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Using `sys.executable` to run Python in a sub-shell doesn't always work in a virtual environment as the `sys.executable` Python is not necessarily compatible with any loaded spack/other virtual environment.
- revert use of sys.executable to print out subshell environment (#14496)
- try instead to use an available python, then if there *is not* one, use `sys.executable`
- this addresses RHEL8 (where there is no `python` and `PYTHONHOME` issue in a simpler way
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* Fix use of sys.executable for module/env commands
* Fix unit tests
* More consistent quotation, less duplication
* Fix import syntax
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When removing packages from a view, extensions were being deactivated
in an arbitrary order. Extensions must be deactivated in preorder
traversal (dependents before dependencies), so when this order was
violated the view update would fail.
This commit ensures that views deactivate extensions based on a
preorder traversal and adds a test for it.
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Despite trying very hard to keep dicts out of our hash algorithm, we seem
to still accidentally add them in ways that the tests can't catch. This
can cause errors when hashes are not computed deterministically.
This fixes an error we saw with Python 3.5, where dictionary iteration
order is random. In this instance, we saw a bug when reading Spack
environment lockfiles -- The load would fail like this:
```
...
File "/sw/spack/lib/spack/spack/environment.py", line 1249, in concretized_specs
yield (s, self.specs_by_hash[h])
KeyError: 'qcttqplkwgxzjlycbs4rfxxladnt423p'
```
This was because the hashes differed depending on whether we wrote `path`
or `module` first when recomputing the build hash as part of reading a
Spack lockfile. We can fix it by ensuring a determistic iteration order.
- [x] Fix two places (one that caused an issue, and one that did
not... yet) where our to_node_dict-like methods were using regular python
dicts.
- [x] Also add a check that statically analyzes our to_node_dict
functions and flags any that use Python dicts.
The test found the two errors fixed here, specifically:
```
E AssertionError: assert [] == ['Use syaml_dict instead of ...pack/spack/spec.py:1495:28']
E Right contains more items, first extra item: 'Use syaml_dict instead of dict at /Users/gamblin2/src/spack/lib/spack/spack/spec.py:1495:28'
E Full diff:
E - []
E + ['Use syaml_dict instead of dict at '
E + '/Users/gamblin2/src/spack/lib/spack/spack/spec.py:1495:28']
```
and
```
E AssertionError: assert [] == ['Use syaml_dict instead of ...ack/architecture.py:359:15']
E Right contains more items, first extra item: 'Use syaml_dict instead of dict at /Users/gamblin2/src/spack/lib/spack/spack/architecture.py:359:15'
E Full diff:
E - []
E + ['Use syaml_dict instead of dict at '
E + '/Users/gamblin2/src/spack/lib/spack/spack/architecture.py:359:15']
```
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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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`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
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* 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
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`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
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Fixes #13529
Fixes #13509
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* 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.
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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.
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path (which includes the file name) (#13727)
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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.
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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.
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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
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* environments: make shell modifications partially unconditional
* flake
* missing module name
* add regression test
* flake
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* 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
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- [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
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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`.
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* fix issue where spack.util.url.join() failed to correctly handle absolute path components
* add url util tests
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This fixes a UnicodeDecodeError in the sbang patching function.
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