This PR will add a new audit, specifically for spack package homepage urls (and eventually
other kinds I suspect) to see if there is an http address that can be changed to https.
Usage is as follows:
```bash
$ spack audit packages-https <package>
```
And in list view:
```bash
$ spack audit list
generic:
Generic checks relying on global variables
configs:
Sanity checks on compilers.yaml
Sanity checks on packages.yaml
packages:
Sanity checks on specs used in directives
packages-https:
Sanity checks on https checks of package urls, etc.
```
I think it would be unwise to include with packages, because when run for all, since we do requests it takes a long time. I also like the idea of more well scoped checks - likely there will be other addresses for http/https within a package that we eventually check. For now, there are two error cases - one is when an https url is tried but there is some SSL error (or other error that means we cannot update to https):
```bash
$ spack audit packages-https zoltan
PKG-HTTPS-DIRECTIVES: 1 issue found
1. Error with attempting https for "zoltan":
<urlopen error [SSL: CERTIFICATE_VERIFY_FAILED] certificate verify failed: Hostname mismatch, certificate is not valid for 'www.cs.sandia.gov'. (_ssl.c:1125)>
```
This is either not fixable, or could be fixed with a change to the url or (better) contacting the site owners to ask about some certificate or similar.
The second case is when there is an http that needs to be https, which is a huge issue now, but hopefully not after this spack PR.
```bash
$ spack audit packages-https xman
Package "xman" uses http but has a valid https endpoint.
```
And then when a package is fixed:
```bash
$ spack audit packages-https zlib
PKG-HTTPS-DIRECTIVES: 0 issues found.
```
And that's mostly it. :)
Signed-off-by: vsoch <vsoch@users.noreply.github.com>
Co-authored-by: vsoch <vsoch@users.noreply.github.com>
* Add a __reduce__ method to Spec
fixes#23892
The recursion limit seems to be due to the default
way in which a Spec is serialized, following all
the attributes. It's still not clear to me why this
is related to being in an environment, but in any
case we already have methods to serialize Specs to
disk in JSON and YAML format. Here we use them to
pickle a Spec instance too.
* Downgrade to build-hash
Hopefully nothing will change the package in
between serializing the spec and sending it
to the child process.
* Add support for Python 2
* 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
The gcc compiler can be configured to use `ld.gold` by default. It will
then call `ld.gold` explicitly when linking. When so, spack need to have
a ld.gold wrapper in PATH to inject rpaths link flags etc...
Also I wouldn't be surprised to see some package calling `ld.gold`
directly.
As for ld.gold, the argument could be made that we want to support any
package that could call ld.lld.
* Add a __reduce__ method to SpecBuildInterface
This class was confusing pickle when being serialized,
due to its scary nature of being an object that disguise
as another type.
* Add more MacOS tests, switch them to clingo
* Fix condition syntax
* Remove Python v3.6 and v3.9 with macOS
* Conditionally remove 'context' from kwargs in _urlopen
Previously, 'context' is purged from kwargs in _urlopen to
conform to varying support for 'context' in different versions
of urllib. This fix tries to use 'context', and then removes
it if an exception is thrown and tries again.
* Specify error type in try statement in _urlopen
Specify TypeError when checking if 'context' is in kwargs
for _urlopen. Also, if try fails, check that 'context' is
in the error message before removing from kwargs.
This is a direct followup to #13557 which caches additional attributes that were added in #24095 that are expensive to compute. I had to reopen#25556 in another PR to invalidate the GitLab CI cache, but see #25556 for prior discussion.
### Before
```console
$ time spack env activate .
real 2m13.037s
user 1m25.584s
sys 0m43.654s
$ time spack env view regenerate
==> Updating view at /Users/Adam/.spack/.spack-env/view
real 16m3.541s
user 10m28.892s
sys 4m57.816s
$ time spack env deactivate
real 2m30.974s
user 1m38.090s
sys 0m49.781s
```
### After
```console
$ time spack env activate .
real 0m8.937s
user 0m7.323s
sys 0m1.074s
$ time spack env view regenerate
==> Updating view at /Users/Adam/.spack/.spack-env/view
real 2m22.024s
user 1m44.739s
sys 0m30.717s
$ time spack env deactivate
real 0m10.398s
user 0m8.414s
sys 0m1.630s
```
Fixes#25555Fixes#25541
* Speedup environment activation, part 2
* Only query distutils a single time
* Fix KeyError bug
* Make vermin happy
* Manual memoize
* Add comment on cross-compiling
* Use platform-specific include directory
* Fix multiple bugs
* Fix python_inc discrepancy
* Fix import tests
* Set pubkey trust to ultimate during `gpg trust`
Tries to solve the same problem as #24760 without surpressing stderr
from gpg commands.
This PR makes every imported key trusted in the gpg database.
Note: I've outlined
[here](https://github.com/spack/spack/pull/24760#issuecomment-883183175)
that gpg's trust model makes sense, since how can we trust a random
public key we download from a binary cache?
* Fix test
Fixes#25603
This commit adds a new context manager to temporarily
deactivate active environments. This context manager
is used when setting up bootstrapping configuration to
make sure that the current environment is not affected
by operations on the bootstrap store.
* Preserve exit code 1 if nothing is found
* Use context manager for the environment
This commit adds a regression test for version selection
with preferences in `packages.yaml`. Before PR 25585 we
used negative weights in a minimization to select the
optimal version. This may lead to situations where a
dependency may make the version score of dependents
"better" if it is preferred in packages.yaml.
PackageInstaller and Package.installed disagree over what it means
for a package to be installed: PackageInstaller believes it should be
enough for a database entry to exist, whereas Package.installed
requires a database entry & a prefix directory.
This leads to the following niche issue:
* a develop spec in an environment is successfully installed
* then somehow its install prefix is removed (e.g. through a bug fixed
in #25583)
* you modify the sources and reinstall the environment
1. spack checks pkg.installed and realizes the develop spec is NOT
installed, therefore it doesn't need to have 'overwrite: true'
2. the installer gets the build task and checks the database and
realizes the spec IS installed, hence it doesn't have to install it.
3. the develop spec is not rebuilt.
The solution is to make PackageInstaller and pkg.installed agree over
what it means to be installed, and this PR does that by dropping the
prefix directory check from pkg.installed, so that it only checks the
database.
As a result, spack will create a build task with overwrite: true for
the develop spec, and the installer in fact handles overwrite requests
fine even if the install prefix doesn't exist (it just does a normal
install).
see #25563
When we have a concrete environment and we ask to install a
concrete spec from a file, currently Spack returns a list of
specs that are all the one that match the argument DAG hash.
Instead we want to compare build hashes, which also account
for build-only dependencies.
#25303 filtered padding from build output, but it's still there in binary install/relocate output,
so our CI logs are still quite long and frequently hit the limit.
- [x] add context handler from #25303 to buildcache installation as well
This allows you to run `spack graph --installed` from within an environment and get a dot graph of
its concrete specs.
- [x] make `spack graph -i` environment-aware
- [x] add code to the generated dot graph to ensure roots have min rank (i.e., they're all at the
top or left of the DAG)
Bootstrapping clingo on macOS on `develop` gives errors like this:
```
==> Error: RuntimeError: Unable to locate python command in /System/Library/Frameworks/Python.framework/Versions/2.7/Resources/Python.app/Contents/bin
/Users/gamblin2/Workspace/spack/var/spack/repos/builtin/packages/python/package.py:662, in command:
659 return Executable(path)
660 else:
661 msg = 'Unable to locate {0} command in {1}'
>> 662 raise RuntimeError(msg.format(self.name, self.prefix.bin))
```
On macOS, `python` is laid out differently. In particular, `sys.executable` is here:
```console
Python 2.7.16 (default, May 8 2021, 11:48:02)
[GCC Apple LLVM 12.0.5 (clang-1205.0.19.59.6) [+internal-os, ptrauth-isa=deploy on darwin
Type "help", "copyright", "credits" or "license" for more information.
>>> import sys
>>> sys.executable
'/System/Library/Frameworks/Python.framework/Versions/2.7/Resources/Python.app/Contents/MacOS/Python'
```
Based on that, you'd think that
`/System/Library/Frameworks/Python.framework/Versions/2.7/Resources/Python.app/Contents` would be
where you'd look for a `bin` directory, but you (and Spack) would be wrong:
```console
$ ls /System/Library/Frameworks/Python.framework/Versions/2.7/Resources/Python.app/Contents/
Info.plist MacOS/ PkgInfo Resources/ _CodeSignature/ version.plist
```
You need to look in `sys.exec_prefix`
```
>>> sys.exec_prefix
'/System/Library/Frameworks/Python.framework/Versions/2.7'
```
Which looks much more like a standard prefix, with understandable `bin`, `lib`, and `include`
directories:
```console
$ ls /System/Library/Frameworks/Python.framework/Versions/2.7
Extras/ Mac/ Resources/ bin/ lib/
Headers@ Python* _CodeSignature/ include/
$ ls -l /System/Library/Frameworks/Python.framework/Versions/2.7/bin/python
lrwxr-xr-x 1 root wheel 7B Jan 1 2020 /System/Library/Frameworks/Python.framework/Versions/2.7/bin/python@ -> python2
```
- [x] change `bootstrap.py` to use the `sys.exec_prefix` as the external prefix, instead of just
getting the parent directory of the executable.
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).
This commit rework version facts so that:
1. All the information on versions is collected
before emitting the facts
2. The same kind of atom is emitted for versions
stemming from different origins (package.py
vs. packages.yaml)
In the end all the possible versions for a given
package are totally ordered and they are given
different and increasing weights staring from zero.
This refactor allow us to avoid using negative
weights, which in some configurations may make
parent node score "better" and lead to unexpected
"optimal" results.
Once PR binary graduation is deployed, the shared PR mirror will
contain binaries just built by a merged PR, before the subsequent
develop pipeline has had time to finish. Using the shared PR mirror
as a source of binaries will reduce the number of times we have to
rebuild the same full hash.
* 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.
* Bootstrap clingo from binaries
* Move information on clingo binaries to a JSON file
* Add support to bootstrap on Cray
Bootstrapping on Cray requires, at the moment, to
swap the platform when looking for binaries - due
to #22800.
* Add SHA256 verification for bootstrapped software
Use sha256 verification for binaries necessary to bootstrap
the concretizer and gpg for signature verification
* patchelf: use Spec._old_concretize() to bootstrap
As noted in #24450 we may happen to need the
concretizer when bootstrapping clingo. In that case
only the old concretizer is available.
* Add a schema for bootstrapping methods
Two fields have been added to bootstrap.yaml:
"sources" which lists the methods available for
bootstrapping software
"trusted" which records if a source is trusted or not
A subcommand has been added to "spack bootstrap" to list
the sources currently available.
* Methods used for bootstrapping are configurable from bootstrap:sources
The function that tries to ensure a given Python module
is importable now tries bootstrapping methods in the same
order as they are defined in `bootstrap.yaml`
* Permit to trust/untrust bootstrapping methods
* Add binary tests for MacOS, Ubuntu
* Add documentation
* Add a note on bash
Spack is internally using a patched version of `argparse` mainly to backport Python 3 functionality
into Python 2. This PR makes it such that for the supported Python 3 versions we use `argparse`
from the standard Python library. This PR has been extracted from #25371 where it was needed
to be able to use recent versions of `pytest`.
* Fixed formatting issues when using a pristine argparse.py
* Fix error message for Python 3.X when missing positional arguments
* Account for the change of API in Python 3.7
* Layout multi-valued args into columns in error messages
* Seamless transition in develop if argparse.pyc is in external
* Be more defensive in case we can't remove the file.
Add link type to spack.yaml format
Add tests to verify link behavior is correct for installed files
for all three view types
Co-authored-by: vsoch <vsoch@users.noreply.github.com>
The commands have been deprecated in #7098, and have
been failing with an error message since then.
Cleaning the code since it is unlikely that somebody
is still using them.
Preferred providers had a non-zero weight because in an earlier formulation of the logic program that was needed to prefer external providers over default providers. With the current formulation for externals this is not needed anymore, so we can give a weight of zero to both default choices and providers that are externals. _Using zero ensures that we don't introduce any drift towards having less providers, which was happening when minimizing positive weights_.
Modifications:
- [x] Default weight for providers starts at 0 (instead of 10, needed before to prefer externals)
- [x] Rules to compute the `provider_weight` have been refactored. There are multiple possible weights for a given `Virtual`. Only one gets selected by the solver (the one that minimizes the objective function).
- [x] `provider_weight` are now accounting for each different `Virtual`. Before there was a single weight per provider, even if the package was providing multiple virtuals.
* Give preferred providers a weight of zero
Preferred providers had a non-zero weight because in an earlier
formulation of the logic program that was needed to prefer
external providers over default providers.
With the current formulation for externals this is not needed anymore,
so we can give a weight of zero to default choices. Using zero
ensures that we don't introduce any drift towards having
less providers, which was happening when minimizing positive weights.
* Simplify how we compute weights for providers
Rewrite rules so that specific events (i.e. being
an external) unlock the possibility to use certain
weights. The weight being considered is then selected
by the minimization process to be the one that gives
the best score.
* Allow providers to have different weights for different virtuals
Before this change we didn't differentiate providers based on
the virtual they provide, which meant that packages providing
more than one virtual had nonetheless a single weight.
With this change there will be a weight per virtual.
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
`compare_specs()` had a `colorful` keyword argument, but everything else in
spack uses `color` for this.
- [x] rename the argument
- [x] make the default follow spack's `--color=always/never/auto` setting
Add a workflow to test bootstrapping clingo on
different platforms so that we can detect changes
that break it.
Compute `site_packages_dir` in `bootstrap.py` as it was
before #24095, until we figure a better way to override
that attribute.
Long, padded install paths can get to be very long in the verbose install
output. This has to be filtered out by the Executable class, as it
generates these debug messages.
- [x] add ability to filter paths from Executable output.
- [x] add a context manager that can enable path filtering
- [x] make `build_process` in `installer.py`
This should hopefully allow us to see most of the build output in
Gitlab pipeline builds again.
`build_process` has been around a long time but it's become a very large,
unwieldy method. It's hard to work with because it has a lot of local
variables that need to persist across all of the code.
- [x] To address this, convert it its own `BuildInfoProcess` class.
- [x] Start breaking the method apart by factoring out the main
installation logic into its own function.
When context managers are used to save and restore values, we need to remember
to use try/finally around the yield in case an exception is thrown. Otherwise,
the cleanup will be skipped.
- Change config from the undocumented `use_curl: true/false` to `url_fetch_method: urllib/curl`.
- Documentation of `url_fetch_method` in `defaults/config.yaml`
- Default fetch option explicitly set to `urllib` for users who may not have curl on their system
To upgrade from `use_curl` to `url_fetch_method`, run `spack config update config`
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.
When a spec fails to build on `develop`, instead of storing an empty file as the entry in the broken specs list, this change stores the full spec yaml as well as links to the failing pipeline and job.
A `spack diff` will take two specs, and then use the spack.solver.asp.SpackSolverSetup to generate
lists of facts about each (e.g., nodes, variants, etc.) and then take a set difference between the
two to show the user the differences.
Example output:
$ spack diff python@2.7.8 python@3.8.11
==> Warning: This interface is subject to change.
--- python@2.7.8/tsxdi6gl4lihp25qrm4d6nys3nypufbf
+++ python@3.8.11/yjtseru4nbpllbaxb46q7wfkyxbuvzxx
@@ variant_value @@
- python patches a8c52415a8b03c0e5f28b5d52ae498f7a7e602007db2b9554df28cd5685839b8
+ python patches 0d98e93189bc278fbc37a50ed7f183bd8aaf249a8e1670a465f0db6bb4f8cf87
@@ version @@
- openssl Version(1.0.2u)
+ openssl Version(1.1.1k)
- python Version(2.7.8)
+ python Version(3.8.11)
Currently this uses diff-like output but we will attempt to improve on this in the future.
One use case for `spack diff` is whenever a user has a disambiguate situation and cannot
remember how two different installs are different. The command can also output `--json` in
the case of a more analysis type use case where we want to save complete data with all
diffs and the intersection. However, the command is really more intended for a command
line use case, and we likely will have an analyzer more suited to saving data
Signed-off-by: vsoch <vsoch@users.noreply.github.com>
Co-authored-by: vsoch <vsoch@users.noreply.github.com>
Co-authored-by: Tamara Dahlgren <35777542+tldahlgren@users.noreply.github.com>
Co-authored-by: Todd Gamblin <tgamblin@llnl.gov>
* Catch ConnectionError from CDash reporter
Catch ConnectionError when attempting to upload the results of `spack install`
to CDash. This follows in the spirit of #24299. We do not want `spack install`
to exit with a non-zero status when something goes wrong while attempting to
report results to CDash.
* Catch HTTP Error 400 (Bad Request) in relate_cdash_builds()
`spack style` previously used a Travis CI variable to figure out
what the base branch of a PR was, and this was apparently also set
on `develop`. We switched to `GITHUB_BASE_REF` to support GitHub
Actions, but it looks like this is set to `""` in pushes to develop,
so `spack style` breaks there.
This PR does two things:
- [x] Remove `GITHUB_BASE_REF` knowledge from `spack style` entirely
- [x] Handle `GITHUB_BASE_REF` in style scripts instead, and explicitly
pass the base ref if it is present, but don't otherwise.
This makes `spack style` *not* dependent on the environment and fixes
handling of the base branch in the right place.
This adds a `--root` option so that `spack style` can check style for
a spack instance other than its own.
We also change the inner workings of `spack style` so that `--config FILE`
(and similar options for the various tools) options are used. This ensures
that when `spack style` runs, it always uses the config from the running spack,
and does *not* pick up configuration from the external root.
- [x] add `--root` option to `spack style`
- [x] add `--config` (or similar) option when invoking style tools
- [x] add a test that verifies we can check an external instance
Intel oneAPI installs maintain a lock file in XDG_RUNTIME_DIR,
which by default exists in /tmp (and is shared by all component
installs). This prevented multiple oneAPI components from being
installed in parallel. This commit sets XDG_RUNTIME_DIR to exist
within Spack's installation Stage, so allows multiple components
to be installed at the same time.
This uses our bootstrapping logic to automatically install dependencies for
`spack style`. Users should no longer have to pre-install all of the tools
(`isort`, `mypy`, `black`, `flake8`). The command will do it for them.
- [x] add logic to bootstrap specs with specific version requirements in `spack style`
- [x] remove style tools from CI requirements (to ensure we test bootstrapping)
- [x] rework dependencies for `mypy` and `py-typed-ast`
- `py-typed-ast` needs to be a link dependency
- it needs to be at 1.4.1 or higher to work with python 3.9
Signed-off-by: vsoch <vsoch@users.noreply.github.com>
#24095 introduced a couple of bugs, which are fixed here:
1. The module path is computed incorrectly for bootstrapped clingo
2. We remove too many paths for `sys.path` in case of failures
Third-party Python libraries may be installed in one of several directories:
1. `lib/pythonX.Y/site-packages` for Spack-installed Python
2. `lib64/pythonX.Y/site-packages` for system Python on RHEL/CentOS/Fedora
3. `lib/pythonX/dist-packages` for system Python on Debian/Ubuntu
Previously, Spack packages were hard-coded to use the (1). Now, we query the Python installation itself and ask it which to use. Ever since #21446 this is how we've been determining where to install Python libraries anyway.
Note: there are still many packages that are hard-coded to use (1). I can change them in this PR, but I don't have the bandwidth to test all of them.
* Python: handle dist-packages and site-packages
* Query Python to find site-packages directory
* Add try-except statements for when distutils isn't installed
* Catch more errors
* Fix root directory used in import tests
* Rely on site_packages_dir property
* Permit to enable/disable bootstrapping and customize store location
This PR adds configuration handles to allow enabling
and disabling bootstrapping, and to customize the store
location.
* Move bootstrap related configuration into its own YAML file
* Add a bootstrap command to manage configuration
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.
015e29efe1 that introduced this section to the
documentation said “two” here instead of the actual count, three.
9f54cea5c5 then added a fourth, BLAS/LAPACK.
Rather than trying to keep this leading count in sync, this change just replaces
the wording with something more generic/stable.
* 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.
`dateutil.parser` was an optional dependency for CVS tests. It was failing on macOS
beacuse the dateutil types were not being installed, and mypy was failing *even when the
CVS tests were skipped*. This seems like it was an oversight on macOS --
`types-dateutil-parser` was not installed there, though it was on Linux unit tests.
It takes 6 lines of YAML and some weird test-skipping logic to get `python-dateutil` and
`types-python-dateutil` installed in all the tests where we need them, but it only takes
4 lines of code to write the date parser we need for CVS, so I just did that instead.
Note that CVS date format can vary from system to system, but it seems like it's always
pretty similar for the parts we care about.
- [x] Replace dateutil.parser with a simpler date regex
- [x] Lose the dependency on `dateutil.parser`
Previous tests of `spack style` didn't really run the tools --
they just ensure that the commands worked enough to get coverage.
This adds several real tests and ensures that we hit the corner
cases in `spack style`. This also tests sucess as well as failure
cases.
This consolidates code across tools in `spack style` so that each
`run_<tool>` function can be called indirecty through a dictionary
of handlers, and os that checks like finding the executable for the
tool can be shared across commands.
- [x] rework `spack style` to use decorators to register tools
- [x] define tool order in one place in `spack style`
- [x] fix python 2/3 issues to Get `isort` checks working
- [x] make isort error regex more robust across versions
- [x] remove unused output option
- [x] change vestigial `TRAVIS_BRANCH` to `GITHUB_BASE_REF`
- [x] update completion
We should not fail the generate stage simply due to the presence of
a broken-spec somewhere in the DAG. Only fail if the known broken
spec needs to be rebuilt.
This PR adds a context manager that permit to group the common part of a `when=` argument and add that to the context:
```python
class Gcc(AutotoolsPackage):
with when('+nvptx'):
depends_on('cuda')
conflicts('@:6', msg='NVPTX only supported in gcc 7 and above')
conflicts('languages=ada')
conflicts('languages=brig')
conflicts('languages=go')
```
The above snippet is equivalent to:
```python
class Gcc(AutotoolsPackage):
depends_on('cuda', when='+nvptx')
conflicts('@:6', when='+nvptx', msg='NVPTX only supported in gcc 7 and above')
conflicts('languages=ada', when='+nvptx')
conflicts('languages=brig', when='+nvptx')
conflicts('languages=go', when='+nvptx')
```
which needs a repetition of the `when='+nvptx'` argument. The context manager might help improving readability and permits to group together directives related to the same semantic aspect (e.g. all the directives needed to model the behavior of `gcc` when `+nvptx` is active).
Modifications:
- [x] Added a `when` context manager to be used with package directives
- [x] Add unit tests and documentation for the new feature
- [x] Modified `cp2k` and `gcc` to show the use of the context manager
ci: only write to broken-specs list on SpackError
Only write to the broken-specs list when `spack install` raises a SpackError,
instead of writing to this list unnecessarily when infrastructure-related problems
prevent a develop job from completing successfully.
If two Specs have the same hash (and prefix) but are not equal, Spack
originally had logic to detect this and raise an error (since both
cannot be installed in the same place). Recently this has eroded and
the check no-longer works; moreover, when defining projections (which
may truncate the hash or other distinguishing properties from the
prefix) Spack was also failing to detect collisions (in both of these
cases, Spack would overwrite the old prefix with the new Spec).
This PR maintains a list of all "taken" prefixes: if a hash is not
registered (i.e. recorded as installed in the database) but the prefix
is occupied, that is a collision. This can detect collisions created
by defining projections (specifically when they omit the hash).
The PR does not detect collisions where specs have the same hash
(and prefix) but are not equal.
Prior to any Spack build, Spack modifies PATH etc. to help the build
find the dependencies it needs. It also allows any package to define
custom environment modifications (and furthermore a package can
specify environment modifications to apply when it is used as a
dependency). If an external package defines custom environment
modifications that alter PATH, and the external package is in a merged
or system prefix, then that prefix could "override" the Spack-built
packages.
This commit reorders environment modifications so that PrependPath
actions which expose Spack-built packages override PrependPath actions
for custom environment modifications of external packages.
In more detail, the original order of environment modifications is:
* Modules
* Compiler flag variables
* PATH, CMAKE_PREFIX_PATH, and PKG_CONFIG_PATH for dependencies
* Custom package.py modifications in the following order:
* dependencies
* root
This commit changes the order:
* Modules
* Compiler flag variables
* For each external dependency
* PATH, CMAKE_PREFIX_PATH, and PKG_CONFIG_PATH modifications
* Custom modifications
* For each Spack-built dependency
* PATH, CMAKE_PREFIX_PATH, and PKG_CONFIG_PATH modifications
* Custom modifications
Spack pipelines need to take specific actions internally that depend
on whether the pipeline is being run on a PR to spack or a merge to
the develop branch. Pipelines can also run in other repositories,
which represents other possible use cases than just the two mentioned
above. This PR creates a "SPACK_PIPELINE_TYPE" gitlab variable which
is propagated to rebuild jobs, and is also used internally to determine
which pipeline-specific tasks to run.
One goal of the PR is fix an issue where rebuild jobs which failed on
develop pipelines did not properly report the broken full hash to the
"broken-specs-url".
* Add Externally Findable section to info command
* Use comma delimited detection attributes in addition to boolean value
* Unit test externally detectable part of spack info
* Force the Python interpreter with an env variable
This commit forces the Python interpreter with an
environment variable, to ensure that the Python set
by the "setup-python" action is the one being used.
Due to the policy adopted by Spack to prefer python3
over python we may end up picking a Python 3.X
interpreter where Python 2.7 was meant to be used.
* Revert "Update conftest.py (#24473)"
This reverts commit 477c8ce820.
* Make python-dateutil a soft dependency for unit tests
Before #23212 people could clone spack and run
```
spack unit-tests
```
while now this is not possible, since python-dateutil is
a required but not vendored dependency. This change makes
it not a hard requirement, i.e. it will be used if found
in the current interpreter.
* Workaround mypy complaint
This commit fixes a subtle bug that may occur when
a package is a "possible_provider" of a virtual but
no "provides_virtual" can be deduced. In that case
the cardinality constraint on "provides_virtual"
may arbitrarily assign a package the role of provider
even if the constraints for it to be one are not fulfilled.
The fix reworks the logic around three concepts:
- "possible_provider": a package may provide a virtual if some constraints are met
- "provides_virtual": a package meet the constraints to provide a virtual
- "provider": a package selected to provide a virtual
Spack packages can now fetch versions from CVS repositories. Note
this fetch mechanism is unsafe unless using :extssh:. Most public
CVS repositories use an insecure protocol implemented as part of CVS.
Here we are adding an install_times.json into the spack install metadata folder.
We record a total, global time, along with the times for each phase. The type
of phase or install start / end is included (e.g., build or fail)
Signed-off-by: vsoch <vsoch@users.noreply.github.com>
Co-authored-by: vsoch <vsoch@users.noreply.github.com>
Add a new "spack audit" command. This command can check for issues
with configuration or with packages and is intended to help a
user debug a failed Spack build.
In some cases the reported issues are always errors but are too
costly to check for (e.g. packages that specify missing variants on
dependencies). In other cases the issues may be legitimate but
uncommon usage of Spack and we want to be sure the user intended the
behavior (e.g. duplicate compiler definitions).
Audits are grouped by theme, and for now the two themes are packages
and configuration. For example you can run all available audits
on packages with "spack audit packages". It is intended that in
the future users will be able to define their own audits.
The package audits are good candidates for running in package_sanity
(i.e. they could catch bugs in user-submitted packages before they
are merged) but that is left for a later PR.
This should get us most of the way there to support using monitor during a spack container build, for both Singularity and Docker. Some quick notes:
### Docker
Docker works by way of BUILDKIT and being able to specify --secret. What this means is that you can prefix a line with a mount of type secret as follows:
```bash
# Install the software, remove unnecessary deps
RUN --mount=type=secret,id=su --mount=type=secret,id=st cd /opt/spack-environment && spack env activate . && export SPACKMON_USER=$(cat /run/secrets/su) && export SPACKMON_TOKEN=$(cat /run/secrets/st) && spack install --monitor --fail-fast && spack gc -y
```
Where the id for one or more secrets corresponds to the file mounted at `/run/secrets/<name>`. So, for example, to build this container with su (spackmon user) and sv (spackmon token) defined I would export them on my host and do:
```bash
$ DOCKER_BUILDKIT=1 docker build --network="host" --secret id=st,env=SPACKMON_TOKEN --secret id=su,env=SPACKMON_USER -t spack/container .
```
And when we add `env` to the secret definition that tells the build to look for the secret with id "st" in the environment variable `SPACKMON_TOKEN` for example.
If the user is building locally with a local spack monitor, we also need to set the `--network` to be the host, otherwise you can't connect to it (a la isolation of course.)
## Singularity
Singularity doesn't have as nice an ability to clearly specify secrets, so (hoping this eventually gets implemented) what I'm doing now is providing the user instructions to write the credentials to a file, add it to the container to source, and remove when done.
## Tags
Note that the tags PR https://github.com/spack/spack/pull/23712 will need to be merged before `--monitor-tags` will actually work because I'm checking for the attribute (that doesn't exist yet):
```bash
"tags": getattr(args, "monitor_tags", None)
```
So when that PR is merged to update the argument group, it will work here, and I can either update the PR here to not check if the attribute is there (it will be) or open another one in the case this PR is already merged.
Finally, I added a bunch of documetation for how to use monitor with containerize. I say "mostly working" because I can't do a full test run with this new version until the container base is built with the updated spack (the request to the monitor server for an env install was missing so I had to add it here).
Signed-off-by: vsoch <vsoch@users.noreply.github.com>
Co-authored-by: vsoch <vsoch@users.noreply.github.com>
When running executables from build dependencies, we want to avoid that
`LD_PRELOAD` and `DYLD_INSERT_LIBRARIES` any of their shared libs build
by spack with system libraries.
this will first support uploads for spack monitor, and eventually could be
used for other kinds of spack uploads
Signed-off-by: vsoch <vsoch@users.noreply.github.com>
Co-authored-by: vsoch <vsoch@users.noreply.github.com>
* extending example for buildcaches
I was attempting to create a local build cache from a directory, and I found the
docs for both buildcaches and mirrors, but did not connect the docs that the
url variable could be the local filesystem variable. I am extending the docs for
buildcaches with an example of creating and interacting with one on the filesystem
because I suspect other users will run into this need and possibly not find what
they are looking for.
Signed-off-by: vsoch <vsoch@users.noreply.github.com>
* adding as follows to spack mirror list
Co-authored-by: Tamara Dahlgren <35777542+tldahlgren@users.noreply.github.com>
Co-authored-by: vsoch <vsoch@users.noreply.github.com>
Co-authored-by: Tamara Dahlgren <35777542+tldahlgren@users.noreply.github.com>
It is currently kind of confusing to the reader to distinguish spack buildcache install
and spack install, and it is not clear how to use a build cache once a mirror is added.
Hopefully this little big of description can help (and I hope I got it right!)
Signed-off-by: vsoch <vsoch@users.noreply.github.com>
Co-authored-by: vsoch <vsoch@users.noreply.github.com>
Use the 'version_yearlike' attribute instead of 'version' to
check if the SPACK_COMPILER_EXTRA_RPATHS should be set to include
the built-in 'libfabrics'.
When using the bare 'version', the comparison is wrong when
building with 'intel-parallel-studio', which has the version
format '<edition>.YYYY.Nupdate', due to the leading '<edition>'.
Extracting specs for the result of a solve has been factored
as a method into the asp.Result class. The method account for
virtual specs being passed as initial requests.
Minimizing compiler mismatches in the DAG and preferring newer
versions of packages are now higher priority than trying to use as
many default values as possible in multi-valued variants.
