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.
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.
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.
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.
* 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.
`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.
`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.
`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.
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()`
`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.
Users can now list mirrors of the main url in packages.
- [x] Instead of just a single `url` attribute, users can provide a list (`urls`) in the package, and these will be tried by in order by the fetch strategy.
- [x] To handle one of the most common mirror cases, define a `GNUMirrorPackage` mixin to handle all the standard GNU mirrors. GNU packages can set `gnu_mirror_path` to define the path within a mirror, and the mixin handles setting up all the requisite GNU mirror URLs.
- [x] update all GNU packages in `builtin` to use the `GNUMirrorPackage` mixin.
* Add symbols patch
* Apply symbols patch to pgmath
* Add github issue number for symbols patch.
* Add naromero77 as a maintainer.
* Patch only applied to March 2019 release and master.
* Record that old versions of ROOT don't support modern GCC
* Well, actually I don't know about 6.07
* Fix typo and follow odd version recommendation from @chissg
* Add QE 6.5
* Support for serial HDF5 case with serial (no mpi) QE is now supported but requires a patch for 6.4.1 and 6.5.
* Add naromero77 as a maintainer.
* Start cinema package
* Remove boilerplate and add description
* Formatting for pep8
* Correct milestone tag
* 'master' instead of 'develop'
Co-Authored-By: Adam J. Stewart <ajstewart426@gmail.com>
* Two variants, both with numpy and other small changes
* When +image for scikit
Co-authored-by: Adam J. Stewart <ajstewart426@gmail.com>
