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2019-12-18package_sanity: add a test to enforce no nonexisting dependencies in builtinTodd Gamblin1-0/+16
We shouldn't allow packages to have missing dependencies in the mainline. - [x] Add a test to enforce this.
2019-12-18possible_dependencies() now reports missing dependenciesTodd Gamblin2-15/+48
- Add an optional argument so that `possible_dependencies()` will report missing dependencies. - Add a test to ensure it works. - Ignore missing dependencies in `possible_dependencies()` by default.
2019-12-18package: add spack.package.possible_dependencies methodTodd Gamblin2-4/+53
- this version allows getting possible dependencies of multiple packages or specs at once. - New method handles calling `PackageBase.possible_dependencies` multiple times and passing `visited` dict around.
2019-12-18performance: speed up `spack find` in environmentsTodd Gamblin1-7/+11
`Environment.added_specs()` has a loop around calls to `Package.installed()`, which can result in repeated DB queries. Optimize this with a read transaction in `Environment`.
2019-12-18performance: `spack spec` should use a read transacction with -ITodd Gamblin1-9/+26
`spack spec -I` queries the database for installation status and should use a read transaction around calls to `Spec.tree()`.
2019-12-18concretization: improve performance by avoiding database locksTodd Gamblin1-4/+6
Checks for deprecated specs were repeatedly taking out read locks on the database, which can be very slow. - [x] put a read transaction around the deprecation check
2019-12-18performance: memoize spack.architecture.get_platform()Todd Gamblin2-0/+8
`get_platform()` is pretty expensive and can be called many times in a spack invocation. - [x] memoize `get_platform()`
2019-12-18bugfix: don't fail if checking for "real" compiler versionTodd Gamblin1-1/+6
doesn't understand a custom, user-defined compiler version. However, if the compiler's version check fails, you can't build anything with the custom compiler. - [x] Be more lenient: fall back to the custom compiler version and use it verbatim if the version check fails.
2019-12-18bugfix: `pgcc -V` returns 2 on power machinesTodd Gamblin2-3/+9
`pgcc -V` was failing on power machines because it returns 2 (despite correctly printing version information). On x86_64 machines the same command returns 0 and doesn't cause an error. - [x] Ignore return value of 2 for pgcc when doign a version check
2019-12-17Fix argparse rST parsing of help messages (#14014)Adam J. Stewart1-2/+3
Thanks!
2019-12-17microarchitectures: readable names for AArch64 vendors (#13825)Massimiliano Culpo4-29/+102
Vendors for ARM come out of `/proc/cpuinfo` as hex numbers instead of readable strings. - Add support for associating vendor names with the hex numbers. - Also move these mappings from Python code to `microarchitectures.json` - Move darwin feature name mappings to `microarchitectures.json` as well
2019-12-14match bootstrapped compiler to architecture (#14059)Greg Becker1-0/+1
2019-12-14package hash: gracefully handle @when with non-string args (#14153)Peter Scheibel2-26/+45
* when constructing package hash, default to including a method in the content hash if we can't determine whether it would be included by examining the AST * add a test for updated content-hash calculations * refactor content hash tests to eliminate repeated lines
2019-12-13Split out CDash options to a separate help document (#13704)Zack Galbreath2-12/+57
Prevent `spack help install` from getting too cluttered with CDash-specific documentation.
2019-12-13Patch fetching: remove unnecessary argumentPeter Josef Scheibel3-8/+4
2019-12-13Mirrors: skip attempts to fetch BundlePackagesPeter Josef Scheibel1-0/+10
BundlePackages use a noop fetch strategy. The mirror logic was assuming that the fetcher had a resource to cach after performing a fetch. This adds a special check to skip caching if the stage is associated with a BundleFetchStrategy. Note that this should allow caching resources associated with BundlePackages.
2019-12-13Mirrors: avoid re-downloading patchesPeter Josef Scheibel2-20/+28
When updating a mirror, Spack was re-retrieving all patches (since the fetch logic for patches is separate). This updates the patch logic to allow the mirror logic to avoid this.
2019-12-13Mirrors: perform checksum of fetched sourcesPeter Josef Scheibel1-0/+1
Since cache_mirror does the fetch itself, it also needs to do the checksum itself if it wants to verify that the source stored in the mirror is valid. Note that this isn't strictly required because fetching (including from mirrors) always separately verifies the checksum.
2019-12-13Mirrors: fix cosmetic symlink targetsPeter Josef Scheibel2-1/+34
The targets for the cosmetic paths in mirrrors were being calculated incorrectly as of fb3a3ba: the symlinks used relative paths as targets, and the relative path was computed relative to the wrong directory.
2019-12-13Allow repeated invocations of 'mirror create'Peter Josef Scheibel1-0/+6
When creating a cosmetic symlink for a resource in a mirror, remove it if it already exists. The symlink is removed in case the logic to create the symlink has changed.
2019-12-10pytest: add __init__ files for all test subdirs (#13889)Greg Becker5-6/+22
* pytest: add __init__ files for all test subdirs * add licenses to empty files * Fix Sphinx warning message about comment within docstring * Further fixes to Sphinx docstring
2019-12-10Better error message when setting unknown variants during concretization ↵Massimiliano Culpo3-8/+17
(#13128) fixes #13124
2019-12-09Follow up/11117 fixes and testing (#13607)Omar Padron10-158/+272
* fix docstring in generate_package_index() refering to "public" keys as "signing" keys * use explicit kwargs in push_to_url() * simplify url_util.parse() per tgamblin's suggestion * replace standardize_header_names() with the much simpler get_header() * add some basic tests * update s3_fetch tests * update S3 list code to strip leading slashes from prefix * correct minor warning regression introduced in #11117 * add more tests * flake8 fixes * add capsys fixture to mirror_crud test * add get_header() tests * use get_header() in more places * incorporate review comments
2019-12-09environments: allow 'add' command to add virtuals (#13787)Greg Becker2-2/+26
This PR allows virtual packages to be added to the specs list using the add command. Virtual packages are already allowed in named lists in spack environments/stacks, and they are already allowed in the specs list when added using the yaml directly.
2019-12-09Apply URLFetchStrategy to ftp:// and ftps:// url schemes (#13939)Andras Wacha1-1/+3
* Apply URLFetchStrategy to ftp:// and ftps:// url schemes * Corrected trailing whitespace error
2019-12-08Tuneup docs re setting up sphinx for building docs (#14005)George Hartzell1-6/+14
I have, more than once, tried to install the list of things that need to build the docs, only to discover that the list doesn't use Spack's package names. I'm tired of facepalming.... While I was there I touched up the prose about activating the new Python packages; activating a python package doesn't add anything to your PYTHONPATH, it links things into a directory that's *already* on your PYTHONPATH. Note that this all presupposes that you're using that same python....
2019-12-06Spec Header Dirs: Only first include/ (#13991)Axel Huebl2-2/+16
* CUDA HeaderList: Unit Test * Spec Header Dirs: Only first include/ Avoid matching recurringly nested include paths that usually refer to internally shipped libraries in packages. Example in CUDA Toolkit, shipping a libc++ fork internally with libcu++ since 10.2.89: `<prefix>/include/cuda/some/more/details/include/` or `<prefix>/include/cuda/std/detail/libcxx/include` regex: non-greedy first match of include Co-Authored-By: Massimiliano Culpo <massimiliano.culpo@gmail.com> * CUDA: Re-Enable 10.2.89 as Default
2019-12-06docs: Alphabetize create cmd template options (#13993)Tamara Dahlgren1-1/+2
* Bugfix: Display template options for create command. * Alphabetize "spack create" template options for readability * Revert template choices format; alphabetize list * flake8 fix
2019-12-06Bugfix: spack find -p fails in environment (#13972)Greg Becker3-1/+26
* force spack find -p to print abstract specs without prefixes * hashes have the same issue; improve handling of find -L to match find -l
2019-12-06docs: Minimal BundlePackage build system doc (#13992)Tamara Dahlgren2-0/+53
* Minimal BundlePackage build system doc * Add link to new bundlepackage file * Fixed link bug and added create command example
2019-12-05cdash: fix reporting issue with python 3Scott Wittenburg1-1/+4
2019-12-04patching: do strict version range checking (#13989)Peter Scheibel3-2/+19
* apply strict constraint checks for patches, otherwise Spack may incorrectly treat a version range constraint as satisfied when mixing x.y and x.y.z versions * add mixed version checks to version comparison tests
2019-12-04version bump: 0.13.2Todd Gamblin1-1/+1
2019-12-04Bugfix: allow missing modules if they are blacklisted (#13540)Peter Scheibel4-30/+115
`spack module loads` and `spack module find` previously failed if any upstream modules were missing. This prevented it from being used with upstreams (or, really, any spack instance) that blacklisted modules. This PR makes module finding is now more lenient (especially for blacklisted modules). - `spack module find` now does not report an error if the spec is blacklisted - instead, it prints a single warning if any modules will be omitted from the loads file - It comments the missing modules out of the loads file so the user can see what's missing - Debug messages are also printed so users can check this with `spack -d...` - also added tests for new functionality
2019-12-04Fix spack test when SPACK_ROOT isn't set (#13980)Adam J. Stewart1-3/+4
2019-12-04Fixed x86-64 optimization flags for clang (#13913)Massimiliano Culpo3-53/+32
* Fixed x86-64 optimization flags for clang * Fixed expected results in unit tests Before the flags used where the one for llc, the underlying compiler from LLVM IR to machine assembly. It turns out that the semantic of `-march`, `-mtune` and `-mcpu` changes from clang front-end to llc. I found no definitive reference for the flags submitted in this PR, but I checked the assembly on a vectorizable function using Godbolt's web-site.
2019-12-02Speedup environment activation (#13557)Massimiliano Culpo2-2/+13
* Add a transaction around repeated calls to `spec.prefix` in the activation process * cache the computation of home in the python package to speed up setting deps * ensure that module-scope variables are only set *once* per module
2019-12-02Version bump: 1.13.1 (#13942)Adam J. Stewart1-1/+1
2019-11-30Armor test script against shebang character limit if appropriate. (#12447)Chris Green1-0/+2
2019-11-29Mass conversion of setup_(dependent_)?environment (#13924)Adam J. Stewart3-10/+10
* Mass conversion of setup_(dependent_)?environment * prefix -> self.prefix
2019-11-26use semicolons instead of newlines in module/python command (#13904)Greg Becker1-1/+1
2019-11-26IntelPackage: setup_env -> setup_build_env (#13888)Adam J. Stewart1-47/+24
2019-11-26buildcache list: do not display duplicate specs (#13758)Massimiliano Culpo2-6/+25
fixes #13757
2019-11-26Remove warning from the "Custom Extensions" section of the docs (#13804)Massimiliano Culpo1-6/+0
Extensions have been available for a while and the overall design seems solid enough to be feasible for extensions without losing backward compatibility.
2019-11-25add package cuda@10.2.89 (#13819)René Widera1-3/+10
* add package cuda@10.2.89 add CUDA 10.2 support * CudaPackage: Add 10.2 Conflicts * CUDA: Modernize Run Environment See #11115
2019-11-22cmd/install: remove unused install_status option (#13751)Greg Becker1-1/+1
* cmd/install: remove unused install_status option * update bash completions for spack install
2019-11-21Fixed detection for cascadelake microarchitecture (#13820)Massimiliano Culpo3-1/+23
fixes #13803
2019-11-20mirror bug fixes: symlinks, duplicate patch names, and exception handling ↵Paul Ferrell4-17/+24
(#13789) * Some packages (e.g. mpfr at the time of this patch) can have patches with the same name but different contents (which apply to different versions of the package). This appends part of the patch hash to the cache file name to avoid conflicts. * Some exceptions which occur during fetching are not a subclass of SpackError and therefore do not have a 'message' attribute. This updates the logic for mirroring a single spec (add_single_spec) to produce an appropriate error message in that case (where before it failed with an AttributeError) * In various circumstances, a mirror can contain the universal storage path but not a cosmetic symlink; in this case it would not generate a symlink. Now "spack mirror create" will create a symlink for any package that doesn't have one.
2019-11-20Features/expand microarch for aarch64 (#13780)t-karatsu4-0/+117
* Add process to determine aarch64 microarchitecture * add microarchitectures for thunderx2 and a64fx * Add optimize flags for gcc on aarch64 family processors thunderx2 and a64fx. * Add optimize flags for clang on aarch64 family processors thunderx2 and a64fx * Add testing for thunderx2 and a64fx microarchitectures
2019-11-18binary distribution: relocate text files properly in relative binaries (#13578)Greg Becker2-10/+12
* Make relative binaries relocate text files properly * rb strings aren't valid in python 2 * move perl to new interface for setup_environment family methods