* This fixes a bug in concretization. Before the recent change to the
algorithm, the intent was that the @develop version, although
"greater" than numberic versions, is never preferred BY DEFAULT over
numeric versions.
To test this... suppose you have a package with no `preferred=True` in
it, and nothing in `packages.yaml`, but with a `develop` version. For
the sake of this example, I've hacked my `python/package.py` to work
this way.
Without bugfix (WRONG: user should never get develop by default):
```
python@develop%clang@7.3.0-apple~tk~ucs4 arch=darwin-elcapitan-x86_64
...
```
With bugfix (RIGHT: largest numeric version selected):
```
python@3.5.2%clang@7.3.0-apple~tk~ucs4 arch=darwin-elcapitan-x86_64
...
```
* Documented version selection in concretization algo.
* Fix typos
* flake8
* Fix various documentation bugs
* Keep long option names, but don't include in Command Index
* Use long option name
* Explicitly designate sections to be listed in the Command Index
* Consistent menu bar titles
Input/output/error streams not directed to None or 'str' were not being closed
because `close()` method was being called on the argument value (a string type)
instead of the open file descriptor object.
* Fix bug in handling of precedence of preferred=True vs. versions given in packages.yaml (#1556)
* Standardized comparison of versions: numeric versions are always greater than non-numeric versions; and non-numeric versions are sorted alphabetically.
This is
a) simple
b) ensures that non-numeric versions (such as 'develop') in package.py are not chosen ahead of numeric versions, when nothing is specified in packages.yaml
Fixes Issue #1557
* Removed debugging output
* Fix variable shadowing bug
* Ensure develop < numeric version.
* Bug fix.
* Passes all unit tests in versions.py
* flake8 fixes
* flake8 fixes
* Changed type test to be more correct.
See http://stackoverflow.com/questions/8203336/difference-between-int-and-numbers-integral-in-python
This closes#1757 which provides an example of a url scheme where the
version appears after the extension. Instead of extending the parsing
logic to handle this case, this commit allows the user to specify
their extension type. This helps Spack choose the appropriate
decompressor and mirror archive filename.
* Transferred pending changes from efischer/develop
* 1. Rewrite of "Getting Started": everything you need to set up Spack, even on old/ornery systems. This is not a reference manual section; items covered here are covered more systematically elsewhere in the manual. Some sections were moved here from elsewhere.
2. Beginning to write three methods of application developer support. Two methods were moved from elsewhere.
* Edits...
* Moved sections in preparation for additional text to be added from old efischer/docs branch.
* Moved 2 more sections.
* Avoid accid
* Applied proofreading edits from @adamjstewart
* Fixed non-standard section characters.
* Moved section on profiling to the developer's guide.
* Still working on Spack workflows...
* Finished draft of packaging_guide.rst
* Renamed sample projects.
* Updates to docstrings
* Added documentation to resolve#638 (content taken from #846)
* Added section on resolving inconsistent run dependencies. Addresses #645
* Showed how to build Python extensions only compatible with certain versions of Python.
* Added examples of getting the right behavior from depends_on(). See #1035
* Added section on Intel compilers and their GCC masquerading feature. Addresses #638, #1687.
* Fixed formatting
* Added fixes to filesystem views. Added a caveats section to ``spack setup``.
* Updated section on Intel compiler configuration because compiler flags currently do not work (see #1687)
* Defined trusted downloads, and updated text based on them. (See #1696)
* Added workflow to deal with buggy upstream software. See #1683
* Added proper separation between Spack Docs vs. Reference Manual
* Renamed spack_workflows to workflows. Resolves a conflict with the .gitignore file.
* Removed repeated section.
* Created new "Vendor Specific Compiler Configuration" section and organized existing Intel section into it. Added new PGI and NAG sections; but they need to be expanded / rewritten based on the existing text plus research through Spack issues on GitHub.
* Fixed text on `spack load --dependencies` to conform to reality. See #1662
* Added patching as option for upstream bugfixes.
* Added section on using licensed compilers.
* Added section on non-downloadable tarballs.
* Wrote sections on NAG and PGI. Arranged compilers in alphabetical order.
* Fix indent.
* Fixed typos.
* Clarified dependency types.
* Applied edits from Adam J. Stewart. Spellchecked workflows and getting_started.
* Removed spurious header
* Fixed Sphinx errors
* Fixed erroneous symbol in docstring.
* Fix many typos and formatting problems.
* Spacing changes
* Added section on fixing Git problems. See #1779
* Fixed signature of install() method.
* Addressed system packages in greater detail. See #1794#1795
* Fixed typos
* Fixed quotes
* Duplicate section on Spack profiling removed from configuration.rst. It had earlier been moved to developer_guide.rst, where it fits better.
* Minor edits
- Tweak supported platform language.
- Various small changes to the new getting started guide.
* Fixed bug with quotes.
- Fixed up dependency management so that:
- build deps go in PATH and -I
- link deps go in -L args
- only *immediate* link deps are RPATH'd
The latter reduces the number of libraries that need to be added to
DT_NEEDED / LC_RPATH. This removes redundant RPATHs to transitive
dependencies.
* Fixes#1720: spack reindex fails with invalid ref count.
- Database graph wasn't being built properly; dependencies were set up
incorrectly in the nodes that ended up in the graph on reindex.
- Reworked _add to increment ref count properly and to always build
bottom-up to make the logic simpler to understand.
* Add checks to ensure DB is a valid merkle tree.
- Distinguish between static (package) and dynamic (spec) graphs.
- static graphs ignore conditions and multiple instances (hashes) and
plot raw dependencies among packages.
- dynamic graphs include information from particular specs (instances of
packages) and can have multiple instances with hashes.
- Allow graphing all packages in the install DB.
- useful for debugging.
* Perform shebang fix for all files
* Fix sbang for perl scripts
Otherwise perl would look at the #! line and call sbang again, resulting
in an infinite loop.
* Turned <provider>_libs into an iterable
Modifications :
- added class LibraryList + unit tests
- added convenience functions `find_libraries` and `dedupe`
- modifed non Intel blas/lapack providers
- modified packages using blas_shared_libs and similar functions
* atlas : added pthread variant
* intel packages : added lapack_libs and blas_libs
* find_library_path : removed unused function
* PR review : fixed last issues
* LibraryList : added test on __add__ return type
* LibraryList : added __radd__ fixed unit tests
fix : failing unit tests due to missing `self`
* cp2k and dependecies : fixed blas-lapack related statements in package.py
* Fixed bug propagating --dirty flag to sub-installs.
* Fix syntax error
* Allow --dirty flag to be set with SPACK_DIRTY env var.
* Added dirty flag to `spack diy` and `spack setup`, as is currently in `spack install`
* flake8
Includes :
- treatment of a generic hierarchy (i.e. lapack + mpi + compiler)
- possibility to specify which compilers are to be considered Core
- correct treatment of the 'family' directive
- unit tests for most new features
When re-using previously downloaded tarballs, spack copies from
`var/spack/stage/PACKAGE-VERSION-HASH/downloaded_file` to
`var/spack/cache/PACKAGE/downloaded_file`. This fails if the source is owned by
a different user (`shutil.copy` tries to retain all meta data including file
ownership). Change to a non-meta-data copy function (`shutil.copyfile`).
This closes#1308, where fetching a non-expanded resource from a mirror
will cause an error.
This also ensures that when a URL resource is fetched from a mirror,
that it will be named as though it were retrieved from the original
URL. This is particularly useful for non-expanded resources since it
ensures that the resource name is consistent for the installation
(this is less important for expanded resources because the build takes
place inside the expanded resource).
- Spec._dup() incorrectly copied cached hashes and normal/concrete values
even when dependency structure was not preserved.
- Now these are only copied when *all* dependencies are copied.
- Currently, build dependencies are not currently hashed; we are waiting
to hash these until we have smarter concretization that can reuse more
installed specs. The layout needs to account for this when checking
whethert things are installed.
- Transaction logic had gotten complicated -- DB would not reindex when
corrupt, rather the error would be reported (ugh).
- DB will now print the error and force a rebuild when errors are
detected reading the old databse.
- Spack currently not hashing build deps (to allow more reuse of packages
and less frequent re-installing)
- Fast in-memory hash should still hash *all* deptypes, and installed
specs will only reflect link and run deps.
- We'll revert this when we can concretize more liberally based on what
is already installed.
- can now pass these to Spec.copy() and Spec._dup():
- deps=True
- deps=False
- deps=(list of deptypes)
- Makes it easy to filter out only part of a spec.
Everything in the __all__ list in the spack module is from some other
module, so only do their documentation in their original location. This
also avoids issues like the fact that some directive names shadow spack
core module names.
The header append lines were too long, so I just converted it into a
multi-line string template so it's all one piece now instead of a bunch
of appends.
Major stuff:
- Created a FileCache for managing user cache files in Spack. Currently just
handles virtuals.
- Moved virtual cache from the repository to the home directory so that users do
not need write access to Spack repositories to use them.
- Refactored `Transaction` class in `database.py` -- moved it to
`LockTransaction` in `lock.py` and made it reusable by other classes.
Other additions:
- Added tests for file cache and transactions.
- Added a few more tests for database
- Fixed bug in DB where writes could happen even if exceptions were raised
during a transaction.
- `spack uninstall` now attempts to repair the database when it discovers that a
prefix doesn't exist but a DB record does.
- Spack will check if the index needs updating, and will only parse
all package files if it does.
- Spack tries to parse as few package files as necessary.
- Don't need to list all packages unless we have to.
- Only use the list of all packages for existence checks if we have
generated it for some other purpose.
This PR will catch the error where the url can not be determined from a
VCS URL, such as git. It will print a message to the console and move on
because it should not be a fatal error at this point in the process.
This should fix#1459.
The archive_version variable should only get set if versions will be
checked and that is only if there is a list_url in the package file. For
VCS repos setting the variable triggers an error from web.py as it
parses the default_fetcher object.
This should fix#1422.
Assuming a bash interactive environment will be correctly formed on login, we
should prefer to probe the environment using a shell that reports itself as
`bash` instead of `sh` which may not source files that set the
environment modules in statements like:
```
case "$is" in
bash) test -s /etc/bash.bashrc.local && . /etc/bash.bashrc.local ;;
ksh) test -s /etc/ksh.kshrc.local && . /etc/ksh.kshrc.local ;;
zsh) test -s /etc/zsh.zshrc.local && . /etc/zsh.zshrc.local ;;
ash) test -s /etc/ash.ashrc.local && . /etc/ash.ashrc.local
esac
test -s /etc/sh.shrc.local && . /etc/sh.shrc.local
```
The list of default environment modules is obtained by calling
`module list -lt`
from a subshell with a wiped environment. This allows `/etc/profile` and other
init scripts to be fully sourced which should generally include loading the
default modules.
The list of default modules is then parsed for the first acceptable CPU target,
assumed to be the back_end target.
A platform to generically cover all Cray systems is introduced to avoid having
specific platforms for each of XK (XE, XT), XC, and future systems using CrayPE
and CNL.
The platform searches for 'front_end' and 'back_end' targets, in order, from:
* Environment variables 'SPACK_FRONT_END' and 'SPACK_BACK_END'
* A spack configuration file 'targets.yaml'
* Parsing `/etc/bash.bashrc.local` for first loaded CrayPE CPU target.
If a back_end target is not found through one of these methods, an exception is
raised. Otherwise, the back_end is set as the default target. The shell init
script search is based on recommendations in Crayports case #144359.
No automagic way of determining front_end targets has been found (to date) so if
a front_end is not specified through configuration, it is ignored which should
leave a spack instance in a consistant state.
In addition to `list_url` make sure the package has the `url` attribute
set before attempting to add urls from a list. This is to cover the case
where there may be a `list_url` specified in tandem with a
`url_for_version`.
This commit will make urls from list_url only checked if `list_url` is
set in the package file. This makes more sense as there is no need to
check for those if the attribute is not present. If `url` is present and
`list_url` is not then it would result in the same url. If
`url_for_version` is used then that will not work anyway.
This PR allows archive file retrieval from urls derived from the
`list_url` setting in a package file. This allows for continued
retrieval of checksummed archive files even when they are moved to a new
remote location when a package is updated upstream.
Set up the environment for the Intel compilers and tools. This commit
does the following:
- Unset variables that were incorrect from the auto guess prefix
inspections.
- Add a RemovePath environment_modifications_formats for dotkit.
- Set the module environment variables appropriate for the different
variants.
- Change the component logic so that the '+all' variant works. It was
getting split by letter and leaving COMPONENTS empty.
- Added a variant checking function.
- Added NONRPM_DB_DIR to the silent.cfg so that the product database
goes to the installation directory.
- With the product database in prefix the code to remove the product
database file from the home directory is no longer needed and was
removed.
- Reformat the 'tools' variant description.
There are probably more variables needed for the '+tools' for the
'professional' product version but I do not have access to that.
- Default scope is versioned with spack and can be overridden by site
or user config.
- Default scope provides sensible default concretization preferences
for all of Spack.
- per-platform concretization scope can be added later (to force a
particular MPI on, e.g., Cray systems)
- Consolidated code to read spec.yaml and database index.yaml into
one method (`read_yaml_dep_specs()`) in spec.py.
- Code understands old hash format, tuple format, and dicts for dep
specs, for backward compatibility.
- Spec YAML now uses a dict with keys to represent dep specs (this is
more future-proof).
- Dep specs no longer contain !!py-tuple entries in YAML (only lists
properly YAML-ize)
- bump database version.
deptypes: allow for different queries
For things like Python modules, they are required for the build and
runtime, but rather than adding a new parameter for what to query across
the dependency DAG, just expose the recursive query parameter.
When var/spack/stage is a symlink, the tests fail since realpath is used
on the resulting path, but not the original path, so the string compare
fails. Smarter path testing might be a better option.
This list was not formatted correctly on [the ReadTheDocs site](http://software.llnl.gov/spack/basic_usage.html#specs-dependencies).
I'm not a .rst expert, but I think that it was improperly indented.
The example includes an `arch=...` string but *arch* is not listed in the valid compiler flag specifiers or architecture specifiers. Should it be, or is it considered an "optional variant specifier?
Modifications :
- added EditableMakefile to PackageBase subclasses
- astyle modified as an example
- preliminary hook to stop at a certain phase of install
- add macports to things that are cleaned out of the environment.
- linker incompatibilities cause issues with packages like OpenSSL.
- also clean up NOQA stuff in OpenSSL
- Common cli arguments now are in their own module
- Moved utilities that can be reused by different commands into spack.cmd.__init__.py
- Modifications to `spack module loads`
Removed examples of Cray config files and added them under Spack on
Cray. Any users of Cray can just look at the Spack on Cray section to
get an idea of what's used. If they want more information they can click
links to the sections.
# Conflicts:
# lib/spack/docs/packaging_guide.rst
# lib/spack/spack/package.py
Mostly minor/formatting issues in lib/spack/spack/package.py (the heavyweight merge was already done recently). Only one serious issue: it looks like the feature branch had accidentally deleted the line `spack.hooks.post_install(self)`. This got added back in from develop.
config :
- added `hash_length` under the modules section
EnvModules :
- take into consideration hash_length when constructing `file_name`
- added logic to warn and skip module file writing in case of file name clash
If you want to bootstrap from a fork, the `--remote` option may be used
to select it.
Also limit the branches to 'develop' and 'master' if the remote is
'origin' since those are the actual integration branches used (other
branches on 'origin' are just PR branches).
spack module :
- refresh accepts a constraint
- find and refresh share common cli options
- ask for confirmation before refreshing
- deleting the module file tree is now optional
Updating how to use compilers.yaml on Cray as well as setting up
external packages. Also includes what needs to be set up for usage on
Cray and explains what needs to be done to get Spack properly working.
Also explain the architecture spec and what it does.
Building OpenMPI without fortran is possible, and was already handled.
Raising an install error we effectively renounce at clang+OpenMPI.
build_environment : sets 'CC', 'CXX', and similar variables only if a compiler is found
