Modifications:
- [x] Change `defaults/config.yaml`
- [x] Add a fix for bootstrapping patchelf from sources if `compilers.yaml` is empty
- [x] Make `SPACK_TEST_SOLVER=clingo` the default for unit-tests
- [x] Fix package failures in the e4s pipeline
Caveats:
1. CentOS 6 still uses the original concretizer as it can't connect to the buildcache due to issues with `ssl` (bootstrapping from sources requires a C++14 capable compiler)
1. I had to update the image tag for GitlabCI in e699f14.
1. libtool v2.4.2 has been deprecated and other packages received some update
This will allow a user to (from anywhere a Spec is parsed including both name and version) refer to a git commit in lieu of
a package version, and be able to make comparisons with releases in the history based on commits (or with other commits). We do this by way of:
- Adding a property, is_commit, to a version, meaning I can always check if a version is a commit and then change some action.
- Adding an attribute to the Version object which can lookup commits from a git repo and find the last known version before that commit, and the distance
- Construct new Version comparators, which are tuples. For normal versions, they are unchanged. For commits with a previous version x.y.z, d commits away, the comparator is (x, y, z, '', d). For commits with no previous version, the comparator is ('', d) where d is the distance from the first commit in the repo.
- Metadata on git commits is cached in the misc_cache, for quick lookup later.
- Git repos are cached as bare repos in `~/.spack/git_repos`
- In both caches, git repo urls are turned into file paths within the cache
If a commit cannot be found in the cached git repo, we fetch from the repo. If a commit is found in the cached metadata, we do not recompare to newly downloaded tags (assuming repo structure does not change). The cached metadata may be thrown out by using the `spack clean -m` option if you know the repo structure has changed in a way that invalidates existing entries. Future work will include automatic updates.
# Finding previous versions
Spack will search the repo for any tags that match the string of a version given by the `version` directive. Spack will also search for any tags that match `v + string` for any version string. Beyond that, Spack will search for tags that match a SEMVER regex (i.e., tags of the form x.y.z) and interpret those tags as valid versions as well. Future work will increase the breadth of tags understood by Spack
For each tag, Spack queries git to determine whether the tag is an ancestor of the commit in question or not. Spack then sorts the tags that are ancestors of the commit by commit-distance in the repo, and takes the nearest ancestor. The version represented by that tag is listed as the previous version for the commit.
Not all commits will find a previous version, depending on the package workflow. Future work may enable more tangential relationships between commits and versions to be discovered, but many commits in real world git repos require human knowledge to associate with a most recent previous version. Future work will also allow packages to specify commit/tag/version relationships manually for such situations.
# Version comparisons.
The empty string is a valid component of a Spack version tuple, and is in fact the lowest-valued component. It cannot be generated as part of any valid version. These two characteristics make it perfect for delineating previous versions from distances. For any version x.y.z, (x, y, z, '', _) will be less than any "real" version beginning x.y.z. This ensures that no distance from a release will cause the commit to be interpreted as "greater than" a version which is not an ancestor of it.
Signed-off-by: vsoch <vsoch@users.noreply.github.com>
Co-authored-by: vsoch <vsoch@users.noreply.github.com>
Co-authored-by: Gregory Becker <becker33@llnl.gov>
Co-authored-by: Todd Gamblin <tgamblin@llnl.gov>
This PR coincides with tiny changes to spack to support spack monitor using the new spec
the corresponding spack monitor PR is at https://github.com/spack/spack-monitor/pull/31.
Since there are no changes to the database we can actually update the current server
fairly easily, so either someone can test locally or we can just update and then
test from that (and update as needed).
Signed-off-by: vsoch <vsoch@users.noreply.github.com>
Co-authored-by: vsoch <vsoch@users.noreply.github.com>
* ESMF and NEMSIO changes.
- Updating ESMF to set the COMM correctly when using Intel oneapi.
- Explicitly setting the CMake MPI Fortran compiler for NEMSIO.
* Update UFS utils CMake to use MPI_<lang>_COMPILER.
#22845 revealed a long-standing bug that had never been triggered before, because the
hashing algorithm had been stable for multiple years while the bug was in production. The
bug was that when reading a concretized environment, Spack did not properly read in the
build hashes associated with the specs in the environment. Those hashes were recomputed
(and as long as we didn't change the algorithm, were recomputed identically). Spack's
policy, though, is never to recompute a hash. Once something is installed, we respect its
metadata hash forever -- even if internally Spack changes the hashing method. Put
differently, once something is concretized, it has a concrete hash, and that's it -- forever.
When we changed the hashing algorithm for performance in #22845 we exposed the bug.
This PR fixes the bug at its source, but properly reading in the cached build hash attributes
associated with the specs. I've also renamed some variables in the Environment class
methods to make a mistake of this sort more difficult to make in the future.
* ensure environment build hashes are never recomputed
* add comment clarifying reattachment of env build hashes
* bump lockfile version and include specfile version in env meta
* Fix unit-test for v1 to v2 conversion
Co-authored-by: Massimiliano Culpo <massimiliano.culpo@gmail.com>
* Refactor platform etc. to avoid circular dependencies
All the base classes in spack.architecture have been
moved to the corresponding specialized subpackages,
e.g. Platform is now defined within spack.platforms.
This resolves a circular dependency where spack.architecture
was both:
- Defining the base classes for spack.platforms, etc.
- Collecting derived classes from spack.platforms, etc.
Now it dopes only the latter.
* Move a few platform related functions to "spack.platforms"
* Removed spack.architecture.sys_type()
* Fixup for docs
* Rename Python modules according to review
* dvsdk: Turn off variants by default
This allows an install to more easily be explicit about which pieces to
turn on as more variants are added
* dvsdk: effectively disable the broken variants
* Switch http to https where latter exists
* Hopefully restore original permissions
* Add URL updates after include the -L curl option
* Manual corrections to select URL format strings
* Tell gtk-doc where the XML catalog is
The gtk-doc configure script has an option for specifying the path to
the XML catalog. If this is not set the configure script will search
a defined set of directories for a catalog file and will set
`with_xml_catalog` based on that. Only if no system catalog is found will
the XML_CATALOG_FILES be looked at. In order to make sure that the spack
provided catalog is used, pass the `--with-xml-catalog` option.
* Use the property from docbook-xml
Currently as part of installing a package, we lock a prefix, check if
it exists, and create it if not; the logic for creating the prefix
included a check for the existence of that prefix (and raised an
exception if it did), which was redundant.
This also includes removal of tests which were not verifying
anything (they pass with or without the modifications in this PR).
- Parallel install was failing to generate a config file.
- OpenSSH has an extensive test suite, run it if requested.
- 'executables' wrongly had 'rsh', replaced the openssh tools.
There are two ways to build SQLite: With the Autotools setup or the
so-called "amalgamation" which is a single large C file containing the
SQLite implementation. The amalgamation build is controlled by
pre-processor flags and the Spack setup was using an amalgamation
pre-processor flag for a feature that is controlled by an option of the
configure script. As a consequence, until now Spack has always built
SQLite with the rtree feature enabled.
Knowing that spack has patched the code and organized the build is potentially valuable information for GROMACS users and developers troubleshooting their builds.
PLUMED does further patches to GROMACS, so that is expressed directly also.
