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This PR adds the paper library to spack.
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* added build dependences required after cairo package change
* fixed pango build dependencies
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* patch cairo build files for build without fontconfig
* added build dependencies for cairo
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* Add Avizo Recipe
* make changes as per review
* fix home url and linting
* Fix url
* fix identation
* change checksum to sha256 instead of md5
* fix installation
* fix lint
* fix identation
* make it compatible with python 2.6
* enhancing recipe and fixing avizo licensing
changes as per suggestions from reviewer; fix licensing
* fix identation
* use new setup_run_environment function
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* aspa: Fix common errors.
* defined new member 'Vec_value_type' in 'self' namespace.
* fix narrowing error.
* fix patch about typecast.
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This PR moves build smoke tests from TravisCI and migrates them to Github Actions. The result is that build tests are performed in parallel with unit tests and they don't hog additional resources on Travis. The workflow will not run if a PR only changes packages in the built-in repository, but will always run on pushes to develop or master.
* Removed build tests from Travis and passed them to Github Actions
* Store ~/.ccache in Github Actions cache
* Add filters on paths and make sure this workflow don't run
* Use paths-ignore and exclude only files in the built-in repo
* Added a badge to README.md
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Remove a few remaining mentions of the pyqver package, which was removed in #14289.
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This commit removes the `python_version.py` unit test module
and the vendored dependencies `pyqver2.py` and `pyqver3.py`.
It substitutes them with an equivalent check done using
`vermin` that is run as a separate workflow via Github Actions.
This allows us to delete 2 vendored dependencies that are unmaintained
and substitutes them with a maintained tool.
Also, updates the list of vendored dependencies.
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Before this commit we used to run the entire unit test suite
in the presence of a failure. Since we currently rely a lot
on the state of the filesystem etc. the end report was most
of the time showing spurious failures that were a consequence
of the first failing test.
This PR makes unit tests exit at the first failing test
Also, pin codecov at v4.5.4 (last one supporting Python 2.6)
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`ViewDescriptor.regenerate()` calls `get_all_specs()`, which reads
`spec.yaml` files, which is slow. It's fine to do this once, but
`view.remove_specs()` *also* calls it immediately afterwards.
- [x] Pass the result of `get_all_specs()` as an optional parameter to
`view.remove_specs()` to avoid reading `spec.yaml` files twice.
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`ViewDescriptor.regenerate()` was copying specs and stripping build
dependencies, which clears `_hash` and other cached fields on concrete
specs, which causes a bunch of YAML hashes to be recomputed.
- [x] Preserve the `_hash` and `_normal` fields on stripped specs, as
these will be unchanged.
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`os.path.exists()` will report False if the target of a symlink doesn't
exist, so we can avoid a costly call to realpath here.
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`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.
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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
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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.
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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.
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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()`
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`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.
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`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`.
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`spack spec -I` queries the database for installation status and should
use a read transaction around calls to `Spec.tree()`.
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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
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`get_platform()` is pretty expensive and can be called many times in a
spack invocation.
- [x] memoize `get_platform()`
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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.
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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.
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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.
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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.
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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.
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(#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.
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`ViewDescriptor.regenerate()` calls `get_all_specs()`, which reads
`spec.yaml` files, which is slow. It's fine to do this once, but
`view.remove_specs()` *also* calls it immediately afterwards.
- [x] Pass the result of `get_all_specs()` as an optional parameter to
`view.remove_specs()` to avoid reading `spec.yaml` files twice.
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`ViewDescriptor.regenerate()` was copying specs and stripping build
dependencies, which clears `_hash` and other cached fields on concrete
specs, which causes a bunch of YAML hashes to be recomputed.
- [x] Preserve the `_hash` and `_normal` fields on stripped specs, as
these will be unchanged.
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`os.path.exists()` will report False if the target of a symlink doesn't
exist, so we can avoid a costly call to realpath here.
|
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`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.
|
|
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
|
|
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.
|
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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.
|
|
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()`
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`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.
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comments. (#14281)
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