD=0 needs for the single threaded version +# The USE_LOCKING=1 needs for thread safe version (if threaded software calls OpenBLAS, without it +# OpenBLAS is not thread safe (so only single threaded software would be able to use it) buildopts = "INTERFACE64=1 USE_OPENMP=0 USE_THREAD=0 USE_LOCKING=1 " -testopts = "INTERFACE64=1 USE_OPENMP=0 USE_THREAD=0 USE_LOCKING=1 " -installopts = "INTERFACE64=1 USE_OPENMP=0 USE_THREAD=0 USE_LOCKING=1 " +testopts = buildopts +installopts = buildopts run_lapack_tests = True max_failing_lapack_tests_num_errors = 150 From ca81bd89d82cb032dc3723f64313360e063f96fd Mon Sep 17 00:00:00 2001 From: ocaisa Date: Tue, 5 Nov 2024 19:51:18 +0100 Subject: [PATCH 80/85] Update .github/workflows/tagbot.yml --- .github/workflows/tagbot.yml | 2 +- 1 file changed, 1 insertion(+), 1 deletion(-) diff --git a/.github/workflows/tagbot.yml b/.github/workflows/tagbot.yml index e14752f1f860..6a518cbe03d0 100644 --- a/.github/workflows/tagbot.yml +++ b/.github/workflows/tagbot.yml @@ -8,7 +8,7 @@ concurrency: jobs: tagbot: # Note: can't rely on github.event.pull_request.merge_commit_sha because pull_request_target - # does not wait github mergability check, and the value is outdated. + # does not wait for github mergability check, and the value is outdated. # Instead we merge manually in a temporary subdir "pr" runs-on: ubuntu-24.04 permissions: From aaa25360d0ea1e4f47af2ea7736b72b6d07e1c9e Mon Sep 17 00:00:00 2001 From: Balazs Hajgato Date: Wed, 6 Nov 2024 15:26:20 +0100 Subject: [PATCH 81/85] {numlib}[GCC-13.3.0] OpenBLAS 0.3.27 sequential with 64 bit interface --- .../OpenBLAS-0.3.27-GCC-13.3.0-seq-iface64.eb | 60 +++++++++++++++++++ 1 file changed, 60 insertions(+) create mode 100644 easybuild/easyconfigs/o/OpenBLAS/OpenBLAS-0.3.27-GCC-13.3.0-seq-iface64.eb diff --git a/easybuild/easyconfigs/o/OpenBLAS/OpenBLAS-0.3.27-GCC-13.3.0-seq-iface64.eb b/easybuild/easyconfigs/o/OpenBLAS/OpenBLAS-0.3.27-GCC-13.3.0-seq-iface64.eb new file mode 100644 index 000000000000..5527c667f663 --- /dev/null +++ b/easybuild/easyconfigs/o/OpenBLAS/OpenBLAS-0.3.27-GCC-13.3.0-seq-iface64.eb @@ -0,0 +1,60 @@ +name = 'OpenBLAS' +version = '0.3.27' +versionsuffix = '-seq-iface64' + +homepage = 'https://www.openblas.net/' +description = "OpenBLAS is an optimized BLAS library based on GotoBLAS2 1.13 BSD version." + +toolchain = {'name': 'GCC', 'version': '13.3.0'} + +source_urls = [ + # order matters, trying to download the large.tgz/timing.tgz LAPACK tarballs from GitHub causes trouble + 'https://www.netlib.org/lapack/timing/', + 'https://github.com/xianyi/OpenBLAS/archive/', +] +sources = ['v%(version)s.tar.gz'] +patches = [ + ('large.tgz', '.'), + ('timing.tgz', '.'), + 'OpenBLAS-0.3.15_workaround-gcc-miscompilation.patch', + 'OpenBLAS-0.3.21_fix-order-vectorization.patch', + 'OpenBLAS-0.3.26_lapack_qr_noninittest.patch', + 'OpenBLAS-0.3.27_fix_zscal.patch', + 'OpenBLAS-0.3.27_riscv-drop-static-fortran-flag.patch', +] +checksums = [ + {'v0.3.27.tar.gz': 'aa2d68b1564fe2b13bc292672608e9cdeeeb6dc34995512e65c3b10f4599e897'}, + {'large.tgz': 'f328d88b7fa97722f271d7d0cfea1c220e0f8e5ed5ff01d8ef1eb51d6f4243a1'}, + {'timing.tgz': '999c65f8ea8bd4eac7f1c7f3463d4946917afd20a997807300fe35d70122f3af'}, + {'OpenBLAS-0.3.15_workaround-gcc-miscompilation.patch': + 'e6b326fb8c4a8a6fd07741d9983c37a72c55c9ff9a4f74a80e1352ce5f975971'}, + {'OpenBLAS-0.3.21_fix-order-vectorization.patch': + '08af834e5d60441fd35c128758ed9c092ba6887c829e0471ecd489079539047d'}, + {'OpenBLAS-0.3.26_lapack_qr_noninittest.patch': '4781bf1d7b239374fd8069e15b4e2c0ef0e8efaa1a7d4c33557bd5b27e5de77c'}, + {'OpenBLAS-0.3.27_fix_zscal.patch': '9210d7b66538dabaddbe1bfceb16f8225708856f60876ca5561b19d3599f9fd1'}, + {'OpenBLAS-0.3.27_riscv-drop-static-fortran-flag.patch': + 'f374e41efffd592ab1c9034df9e7abf1045ed151f4fc0fd0da618ce9826f2d4b'}, +] + +builddependencies = [ + ('make', '4.4.1'), + # required by LAPACK test suite + ('Python', '3.12.3'), +] + +# INTERFACE64=1 needs if you link OpenBLAS for fortran code compied with 64 bit integers (-i8) +# This would be in intel library naming convention ilp64 +# The USE_OPENMP=0 and USE_THREAD=0 needs for the single threaded version +# The USE_LOCKING=1 needs for thread safe version (if threaded software calls OpenBLAS, without it +# OpenBLAS is not thread safe (so only single threaded software would be able to use it) +buildopts = "INTERFACE64=1 USE_OPENMP=0 USE_THREAD=0 USE_LOCKING=1 " +testopts = buildopts +installopts = buildopts + +run_lapack_tests = True +max_failing_lapack_tests_num_errors = 150 + +# extensive testing can be enabled by uncommenting the line below +# runtest = 'PATH=.:$PATH lapack-timing' + +moduleclass = 'numlib' From 628a7ebd15550dba4d76f51e2ba83899b23fe639 Mon Sep 17 00:00:00 2001 From: =?UTF-8?q?Mikael=20=C3=96hman?= Date: Wed, 6 Nov 2024 15:48:25 +0100 Subject: [PATCH 82/85] Fix tagbot concurrency group Can't use github.ref when using pull_request_target, since that value also points to base ref. --- .github/workflows/tagbot.yml | 2 +- 1 file changed, 1 insertion(+), 1 deletion(-) diff --git a/.github/workflows/tagbot.yml b/.github/workflows/tagbot.yml index 6a518cbe03d0..811599999fd9 100644 --- a/.github/workflows/tagbot.yml +++ b/.github/workflows/tagbot.yml @@ -2,7 +2,7 @@ name: Tagbot on: [pull_request_target] concurrency: - group: "${{ github.workflow }}-${{ github.ref }}" + group: "${{ github.workflow }}-${{ github.event.pull_request.number }}" cancel-in-progress: true jobs: From 219e64c2fc8d572424b6c77defe472ef6671037c Mon Sep 17 00:00:00 2001 From: =?UTF-8?q?Mikael=20=C3=96hman?= Date: Wed, 6 Nov 2024 17:22:04 +0100 Subject: [PATCH 83/85] Actually perform temporary merge in checkout to determine PR changes --- .github/workflows/tagbot.yml | 2 +- 1 file changed, 1 insertion(+), 1 deletion(-) diff --git a/.github/workflows/tagbot.yml b/.github/workflows/tagbot.yml index 6a518cbe03d0..958a776d46ad 100644 --- a/.github/workflows/tagbot.yml +++ b/.github/workflows/tagbot.yml @@ -29,7 +29,7 @@ jobs: run: | git config user.name "github-workflow" git config user.email "github-workflow@github.com" - git merge --no-commit --no-ff origin/${{ github.event.pull_request.base.ref }} + git merge --no-edit --no-ff origin/${{ github.event.pull_request.base.ref }} continue-on-error: true working-directory: pr From 3e35d8a5c170dedfdd24f6825f1c9537a08b5bf8 Mon Sep 17 00:00:00 2001 From: Jakob Schiotz Date: Wed, 6 Nov 2024 18:20:41 +0100 Subject: [PATCH 84/85] Update libvdwxc webpage as old URL has been taken over by evildoers. --- easybuild/easyconfigs/l/libvdwxc/libvdwxc-0.3.2-foss-2018b.eb | 2 +- easybuild/easyconfigs/l/libvdwxc/libvdwxc-0.4.0-foss-2019a.eb | 2 +- 2 files changed, 2 insertions(+), 2 deletions(-) diff --git a/easybuild/easyconfigs/l/libvdwxc/libvdwxc-0.3.2-foss-2018b.eb b/easybuild/easyconfigs/l/libvdwxc/libvdwxc-0.3.2-foss-2018b.eb index df2d4d407fea..411ee1867d80 100644 --- a/easybuild/easyconfigs/l/libvdwxc/libvdwxc-0.3.2-foss-2018b.eb +++ b/easybuild/easyconfigs/l/libvdwxc/libvdwxc-0.3.2-foss-2018b.eb @@ -3,7 +3,7 @@ easyblock = 'ConfigureMake' name = 'libvdwxc' version = '0.3.2' -homepage = 'http://libvdwxc.org' +homepage = 'https://libvdwxc.materialsmodeling.org/' description = """libvdwxc is a general library for evaluating energy and potential for exchange-correlation (XC) functionals from the vdW-DF family that can be used with various of density functional theory (DFT) codes.""" diff --git a/easybuild/easyconfigs/l/libvdwxc/libvdwxc-0.4.0-foss-2019a.eb b/easybuild/easyconfigs/l/libvdwxc/libvdwxc-0.4.0-foss-2019a.eb index 999145324337..b750b9a414f2 100644 --- a/easybuild/easyconfigs/l/libvdwxc/libvdwxc-0.4.0-foss-2019a.eb +++ b/easybuild/easyconfigs/l/libvdwxc/libvdwxc-0.4.0-foss-2019a.eb @@ -3,7 +3,7 @@ easyblock = 'ConfigureMake' name = 'libvdwxc' version = '0.4.0' -homepage = 'http://libvdwxc.org' +homepage = 'https://libvdwxc.materialsmodeling.org/' description = """libvdwxc is a general library for evaluating energy and potential for exchange-correlation (XC) functionals from the vdW-DF family that can be used with various of density functional theory (DFT) codes.""" From f2a65af3049b3a71f82a77a7c402d2835ecbfc6a Mon Sep 17 00:00:00 2001 From: Jakob Schiotz Date: Wed, 6 Nov 2024 18:25:25 +0100 Subject: [PATCH 85/85] Update libvdwxc webpage as old URL has been taken over by evildoers. --- easybuild/easyconfigs/l/libvdwxc/libvdwxc-0.4.0-foss-2019b.eb | 2 +- easybuild/easyconfigs/l/libvdwxc/libvdwxc-0.4.0-foss-2020a.eb | 2 +- easybuild/easyconfigs/l/libvdwxc/libvdwxc-0.4.0-foss-2020b.eb | 2 +- easybuild/easyconfigs/l/libvdwxc/libvdwxc-0.4.0-foss-2021a.eb | 2 +- easybuild/easyconfigs/l/libvdwxc/libvdwxc-0.4.0-foss-2021b.eb | 2 +- easybuild/easyconfigs/l/libvdwxc/libvdwxc-0.4.0-foss-2022a.eb | 2 +- easybuild/easyconfigs/l/libvdwxc/libvdwxc-0.4.0-foss-2023a.eb | 2 +- easybuild/easyconfigs/l/libvdwxc/libvdwxc-0.4.0-intel-2020b.eb | 2 +- easybuild/easyconfigs/l/libvdwxc/libvdwxc-0.4.0-intel-2021a.eb | 2 +- easybuild/easyconfigs/l/libvdwxc/libvdwxc-0.4.0-intel-2021b.eb | 2 +- 10 files changed, 10 insertions(+), 10 deletions(-) diff --git a/easybuild/easyconfigs/l/libvdwxc/libvdwxc-0.4.0-foss-2019b.eb b/easybuild/easyconfigs/l/libvdwxc/libvdwxc-0.4.0-foss-2019b.eb index c9f93a8ff91b..a04a99002a9f 100644 --- a/easybuild/easyconfigs/l/libvdwxc/libvdwxc-0.4.0-foss-2019b.eb +++ b/easybuild/easyconfigs/l/libvdwxc/libvdwxc-0.4.0-foss-2019b.eb @@ -3,7 +3,7 @@ easyblock = 'ConfigureMake' name = 'libvdwxc' version = '0.4.0' -homepage = 'https://libvdwxc.org' +homepage = 'https://libvdwxc.materialsmodeling.org/' description = """libvdwxc is a general library for evaluating energy and potential for exchange-correlation (XC) functionals from the vdW-DF family that can be used with various of density functional theory (DFT) codes.""" diff --git a/easybuild/easyconfigs/l/libvdwxc/libvdwxc-0.4.0-foss-2020a.eb b/easybuild/easyconfigs/l/libvdwxc/libvdwxc-0.4.0-foss-2020a.eb index c6769e531571..dd9797af7349 100644 --- a/easybuild/easyconfigs/l/libvdwxc/libvdwxc-0.4.0-foss-2020a.eb +++ b/easybuild/easyconfigs/l/libvdwxc/libvdwxc-0.4.0-foss-2020a.eb @@ -3,7 +3,7 @@ easyblock = 'ConfigureMake' name = 'libvdwxc' version = '0.4.0' -homepage = 'https://libvdwxc.org' +homepage = 'https://libvdwxc.materialsmodeling.org/' description = """libvdwxc is a general library for evaluating energy and potential for exchange-correlation (XC) functionals from the vdW-DF family that can be used with various of density functional theory (DFT) codes.""" diff --git a/easybuild/easyconfigs/l/libvdwxc/libvdwxc-0.4.0-foss-2020b.eb b/easybuild/easyconfigs/l/libvdwxc/libvdwxc-0.4.0-foss-2020b.eb index 9dee6b6ef267..0e414c5d729b 100644 --- a/easybuild/easyconfigs/l/libvdwxc/libvdwxc-0.4.0-foss-2020b.eb +++ b/easybuild/easyconfigs/l/libvdwxc/libvdwxc-0.4.0-foss-2020b.eb @@ -3,7 +3,7 @@ easyblock = 'ConfigureMake' name = 'libvdwxc' version = '0.4.0' -homepage = 'https://libvdwxc.org' +homepage = 'https://libvdwxc.materialsmodeling.org/' description = """libvdwxc is a general library for evaluating energy and potential for exchange-correlation (XC) functionals from the vdW-DF family that can be used with various of density functional theory (DFT) codes.""" diff --git a/easybuild/easyconfigs/l/libvdwxc/libvdwxc-0.4.0-foss-2021a.eb b/easybuild/easyconfigs/l/libvdwxc/libvdwxc-0.4.0-foss-2021a.eb index eb7dd54a47d7..843a00aaac2b 100644 --- a/easybuild/easyconfigs/l/libvdwxc/libvdwxc-0.4.0-foss-2021a.eb +++ b/easybuild/easyconfigs/l/libvdwxc/libvdwxc-0.4.0-foss-2021a.eb @@ -3,7 +3,7 @@ easyblock = 'ConfigureMake' name = 'libvdwxc' version = '0.4.0' -homepage = 'https://libvdwxc.org' +homepage = 'https://libvdwxc.materialsmodeling.org/' description = """libvdwxc is a general library for evaluating energy and potential for exchange-correlation (XC) functionals from the vdW-DF family that can be used with various of density functional theory (DFT) codes.""" diff --git a/easybuild/easyconfigs/l/libvdwxc/libvdwxc-0.4.0-foss-2021b.eb b/easybuild/easyconfigs/l/libvdwxc/libvdwxc-0.4.0-foss-2021b.eb index c5a0fad835bc..1050fbf314f9 100644 --- a/easybuild/easyconfigs/l/libvdwxc/libvdwxc-0.4.0-foss-2021b.eb +++ b/easybuild/easyconfigs/l/libvdwxc/libvdwxc-0.4.0-foss-2021b.eb @@ -3,7 +3,7 @@ easyblock = 'ConfigureMake' name = 'libvdwxc' version = '0.4.0' -homepage = 'https://libvdwxc.org' +homepage = 'https://libvdwxc.materialsmodeling.org/' description = """libvdwxc is a general library for evaluating energy and potential for exchange-correlation (XC) functionals from the vdW-DF family that can be used with various of density functional theory (DFT) codes.""" diff --git a/easybuild/easyconfigs/l/libvdwxc/libvdwxc-0.4.0-foss-2022a.eb b/easybuild/easyconfigs/l/libvdwxc/libvdwxc-0.4.0-foss-2022a.eb index b1785ef119b2..3b14a5ca7076 100644 --- a/easybuild/easyconfigs/l/libvdwxc/libvdwxc-0.4.0-foss-2022a.eb +++ b/easybuild/easyconfigs/l/libvdwxc/libvdwxc-0.4.0-foss-2022a.eb @@ -3,7 +3,7 @@ easyblock = 'ConfigureMake' name = 'libvdwxc' version = '0.4.0' -homepage = 'https://libvdwxc.org' +homepage = 'https://libvdwxc.materialsmodeling.org/' description = """libvdwxc is a general library for evaluating energy and potential for exchange-correlation (XC) functionals from the vdW-DF family that can be used with various of density functional theory (DFT) codes.""" diff --git a/easybuild/easyconfigs/l/libvdwxc/libvdwxc-0.4.0-foss-2023a.eb b/easybuild/easyconfigs/l/libvdwxc/libvdwxc-0.4.0-foss-2023a.eb index 9cf45cc3abe2..7c8c009c9d0d 100644 --- a/easybuild/easyconfigs/l/libvdwxc/libvdwxc-0.4.0-foss-2023a.eb +++ b/easybuild/easyconfigs/l/libvdwxc/libvdwxc-0.4.0-foss-2023a.eb @@ -3,7 +3,7 @@ easyblock = 'ConfigureMake' name = 'libvdwxc' version = '0.4.0' -homepage = 'https://libvdwxc.org' +homepage = 'https://libvdwxc.materialsmodeling.org/' description = """libvdwxc is a general library for evaluating energy and potential for exchange-correlation (XC) functionals from the vdW-DF family that can be used with various of density functional theory (DFT) codes.""" diff --git a/easybuild/easyconfigs/l/libvdwxc/libvdwxc-0.4.0-intel-2020b.eb b/easybuild/easyconfigs/l/libvdwxc/libvdwxc-0.4.0-intel-2020b.eb index 751488a0728d..a610d3ec7735 100644 --- a/easybuild/easyconfigs/l/libvdwxc/libvdwxc-0.4.0-intel-2020b.eb +++ b/easybuild/easyconfigs/l/libvdwxc/libvdwxc-0.4.0-intel-2020b.eb @@ -3,7 +3,7 @@ easyblock = 'ConfigureMake' name = 'libvdwxc' version = '0.4.0' -homepage = 'https://libvdwxc.org' +homepage = 'https://libvdwxc.materialsmodeling.org/' description = """libvdwxc is a general library for evaluating energy and potential for exchange-correlation (XC) functionals from the vdW-DF family that can be used with various of density functional theory (DFT) codes.""" diff --git a/easybuild/easyconfigs/l/libvdwxc/libvdwxc-0.4.0-intel-2021a.eb b/easybuild/easyconfigs/l/libvdwxc/libvdwxc-0.4.0-intel-2021a.eb index cdc3abd5a19d..e137148b85c4 100644 --- a/easybuild/easyconfigs/l/libvdwxc/libvdwxc-0.4.0-intel-2021a.eb +++ b/easybuild/easyconfigs/l/libvdwxc/libvdwxc-0.4.0-intel-2021a.eb @@ -3,7 +3,7 @@ easyblock = 'ConfigureMake' name = 'libvdwxc' version = '0.4.0' -homepage = 'https://libvdwxc.org' +homepage = 'https://libvdwxc.materialsmodeling.org/' description = """libvdwxc is a general library for evaluating energy and potential for exchange-correlation (XC) functionals from the vdW-DF family that can be used with various of density functional theory (DFT) codes.""" diff --git a/easybuild/easyconfigs/l/libvdwxc/libvdwxc-0.4.0-intel-2021b.eb b/easybuild/easyconfigs/l/libvdwxc/libvdwxc-0.4.0-intel-2021b.eb index c8c0d2a86440..5df0f660f1d9 100644 --- a/easybuild/easyconfigs/l/libvdwxc/libvdwxc-0.4.0-intel-2021b.eb +++ b/easybuild/easyconfigs/l/libvdwxc/libvdwxc-0.4.0-intel-2021b.eb @@ -3,7 +3,7 @@ easyblock = 'ConfigureMake' name = 'libvdwxc' version = '0.4.0' -homepage = 'https://libvdwxc.org' +homepage = 'https://libvdwxc.materialsmodeling.org/' description = """libvdwxc is a general library for evaluating energy and potential for exchange-correlation (XC) functionals from the vdW-DF family that can be used with various of density functional theory (DFT) codes."""