* switch from bool to int debug levels
* Added debug options and changed lock logging to use more detailed values
* Limit installer and timestamp PIDs to standard debug output
* Reduced verbosity of fetch/stage/install output, changing most to debug level 1
* Combine lock log methods; change build process install to debug
* Changed binary cache install messages to extraction messages
* bugfix: make compiler preferences slightly saner
This fixes two issues with the way we currently select compilers.
If multiple compilers have the same "id" (os/arch/compiler/version), we
currently prefer them by picking this one with the most supported
languages. This can have some surprising effects:
* If you have no `gfortran` but you have `gfortran-8`, you can detect
`clang` that has no configured C compiler -- just `f77` and `f90`. This
happens frequently on macOS with homebrew. The bug is due to some
kludginess about the way we detect mixed `clang`/`gfortran`.
* We can prefer suffixed versions of compilers to non-suffixed versions,
which means we may select `clang-gpu` over `clang` at LLNL. But,
`clang-gpu` is not actually clang, and it can break builds. We should
prefer `clang` if it's available.
- [x] prefer compilers that have C compilers and prefer no name variation
to variation.
* tests: add test for which()
Apple's gcc is really clang. We previously ignored it by default but
there was a regression in #17110.
Originally we checked for all clang versions with this, but I know of
none other than `gcc` on macos that actually do this, so limiting to
`apple-clang` should be ok.
- [x] Fix check for `apple-clang` in `gcc.py` to use version detection
from `spack.compilers.apple_clang`
The `spack-build-env.txt` file may contains many secrets, but the obvious one is the private signing key in `SPACK_SIGNING_KEY`. This file is nonetheless uploaded as a build artifact to gitlab. For anyone running CI on a public version of Gitlab this is a major security problem. Even for private Gitlab instances it can be very problematic.
Co-authored-by: Scott Wittenburg <scott.wittenburg@kitware.com>
Fixes#17299
Cray Shasta systems appear to use an unmodified Sles or other Linux operating system on the backend (like Cray "Cluster" systems and unlike Cray "XC40" systems that use CNL).
This updates the CNL version detection to properly note that this is the underlying OS instead of CNL and delegate to LinuxDistro.
* environment-views: fix bug where missing recipe/repo breaks env commands
When a recipe or a repo has been removed from Spack and an environment
is active, it causes the view activation to crash Spack before any
commands can be executed. Further, the error message it not at all clear
in explaining the issue.
This forces view regeneration to always start from scratch to avoid the
missing package recipes, and defaults add_view=False in main for views activated
by the `spack -e` option.
* add messages to env status and deactivate
Warn users that a view may be corrupt when deactivating an environment
or checking its status while active. Updated message for activate.
* tests for view checking
Co-authored-by: Gregory Becker <becker33@llnl.gov>
* switch from bool to int debug levels
* Added debug options and changed lock logging to use more detailed values
* Limit installer and timestamp PIDs to standard debug output
* Reduced verbosity of fetch/stage/install output, changing most to debug level 1
* Combine lock log methods; change build process install to debug
* Changed binary cache install messages to extraction messages
* bugfix: make compiler preferences slightly saner
This fixes two issues with the way we currently select compilers.
If multiple compilers have the same "id" (os/arch/compiler/version), we
currently prefer them by picking this one with the most supported
languages. This can have some surprising effects:
* If you have no `gfortran` but you have `gfortran-8`, you can detect
`clang` that has no configured C compiler -- just `f77` and `f90`. This
happens frequently on macOS with homebrew. The bug is due to some
kludginess about the way we detect mixed `clang`/`gfortran`.
* We can prefer suffixed versions of compilers to non-suffixed versions,
which means we may select `clang-gpu` over `clang` at LLNL. But,
`clang-gpu` is not actually clang, and it can break builds. We should
prefer `clang` if it's available.
- [x] prefer compilers that have C compilers and prefer no name variation
to variation.
* tests: add test for which()
Apple's gcc is really clang. We previously ignored it by default but
there was a regression in #17110.
Originally we checked for all clang versions with this, but I know of
none other than `gcc` on macos that actually do this, so limiting to
`apple-clang` should be ok.
- [x] Fix check for `apple-clang` in `gcc.py` to use version detection
from `spack.compilers.apple_clang`
Spack did not support usage of the `--config-scope` option in
combination with an environment: In `lib/spack/spack/main.py`,
`spack.config.command_line_scopes` is set equal to any config scopes
passed by the `--config-scope` option. However, this is done after
activating an environment. In the process of activating an environment,
the `spack.config.config` singleton is instantiated, so later setting of
`spack.config.command_line_scopes` is ignored.
This commit sets command line scopes before activating an environment to
ensure that they are included in the configuration.
Co-authored-by: Tim Fuller <tjfulle@sandia.gov>
The `spack-build-env.txt` file may contains many secrets, but the obvious one is the private signing key in `SPACK_SIGNING_KEY`. This file is nonetheless uploaded as a build artifact to gitlab. For anyone running CI on a public version of Gitlab this is a major security problem. Even for private Gitlab instances it can be very problematic.
Co-authored-by: Scott Wittenburg <scott.wittenburg@kitware.com>
For normal users, `-o` or `--no-same-owner` (GNU extension) is
the default behavior, but for the root user, `tar` attempts to preserve
the ownership from the tarball.
This makes `tar` use `-o` all the time. This should improve untarring
files owned by users not available in rootless Docker builds.
The error message was not updated when the behavior of Spack environments
was changed to not automatically activate the local environment in #17258.
The previous error message no longer makes sense.
When Spack installs a package, it stores repository package.py files
for it and all of its dependencies - any package with a Spack metadata
directory in its installation prefix.
It turns out this was too broad: this ends up including external
packages installed by Spack (e.g. installed by another Spack instance).
Currently Spack doesn't store the namespace properly for such packages,
so even though the package file could be fetched from the external,
Spack is unable to locate it.
This commit avoids the issue by skipping any attempt to locate and copy
from the package repository of externals, regardless of whether they
have a Spack repo directory.
Spack was attempting to calculate abspath on the located config.guess
path even when it was not found (None); this commit skips the abspath
calculation when config.guess is not found.
The error message was not updated when the behavior of Spack environments
was changed to not automatically activate the local environment in #17258.
The previous error message no longer makes sense.
When Spack installs a package, it stores repository package.py files
for it and all of its dependencies - any package with a Spack metadata
directory in its installation prefix.
It turns out this was too broad: this ends up including external
packages installed by Spack (e.g. installed by another Spack instance).
Currently Spack doesn't store the namespace properly for such packages,
so even though the package file could be fetched from the external,
Spack is unable to locate it.
This commit avoids the issue by skipping any attempt to locate and copy
from the package repository of externals, regardless of whether they
have a Spack repo directory.
* Buildcache:
* Try mocking an install of quux, corge and garply using prebuilt binaries
* Put patchelf install after ccache restore
* Add script to install patchelf from source so it can be used on Ubuntu:Trusty which does not have a patchelf pat package. The script will skip building on macOS
* Remove mirror at end of bindist test
* Add patchelf to Ubuntu build env
* Revert mock patchelf package to allow other tests to run.
* Remove depends_on('patchelf', type='build') relying instead on
* Test fixture to ensure patchelf is available.
* Call g++ command to build libraries directly during test build
* Flake8
* Install patchelf in before_install stage using apt unless on Trusty where a build is done.
* Add some symbolic links between packages
* Flake8
* Flake8:
* Update mock packages to write their own source files
* Create the stage because spec search does not create it any longer
* updates after change of list command arguments
* cleanup after merge
* flake8
fixes#17396
This prevents the class attribute to be inherited and
saves current maintainers from becoming the default
maintainers of every Cuda package.
We got rid of `master` after #17377, but users still want a way to get
the latest stable release without knowing its number.
We've added a `releases/latest` tag to replace what was once `master`.
Co-authored-by: Massimiliano Culpo <massimiliano.culpo@gmail.com>
Fixes#16478
This allows an uninstall to proceed even when encountering pre-uninstall
hook failures if the user chooses the --force option for the uninstall.
This also prevents post-uninstall hook failures from raising an exception,
which would terminate a sequence of uninstalls. This isn't likely essential
for #16478, but I think overall it will improve the user experience: if
the post-uninstall hook fails, there isn't much point in terminating a
sequence of spec uninstalls because at the point where the post-uninstall
hook is run, the spec has already been removed from the database (so it
will never have another chance to run).
Notes:
* When doing spack uninstall -a, certain pre/post-uninstall hooks aren't
important to run, but this isn't easy to track with the current model.
For example: if you are uninstalling a package and its extension, you
do not have to do the activation check for the extension.
* This doesn't handle the uninstallation of specs that are not in the DB,
so it may leave "dangling" specs in the installation prefix
- [x] Remove references to `master` branch
- [x] Document how release branches are structured
- [x] Document how to make a major release
- [x] Document how to make a point release
- [x] Document how to do work in our release projects
Spack was attempting to calculate abspath on the located config.guess
path even when it was not found (None); this commit skips the abspath
calculation when config.guess is not found.
* Move flake8 tests on Github Actions
* Move shell test to Github Actions
* Moved documentation build to Github Action
* Don't run coverage on Python 2.6
Since we get connection errors consistently on Travis
when trying to upload coverage results for Python 2.6,
avoid computing coverage entirely to speed-up tests.
* share/spack/setup-env.fish file to setup environment in fish shell
* setup-env.fish testing script
* Update share/spack/setup-env.fish
Co-Authored-By: Elsa Gonsiorowski, PhD <gonsie@me.com>
* Update share/spack/qa/setup-env-test.fish
Co-Authored-By: Adam J. Stewart <ajstewart426@gmail.com>
* updates completions using `spack commands --update-completion`
* added stderr-nocaret warning
* added fish shell tests to CI system
Co-authored-by: becker33 <becker33@llnl.gov>
Co-authored-by: Adam J. Stewart <ajstewart426@gmail.com>
Co-authored-by: Elsa Gonsiorowski, PhD <gonsie@me.com>
* cray: detect frontend compilers automatically
This commit permits to detect frontend compilers
automatically, with the exception of cce.
Co-authored-by: Gregory Becker <becker33.llnl.gov>
[george.hartzell@172-16-193-97 spack-explore-docker]$ spack containerize
Running `spack containerize` with the example `spack.yaml` file fails
with an error that ends like so:
```
[...]
File "/local_scratch/hartzell/tmp/spack-explore-docker/lib/spack/external/ruamel/yaml/scanner.py", line 165, in need_more_tokens
self.stale_possible_simple_keys()
File "/local_scratch/hartzell/tmp/spack-explore-docker/lib/spack/external/ruamel/yaml/scanner.py", line 309, in stale_possible_simple_keys
"could not find expected ':'", self.get_mark())
ruamel.yaml.scanner.ScannerError: while scanning a simple key
in "/local_scratch/hartzell/tmp/spack-explore-docker/spack.yaml", line 26, column 1
could not find expected ':'
in "/local_scratch/hartzell/tmp/spack-explore-docker/spack.yaml", line 28, column 5
```
Indenting the block string fixes the problem for me.
CentOS 7,
```
$ spack --version
0.14.2-1529-ec58f28c2
```
* env: no automatic activation
* Ensure ci rebuild jobs activate the environment (no longer automagic)
Co-authored-by: Scott Wittenburg <scott.wittenburg@kitware.com>
* Start moving toward a json buildcache index
* Add spec and database index schemas
* Add a schema for buildcache spec.yaml files
* Provide a mode for database class to generate buildcache index
* Update db and ci tests to validate object w/ new schema
* Remove unused temporary upload-s3 command
* Use database class to generate buildcache index
* Do not generate index with each buildcache creation
* Make buildcache index mode into a couple of constructor args to Database class
* Use keyword args for _createtarball
* Parse new json index when we get specs from buildcache
Now that only one index file per mirror needs to be fetched in
order to have all the concrete specs for binaries available on the
mirror, we can just fetch and refresh the cached specs every time
instead of needing to use the '-f' flag to force re-reading.
* First fix for SPACK_DEPENDENCIES problem when doing setup
* Get rid of transitive include path in setup.
* Export SPACK_INCLUDE_DIRS into spconfig.py
* add buildcache create test
* add functionality and test to create buildcache from environment
* use env.concretized_user_specs rather than env.roots to get concretized specs, as suggested in review from becker33
* Allow `spack remove -f` and `spack uninstall` to work on matrices
Allow Environment.remove(force=True) to remove the concrete spec from the environment
even when the user spec cannot be removed because it is in a matrix.
* Separate Apple Clang from LLVM Clang
Apple Clang is a compiler of its own. All places
referring to "-apple" suffix have been updated.
* Hack to use a dash in 'apple-clang'
To be able to use autodoc from Sphinx we need
a valid Python name for the module that contains
Apple's Clang code.
* Updated packages to account for the existence of apple-clang
Co-authored-by: Adam J. Stewart <ajstewart426@gmail.com>
* Added unit test for XCode related functions
Co-authored-by: Gregory Becker <becker33@llnl.gov>
Co-authored-by: Adam J. Stewart <ajstewart426@gmail.com>
* short-circuit is_activated check when the extendee is installed upstream
* add test for checking activation status of packages with an extendee installed upstream
spack config add <value>: add nested value value to the configuration scope specified
spack config remove/rm: remove specified configuration from the relevant scope
* Some minor fixes to set_permissions() in file_permissions.py
The set_permissions() routine claims to prevent users from creating
world writable suid binaries. However, it seems to only be checking
for/preventing group writable suid binaries.
This patch modifies the routine to check for both world and group
writable suid binaries, and complain appropriately.
* permissions.py: Add test to check blocks world writable SUID files
The original test_chmod_rejects_group_writable_suid tested
that the set_permissions() function in
lib/spack/spack/util/file_permissions.py
would raise an exception if changed permission on a file with
both SUID and SGID plus sticky bits is chmod-ed to g+rwx and o+rwx.
I have modified so that more narrowly tests a file with SUID
(and no SGID or sticky bit) set is chmod-ed to g+w.
I have added a second test test_chmod_rejects_world_writable_suid
that checks that exception is raised if an SUID file is chmod-ed
to o+w
* file_permissions.py: Raise exception when try to make sgid file world writable
Updated set_permissions() in file_permissions.py to also raise
an exception if try to make an SGID file world writable. And
added corresponding unit test as well.
* Remove debugging prints from permissions.py
* Module index should not be unconditionally overwritten
Uncovered after we switched our CI to generate modules for packages
one-by-one rather than in bulk. This overwrote a complete module index
with an index with a single entry, and broke our downstream Spack
instances that needed the upstream module index.
* Changed the 'include' config section to use 'substitute_path_variables' to allow for Spack config variables to be used (e.g. $spack).
* Fixed a bug with 'include' section path expansion and added a test case for 'include' paths with embedded config variables.
* Cray: fix Blue Waters support
* pkg-config env vars needed on Blue Waters
* cray platform: fix support for user-build MPI on cray machines
* reintroduce cray environment cleaning behind cnl version guard
* cray platform: fix support for user-build MPI on cray machines
Co-authored-by: Gregory <becker33@llnl.gov>
Builds can be stopped before the final install phase due to user requests. Those builds
should not be registered as installed in the database.
We had code intended to handle this but:
1. It caught the wrong type of exception
2. We were catching these exceptions to suppress them at a lower level in the stack
This PR allows the StopIteration to propagate through a ChildError, and catches it
properly. Also added to an existing test to prevent regression.
This fixes a fork bomb in `spack versions`. Recursive generation of pools
to scrape URLs in `_spider` was creating large numbers of processes.
Instead of recursively creating process pools, we now use a single
`ThreadPool` with a concurrency limit.
More on the issue: having ~10 users running at the same time spack
versions on front-end nodes caused kernel lockup due to the high number
of sockets opened (sys-admin reports ~210k distributed over 3 nodes).
Users were internal, so they had ulimit -n set to ~70k.
The forking behavior could be observed by just running:
$ spack versions boost
and checking the number of processes spawned. Number of processes
per se was not the issue, but each one of them opens a socket
which can stress `iptables`.
In the original issue the kernel watchdog was reporting:
Message from syslogd@login03 at May 19 12:01:30 ...
kernel:Watchdog CPU:110 Hard LOCKUP
Message from syslogd@login03 at May 19 12:01:31 ...
kernel:watchdog: BUG: soft lockup - CPU#110 stuck for 23s! [python3:2756]
Message from syslogd@login03 at May 19 12:01:31 ...
kernel:watchdog: BUG: soft lockup - CPU#94 stuck for 22s! [iptables:5603]
* add an --exclude-file option to 'spack mirror create' which allows a user to specify a file of specs to exclude when creating a mirror. this is anticipated to be useful especially when using the '--all' option
* allow specifying number of versions when mirroring all packages
* when mirroring all specs within an environment, include dependencies of root specs
* add '--exclude-specs' option to allow user to specify that specs should be excluded on the command line
* add test for excluding specs
fixes#12527
Mention that specs can be uninstalled by hash also in
the help message. Reference `spack gc` in case people
are looking for ways to clean the store from build time
dependencies.
Use "spec" instead of "package" to avoid ambiguity in
the error message.
* Unify tests for compiler command in the same file
Tests for the "spack compiler" command were previously
scattered among different files.
* Tests should use mutable_config, since they modify the compiler list
Because of the way abstract variants are implemented, the following
spec matrix does not work as intended:
```
matrix:
- [foo]
- [bar=a, bar=b]
exclude:
- bar=a
```
because abstract variants always satisfy any variant of the same
name, regardless of values.
This PR converts abstract variants to whatever their appropriate
type is before running satisfaction checks for the excludes clause
in a matrix.
fixes#16841
Now that the version number of GCC reached double digits, an update
to the regex is needed to recognize gcc-10 as an executable to be
inspected when searching for compilers.
* make_link_relative: added docstring
* make_elf_binaries_relative: added docstring, unit tests
* raise_if_not_relocatable: added docstring, added unit test for exceptional case
* relocate_links: removed unused arguments, added docstring and comments
Also fixed a possible bug that was issuing spurious
warning when a file was relocated successfully
* relocate_text: added docstring and comments, renamed arguments
* relocate_text_bin: added docstring and comments, renamed arguments, unit tests
Problem: when calling `static_to_shared_library` on the `cray` arch, it
produces a non-sensical compiler command with no input files. For
example, when installing lua@5.2.4, it produced:
'gcc -lm -ldl -o /big-long-spack-path/liblua.so.5.2.4'
Solution: do the same thing on `cray` that is done for `linux`
* account for schema validation errors where the associated instance doesn't have a line number
* fix unrelated flake error (but it must be fixed because this PR touches this file and the flake rules have been updated since the last edit to this file)
Allows `all` to be configured non-buildable in packages.yaml.
The following config would only allow zlib to be built by Spack, all other packages would have to be found as externals.
```
packages:
all:
buildable: False
zlib:
buildable: True
```
This change also adds a code path through the spack ci pipelines
infrastructure which supports PR testing on the Spack repository.
Gitlab pipelines run as a result of a PR (either creation or pushing
to a PR branch) will only verify that the packages in the environment
build without error. When the PR branch is merged to develop,
another pipeline will run which results in the generated binaries
getting pushed to the binary mirror.
Providing only $padding or ${padding} results in an attempt to
substitute a padding of maximum system path length, while leaving
room for the parts of the install path spack generates. Providing
$padding-<len> or ${padding-<len>} simply substitutes padding of
the specified length.
Packages built with lmod core_compiler are placed in `Core`.
Other packages may belong in `Core`. For example, python may be built with a proprietary compiler for performance, but belong on the `Core` directory.
With this PR, lmod config can include a `core_specs` list. Any package that satisfies a spec in that list is placed in `Core`, regardless of its compiler or dependencies.
This improves the documentation for `spack external find` in several ways:
* Provide a code example of implementing `determine_spec_details` for a package
* Explain how to define executables to look for (and also e.g. that they are treated as regular expressions and so can pull in unexpected files).
* Add the "why" for a couple of constraints (i.e. explain that this logic only works for build/run deps because it examines `PATH` for executables)
* Spread the docs between build customization and packaging sections
* Add cross-references
* Add a label so that `spack external find` is linked from the command reference.
* Add pmi support (required by ucx, ofi, and gni backends)
* Add support for ucx backend
* Add dependency on MPI for pmi=simplepmi, slurmpmi, or slurmpmi2
* Remove charmpp as an MPI provider since the changes in this PR can
add MPI as a dependency (mentioned previously)
* Install into transport_protocol-OS-arch subdirectory to match
default charmpp installation behavior (which helps dependents find it)
- add docstrings and make parameter names consistent in `relocate.py`
- Make `replace_prefix_*` and other functions private (as they are implementation details)
- remove unused function _replace_prefix_nullterm()
- Add unit tests for `relocate.py` functions
- add patchelf to Travis and use it during tests
- add hello_world fixture with a compiled binary, so we can test relocation
After migrating to `travis-ci.com`, we saw I/O issues in our tests --
tests that relied on `capfd` and `capsys` were failing. We've also seen
this in GitHub actions, and it's kept us from switching to them so far.
Turns out that the issue is that using streams like `sys.stdout` as
default arguments doesn't play well with `pytest` and output redirection,
as `pytest` changes the values of `sys.stdout` and `sys.stderr`. if these
values are evaluated before output redirection (as they are when used as
default arg values), output won't be captured properly later.
- [x] replace all stream default arg values with `None`, and only assign stream
values inside functions.
- [x] fix tests we didn't notice were relying on this erroneous behavior
This adds the `url` alternative `urls` to `package.all_urls`. With
this addition, one can find again new versions with
`spack versions <package>` for packages that are populated with
from mixin mirror `urls`.
Example: `util-macros` from x.org mixin.
