Modifications:
- [x] Removed `centos:6` unit test, adjusted vermin checks
- [x] Removed backport of `collections.OrderedDict`
- [x] Removed backport of `functools.total_ordering`
- [x] Removed Python 2.6 specific skip markers in unit tests
- [x] Fixed a few minor Python 2.6 related TODOs in code
Updating the vendored dependencies will be done in separate PRs
This PR permits to specify the `url` and `ref` of the Spack instance used in a container recipe simply by expanding the YAML schema as outlined in #20442:
```yaml
container:
images:
os: amazonlinux:2
spack:
ref: develop
resolve_sha: true
```
The `resolve_sha` option, if true, verifies the `ref` by cloning the Spack repository in a temporary directory and transforming any tag or branch name to a commit sha. When this new ability is leveraged an additional "bootstrap" stage is added, which builds an image with Spack setup and ready to install software. The Spack repository to be used can be customized with the `url` keyword under `spack`.
Modifications:
- [x] Permit to pin the version of Spack, either by branch or tag or sha
- [x] Added a few new OSes (centos:8, amazonlinux:2, ubuntu:20.04, alpine:3, cuda:11.2.1)
- [x] Permit to print the bootstrap image as a standalone
- [x] Add documentation on the new part of the schema
- [x] Add unit tests for different use cases
* py-vermin: add latest version 1.3.1
* Exclude line from Vermin since version is already being checked for
Vermin 1.3.1 finds that `encoding` kwarg of builtin `open()` requires Python 3+.
Installing packages with a lot of dependencies does not have an easy way
of judging the current progress (apart from running `spack spec -I pkg`
in another terminal). This change allows Spack to update the terminal's
title with status information, including its current progress as well as
information about the current and total number of packages.
Spack has logic to preserve an installation prefix when it is being
overwritten: if the new install fails, the old files are restored.
This PR adds error handling for when this backup restoration fails
(i.e. the new install fails, and then some unexpected error prevents
restoration from the backup).
* Make sure PackageInstaller does not remove the just-restored
install dir after failure in spack install --overwrite
* Remove cryptic error message and rethrow actual error
This adds lockfile tracking to Spack's lock mechanism, so that we ensure that there
is only one open file descriptor per inode.
The `fcntl` locks that Spack uses are associated with an inode and a process.
This is convenient, because if a process exits, it releases its locks.
Unfortunately, this also means that if you close a file, *all* locks associated
with that file's inode are released, regardless of whether the process has any
other open file descriptors on it.
Because of this, we need to track open lock files so that we only close them when
a process no longer needs them. We do this by tracking each lockfile by its
inode and process id. This has several nice properties:
1. Tracking by pid ensures that, if we fork, we don't inadvertently track the parent
process's lockfiles. `fcntl` locks are not inherited across forks, so we'll
just track new lockfiles in the child.
2. Tracking by inode ensures that referencs are counted per inode, and that we don't
inadvertently close a file whose inode still has open locks.
3. Tracking by both pid and inode ensures that we only open lockfiles the minimum
number of times necessary for the locks we have.
Note: as mentioned elsewhere, these locks aren't thread safe -- they're designed to
work in Python and assume the GIL.
Tasks:
- [x] Introduce an `OpenFileTracker` class to track open file descriptors by inode.
- [x] Reference-count open file descriptors and only close them if they're no longer
needed (this avoids inadvertently releasing locks that should not be released).
* Refactor active environment getters
- Make `spack.environment.active_environment` a trivial getter for the active
environment, replacing `spack.environment.get_env` when the arguments are
not needed
- New method `spack.cmd.require_active_environment(cmd_name)` for
commands that require an environment (rather than abusing
get_env/active_environment)
- Clean up calling code to call spack.environment.active_environment or
spack.cmd.require_active_environment as appropriate
- Remove the `-e` parsing from `active_environment`, because `main.py` is
responsible for processing `-e` and already activates the environment.
- Move `spack.environment.find_environment` to
`spack.cmd.find_environment`, to avoid having spack.environment aware
of argparse.
- Refactor `spack install` command so argument parsing is all handled in the
command, no argparse in spack.environment or spack.installer
- Update documentation
* Python 2: toplevel import errors only with 'as ev'
In two files, `import spack.environment as ev` leads to errors
These errors are not well understood ("'module' object has no attribute
'environment'"). All other files standardize on the above syntax.
This is both a bugfix and a generalization of #25168. In #25168, we attempted to filter padding
*just* from the debug output of `spack.util.executable.Executable` objects. It turns out we got it
wrong -- filtering the command line string instead of the arg list resulted in output like this:
```
==> [2021-08-05-21:34:19.918576] ["'", '/', 'b', 'i', 'n', '/', 't', 'a', 'r', "'", ' ', "'", '-', 'o', 'x', 'f', "'", ' ', "'", '/', 't', 'm', 'p', '/', 'r', 'o', 'o', 't', '/', 's', 'p', 'a', 'c', 'k', '-', 's', 't', 'a', 'g', 'e', '/', 's', 'p', 'a', 'c', 'k', '-', 's', 't', 'a', 'g', 'e', '-', 'p', 'a', 't', 'c', 'h', 'e', 'l', 'f', '-', '0', '.', '1', '3', '-', 'w', 'p', 'h', 'p', 't', 'l', 'h', 'w', 'u', 's', 'e', 'i', 'a', '4', 'k', 'p', 'g', 'y', 'd', 'q', 'l', 'l', 'i', '2', '4', 'q', 'b', '5', '5', 'q', 'u', '4', '/', 'p', 'a', 't', 'c', 'h', 'e', 'l', 'f', '-', '0', '.', '1', '3', '.', 't', 'a', 'r', '.', 'b', 'z', '2', "'"]
```
Additionally, plenty of builds output padded paths in other plcaes -- e.g., not just command
arguments, but in other `tty` messages via `llnl.util.filesystem` and other places. `Executable`
isn't really the right place for this.
This PR reverts the changes to `Executable` and moves the filtering into `llnl.util.tty`. There is
now a context manager there that you can use to install a filter for all output.
`spack.installer.build_process()` now uses this context manager to make `tty` do path filtering
when padding is enabled.
- [x] revert filtering in `Executable`
- [x] add ability for `tty` to filter output
- [x] install output filter in `build_process()`
- [x] tests
The output order for `spack diff` is nondeterministic for larger diffs -- if you
ran it several times it will not put the fields in the spec in the same order on
successive invocations.
This makes a few fixes to `spack diff`:
- [x] Implement the change discussed in https://github.com/spack/spack/pull/22283#discussion_r598337448
to make `AspFunction` comparable in and of itself and to eliminate the need for `to_tuple()`
- [x] Sort the lists of diff properties so that the output is always in the same order.
- [x] Make the output for different fields the same as what we use in the solver. Previously, we
would use `Type(value)` for non-string values and `value` for strings. Now we just use
the value. So the output looks a little cleaner:
```
== Old ========================== == New ====================
@@ node_target @@ @@ node_target @@
- gdbm Target(x86_64) - gdbm x86_64
+ zlib Target(skylake) + zlib skylake
@@ variant_value @@ @@ variant_value @@
- ncurses symlinks bool(False) - ncurses symlinks False
+ zlib optimize bool(True) + zlib optimize True
@@ version @@ @@ version @@
- gdbm Version(1.18.1) - gdbm 1.18.1
+ zlib Version(1.2.11) + zlib 1.2.11
@@ node_os @@ @@ node_os @@
- gdbm catalina - gdbm catalina
+ zlib catalina + zlib catalina
```
I suppose if we want to use `repr()` in the output we could do that and could be
consistent but we don't do that elsewhere -- the types of things in Specs are
all stringifiable so the string and the name of the attribute (`version`, `node_os`,
etc.) are sufficient to know what they are.
Spack allows users to set `padded_length` to pad out the installation path in
build farms so that any binaries created are more easily relocatable. The issue
with this is that the padding dominates installation output and makes it
difficult to see what is going on. The padding also causes logs to easily
exceed size limits for things like GitLab artifacts.
This PR fixes this by adding a filter in the logger daemon. If you use a
setting like this:
config:
install_tree:
padded_length: 512
Then lines like this in the output:
==> [2021-06-23-15:59:05.020387] './configure' '--prefix=/Users/gamblin2/padding-log-test/opt/__spack_path_placeholder__/__spack_path_placeholder__/__spack_path_placeholder__/__spack_path_placeholder__/__spack_path_placeholder__/__spack_path_placeholder__/__spack_path_placeholder__/__spack_path_placeholder__/__spack_path_placeholder__/__spack_path_placeholder__/__spack_path_placeholder__/__spack_path_placeholder__/__spack_path_placeholder__/__spack_path_placeholder__/__spack_path_placeholder__/__spack_path_placeholder__/__spack_path_placeholder__/__spack_path_pla/darwin-bigsur-skylake/apple-clang-12.0.5/zlib-1.2.11-74mwnxgn6nujehpyyalhwizwojwn5zga
will be replaced with the much more readable:
==> [2021-06-23-15:59:05.020387] './configure' '--prefix=/Users/gamblin2/padding-log-test/opt/[padded-to-512-chars]/darwin-bigsur-skylake/apple-clang-12.0.5/zlib-1.2.11-74mwnxgn6nujehpyyalhwizwojwn5zga
You can see that the padding has been replaced with `[padded-to-512-chars]` to
indicate the total number of characters in the padded prefix. Over a long log
file, this should save a lot of space and allow us to see error messages in
GitHub/GitLab log output.
The *actual* build logs still have full paths in them. Also lines that are
output by Spack and not by a package build are not filtered and will still
display the fully padded path. There aren't that many of these, so the change
should still help reduce file size and readability quite a bit.
* fix remaining flake8 errors
* imports: sort imports everywhere in Spack
We enabled import order checking in #23947, but fixing things manually drives
people crazy. This used `spack style --fix --all` from #24071 to automatically
sort everything in Spack so PR submitters won't have to deal with it.
This should go in after #24071, as it assumes we're using `isort`, not
`flake8-import-order` to order things. `isort` seems to be more flexible and
allows `llnl` mports to be in their own group before `spack` ones, so this
seems like a good switch.
* util.tty.log: read up to 100 lines if ready
Rework to read up to 100 lines from the captured stdin as long as data
is ready to be read immediately. Adds a helper function to poll with
`select` for ready data. This showed a roughly 5-10x perf improvement
for high-rate writes through the logger with relatively short lines.
* util.tty.log: Defer flushes to end of ready reads
Rather than flush per line, flush per set of reads. Since this is a
non-blocking loop, the total perceived wait is short.
* util.tty.log: only scan each line once, usually
Rather than always find all control characters then substitute them all,
use `subn` to count the number of control characters replaced. Only if
control characters exist find out what they are. This could be made
truly single pass with sub with a function, but it's a more intrusive
change and this got 99%ish of the performance improvement (roughly
another 2x in some cases).
* util.tty.log: remove check for `readable`
Python < 3 does not support a readable check on streams, should not be
necessary here since we control the only use and it's explicitly a
stream to be read.
The loading protocol mandates that the the module we are going
to import needs to be already in sys.modules before its code is
executed, so to prevent unbounded recursions and multiple loading.
Loading a module from file exits early if the module is already
in sys.modules
In debug mode, processes taking an exclusive lock write out their node name to
the lock file. We were using `getfqdn()` for this, but it seems to produce
inconsistent results when used from within some github actions containers.
We get this error because getfqdn() seems to return a short name in one place
and a fully qualified name in another:
```
File "/home/runner/work/spack/spack/lib/spack/spack/test/llnl/util/lock.py", line 1211, in p1
assert lock.host == self.host
AssertionError: assert 'fv-az290-764....cloudapp.net' == 'fv-az290-764'
- fv-az290-764.internal.cloudapp.net
+ fv-az290-764
!!!!!!!!!!!!!!!!!!!! Interrupted: stopping after 1 failures !!!!!!!!!!!!!!!!!!!!
== 1 failed, 2547 passed, 7 skipped, 22 xfailed, 2 xpassed in 1238.67 seconds ==
```
This seems to stem from https://bugs.python.org/issue5004.
We don't really need to get a fully qualified hostname for debugging, so use
`gethostname()` because its results are more consistent. This seems to fix the
issue.
Signed-off-by: vsoch <vsoch@users.noreply.github.com>
We set LC_ALL=C to encourage a build process to generate ASCII
output (so our logger daemon can decode it). Most packages
respect this but it appears that intel-oneapi-compilers does
not in some cases (see #22813). This reads the output of the build
process as UTF-8, which still works if the build process respects
LC_ALL=C but also works if the process generates UTF-8 output.
For Python >= 3.7 all files are opened with UTF-8 encoding by
default. Python 2 does not support the encoding argument on
'open', so to support Python 2 the files would have to be
opened in byte mode and explicitly decoded (as a side note,
this would be the only way to handle other encodings without
being informed of them in advance).
We have been using the `@llnl.util.lang.key_ordering` decorator for specs
and most of their components. This leverages the fact that in Python,
tuple comparison is lexicographic. It allows you to implement a
`_cmp_key` method on your class, and have `__eq__`, `__lt__`, etc.
implemented automatically using that key. For example, you might use
tuple keys to implement comparison, e.g.:
```python
class Widget:
# author implements this
def _cmp_key(self):
return (
self.a,
self.b,
(self.c, self.d),
self.e
)
# operators are generated by @key_ordering
def __eq__(self, other):
return self._cmp_key() == other._cmp_key()
def __lt__(self):
return self._cmp_key() < other._cmp_key()
# etc.
```
The issue there for simple comparators is that we have to bulid the
tuples *and* we have to generate all the values in them up front. When
implementing comparisons for large data structures, this can be costly.
This PR replaces `@key_ordering` with a new decorator,
`@lazy_lexicographic_ordering`. Lazy lexicographic comparison maps the
tuple comparison shown above to generator functions. Instead of comparing
based on pre-constructed tuple keys, users of this decorator can compare
using elements from a generator. So, you'd write:
```python
@lazy_lexicographic_ordering
class Widget:
def _cmp_iter(self):
yield a
yield b
def cd_fun():
yield c
yield d
yield cd_fun
yield e
# operators are added by decorator (but are a bit more complex)
There are no tuples that have to be pre-constructed, and the generator
does not have to complete. Instead of tuples, we simply make functions
that lazily yield what would've been in the tuple. If a yielded value is
a `callable`, the comparison functions will call it and recursively
compar it. The comparator just walks the data structure like you'd expect
it to.
The ``@lazy_lexicographic_ordering`` decorator handles the details of
implementing comparison operators, and the ``Widget`` implementor only
has to worry about writing ``_cmp_iter``, and making sure the elements in
it are also comparable.
Using this PR shaves another 1.5 sec off the runtime of `spack buildcache
list`, and it also speeds up Spec comparison by about 30%. The runtime
improvement comes mostly from *not* calling `hash()` `_cmp_iter()`.
Sometimes we need to patch a file that is a dependency for some other
automatically generated file that comes in a release tarball. As a
result, make tries to regenerate the dependent file using additional
tools (e.g. help2man), which would not be needed otherwise.
In some cases, it's preferable to avoid that (e.g. see #21255). A way
to do that is to save the modification timestamps before patching and
restoring them afterwards. This PR introduces a context wrapper that
does that.
* sbang pushed back to callers;
star moved to util.lang
* updated unit test
* sbang test moved; local tests pass
Co-authored-by: Nathan Hanford <hanford1@llnl.gov>
- [x] add `concretize.lp`, `spack.yaml`, etc. to licensed files
- [x] update all licensed files to say 2013-2021 using
`spack license update-copyright-year`
- [x] appease mypy with some additions to package.py that needed
for oneapi.py
I lost my mind a bit after getting the completion stuff working and
decided to get Mypy working for spack as well. This adds a
`.mypy.ini` that checks all of the spack and llnl modules, though
not yet packages, and fixes all of the identified missing types and
type issues for the spack library.
In addition to these changes, this includes:
* rename `spack flake8` to `spack style`
Aliases flake8 to style, and just runs flake8 as before, but with
a warning. The style command runs both `flake8` and `mypy`,
in sequence. Added --no-<tool> options to turn off one or the
other, they are on by default. Fixed two issues caught by the tools.
* stub typing module for python2.x
We don't support typing in Spack for python 2.x. To allow 2.x to
support `import typing` and `from typing import ...` without a
try/except dance to support old versions, this adds a stub module
*just* for python 2.x. Doing it this way means we can only reliably
use all type hints in python3.7+, and mypi.ini has been updated to
reflect that.
* add non-default black check to spack style
This is a first step to requiring black. It doesn't enforce it by
default, but it will check it if requested. Currently enforcing the
line length of 79 since that's what flake8 requires, but it's a bit odd
for a black formatted project to be quite that narrow. All settings are
in the style command since spack has no pyproject.toml and I don't
want to add one until more discussion happens. Also re-format
`style.py` since it no longer passed the black style check
with the new length.
* use style check in github action
Update the style and docs action to use `spack style`, adding in mypy
and black to the action even if it isn't running black right now.
Users can add test() methods to their packages to run smoke tests on
installations with the new `spack test` command (the old `spack test` is
now `spack unit-test`). spack test is environment-aware, so you can
`spack install` an environment and then run `spack test run` to run smoke
tests on all of its packages. Historical test logs can be perused with
`spack test results`. Generic smoke tests for MPI implementations, C,
C++, and Fortran compilers as well as specific smoke tests for 18
packages.
Inside the test method, individual tests can be run separately (and
continue to run best-effort after a test failure) using the `run_test`
method. The `run_test` method encapsulates finding test executables,
running and checking return codes, checking output, and error handling.
This handles the following trickier aspects of testing with direct
support in Spack's package API:
- [x] Caching source or intermediate build files at build time for
use at test time.
- [x] Test dependencies,
- [x] packages that require a compiler for testing (such as library only
packages).
See the packaging guide for more details on using Spack testing support.
Included is support for package.py files for virtual packages. This does
not change the Spack interface, but is a major change in internals.
Co-authored-by: Tamara Dahlgren <dahlgren1@llnl.gov>
Co-authored-by: wspear <wjspear@gmail.com>
Co-authored-by: Adam J. Stewart <ajstewart426@gmail.com>
- [x] Solver now uses the Python interface to clingo
- [x] can extract unsatisfiable cores from problems when things go wrong
- [x] use Python callbacks for versions instead of choice rules (this may
ultimately hurt performance)
Spack creates a separate process to do package installation. Different
operating systems and Python versions use different methods to create
it but up until Python 3.8 both Linux and Mac OS used "fork" (which
duplicates process memory, file descriptor table, etc.).
Python >= 3.8 on Mac OS prefers creating an entirely new process
(referred to as the "spawn" start method) because "fork" was found to
cause issues (in other words "spawn" is the default start method used
by multiprocessing.Process). Spack was dependent on the particular
behavior of fork to replicate process memory and transmit file
descriptors.
This PR refactors the Spack internals to support starting a child
process with the "spawn" method. To achieve this, it makes the
following changes:
- ensure that the package repository and other global state are
transmitted to the child process
- ensure that file descriptors are transmitted to the child process in
a way that works with multiprocessing and spawn
- make all the state needed for the build process and tests picklable
(package, stage, etc.)
- move a number of locally-defined functions into global scope so that
they can be pickled
- rework tests where needed to avoid using local functions
This PR also reworks sbang tests to work on macOS, where temporary
directories are deeper than the Linux sbang limit. We make the limit
platform-dependent (macOS supports 512-character shebangs)
See: #14102
* allow environments to specify dev-build packages
* spack develop and spack undevelop commands
* never pull dev-build packges from bincache
* reinstall dev_specs when code has changed; reinstall dependents too
* preserve dev info paths and versions in concretization as special variant
* move install overwrite transaction into installer
* move dev-build argument handling to package.do_install
now that specs are dev-aware, package.do_install can add
necessary args (keep_stage=True, use_cache=False) to dev
builds. This simplifies driving logic in cmd and env._install
* allow 'any' as wildcard for variants
* spec: allow anonymous dependencies
raise an error when constraining by or normalizing an anonymous dep
refactor concretize_develop to remove dev_build variant
refactor tests to check for ^dev_path=any instead of +dev_build
* fix variant class hierarchy
Fixes#18441
When writing an environment, there are cases where the lock file for
the environment may be removed. In this case there was a period
between removing the lock file and writing the new manifest file
where an exception could leave the manifest in its old state (in
which case the lock and manifest would be out of sync).
This adds a context manager which is used to restore the prior lock
file state in cases where the manifest file cannot be written.
As detailed in https://bugs.python.org/issue33725, starting new
processes with 'fork' on Mac OS is not guaranteed to work in general.
As of Python 3.8 the default process spawning mechanism was changed
to avoid this issue.
Spack depends on the fork-based method to preserve file descriptors
transparently, to preserve global state, and to avoid pickling some
objects. An effort is underway to remove dependence on fork-based
process spawning (see #18205). In the meantime, this allows Spack to
run with Python 3.8 on Mac OS by explicitly choosing to use 'fork'.
Co-authored-by: Peter Josef Scheibel <scheibel1@llnl.gov>
Co-authored-by: Adam J. Stewart <ajstewart426@gmail.com>
Co-authored-by: Todd Gamblin <tgamblin@llnl.gov>
Some of the feature flags are named differently and clwb is missing on
my i7-1065G7. cascadelake and cannonlake might have similar problems but
I do not have access to those architectures to test.
The YAML config for paths and modules of external packages has
changed: the new format allows a single spec to load multiple
modules. Spack will automatically convert from the old format
when reading the configs (the updates do not add new essential
properties, so this change in Spack is backwards-compatible).
With this update, Spack cannot modify existing configs/environments
without updating them (e.g. “spack config add” will fail if the
configuration is in a format that predates this PR). The user is
prompted to do this explicitly and commands are provided. All
config scopes can be updated at once. Each environment must be
updated one at a time.
* switch from bool to int debug levels
* Added debug options and changed lock logging to use more detailed values
* Limit installer and timestamp PIDs to standard debug output
* Reduced verbosity of fetch/stage/install output, changing most to debug level 1
* Combine lock log methods; change build process install to debug
* Changed binary cache install messages to extraction messages
* Separate Apple Clang from LLVM Clang
Apple Clang is a compiler of its own. All places
referring to "-apple" suffix have been updated.
* Hack to use a dash in 'apple-clang'
To be able to use autodoc from Sphinx we need
a valid Python name for the module that contains
Apple's Clang code.
* Updated packages to account for the existence of apple-clang
Co-authored-by: Adam J. Stewart <ajstewart426@gmail.com>
* Added unit test for XCode related functions
Co-authored-by: Gregory Becker <becker33@llnl.gov>
Co-authored-by: Adam J. Stewart <ajstewart426@gmail.com>
After migrating to `travis-ci.com`, we saw I/O issues in our tests --
tests that relied on `capfd` and `capsys` were failing. We've also seen
this in GitHub actions, and it's kept us from switching to them so far.
Turns out that the issue is that using streams like `sys.stdout` as
default arguments doesn't play well with `pytest` and output redirection,
as `pytest` changes the values of `sys.stdout` and `sys.stderr`. if these
values are evaluated before output redirection (as they are when used as
default arg values), output won't be captured properly later.
- [x] replace all stream default arg values with `None`, and only assign stream
values inside functions.
- [x] fix tests we didn't notice were relying on this erroneous behavior
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>
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.
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.
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
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.
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>
`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()`
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.
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()`
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
* 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
* 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 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
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).
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.
Custom string versions for compilers were raising a ValueError on
conversion to int. This commit fixes the behavior by trying to detect
the underlying compiler version when in presence of a custom string
version.
* Refactor code that deals with custom versions for better readability
* Partition version components with a regex
* Fix semantic of custom compiler versions with a suffix
* clang@x.y-apple has been special-cased
* Add unit tests
* Added architecture specific optimization flags for Clang / LLVM
* Disallow compiler optimizations for mixed toolchains
* We emit a warning when building for a mixed toolchain
* Fixed issues with suffixed versions of compilers; Apple's Clang will,
for the time being, fall back on x86-64 for every compilation.
Since the backup file is only created on the first invocation, it will
contain the original file without any modifications. Further invocations
will then read the backup file, effectively reverting prior invocations.
This can be reproduced easily by trying to install likwid, which will
try to install into /usr/local. Work around this by creating a temporary
file to read from.
* This updates stage names to use "spack-stage-" as a prefix.
This avoids removing non-Spack directories in "spack clean" as
c141e99 did (in this case so long as they don't contain the
prefix "spack-stage-"), and also addresses a follow-up issue
where Spack stage directories were not removed.
* Spack now does more-stringent checking of expected permissions for
staging directories. For a given stage root that includes a user
component, all directories before the user component that are
created by Spack are expected to match the permissions of their
parent; the user component and all deeper directories are expected
to be accessible to the user (read/write/execute).
This feature generates a verification manifest for each installed
package and provides a command, "spack verify", which can be used to
compare the current file checksums/permissions with those calculated
at installed time.
Verification includes
* Checksums of files
* File permissions
* Modification time
* File size
Packages installed before this PR will be skipped during verification.
To verify such a package you must reinstall it.
The spack verify command has three modes.
* With the -a,--all option it will check every installed package.
* With the -f,--files option, it will check some specific files,
determine which package they belong to, and confirm that they have
not been changed.
* With the -s,--specs option or by default, it will check some
specific packages that no files havae changed.
From Python docs:
--
'surrogateescape' will represent any incorrect bytes as code points in
the Unicode Private Use Area ranging from U+DC80 to U+DCFF. These
private code points will then be turned back into the same bytes when
the surrogateescape error handler is used when writing data. This is
useful for processing files in an unknown encoding.
--
This will allow us to process files with unknown encodings.
To accommodate the case of self-extracting bash scripts, filter_file
can now stop filtering text input if a certain marker is found. The
marker must be passed at call time via the "stop_at" function argument.
At that point the file will be reopened in binary mode and copied
verbatim.
* use "surrogateescape" error handling to ignore unknown chars
* permit to stop filtering if a marker is found
* add unit tests for non-ASCII and mixed text/binary files
Both floating-point and NEON are required in all standard ARMv8
implementations. Theoretically though specialized markets can support
no NEON or floating-point at all. Source:
https://developer.arm.com/docs/den0024/latest/aarch64-floating-point-and-neon
On the other hand the base procedure call standard for Aarch64
"assumes the availability of the vector registers for passing
floating-point and SIMD arguments". Further "the Arm 64-bit
architecture defines two mandatory register banks: a general-purpose
register bank which can be used for scalar integer processing and
pointer arithmetic; and a SIMD and Floating-Point register bank".
Source:
https://developer.arm.com/docs/ihi0055/latest/procedure-call-standard-for-the-arm-64-bit-architecture
This makes customization of Aarch64 with no NEON instruction set
available so unlikely that we can consider them a feature of the
generic family.
The output of subprocess.check_output is a byte string in Python 3. This causes dictionary lookup to fail later on.
A try-except around this function prevented this error from being noticed. Removed this so that more errors can propagate out.
* microarchitectures: zen starts from x86_64, not from excavator
* Unit tests: fixed a test that is wrong with the new modeling
* microarchitectures: fixed features and inheritance for 15h family
bulldozer doesn't inherit from barcelona (10h) + added xop, lwp and tbm
instruction sets to the 15h family (it distinguish the family from 17h)
- This is needed to support Cray machines -- we need an architecture
mic_knl > x86_64
- We used Cray's naming scheme for this target to make it work seamlessly
with the module-based detection sccheme on Cray. mic_knl is pretty
much dead, so this will be the last succh target. We will need to work
wtih Cray and other vendors in the future.
Spack can now:
- label ppc64, ppc64le, x86_64, etc. builds with specific
microarchitecture-specific names, like 'haswell', 'skylake' or
'icelake'.
- detect the host architecture of a machine from /proc/cpuinfo or similar
tools.
- Understand which microarchitectures are compatible with which (for
binary reuse)
- Understand which compiler flags are needed (for GCC, so far) to build
binaries for particular microarchitectures.
All of this is managed through a JSON file (microarchitectures.json) that
contains detailed auto-detection, compiler flag, and compatibility
information for specific microarchitecture targets. The `llnl.util.cpu`
module implements a library that allows detection and comparison of
microarchitectures based on the data in this file.
The `target` part of Spack specs is now essentially a Microarchitecture
object, and Specs' targets can be compared for compatibility as well.
This allows us to label optimized binary packages at a granularity that
enables them to be reused on compatible machines. Previously, we only
knew that a package was built for x86_64, NOT which x86_64 machines it
was usable on.
Currently this feature supports Intel, Power, and AMD chips. Support for
ARM is forthcoming.
Specifics:
- Add microarchitectures.json with descriptions of architectures
- Relaxed semantic of compiler's "target" attribute. Before this change
the semantic to check if a compiler could be viable for a given target
was exact match. This made sense as the finest granularity of targets
was architecture families. As now we can target micro-architectures,
this commit changes the semantic by interpreting as the architecture
family what is stored in the compiler's "target" attribute. A compiler
is then a viable choice if the target being concretized belongs to the
same family. Similarly when a new compiler is detected the architecture
family is stored in the "target" attribute.
- Make Spack's `cc` compiler wrapper inject target-specific flags on the
command line
- Architecture concretization updated to use the same algorithm as
compiler concretization
- Micro-architecture features, vendor, generation etc. are included in
the package hash. Generic architectures, such as x86_64 or ppc64, are
still dumped using the name only.
- If the compiler for a target is not supported exit with an intelligible
error message. If the compiler support is unknown don't try to use
optimization flags.
- Support and define feature aliases (e.g., sse3 -> ssse3) in
microarchitectures.json and on Microarchitecture objects. Feature
aliases are defined in targets.json and map a name (the "alias") to a
list of rules that must be met for the test to be successful. The rules
that are available can be extended later using a decorator.
- Implement subset semantics for comparing microarchitectures (treat
microarchitectures as a partial order, i.e. (a < b), (a == b) and (b <
a) can all be false.
- Implement logic to automatically demote the default target if the
compiler being used is too old to optimize for it. Updated docs to make
this behavior explicit. This avoids surprising the user if the default
compiler is older than the host architecture.
This commit adds unit tests to verify the semantics of target ranges and
target lists in constraints. The implementation to allow target ranges
and lists is minimal and doesn't add any new type. A more careful
refactor that takes into account the type system might be due later.
Co-authored-by: Gregory Becker <becker33.llnl.gov>
Add llnl.util.cpu_name, with initial support for detecting different
microarchitectures on Linux. This also adds preliminary changes for
compiler support and variants to control the optimizatoin levels by
target.
This does not yet include translations of targets to particular
compilers; that is left to another PR.
Co-authored-by: Massimiliano Culpo <massimiliano.culpo@gmail.com>
* implicit_rpaths are now removed from compilers.yaml config and are always instantiated dynamically, this occurs one time in the build_environment module
* per-compiler list required libraries (e.g. libstdc++, libgfortran) and whitelist directories from rpaths including those libraries. Remove non-whitelisted implicit rpaths. Some libraries default for all compilers.
* reintroduce 'implicit_rpaths' as a config variable that can be used to disable Spack insertion of compiler RPATHs generated at build time.
- mkdirp now takes arguments to allow it to properly set permissions on created directories.
- Two arguments (group and mode) set permissions for the leaf directory.
- Intermediate directories can inherit permissions from either the topmost existing directory (the parent) or the leaf.
Fixes#11163
The goal of this work is to simplify stage directory structures by eliminating use of symbolic links. This means, among other things, that` $spack/var/spack/stage` will no longer be the core staging directory. Instead, the first accessible `config:build_stage` path will be used.
Spack will no longer automatically append `spack-stage` (or the like) to configured build stage directories so the onus of distinguishing the directory from other work -- so the other work is not automatically removed with a `spack clean` operation -- falls on the user.
* extends mkdirs with permissions for intermediate folders
Does not use os.makedirs mode parameter because its behavior is changed
with Python 3.7 (it ignores it for intermediate dirs), and moreover it
was not possible to set different modes for newly-created folders
and leaf folder.
reference:
- https://bugs.python.org/issue19930
- https://docs.python.org/3.7/library/os.html#os.makedirs
* comment mkdirp step easing code understanding
* revert mkdir to default for package metapath
since metapath is nested in package folder, there is no need
to specify permissions for intermediate folders because the prefix
already exists.
* comment create_install_directory package modes
The default library search for a package checks the lib/ and lib64/
directories for libraries before the root prefix, in order to save
time when searching for libraries provided by externals (which e.g.
may have '/usr/' as their root).
This moves that logic into the "find_libraries" utility method so
packages implementing their own custom library search logic can
benefit from it.
This also updates packages which appear to be replicating this logic
exactly, replacing it with a single call to "find_libraries".
Fixes#11782
Spack was not properly resolving relative paths to absolute paths
when a relative path was passed to "spack compiler add [PATH]".
Now, if provided a relative path, the absolute path is written to
compilers.yaml rather than the relative path.
For resources, it is desirable to use the expanded archive name of
the resource as the name of the directory when adding it to the root
staging area.
#11528 established 'spack-src' as the universal directory where
source files are placed, which also affected the behavior of
resources managed with Stages.
This adds a new property ('srcdir') to Stage to remember the name of
the expanded source directory, and uses this as the default name when
placing a resource directory in the root staging area.
This also:
* Ensures that downloaded sources are archived using the expanded
archive name (otherwise Spack will not be able to determine the
original directory name when using a cached archive).
* Updates working_dir context manager to guarantee restoration of
original working directory when an exception occurs
* Adds a "temp_cwd" context manager which creates a temporary
directory and sets it as the working directory
- spack.compilers.find_compilers now uses a multiprocess.pool.ThreadPool to execute
system commands for the detection of compiler versions.
- A few memoized functions have been introduced to avoid poking the filesystem multiple
times for the same results.
- Performance is much improved, and Spack no longer fork-bombs the system when doing a `compiler find`
- make tty.msg, tty.info, etc. print the exception type and stringified
message if the message argument is an exception.
- simplify parts of the code that call tty.debug(str(e))
- add extra tty.debug statements in places where exceptions were
previously ignored
The Spack documentation currently hard-codes some functionality in
`conf.py`, which makes the doc build less "pluggable" for things like
localized doc builds.
In particular, we unconditionally generate an index of commands and a
package list as part of the docs, but those should really only be done if
things are not up to date.
This commit does the following:
- Add `--header` option to `spack commands` so that it can do the work of
prepending text to its output.
- Add `--update FILE` option to `spack commands` that makes it generate a
new command index *only* if FILE is out of date w.r.t. commands in the
Spack source.
- Simplify code in `conf.py` to use these options and only update the
command index when needed.
Environments are nowm by default, created with views. When activated, if an environment includes a view, this view will be added to `PATH`, `CPATH`, and other shell variables to expose the Spack environment in the user's shell.
Example:
```
spack env create e1 #by default this will maintain a view in the directory Spack maintains for the env
spack env create e1 --with-view=/abs/path/to/anywhere
spack env create e1 --without-view
```
The `spack.yaml` manifest file now looks like this:
```
spack:
specs:
- python
view: true #or false, or a string
```
These commands can be used to control the view configuration for the active environment, without hand-editing the `spack.yaml` file:
```
spack env view enable
spack env view envable /abs/path/to/anywhere
spack env view disable
```
Views are automatically updated when specs are installed to an environment. A view only maintains one copy of any package. An environment may refer to a package multiple times, in particular if it appears as a dependency. This PR establishes a prioritization for which environment specs are added to views: a spec has higher priority if it was concretized first. This does not necessarily exactly match the order in which specs were added, for example, given `X->Z` and `Y->Z'`:
```
spack env activate e1
spack add X
spack install Y # immediately concretizes and installs Y and Z'
spack install # concretizes X and Z
```
In this case `Z'` will be favored over `Z`.
Specs in the environment must be concrete and installed to be added to the view, so there is another minor ordering effect: by default the view maintained for the environment ignores file conflicts between packages. If packages are not installed in order, and there are file conflicts, then the version chosen depends on the order.
Both ordering issues are avoided if `spack install`/`spack add` and `spack install <spec>` are not mixed.
Replace the original implementation of the "memoized" decorator with
an implementation that exposes the docstring and arguments of the
wrapped function. This is achieved using functools.wraps.
This provides a mechanism to implement a new Spack command in a
separate directory, and with a small configuration change point Spack
to the new command.
To register the command, the directory must be added to the
"extensions" section of config.yaml. The command directory name must
have the prefix "spack-", and have the following layout:
spack-X/
pytest.ini #optional, for testing
X/
cmd/
name-of-command1.py
name-of-command2.py
...
tests/ #optional
conftest.py
test_name-of-command1.py
templates/ #optional jinja templates, if needed
And in config.yaml:
config:
extensions:
- /path/to/spack-X
If the extension includes tests, you can run them via spack by adding
the --extension option, like "spack test --extension=X"
Currently, only C headers are considered, causing build failures for
packages depending on, e.g., netcdf-fortran and xerces-c. Additionally,
the regex used to look for the include path component did not consider
word boundaries, causing false matches.
* Added the `spack buildcache preview` sub-command
This is similar to `spack spec -I` but highlights which nodes in a DAG
are relocatable and which are not.
spec.tree has been generalized a little to accept a status function,
instead of always showing the install status
The current implementation works only for ELF, and needs to be
generalized to other platforms.
* Added a test to check if an executable is relocatable or not
This test requires a few commands to be present in the environment.
Currently it will run only under python 3.7 (which uses Xenial instead
of Trusty).
* Added tests for the 'buildcache preview' command.
* Fixed codebase after rebase
* Fixed the list of apt addons for Python 3.7 in travis.yaml
* Only check ELF executables and shared libraries. Skip checking virtual or external packages. (#229)
* Fixed flake8 issues
* Add handling for macOS mach binaries (#231)
This restores the use of Package.headers when computing -I options
for building a package that was added in #8136 and reverted in
#10604. #8136 used utility logic that located all header files in
an installation prefix, and calculated the -I options as the
immediate roots containing those header files.
In some cases, for a package containing a directory structure like
prefix/
include/
ex1.h
subdir/
ex2.h
dependents may expect to include ex2.h relative to 'include', and
adding 'prefix/include/subdir' as a -I was causing errors,
in particular if ex2.h has the same name as a system header.
This updates header utility logic to by default return the base
"include" directory when it exists, rather than subdirectories.
It also makes it possible for package implementers to override
Package.headers to return the subdirectory when it is required
(for example with libxml2).
This PR improves the validation of `modules.yaml` by introducing a custom validator that checks if an attribute listed in `properties` or `patternProperties` is a valid spec. This new check applied to the test case in #9857 gives:
```console
$ spack install szip
==> Error: /home/mculpo/.spack/linux/modules.yaml:5: "^python@2.7@" is an invalid spec [Invalid version specifier]
```
Details:
* Moved the set-up of a custom validator class to spack.schema
* In Spack we use `jsonschema` to validate configuration files
against a schema. We also need custom validators to enforce
writing default values within "properties" or "patternProperties"
attributes.
* Currently, validators were customized at the place of use and with the
recent introduction of environments that meant we were setting-up and
using 2 different validator classes in two different modules.
* This commit moves the set-up of a custom validator class in the
`spack.schema` module and refactors the code in `spack.config` and
`spack.environments` to use it.
* Added a custom validator to check if an attribute is a valid spec
* Added a custom validator that can be used on objects, which yields an
error if the attribute is not a valid spec.
* Updated the schema for modules.yaml
* Updated modules.yaml to fix a few inconsistencies:
- a few attributes were not tested properly using 'anyOf'
- suffixes has been updated to also check that the attribute is a spec
- hierarchical_scheme has been updated to hierarchy
* Removed $ref from every schema
* $ref is not composable or particularly legible
* Use python dicts and regular old variables instead.
- `spack env create <name>` works as before
- `spack env create <path>` now works as well -- environments can be
created in their own directories outside of Spack.
- `spack install` will look for a `spack.yaml` file in the current
directory, and will install the entire project from the environment
- The Environment class has been refactored so that it does not depend on
the internal Spack environment root; it just takes a path and operates
on an environment in that path (so internal and external envs are
handled the same)
- The named environment interface has been hoisted to the
spack.environment module level.
- env.yaml is now spack.yaml in all places. It was easier to go with one
name for these files than to try to handle logic for both env.yaml and
spack.yaml.
- add `SingleFileScope` to configuration, which allows us to pull config
sections from a single file.
- update `env.yaml` and tests to ensure that the env.yaml schema works
when pulling configurtion from the env file.
- #8773 made the default mode 0o777, which is what's documented but
mkdirp actually takes the OS default or umask by default
- revert to the Python default by default, and only set the mode when
asked explicitly.
- remove the old LGPL license headers from all files in Spack
- add SPDX headers to all files
- core and most packages are (Apache-2.0 OR MIT)
- a very small number of remaining packages are LGPL-2.1-only
Spack can now be configured to assign permissions to the files installed by a package.
In the `packages.yaml` file under `permissions`, the attributes `read`, `write`, and `group` control the package permissions. These attributes can be set per-package, or for all packages under `all`. If permissions are set under `all` and for a specific package, the package-specific settings take precedence. The `read` and `write` attributes take one of `user`, `group`, and `world`.
packages:
all:
permissions:
write: group
group: spack
my_app:
permissions:
read: group
group: my_team
Fixes#9166
This is intended to reduce errors related to lock timeouts by making
the following changes:
* Improves error reporting when acquiring a lock fails (addressing
#9166) - there is no longer an attempt to release the lock if an
acquire fails
* By default locks taken on individual packages no longer have a
timeout. This allows multiple spack instances to install overlapping
dependency DAGs. For debugging purposes, a timeout can be added by
setting 'package_lock_timeout' in config.yaml
* Reduces the polling frequency when trying to acquire a lock, to
reduce impact in the case where NFS is overtaxed. A simple
adaptive strategy is implemented, which starts with a polling
interval of .1 seconds and quickly increases to .5 seconds
(originally it would poll up to 10^5 times per second).
A test is added to check the polling interval generation logic.
* The timeout for Spack's whole-database lock (e.g. for managing
information about installed packages) is increased from 60s to
120s
* Users can configure the whole-database lock timeout using the
'db_lock_timout' setting in config.yaml
Generally, Spack locks (those created using spack.llnl.util.lock.Lock)
now have no timeout by default
This does not address implementations of NFS that do not support file
locking, or detect cases where services that may be required
(nfslock/statd) aren't running.
Users may want to be able to more-aggressively release locks when
they know they are the only one using their Spack instance, and they
encounter lock errors after a crash (e.g. a remote terminal disconnect
mentioned in #8915).
Fixes#9001#8289 added support for install_tree and copy_tree to merge into an existing
directory structure. However, it did not properly handle relative symlinks and
also removed support for the 'ignore' keyword. Additionally, some of the tests
were overly-strict when checking the permissions on the copied files.
This updates the install_tree/copy_tree methods and their tests:
* copy_tree/install_tree now preserve relative link targets (if the symlink in the
source directory structure is relative, the symlink created in the destination
will be relative)
* Added support for 'ignore' argument back to copy_tree/install_tree (removed
in #8289). It is no longer the object output by shutil.ignore_patterns: you pass a
function that accepts a path relative to the source and returns whether that
path should be copied.
* The openfoam packages (currently the only ones making use of the 'ignore'
argument) are updated for the new API
* When a symlink target is absolute, copy_tree and install_tree now rewrite the
source prefix to be the destination prefix
* copy_tree tests no longer check permissions: copy_tree doesn't enforce
anything about permissions so its tests don't check for that
* install_tree tests no longer check for exact permission matching since it can add
file permissions
Replace use of `shutil.copytree` with `copy_tree` and `install_tree` functions in `llnl.util.filesystem`.
- `copy_tree` copies without setting permissions. It should be used to copy files around in the build directory.
- `install_tree` copies files and sets permissions. It should be used to copy files into the installation directory.
- `install` and `copy` are analogous single-file functions.
- add more extensive tests for these functions
- update packages to use these functions.
* Fix performance issue when compiling.
Spack was doing active wait when compiling, spoiling one core.
My fix consists in not setting any timeout for select, instead of
the previous 0 second.
* Fix comments about select.select timeout
- This was a nasty workaround due to the way our compiler wrappers used
to work. We don't want to have to modify our elfutils installation to
install libdwarf.
- Since cd9691de5, we no longer need this because the package will always
come before dependencies in our include order.
- repo membership test was broken by the refactor of spack/__init__.py
- refactor singleton so that 'spec in repo' works again for `spack.repo.path`
- fix spec command and add basic tests for `spack spec` and `spack spec --yaml`
- Fixes a bug in `llnl.util.lock`
- Locks in the current directory would fail because the parent directory
was the empty string.
- Fix this and return '.' for the parent of locks in the current
directory.
- Clean up error messages for when a lock can't be created, or when an
exclusive (write) lock can't be taken on a file.
- Add a number of subclasses of LockError to distinguish timeouts from
permission issues.
- Add an explicit check to prevent the user from taking a write lock on a
read-only file.
- We had a check for this for when we try to *upgrade* a lock on an RO
file, but not for an initial write lock attempt.
- Add more tests for different lock permission scenarios.
- write locks previously wrote information about the lock holder (host
and pid), and read locks woudl read this in.
- This is really only for debugging, so only enable it then
- add some tests that target debug info, and improve multiproc lock test
output
Functional updates:
- `python` now creates a copy of the `python` binaries when it is added
to a view
- Python extensions (packages which subclass `PythonPackage`) rewrite
their shebang lines to refer to python in the view
- Python packages in the same namespace will not generate conflicts if
both have `...lib/site-packages/namespace-example/__init__.py`
- These `__init__` files will also remain when removing any package in
the namespace until the last package in the namespace is removed
Generally (Updated 2/16):
- Any package can define `add_files_to_view` to customize how it is added
to a view (and at the moment custom definitions are included for
`python` and `PythonPackage`)
- Likewise any package can define `remove_files_from_view` to customize
which files are removed (e.g. you don't always want to remove the
namespace `__init__`)
- Any package can define `view_file_conflicts` to customize what it
considers a merge conflict
- Global activations are handled like views (where the view root is the
spec prefix of the extendee)
- Benefit: filesystem-management aspects of activating extensions are
now placed in views (e.g. now one can hardlink a global activation)
- Benefit: overriding `Package.activate` is more straightforward (see
`Python.activate`)
- Complication: extension packages which have special-purpose logic
*only* when activated outside of the extendee prefix must check for
this in their `add_files_to_view` method (see `PythonPackage`)
- `LinkTree` is refactored to have separate methods for copying a
directory structure and for copying files (since it was found that
generally packages may want to alter how files are copied but still
wanted to copy directories in the same way)
TODOs (updated 2/20):
- [x] additional testing (there is some unit testing added at this point
but more would be useful)
- [x] refactor or reorganize `LinkTree` methods: currently there is a
separate set of methods for replicating just the directory structure
without the files, and a set for replicating everything
- [x] Right now external views (i.e. those not used for global
activations) call `view.add_extension`, but global activations do not
to avoid some extra work that goes into maintaining external views. I'm
not sure if addressing that needs to be done here but I'd like to
clarify it in the comments (UPDATE: for now I have added a TODO and in
my opinion this can be merged now and the refactor handled later)
- [x] Several method descriptions (e.g. for `Package.activate`) are out
of date and reference a distinction between global activations and
views, they need to be updated
- [x] Update aspell package activations
- Spack was assuming that a group with gid == current uid would always exist.
- This was breaking the travis build for macos.
- also fix issue with the DB tarball test finding coverage filesx
- spack.util.lock behaves the same as llnl.util.lock, but Lock._lock and
Lock._unlock do nothing.
- can be disabled with a control variable.
- configuration options can enable/disable locking:
- `locks` option in spack configuration controls whether Spack will use filesystem locks or not.
- `-l` and `-L` command-line options can force-disable or force-enable locking.
- Spack will check for group- and world-writability before disabling
locks, and it will not allow a group- or world-writable instance to
have locks disabled.
- update documentation
- simplify the singleton pattern across the codebase
- reduce lines of code needed for crufty initialization
- reduce functions that need to mess with a global
- Singletons whose semantics changed:
- spack.store.store() -> spack.store
- spack.repo.path() -> spack.repo.path
- spack.config.config() -> spack.config.config
- spack.caches.fetch_cache() -> spack.caches.fetch_cache
- spack.caches.misc_cache() -> spack.caches.misc_cache
* Added installation date and time to the database
Information on the date and time of installation of a spec is recorded
into the database. The information is retained on reindexing.
* Expose the possibility to query for installation date
The DB can now be queried for specs that have been installed in a given
time window. This query possibility is exposed to command line via two
new options of the `find` command.
* Extended docstring for Database._add
* Use timestamps since the epoch instead of formatted date in the DB
* Allow 'pretty date' formats from command line
* Substituted kwargs with explicit arguments
* Simplified regex for pretty date strings. Added unit tests.
This updates the fix_darwin_install_name function to use the Spack
Executable object to run install_name_tool, which ensures that
process output is formatted as a 'str' for python2 and python3.
Originally fix_darwin_install_name was invoking subprocess.Popen
directly.
Following the discussion with Todd and Adam, find has been modified to
accept glob expressions. This should not affect performance as every
glob implementation I inspected has 3 cases (no wildcard, wildcard but
no directories involved, wildcard and directories involved) and uses
fnmatch underneath.
Mixins have been changed to do by default a non-recursive search (but
a recursive search can still be triggered using the recursive keyword).
Following comments from Todd:
- the call to tty.debug has been moved deeper, to log the filtering of each file
- the shadowing on the name "kwargs" is avoided
- command reference now includes usage for all Spack commands as output
by `spack help`. Each command usage links to any related section in
the docs.
- added `spack commands` command which can list command names,
subcommands, and generate RST docs for commands.
- added `llnl.util.argparsewriter`, which analyzes an argparse parser and
calls hooks for description, usage, options, and subcommands
'spack install' can now reinstall a spec even if it has dependents, via
the --overwrite option. This option moves the current installation in a
temporary directory. If the reinstallation is successful the temporary
is removed, otherwise a rollback is performed.
- When you don't use wildcards, flake8 will find places where you used an
undefined name.
- This commit has all the bugfixes resulting from this static check.
I'm tracking down a problem with the perl package that's been
generating this error:
```
OSError: OSError: [Errno 2] No such file or directory: '/blah/blah/blah/lib/5.24.1/x86_64-linux/Config.pm~'
```
The real problem is upstream, but it's being masked by an exception
raised in `filter_file`s finally block.
In my case, `backup` is `False`.
The backup is created around line 127, the `re.sub()` calls
fails (working on that), the `except` block fires and moves the backup
file back, then the finally block tries to remove the non-existent
backup file.
This change just avoids trying to remove the non-existent file.
`spack blame` prints out the contributors to a package.
By modification time:
```
$ spack blame --time llvm
LAST_COMMIT LINES % AUTHOR EMAIL
3 days ago 2 0.6 Andrey Prokopenko <andrey.prok@gmail.com>
3 weeks ago 125 34.7 Massimiliano Culpo <massimiliano.culpo@epfl.ch>
3 weeks ago 3 0.8 Peter Scheibel <scheibel1@llnl.gov>
2 months ago 21 5.8 Adam J. Stewart <ajstewart426@gmail.com>
2 months ago 1 0.3 Gregory Becker <becker33@llnl.gov>
3 months ago 116 32.2 Todd Gamblin <tgamblin@llnl.gov>
5 months ago 2 0.6 Jimmy Tang <jcftang@gmail.com>
5 months ago 6 1.7 Jean-Paul Pelteret <jppelteret@gmail.com>
7 months ago 65 18.1 Tom Scogland <tscogland@llnl.gov>
11 months ago 13 3.6 Kelly (KT) Thompson <kgt@lanl.gov>
a year ago 1 0.3 Scott Pakin <pakin@lanl.gov>
a year ago 3 0.8 Erik Schnetter <schnetter@gmail.com>
3 years ago 2 0.6 David Beckingsale <davidbeckingsale@gmail.com>
3 days ago 360 100.0
```
Or by percent contribution:
```
$ spack blame --percent llvm
LAST_COMMIT LINES % AUTHOR EMAIL
3 weeks ago 125 34.7 Massimiliano Culpo <massimiliano.culpo@epfl.ch>
3 months ago 116 32.2 Todd Gamblin <tgamblin@llnl.gov>
7 months ago 65 18.1 Tom Scogland <tscogland@llnl.gov>
2 months ago 21 5.8 Adam J. Stewart <ajstewart426@gmail.com>
11 months ago 13 3.6 Kelly (KT) Thompson <kgt@lanl.gov>
5 months ago 6 1.7 Jean-Paul Pelteret <jppelteret@gmail.com>
3 weeks ago 3 0.8 Peter Scheibel <scheibel1@llnl.gov>
a year ago 3 0.8 Erik Schnetter <schnetter@gmail.com>
3 years ago 2 0.6 David Beckingsale <davidbeckingsale@gmail.com>
3 days ago 2 0.6 Andrey Prokopenko <andrey.prok@gmail.com>
5 months ago 2 0.6 Jimmy Tang <jcftang@gmail.com>
2 months ago 1 0.3 Gregory Becker <becker33@llnl.gov>
a year ago 1 0.3 Scott Pakin <pakin@lanl.gov>
3 days ago 360 100.0
```
- Python I/O would not properly interleave (or appear) with output from
subcommands.
- Add a flusing wrapper around sys.stdout and sys.stderr when
redirecting, so that Python output is synchronous with that of
subcommands.
- 'v' toggle was previously only good for the current install.
- subsequent installs needed user to press 'v' again.
- 'v' state is now preserved across dependency installs.
- Simplify interface to log_output. New interface requires only one
context handler instead of two. Before:
with log_output('logfile.txt') as log_redirection:
with log_redirection:
# do things ... output will be logged
After:
with log_output('logfile.txt'):
# do things ... output will be logged
If you also want the output to be echoed to ``stdout``, use the
`echo` parameter::
with log_output('logfile.txt', echo=True):
# do things ... output will be logged and printed out
And, if you just want to echo *some* stuff from the parent, use
``force_echo``:
with log_output('logfile.txt', echo=False) as logger:
# do things ... output will be logged
with logger.force_echo():
# things here will be echoed *and* logged
A key difference between this and the previous implementation is that
*everything* in the context handler is logged. Previously, things like
`Executing phase 'configure'` would not be logged, only output to the
screen, so understanding phases in the build log was difficult.
- The implementation of `log_output()` is different in two major ways:
1. This implementation avoids race cases by using only one pipe (before
we had a multiprocessing pipe and a unix pipe). The logger daemon
stops naturally when the input stream is closed, which avoids a race
in the previous implementation where we'd miss some lines of output
because the parent would shut the daemon down before it was done
with all output.
2. Instead of turning output redirection on and off, which prevented
some things from being logged, this version uses control characters
in the output stream to enable/disable forced echoing. We're using
the time-honored xon and xoff codes, which tell the daemon to echo
anything between them AND write it to the log. This is how
`logger.force_echo()` works.
- Fix places where output could get stuck in buffers by flushing more
aggressively. This makes the output printed to the terminal the same
as that which would be printed through a pipe to `cat` or to a file.
Previously these could be weirdly different, and some output would be
missing when redirecting Spack to a file or pipe.
- Simplify input and color handling in both `build_environment.fork()`
and `llnl.util.tty.log.log_output()`. Neither requires an input_stream
parameter anymore; we assume stdin will be forwarded if possible.
- remove `llnl.util.lang.duplicate_stream()` and remove associated
monkey-patching in tests, as these aren't needed if you just check
whether stdin is a tty and has a fileno attribute.
* Disable spec colorization when redirecting stdout and add command line flag to re-enable
* Add command line `--color` flag to control output colorization
* Add options to `llnl.util.tty.color` to allow color to be auto/always/never
* Add `Spec.cformat()` function to be used when `format()` should have auto-coloring
- Lock test can be run either as a node-local test or as an MPI test.
- Lock test is now parametrized by filesystem, so you can test the
locking capabilities of your NFS, Lustre, or GPFS filesystem. See docs
for details.
PR #3367 inadvertently changed the semantics of _find_recursive and
_find_non_recursive so that the returned list are not ordered as the
input search list. This commit restores the original semantic, and adds
tests to verify it.
Modifications:
- added support for multi-valued variants
- refactored code related to variants into variant.py
- added new generic features to AutotoolsPackage that leverage multi-valued variants
- modified openmpi to use new features
- added unit tests for the new semantics
## Motivation
Python installations are both important and unfortunately inconsistent. Depending on the Python version, OS, and the strength of the Earth's magnetic field when it was installed, the name of the Python executable, directory containing its libraries, library names, and the directory containing its headers can vary drastically.
I originally got into this mess with #3274, where I discovered that Boost could not be built with Python 3 because the executable is called `python3` and we were telling it to use `python`. I got deeper into this mess when I started hacking on #3140, where I discovered just how difficult it is to find the location and name of the Python libraries and headers.
Currently, half of the packages that depend on Python and need to know this information jump through hoops to determine the correct information. The other half are hard-coded to use `python`, `spec['python'].prefix.lib`, and `spec['python'].prefix.include`. Obviously, none of these packages would work for Python 3, and there's no reason to duplicate the effort. The Python package itself should contain all of the information necessary to use it properly. This is in line with the recent work by @alalazo and @davydden with respect to `spec['blas'].libs` and friends.
## Prefix
For most packages in Spack, we assume that the installation directory is `spec['python'].prefix`. This generally works for anything installed with Spack, but gets complicated when we include external packages. Python is a commonly used external package (it needs to be installed just to run Spack). If it was installed with Homebrew, `which python` would return `/usr/local/bin/python`, and most users would erroneously assume that `/usr/local` is the installation directory. If you peruse through #2173, you'll immediately see why this is not the case. Homebrew actually installs Python in `/usr/local/Cellar/python/2.7.12_2` and symlinks the executable to `/usr/local/bin/python`. `PYTHONHOME` (and presumably most things that need to know where Python is installed) needs to be set to the actual installation directory, not `/usr/local`.
Normally I would say, "sounds like user error, make sure to use the real installation directory in your `packages.yaml`". But I think we can make a special case for Python. That's what we decided in #2173 anyway. If we change our minds, I would be more than happy to simplify things.
To solve this problem, I created a `spec['python'].home` attribute that works the same way as `spec['python'].prefix` but queries Python to figure out where it was actually installed. @tgamblin Is there any way to overwrite `spec['python'].prefix`? I think it's currently immutable.
## Command
In general, Python 2 comes with both `python` and `python2` commands, while Python 3 only comes with a `python3` command. But this is up to the OS developers. For example, `/usr/bin/python` on Gentoo is actually Python 3. Worse yet, if someone is using an externally installed Python, all 3 commands may exist in the same directory! Here's what I'm thinking:
If the spec is for Python 3, try searching for the `python3` command.
If the spec is for Python 2, try searching for the `python2` command.
If neither are found, try searching for the `python` command.
## Libraries
Spack installs Python libraries in `spec['python'].prefix.lib`. Except on openSUSE 13, where it installs to `spec['python'].prefix.lib64` (see #2295 and #2253). On my CentOS 6 machine, the Python libraries are installed in `/usr/lib64`. Both need to work.
The libraries themselves change name depending on OS and Python version. For Python 2.7 on macOS, I'm seeing:
```
lib/libpython2.7.dylib
```
For Python 3.6 on CentOS 6, I'm seeing:
```
lib/libpython3.so
lib/libpython3.6m.so.1.0
lib/libpython3.6m.so -> lib/libpython3.6m.so.1.0
```
Notice the `m` after the version number. Yeah, that's a thing.
## Headers
In Python 2.7, I'm seeing:
```
include/python2.7/pyconfig.h
```
In Python 3.6, I'm seeing:
```
include/python3.6m/pyconfig.h
```
It looks like all Python 3 installations have this `m`. Tested with Python 3.2 and 3.6 on macOS and CentOS 6
Spack has really nice support for libraries (`find_libraries` and `LibraryList`), but nothing for headers. Fixed.
`set_executable` now checks if a user/group.other had read permission
on a file and if it does then it sets the corresponding executable
bit.
See #1483.
- Get rid of pkgsort() usage for preferred variants.
- Concretization is now entirely based on key-based sorting.
- Remove PreferredPackages class and various spec cmp() methods.
- Replace with PackagePrefs class that implements a key function for
sorting according to packages.yaml.
- Clear package pref caches on config test.
- Explicit compare methods instead of total_ordering in Version.
- Our total_ordering backport wasn't making Python 3 happy for some
reason.
- Python 3's functools.total_ordering and spelling the operators out
fixes the problem.
- Fix unicode issues with spec hashes, json, & YAML
- Try to use str everywhere and avoid unicode objects in python 2.
- convert print, StringIO, except as, octals, izip
- convert print statement to print function
- convert StringIO to six.StringIO
- remove usage of csv reader in Spec, in favor of simple regex
- csv reader only does byte strings
- convert 0755 octal literals to 0o755
- convert `except Foo, e` to `except Foo as e`
- fix a few places `str` is used.
- may need to switch everything to str later.
- convert iteritems usages to use six.iteritems
- fix urllib and HTMLParser
- port metaclasses to use six.with_metaclass
- More octal literal conversions for Python 2/3
- Fix a new octal literal.
- Convert `basestring` to `six.string_types`
- Convert xrange -> range
- Fix various issues with encoding, iteritems, and Python3 semantics.
- Convert contextlib.nested to explicitly nexted context managers.
- Convert use of filter() to list comprehensions.
- Replace reduce() with list comprehensions.
- Clean up composite: replace inspect.ismethod() with callable()
- Python 3 doesn't have "method" objects; inspect.ismethod returns False.
- Need to use callable in Composite to make it work.
- Update colify to use future division.
- Fix zip() usages that need to be lists.
- Python3: Use line-buffered logging instead of unbuffered.
- Python3 raises an error with unbuffered I/O
- See https://bugs.python.org/issue17404
- Added a new interface for Specs to pass build information
- Calls forwarded from Spec to Package are now explicit
- Added descriptor within Spec to manage forwarding
- Added state in Spec to maintain query information
- Modified a few packages (the one involved in spack install pexsi) to showcase changes
- This uses an object wrapper to `spec` to implement the `libs` sub-calls.
- wrapper is returned from `__getitem__` only if spec is concrete
- allows packagers to access build information easily
Previously, fix_darwin_install_name would only handle dependencies that have no path set, and it ignore dependencies that have the build directory as path baked in. Catch this, and replace it by the install directory.
* Porting: substitute nose with ytest
This huge commit substitutes nose with pytest as a testing system. Things done here:
* deleted external/nose as it is no longer used
* moved mock resources in their own directory 'test/mock/'
* ported two tests (cmd/find, build_system) to pytest native syntax as an example
* build_environment, log: used monkeypatch instead of try/catch
* moved global mocking of fetch_cache to an auto-used fixture
* moved global mocking from test/__init__.py to conftest.py
* made `spack test` a wrapper around pytest
* run-unit-tests: avoid running python 2.6 tests under coverage to speed them up
* use `pytest --cov` instead of coverage run to cut down testing time
* mock/packages_test: moved mock yaml configuration to files instead of leaving it in the code as string literals
* concretize.py: ported tests to native pytest, reverted multiprocessing in pytest.ini as it was creating the wrong report for coveralls
* conftest.py, fixtures: added docstrings
* concretize_preferences.py: uses fixtures instead of subclassing MockPackagesTest
* directory_layout.py: uses fixtures instead of subclassing MockPackagesTest
* install.py: uses fixtures instead of subclassing MockPackagesTest
* optional_deps.py: uses fixtures instead of subclassing MockPackagesTest
optional_deps.py: uses fixtures instead of subclassing MockPackagesTest
* packages.py: uses fixtures instead of subclassing MockPackagesTest
* provider_index.py: uses fixtures instead of subclassing MockPackagesTest
* spec_yaml.py: uses fixtures instead of subclassing MockPackagesTest
* multimethod.py: uses fixtures instead of subclassing MockPackagesTest
* install.py: now uses mock_archive_url
* git_fetch.py: uses fixtures instead of subclassing MockPackagesTest
* hg_fetch.py: uses fixtures instead of subclassing MockPackagesTest
* svn_fetch.py, mirror.py: uses fixtures instead of subclassing MockPackagesTest
repo.py: deleted
* test_compiler_cmd.py: uses fixtures instead of subclassing MockPackagesTest
* cmd/module.py, cmd/uninstall.py: uses fixtures instead of subclassing MockDatabase
* database.py: uses fixtures instead of subclassing MockDatabase, removed mock/database
* pytest: uncluttering fixture implementations
* database: changing the scope to 'module'
* config.py: uses fixtures instead of subclassing MockPackagesTest
* spec_dag.py, spec_semantics.py: uses fixtures instead of subclassing MockPackagesTest
* stage.py: uses fixtures instead of subclassing MockPackagesTest. Removed mock directory
* pytest: added docstrings to all the fixtures
* pytest: final cleanup
* build_system_guess.py: fixed naming and docstrings as suggested by @scheibelp
* spec_syntax.py: added expected failure on parsing multiple specs closes#1976
* Add pytest and pytest-cov to Spack externals.
* Make `spack flake8` ignore externals.
* run-unit-tests runs spack test and not pytest.
* Remove all the special stuff for `spack test`
- Remove `conftest.py` magic and all the special case stuff in `bin/spack`
- Spack commands can optionally take unknown arguments, if they want to
handle them.
- `spack test` is now a command like the others.
- `spack test` now just delegates its arguments to `pytest`, but it does
it by receiving unknown arguments and NOT taking an explicit
help argument.
* Fix error in fixtures.
* Improve `spack test` command a bit.
- Now supports an approximation of the old simple interface
- Also supports full pytest options if you want them.
* Use external coverage instead of pytest-cov
* Make coverage use parallel-mode.
* change __init__.py docs to include pytest
* inheritance of directives: using meta-classes to inject attributes coming from directives into packages + lazy directives
* _dep_types -> dependency_types
* using a meta-class to inject directives into packages
* directives are lazy
fixes#2466
* directives.py: allows for multiple inheritance. Added blank lines as suggested by @tgamblin
* directives.py: added a test for simple inheritance of directives
* Minor improvement requested by @tgamblin
CMakePackage: importing names from spack.directives
directives: wrap __new__ to respect pep8
* Refactoring requested by @tgamblin
directives: removed global variables in favor of class variables. Simplified the interface for directives (they return a callable on a package or a list of them).
The option -s now causes file and line number information to be printed
along with any invocation of msg, info, etc...
This will greatly ease debugging.
* spack install: forward sys.stdin to child processes fixes#2140
- [ ] redirection process is spawned in __enter__ instead of __init__
- [ ] sys.stdin is forwarded to child processes
* log: wrapped __init__ definition
- Closing and re-opening to upgrade to write will lose all existing read
locks on this process.
- If we didn't allow ranges, sleeping until no reads would work.
- With ranges, we may never be able to take some legal write locks
without invalidating all reads. e.g., if a write lock has distinct
range from all reads, it should just work, but we'd have to close the
file, reopen, and re-take reads.
- It's easier to just check whether the file is writable in the first
place and open for writing from the start.
- Lock now only opens files read-only if we *can't* write them.
A use case where the previous approach was failing is :
- more than one spack process running on compute nodes
- stage directory is a link to fast LOCAL storage
In this case the processes may try to unlink something that is "dead" for them, but actually used by other processes on storage they cannot see.
* Turned <provider>_libs into an iterable
Modifications :
- added class LibraryList + unit tests
- added convenience functions `find_libraries` and `dedupe`
- modifed non Intel blas/lapack providers
- modified packages using blas_shared_libs and similar functions
* atlas : added pthread variant
* intel packages : added lapack_libs and blas_libs
* find_library_path : removed unused function
* PR review : fixed last issues
* LibraryList : added test on __add__ return type
* LibraryList : added __radd__ fixed unit tests
fix : failing unit tests due to missing `self`
* cp2k and dependecies : fixed blas-lapack related statements in package.py
