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2020-07-27Relocate rpaths for all binaries, then do text bin replacement if the rpaths ↵Patrick Gartung1-7/+10
still exist after running patchelf/otool (#17418)
2020-07-27add tutorial setup script to share/spack (#17705)Greg Becker1-0/+123
* add tutorial setup script to share/spack * Add check for Ubuntu 18, fix xvda check, fix apt-get errors - now works on t2.micro, t2.small, and m instances - apt-get needs retries around it to work Co-authored-by: Todd Gamblin <tgamblin@llnl.gov>
2020-07-26bugfix: don't redundantly print ChildErrors (#17709)Todd Gamblin2-5/+12
A bug was introduced in #13100 where ChildErrors would be redundantly printed when raised during a build. We should eventually revisit error handling in builds and figure out what the right separation of responsibilities is for distributed builds, but for now just skip printing. - [x] SpackErrors were designed to be printed by the forked process, not by the parent, so check if they've already been printed. - [x] update tests
2020-07-23update changelog for 0.15.2v0.15.2Gregory Becker1-0/+19
2020-07-23bump version number for 0.15.2Gregory Becker3-6/+10
2020-07-23add tutorial public key to share/spack/keys dir (#17684)Greg Becker1-0/+38
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
2020-07-23Reduce 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
2020-07-23bugfix: use getattr for variation.prefix/suffix (#17669)eugeneswalker1-2/+2
2020-07-23bugfix: 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()
2020-07-23ci pipelines: activate environment without view (#17440)Harmen Stoppels1-1/+1
2020-07-23bugfix: 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`
2020-07-23buildcache: list all mirrors even if one failsScott Wittenburg1-2/+2
2020-07-23Bugfix/install missing compiler from buildcache (#17536)Scott Wittenburg2-0/+40
Ensure compilers installed from buildcache are registered.
2020-07-23adept-utils: 1.0.1 does not build w/ boost 1.73.0 or newer (#17560)Scott Wittenburg1-1/+1
2020-07-23Fix 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>
2020-07-23llvm-flang: Only build offload code if cuda enabled (#17466)Dr Owain Kenway1-3/+4
* llvm-flang Only build offload code if cuda enabled The current version executes `cmake(*args)` always as part of the post install. If device offload is not part of the build, this results in referencing `args` without it being set and the error: ``` ==> Error: UnboundLocalError: local variable 'args' referenced before assignment ``` Looking at prevoous version of `llvm-package.py` this whole routine appears to be only required for offload, some indent `cmake/make/install` to be under the `if`. * Update package.py Add comment
2020-07-23clear mpicc and friends before each build (#17450)Sajid Ali1-0/+8
* clear mpi env vars
2020-07-10Bump version to 0.15.1; update CHANGELOG and version referencesv0.15.1Peter Josef Scheibel4-6/+26
2020-07-10spack install: improve error message with no args (#17454)Greg Becker2-2/+37
The error message was not updated when the behavior of Spack environments was changed to not automatically activate the local environment in #17258. The previous error message no longer makes sense.
2020-07-10installation: skip repository metadata for externals (#16954)Greg Becker1-3/+8
When Spack installs a package, it stores repository package.py files for it and all of its dependencies - any package with a Spack metadata directory in its installation prefix. It turns out this was too broad: this ends up including external packages installed by Spack (e.g. installed by another Spack instance). Currently Spack doesn't store the namespace properly for such packages, so even though the package file could be fetched from the external, Spack is unable to locate it. This commit avoids the issue by skipping any attempt to locate and copy from the package repository of externals, regardless of whether they have a Spack repo directory.
2020-07-10add public spack mirror (#17077)Peter Scheibel1-0/+2
2020-07-10bugfix: no infinite recursion in setup-env.sh on CrayTodd Gamblin3-0/+29
On Cray platforms, we rely heavily on the module system to figure out what targets, compilers, etc. are available. This unfortunately means that we shell out to the `module` command as part of platform initialization. Because we run subcommands in a shell, we can get infinite recursion if `setup-env.sh` and friends are in some init script like `.bashrc`. This fixes the infinite loop by adding guards around `setup-env.sh`, `setup-env.csh`, and `setup-env.fish`, to prevent recursive initializations of Spack. This is safe because Spack never shells out to itself, so we do not need it to be initialized in subshells. - [x] add recursion guard around `setup-env.sh` - [x] add recursion guard around `setup-env.csh` - [x] add recursion guard around `setup-env.fish`
2020-07-10Fix gcc + binutils compilation. (#9024)cedricchevalier191-3/+1
* fix binutils deptype for gcc binutils needs to be a run dependency of gcc * Fix gcc+binutils build on RHEL7+ static-libstdc++ is not available with system gcc. Anyway, as it is for bootstraping, we do not really care depending on a shared libstdc++. Co-authored-by: Michael Kuhn <michael@ikkoku.de>
2020-07-10autotools bugfix: handle missing config.guess (#17356)Michael Kuhn1-2/+2
Spack was attempting to calculate abspath on the located config.guess path even when it was not found (None); this commit skips the abspath calculation when config.guess is not found.
2020-07-10inel-mpi: fix for wrong structure name instroduced in ea8a0be4 (#17382)TZ1-1/+1
it's mpi_compiler_wrappers and not mpi_compiler._wrappers fixes 2nd part of #17371
2020-07-10Fix Intel MPI super invocation, again (#17378)Adam J. Stewart1-1/+1
2020-07-10autotools: Fix config.guess detection, take two (#17333)Michael Kuhn1-5/+3
The previous fix from #17149 contained a thinko that produced errors for packages that overwrite configure_directory.
2020-06-30changelog for v0.15.0v0.15.0Gregory Becker1-2/+96
2020-06-30bump version numberGregory Becker3-7/+12
2020-06-30Activate environment in container file (#17316)Glenn Johnson2-2/+4
* Activate environment in container file This PR will ensure that the container recipes will build the spack environment by first activating the environment. * Deactivate environment before environment collection For Singularity, the environment must be deactivated before running the command to collect the environment variables. This is because the environment collection uses `spack env activate`.
2020-06-30run github workflows on release branches (#17317)Greg Becker4-0/+4
2020-06-30Don't detect "classic" on Cray to avoid a compiler bug (#17314)Massimiliano Culpo4-2/+16
* Don't detect "classic" on Cray to avoid a compiler bug * add tests Co-authored-by: Gregory Becker <becker33@llnl.gov>
2020-06-30Add fish shell support (#9279)Johannes Blaschke10-6/+1171
* share/spack/setup-env.fish file to setup environment in fish shell * setup-env.fish testing script * Update share/spack/setup-env.fish Co-Authored-By: Elsa Gonsiorowski, PhD <gonsie@me.com> * Update share/spack/qa/setup-env-test.fish Co-Authored-By: Adam J. Stewart <ajstewart426@gmail.com> * updates completions using `spack commands --update-completion` * added stderr-nocaret warning * added fish shell tests to CI system Co-authored-by: becker33 <becker33@llnl.gov> Co-authored-by: Adam J. Stewart <ajstewart426@gmail.com> Co-authored-by: Elsa Gonsiorowski, PhD <gonsie@me.com>
2020-06-30Cray compiler: fix implicit rpaths for classic versions (#17310)Greg Becker4-14/+41
* check link dirs for existence
2020-06-30cmake v3.17.3 (#17313)Andrew Gaspar1-0/+1
2020-06-30half: fix __F16C__ include of immintrin.h (#17272)Andrew W Elble2-0/+25
Small fix so that immintrin.h gets included properly when the compiler sets __F16C__. Upstream has been notified.
2020-06-30filebench:remove autoreconf() (#17305)darmac1-8/+0
2020-06-30add constrain for hpx 1.4.* and boost 1.73.0 (#17307)albestro1-0/+4
https://github.com/STEllAR-GROUP/hpx/issues/4728#issuecomment-640685308
2020-06-30cleverleaf: Add C++ link flags for Fujitsu. (#17308)Tomoki, Karatsu2-0/+14
2020-06-30Add OpenFOAM 2006 (2020-06) release (#17309)Mark Olesen1-0/+1
Co-authored-by: Mark Olesen <Mark.Olesen@esi-group.com>
2020-06-30Catch2 v2.12.3 (#17312)Andrew Gaspar1-1/+7
Added master branch, too
2020-06-30[whizard] Fix Runtime Compiler Paths (#17300)vvolkl1-0/+12
* [whizard] fix runtime compilers fix * [whizard] flake8 * [whizard] add master branch
2020-06-30[py-mdanalysis] new version and added dependencies (#16819)Jen Herting1-10/+36
* [py-mdanalysis] new version and added dependencies Original commit message: Author: Andrew Elble <aweits@rit.edu> Date: Thu Nov 14 08:35:14 2019 -0500 mdanalysis * [py-mdanalysis] python is type build/run * [py-mdanalysis] updated numpy version requirement for all listed versions of py-mdanalysis * [py-mdanalysis] updated biopython version requirement for all listed versions of py-mdanalysis * [py-mdanalysis] updated py-griddataformats version requirement for all listed versions of py-mdanalysis * [py-mdanalysis] gsd only required after version 1.17.0 and requires gsd@1.4.0 * [py-mdanalysis] only requires mmtf-python after version 0.16.0 and requires version 1.0.0 * [py-mdanalysis] has required py-joblib since version 0.16 * [py-mdanalysis] updated py-scipy version requirement for all listed versions of py-mdanalysis * [py-mdanalysis] updated py-matplotlib version requirement for all listed versions of py-mdanalysis * [py-mdanalysis] has required py-mock since version 0.18.0 * [py-mdanalysis] py-scikit-learn only required after version 0.16.0 and only for +analysis variant * [py-mdanalysis] Reordered and reformatted for readability * [py-mdanalysis] flake8 fixes * [py-mdanalysis] proactively adding version 1.0.0 while I'm here since major release * [py-mdanalysis] fixing some forgotten colons
2020-06-30[py-crossmap] added version 0.3.9 (#17233)Jen Herting1-2/+2
* [py-crossmap] added version 0.3.9 * [py-crossmap] py-numpy not required * [py-crossmap] py-cython must be >= 0.17
2020-06-30[ruby] fixing path to gcc such that users can use gem to install nati… ↵Jen Herting1-0/+11
(#17141) * [ruby] fixing path to gcc such that users can use gem to install native gems to their home directory * [ruby] working on making flake8 happier * [ruby] Line can't really be split cleanly. Enhancing flake8's calm. ya learn something new every day... * [ruby] line break where requested * [ruby] make raw string * [ruby] only running for x86_64-linux everything else is untested * [ruby] finding rbconfig.rb in a cross platform manner
2020-06-30New package/graphblast (#17289)Sinan1-0/+42
* new package: GraphBlast * polish * add cuda_arch setup * flake8 * the package requires cuda variant and dependency * add comments * define cuda_arch * implement multiple and custom cuda arches * tidy up, improve * flake8 * improve style * add variant description * use patch method, add new version for latest commit building since master now fails * remove gcc conflict, tidy up * also indicate build range for boost Co-authored-by: Sinan81 <sbulut@3vgeomatics.com> Co-authored-by: Sinan81 <Sinan81@github>
2020-06-30dssp: new package at v3.1.4 (#17188)Harsh Bhatia2-5/+42
Renamed xspp to hspp