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2019-12-23performance: only regenerate env views once in `spack install`Todd Gamblin2-9/+29
`spack install` previously concretized, writes the entire environment out, regenerated views, then wrote and regenerated views again. Regenerating views is slow, so ensure that we only do that once. - [x] add an option to env.write() to skip view regeneration - [x] add a note on whether regenerate_views() shouldn't just be a separate operation -- not clear if we want to keep it as part of write to ensure consistency, or take it out to avoid performance issues.
2019-12-23performance: add read transactions for `install_all()` and `install()`Todd Gamblin1-31/+35
Environments need to read the DB a lot when installing all specs. - [x] Put a read transaction around `install_all()` and `install()` to avoid repeated locking
2019-12-23lock transactions: avoid redundant reading in write transactionsTodd Gamblin2-1/+62
Our `LockTransaction` class was reading overly aggressively. In cases like this: ``` 1 with spack.store.db.read_transaction(): 2 with spack.store.db.write_transaction(): 3 ... ``` The `ReadTransaction` on line 1 would read in the DB, but the WriteTransaction on line 2 would read in the DB *again*, even though we had a read lock the whole time. `WriteTransaction`s were only considering nested writes to decide when to read, but they didn't know when we already had a read lock. - [x] `Lock.acquire_write()` return `False` in cases where we already had a read lock.
2019-12-23lock transactions: ensure that nested write transactions writeTodd Gamblin2-1/+64
If a write transaction was nested inside a read transaction, it would not write properly on release, e.g., in a sequence like this, inside our `LockTransaction` class: ``` 1 with spack.store.db.read_transaction(): 2 with spack.store.db.write_transaction(): 3 ... 4 with spack.store.db.read_transaction(): ... ``` The WriteTransaction on line 2 had no way of knowing that its `__exit__()` call was the last *write* in the nesting, and it would skip calling its write function. The `__exit__()` call of the `ReadTransaction` on line 1 wouldn't know how to write, and the file would never be written. The DB would be correct in memory, but the `ReadTransaction` on line 4 would re-read the whole DB assuming that other processes may have modified it. Since the DB was never written, we got stale data. - [x] Make `Lock.release_write()` return `True` whenever we release the *last write* in a nest.
2019-12-23lock transactions: fix non-transactional writesTodd Gamblin4-172/+285
Lock transactions were actually writing *after* the lock was released. The code was looking at the result of `release_write()` before writing, then writing based on whether the lock was released. This is pretty obviously wrong. - [x] Refactor `Lock` so that a release function can be passed to the `Lock` and called *only* when a lock is really released. - [x] Refactor `LockTransaction` classes to use the release function instead of checking the return value of `release_read()` / `release_write()`
2019-12-23performance: avoid repeated DB locking on view generationTodd Gamblin1-10/+13
`ViewDescriptor.regenerate()` checks repeatedly whether packages are installed and also does a lot of DB queries. Put a read transaction around the whole thing to avoid repeatedly locking and unlocking the DB.
2019-12-23performance: 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`.
2019-12-23performance: `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()`.
2019-12-23concretization: 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
2019-12-23performance: 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()`
2019-12-23use `sys.executable` instead of `python` in `_source_single_file` (#14252)Sajid Ali1-1/+1
2019-12-23Patch fetching: remove unnecessary argumentPeter Josef Scheibel3-8/+4
2019-12-23Mirrors: 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.
2019-12-23Mirrors: 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.
2019-12-23Mirrors: 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.
2019-12-23Mirrors: 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.
2019-12-23Allow 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.
2019-12-23mirror 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.
2019-12-04update CHANGELOG.md for 0.13.2v0.13.2Todd Gamblin1-0/+40
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
2019-12-02Speedup environment activation (#13557)Massimiliano Culpo3-4/+21
* 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
2019-12-01bugfix: mirror path works for unknown versions (#13626)Todd Gamblin2-2/+8
`mirror_archive_path` was failing to account for the case where the fetched version isn't known to Spack. - [x] don't require the fetched version to be in `Package.versions` - [x] add regression test for mirror paths when package does not have a version
2019-12-01environments: don't try to modify run-env if a spec is not installed (#13589)Adam J. Stewart1-2/+2
Fixes #13529 Fixes #13509
2019-12-01use semicolons instead of newlines in module/python command (#13904)Greg Becker1-1/+1
2019-12-01verify.py: os.path.exists exception handling (#13656)Daryl W. Grunau1-14/+16
2019-11-17Document use of the maintainers field (#13748)Adam J. Stewart2-0/+19
2019-11-15Bugfix/config caching 13754 (#13759)Greg Becker1-2/+3
* remove reference to `spack.store` in method definition Referencing `spack.store` in method definition will cache the `spack.config.config` singleton variable too early, before we have a chance to add command line and environment scopes.
2019-11-15hwloc: added 'master' version pointing at the HEAD of the master branch (#13734)Massimiliano Culpo1-4/+6
2019-11-14Config option to allow gpg warning suppression (#13744)Greg Becker4-3/+17
Add a configuration option to suppress gpg warnings during binary package verification. This only suppresses warnings: a gpg failure will still fail the install. This allows users who have already explicitly trusted the gpg key they are using to avoid seeing repeated warnings that it is self-signed.
2019-11-14determine target relative to the link directory rather than the full link ↵Peter Scheibel1-3/+3
path (which includes the file name) (#13727)
2019-11-13Allow binary relocation of strings in relative binaries (#13724)Greg Becker2-15/+25
Binaries with relative RPATHS currently do not relocate strings hard-coded in binaries This PR extends the best-effort relocation of strings hard-coded in binaries to those whose RPATHs have been relativized.
2019-11-05`spack find` now displays variants and other spec constraintsv0.13.1Todd Gamblin3-4/+23
If you do this in a spack environment: spack add hdf5+hl hdf5+hl will be the root added to the `spack.yaml` file, and you should really expect `hdf5+hl` to display as a root in the environment. - [x] Add decoration to roots so that you can see the details about what is required to build. - [x] Add a test.
2019-11-05bugfix: uninstall should find concrete specs by DAG hashTodd Gamblin1-1/+9
This fixes a regression introduced in #10792. `spack uninstall` in an environment would not match concrete query specs properly after the index hash of enviroments changed. - [x] Search by DAG hash for specs to remove instead of by build hash
2019-11-04environments: make shell modifications partially unconditional (#13523)Greg Becker2-1/+37
* environments: make shell modifications partially unconditional * flake * missing module name * add regression test * flake
2019-11-04binary distribution: relocate text files properly in relative binaries (#13578)Greg Becker3-17/+37
* 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
2019-11-03bugfix: fetch prefers to fetch local mirrors over remote resources (#13545)Omar Padron3-8/+11
- [x] insert at beginning of list so fetch grabs local mirrors before remote resources - [x] update the S3FetchStrategy so that it throws a SpackError if the fetch fails. Before, it was throwing URLError, which was not being caught in stage.py. - [x] move error handling out of S3FetchStrategy and into web_util.read_from_url() - [x] pass string instead of URLError to SpackWebError
2019-11-03environments: only write when necessary (#13546)Greg Becker4-25/+66
This changes Spack environments so that the YAML file associated with the environment is *only* written when necessary (i.e., if it is changed *by spack*). The lockfile is still written out as before. There is a larger question here of which part of Spack should be responsible for setting defaults in config files, and how we can get rid of empty lists and data structures currently cluttering files like `compilers.yaml`. But that probably requires a rework of the default-setting validator in `spack.config`, as well as the code that uses `spack.config`. This will at least help for `spack.yaml`.
2019-11-01version bump: 0.13.1Todd Gamblin1-1/+1
2019-11-01bugfix: spack.util.url.join() now handles absolute paths correctly (#13488)Omar Padron3-2/+379
* fix issue where spack.util.url.join() failed to correctly handle absolute path components * add url util tests
2019-11-01sbang: use utf-8 for encoding when patching (#13490)Gregory Lee1-4/+13
This fixes a UnicodeDecodeError in the sbang patching function.
2019-11-01Specs with quoted flags containing spaces are parsed correctly (#13521)Massimiliano Culpo2-1/+22
2019-11-01targets: print a warning message before downgrading (#13513)Massimiliano Culpo2-25/+57
* Make package preferences a soft failure for targets, instead of a hard failure. * Added unit tests for preferences expressed via packages.yaml
2019-11-01Travis CI: Test Python 3.8 (#13347)Adam J. Stewart4-15/+35
* Travis CI: Test Python 3.8 * Fix use of deprecated cgi.escape method * Fix version comparison * Fix flake8 F811 change in Python 3.8 * Make flake8 happy * Use Python 3.8 for all test categories
2019-11-01Documentation: Database.query methods share docstrings (#13515)Greg Becker1-41/+53
Currently, query arguments in the Spack core are documented on the Database._query method, where the functionality is defined. For users of the spack python command, this makes the python builtin method help less than ideally useful, as help(spack.store.db.query) and help(spack.store.db.query_local) do not show relevant information. This PR updates the doc attributes for the Database.query and Database.query_local arguments to mirror everything after the first line of the Database._query docstring.
2019-11-01cuda: fix conflict statements for x86-64 targets (#13472)Massimiliano Culpo1-4/+6
* cuda: fix conflict statements for x86-64 targets fixes #13462 This build system mixin was not updated after the support for specific targets has been merged. * Updated the version range of cuda that conflicts with gcc@8: * Updated the version range of cuda that conflicts with gcc@8: for ppc64le * Relaxed conflicts for version > 10.1 * Updated versions in conflicts Co-Authored-By: Axel Huebl <axel.huebl@plasma.ninja>
2019-11-01cpu: fix clang flags for generic x86_64 (#13491)Greg Becker2-8/+16
* cpu: differentiate flags used for pristine LLVM vs. Apple's version
2019-11-01syaml_int type should use int.__repr__ rather than str.__repr__ (#13487)Peter Scheibel1-1/+1
2019-10-31elpa: prefer 2016.05.004 until sse/avx/avx2 issues are resolved (#13530)eugeneswalker1-1/+1
- configuration fails on newer versions when enabling sse/avx/avx2 - prefer an older version that will build with these features
2019-10-31trilinos: temporarily constrain netcdf@:4.7.1 (#13526)eugeneswalker1-1/+1
remove this when issues are resolved with `trilinos^netcdf@4.7.2`