* Add checksum for py-skl2onnx 1.12
* Update var/spack/repos/builtin/packages/py-skl2onnx/package.py
Co-authored-by: Adam J. Stewart <ajstewart426@gmail.com>
* Update package.py
Co-authored-by: Adam J. Stewart <ajstewart426@gmail.com>
* Add checksum for py-tables 3.7.0
* Update package.py
* Update var/spack/repos/builtin/packages/py-tables/package.py
Co-authored-by: Adam J. Stewart <ajstewart426@gmail.com>
Co-authored-by: Adam J. Stewart <ajstewart426@gmail.com>
ROOT has a webgui which is available with the `+root7` variant. This is a fairly large part of a ROOT install (275MB out of 732MB on my system) which is not necessarily useful in all use cases (e.g. inside containers on network-restricted HPC/HTC compute nodes). This new variant adds the option to retain the ROOT7 functionality but not necessarily include the `webgui` aspects.
`__unused__` defined in `general.h` conflict with the one defined by libc headers,
so change it to `__attribute__unused__` according to s.zharkoff:
https://bugs.gentoo.org/828550#c11
cmd:
`grep -rl "__unused__" . | xargs -n1 sed -i -e 's/\b__unused__\b/__attribute__unused__/g' -e 's/(unused)/(__unused__)/g'`
Basic stack of ML packages we would like to test and generate binaries for in CI.
Spack now has a large CI framework in GitLab for PR testing and public binary generation.
We should take advantage of this to test and distribute optimized binaries for popular ML
frameworks.
This is a pretty extensive initial set, including CPU, ROCm, and CUDA versions of a core
`x96_64_v4` stack.
### Core ML frameworks
These are all popular core ML frameworks already available in Spack.
- [x] PyTorch
- [x] TensorFlow
- [x] Scikit-learn
- [x] MXNet
- [x] CNTK
- [x] Caffe
- [x] Chainer
- [x] XGBoost
- [x] Theano
### ML extensions
These are domain libraries and wrappers that build on top of core ML libraries
- [x] Keras
- [x] TensorBoard
- [x] torchvision
- [x] torchtext
- [x] torchaudio
- [x] TorchGeo
- [x] PyTorch Lightning
- [x] torchmetrics
- [x] GPyTorch
- [x] Horovod
### ML-adjacent libraries
These are libraries that aren't specific to ML but are still core libraries used in ML pipelines
- [x] numpy
- [x] scipy
- [x] pandas
- [x] ONNX
- [x] bazel
Co-authored-by: Jonathon Anderson <17242663+blue42u@users.noreply.github.com>
* Add checksum for py-scikit-build 0.15.0 and use sources from pypi
* Update var/spack/repos/builtin/packages/py-scikit-build/package.py
Co-authored-by: Adam J. Stewart <ajstewart426@gmail.com>
Co-authored-by: Adam J. Stewart <ajstewart426@gmail.com>
* Add checksum for py-terminado 0.15.0
* Update var/spack/repos/builtin/packages/py-terminado/package.py
Co-authored-by: Adam J. Stewart <ajstewart426@gmail.com>
Co-authored-by: Adam J. Stewart <ajstewart426@gmail.com>
* added metaphlan v4, cleaned up phylophlan
* added iqtree2
* fixed phylophlan, builds now
* changed config.yaml to default
* fixed style
* py-jsonschema: add 4.16.0 and new package py-hatch-fancy-pypi-readme (#32929)
* acfl: add v22.1 (#32915)
Co-authored-by: Annop Wongwathanarat <annop.wongwathanarat@arm.com>
* Fixup errors introduced by Clingo Pr: (#32905)
* re2c depends on cmake on Windows
* Winbison properly added to bootstrap package search list
* Set CMAKE_HIP_ARCHITECTURES with the value of amdgpu_target (#32901)
* libtiff: default to +zlib+jpeg (#32945)
* octave: add version 7.2.0 (#32943)
* simgrid new releases (#32920)
* [rocksdb] Added rtti variant (#32918)
* rvs binary path updated for 5.2 rocm release (#32892)
* Add checksum for py-pytest-runner 6.0.0 (#32957)
* py-einops: add v0.5.0 (#32959)
* Replace repo with the NVIDIA one (#32951)
* Add checksum for py-tomli 2.0.1 (#32949)
* QMCPACK: add @3.15.0 (#32931)
* Tidied up configure arguments to use special spack autotools features. (#32930)
* casper: old domain fell off, adding github repo (#32928)
* unifyfs: pin mercury version; add boost variant (#32911)
Mercury has a new version (v2.2) releasing soon that UnifyFS does not build with and hasn't been tested with. This pins UnifyFS to the last version of Mercury used/tested.
Add a variant to avoid building/using boost
Append -std=gnu99 to cflags if building with gcc@4. Needed for mochi-margo to compile
* trilinos: constrain superlu-dist version (#32889)
* trilinos: constrain superlu-dist version for 13.x
* syntax
* FEniCSx: Updates for 0.5.1 (#32665)
* Updates for DOLFINx 0.5.1 and associated packages
* xtensor needed on anything less than main
* Switch back to Python 3.7 minimum.
* Might be good to point out in our README how to fix Python version?
* Fix basix, xtensor dep
* Add numba feature
* Fix checksum
* Make slepc optional
Co-authored-by: Tamara Dahlgren <35777542+tldahlgren@users.noreply.github.com>
* simgrid: add variant and remove flag (#32797)
* simgrid: remove std c++11 flag
* simgrid: add msg variant
* Axom: bring in changes from axom repo (#32643)
* bring in changes from axom repo
Co-authored-by: white238 <white238@users.noreply.github.com>
Co-authored-by: Tamara Dahlgren <35777542+tldahlgren@users.noreply.github.com>
* Add checksum for py-pyparsing 3.0.9 (#32952)
* rdma-core: fix syntax for external discoverability (#32962)
* Add checksum for py-flatbuffers 2.0.7 (#32955)
* amrex: add v22.10 (#32966)
* Remove CMakePackage.define alias from most packages (#32950)
* Bug fix for `ca-certificates-mozilla/package.py` to enable `spack install --source` (#32953)
* made suggested changes to iqtree2, py-dendropy, py-metaphlan, and py-pkgconfig. Poetry install still broken
* reverted py-pkgconfig deps to poetry-core
* made iqtree2 less dedundant, changes to py-dendropy and py-pkgconfig deps
Co-authored-by: Manuela Kuhn <36827019+manuelakuhn@users.noreply.github.com>
Co-authored-by: Annop Wongwathanarat <annop.wongwathanarat@gmail.com>
Co-authored-by: Annop Wongwathanarat <annop.wongwathanarat@arm.com>
Co-authored-by: John W. Parent <45471568+johnwparent@users.noreply.github.com>
Co-authored-by: Auriane R <48684432+aurianer@users.noreply.github.com>
Co-authored-by: Adam J. Stewart <ajstewart426@gmail.com>
Co-authored-by: Kai Torben Ohlhus <k.ohlhus@gmail.com>
Co-authored-by: Vinícius <viniciusvgp@gmail.com>
Co-authored-by: Matthieu Dorier <mdorier@anl.gov>
Co-authored-by: renjithravindrankannath <94420380+renjithravindrankannath@users.noreply.github.com>
Co-authored-by: iarspider <iarspider@gmail.com>
Co-authored-by: Paul R. C. Kent <kentpr@ornl.gov>
Co-authored-by: Brian Van Essen <vanessen1@llnl.gov>
Co-authored-by: snehring <7978778+snehring@users.noreply.github.com>
Co-authored-by: Cameron Stanavige <stanavige1@llnl.gov>
Co-authored-by: Cody Balos <balos1@llnl.gov>
Co-authored-by: Jack S. Hale <mail@jackhale.co.uk>
Co-authored-by: Tamara Dahlgren <35777542+tldahlgren@users.noreply.github.com>
Co-authored-by: Lucas Nesi <lucas31nesi@hotmail.com>
Co-authored-by: Chris White <white238@llnl.gov>
Co-authored-by: white238 <white238@users.noreply.github.com>
Co-authored-by: Martin Pokorny <mpokorny@caltech.edu>
Co-authored-by: Weiqun Zhang <WeiqunZhang@lbl.gov>
Co-authored-by: Massimiliano Culpo <massimiliano.culpo@gmail.com>
Co-authored-by: Dom Heinzeller <dom.heinzeller@icloud.com>
* filter_file: introduce argument 'start_at'
* autotools: extend patching of the libtool script
* autotools: refactor _patch_usr_bin_file
* autotools: improve readability of the filtering
* autotools: keep the modification time of the configure scripts
* autotools: do not try to patch directories
* autotools: explain libtool patching for posterity
Co-authored-by: Massimiliano Culpo <massimiliano.culpo@gmail.com>
Co-authored-by: Harmen Stoppels <harmenstoppels@gmail.com>
