`DYLD_LIBRARY_PATH` can frequently break builtin macOS software when
pointed at Spack libraries. This is because it takes *higher* precedence
than the default library search paths, which are used by system software.
`DYLD_FALLBACK_LIBRARY_PATH`, on the other hand, takes lower precedence.
At first glance, this might seem bad, because the software installed by
Spack in an environment needs to find *its* libraries, and it should not
use the defaults. However, Spack's isntallations are always `RPATH`'d,
so they do not have this problem.
`DYLD_FALLBACK_LIBRARY_PATH` is thus useful for things built in an
environment that need to use Spack's libraries, that don't set *their*
RPATHs correctly for whatever reason. We now prefer it to
`DYLD_LIBRARY_PATH` in modules and in environments because it helps a
little bit, and it is much less intrusive.
provided (#15662).
Prior to this fix, the checked Spec object would not be populated, and
concretization would fail.
Co-authored-by: Marc Allen <mrcall@amazon.com>
`spack test` has a spurious '[+] ' in the output:
```
lib/spack/spack/test/install.py .........[+] ......
```
Output is properly suppressed:
```
lib/spack/spack/test/install.py ...............
```
Makes the following changes:
* (Fixes#15620) tty configuration was failing when stdout was
redirected. The implementation now creates a pseudo terminal for
stdin and checks stdout properly, so redirections of stdin/out/err
should be handled now.
* Handles terminal configuration when the Spack process moves between
the foreground and background (possibly multiple times) during a
build.
* Spack adjusts terminal settings to allow users to to enable/disable
build process output to the terminal using a "v" toggle, abnormal
exit cases (like CTRL-C) could leave the terminal in an unusable
state. This is addressed here with a special-case handler which
restores terminal settings.
Significantly extend testing of process output logger:
* New PseudoShell object for setting up a master and child process
and configuring file descriptor inheritance between the two
* Tests for "v" verbosity toggle making use of the added PseudoShell
object
* Added `uniq` function which takes a list of elements and replaces
any consecutive sequence of duplicate elements with a single
instance (e.g. "112211" -> "121")
Co-authored-by: Adam J. Stewart <ajstewart426@gmail.com>
The performance improvements done in #14693 where leaving the DB in an inconsistent state when specs were removed from it. This PR updates the DB internal state whenever the DB is written to a file.
Note that we still cannot properly enumerate installed dependents, so there is a TODO in this code. Fixing that will require the dependents dictionaries in specs to be re-keyed (either by hash, or not keyed at all -- a list would do). See #11983 for details.
Reading the database repeatedly can be quite slow. We need a way to speed
up Spack when it reads the DB multiple times, but the DB has not been
modified between reads (which is nearly all the time).
- [x] Add a file containing a unique uuid that is regenerated at database
write time. Use this uuid to suppress re-parsing the database
contents if we know a previous uuid and the uuid has not changed.
- [x] Fix mutable_database fixture so that it resets the last seen
verifier when it resets.
- [x] Enable not rereading the database immediately after a write. Make
the tests reset the last seen verifier in between tests that use the
database fixture.
- [x] make presence of uuid module optional
Removed the code that was converting the old index.yaml format into
index.json. Since the change happened in #2189 it should be
considered safe to drop this (untested) code.
* only override spec prefix for non-external packages
* add test that environment shell modifications respect explicitly-specified prefixes for external packages
* add clarifying comment
spack.util.environment_after_sourcing_files compares the local
environment against a shell environment after having sourced a
file; but this ends up including the default shell profile and
rc, which might differ from the local environment.
To change this, compare against the default shell environment,
expressed here as 'source /dev/null'.
According to my nightly CI/CD tests, x.org is another large provider
of software in common build chains that is often down.
Added a hand-selected amount of mirrors that is well up-to-sync.
Tested with `util-macros` that has a quite "recent" patch release.
Other packages to follow in an individual PR.
Makes the following changes:
* (Fixes#15620) tty configuration was failing when stdout was
redirected. The implementation now creates a pseudo terminal for
stdin and checks stdout properly, so redirections of stdin/out/err
should be handled now.
* Handles terminal configuration when the Spack process moves between
the foreground and background (possibly multiple times) during a
build.
* Spack adjusts terminal settings to allow users to to enable/disable
build process output to the terminal using a "v" toggle, abnormal
exit cases (like CTRL-C) could leave the terminal in an unusable
state. This is addressed here with a special-case handler which
restores terminal settings.
Significantly extend testing of process output logger:
* New PseudoShell object for setting up a master and child process
and configuring file descriptor inheritance between the two
* Tests for "v" verbosity toggle making use of the added PseudoShell
object
* Added `uniq` function which takes a list of elements and replaces
any consecutive sequence of duplicate elements with a single
instance (e.g. "112211" -> "121")
Co-authored-by: Adam J. Stewart <ajstewart426@gmail.com>
* Moved link to the right place in the docs
* Fixed a few minor issues in extensions docs
Fixed a typo, added a subsubsection for better
navigation, reworded "modules in Python" as
"Python packages"
sourceware.org is often quite overrun and times out or results in
certificate errors.
Since libffi, bzip2, elfutils, etc. are quite fundamental in
build chains, lets add some official mirrors.
libffi, bzip2, elfutils, lvm2, valgrind: add mirrors
The performance improvements done in #14693 where leaving the DB in an inconsistent state when specs were removed from it. This PR updates the DB internal state whenever the DB is written to a file.
Note that we still cannot properly enumerate installed dependents, so there is a TODO in this code. Fixing that will require the dependents dictionaries in specs to be re-keyed (either by hash, or not keyed at all -- a list would do). See #11983 for details.
* Skip collection of compiler link paths if compiler does not define a verbose flag
* modules config bug: allow user to configure a compiler without an explicit entry for loaded modules
* Add capability for detecting build number for Arm compilers
* Fixing fleck8 errors and updating test_arm_version_detection function for more detailed Arm compielr version detection
* Ran flake8 locally and corrected errors
* Altering Arm compielr version check to remove else clause and be more consistent with other compielr version checks. Added test case so both the 'if' and 'else' conditionals of the Arm compiler version check have a test case
Co-authored-by: EC2 Default User <ec2-user@ip-172-31-7-135.us-east-2.compute.internal>
spack.util.environment_after_sourcing_files compares the local
environment against a shell environment after having sourced a
file; but this ends up including the default shell profile and
rc, which might differ from the local environment.
To change this, compare against the default shell environment,
expressed here as 'source /dev/null'.
* only override spec prefix for non-external packages
* add test that environment shell modifications respect explicitly-specified prefixes for external packages
* add clarifying comment
Currently, to force Spack to use an external MPI, you have to specify `buildable: False`
for every MPI provider in Spack in your packages.yaml file. This is both tedious and
fragile, as new MPI providers can be added and break your workflow when you do a
git pull.
This PR allows you to specify an entire virtual dependency as non-buildable, and
specify particular implementations to be built:
```
packages:
all:
providers:
mpi: [mpich]
mpi:
buildable: false
paths:
mpich@3.2 %gcc@7.3.0: /usr/packages/mpich-3.2-gcc-7.3.0
```
will force all Spack builds to use the specified `mpich` install.
Removed provider_index use of 'import from' and refactored a few routines to a further subclassing of _IndexBase for implementing user defined bindings of provider specs.
* relocate: removed import from statements
* relocate: renamed *Exception to *Error
This aims at consistency in naming with both
the standard library (ValueError, AttributeError,
etc.) and other errors in 'spack.error'.
Improved existing docstrings
* relocate: simplified search function by un-nesting conditionals
The search function that searches for patchelf has been
refactored to remove deeply nested conditionals.
Extended docstring.
* relocate: removed a condition specific to unit tests
* relocate: added test for _patchelf
Our unit tests run many times. Any unit test which actually installs
a package (which involves fetching code on the internet) is a severe
bug because it runs an installation many times (i.e. re-downloading
the same package for each version of Python that we run unit tests
for).
This reverts commit 25893f1, which added tests that install real
packages.
If the Python used by Spack does not include Setuptools, then
'spack test' will fail because Spack's vendored pytest dependency
imports and uses Setuptools in some of its functions. It turns out
that Spack doesn't use the functionality those methods enable, so
this PR removes those functions and thereby allows 'spack test' to
run without Setuptools.
For any Spack test using Spack's YAML configuration, avoid using real
Spack configuration that has been cached by other tests and Spack
startup logic. Previously this was only done for tests using
'mutable_config' (i.e. those which expected to *change* the
configuration of Spack), but in fact all tests that read Spack config
should use it.
This was an issue when running tests within an environment, because
compiler configuration ends up being queried earlier, and the user's
real config "leaks" into the cache. Outside an environment, the cache
is never set until tests touch it, so we weren't seeing this issue.
`spack test` has a spurious '[+] ' in the output:
```
lib/spack/spack/test/install.py .........[+] ......
```
Output is properly suppressed:
```
lib/spack/spack/test/install.py ...............
```
Reading the database repeatedly can be quite slow. We need a way to speed
up Spack when it reads the DB multiple times, but the DB has not been
modified between reads (which is nearly all the time).
- [x] Add a file containing a unique uuid that is regenerated at database
write time. Use this uuid to suppress re-parsing the database
contents if we know a previous uuid and the uuid has not changed.
- [x] Fix mutable_database fixture so that it resets the last seen
verifier when it resets.
- [x] Enable not rereading the database immediately after a write. Make
the tests reset the last seen verifier in between tests that use the
database fixture.
- [x] make presence of uuid module optional
Spack currently cannot run as a background process uninterrupted because some of the logging functions used in the install method (especially to create the dynamic verbosity toggle with the v key) cause the OS to issue a SIGTTOU to Spack when it's backgrounded.
This PR puts the necessary gatekeeping in place so that Spack doesn't do anything that will cause a signal to stop the process when operating as a background process.
Spack currently cannot run as a background process uninterrupted because some of the logging functions used in the install method (especially to create the dynamic verbosity toggle with the v key) cause the OS to issue a SIGTTOU to Spack when it's backgrounded.
This PR puts the necessary gatekeeping in place so that Spack doesn't do anything that will cause a signal to stop the process when operating as a background process.
This makes sure that a package's fetch_options are used when fetching
new versions to checksum. This allows working around problems with
slow servers or those requiring a cookie to be set.
Bug: Spack hangs on some Cray machines
Reason: The TERM environment variable is necessary to run bash -lc "echo $CRAY_CPU_TARGET", but we run that command within env -i, which wipes the environment.
Fix: Manually forward the TERM environment variable to env -i /bin/bash -lc "echo $CRAY_CPU_TARGET"
When trying to use an upstream Spack repository, as of f2aca86 Spack
was attempting to write to the upstream DB based on a new metadata
directory added in that commit. Upstream DBs are read-only, so this
should not occur.
This adds a check to prevent Spack from writing to the upstream DB
fixes#15449
Before this PR a call to pkg.url_for_version was modifying
class attributes determining different results for subsequents
calls and an error when the urls was empty.
This recovers the old behavior of replace_prefix_bin that was
modified to work with elf binaries by prefixing os.sep to new prefix
until length is the same as old prefix.
Testing the install StopIteration exception resulted in an attribute error:
AttributeError: 'StopIteration' object has no attribute 'message'
This PR adds a unit test and resolves that error.
The new build process, introduced in #13100 , relies on a spec's dependents in addition to their dependencies. Loading a spec from a yaml file was not initializing the dependents.
- [x] populate dependents when loading from yaml
The distributed build PR (#13100) -- did not check the install status of dependencies when using the `--only package` option so would refuse to install a package with the claim that it had uninstalled dependencies whether that was the case or not.
- [x] add install status checks for the `--only package` case.
- [x] add initial set of tests
This change stores packages' configure arguments during build and makes
use of them while refreshing module files. This fixes problems such as in
#10716.
Bug: Spack hangs on some Cray machines
Reason: The TERM environment variable is necessary to run bash -lc "echo $CRAY_CPU_TARGET", but we run that command within env -i, which wipes the environment.
Fix: Manually forward the TERM environment variable to env -i /bin/bash -lc "echo $CRAY_CPU_TARGET"
- [x] move some logic for handling virtual packages from the `spack
dependencies` command into `spack.package.possible_dependencies()`
- [x] rework possible dependencies tests so that expected and actual
output are on the left/right respectively
When trying to use an upstream Spack repository, as of f2aca86 Spack
was attempting to write to the upstream DB based on a new metadata
directory added in that commit. Upstream DBs are read-only, so this
should not occur.
This adds a check to prevent Spack from writing to the upstream DB
* try extend path to solve PyQt5.sip not found issue
* disable private sip installation in sippackage class
* undo manual PyQt5 dir creation in py-sip site-packages dir
* fix typo
* fix typo
* also apply fix to PyQt4
* tidy up
* flake8 and tidy up
* tidy and undo hardcoding of python_include_dir
* replace hardcoded python inc dir
* fix minor issues
* rethink include dir variable name
* improve style
* add new versions
* implement new sip setup to qsci installation
* set sip-incdir correctly for the new setup
* setup extend_path thing before qsci python bindings
* take care of conflict
* flake8
* also extend for PyQt4
* improve style
* improve style
* SipPackage build sys should depend on py-sip
* consolidate extend_path fixes into SipPackage
* fix typo
* fix bugs
* flake8
* revert sip doc to pre-resource setup
* import os module
* flake8
Co-authored-by: Sinan81 <sbulut@3vgeomatics.com>
Add a 'define_from_variant` helper function to CMake-based Spack
packages to convert package variants into CMake arguments. For
example:
args.append('-DFOO=%s' % ('ON' if '+foo' in self.spec else 'OFF'))
can be replaced with:
args.append(self.define_from_variant('foo'))
The following conversions are handled automatically:
* Flag variants will be converted to CMake booleans
* Multivalued variants will be converted to semicolon-separated strings
* Other variant values are converted to CMake string arguments
This also adds a 'define' helper method to convert any variable to
a CMake argument. It has the same conversion rules as
'define_from_variant' (but operates directly on values rather than
requiring the user to supply the name of a package variant).
* Buildcache: Install into non-default directory layouts
Store a dictionary mapping of original dependency prefixes to dependency hashes
Use the loaded spec to grab the new dependency prefixes in the new directory layout.
Map the original dependency prefixes to the new dependency prefixes using the dependency hashes.
Use the dependency prefixes map to replace original rpaths with new rpaths preserving the order.
For mach-o binaries, use the dependency prefixes map to replace the dependency library entires for libraries and executables and the replace the library id for libraries.
On Linux, patchelf is used to replace the rpaths of elf binaries.
On macOS, install_name_tool is used to replace the rpaths and dependency libraries of mach-o binaries and the id of mach-o libraries.
On Linux, macholib is used to replace the dependency libraries of mach-o binaries and the id of mach-o libraries.
Binary text with padding replacement is attempted for all binaries for the following paths:
spack layout root
spack prefix
sbang script location
dependency prefixes
package prefix
Text replacement is attempted for all text files using the paths above.
Symbolic links to the absolute path of the package install prefix are replaced, all others produce warnings.
PR #15212 added a new connect_timeout option that can be overridden
using fetch_options but had to specified per-version. This adds a new
per-package variable that can be used to override fetch_options for
all versions in the package. This includes connect_timeout as well
as 'cookie' (e.g. for the jdk package).
Packages can combine package-level fetch_options with per-version
fetch_options, in which case the version fetch_options completely
override the package-level fetch_options.
This commit includes tests for the added behavior.
fixes#15449
Before this PR a call to pkg.url_for_version was modifying
class attributes determining different results for subsequents
calls and an error when the urls was empty.
* add --skip-unstable-versions option to 'spack mirror create' which skips sources/resource for packages if their version is not stable (i.e. if they are the head of a git branch rather than a fixed commit)
* '--skip-unstable-versions' should skip all VCS sources/resources, not just those which are not cachable
Allows spack.config InternalConfigScope and Configuration.set() to
handle keys with trailing ':' to indicate replacement vs merge
behavior with respect to lower priority scopes.
Lists may now be replaced rather than merged (this behavior was
previously only available for dictionaries).
This commit adds tests for the new behavior.
Testing the install StopIteration exception resulted in an attribute error:
AttributeError: 'StopIteration' object has no attribute 'message'
This PR adds a unit test and resolves that error.
This recovers the old behavior of replace_prefix_bin that was
modified to work with elf binaries by prefixing os.sep to new prefix
until length is the same as old prefix.
Removed the code that was converting the old index.yaml format into
index.json. Since the change happened in #2189 it should be
considered safe to drop this (untested) code.
Spack's fflags are meant for both f77 and fc. Therefore, they must
be passed as FFLAGS and FCFLAGS to the configure scripts of
Autotools-based packages.
The distributed build PR (#13100) -- did not check the install status of dependencies when using the `--only package` option so would refuse to install a package with the claim that it had uninstalled dependencies whether that was the case or not.
- [x] add install status checks for the `--only package` case.
- [x] add initial set of tests
connect_timeout can be used to increase the time Spack waits for the
server to answer. This can be used to work around slow connections or
servers.
Fixes#14700
* CudaPackage: add support for Tesla K80 and older CUDA
* Flake8 fixes
* Fix cuda_arch when no arch is set
* Fine-tune cuda_arch=37,50 supported CUDA versions
* CUDA 6.5+ supports SM_37
* Add @svenevs as a maintainer
The new build process, introduced in #13100 , relies on a spec's dependents in addition to their dependencies. Loading a spec from a yaml file was not initializing the dependents.
- [x] populate dependents when loading from yaml
* Buildcache command: add install option -o/--otherarch
This will allow matching specs from other archs, for example
installing macOS buildcaches on linux hosts.
* spack commands --update-completion
args.specs is a list, which results in output like this:
```
eval `spack load --sh ['libxml2', 'xz']`
```
We want this instead:
```
eval `spack load --sh libxml2 xz`
```
This change stores packages' configure arguments during build and makes
use of them while refreshing module files. This fixes problems such as in
#10716.
* Emit a sensible error message if compiler's target is overly specific
fixes#14798fixes#13733
Compiler specifications require a generic architecture family as
their target. This commit improves the error message that is
displayed to users if they edit compilers.yaml and use an overly
specific name.
The hashing logic looks for function calls that are Spack directives.
It expects that when a Spack directive is used that it is referenced
directly by name, and that the directive function is not itself
retrieved by calling another function. When the hashing logic
encountered a function call where the function was determined
dynamically, it would fail (attempting to access a name attribute
that does not happen to exist in this case).
This updates the hashing logic to filter out function calls where the
function is determined dynamically when looking for uses of Spack
directives.
Spack now requires an exact match of the compiler version
requested by the user. A loose constraint can be given to
Spack by using a version range instead of a concrete version
(e.g. 4.5: instead of 4.5).
Sometimes one needs to preserve the (relative order) of
mtimes on installed files. So it's better to just copy
over all the metadata from the source tree to the install
tree. If permissions need fixing, that will be done anyway
afterwards.
One major use case are resource()s:
They're unpacked in one place and then copied to their
final place using install_tree(). If the resource is a
source tree using autoconf/automake, resetting mtimes
uncorrectly might force unwanted autoconf/etc calls.
If the mimetype returned from `file -h -b --mime-type` contains slashes
in its subtype, the tuple returned from `spack.relocate.mime_type` will
have a size larger than two, which leads to errors.
Change-Id: I31de477e69f114ffdc9ae122d00c573f5f749dbb
Fixes#9394Closes#13217.
## Background
Spack provides the ability to enable/disable parallel builds through two options: package `parallel` and configuration `build_jobs`. This PR changes the algorithm to allow multiple, simultaneous processes to coordinate the installation of the same spec (and specs with overlapping dependencies.).
The `parallel` (boolean) property sets the default for its package though the value can be overridden in the `install` method.
Spack's current parallel builds are limited to build tools supporting `jobs` arguments (e.g., `Makefiles`). The number of jobs actually used is calculated as`min(config:build_jobs, # cores, 16)`, which can be overridden in the package or on the command line (i.e., `spack install -j <# jobs>`).
This PR adds support for distributed (single- and multi-node) parallel builds. The goals of this work include improving the efficiency of installing packages with many dependencies and reducing the repetition associated with concurrent installations of (dependency) packages.
## Approach
### File System Locks
Coordination between concurrent installs of overlapping packages to a Spack instance is accomplished through bottom-up dependency DAG processing and file system locks. The runs can be a combination of interactive and batch processes affecting the same file system. Exclusive prefix locks are required to install a package while shared prefix locks are required to check if the package is installed.
Failures are communicated through a separate exclusive prefix failure lock, for concurrent processes, combined with a persistent store, for separate, related build processes. The resulting file contains the failing spec to facilitate manual debugging.
### Priority Queue
Management of dependency builds changed from reliance on recursion to use of a priority queue where the priority of a spec is based on the number of its remaining uninstalled dependencies.
Using a queue required a change to dependency build exception handling with the most visible issue being that the `install` method *must* install something in the prefix. Consequently, packages can no longer get away with an install method consisting of `pass`, for example.
## Caveats
- This still only parallelizes a single-rooted build. Multi-rooted installs (e.g., for environments) are TBD in a future PR.
Tasks:
- [x] Adjust package lock timeout to correspond to value used in the demo
- [x] Adjust database lock timeout to reduce contention on startup of concurrent
`spack install <spec>` calls
- [x] Replace (test) package's `install: pass` methods with file creation since post-install
`sanity_check_prefix` will otherwise error out with `Install failed .. Nothing was installed!`
- [x] Resolve remaining existing test failures
- [x] Respond to alalazo's initial feedback
- [x] Remove `bin/demo-locks.py`
- [x] Add new tests to address new coverage issues
- [x] Replace built-in package's `def install(..): pass` to "install" something
(i.e., only `apple-libunwind`)
- [x] Increase code coverage
* Buildcache creation change the way prefix is copied to workdir.
* install_tree copies hardlinked files
* tarfile creates hardlinked files on extraction.
* create a temporary tarfile from prefix and extract it to workdir
* Use temp tarfile to move workdir to prefix to preserve hardlinks instead of copying
It's often useful to run a module with `python -m`, e.g.:
python -m pyinstrument script.py
Running a python script this way was hard, though, as `spack python` did
not have a similar `-m` option. This PR adds a `-m` option to `spack
python` so that we can do things like this:
spack python -m pyinstrument ./test.py
This makes it easy to write a script that uses a small part of Spack and
then profile it. Previously thee easiest way to do this was to write a
custom Spack command, which is often overkill.
Fixes#10019
If multiple instances of a package were installed in a single
instance of Spack, and they differed in terms of dependencies, then
"spack find" would not distinguish specs based on their dependencies.
For example if two instances of X were installed, one with Y and one
with Z, then "spack find X ^Y" would display both instances of X.
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
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.
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']
```
This commit introduces a `--no-check-signature` option for
`spack install` so that unsigned packages can be installed. It is
off by default (signatures required).
VSX alitvec extensions are supported by PowerISA from v2.06 (Power7+), but might
not be listed in features.
FMA has been supported by PowerISA since Power1, but might not be listed in
features.
This commit adds these features to all the power ISA family sets.
Add an optional 'submodules_delete' field to Git versions in Spack
packages that allows them to remove specific submodules.
For example: the nervanagpu submodule has become unavailable for the
PyTorch project (see issue 19457 at
https://github.com/pytorch/pytorch/issues/). Removing this submodule
allows 0.4.1 to build.
* Initialize _cached_specs at the file level and check for spec in it before searching mirrors in try_download_spec.
* Make _cached_specs a set to avoid duplicates
* Fix packaging test
* Ignore build_cache in stage when spec.yaml files are downloaded.
`spack -V` previously always returned the version of spack from
`spack.spack_version`. This gives us a general idea of what version
users are on, but if they're on `develop` or on some branch, we have to
ask more questions.
This PR makes `spack -V` check whether this instance of Spack is a git
repository, and if it is, it appends useful information from `git
describe --tags` to the version. Specifically, it adds:
- number of commits since the last release tag
- abbreviated (but unique) commit hash
So, if you're on `develop` you might get something like this:
$ spack -V
0.13.3-912-3519a1762
This means you're on commit 3519a1762, which is 912 commits ahead of
the 0.13.3 release.
If you are on a release branch, or if you are using a tarball of Spack,
you'll get the usual `spack.spack_version`:
$ spack -V
0.13.3
This should help when asking users what version they are on, since a lot
of people use the `develop` branch.
This PR adds a new command to Spack:
```console
$ spack containerize -h
usage: spack containerize [-h] [--config CONFIG]
creates recipes to build images for different container runtimes
optional arguments:
-h, --help show this help message and exit
--config CONFIG configuration for the container recipe that will be generated
```
which takes an environment with an additional `container` section:
```yaml
spack:
specs:
- gromacs build_type=Release
- mpich
- fftw precision=float
packages:
all:
target: [broadwell]
container:
# Select the format of the recipe e.g. docker,
# singularity or anything else that is currently supported
format: docker
# Select from a valid list of images
base:
image: "ubuntu:18.04"
spack: prerelease
# Additional system packages that are needed at runtime
os_packages:
- libgomp1
```
and turns it into a `Dockerfile` or a Singularity definition file, for instance:
```Dockerfile
# Build stage with Spack pre-installed and ready to be used
FROM spack/ubuntu-bionic:prerelease as builder
# What we want to install and how we want to install it
# is specified in a manifest file (spack.yaml)
RUN mkdir /opt/spack-environment \
&& (echo "spack:" \
&& echo " specs:" \
&& echo " - gromacs build_type=Release" \
&& echo " - mpich" \
&& echo " - fftw precision=float" \
&& echo " packages:" \
&& echo " all:" \
&& echo " target:" \
&& echo " - broadwell" \
&& echo " config:" \
&& echo " install_tree: /opt/software" \
&& echo " concretization: together" \
&& echo " view: /opt/view") > /opt/spack-environment/spack.yaml
# Install the software, remove unecessary deps and strip executables
RUN cd /opt/spack-environment && spack install && spack autoremove -y
RUN find -L /opt/view/* -type f -exec readlink -f '{}' \; | \
xargs file -i | \
grep 'charset=binary' | \
grep 'x-executable\|x-archive\|x-sharedlib' | \
awk -F: '{print $1}' | xargs strip -s
# Modifications to the environment that are necessary to run
RUN cd /opt/spack-environment && \
spack env activate --sh -d . >> /etc/profile.d/z10_spack_environment.sh
# Bare OS image to run the installed executables
FROM ubuntu:18.04
COPY --from=builder /opt/spack-environment /opt/spack-environment
COPY --from=builder /opt/software /opt/software
COPY --from=builder /opt/view /opt/view
COPY --from=builder /etc/profile.d/z10_spack_environment.sh /etc/profile.d/z10_spack_environment.sh
RUN apt-get -yqq update && apt-get -yqq upgrade \
&& apt-get -yqq install libgomp1 \
&& rm -rf /var/lib/apt/lists/*
ENTRYPOINT ["/bin/bash", "--rcfile", "/etc/profile", "-l"]
```
* Add binary_distribution::get_spec which takes concretized spec
Add binary_distribution::try_download_specs for downloading of spec.yaml files to cache
get_spec is used by package::try_install_from_binary_cache to download only the spec.yaml
for the concretized spec if it exists.
The Spec parser currently calls `spec.traverse()` after every parse, in
order to set the platform if it's not set. We don't need to do a full
traverse -- we can just check the platforrm as new specs are parsed.
This takes about a second off the time required to import all packages in
Spack (from 8s to 7s).
- [x] simplify platform-setting logic in `SpecParser`.
`filename_for_package_name()` and `dirname_for_package_name()`
automatically construct a Spec from their arguments, which adds a fair
amount of overhead to importing lots of packages. Removing this removes
about 11% of the runtime of importing all packages in Spack (9s -> 8s).
- [x] `filename_for_package_name()` and `dirname_for_package_name()` now
take a string `pkg_name` arguments instead of specs.
* `Environment.__init__` is now synchronized with all writing operations
* `spack uninstall` now synchronizes its updates to any associated environment
* A side effect of this is that the environment is no longer updated piecemeal as specs are uninstalled - all specs are removed from the environment before they are uninstalled
This commit makes two fundamental corrections to tests:
1) Changes 'matches' to the correct 'match' argument for 'pytest.raises' (for all affected tests except those checking for 'SystemExit');
2) Replaces the 'match' argument for tests expecting 'SystemExit' (since the exit code is retained instead) with 'capsys' error message capture.
Both changes are needed to ensure the associated exception message is actually checked.
Updates to environments were not multi-process safe, which prevented them from taking advantage of parallel builds as implemented in #13100. This is a minimal set of changes to enable `spack install` in an environment to be parallelized:
- [x] add an internal lock, stored in the `.spack-env` directory,
to synchronize updates to `spack.yaml` and `spack.lock`
- [x] add `Environment.write_transaction` interface for this lock
- [x] makes use of `Environment.write_transaction` in `install`,
`add`, and `remove` commands
- `uninstall` is not synchronized yet; that is left for a future PR.
Spack commands referring to upstream-installed specs by hash have
been broken since 6b619da (merged September 2019), which added a new
Database function specifically for parsing hashes from command-line
specs; this function was inappropriately attempting to acquire locks
on upstream databases.
This PR updates the offending function to avoid locking upstream
databases and also updates associated tests to catch regression
errors: the upstream database created for these tests was not
explicitly set as an upstream (i.e. initialized with upstream=True)
so it was not guarding against inappropriate accesses.
* Unified environment modifications in config files
fixes#13357
This commit factors all the code that is involved in
the validation (schema) and parsing of environment modifications
from configuration files in a single place. The factored out
code is then used for module files and compiler configuration.
Attributes were separated by dashes in `compilers.yaml` files and
by underscores in `modules.yaml` files. This PR unifies the syntax
on attributes separated by underscores.
Unit testing of environment modifications in compilers
has been refactored and simplified.
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
Openblas target is now determined automatically upon inspection of
`TargetList.txt`. If the spack target is a generic architecture family
(like x86_64 or aarch64) the DYNAMIC_ARCH setting is used
instead of targeting a specific microarchitecture.
Instead of another script, this adds a simple argument to `spack
commands` that updates the completion script. Developers can now just
run:
spack commands --update-completion
This should make it simpler for developers to remember to run this
*before* the tests fail. Also, this version tab-completes.
Previously the `spack load` command was a wrapper around `module load`. This required some bootstrapping of modules to make `spack load` work properly.
With this PR, the `spack` shell function handles the environment modifications necessary to add packages to your user environment. This removes the dependence on environment modules or lmod and removes the requirement to bootstrap spack (beyond using the setup-env scripts).
Included in this PR is support for MacOS when using Apple's System Integrity Protection (SIP), which is enabled by default in modern MacOS versions. SIP clears the `LD_LIBRARY_PATH` and `DYLD_LIBRARY_PATH` variables on process startup for executables that live in `/usr` (but not '/usr/local', `/System`, `/bin`, and `/sbin` among other system locations. Spack cannot know the `LD_LIBRARY_PATH` of the calling process when executed using `/bin/sh` and `/usr/bin/python`. The `spack` shell function now manually forwards these two variables, if they are present, as `SPACK_<VAR>` and recovers those values on startup.
- [x] spack load/unload no longer delegate to modules
- [x] refactor user_environment modification calculations
- [x] update documentation for spack load/unload
Co-authored-by: Todd Gamblin <tgamblin@llnl.gov>
This PR adds a `--format=bash` option to `spack commands` to
auto-generate the Bash programmable tab completion script. It can be
extended to work for other shells.
Progress:
- [x] Fix bug in superclass initialization in `ArgparseWriter`
- [x] Refactor `ArgparseWriter` (see below)
- [x] Ensure that output of old `--format` options remains the same
- [x] Add `ArgparseCompletionWriter` and `BashCompletionWriter`
- [x] Add `--aliases` option to add command aliases
- [x] Standardize positional argument names
- [x] Tests for `spack commands --format=bash` coverage
- [x] Tests to make sure `spack-completion.bash` stays up-to-date
- [x] Tests for `spack-completion.bash` coverage
- [x] Speed up `spack-completion.bash` by caching subroutine calls
This PR also necessitates a significant refactoring of
`ArgparseWriter`. Previously, `ArgparseWriter` was mostly a single
`_write` method which handled everything from extracting the information
we care about from the parser to formatting the output. Now, `_write`
only handles recursion, while the information extraction is split into a
separate `parse` method, and the formatting is handled by `format`. This
allows subclasses to completely redefine how the format will appear
without overriding all of `_write`.
Co-Authored-by: Todd Gamblin <tgamblin@llnl.gov>
The gpg2 command isn't always around; it's sometimes called gpg. This is
the case with the brew-installed version, and it's breaking our tests.
- [x] Look for both 'gpg2' and 'gpg' when finding the command
- [x] If we find 'gpg', ensure the version is 2 or higher
- [x] Add tests for version detection.
- [x] Factored to a common place the fixture `testing_gpg_directory`, renamed it as
`mock_gnupghome`
- [x] Removed altogether the function `has_gnupg2`
For `has_gnupg2`, since we were not trying to parse the version from the output of:
```console
$ gpg2 --version
```
this is effectively equivalent to check if `spack.util.gpg.GPG.gpg()` was found. If we need to ensure version is `^2.X` it's probably better to do it in `spack.util.gpg.GPG.gpg()` than in a separate function.
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']
```
Rework Spack's continuous integration workflow to be environment-based.
- Add the `spack ci` command, which replaces the many scripts in `bin/`
- `spack ci` decouples the CI workflow from the spack instance:
- CI is defined in a spack environment
- environment is in its own (single) git repository, separate from Spack
- spack instance used to run the pipeline is up to the user
- A new `gitlab-ci` section in environments allows users to configure how
specs in the environment should be mapped to runners
- Compilers can be bootstrapped in the new pipeline workflow
- Add extensive documentation on pipelines (see `pipelines.rst` for further details)
- Add extensive tests for pipeline code
* Reorder GNU mirrors (#14395)
As @adamjstewart commented in #14395, GNU suggests to use
their mirror. So reorder the mirror to the top.
GNU Doc: https://www.gnu.org/prep/ftp.en.html
* Use spack.util.url.join for URLs in GNU mirrors (#14395)
One should not use os.path.join for URLs. This does only
work on POSIX systems.
Instead use spack.util.url.join.
So every part in spack uses the same url joining method.
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.
* Spack can uninstall unused specs
fixes#4382
Added an option to spack uninstall that removes all unused specs i.e.
build dependencies or transitive dependencies that are left
in the store after the specs that pulled them in have been removed.
* Moved the functionality to its own command
The command has been named 'spack autoremove' to follow the naming used
for the same functionality by other widely known package managers i.e.
yum and apt.
* Speed-up autoremoving specs by not locking and re-reading the scratch DB
* Make autoremove work directly on Spack's store
* Added unit tests for the new command
* Display a terser output to the user
* Renamed the "autoremove" command "gc"
Following discussion there's more consensus around
the latter name.
* Preserve root specs in env contexts
* Instead of preserving specs, restrict gc to the active environment
* Added docs
* Added a unit test for gc within an environment
* Updated copyright to 2020
* Updated documentation according to review
Rephrased a couple of sentences, added references to
`spack find` and dependency types.
* Updated function naming and docstrings
* Simplified computation of unused specs
Since the new approach uses private attributes of the DB
it has been coded as a method of that class rather than a
freestanding function.
The imports in `spec.py` are getting to be pretty unwieldy.
- [x] Remove all of the `import from` style imports and replace them with
`import` or `import as`
- [x] Remove a number names that were exported by `spack.spec` that
weren't even in `spack.spec`
Previously, `spack test` automatically passed all of its arguments to
`pytest -k` if no options were provided, and to `pytest` if they were.
`spack test -l` also provided a list of test filenames, but they didn't
really let you completely narrow down which tests you wanted to run.
Instead of trying to do our own weird thing, this passes `spack test`
args directly to `pytest`, and omits the implicit `-k`. This means we
can now run, e.g.:
```console
$ spack test spec_syntax.py::TestSpecSyntax::test_ambiguous
```
This wasn't possible before, because we'd pass the fully qualified name
to `pytest -k` and get an error.
Because `pytest` doesn't have the greatest ability to list tests, I've
tweaked the `-l`/`--list`, `-L`/`--list-long`, and `-N`/`--list-names`
options to `spack test` so that they help you understand the names
better. you can combine these options with `-k` or other arguments to do
pretty powerful searches.
This one makes it easy to get a list of names so you can run tests in
different orders (something I find useful for debugging `pytest` issues):
```console
$ spack test --list-names -k "spec and concretize"
cmd/env.py::test_concretize_user_specs_together
concretize.py::TestConcretize::test_conflicts_in_spec
concretize.py::TestConcretize::test_find_spec_children
concretize.py::TestConcretize::test_find_spec_none
concretize.py::TestConcretize::test_find_spec_parents
concretize.py::TestConcretize::test_find_spec_self
concretize.py::TestConcretize::test_find_spec_sibling
concretize.py::TestConcretize::test_no_matching_compiler_specs
concretize.py::TestConcretize::test_simultaneous_concretization_of_specs
spec_dag.py::TestSpecDag::test_concretize_deptypes
spec_dag.py::TestSpecDag::test_copy_concretized
```
You can combine any list option with keywords:
```console
$ spack test --list -k microarchitecture
llnl/util/cpu.py modules/lmod.py
```
```console
$ spack test --list-long -k microarchitecture
llnl/util/cpu.py::
test_generic_microarchitecture
modules/lmod.py::TestLmod::
test_only_generic_microarchitectures_in_root
```
Or just list specific files:
```console
$ spack test --list-long cmd/test.py
cmd/test.py::
test_list test_list_names_with_pytest_arg
test_list_long test_list_with_keywords
test_list_long_with_pytest_arg test_list_with_pytest_arg
test_list_names
```
Hopefully this stuff will help with debugging test issues.
- [x] make `spack test` send args directly to `pytest` instead of trying
to do fancy things.
- [x] rework `--list`, `--list-long`, and add `--list-names` to make
searching for tests easier.
- [x] make it possible to mix Spack's list args with `pytest` args
(they're just fancy parsing around `pytest --collect-only`)
- [x] add docs
- [x] add tests
- [x] update spack completion
Test configuration files (except modules.yaml) were in the root level of
test/data, but should really just be in their own directory. The absence
of modules.yaml was also breaking module tests if we got module
preferences after tests started, as the mock modules.yaml was not in the
test directory.
The module hook would previously fail if there were no enabled module types.
- Instead of looking for a `KeyError`, default to empty list when the
config variable is not present.
- Convert lambdas to real functions for clarity.
- Remove legacy yaml_version_check() hook
- Remove the pre_run hook from `hook/__init__.py` and `main.py`
We want to discourage the use of pre-run hooks because they have to run
at startup. To keep Spack fast, we should do things like this lazily
instead of in hooks that require spidering directories full of modules.
Continuing to shave small bits of time off startup --
`spack.cmd.common.arguments` constructs many `Args` objects at module
scope, which has to be done for all commands that import it. Instead of
doing this at load time, do it lazily.
- [x] construct Args objects lazily
- [x] remove the module-scoped argparse fixture
- [x] make the mock config scope set dirty to False by default (like the
regular scope)
This *seems* to reduce load time slightly
Previously, fixtures like `config`, `database`, and `store` were
module-scoped, but frequently used as test function arguments. These
fixtures swap out global on setup and restore them on teardown. As
function arguments, they would do the right set-up, but they'd leave the
global changes in place for the whole module the function lived in. This
meant that if you use `config` once, other functions in the same module
would inadvertently inherit the mock Spack configuration, as it would
only be torn down once all tests in the module were complete.
In general, we should module- or session-scope the *STATE* required for
these global objects (as it's expensive to create0, but we shouldn't
module-or session scope the activation/use of them, or things can get
really confusing.
- [x] Make generic context managers for global-modifying fixtures.
- [x] Make session- and module-scoped fixtures that ONLY build filesystem
state and create objects, but do not swap out any variables.
- [x] Make seeparate function-scoped fixtures that *use* the session
scoped fixtures and actually swap out (and back in) the global
variables like `config`, `database`, and `store`.
These changes make it so that global changes are *only* ever alive for a
singlee test function, and we don't get weird dependencies because a
global fixture hasn't been destroyed.
`PackagePrefs` has had a class-level cache of data from `packages.yaml` for
a long time, but it complicates testing and leads to subtle errors,
especially now that we frequently manipulate custom config scopes and
environments.
Moving the cache to instance-level doesn't slow down concretization or
the test suite, and it just caches for the life of a `PackagePrefs`
instance (i.e., for a single cocncretization) so we don't need to worry
about global state anymore.
- [x] Remove class-level caches from `PackagePrefs`
- [x] Add a cached _spec_order object on each `PackagePrefs` instance
- [x] Remove all calls to `PackagePrefs.clear_caches()`
Commands like `spack blame` were printig poorly when redirected to files,
as colify reverts to a single column when redirected. This works for
list data but not tables.
- [x] Force a table by always passing `tty=True` from `colify_table()`
In "spack info" the Variants header currently has two blank
lines under it. That's too much. It looks like the actual
content belongs to something else.
Instead underline the headers to make things more obvious.
This commit removes the `python_version.py` unit test module
and the vendored dependencies `pyqver2.py` and `pyqver3.py`.
It substitutes them with an equivalent check done using
`vermin` that is run as a separate workflow via Github Actions.
This allows us to delete 2 vendored dependencies that are unmaintained
and substitutes them with a maintained tool.
Also, updates the list of vendored dependencies.
`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.
`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`.
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
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.
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 an optional argument so that `possible_dependencies()` will report
missing dependencies.
- Add a test to ensure it works.
- Ignore missing dependencies in `possible_dependencies()` by default.
- this version allows getting possible dependencies of multiple packages
or specs at once.
- New method handles calling `PackageBase.possible_dependencies` multiple
times and passing `visited` dict around.
`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`.
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
doesn't understand a custom, user-defined compiler version. However, if
the compiler's version check fails, you can't build anything with the
custom compiler.
- [x] Be more lenient: fall back to the custom compiler version and use
it verbatim if the version check fails.
`pgcc -V` was failing on power machines because it returns 2 (despite
correctly printing version information). On x86_64 machines the same
command returns 0 and doesn't cause an error.
- [x] Ignore return value of 2 for pgcc when doign a version check
Vendors for ARM come out of `/proc/cpuinfo` as hex numbers instead of readable strings.
- Add support for associating vendor names with the hex numbers.
- Also move these mappings from Python code to `microarchitectures.json`
- Move darwin feature name mappings to `microarchitectures.json` as well
* when constructing package hash, default to including a method in the content hash if we can't determine whether it would be included by examining the AST
* add a test for updated content-hash calculations
* refactor content hash tests to eliminate repeated lines
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.
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.
* pytest: add __init__ files for all test subdirs
* add licenses to empty files
* Fix Sphinx warning message about comment within docstring
* Further fixes to Sphinx docstring
* fix docstring in generate_package_index() refering to "public" keys as "signing" keys
* use explicit kwargs in push_to_url()
* simplify url_util.parse() per tgamblin's suggestion
* replace standardize_header_names() with the much simpler get_header()
* add some basic tests
* update s3_fetch tests
* update S3 list code to strip leading slashes from prefix
* correct minor warning regression introduced in #11117
* add more tests
* flake8 fixes
* add capsys fixture to mirror_crud test
* add get_header() tests
* use get_header() in more places
* incorporate review comments
This PR allows virtual packages to be added to the specs list using
the add command.
Virtual packages are already allowed in named lists in spack
environments/stacks, and they are already allowed in the specs list
when added using the yaml directly.
I have, more than once, tried to install the list of things that need
to build the docs, only to discover that the list doesn't use Spack's
package names. I'm tired of facepalming....
While I was there I touched up the prose about activating the new
Python packages; activating a python package doesn't add anything to
your PYTHONPATH, it links things into a directory that's *already* on
your PYTHONPATH. Note that this all presupposes that you're using
that same python....
* CUDA HeaderList: Unit Test
* Spec Header Dirs: Only first include/
Avoid matching recurringly nested include paths that usually
refer to internally shipped libraries in packages.
Example in CUDA Toolkit, shipping a libc++ fork internally
with libcu++ since 10.2.89:
`<prefix>/include/cuda/some/more/details/include/` or
`<prefix>/include/cuda/std/detail/libcxx/include`
regex: non-greedy first match of include
Co-Authored-By: Massimiliano Culpo <massimiliano.culpo@gmail.com>
* CUDA: Re-Enable 10.2.89 as Default
* apply strict constraint checks for patches, otherwise Spack may incorrectly treat a version range constraint as satisfied when mixing x.y and x.y.z versions
* add mixed version checks to version comparison tests
`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
`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
* Fixed x86-64 optimization flags for clang
* Fixed expected results in unit tests
Before the flags used where the one for llc, the underlying compiler from LLVM IR to machine assembly. It turns out that the semantic of `-march`, `-mtune` and `-mcpu` changes from clang front-end to llc.
I found no definitive reference for the flags submitted in this PR, but I checked the assembly on a vectorizable function using Godbolt's web-site.
* 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
* 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
`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
Extensions have been available for a while and the overall design
seems solid enough to be feasible for extensions without losing
backward compatibility.
* 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.
* Add process to determine aarch64 microarchitecture
* add microarchitectures for thunderx2 and a64fx
* Add optimize flags for gcc on aarch64 family processors thunderx2 and a64fx.
* Add optimize flags for clang on aarch64 family processors thunderx2 and a64fx
* Add testing for thunderx2 and a64fx microarchitectures
* 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
* 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.
* 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.
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.
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.
when making a package relative, relocate links relative to link directory
rather than the full link path (which includes the file name) because `os.path.relpath` expects a directory.
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.
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.
* Docs update for deprecated `spack sha256`
* Added macOS shasum
* Update lib/spack/docs/packaging_guide.rst
Co-Authored-By: Adam J. Stewart <ajstewart426@gmail.com>
- [x] Use higher contrast terminal output font
- [x] Use higher contrast code block background color than default
- [x] Use a noticeable prompt character
See also https://github.com/spack/spack-tutorial/pull/10.
`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
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
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.
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.
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
* 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
- [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
- [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
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`.
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`.
Commands like "spack mirror list" were displaying mirrors in a
different order than what was listed in the corresponding mirrors.yaml
file.
This restores commands to iterate over mirrors in the order that
they appear in the config file.
* Travis CI: Test Python 3.8
* Fix use of deprecated cgi.escape method
* Fix version comparison
* Fix flake8 F811 change in Python 3.8
* Make flake8 happy
* Use Python 3.8 for all test categories
Currently, query arguments in the Spack core are documented on the
Database._query method, where the functionality is defined.
For users of the spack python command, this makes the python builtin
method help less than ideally useful, as help(spack.store.db.query)
and help(spack.store.db.query_local) do not show relevant information.
This PR updates the doc attributes for the Database.query and
Database.query_local arguments to mirror everything after the first
line of the Database._query docstring.
* cuda: fix conflict statements for x86-64 targets
fixes#13462
This build system mixin was not updated after the support for specific
targets has been merged.
* Updated the version range of cuda that conflicts with gcc@8:
* Updated the version range of cuda that conflicts with gcc@8: for ppc64le
* Relaxed conflicts for version > 10.1
* Updated versions in conflicts
Co-Authored-By: Axel Huebl <axel.huebl@plasma.ninja>
4af4487 added a mirror_id function to most FetchStrategy
implementations that is used to calculate resource locations in
mirrors. It left out BundleFetchStrategy which broke all packages
making use of BundlePackage (e.g. xsdk). This adds a noop
implementation of mirror_id to BundleFetchStrategy so that the
download/installation of BundlePackages can proceed as normal.
* Travis CI: Test Python 3.8
* Fix use of deprecated cgi.escape method
* Fix version comparison
* Fix flake8 F811 change in Python 3.8
* Make flake8 happy
* Use Python 3.8 for all test categories
Currently, query arguments in the Spack core are documented on the
Database._query method, where the functionality is defined.
For users of the spack python command, this makes the python builtin
method help less than ideally useful, as help(spack.store.db.query)
and help(spack.store.db.query_local) do not show relevant information.
This PR updates the doc attributes for the Database.query and
Database.query_local arguments to mirror everything after the first
line of the Database._query docstring.
* cuda: fix conflict statements for x86-64 targets
fixes#13462
This build system mixin was not updated after the support for specific
targets has been merged.
* Updated the version range of cuda that conflicts with gcc@8:
* Updated the version range of cuda that conflicts with gcc@8: for ppc64le
* Relaxed conflicts for version > 10.1
* Updated versions in conflicts
Co-Authored-By: Axel Huebl <axel.huebl@plasma.ninja>
The `test_changed_files` in `test/cmd/flake8.py` was failing because it calls
`ArgumentParser.parse_args()` without arguments. Normally that would just
parse `sys.argv` but it seems to fail because of something in either `spack test`
or `pytest`. Call it with an empty array so that it doesn't try to touch`sys.argv`
at all.
- [x] allow `-d` spack option for `test_changed_files`
* docs: add a spack environment for building the docs
* docs: remove tutorial and link to spack-tutorial.readthedocs.io
The tutorial now has its own standalone website, versioned by instances
of the tutorial. Link to that instead of versioning it directly with Spack.
Support mirroring all packages with `spack mirror create --all`.
In this mode there is no concretization:
* Spack pulls every version of every package into the created mirror.
* It also makes multiple attempts for each package/version combination
(if there is a temporary connection failure).
* Continues if all attempts fail. i.e., this makes its best effort to
fetch evrerything, even if all attempts to fetch one package fail.
This also changes mirroring logic to prefer storing sources by their hash
or by a unique name derived from the source. For example:
* Archives with checksums are named by the sha256 sum, i.e.,
`archive/f6/f6cf3bd233f9ea6147b21c7c02cac24e5363570ce4fd6be11dab9f499ed6a7d8.tar.gz`
vs the previous `<package-name>-package-version>.tar.gz`
* VCS repositories are stored by a path derived from their URL,
e.g. `git/google/leveldb.git/master.tar.gz`.
The new mirror layout allows different packages to refer to the same
resource or source without duplicating that download in the
mirror/cache. This change is not essential to mirroring everything but is
expected to save space when mirroring packages that all use the same
resource.
The new structure of the mirror is:
```
<base directory>/
_source-cache/ <-- the _source-cache directory is new
archive/ <-- archives/resources/patches stored by hash
00/ <-- 2-letter sha256 prefix
002748bdd0319d5ab82606cf92dc210fc1c05d0607a2e1d5538f60512b029056.tar.gz
01/
0154c25c45b5506b6d618ca8e18d0ef093dac47946ac0df464fb21e77b504118.tar.gz
0173a74a515211997a3117a47e7b9ea43594a04b865b69da5a71c0886fa829ea.tar.gz
...
git/
OpenFAST/
openfast.git/
master.tar.gz <-- repo by branch name
PHASTA/
phasta.git/
11f431f2d1a53a529dab4b0f079ab8aab7ca1109.tar.gz <-- repo by commit
...
svn/ <-- each fetch strategy has its own subdirectory
...
openmpi/ <-- the remaining package directories have the old format
openmpi-1.10.1.tar.gz <-- human-readable name is symlink to _source-cache
```
In addition to the archive names as described above, `mirror create` now
also creates symlinks with the old format to help users understand which
package each mirrored archive is associated with, and to allow mirrors to
work with old spack versions. The symlinks are relative so the mirror
directory can still itself be archived.
Other improvements:
* `spack mirror create` will not re-download resources that have already
been placed in it.
* When creating a mirror, the resources downloaded to the mirror will not
be cached (things are not stored twice).
reindexing takes a significant amount of time, and there's no reason to
do it from DB version 0.9.3 to version 5. The only difference is that v5
can contain "deprecated_for" fields.
- [x] Add a `_skip_reindex` list at the start of `database.py`
- [x] Skip the reindex for upgrades in this list. The new version will
just be written to the file the first time we actually have to write
the DB out (e.g., after an install), and reads will still work fine.
Previously, spack would error out if we tried to fetch something with no
code, but that would prevent fetching dependencies. In particular, this
would fail:
spack fetch --dependencies xsdk
- [x] Instead of raising an error, just print a message that there is nothing
to be fetched for packages like xsdk that do not have code.
- [x] Make BundleFetchStrategy a bit more quiet about doing nothing.
We've had `spack spec --yaml` for a while, and we've had methods for JSON
for a while as well. We just haven't has a `--json` argument for `spack spec`.
- [x] Add a `--json` argument to `spack spec`, just like `--yaml`
New entry for K10 microarchitecture.
Reorder Zen* microarchitectures to avoid triggering as k10.
Remove some desktop-specific flags that were preventing Opteron Bulldozer/Piledriver/Steamroller/Excavator CPUs from being recognized as such.
Remove one or two flags which weren't produced in /proc/cpuinfo on older OS (RHEL6 and friends).
Rename the `spack diy` command to `spack dev-build` to make the use case clearer.
The `spack diy` command has some useful functionality for developers using Spack to build their dependencies and configure/build/install the code they are developing. Developers do not notice it, partly because of the obscure name.
The `spack dev-build` command has a `-u/--until PHASE` option to stop after a given phase of the build. This can be used to configure your project, run cmake on your project, or similarly stop after any stage of the build the user wants. These options are analogous to the existing `spack configure` and `spack build` commands, but for developer builds.
To unify the syntax, we have deprecated the `spack configure` and `spack build` commands, and added a `-u/--until PHASE` option to the `spack install` command as well.
The functionality in `spack dev-build` (specifically `spack dev-build -u cmake`) may be able to supersede the `spack setup` command, but this PR does not deprecate that command as that will require slightly more thought.
fd58c98 formats the `Stage`'s `archive_path` in `Stage.archive` (as part of `web.push_to_url`). This is not needed and if the formatted differs from the original path (for example if the archive file name contains a URL query suffix), then the copy fails.
This removes the formatting that occurs in `web.push_to_url`.
We should figure out a way to handle bad cases like this *and* to have nicer filenames for downloaded files. One option that would work in this particular case would be to also pass `-J` / `--remote-header-name` to `curl`. We'll need to do follow-up work to determine if we can use `-J` everywhere.
See also: https://github.com/spack/spack/pull/11117#discussion_r338301058
Add a new entry in `config.yaml`:
config:
shared_linking: 'rpath'
If this variable is set to `rpath` (the default) Spack will set RPATH in ELF binaries. If set to `runpath` it will set RUNPATH.
Details:
* Spack cc wrapper explicitly adds `--disable-new-dtags` when linking
* cc wrapper also strips `--enable-new-dtags` from the compile line
when disabling (and vice versa)
* We specifically do *not* add any dtags flags on macOS, which uses
Mach-O binaries, not ELF, so there's no RUNPATH)
`spack deprecate` allows for the removal of insecure packages with minimal impact to their dependents. It allows one package to be symlinked into the prefix of another to provide seamless transition for rpath'd and hard-coded applications using the old version.
Example usage:
spack deprecate /hash-of-old-openssl /hash-of-new-openssl
The spack deprecate command is designed for use only in extroardinary circumstances. The spack deprecate command makes no promises about binary compatibility. It is up to the user to ensure the replacement is suitable for the deprecated package.
Previously this command only showed total counts for each regular
expression. This doesn't give you a sense of which regexes are working
well and which ones are not. We now display the number of right, wrong,
and total URL parses per regex.
It's easier to see where we might improve the URL parsing with this
change.
This updates the configuration loading/dumping logic (now called
load_config/dump_config) in spack_yaml to preserve comments (by using
ruamel.yaml's RoundTripLoader). This has two effects:
* environment spack.yaml files expect to retain comments, which
load_config now supports. By using load_config, users can now use the
':' override syntax that was previously unavailable for environment
configs (but was available for other config files).
* config files now retain user comments by default (although in cases
where Spack updates/overwrites config, the comments can still be
removed).
Details:
* Subclasses `RoundTripLoader`/`RoundTripDumper` to parse yaml into
ruamel's `CommentedMap` and analogous data structures
* Applies filename info directly to ruamel objects in cases where the
updated loader returns those
* Copies management of sections in `SingleFileScope` from #10651 to allow
overrides to occur
* Updates the loader/dumper to handle the processing of overrides by
specifically checking for the `:` character
* Possibly the most controversial aspect, but without that, the parsed
objects have to be reconstructed (i.e. as was done in
`mark_overrides`). It is possible that `mark_overrides` could remain
and a deep copy will not cause problems, but IMO that's generally
worth avoiding.
* This is also possibly controversial because Spack YAML strings can
include `:`. My reckoning is that this only occurs for version
specifications, so it is safe to check for `endswith(':') and not
('@' in string)`
* As a consequence, this PR ends up reserving spack yaml functions
load_config/dump_config exclusively for the purpose of storing spack
config
`test_envoronment_status()` was printing extra output during tests.
- [x] disable output only for `env('status')` calls instead of disabling
it for the whole test.
This PR ensures that environment activation sets all environment variables set by the equivalent `module load` operations, except that the spec prefixes are "rebased" to the view associated with the environment.
Currently, Spack blindly adds paths relative to the environment view root to the user environment on activation. Issue #12731 points out ways in which this behavior is insufficient.
This PR changes that behavior to use the `setup_run_environment` logic for each package to augment the prefix inspections (as in Spack's modulefile generation logic) to ensure that all necessary variables are set to make use of the packages in the environment.
See #12731 for details on the previous problems in behavior.
This PR also updates the `ViewDescriptor` object in `spack.environment` to have a `__contains__` method. This allows for checks like `if spec in self.default_view`. The `__contains__` operator for `ViewDescriptor` objects checks whether the spec satisfies the filters of the View descriptor, not whether the spec is already linked into the underlying `FilesystemView` object.
This PR ensures that on Darwin we always append /sbin and /usr/sbin to PATH, if they are not already present, when looking for sysctl.
* Make sure we look into /sbin and /usr/sbin for sysctl
* Refactor sysctl for better readability
* Remove marker to make test pass
These changes update our gcc microarchitecture descriptions based on manuals found here https://gcc.gnu.org/onlinedocs/ and assuming that new architectures are not added during patch releases.
