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2021-04-13genemark-et package: add version 4.65 and new dependencies (#22966)Glenn Johnson4-2/+64
New version has new dependencies (which are also added here as new packages): * perl-mce * perl-threads * perl-thread-queue The new version of genemark-et also has a different URL scheme.
2021-04-13rdma-core bugfix: help CMake find Python dependency (#22891)Tamara Dahlgren1-3/+7
2021-04-13eccodes: add version 2.21.0 (#22901)Sergey Kosukhin1-5/+8
The CMake option ENABLE_PYTHON has been renamed to ENABLE_PYTHON2 starting version 2.20.0
2021-04-13elmerfem: add version 9.0; fix version 8.4; add +gui variant (#22931)Andrew W Elble1-2/+23
* Add a +gui variant (default off) which adds dependencies on qt, paraview, and qwt * Backport upstream patch when installing version 8.4 (this patch is already applied for versions >= 9.0)
2021-04-13New package: r-tester (#22945)Jen Herting1-0/+18
Co-authored-by: Alex C Leute <aclrc@rit.edu>
2021-04-13BRAKER package: Add version 2.1.6 (#22965)Glenn Johnson1-0/+1
2021-04-13git: add version 2.31.1 (#22974)Robert Mijakovic1-0/+5
2021-04-13Python: add versions 3.8.9, 3.9.4 (#22975)Robert Mijakovic1-1/+3
2021-04-13gaussian-view/vmd: add deps on X11/GL libraries (#22322)Tiziano Müller7-0/+62
Both binary packages would otherwise require X11 and Mesa libraries to be installed on the host to run. Make sure they use the Spack-provided libraries by patching the `rpath` via `patchelf`.
2021-04-13Documentation: update intel-parallel-studio instructions (#22248)Tiziano Müller1-36/+36
* Clarify stub compiler definition in compilers.yaml * Update explanation of why stub compiler definition is needed * Add note about required module definition when using Spack-installed intel-parallel-studio as intel-compiler * Add suggestion about updating package config preferences based on choice of variants when installing intel-parallel-studio to avoid reinstallation
2021-04-13add darshan 3.3.0-pre1 pre-release (#22942)shanedsnyder2-2/+4
2021-04-13netlib-lapack: New versions (#22964)G-Ragghianti1-6/+6
2021-04-13added dyninst 11.0.0 (#22949)Gregory Lee1-0/+1
2021-04-13amrex: allow builds with clang and apple-clang (#22967)mic841-2/+0
2021-04-13VTKM: change preferred version (#22950)Vicente Bolea1-2/+2
2021-04-13bcftools: add v1.12 (#22883)Glenn Johnson1-0/+2
2021-04-13htslib: add version 1.12 (#22882)Glenn Johnson1-0/+1
2021-04-13bump cmake (#22961)Harmen Stoppels1-0/+2
2021-04-13py-pandas: add v1.2.4 (#22944)Adam J. Stewart1-0/+1
2021-04-13changes to enable rocm builds using git repo (#22943)Sreenivasa Murthy Kolam5-2/+13
2021-04-13Fix issue where binutils builds ld with ~ld (#22959)Harmen Stoppels1-21/+14
Let's be very explicit and always add --enable or --disable.
2021-04-13berkeley-db: making +cxx and +stl default to True (#22960)Matthieu Dorier1-2/+2
2021-04-13spfft: add version 1.0.2 (#22958)Simon Frasch1-0/+1
2021-04-13intel-parallel-studio: fix vtune installation for 2020+ (#22255)Tiziano Müller1-3/+5
vtune_amplifier got renamed to vtune_profiler for the 2020+ suite
2021-04-13SIRIUS and SpFFT versions need ROCm < 4.1 (#22957)Harmen Stoppels2-0/+6
FindHIP.cmake script is not working for both 4.0 and 4.1. It's fixed in their develop branches
2021-04-13spglib: fix libs property for some multilib distros (#22956)Tiziano Müller1-2/+2
on multilib distros with lib/lib64 (rather than lib32/lib) the library ends up in a dir lib64/ instead of lib/, breaking the libs property (and the cp2k+spglib build)
2021-04-13gcc: add v10.3 (#22894)yellowhat1-0/+1
2021-04-12New package: r-tictoc (#22937)Jen Herting1-0/+28
2021-04-12vtk: new version, 9.0.1 (#22880)Robert Mijakovic1-1/+2
Co-authored-by: Robert Mijakovic <robert.mijakovic@lxp.lu>
2021-04-12New Package: r-assertive-types (#22933)Jen Herting1-0/+27
2021-04-12Add new versions of patchelf (#22939)Harmen Stoppels1-1/+9
2021-04-12Bump hiop version (#22884)Asher Mancinelli1-0/+1
2021-04-12samtools: add version 1.12 (#22885)Glenn Johnson1-0/+2
2021-04-12ROCm relase 4.1.0: Bump up version of rocm-validation-suite (#22946)arjun-raj-kuppala2-1/+16
2021-04-12Add conflict for Mac OS for STAT package (#22919)Pramod Kumbhar1-0/+3
See https://github.com/LLNL/STAT/issues/19
2021-04-12packages/phist: new version 1.9.4 (#22922)jthies1-1/+2
fix version 1.7.4 checksum re 22758: phist-1.9.4 should resolve this issue, once confirmed I will add a patch for older versions.
2021-04-12openPMD-api: 0.13.3 (#22910)Axel Huebl1-2/+3
2021-04-12Externals with merged prefixes (#22653)Peter Scheibel2-17/+85
We remove system paths from search variables like PATH and from -L options because they may contain many packages and could interfere with Spack-built packages. External packages may be installed to prefixes that are not actually system paths but are still "merged" in the sense that many other packages are installed there. To avoid conflicts, this PR places all external packages at the end of search paths.
2021-04-12maker: add v3.01.03 (#22915)Glenn Johnson1-1/+2
2021-04-12blt: add v0.4.0 (#22917)Chris White1-2/+3
2021-04-12bart: update package (#22926)Glenn Johnson2-4/+38
- add version 0.7.00 - make build work with intel-oneapi-mkl - Add myself as maintainer
2021-04-12casacore: change FFT variants for correct, version dependent, FFT choices ↵Martin Pokorny1-7/+11
(#22925) Required dependency on FFTW for casacore@3.4.0:; optional for casacore@:3.4.0, depending selection of FFTPack
2021-04-12mumax: constrain go version (#22927)Glenn Johnson1-1/+1
Mumax will not build with go-1.16.
2021-04-12qt: restrict python version when +webkit (#22928)Seth R. Johnson1-0/+1
See #17270. ``` make[2]: Entering directory `/tmp/vavolkl/spack-stage/spack-stage-qt-5.14.2-63dapppjbq6vqh3le7pazsprijls7cfl/spack-src/qtwebengine/src' /bin/sh: -c: line 0: syntax error near unexpected token `(' /bin/sh: -c: line 0: `echo Modules will not be built. Python version 2 (2.7.5 or later) is required to build QtWebEngine.' make[2]: *** [errorbuild] Error 1 ```
2021-04-12tfel: add missing variant (#22558)thelfer1-0/+2
The variant was used but not defined.
2021-04-12libsakura: Change precision for fftw dependency depending on libsakura ↵Martin Pokorny1-1/+2
version (#22924) Co-authored-by: Harmen Stoppels <harmenstoppels@gmail.com>
2021-04-11ASP-based solver: assign OS correctly with inheritance from parent (#22896)Massimiliano Culpo3-0/+28
fixes #22871 When in presence of multiple choices for the operating system we were lacking a rule to derive the node OS if it was inherited.
2021-04-10fix 22802- fix incorrect arch list for rocblas (#22881)Sreenivasa Murthy Kolam3-2/+11
2021-04-09Drop cxx berkeley-db (#22899)Harmen Stoppels1-2/+7
2021-04-09Build process output: handle UTF-8 for python 3.x to 3.7 (#22888)Peter Scheibel1-2/+9
We set LC_ALL=C to encourage a build process to generate ASCII output (so our logger daemon can decode it). Most packages respect this but it appears that intel-oneapi-compilers does not in some cases (see #22813). This reads the output of the build process as UTF-8, which still works if the build process respects LC_ALL=C but also works if the process generates UTF-8 output. For Python >= 3.7 all files are opened with UTF-8 encoding by default. Python 2 does not support the encoding argument on 'open', so to support Python 2 the files would have to be opened in byte mode and explicitly decoded (as a side note, this would be the only way to handle other encodings without being informed of them in advance).