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2020-07-23cray: detect shasta os properly (#17467)Greg Becker2-1/+4
Fixes #17299 Cray Shasta systems appear to use an unmodified Sles or other Linux operating system on the backend (like Cray "Cluster" systems and unlike Cray "XC40" systems that use CNL). This updates the CNL version detection to properly note that this is the underlying OS instead of CNL and delegate to LinuxDistro.
2020-07-23environment-views: fix bug where missing recipe/repo breaks env commands ↵robo-wylder5-19/+104
(#17608) * environment-views: fix bug where missing recipe/repo breaks env commands When a recipe or a repo has been removed from Spack and an environment is active, it causes the view activation to crash Spack before any commands can be executed. Further, the error message it not at all clear in explaining the issue. This forces view regeneration to always start from scratch to avoid the missing package recipes, and defaults add_view=False in main for views activated by the `spack -e` option. * add messages to env status and deactivate Warn users that a view may be corrupt when deactivating an environment or checking its status while active. Updated message for activate. * tests for view checking Co-authored-by: Gregory Becker <becker33@llnl.gov>
2020-07-23Update fetch order to match iteration order of MirrorReference (#17572)Peter Scheibel1-3/+5
2020-07-23util.executable.which: handle path separators like /bin/which (#17668)Greg Becker2-2/+37
* util.executable.which: handle path separators like /bin/which Co-authored-by: Massimiliano Culpo <massimiliano.culpo@gmail.com>
2020-07-23csa-c: added new package at master (#17676)ilbiondo1-0/+19
Co-authored-by: Massimiliano Culpo <massimiliano.culpo@gmail.com>
2020-07-23nn-c: added new package at v1.86.2 (#17675)ilbiondo1-0/+33
Co-authored-by: Massimiliano Culpo <massimiliano.culpo@gmail.com>
2020-07-23Shapeit4: added new package at v4.1.3 (#17674)ilbiondo1-0/+55
2020-07-23Reduce output verbosity with debug levels (#17546)Tamara Dahlgren15-165/+342
* switch from bool to int debug levels * Added debug options and changed lock logging to use more detailed values * Limit installer and timestamp PIDs to standard debug output * Reduced verbosity of fetch/stage/install output, changing most to debug level 1 * Combine lock log methods; change build process install to debug * Changed binary cache install messages to extraction messages
2020-07-22[M4] Add missing compiler flag on Cray Compiler (#17604)Nick Robison1-0/+3
* [M4] Add missing compiler flag on Cray Compiler The new version of the Cray Compiler are based on Clang, which means we need to add the same LDFLAG as other clang environments.
2020-07-22Cython: add v0.29.21 (#17650)Adam J. Stewart1-1/+2
2020-07-22New Package: py-boto (#17639)Jen Herting1-0/+19
Added py-boto package
2020-07-22precice: Add version 2.1.0 (#17644)Frédéric Simonis1-0/+2
2020-07-22bugfix: use getattr for variation.prefix/suffix (#17669)eugeneswalker1-2/+2
2020-07-22hpctoolkit: add version 2020.07.21 (#17645)Mark W. Krentel1-0/+1
2020-07-22Added variant to enable Legion SPY logging. (#17637)Ben Bergen1-0/+5
2020-07-22[acts] Add version 0.28.0 (#17622)Hadrien G1-0/+1
Add acts v0.28.0
2020-07-21hisat2 (package): add version 2.2.0, update homepage (#17600)Justin S1-2/+7
2020-07-21New packages: py-azure-cli and dependencies (#17585)Adam J. Stewart95-12/+1745
2020-07-21bugfix: make compiler preferences slightly saner (#17590)Todd Gamblin5-19/+191
* bugfix: make compiler preferences slightly saner This fixes two issues with the way we currently select compilers. If multiple compilers have the same "id" (os/arch/compiler/version), we currently prefer them by picking this one with the most supported languages. This can have some surprising effects: * If you have no `gfortran` but you have `gfortran-8`, you can detect `clang` that has no configured C compiler -- just `f77` and `f90`. This happens frequently on macOS with homebrew. The bug is due to some kludginess about the way we detect mixed `clang`/`gfortran`. * We can prefer suffixed versions of compilers to non-suffixed versions, which means we may select `clang-gpu` over `clang` at LLNL. But, `clang-gpu` is not actually clang, and it can break builds. We should prefer `clang` if it's available. - [x] prefer compilers that have C compilers and prefer no name variation to variation. * tests: add test for which()
2020-07-21[acts] Add 0.27.x series (#17621)Hadrien G1-0/+2
Add acts v0.27 and v0.27.1
2020-07-21ci pipelines: activate environment without view (#17440)Harmen Stoppels1-1/+1
2020-07-21cp2k: make libint optional (#17618)Tiziano Müller1-23/+30
2020-07-20aegean (package): remove -m64 on aarch64 (#17615)t-nojiri1-0/+3
2020-07-21acts: added v0.26 (#17602)Hadrien G1-1/+3
2020-07-21flatbuffers: added v0.12.0 (#17603)Nick Robison1-0/+1
2020-07-21qt4: add missing libSM dependency (#17611)Seth R. Johnson1-0/+1
See https://github.com/spack/spack/issues/15082 and https://github.com/spack/spack/pull/16226
2020-07-21hpcviewer, ibm-java: new versions (#17612)Mark W. Krentel2-0/+8
Add hpcviewer version 2020.07 and ibm-java 8.0.6.11.
2020-07-20Bugfix: Do not raise InstallError for ascent_ver (#17578)Tamara Dahlgren1-3/+3
2020-07-20bugfix: ignore Apple's "gcc" by default (#17589)Todd Gamblin3-29/+51
Apple's gcc is really clang. We previously ignored it by default but there was a regression in #17110. Originally we checked for all clang versions with this, but I know of none other than `gcc` on macos that actually do this, so limiting to `apple-clang` should be ok. - [x] Fix check for `apple-clang` in `gcc.py` to use version detection from `spack.compilers.apple_clang`
2020-07-20Fix MacOS build tests (#17542)Massimiliano Culpo2-11/+35
* MacOS build tests - Run on PR that modify the YAML file of the workflow - Don't clone Spack, since we are in the Spack repo now * Try to add opengl to configuration to build jupyter * fixup
2020-07-20Configuration: allow usage of command-line scopes with environments (#14608)Dr. Christian Tacke1-4/+4
Spack did not support usage of the `--config-scope` option in combination with an environment: In `lib/spack/spack/main.py`, `spack.config.command_line_scopes` is set equal to any config scopes passed by the `--config-scope` option. However, this is done after activating an environment. In the process of activating an environment, the `spack.config.config` singleton is instantiated, so later setting of `spack.config.command_line_scopes` is ignored. This commit sets command line scopes before activating an environment to ensure that they are included in the configuration. Co-authored-by: Tim Fuller <tjfulle@sandia.gov>
2020-07-20py-dp-gp-cluster: new package at 2019-09-22 (#17549)Justin S1-0/+33
* py-dp-gp-cluster: new package * py-dp-gp-cluster: remove master, add 2019-09-22 * py-dp-gp-cluster: require python2, older gpy, sklearn * py-dp-gp-cluster: remove cython runtime dep
2020-07-18update ascent package with recent ver dep logic, and dray support (#17502)Cyrus Harrison1-19/+66
* update ascent package with recent ver dep logic, and dray support * update pmt name, make babelflow logic dep on mpi
2020-07-18Add texlive 2020 version (#17559)Jon Rood3-4/+21
* Add new versions of texlive and poppler. * Add new versions of harfbuzz which also relocated source location to github. * Update var/spack/repos/builtin/packages/harfbuzz/package.py Co-authored-by: Adam J. Stewart <ajstewart426@gmail.com> * Restore deleted url line in harfbuzz. Co-authored-by: Adam J. Stewart <ajstewart426@gmail.com>
2020-07-17allow GNUPGHOME to come from SPACK_GNUPGHOME in env, if set (#17139)eugeneswalker1-1/+1
2020-07-17r-devtools: add version 2.3.0; update dependencies (#17408)Amjad Kotobi1-8/+31
2020-07-17libint (package): add tuning options for MOLGW (#17329)Fabien Bruneval1-0/+23
2020-07-17New package: parallelmergetree (#17501)Cyrus Harrison1-0/+34
2020-07-17Bugfix/install missing compiler from buildcache (#17536)Scott Wittenburg2-0/+40
Ensure compilers installed from buildcache are registered.
2020-07-17py-matplotlib: add v3.3.0Adam J. Stewart1-5/+7
2020-07-17buildcache: list all mirrors even if one failsScott Wittenburg1-2/+2
2020-07-17subversion: added v1.14.0 amd v1.13.0, added new url (#17519)Amjad Kotobi1-1/+6
2020-07-16add devil ray package (#17495)Cyrus Harrison1-0/+318
* add dray with mid-review changes * remove env import since its impliclity included
2020-07-16Updates to maestrowf package (#17470)Francesco Di Natale2-18/+46
* Addition of Chainmap to satisfy Maestro dependency. * Additional versions and dependencies for Maestro. * Updated URL to point to pypi. * Updates to chainmap hashes. * Updates to pull version from PyPi. * Corrections to flake8 errors. * Stricter restrictions on Python versioning. Maestro actually supports Python 3.5 and later. Co-authored-by: Adam J. Stewart <ajstewart426@gmail.com> * Only install chainmap for Python2 versions. Co-authored-by: Adam J. Stewart <ajstewart426@gmail.com> * Removal of setuptools python cond. * Removal of version constaints on setuptools. Co-authored-by: Adam J. Stewart <ajstewart426@gmail.com>
2020-07-16Version 1.13.2 still needs the XL patch. (#17561)Kelly (KT) Thompson2-0/+14
2020-07-16adept-utils: 1.0.1 does not build w/ boost 1.73.0 or newer (#17560)Scott Wittenburg1-1/+1
2020-07-16Mark old icu4c as conflicting (#17562)Seth R. Johnson1-0/+2
GCC 4.8.5 on rhel6: ``` utext.cpp:572:5: error: 'max_align_t' in namespace 'std' does not name a type std::max_align_t extension; ^ utext.cpp: In function 'UText* utext_setup_67(UText*, int32_t, UErrorCode*)': utext.cpp:587:73: error: 'max_align_t' is not a member of 'std' spaceRequired = sizeof(ExtendedUText) + extraSpace - sizeof(std::max_align_t); ^ utext.cpp:587:73: note: suggested alternative: In file included from /projects/spack/opt/spack/gcc-4.4.7/gcc/6ln2t7b/include/c++/4.8.5/cstddef:42:0, from utext.cpp:19: /projects/spack/opt/spack/gcc-4.4.7/gcc/6ln2t7b/lib/gcc/x86_64-unknown-linux-gnu/4.8.5/include/stddef.h: 425:3: note: 'max_align_t' } max_align_t; ^ utext.cpp:598:57: error: 'struct ExtendedUText' has no member named 'extension' ut->pExtra = &((ExtendedUText *)ut)->extension; ^ g++ ... loadednormalizer2impl.cpp g++ ... chariter.cpp ```
2020-07-16Fix security issue in CI (#17545)Harmen Stoppels2-9/+1
The `spack-build-env.txt` file may contains many secrets, but the obvious one is the private signing key in `SPACK_SIGNING_KEY`. This file is nonetheless uploaded as a build artifact to gitlab. For anyone running CI on a public version of Gitlab this is a major security problem. Even for private Gitlab instances it can be very problematic. Co-authored-by: Scott Wittenburg <scott.wittenburg@kitware.com>
2020-07-16Add new dependencies required in latest rsync. (#17558)Jon Rood2-0/+5
2020-07-16PySCF new package (#17474)Nichols A. Romero2-0/+45
* Initial version of PySCF. * Add master branch to xcfun library * PySCF only compatible with specific commit of xcfun library * Update var/spack/repos/builtin/packages/py-pyscf/package.py Co-authored-by: Adam J. Stewart <ajstewart426@gmail.com> * Update var/spack/repos/builtin/packages/py-pyscf/package.py Co-authored-by: Adam J. Stewart <ajstewart426@gmail.com> * Revert "PySCF only compatible with specific commit of xcfun library" This reverts commit 8296005400fbe76d0c8339b7ca06e71a801f0a22. * Revert "Add master branch to xcfun library" This reverts commit f2b69989316a6bece6530d5d63f1d120ab4c14a8. * Issues conflict for xcfun library version rather than relying on a random commit. * Add version xcfun 2.0.0a2 which is needed by PySCF. * Remove xcfun conflict and express dependency more explictly. Add comment as to why this is necessary. Co-authored-by: Adam J. Stewart <ajstewart426@gmail.com>