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2019-07-17Add support for .txz and .tbz2 file extensions (#12048)Adam J. Stewart3-1/+46
2019-07-17tests: uninstall_by_spec error and rpath_args tests (#11971)Tamara Dahlgren2-0/+26
* tests: Add uninstall_by_spec error tests. These tests were originally included in PR #11797.
2019-07-17feature: Allow developers to use Spack for partial builds (#12006)Greg Becker1-1/+5
Added new diy option.
2019-07-16Ignore Modules v4 environment variables in `from_sourcing_file` (#10753)Massimiliano Culpo3-117/+311
* from_sourcing_file: fixed a bug + added a few ignored variables closes #7536 Credits for this change goes to mgsternberg (original author of #7536) The new variables being ignored are specific to Modules v4. * Use Spack Executable in 'EnvironmentModifications.from_sourcing_file' Using this class avoids duplicating lower level logic to decode stdout and handle non-zero return codes * Extracted a function that returns the environment after sourcing files The logic in `EnvironmentModifications.from_sourcing_file` has been simplified by extracting a function that returns a dictionary with the environment one would have after sourcing the files passed as argument. * Further refactoring of EnvironmentModifications.from_sourcing_file Extracted a function that sanitizes a dictionary removing keys that are blacklisted, but keeping those that are whitelisted. Blacklisting and whitelisting can be done on literals or regex. Extracted a new factory that creates an instance of EnvironmentModifications from a diff of two environments. * Added unit tests * PS1 is blacklisted + more readable names for some variables
2019-07-15Fix build_jobs exceeding number of coresMichael Kuhn1-0/+1
All documentation mentions that `build_jobs` is limited by the number of cores available in the system. This is also enforced when setting it via `--jobs`. However, when setting it via `config.yaml`, it can exceed the number of cores available, making builds run out of memory.
2019-07-15Add auto-dispatch specification to Intel packages (#11697)Glenn Johnson1-1/+33
This PR adds the ability to specify the auto-dispatch targets that can be used by the Intel compilers. The `-ax` flag will be written to the respective compiler configuration files. This ability is very handy when wanting to build optimized builds for various architectures. This PR does not set any optimization flags, however.
2019-07-15spack uninstall can uninstall specs with multiple roots (#11977)Massimiliano Culpo2-14/+52
Fixes #3690 Fixes #5637 Uninstalling dependents of a spec was relying on a traversal of the parents done by inspecting spec._dependents. This is in turn a DependencyMap that maps a package name to a single DependencySpec object (an edge in the DAG) and cannot thus model the case where a spec has multiple configurations of the same parent package installed (for example if different versions of the same Python library depend on the same Python installation). This commit works around this issue by constructing the list of specs to be uninstalled in an alternative way, and adds tests to verify the behavior. The core issue with DependencyMap is not resolved here.
2019-07-12find_libraries searches lib and lib64 before prefix (#11958)Tim Fuller2-15/+23
The default library search for a package checks the lib/ and lib64/ directories for libraries before the root prefix, in order to save time when searching for libraries provided by externals (which e.g. may have '/usr/' as their root). This moves that logic into the "find_libraries" utility method so packages implementing their own custom library search logic can benefit from it. This also updates packages which appear to be replicating this logic exactly, replacing it with a single call to "find_libraries".
2019-07-12Copy --{use,no}-cache from install to bootstrap (#11786)Oliver Breitwieser1-1/+10
2019-07-12'spack compiler add' resolves relative path to absolute path (#11792)Carson Woods1-0/+1
Fixes #11782 Spack was not properly resolving relative paths to absolute paths when a relative path was passed to "spack compiler add [PATH]". Now, if provided a relative path, the absolute path is written to compilers.yaml rather than the relative path.
2019-07-12Add template creation test, --skip-editor option (#11970)Tamara Dahlgren2-2/+63
* Add template creation test * Added --skip-editor option to "spack create": normally "spack create" opens an editor for the user after generating a package file; when the --skip-editor option is used, "spack create" only generates the package file and does not open an editor * Added --skip-editor option to bash completion
2019-07-12Fix pic_flag and test contents about Fujitsu compiler. (#11996)t-karatsu2-6/+6
2019-07-12bugfix: show dot after namespaces in `spack find -N` (#11945)Todd Gamblin2-1/+14
- Namepsaces were shown without dots after the new format strings were added. - Add a test for `spack find` to ensure that find -N shows the right output.
2019-07-11test: Extra possible-dependencies coverage check (#11988)Tamara Dahlgren1-1/+10
2019-07-11Rename build logs and make names consistent (#11806)Tamara Dahlgren9-92/+228
Fixes #11781 * Rename build log to spack-build-log.txt * Rename environment variables file to spack-build-env.txt * The name of the log and env files is now the same during the build and after the build completes * Update packages which referred to the build log/env files * For packages installed before this commit using older names for the build and env files, search for the older names
2019-07-10tutorial: correct image link on tutorial pageTodd Gamblin1-1/+1
2019-07-10tutorial: updates slides for DOE/NSF workshop.Todd Gamblin1-9/+8
2019-07-08bugfix: conflicts should print out the spec that has the conflict (#11947)Todd Gamblin1-1/+6
- Fix a bug introdcued by removing parse_anonymous_spec() - Conflicts' when specs are now *actually* anonymous, and the name of the package is implicit, so we need to remember to add it back to error messages.
2019-07-05bugfix: always generate a stack trace when spack is run with --debug (#11940)Todd Gamblin1-0/+5
- We weren't previously printing stack traces on SystemExit or KeyboardInterrupts. - Either raise or print the stacktrace in these cases.
2019-07-01specs: remove parse_anonymous_spec(); use Spec() insteadTodd Gamblin6-144/+168
- `parse_anonymous_spec()` is a vestige of the days when Spack didn't support nameless specs. We don't need it anymore because now we can write Spec() for a spec that will match anything, and satisfies() semantics work properly for anonymous specs. - Delete `parse_anonymous_spec()` and replace its uses with simple calls to the Spec() constructor. - make then handling of when='...' specs in directives more consistent. - clean up Spec.__contains__() - refactor directives and tests slightly to accommodate the change.
2019-07-01cray: use the cle-release file to determine CNL versionTodd Gamblin2-6/+72
- CNL OS previously used the *Cray PE* version to determine the OS version. Cray does not synchronize PE and CLE releases; you can run CLE7 with PrgEnv 6 (and NERSC currently does). - Fix Spack's OS detection by using the cle-release file to detect the OS version. This file is updated with every CLE OS release. - Add some tests for our parsing logic
2019-07-01buildcache: add replace_prefix_bin function to deal with hard coded paths in ↵Patrick Gartung1-8/+27
libraries and executables. (#11882)
2019-06-30style: remove unnecessary NOQA exceptionsTodd Gamblin1-9/+9
2019-06-29Allow uninstalling missing packages (#11874)Peter Scheibel2-6/+19
Remove package access from directory_layout; add regression test to ensure that specs can be uninstalled without a package being known
2019-06-28docs: add example for an external module in packages.yamlMark W. Krentel1-2/+12
Add an example of a 'modules:' entry for an external package in packages.yaml. The 'External Packages' section of 'Build Customization' mentions 'paths:' and 'modules:' and gives an example of paths, but not modules.
2019-06-26Add --frontend and --backend option to spack arch command (#11746)Toyohisa Kameyama2-2/+26
2019-06-24Fix for #10063 : install from source if buildcache with different DAG exist ↵Patrick Gartung1-1/+6
(#11834) * Fix for #10063 : install from source if buildcache with different DAG exist * Flake8
2019-06-21Use Stage.archive_file to access non-expanded download (#11817)Peter Scheibel2-4/+25
Fixes #11816 Allow packages to refer to non-expanded downloads (e.g. a single script) using Stage.archive_file. This addresses a regression from #11688 and adds a unit test for it.
2019-06-20Ignore pgcc-llvm and friends, default to pgcc (#11703)Adam J. Stewart1-4/+0
This change reverts to the previous behavior of only looking for pgcc and friends, not pgcc-llvm and friends. The llvm variant doesn't support all the same features as the traditional variant of the pgi code generator; this change avoids treating the llvm variant as a default pgi compiler. This retains the changes in #10704 which accept the "LLVM" suffix of the version string of the PGI compiler, which allows users to explicitly add the llvm-pgi compiler if desired.
2019-06-20Resources: use expanded archive name by default (#11688)Peter Scheibel4-45/+135
For resources, it is desirable to use the expanded archive name of the resource as the name of the directory when adding it to the root staging area. #11528 established 'spack-src' as the universal directory where source files are placed, which also affected the behavior of resources managed with Stages. This adds a new property ('srcdir') to Stage to remember the name of the expanded source directory, and uses this as the default name when placing a resource directory in the root staging area. This also: * Ensures that downloaded sources are archived using the expanded archive name (otherwise Spack will not be able to determine the original directory name when using a cached archive). * Updates working_dir context manager to guarantee restoration of original working directory when an exception occurs * Adds a "temp_cwd" context manager which creates a temporary directory and sets it as the working directory
2019-06-19fixed spec dependence attribute writing. Fixes #11686 (#11776)Gregory Lee1-1/+1
2019-06-18Remove test dependency on /usr/bin/gcc (#11769)Greg Becker1-3/+10
The regression test for #11678 fails on at least some Mac OS systems because they have a /usr/bin/gcc that is secretly clang. This PR replaces the dependency on a system gcc executable with a test-generated script that generates the expected output for the compiler logic.
2019-06-18Rename build.out to build.txt (#11749)Elizabeth Fischer3-5/+5
Rename build.out to build.txt; makes it easier when people post log files to the Spack mailing list.
2019-06-17bugfix: use config fixture for stage tests (#11701)Tamara Dahlgren2-6/+23
Some tests introduced in #11528 temporarily set the user's `config:build_stage`, which affected (or created) a config.yaml file in the user's `$HOME/.spack` directory that could leave entries behind if the tests fail. This change ensures only temporary configuration files are used/affected by these tests.
2019-06-17docs: updates for `stage.source_path` (#11702)Tamara Dahlgren3-13/+37
2019-06-16docs: update tutorial page for ISC19 tutorial (#11742)Todd Gamblin1-10/+13
2019-06-15docs: fix config tutorial (#11715)Michael Kuhn1-30/+35
This fixes a few typos, adds a hint to `spack config blame` and brings the variant specification in line with other docs sections.
2019-06-13Ensure mock configuration directory is cleaned up on session exit. (#11700)Tamara Dahlgren1-1/+4
2019-06-13Add tests for "spack location" command (#11661)Tamara Dahlgren2-0/+135
The "spack location" command was previously untested. This also adds a check to ensure that composite Stages can report whether they were expanded (this property was previously only recorded in Stage but not in CompositeStage).
2019-06-13Always treat DIYStage as expanded (#11663)Tamara Dahlgren2-2/+73
DIYStage, used to treat a user-managed directory as a staging area, should always be considered expanded (i.e. the source has been decompressed if it was stored in an archive). This also: * Adds checks to ensure that the path used to instantiate a DIYStage refers to an existing directory. * Adds tests to check the behavior of DIYStage (including behavior added here, but it was generally untested before).
2019-06-12Update remaining packages to use Stage.source_path (#11662)Tamara Dahlgren2-3/+3
#11528 updated Stage to always store a Package's source in a fixed directory accessible via `Stage.source_path` This left behind a number of packages which were expecting to access the source code via `Stage.path`. This Updates those packages to use `Stage.source_path` instead. This also updates the name of the fixed directory: The original name of the fixed directory was "src", so if an expanded archive created a "src" directory, then users inspecting the directory structure could see paths like "src/src" (which wasn't wrong but could be confusing). Therefore this also updates the name of the fixed directory to "spack-src".
2019-06-12Make "spack compiler find" check PATH by default (#11683)Massimiliano Culpo5-21/+60
Fixes #11678 `spack compiler find` was not searching `PATH` when provided with no arguments. ea7910a updated the API for the search function and the command logic did not update how it called this function. This also adds a test to ensure that `spack compiler find` will collect compilers from `PATH`.
2019-06-11Add additional common C++ and Fortran header file extensions (#11600)Adam J. Stewart1-1/+8
* Add additional common C++ and Fortran header file extensions * Add .hxx extension * Add .txx and .tcc extensions * Add .icc extension
2019-06-11Add extra logic for C std flags on PGI, XL, and Cray (#11635)Chuck Atkins3-7/+57
2019-06-10Fix recursive module find for upstream dependencies (#11304)Peter Scheibel4-64/+223
"spack module tcl find -r <spec>" (and equivalents for other module systems) was failing when a dependency was installed in an upstream Spack instance. This updates the module index to handle locating module files for upstream Spack installations (encapsulating the logic in a new class called UpstreamModuleIndex); the updated index handles the case where a Spack installation has multiple upstream instances. Note that if a module is not available locally but we are using the local package, then we shouldn't use a module (i.e. if the package is also installed upstream, and there is a module file for it, Spack should not use that module). Likewise, if we are instance X using upstreams Y and Z like X->Y->Z, and if we are using a package from instance Y, then we should only use a module from instance Y. This commit includes tests to check that this is handled properly.
2019-06-08concretization: don't apply build-dep constraints for installed packages ↵Peter Scheibel3-5/+85
(#11594) Spack currently tries to unify everything in the DAG, but this is too strict for build dependencies, where it is fine to build a dependency with a tool that conflicts with a version fo that tool for a dependent's build. To enable a workaround for conflicts among build dependencies, so that users can install in multiple steps to avoid these conflicts, make the following changes: * Dont apply package dependency constraints for build deps of installed packages * Avoid applying constraints for installed packages vs. concrete packages * Mark all dependencies of installed packages as visited in normalization method * don't remove dependency links for concrete specs in flat_dependencies Also add tests: * Update test to ensure that link dependencies of installed packages have constraints applied * Add test to check for proper handling of transitive dependencies (which is currently not the case)
2019-06-07spack list: latest version (JSON) (#11652)Axel Huebl4-1/+81
List the latest version of each package in JSON encoding. Preparation for consumption for a "spack badge" service.
2019-06-07Compiler search uses a pool of workers (#10190)Massimiliano Culpo17-302/+503
- spack.compilers.find_compilers now uses a multiprocess.pool.ThreadPool to execute system commands for the detection of compiler versions. - A few memoized functions have been introduced to avoid poking the filesystem multiple times for the same results. - Performance is much improved, and Spack no longer fork-bombs the system when doing a `compiler find`
2019-06-06commands: remove unused `spack list --format=rst` (#11651)Todd Gamblin2-79/+0
- We use `spack list --foramt=html` now, as it is much faster and doesn't make the docs build take forever. - Remove `spack list --format=rst` as it is no longer used.
2019-06-06bugfix: StageComposite must include the `expanded` property` (#11647)Todd Gamblin1-0/+4