See #25249 and https://github.com/spack/spack/pull/27159#issuecomment-958163679.
This adds `spack load --list` as an alias for `spack find --loaded`. The new command is
not as powerful as `spack find --loaded`, as you can't combine it with all the queries or
formats that `spack find` provides. However, it is more intuitively located in the command
structure in that it appears in the output of `spack load --help`.
The idea here is that people can use `spack load --list` for simple stuff but fall back to
`spack find --loaded` if they need more.
- [x] add help to `spack load --list` that references `spack find`
- [x] factor some parts of `spack find` out to be called from `spack load`
- [x] add shell integration
- [x] add shell test
- [x] update completion
- [x] update docs
* trilinos: add @13.2.0, and switch default to cxxstd=14
* trilinos: fix python dependency when using +ifpack or +ifpack2
* trilinos: add conflict for ~epetra +ml when @13.2.0:
* trilinos: keep 13.0.1 as the preferred version
* Update var/spack/repos/builtin/packages/trilinos/package.py
Co-authored-by: Seth R. Johnson <johnsonsr@ornl.gov>
* update
Co-authored-by: Seth R. Johnson <johnsonsr@ornl.gov>
This PR adds error message sentinels to the clingo solve, attached to each of the rules that could fail a solve. The unsat core is then restricted to these messages, which makes the minimization problem tractable. Errors that can only be generated by a bug in the logic program or generating code are prefaced with "Internal error" to make clear to users that something has gone wrong on the Spack side of things.
* minimize unsat cores manually
* only errors messages are choices/assumptions for performance
* pre-check for unreachable nodes
* update tests for new error message
* make clingo concretization errors show up in cdash reports fully
* clingo: make import of clingo.ast parsing routines robust to clingo version
Older `clingo` has `parse_string`; newer `clingo` has `parse_files`. Make the
code work wtih both.
* make AST access functions backward-compatible with clingo 5.4.0
Clingo AST API has changed since 5.4.0; make some functions to help us
handle both versions of the AST.
Co-authored-by: Todd Gamblin <tgamblin@llnl.gov>
This removes `-lpytrilinos` from Makefile.export.Trilinos so that C code
trying to link against a Trilinos built with PyTrilinos does not fail
due to undefined references to python routines (libpytrilinos is only
used when importing PyTrilinos in python, in which case those references
are already defined by Python).
There was already a bit of code to do something similar for C codes
importing Trilinos via a CMake mechanism, this extends that to a basic
Makefile mechanism as well. This patch also updates the comments to
remove a stale link discussing this issue, and replacing with links to
the some Trilinos issue reports related to the matter.
After #26608 I got a report about missing rpaths when building a
downstream package independently using a spack-installed toolchain
(@tmdelellis). This occurred because the spack-installed libraries were
being linked into the downstream app, but the rpaths were not being
manually added. Prior to #26608 autotools-installed libs would retain
their hard-coded path and would thus propagate their link information
into the downstream library on mac.
We could solve this problem *if* the mac linker (ld) respected
`LD_RUN_PATH` like it does on GNU systems, i.e. adding `rpath` entries
to each item in the environment variable. However on mac we would have
to manually add rpaths either using spack's compiler wrapper scripts or
manually (e.g. using `CMAKE_BUILD_RPATH` and pointing to the libraries of
all the autotools-installed spack libraries).
The easier and safer thing to do for now is to simply stop changing the
dylib IDs.
gconf depends on gettext and libintl (dep: intltool)
glibmm, gtkmm, libcanberra and cups need pkgconfig
glibmm needs libsigc++ < 2.9x(which are 3.x pre-releases)
libsigc++@:2.9 depends on m4 for the build
Co-authored-by: Massimiliano Culpo <massimiliano.culpo@gmail.com>
- add version 6.0.5
- add patch to allow fsl to use newer gcc versions
- add patch to allow fsl to use newer cuda versions
- remove constraints on gcc and cuda versions
- add filters to prevent using system headers and libraries
- clean up the installed tree
The `--generic` argument allows printing the best generic target for the
current machine. This can be quite handy when wanting to find the
generic architecture to use when building a shared software stack for
multiple machines.
This PR adds a "spack tags" command to output package tags or
(available) packages with those tags. It also ensures each package
is listed in the tag cache ONLY ONCE per tag.
glib has a few tests which have external dependencies or
try to access the X server. We cannot run those.
Co-authored-by: Massimiliano Culpo <massimiliano.culpo@gmail.com>
* ci: Enable more packages in the DVSDK CI pipeline
* doxygen: Add conflicts for gcc bugs
* dray: Add version constraints for api breakage with newer deps
5.14.2 fails with %gcc@11 with Error: 'numeric_limits' is not a class template
5.8.0 has multiple compile failures as well: Extend the conflict to those too.
- Fix also the confgigure of @5.6.3 (tested with %gcc@11)
* New versions: py-gitdb 4.0.7, 4.0.8, 4.0.9
* Update var/spack/repos/builtin/packages/py-gitdb/package.py
Co-authored-by: Adam J. Stewart <ajstewart426@gmail.com>
* Update package.py
Co-authored-by: Adam J. Stewart <ajstewart426@gmail.com>
* New versions of py-google-auth and py-google-auth-oauthlib
* Update var/spack/repos/builtin/packages/py-google-auth/package.py
Co-authored-by: Adam J. Stewart <ajstewart426@gmail.com>
Co-authored-by: Adam J. Stewart <ajstewart426@gmail.com>
* New verion: py-html5lib 1.1
* Update var/spack/repos/builtin/packages/py-html5lib/package.py
Co-authored-by: Adam J. Stewart <ajstewart426@gmail.com>
* Update var/spack/repos/builtin/packages/py-html5lib/package.py
Co-authored-by: Adam J. Stewart <ajstewart426@gmail.com>
* Update package.py
* Update package.py
* Update package.py
* Update package.py
* Update var/spack/repos/builtin/packages/py-html5lib/package.py
Co-authored-by: Adam J. Stewart <ajstewart426@gmail.com>
* Update var/spack/repos/builtin/packages/py-html5lib/package.py
Co-authored-by: Adam J. Stewart <ajstewart426@gmail.com>
Co-authored-by: Adam J. Stewart <ajstewart426@gmail.com>
* New version: py-importlib-resources 5.3.0
* Update var/spack/repos/builtin/packages/py-importlib-resources/package.py
Co-authored-by: Adam J. Stewart <ajstewart426@gmail.com>
Co-authored-by: Adam J. Stewart <ajstewart426@gmail.com>
* py-slurm-pipeline: Add 4.0.4, Fix base.py: import six for @:3
Before 4.0.0, slurm_pipeline/base.py has: `from six import string_types`
* Added depends_on('py-pytest@6.2.2:', type='build') as requested by Adam
* remove comment requested to be removed
- [x] Allow dding enumerated types and types whose default value is forbidden by the schema
- [x] Add a test for using enumerated types in the tests for `spack config add`
- [x] Make `config add` tests use the `mutable_config` fixture so they do not
affect other tests
Co-authored-by: Todd Gamblin <tgamblin@llnl.gov>
The build-time testsuite which would be run when building
with tests needs docker. Check that it exists before
attempting to execute the tests.
Co-authored-by: Massimiliano Culpo <massimiliano.culpo@gmail.com>
If you don't format `spack.yaml` correctly, `spack config edit` still fails and
you have to edit your `spack.yaml` manually.
- [x] Add some code to `_main()` to defer `ConfigFormatError` when loading the
environment, until we know what command is being run.
- [x] Make `spack config edit` use `SPACK_ENV` instead of the config scope
object to find `spack.yaml`, so it can work even if the environment is bad.
Co-authored-by: scheibelp <scheibel1@llnl.gov>
`spack config get <section>` was erroneously returning just the `spack.yaml`
for the environment.
It should return the combined configuration for that section (including
anything from `spack.yaml`), even in an environment.
- [x] reorder conditions in `cmd/config.py` to fix
`spack --debug config edit` was not working properly -- it would not do show a
stack trace for configuration errors.
- [x] Rework `_main()` and add some notes for maintainers on where things need
to go for configuration to work properly.
- [x] Move config setup to *after* command-line parsing is done.
Co-authored-by: scheibelp <scheibel1@llnl.gov>
`main()` has grown, and in some cases code that can generate errors has gotten
outside the top-level try/catch in there. This means that simple errors like
config issues give you large stack traces, which shouldn't happen without
`--debug`.
- [x] Split `main()` into `main()` for the top-level error handling and
`_main()` with all logic.
There were some loose ends left in ##26735 that cause errors when
using `SPACK_DISABLE_LOCAL_CONFIG`.
- [x] Fix hard-coded `~/.spack` references in `install_test.py` and `monitor.py`
Also, if `SPACK_DISABLE_LOCAL_CONFIG` is used, there is the issue that
`$user_config_path`, when used in configuration files, makes no sense,
because there is no user config scope.
Since we already have `$user_cache_path` in configuration files, and since there
really shouldn't be *any* data stored in a configuration scope (which is what
you'd configure in `config.yaml`/`bootstrap.yaml`/etc., this just removes
`$user_config_path`.
There will *always* be a `$user_cache_path`, as Spack needs to write files, but
we shouldn't rely on the existence of a particular configuration scope in the
Spack code, as scopes are configurable, both in number and location.
- [x] Remove `$user_config_path` substitution.
- [x] Fix reference to `$user_config_path` in `etc/spack/deaults/bootstrap.yaml`
to refer to `$user_cache_path`, which is where it was intended to be.
* Deactivate previous env before activating new one
Currently on develop you can run `spack env activate` multiple times to switch
between environments, but they leave traces, even though Spack only supports
one active environment at a time.
Currently:
```console
$ spack env create a
$ spack env create b
$ spack env activate -p a
[a] $ spack env activate -p b
[b] [a] $ spack env activate -p b
[a] [b] [a] $ spack env activate -p a
[a] [b] [c] $ echo $MANPATH | tr ":" "\n"
/path/to/environments/a/.spack-env/view/share/man
/path/to/environments/a/.spack-env/view/man
/path/to/environments/b/.spack-env/view/share/man
/path/to/environments/b/.spack-env/view/man
```
This PR fixes that:
```console
$ spack env activate -p a
[a] $ spack env activate -p b
[b] $ spack env activate -p a
[a] $ echo $MANPATH | tr ":" "\n"
/path/to/environments/a/.spack-env/view/share/man
/path/to/environments/a/.spack-env/view/man
```
Currently spack is a bit of a bad actor as a zsh plugin, and it was my
fault. The autoload and compinit should really be handled by the user,
as was made abundantly clear when I found spack was doing completion
initialization for *all* of my plugins due to a deferred setup that was
getting messed up by it.
Making this conditional took spack load time from 1.5 seconds (with
module loading disabled) to 0.029 seconds. I can actually afford to load
spack by default with this change in.
Hopefully someday we'll do proper zsh completion support, but for now
this helps a lot.
* use zsh hist expansion in place of dirname
* only run (bash)compinit if compdef/complete missing
* add zsh compiled files to .gitignore
* move changes to .in file, because spack
* Drastically improve YamlFilesystemView file removal via batching
The `remove_file` routine has to check if the file is owned by multiple packages, so it doesn't
remove necessary files. This is done by the `get_all_specs` routine, which walks the entire
package tree. With large numbers of packages on shared file systems, this can take seconds
per file tree traversal, which adds up extremely quickly. For example, a single deactivate
of a largish python package in our software stack on GPFS took approximately 40 minutes.
This patch simply replaces `remove_file` with a batch `remove_files` routine. This routine
removes a list of files rather than a single file, requiring only one traversal per batch. In
practice this means a package can be removed in seconds time, rather than potentially hours,
essentially a ~100x speedup (ignoring initial deactivation logic, which takes about 3 minutes
in our test setup).
* Fix sbang hook for non-writable files
PR #26793 seems to have broken the sbang hook for files with missing
write permissions. Installing perl now breaks with the following error:
```
==> [2021-10-28-12:09:26.832759] Error: PermissionError: [Errno 13] Permission denied: '$SPACK/opt/spack/linux-fedora34-zen2/gcc-11.2.1/perl-5.34.0-afuweplnhphcojcowsc2mb5ngncmczk4/bin/cpanm'
```
Temporarily add write permissions to the original file so it can be
overwritten with the patched one.
And test that file permissions are preserved in sbang even for non-writable files
Co-authored-by: Harmen Stoppels <harmenstoppels@gmail.com>
When relocating a binary distribution, Spack only checks files to see
if they are a link that needs to be relocated. Directories can be
such links as well, however, and need to undergo the same checks
and potential relocation.
`spack list` tests are not using mock packages for some reason, and many
are marked as potentially slow. This isn't really necessary; we don't need
6,000 packages to test the command.
- [x] update tests to use `mock_packages` fixture
- [x] remove `maybeslow` annotations
Currently Spack reads full files containing shebangs to memory as
strings, meaning Spack would have to guess their encoding. Currently
Spack has a fixed guess of UTF-8.
This is unnecessary, since e.g. the Linux kernel does not assume an
encoding on paths at all, it's just bytes and some delimiters on the
byte level.
This commit does the following:
1. Shebangs are treated as bytes, so that e.g. latin1 encoded files do
not throw UnicodeEncoding errors, and adds a test for this.
2. No more bytes than necessary are read to memory, we only have to read
until the first newline, and from there on we an copy the file byte by
bytes instead of decoding and re-encoding text.
3. We cap the number of bytes read to 4096, if no newline is found
before that, we don't attempt to patch it.
4. Add support for luajit too.
This should make Spack both more efficient and usable for non-UTF8
files.
Spack's `system` and `user` scopes provide ways for administrators and
users to set global defaults for all Spack instances, but for use cases
where one wants a clean Spack installation, these scopes can be undesirable.
For example, users may want to opt out of global system configuration, or
they may want to ignore their own home directory settings when running in
a continuous integration environment.
Spack also, by default, keeps various caches and user data in `~/.spack`,
but users may want to override these locations.
Spack provides three environment variables that allow you to override or
opt out of configuration locations:
* `SPACK_USER_CONFIG_PATH`: Override the path to use for the
`user` (`~/.spack`) scope.
* `SPACK_SYSTEM_CONFIG_PATH`: Override the path to use for the
`system` (`/etc/spack`) scope.
* `SPACK_DISABLE_LOCAL_CONFIG`: set this environment variable to completely
disable *both* the system and user configuration directories. Spack will
only consider its own defaults and `site` configuration locations.
And one that allows you to move the default cache location:
* `SPACK_USER_CACHE_PATH`: Override the default path to use for user data
(misc_cache, tests, reports, etc.)
With these settings, if you want to isolate Spack in a CI environment, you can do this:
export SPACK_DISABLE_LOCAL_CONFIG=true
export SPACK_USER_CACHE_PATH=/tmp/spack
This is a stop-gap approach until we have figured out how to deal with
the system and user config scopes more generally, as there are plans to
potentially / eventually get rid of them.
**User config**
Spack is a bit of a pain when you have:
- a shared $HOME folder across different systems.
- multiple Spack versions on the same system.
**System config**
- On shared systems with a versioned programming environment / toolkit,
system administrators want to provide config for each version (e.g.
21.09, 21.10) of the programming environment, and the user Spack
instance should be able to pick this up without a steep learning
curve.
- On shared systems the user should be able to opt out of the
hard-coded config scope in /etc/spack, since it may be incompatible
with their particular instance. Currently Spack can only opt out of all
config scopes through overrides with `"config:":`, `"packages:":`, but that
also drops the defaults config, which would have to be repeated, which
is undesirable, especially the lengthy packages.yaml.
An example use case is: having config in this folder:
```
/path/to/programming/environment/{version}/{compilers,packages}.yaml
```
and have `module load spack-system-config` set the variable
```
SPACK_SYSTEM_CONFIG_PATH=/path/to/programming/environment/{version}
```
where the user no longer has to worry about what `{version}` they are
on.
**Continuous integration**
Finally, there is the use case of continuous integration, which may
clone an arbitrary Spack version, which optimally should not pick up
system or user config from the previous run (like may happen in
classical bare metal non-containerized filesystem side effect ridden
jenkins pipelines). In fact this is very similar to how spack itself
tries to avoid picking up system dependencies during builds...
**But environments solve this?**
- You could do `include`s in environment files to get similar behavior
to the spack_system_config_path example, but environments require you
to:
1) require paths to individual config files, not directories.
2) fail if the listed config file does not exist
- They allow you to override config scopes, but this is generally too
rigurous, as it requires you to repeat the default config, in
particular packages.yaml, and just defies the point of layered config.
Co-authored-by: Tom Scogland <tscogland@llnl.gov>
Co-authored-by: Tim Fuller <tjfulle@sandia.gov>
Co-authored-by: Steve Leak <sleak@lbl.gov>
Co-authored-by: Todd Gamblin <tgamblin@llnl.gov>
Any spec satisfying a default will be symlinked to `default`
If multiple specs have modulefiles in the same directory and satisfy
configured module defaults, then whichever was written last will be
default.
Use of `-R` flag to CTest command causes "empty-14" test to run,
by matching "empty", before the empty-14 target is built.
Patch CTest command in buildscript to match name exactly.
* [geant4] depends_on vecgeom@1.1.8:1.1 range
While previous versions were unclear, the [geant4.10.7 release notes](https://geant4-data.web.cern.ch/ReleaseNotes/ReleaseNotes4.10.7.html) indicate that vecgeom@1.1.8 is a minimum required version, not an exact required version ("Set VecGeom-1.1.8 as minimum required version for optional build with VecGeom."). This will allow some more freedom on the concretizer solutions while allowing geant4 to take advantage of bugfixes and improvements in vecgeom.
* [vecgeom] new version 1.1.17
* For py-torch: Also update dependencies: many version constraints
with an upper bound of @1.9 are now open (e.g. `@1.8.0:1.9` is
converted to `@1.8.0:`).
* For py-torchvision: Also add 0.11.0 and update ^pil constraint
to avoid building with 8.3.0
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
* [pkg][new version] Provide eospac@6.5.0 and mark it as default.
* Merge in changes found in #21629
* Mark all alpha/beta versions as deprecated.
- Addresses @sethrj's recommendation
- Also add a note indicated why these versions are marked this way.
1. Currently it prints not just the spec name, but the dependencies +
their variants + their compilers + their architectures + ...
2. It's clear from the context what spec the message applies to, so,
let's not print the spec at all.
These three rules in `concretize.lp` are overly complex:
```prolog
:- not provider(Package, Virtual),
provides_virtual(Package, Virtual),
virtual_node(Virtual).
```
```prolog
:- provides_virtual(Package, V1), provides_virtual(Package, V2), V1 != V2,
provider(Package, V1), not provider(Package, V2),
virtual_node(V1), virtual_node(V2).
```
```prolog
provider(Package, Virtual) :- root(Package), provides_virtual(Package, Virtual).
```
and they can be simplified to just:
```prolog
provider(Package, Virtual) :- node(Package), provides_virtual(Package, Virtual).
```
- [x] simplify virtual rules to just one implication
- [x] rename `provides_virtual` to `virtual_condition_holds`
fixes#26866
This semantics fits with the way Spack currently treats providers of
virtual dependencies. It needs to be revisited when #15569 is reworked
with a new syntax.
* gcc: support runtime ability to not install spack rpaths
Fixes#26582 .
* gcc: Fix malformed specs file and add docs
The updated docs point out that the spack-modified GCC does *not*
follow the usual behavior of LD_RUN_PATH!
* gcc: fix bad rpath on macOS
This bug has been around since the beginning of the GCC package file:
the rpath command it generates for macOS writes a single (invalid)
rpath entry.
* gcc: only write rpaths for directories with shared libraries
The original lib64+lib was just a hack for "in case either has one" but
it's easy to tell whether either has libraries that can be directly
referenced.
* 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+.
* Update py-aiohttp to 3.7.4 and py-chartdet to 4.0
* Changes from review
* Update package.py
* Update var/spack/repos/builtin/packages/py-chardet/package.py
Co-authored-by: Adam J. Stewart <ajstewart426@gmail.com>
Co-authored-by: Adam J. Stewart <ajstewart426@gmail.com>
The OS should only interpret shebangs, if a file is executable.
Thus, there should be no need to modify files where no execute bit is set.
This solves issues that are e.g. encountered while packaging software as
COVISE (https://github.com/hlrs-vis/covise), which includes example data
in Tecplot format. The sbang post-install hook is applied to every installed
file that starts with the two characters #!, but this fails on the binary Tecplot
files, as they happen to start with #!TDV. Decoding them with UTF-8 fails
and an exception is thrown during post_install.
Co-authored-by: Martin Aumüller <aumuell@reserv.at>
This commit contains changes to support Google Cloud Storage
buckets as mirrors, meant for hosting Spack build-caches. This
feature is beneficial for folks that are running infrastructure on
Google Cloud Platform. On public cloud systems, resources are
ephemeral and in many cases, installing compilers, MPI flavors,
and user packages from scratch takes up considerable time.
Giving users the ability to host a Spack mirror that can store build
caches in GCS buckets offers a clean solution for reducing
application rebuilds for Google Cloud infrastructure.
Co-authored-by: Joe Schoonover <joe@fluidnumerics.com>
* scr/veloc: component releases
Update the ECP-VeloC component packages in preparation for an
upcoming scr@3.0rc2 release.
All
- Add new release versions
- Add new `shared` variant for all components
- Add zlib link dependency to packages that were missing it
- Add maintainers
- Use self.define and self.define_from_variant to clean up cmake_args
axl
- Add independent vendor async support variants
rankstr
- Update older version sha that fails checksum on install
* Fix scr build error
Lock dependencies for scr@3.0rc1 to the versions released at the same
time.
* py-neurokit2: add 0.1.4.1
* Update var/spack/repos/builtin/packages/py-neurokit2/package.py
Co-authored-by: Adam J. Stewart <ajstewart426@gmail.com>
Co-authored-by: Adam J. Stewart <ajstewart426@gmail.com>
* Update cray architecture detection for milan
Update the cray architecture module table with x86-milan -> zen3
Make cray architecture more robust to back off from frontend
architecture to a recent ancestor if necessary. This should make
future cray updates less paingful for users.
Co-authored-by: Gregory Becker <becker33.llnl.gov>
Co-authored-by: Todd Gamblin <gamblin2@llnl.gov>
1. Don't use 16 digits of precision for the seconds, round to 2 digits after the comma
2. Don't print if we don't concretize (i.e. `spack concretize` without `-f` doesn't have to tell me it did nothing in `0.00` seconds)
* Speed-up environment concretization with a process pool
We can exploit the fact that the environment is concretized
separately and use a pool of processes to concretize it.
* Add module spack.util.parallel
Module includes `pool` and `parallel_map` abstractions,
along with implementation details for both.
* Add a new hash type to pass specs across processes
* Add tty msg with concretization time
We use POSIX `patch` to apply patches to files when building, but
`patch` by default prompts the user when it looks like a patch
has already been applied. This means that:
1. If a patch lands in upstream and we don't disable it
in a package, the build will start failing.
2. `spack develop` builds (which keep the stage around) will
fail the second time you try to use them.
To avoid that, we can run `patch` with `-N` (also called
`--forward`, but the long option is not in POSIX). `-N` causes
`patch` to just ignore patches that have already been applied.
This *almost* makes `patch` idempotent, except that it returns 1
when it detects already applied patches with `-N`, so we have to
look at the output of the command to see if it's safe to ignore
the error.
- [x] Remove non-POSIX `-s` option from `patch` call
- [x] Add `-N` option to `patch`
- [x] Ignore error status when `patch` returns 1 due to `-N`
- [x] Add tests for applying a patch twice and applying a bad patch
- [x] Tweak `spack.util.executable` so that it saves the error that
*would have been* raised with `fail_on_error=True`. This lets
us easily re-raise it.
Co-authored-by: Greg Becker <becker33@llnl.gov>
* py-magic: delete redundant package
This package is actually named py-python-magic (since the project itself
is "python-magic").
* New package: libmagic
* Py-python-magic: add required runtime dependency on libmagic and new version
* Py-filemagic: add required runtime dependency
* py-magic: restore and mark as redundant
This reverts commit 4cab7fb69e.
* file: add implicit dependencies and static variant
Replaces redundant libmagic that I added. Compression headers were previously
being picked up from the system.
* Fix py-python-magic dependency
* Update python version requirements
* relocate: call install_name_tool less
* zstd: fix race condition
Multiple times on my mac, trying to install in parallel led to failures
from multiple tasks trying to simultaneously create `$PREFIX/lib`.
* PackageMeta: simplify callback flush
* Relocate: use spack.platforms instead of platform
* Relocate: code improvements
* fix zstd
* Automatically fix rpaths for packages on macOS
* Only change library IDs when the path is already in the rpath
This restores the hardcoded library path for GCC.
* Delete nonexistent rpaths and add more testing
* Relocate: Allow @executable_path and @loader_path
* downgrade_docutils_version
* invalid version
* Update requirements.txt
* Improve spelling and shorten the reference link
* Update spack.yaml
* update version requirement
* update version to maximum of 0.16
Co-authored-by: bernhardkaindl <43588962+bernhardkaindl@users.noreply.github.com>
* py-jupytext: add new package
* Apply suggestions from code review
Co-authored-by: Adam J. Stewart <ajstewart426@gmail.com>
* update jupytext dependencies
* Apply suggestions from code review
Co-authored-by: Adam J. Stewart <ajstewart426@gmail.com>
* py-jupytext: remove py-jupyerlab dependency
Co-authored-by: Adam J. Stewart <ajstewart426@gmail.com>
* py-gevent: add version 1.5
* py-gevent: update dependencies for v1.5.0
* Apply suggestions from code review
Co-authored-by: Adam J. Stewart <ajstewart426@gmail.com>
* Update var/spack/repos/builtin/packages/py-gevent/package.py
Co-authored-by: Adam J. Stewart <ajstewart426@gmail.com>
Co-authored-by: Adam J. Stewart <ajstewart426@gmail.com>
* phist: Prefer 1.9.5 (1.9.6 uses mpi_f08, but not available in CI)
* phist: remove dupe of 1.9.5, missing preferred=True
Also, for 1.9.6, patch the (most, one does not work) tests to use
Currently Spack keeps track of the origin in the code of any
modification to the environment variables. This is very slow
and enabled unconditionally even in code paths where the
origin of the modification is never queried.
The only place where we inspect the origins of environment
modifications is before we start a build, If there's an override
of the type `e.set(...)` after incremental changes like
`e.append_path(..)`, which is a "suspicious" change.
This is very rare though.
If an override like this ever happens, it might mean a package is
broken. If that leads to build errors, we can just ask the user to run
`spack -d install ...` and check the warnings issued by Spack to find
the origins of the problem.
UPP and ncep-post are the same package, so this PR
removes the duplication.
ncep-post was originally named after the upstream repo
that now changed its name to UPP.
It can be frustrating to successfully run `spack test run --alias <name>` only to find you cannot get the results because you already use `<name>` in some previous stand-alone test execution. This PR prevents that from happening.
Primary fix:
Due to a typo in a version range, overlapping PR merges resulted
in a build failure of the latest version:
Don't attempt to remove a non-existing file for version 1.9.6.
Secondary fixes:
update_tpetra_gotypes.patch was mentioned twice, and the version
range has to exclude @1.4.2, to which it cannot be applied.
Add depend_on() py-pytest, py-numpy and pkgconfig with type='test'
@:1.9.0 fail with 'Rank mismatch with gfortran@10:, add a conflicts().
raise InstallError('~mpi not possible with kernel_lib=builtin!')
when applicable.
Fixes for spack install --test=root phist:
mpiexec -n12 puts a lot of stress on a pod and gets stuck in a loop
very often: Reduce the mpiexec procs and the number of threads.
Remove @run_after('build') @on_package_attributes(run_tests=True):
from 'def check()': fixes it from getting called twice
The build script of 'make test_install' for the installcheck expects
the examples to be copied to self.stage.path: Provide them.
* updating the recipe for betterment
* addressing the suggesions received from reviewers
* adding package helper macros
Co-authored-by: mohan002 <mohbabul@amd.com>
Using the Spec.constrain method doesn't work since it might
trigger a repository lookup which could break our directives
and triggers a circular import error.
To fix that we introduce a function to merge abstract anonymous
specs, based only on package names, which does not perform any
lookup in the repository.
Add missing pkgconfig to openslide and its dep perl-alien-libxml2.
Fix shared-mime-info to be a runtime dependency of gdk-pixbuf,
Otherwise, configure cannot detect use gdk-pixbuf without error.
* SEACAS: add a Faodel variant
* Use safer CMake and variant packages instead of directly adding parameters
Add a "+faodel ~mpi" dependency to balance "+faodel +mpi"
The buildcache is now extracted in a temporary folder within the current store,
moved to its final place and relocated.
"spack clean -s" has been extended to also clean the temporary extraction directory.
Add hardlinks with absolute paths for libraries in the corge, garply and quux packages
to detect incorrect handling of hardlinks in tests.
Problem: Flux expects the `FLUX_PMI_LIBRARY_PATH` to point directly at
the `libpmi.so` installed by Flux. When the env var is unset,
prepending to it results in this behavior. In the rare case that the
env var is already set, then the spack `libpmi.so` gets prepended with a
`:`, which Flux then attempts to interpret as a single path.
Solution: don't prepend to the path, instead set the path to point to
the `libpmi.so` (which will be undone when Flux is unloaded).
* flux-core: remove deprecated environment variables
The earliest checksummed version in this package is 0.15.0. As of
0.12.0, wreck (and its associated paths) no longer exist in Flux. As of
0.13.0, the `FLUX_RCX_PATH` variables are no longer used. So clean up
these env vars from the `setup_run_environment`.
gromacs@2018:2020.6 is fixed to build with gcc@11.2.0
by adding #include <limits> to a few header files.
Thanks to Maciej Wójcik <w8jcik@gmail.com> for testing versions.
The `find` command was missing for the examples forcing colorized output. Without this (or another suitable) command, spack produces output that is not using any color. Thus, without the `find` command one does not see any difference between forced colorized and non-colorized output.
There was a bug in 2.36.* of missing Makefile dependencies. The
previous workaround was to require 2.36 to be built serially. This is
now fixed upstream in 2.37 and this PR adds the patch to restore
parallel make to 2.36.
* py-niworkflows: add new package
* Update var/spack/repos/builtin/packages/py-niworkflows/package.py
Co-authored-by: Adam J. Stewart <ajstewart426@gmail.com>
* remove unnecessary comment
Co-authored-by: Adam J. Stewart <ajstewart426@gmail.com>
* py-nistats: add new package
* Update var/spack/repos/builtin/packages/py-nistats/package.py
Co-authored-by: Adam J. Stewart <ajstewart426@gmail.com>
* remove `conflicts`
* remove test dependencies
Co-authored-by: Adam J. Stewart <ajstewart426@gmail.com>
when deployed on kubernetes, the server sends back permanent redirect responses.
This is elegantly handled by the requests library, but not urllib that we have
to use here, so I have to manually handle it by parsing the exception to
get the Location header, and then retrying the request there.
Signed-off-by: vsoch <vsoch@users.noreply.github.com>
* packages/phist, re #26002: force phist to use MPI compiler wrappers (copied from trilinos package)
* packages/phist re #26002, use cmake-provded FindMPI module only
* packages/phist source code formatting
* packages/phist: set MPI_HOME rather than MPI_BASE_DIR, thanks @sethri.
* phist: delete own FindMPI.cmake for older versions (rather than patching it away)
* packages/phist: remove blank line
* phist: adjust sorting of imports
* phist: change order of imports
The ASP-based solver maximizes the number of values in multi-valued
variants (if other higher order constraints are met), to avoid cases
where only a subset of the values that have been specified on the
command line or imposed by another constraint are selected.
Here we swap the priority of this optimization target with the
selection of the default providers, to avoid unexpected results
like the one in #26598
Seems like https://bugs.python.org/issue29699 is relevant. Better to
just ignore errors when removing them tmpdir. The OS will remove it
anyways.
Errors are happening randomly from tests that are using this fixture.
TL;DR: there are matching groups trying to match 1 or more occurrences of
something. We don't use the matching group. Therefore it's sufficient to test
for 1 occurrence. This reduce quadratic complexity to linear time.
---
When parsing logs of an mpich build, I'm getting a 4 minute (!!) wait
with 16 threads for regexes to run:
```
In [1]: %time p.parse("mpich.log")
Wall time: 4min 14s
```
That's really unacceptably slow...
After some digging, it seems a few regexes tend to have `O(n^2)` scaling
where `n` is the string / log line length. I don't think they *necessarily*
should scale like that, but it seems that way. The common pattern is this
```
([^:]+): error
```
which matches `: error` literally, and then one or more non-colons before that. So
for a log line like this:
```
abcdefghijklmnopqrstuvwxyz: error etc etc
```
Any of these are potential group matches when using `search` in Python:
```
abcdefghijklmnopqrstuvwxyz
bcdefghijklmnopqrstuvwxyz
cdefghijklmnopqrstuvwxyz
⋮
yz
z
```
but clearly the capture group should return the longest match.
My hypothesis is that Python has a very bad implementation of `search`
that somehow considers all of these, even though it can be implemented
in linear time by scanning for `: error` first, and then greedily expanding
the longest possible `[^:]+` match to the left. If Python indeed considers
all possible matches, then with `n` matches of length `1 .. n` you
see the `O(n^2)` slowness (i verified this by replacing + with {1,k}
and doubling `k`, it doubles the execution time indeed).
This PR fixes this by removing the `+`, so effectively changing the
O(n^2) into a O(n) worst case.
The reason we are fine with dropping `+` is that we don't use the
capture group anywhere, so, we just ensure `:: error` is not a match
but `x: error` is.
After going from O(n^2) to O(n), the 15MB mpich build log is parsed
in `1.288s`, so about 200x faster.
Just to be sure I've also updated `^CMake Error.*:` to `^CMake Error`,
so that it does not match with all the possible `:`'s in the line.
Another option is to use `.*?` there to make it quit scanning as soon as
possible, but what line that starts with `CMake Error` that does not have
a colon is really a false positive...
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.
* kahip: update to cmake for v3.11, retain scons for older versions
* kahip: update build system to cmake for v3.11, retain SCons for older versions
* address PR comments and add maintainer
* address PR comments - correct version to 2.10, add deprecated and url, and remove scons version
- Do not store the full list of environment variables in
<prefix>/.spack/spack-build-env.txt because it may contain user secrets.
- Only store environment variable modifications upon installation.
- Variables like PATH may still contain user and system paths to make
spack-build-env.txt sourceable. Variables containing paths are
modified through prepending/appending, and if we don't apply these
to the current environment variable, we end up with statements like
`export PATH=/path/to/spack/bin` with system paths missing, meaning
no system binaries are in the path, which is a bad user experience.
- Do write the full environment to spack-build-env.txt in the staging dir,
but ensure it is readonly for the current user, to make it a bit safer
on shared systems.
Creates an environment in a temporary directory and activates it, which
is useful for a quick ephemeral environment:
```
$ spack env activate -p --temp
[spack-1a203lyg] $ spack add zlib
==> Adding zlib to environment /tmp/spack-1a203lyg
==> Updating view at /tmp/spack-1a203lyg/.spack-env/view
```
PR #25904 moved the `--with-tcl` option to only older versions. However,
without this option, the build breaks:
```
checking for Tcl configuration... configure: error: Can't find Tcl configuration definitions. Use --with-tcl to specify a directory containing tclConfig.sh
```
The DB should be what is trusted for certain operations.
If it is not present when read we should assume the
corresponding store is empty, rather than trying a
write operation during a read.
* Add a unit test
* Document what needs to be there in tests
* py-twisted,py-storm: dep on zope.interface, bump storm version
py-twisted and py-storm's import tests need zope.interface.
py-storm: Use pypi and add version 0.25. It didn't change reqs.
zope.infterface@4.5.0 imports removed Feature: Use setuptools@:45
Co-authored-by: Adam J. Stewart <ajstewart426@gmail.com>
* py-storm: all deps updated with type=('build', 'run')
Co-authored-by: Adam J. Stewart <ajstewart426@gmail.com>
* py-bcrypt, py-bleach, py-decorator, py-pygdal: fix python dependency
* Update var/spack/repos/builtin/packages/py-bleach/package.py
Co-authored-by: Adam J. Stewart <ajstewart426@gmail.com>
Co-authored-by: Adam J. Stewart <ajstewart426@gmail.com>
* py-matplotlib: fix 3.4.3
* Update var/spack/repos/builtin/packages/py-matplotlib/package.py
Co-authored-by: Adam J. Stewart <ajstewart426@gmail.com>
Co-authored-by: Adam J. Stewart <ajstewart426@gmail.com>
* py-keras-preprocessing: Add missing deps: six@1.9.0: and numpy@1.9.1:
Add deps: pip download --no-binary :all: keras-preprocessing==1.1.2
Collecting numpy>=1.9.1
Installing build dependencies: started
Collecting six>=1.9.0
* Update var/spack/repos/builtin/packages/py-keras-preprocessing/package.py
Co-authored-by: Adam J. Stewart <ajstewart426@gmail.com>
Co-authored-by: Adam J. Stewart <ajstewart426@gmail.com>
When a symlink to a license file exists but is broken, the license symlink post-install hook fails
because os.path.exists() checks the existence of the target not the symlink itself.
os.path.lexists() is the proper function to use.
* visit: add an external find function (determine_version)
* visit: correct too long comment line
* visit: forgot to set executables
* visit: external find uses signgle dash version
* visit: found as external asking visit version
* fish: adding version 3.3.1
* adding maintainer
* Update var/spack/repos/builtin/packages/fish/package.py
Co-authored-by: Adam J. Stewart <ajstewart426@gmail.com>
Co-authored-by: Adam J. Stewart <ajstewart426@gmail.com>
The most recent release of numactl (2.0.14) fails to build on riscv64
because of a missing "-latomic". This patch from upstream resolves this
issue. It can be dropped once the next version of numactl is released.
Environments push/pop scopes upon activation. If some lazily
evaluated value depending on the current configuration was
computed and cached before the scopes are pushed / popped
there will be an inconsistency in the current state.
This PR fixes the issue for stores, but it would be better
to move away from global state.
The `spack.architecture` module contains an `Arch` class that is very similar to `spack.spec.ArchSpec` but points to platform, operating system and target objects rather than "names". There's a TODO in the class since 2016:
abb0f6e27c/lib/spack/spack/architecture.py (L70-L75)
and this PR basically addresses that. Since there are just a few places where the `Arch` class was used, here we query the relevant platform objects where they are needed directly from `spack.platforms`. This permits to clean the code from vestigial logic.
Modifications:
- [x] Remove the `spack.architecture` module and replace its use by `spack.platforms`
- [x] Remove unneeded tests
* Use gnuconfig package for config file replacement for RISC-V.
This extends the changes in #26035 to handle RISC-V. Before this change,
many packages fail to configure on riscv64 due to config.guess being too
old to know about RISC-V. This is seen out of the box when clingo fails
to build from source due to pkgconfig failing to configure, throwing
error: "configure: error: cannot guess build type; you must specify one".
* Add riscv64 architecture
* Update vendored archspec from upstream project.
These archspec updates include changes needed to support riscv64.
* Update archspec's __init__.py to reflect the commit hash of archspec being used.
Cherry-picked from #25564 so this is standalone.
With this PR we can activate an environment in Spack itself, without computing changes to environment variables only necessary for "shell aware" env activation.
1. Activating an environment:
```python
spack.environment.activate(Environment(xyz)) -> None
```
this basically just sets `_active_environment` and modifies some config scopes.
2. Activating an environment **and** getting environment variable modifications for the shell:
```python
spack.environment.shell.activate(Environment(xyz)) -> EnvironmentModifications
```
This should make it easier/faster to do unit tests and scripting with spack, without the cli interface.
* Isolate bootstrap configuration from user configuration
* Search for build dependencies automatically if bootstrapping from sources
The bootstrapping logic will search for build dependencies
automatically if bootstrapping anything form sources. Any
external spec, if found, is written in a scope that is specific
to bootstrapping.
* Don't clean the bootstrap store with "spack clean -a"
* Copy bootstrap.yaml and config.yaml in the bootstrap area
Reverting from CMake to Make install caused
`-install_path=/usr/local/lib/libzstd.1.dylib` to be hardcoded into the
zstd. Now we explicitly pass the PREFIX into the build command so that
the correct spack install path is saved.
Fixes#26438 and also the ROOT install issue I had :)
- [x] Our wrapper error messages are sometimes hard to differentiate from other build
output, so prefix all errors from `die()` with '[spack cc] ERROR:'
- [x] The error we raise when running, say, `fc` without a Fortran compiler was not
clear enough. Clarify the message and the comment.
This converts everything in cc to POSIX sh, except for the parts currently
handled with bash arrays. Tests are still passing.
This version tries to be as straightforward as possible. Specifically, most conversions
are kept simple -- convert ifs to ifs, handle indirect expansion the way we do in
`setup-env.sh`, only mess with the logic in `cc`, and don't mess with the python code at
all.
The big refactor is for arrays. We can't rely on bash's nice arrays and be ignorant of
separators anymore. So:
1. To avoid complicated separator logic, there are three types of lists. They are:
* `$lsep`-separated lists, which end with `_list`. `lsep` is customizable, but we
picked `^G` (alarm bell) for `$lsep` because it's ASCII and it's unlikely that it
would actually appear in any arguments. If we need to get fancier (and I will lose
faith in the world if we do) then we could consider XON or XOFF.
* `:`-separated directory lists, which end with `_dirs`, `_DIRS`, `PATH`, or `PATHS`
* Whitespace-separated lists (like flags), which can have any other name.
Whitespace and colon-separated lists come with the territory with PATHs from env
vars and lists of flags. `^G` separated lists are what we use for most internal
variables, b/c it's more likely to work.
2. To avoid subshells, use a bunch of functions that do dirty `eval` stuff instead. This
adds 3 functions to deal with lists:
* `append LISTNAME ELEMENT [SEP]` will put `ELEMENT` at the end of the list called
`LISTNAME`. You can optionally say what separator you expect to use. Note that we
are taking advantage of everything being global and passing lists by name.
* `prepend LISTNAME ELEMENT [SEP]` like append, but puts `ELEMENT` at the start of
`LISTNAME`
* `extend LISTNAME1 LISTNAME2 [PREFIX]` appends everything in LISTNAME2 to
LISTNAME1, and optionally prepends `PREFIX` to every element (this is useful for
things like `-I`, `-isystem `, etc.
* `preextend LISTNAME1 LISTNAME2 [PREFIX]` prepends everything in LISTNAME2 to
LISTNAME1 in order, and optionally prepends `PREFIX` to every element.
The routines determine the separator for each argument by its name, so we don't have to
pass around separators everywhere. Amazingly, as long as you do not expand variables'
values within an `eval` environment, you can do all this and still preserve quoting.
When iterating over lists, the user of this API still has to set and unset `IFS`
properly.
We ended up having to ignore shellcheck SC2034 (unused variable), because using evals
all over the place means that shellcheck doesn't notice that our list variables are
actually used.
So far this is looking pretty good. I took the most complex unit test I could find
(which runs a sample link line) and ran the same command line 200 times in a shell
script. Times are roughly as follows:
For this invocation:
```console
$ bash -c 'time (for i in `seq 1 200`; do ~/test_cc.sh > /dev/null; done)'
```
I get the following performance numbers (the listed shells are what I put in `cc`'s
shebang):
**Original**
* Old version of `cc` with arrays and `bash v3.2.57` (macOS builtin): `4.462s` (`.022s` / call)
* Old version of `cc` with arrays and `bash v5.1.8` (Homebrew): `3.267s` (`.016s` / call)
**Using many subshells (#26408)**
* with `bash v3.2.57`: `25.302s` (`.127s` / call)
* with `bash v5.1.8`: `27.801s` (`.139s` / call)
* with `dash`: `15.302s` (`.077s` / call)
This version didn't seem to work with zsh.
**This PR (no subshells)**
* with `bash v3.2.57`: `4.973s` (`.025s` / call)
* with `bash v5.1.8`: `4.984s` (`.025s` / call)
* with `zsh`: `2.995s` (`.015s` / call)
* with `dash`: `1.890s` (`.0095s` / call)
Dash, with the new posix design, is easily the winner.
So there are several interesting things to note here:
1. Running the posix version in `bash` is slower than using `bash` arrays. That is to be
expected because it's doing a bunch of string processing where it likely did not have
to before, at least in `bash`.
2. `zsh`, at least on macOS, is significantly faster than the ancient `bash` they ship
with the system. Using `zsh` with the new version also makes the posix wrappers
faster than `develop`. So it's worth preferring `zsh` if we have it. I suppose we
should also try this with newer `bash` on Linux.
3. `bash v5.1.8` seems to be significantly faster than the old system `bash v3.2.57` for
arrays. For straight POSIX stuff, it's a little slower. It did not seem to matter
whether `--posix` was used.
4. `dash` is way faster than `bash` or `zsh`, so the real payoff just comes from being
able to use it. I am not sure if that is mostly startup time, but it's significant.
`dash` is ~2.4x faster than the original `bash` with arrays.
So, doing a lot of string stuff is slower than arrays, but converting to posix seems
worth it to be able to exploit `dash`.
- [x] Convert all but array-related portions to sh
- [x] Fix basic shellcheck issues.
- [x] Convert arrays to use a few convenience functions: `append` and `extend`
- [x] Get `cc` tests passing.
- [x] Add `cc` tests where needed passing.
- [x] Benchmarking.
Co-authored-by: Tom Scogland <scogland1@llnl.gov>
Co-authored-by: Danny McClanahan <1305167+cosmicexplorer@users.noreply.github.com>
* Add version 0.12.1
* Add variant to build with C++11 standard
build with c++11 standard requires boost threads, and needs explicit setting of
CMAKE_CXX_STANDARD
* intel-tbb: install pkgconfig file
* intel-tbb: install pkgconfig file when @:2021.2.0
* intel-tbb: add blank line
* intel-tbb: fix library name to refer
* intel-tbb: fix library name to refer again
* intel-tbb: use self.prefix.lib.pkgconfig
From the gnupg.org website:
> GnuPG 1.4 is the old, single binary version which still support the
> unsafe PGP-2 keys. However, it lacks many modern features and will
> receive only important updates.
I'm starting to appreciate gpg1 more, because it is relocatable (gng2
has hard-coded paths to gpg-agent and other tools) and it does not
require gpg-agent at all.
* graph500: added option -fcommon for gcc@10.2:, otherwise failed to build with "multiple definition of `column'"
* graph500: moved setting cflag to flag_handler
Work around issues in older hdf5 build and overzealous build flags:
```
>> 1420 /var/folders/j4/fznvdyhx4875h6fhkqjn2kdr4jvyqd/T/9te/spack-stage/spack-stage-hdf5-1.10.4-feyl6tz6hpx5kl7m33avpuacwje2ubul/spack-src/src/H5Odeprec.c:141:8: error: implicit decl
aration of function 'H5CX_set_apl' is invalid in C99 [-Werror,-Wimplicit-function-declaration]
```
The older patch does not apply so the build ends up failing:
```
1539 In file included from /private/var/folders/fy/x2xtwh1n7fn0_0q2kk29xkv9vvmbqb/T/s3j/spack-stage/spack-stage-python-3.8.11
-6jyb6sxztfs6fw26xdbc3ktmbtut3ypr/spack-src/Modules/_tkinter.c:48:
>> 1540 /Applications/Xcode.app/Contents/Developer/Platforms/MacOSX.platform/Developer/SDKs/MacOSX.sdk/usr/include/tk.h:86:11: f
atal error: 'X11/Xlib.h' file not found
1541 # include <X11/Xlib.h>
1542 ^~~~~~~~~~~~
1543 1 error generated.
```
* Explicitly set path to Kokkos for ArborX testing
* Improve formatting
* Update var/spack/repos/builtin/packages/arborx/package.py
Co-authored-by: Seth R. Johnson <johnsonsr@ornl.gov>
* Remove blank line
Co-authored-by: Seth R. Johnson <johnsonsr@ornl.gov>
* -fallow-argument-mismatch flag added when compiling with GCC to avoid a compilation error when using a GCC version > 10.0.
Co-authored-by: Haz99 <jsalamerosanz@gmail.com>
* Filtered every occurrence of "!$OMP SIMD SAFELEN(LVEC2)" when compiling with nvhcp to avoid a compilation error.
Co-authored-by: Haz99 <jsalamerosanz@gmail.com>
* Line with more than 80 characters split into multiple lines.
Co-authored-by: Haz99 <jsalamerosanz@gmail.com>
When using modules for compiler (and/or external package), if a
package's `setup_[dependent_]build_environment` sets `PYTHONHOME`, it
can influence the python subprocess executed to gather module
information.
The error seen was:
```
json.decoder.JSONDecodeError: Expecting value: line 1 column 1 (char 0)
```
But the actual hidden error happened in the `python -c 'import
json...'` subprocess, which made it return an empty string as json:
```
ModuleNotFoundError: No module named 'encodings'
```
This fix uses `python -E` to ignore `PYTHONHOME` and
`PYTHONPATH`. Should be safe here because the python subprocess code
only use packages built-in python.
The python subprocess in `environment.py` was also patched to be safe
and consistent.
* Remove redundant preserve environment code in build environment
* Remove fix for a bug in a module
See https://github.com/spack/spack/issues/3153#issuecomment-280460041,
this shouldn't be part of core spack.
* Don't module unload cray-libsci on all platforms
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).
* Remove vestigial code to be compatible with Spack v0.9.X
* ArchSpec: reworked __repr__ to be more adherent to common Python idioms
* ArchSpec: simplified __init__.py and copy()
closes #26354 and #26358
Previously we did not pass paths for GDB or GMP and ./configure would
get confused about which one to pull from. Be more specific.
Built with all variants enabled and fixed the fixable versions and variants:
@:8.1 were fixable by limiting python versions for these to @:3.6.
7.10.1 and 7.11(.1) were fixable to build with glibc-2.25 and newer
using two long patches.
gdb 7.8 and 7.9 weren't fixable as there is no backport if the fix
to build these with glibc-2.25 and newer:
http://lists.busybox.net/pipermail/buildroot/2017-March/188055.html
Co-authored-by: Bernhard Kaindl <bernhardkaindl7@gmail.com>
Modifications:
- Modify the workflow to build container images without pushing when the workflow file itself is modified
- Strip the leading ghcr.io/spack/ from env.container env.versioned to prepare pushing to multiple registries
- Fixed CentOS 7 and Amazon Linux builds
- Login and push to Docker Hub as well as Github Action
- Add a badge to README.md with the status of docker images
- Specify CMake minimum version more precisely
- Ensure rocBLAS is available at build time
- Limit workaround for missing rocblas include path
to the only affected version (4.1.0)
- Make hip a build and link dependency
- Remove hip's link dependencies
Co-authored-by: Harmen Stoppels <harmenstoppels@gmail.com>
CMake 3.21.3 disables the broken hipcc-as-rocmclang detection again.
From the release notes:
> The AMD ROCm Platform hipcc compiler was identifed by CMake 3.21.0
> through 3.21.2 as a distinct compiler with id ROCMClang. This has been
> removed because it caused regressions. Instead:
> * hipcc may no longer be used as a HIP compiler because it interferes
> with flags CMake needs to pass to Clang. Use Clang directly.
> * hipcc may once again be used as a CXX compiler, and is treated as
> whatever compiler it selects underneath, as CMake 3.20 and below
> did.
* py-snappy: add patch to fix dependencies
* Update var/spack/repos/builtin/packages/py-snappy/req.patch
Co-authored-by: Adam J. Stewart <ajstewart426@gmail.com>
Co-authored-by: Adam J. Stewart <ajstewart426@gmail.com>
* py-jupyter-packaging: add 0.7.12 and 0.10.6
* Update var/spack/repos/builtin/packages/py-jupyter-packaging/package.py
Co-authored-by: Adam J. Stewart <ajstewart426@gmail.com>
* Update var/spack/repos/builtin/packages/py-jupyter-packaging/package.py
Co-authored-by: Adam J. Stewart <ajstewart426@gmail.com>
Co-authored-by: Adam J. Stewart <ajstewart426@gmail.com>
The format of the HPE/Cray supplied module for cray-mvapich2 on HPE apollo systems is
very different from the cray-mpich module supplied on Cray EX and XE
systems.
Recent changes to the cray-mpich package -
https://github.com/spack/spack/pull/23470
broke support for cray-mvapich2 and relies now on the structure of the
cray-mpich module to work properly.
Rather than try to support two very different vendor mpich modules
using the same spack package, just add another one specialized for
the cray-mvapich2 module.
Signed-off-by: Howard Pritchard <hppritcha@gmail.com>
1. Changes the variant of openssl to `certs=mozilla/system/none` so that
users can pick whether they want Spack or system certs, or if they
don't want certs at all.
2. Keeps the default behavior of openssl to use certs=systems.
3. Changes the curl configuration to not guess the ca path during
config, but rather fall back to whatever the tls provider is
configured with. If we don't do this, curl will still pick up system
certs if it finds them.
As a minor fix, it also adds the build dep `pkgconfig` to curl, since
that's being used during the configure phase to get openssl compilation
flags.
* py-mock: fix depends of `@:2.0.0` and bump version
fixes the build of `py-gsutil`, it depends on `'py-mock@:2.0.0'`.
* Update var/spack/repos/builtin/packages/py-mock/package.py
Co-authored-by: Adam J. Stewart <ajstewart426@gmail.com>
* Update var/spack/repos/builtin/packages/py-mock/package.py
Co-authored-by: Adam J. Stewart <ajstewart426@gmail.com>
* Apply the other requested changes
* Add requested change: Add the python@3.6 for newer versions
Co-authored-by: Adam J. Stewart <ajstewart426@gmail.com>
* seacas: new release and fixes for metis/parmetis
* Update to add sha256 checksum for latest seacas release
* Updated the documentation strings with new applications
* Fixed the metis/parmetis variants and logic depending on whether mpi
is enabled/disabled. (There is still a zoltan issue I need to fix,
but this will at least allow seacas to be built without
metis/parmetis or with +mpi+parmetis. The ~mpi+metis still needs
work elsewhere.)
* Enable cpup, slice, zellij in +applications
NetCDF-4.8.1 has been released.
As discussed in https://github.com/Unidata/netcdf-c/issues/2110
(netcdf-c-4.8.1.tar.gz not on ftp site... #2110), the canonical
download site for netCDF releases has been changed and the previous
ftp site is no longer available.
This PR updates the `url` to point to the new recommended download
site and updates the sha256 checksums for the new tar files.
* py-anuga: add git main version to support build with python@3.5:
py-anuga's main branch has been converted to Python-3 recently.
* py-triangle: use pypi, py-anuga: Fixed depends and test suite works now
* py-numba: add 0.54.0 and restrict old dependencies
* Update var/spack/repos/builtin/packages/py-numba/package.py
Co-authored-by: Adam J. Stewart <ajstewart426@gmail.com>
Co-authored-by: Adam J. Stewart <ajstewart426@gmail.com>
* OpenSSL 3.0.0
* Remove openssl constraint in e4s to test 3.0.0
* Restrict openssl
* Restrict openssl to @:1 in unifyfs
* Revert "Remove openssl constraint in e4s to test 3.0.0"
This reverts commit 0f0355609771764280ab1b6a523c80843a4f85d6.
* Prefer 1.x
The logic to perform detection of already installed
packages has been extracted from cmd/external.py
and put into the spack.detection package.
In this way it can be reused programmatically for
other purposes, like bootstrapping.
The new implementation accounts for cases where the
executables are placed in a subdirectory within <prefix>/bin
The build needs `pkgconfig` and `openssl`, `m4` is already added by `autoconf`.
Also add the current version of `libp11` to the list of versions.
Co-authored-by: Bernhard Kaindl <bernhard.kaindl@ait.ac.at>
* Use gnuconfig package for config file replacement
Currently the autotools build system tries to pick up config.sub and
config.guess files from the system (in /usr/share) on arm and power.
This is introduces an implicit system dependency which we can avoid by
distributing config.guess and config.sub files in a separate package,
such as the new `gnuconfig` package which is very lightweight/text only
(unlike automake where we previously pulled these files from as a
backup). This PR adds `gnuconfig` as an unconditional build dependency
for arm and power archs.
In case the user needs a system version of config.sub and config.guess,
they are free to mark `gnuconfig` as an external package with the prefix
pointing to the directory containing the config files:
```yaml
gnuconfig:
externals:
- spec: gnuconfig@master
prefix: /tmp/tmp.ooBlkyAKdw/lol
buildable: false
```
Apart from that, this PR gives some better instructions for users when
replacing config files goes wrong.
* Mock needs this package too now, because autotools adds a depends_on
* Add documentation
* Make patch_config_files a prop, fix the docs, add integrations tests
* Make macOS happy
* py-datalad: move datalad wtf test over from py-datalad-metalad
* Update var/spack/repos/builtin/packages/py-datalad/package.py
Co-authored-by: Adam J. Stewart <ajstewart426@gmail.com>
Co-authored-by: Adam J. Stewart <ajstewart426@gmail.com>
* [vbfnlo] Add doc variant to toggle building of docs
* [openloops] Add scons to dependencies
Make sure that the build_processes does not accidentally pick up a
non-suitable scons version from the underlying system
* [openloops] Set OLPYTHON to make sure the right scons is picked
* [openloops] Fix Flake8 style complaints
Workaround this compile error for gcc by adding -Wno-narrowing for it:
spindle_logd.cc:65:76: error: narrowing conversion of '255' from 'int' to 'char'
spindle_logd.cc:65:76: error: narrowing conversion of '223' from 'int' to 'char'
spindle_logd.cc:65:76: error: narrowing conversion of '191' from 'int' to 'char'
spindle 0.8.1 wants to compile tests with mpi.h, newer versions need mpicc,
thus add: depends_on("mpi"). Spindle supports the --no-mpi to disable MPI.
Fix the perl test case bug Perl/perl5#15544
Variable PATH longer than 1000 characters (as is usual with spack) fails a perl test case
The fix is: Don't test PATH in testcase perlbug.t
Fixes `spack install --test=all` for specs triggering a build and test of perl!
"Long long" is the default type when building trilinos on its own, and
many downstream packages (both in and out of spack) rely on it. E4S
already sets this explicitly to long_long.
When using the ONNX package inside of an environment that specifies a
python3 executable, it will attempt to use a system installed
version. This can lead to a failure where the system python and the
environment python don't agree and the system python ends up with an
invalid environment. Forces ONNX to use the same version of python as
the rest of the spec.
Co-authored-by: Greg Becker <becker33@llnl.gov>
Fix solving/concretizing candle-benchmarks:
py-theano: The requested variant +gpu us now named +cuda
opencv: The requested variants +python and +zlib are now fixed deps
- Match failed autotest tests show the word "FAILED" near the end
- Match "FAIL: ", "FATAL: ", "failed ", "Failed test" of other suites
- autotest " ok"$ means the test passed, independend of text before.
- autoconf messages showing missing tools are fatal later, show them.
dropwatch is a network packet drop checker and it's make check starts
a daemon which does not terminate.
- Skip this test to not block builds.
- Add depends_on('pkgconfig', type='build')
It is needed in case the host does not have pkg-config installed.
- Remove the depends_on('m4', type='build'):
The depends_on('autoconf', type='build') pulls m4 as it needs it.
When using Ubuntu's gcc-8.4.0 on Ubuntu 18.04 to compile rivet-3.1.3,
compilation errors related to UnstableParticles(), "UFS" show up.
Compilation with this compiler is fixed in rivet-3.1.4, adding it.
Adding type='link' to the depends on 'hepmc' and 'hepmc' fixes
the tests to find libHepMC.so.4 in `spack install --tests=all`
Co-authored-by: Valentin Volkl <valentin.volkl@cern.ch>
The cairo test suite is huge, has many backends and the README states
that running and attempting to pass it is not a goal for normal users,
it has so many dependencies into the system, including fonts, that
passing it is not a goal realistically in reach soon:
Skip it, it takes far too long to be practical.
Despite the patch disabling installation of rules, meson's setup
stage looks up the udev package to get `/lib/udev/rules.d`, but as
spack has no `systemd/udev` package, it would fail to build.
Fix such builds by passing `-Dudevrulesdir` and bump version to 3.10.5
* autotoolspackage.rst: No depends_on('m4') with depends_on('autoconf')
- Remove `m4` from the example depends_on() lines for the autoreconf phase.
- Change the branch used as example from develop to master as it is
far more common in the packages of spack's builtin repo.
- Fix the wrong info that libtoolize and aclocal are run explicitly
in the autoreconf phase by default. autoreconf calls these internally
as needed, thus autotools.py also does not call them directly.
- Add that autoreconf() also adds -I<aclocal-prefix>/share/aclocal.
- Add an example how to set autoreconf_extra_args.
- Add an example of a custom autoreconf phase for running autogen.sh.
Co-authored-by: Harmen Stoppels <harmenstoppels@gmail.com>
Based on the original script of R. Mijakovic further improvements of
GPI-2 installation, in particular different official versions,
configuration setups and even testing. Importantly, the non-autotools
way of installation for older versions is also considered, which is
relevant for some packages using GPI-2.
Co-authored-by: Arcesio Castaneda Medina <arcesio.castaneda.medina@itwm.fraunhofer.de>
xload failed with unresolved referenced to libintl functions:
Disabled it's use of gettext calls and added the last "new" version.
Co-authored-by: Bernhard Kaindl <bernhard.kaindl@ait.ac.at>
The hand-written `configure` script of this package does not handle
--without-<feature> at all. The source wants to use `lhapdf` headers
even if support of lhapdf is not indicated using `--with-lhapdf`.
Enable the variant `lhapdf` by default: It fixes the build of the
current package and provides the TauSpinner feature as well.
Fix the build for normal non-root/non-system-user builds, as we cannot
know that we'd have to uninstall these files even if installed as root.
Also add `pkgconfig` and remove not explicitly needed `depends_on('m4')`
* update the Tau package to use the correct ROCm dependencies and prefixes
1st:
When the rocm variant is selected, tau defaults to look for rocm in /opt/rocm
which is not guarenteed to be the correct location -- this has been fixed
to provide the prefix for hsa-rocr-dev (which is now a dependency when +rocm is
selected).
2nd:
the rocprofiler dependency package was not specified correctly, it should
be called rocprofiler-dev, also rocprofiler-dev is a dependency when
+rocprofiler is selected.
added roctracer support
w3m's build fails with `undefined reference to `RAND_egd'` which
is an deprecated insecure feature and from building japanese messages.
Disabling both makes the build of `w3m` work.
This commit shows a template for cut-and-paste into the package to fix it:
```py
==> fast-global-file-status: Executing phase: 'autoreconf'
==> Error: RuntimeError: Cannot generate configure: missing dependencies autoconf, automake, libtool.
Please add the following lines to the package:
depends_on('autoconf', type='build', when='@master')
depends_on('automake', type='build', when='@master')
depends_on('libtool', type='build', when='@master')
Update the version (when='@master') as needed.
```
Co-authored-by: Harmen Stoppels <harmenstoppels@gmail.com>
The build needs pkgconfig and lzma, m4 is already added by autoconf.
Disable generation of kmod manpages as spack does not have xsltproc yet.
Co-authored-by: Bernhard Kaindl <bernhard.kaindl@ait.ac.at>
Assimp searches for zlib (or builds its own version). When it searches, it can find a system install that is not provided by spack. Ref: d286aadbdf/CMakeLists.txt (L451)
Tumbleweed has been broken for a couple of days. The attempt
to fix it in #26170 didn't really work. Let's try to move to
a more stable release series for OpenSuse.
* Make libunwind optional
* Add support for sized_delete and debugalloc
Co-authored-by: Seth R. Johnson <johnsonsr@ornl.gov>
Co-authored-by: Harmen Stoppels <harmenstoppels@gmail.com>
Fix the build of pango and it's 20 dependents: Only provide the versions which
support the build using autotools (conversion to MesonPackage didn't progress)
This only restores the list of versions of August 10, before the build broke.
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).
Spack's source mirror was previously in a plain old S3 bucket. That will still
work, but we can do better. This switches to AWS's CloudFront CDN for hosting
the mirror.
CloudFront is 16x faster (or more) than the old bucket.
- [x] change mirror to https://mirror.spack.io
This PR fixes two problems with clang/llvm's version detection. clang's
version output looks like this:
```
clang version 11.0.0
Target: x86_64-unknown-linux-gnu
```
This caused clang's version to be misdetected as:
```
clang@11.0.0
Target:
```
This resulted in errors when trying to actually use it as a compiler.
When using `spack external find`, we couldn't determine the compiler
version, resulting in errors like this:
```
==> Warning: "llvm@11.0.0+clang+lld+lldb" has been detected on the system but will not be added to packages.yaml [reason=c compiler not found for llvm@11.0.0+clang+lld+lldb]
```
Changing the regex to only match until the end of the line fixes these
problems.
Fixes: #19473
clean_environment(): Unset three more environment variables:
MAKEFLAGS: Affects make, can eg indirectly inhibit enabling parallel build
DISPLAY: Tests of GUI widget libraries might try to connect to an X server
TERM: Could make testsuites attempt to color their output
* Switch Umpire to CMakeCachedPackage
* Fix missing import
* Correct tests option in Umpire
* Switch RAJA to CachedCMakePackage
* Convert CHAI to CachedCMakePackage
* Corrections in RAJA
* Patches in Umpire & RAJA for BLT target export
* Fixup style
* Fixup incorrect use of cmake_cache_string
fixes#25992
Currently the bootstrapping process may need a compiler.
When bootstrapping from sources the need is obvious, while
when bootstrapping from binaries it's currently needed in
case patchelf is not on the system (since it will be then
bootstrapped from sources).
Before this PR we were searching for compilers as the
first operation, in case they were not declared in
the configuration. This fails in case we start
bootstrapping from within an environment.
The fix is to defer the search until we have swapped
configuration.
While debugging #24508, I noticed that we call `basename` in `cc`. The
same can be achieved by using Bash's parameter expansion, saving one
external process per call.
Parameter expansion cannot replace basename for directories in some
cases, but is guaranteed to work for executables.
Git 2.24 introduced a feature flag for repositories with many files, see:
https://github.blog/2019-11-03-highlights-from-git-2-24/#feature-macros
Since Spack's Git repository contains roughly 8,500 files, it can be
worthwhile to enable this, especially on slow file systems such as NFS:
```
$ hyperfine --warmup 3 'cd spack-default; git status' 'cd spack-manyfiles; git status'
Benchmark #1: cd spack-default; git status
Time (mean ± σ): 3.388 s ± 0.095 s [User: 256.2 ms, System: 625.8 ms]
Range (min … max): 3.168 s … 3.535 s 10 runs
Benchmark #2: cd spack-manyfiles; git status
Time (mean ± σ): 168.7 ms ± 10.9 ms [User: 98.6 ms, System: 126.1 ms]
Range (min … max): 144.8 ms … 188.0 ms 19 runs
Summary
'cd spack-manyfiles; git status' ran
20.09 ± 1.42 times faster than 'cd spack-default; git status'
```
* Add support for C++20 to HPX package
* Enable unity builds in HPX package when available
* Add support for HIP/ROCm to HPX package
* Rearrange and update required versions for HPX package
* Add C++20 option to asio package
Modifications:
- [x] Change `defaults/config.yaml`
- [x] Add a fix for bootstrapping patchelf from sources if `compilers.yaml` is empty
- [x] Make `SPACK_TEST_SOLVER=clingo` the default for unit-tests
- [x] Fix package failures in the e4s pipeline
Caveats:
1. CentOS 6 still uses the original concretizer as it can't connect to the buildcache due to issues with `ssl` (bootstrapping from sources requires a C++14 capable compiler)
1. I had to update the image tag for GitlabCI in e699f14.
1. libtool v2.4.2 has been deprecated and other packages received some update
This will allow a user to (from anywhere a Spec is parsed including both name and version) refer to a git commit in lieu of
a package version, and be able to make comparisons with releases in the history based on commits (or with other commits). We do this by way of:
- Adding a property, is_commit, to a version, meaning I can always check if a version is a commit and then change some action.
- Adding an attribute to the Version object which can lookup commits from a git repo and find the last known version before that commit, and the distance
- Construct new Version comparators, which are tuples. For normal versions, they are unchanged. For commits with a previous version x.y.z, d commits away, the comparator is (x, y, z, '', d). For commits with no previous version, the comparator is ('', d) where d is the distance from the first commit in the repo.
- Metadata on git commits is cached in the misc_cache, for quick lookup later.
- Git repos are cached as bare repos in `~/.spack/git_repos`
- In both caches, git repo urls are turned into file paths within the cache
If a commit cannot be found in the cached git repo, we fetch from the repo. If a commit is found in the cached metadata, we do not recompare to newly downloaded tags (assuming repo structure does not change). The cached metadata may be thrown out by using the `spack clean -m` option if you know the repo structure has changed in a way that invalidates existing entries. Future work will include automatic updates.
# Finding previous versions
Spack will search the repo for any tags that match the string of a version given by the `version` directive. Spack will also search for any tags that match `v + string` for any version string. Beyond that, Spack will search for tags that match a SEMVER regex (i.e., tags of the form x.y.z) and interpret those tags as valid versions as well. Future work will increase the breadth of tags understood by Spack
For each tag, Spack queries git to determine whether the tag is an ancestor of the commit in question or not. Spack then sorts the tags that are ancestors of the commit by commit-distance in the repo, and takes the nearest ancestor. The version represented by that tag is listed as the previous version for the commit.
Not all commits will find a previous version, depending on the package workflow. Future work may enable more tangential relationships between commits and versions to be discovered, but many commits in real world git repos require human knowledge to associate with a most recent previous version. Future work will also allow packages to specify commit/tag/version relationships manually for such situations.
# Version comparisons.
The empty string is a valid component of a Spack version tuple, and is in fact the lowest-valued component. It cannot be generated as part of any valid version. These two characteristics make it perfect for delineating previous versions from distances. For any version x.y.z, (x, y, z, '', _) will be less than any "real" version beginning x.y.z. This ensures that no distance from a release will cause the commit to be interpreted as "greater than" a version which is not an ancestor of it.
Signed-off-by: vsoch <vsoch@users.noreply.github.com>
Co-authored-by: vsoch <vsoch@users.noreply.github.com>
Co-authored-by: Gregory Becker <becker33@llnl.gov>
Co-authored-by: Todd Gamblin <tgamblin@llnl.gov>
This PR coincides with tiny changes to spack to support spack monitor using the new spec
the corresponding spack monitor PR is at https://github.com/spack/spack-monitor/pull/31.
Since there are no changes to the database we can actually update the current server
fairly easily, so either someone can test locally or we can just update and then
test from that (and update as needed).
Signed-off-by: vsoch <vsoch@users.noreply.github.com>
Co-authored-by: vsoch <vsoch@users.noreply.github.com>
* ESMF and NEMSIO changes.
- Updating ESMF to set the COMM correctly when using Intel oneapi.
- Explicitly setting the CMake MPI Fortran compiler for NEMSIO.
* Update UFS utils CMake to use MPI_<lang>_COMPILER.
#22845 revealed a long-standing bug that had never been triggered before, because the
hashing algorithm had been stable for multiple years while the bug was in production. The
bug was that when reading a concretized environment, Spack did not properly read in the
build hashes associated with the specs in the environment. Those hashes were recomputed
(and as long as we didn't change the algorithm, were recomputed identically). Spack's
policy, though, is never to recompute a hash. Once something is installed, we respect its
metadata hash forever -- even if internally Spack changes the hashing method. Put
differently, once something is concretized, it has a concrete hash, and that's it -- forever.
When we changed the hashing algorithm for performance in #22845 we exposed the bug.
This PR fixes the bug at its source, but properly reading in the cached build hash attributes
associated with the specs. I've also renamed some variables in the Environment class
methods to make a mistake of this sort more difficult to make in the future.
* ensure environment build hashes are never recomputed
* add comment clarifying reattachment of env build hashes
* bump lockfile version and include specfile version in env meta
* Fix unit-test for v1 to v2 conversion
Co-authored-by: Massimiliano Culpo <massimiliano.culpo@gmail.com>
* Refactor platform etc. to avoid circular dependencies
All the base classes in spack.architecture have been
moved to the corresponding specialized subpackages,
e.g. Platform is now defined within spack.platforms.
This resolves a circular dependency where spack.architecture
was both:
- Defining the base classes for spack.platforms, etc.
- Collecting derived classes from spack.platforms, etc.
Now it dopes only the latter.
* Move a few platform related functions to "spack.platforms"
* Removed spack.architecture.sys_type()
* Fixup for docs
* Rename Python modules according to review
* dvsdk: Turn off variants by default
This allows an install to more easily be explicit about which pieces to
turn on as more variants are added
* dvsdk: effectively disable the broken variants
* Switch http to https where latter exists
* Hopefully restore original permissions
* Add URL updates after include the -L curl option
* Manual corrections to select URL format strings
* Tell gtk-doc where the XML catalog is
The gtk-doc configure script has an option for specifying the path to
the XML catalog. If this is not set the configure script will search
a defined set of directories for a catalog file and will set
`with_xml_catalog` based on that. Only if no system catalog is found will
the XML_CATALOG_FILES be looked at. In order to make sure that the spack
provided catalog is used, pass the `--with-xml-catalog` option.
* Use the property from docbook-xml
Currently as part of installing a package, we lock a prefix, check if
it exists, and create it if not; the logic for creating the prefix
included a check for the existence of that prefix (and raised an
exception if it did), which was redundant.
This also includes removal of tests which were not verifying
anything (they pass with or without the modifications in this PR).
- Parallel install was failing to generate a config file.
- OpenSSH has an extensive test suite, run it if requested.
- 'executables' wrongly had 'rsh', replaced the openssh tools.
There are two ways to build SQLite: With the Autotools setup or the
so-called "amalgamation" which is a single large C file containing the
SQLite implementation. The amalgamation build is controlled by
pre-processor flags and the Spack setup was using an amalgamation
pre-processor flag for a feature that is controlled by an option of the
configure script. As a consequence, until now Spack has always built
SQLite with the rtree feature enabled.
Knowing that spack has patched the code and organized the build is potentially valuable information for GROMACS users and developers troubleshooting their builds.
PLUMED does further patches to GROMACS, so that is expressed directly also.
Modifications:
- Export platforms from spack.platforms directly, so that client modules don't have to import submodules
- Use only plain imports in test/architecture.py
- Parametrized test in test/architecture.py and put most of the setup/teardown in fixtures
This is a major rework of Spack's core core `spec.yaml` metadata format. It moves from `spec.yaml` to `spec.json` for speed, and it changes the format in several ways. Specifically:
1. The spec format now has a `_meta` section with a version (now set to version `2`). This will simplify major changes like this one in the future.
2. The node list in spec dictionaries is no longer keyed by name. Instead, it is a list of records with no required key. The name, hash, etc. are fields in the dictionary records like any other.
3. Dependencies can be keyed by any hash (`hash`, `full_hash`, `build_hash`).
4. `build_spec` provenance from #20262 is included in the spec format. This means that, for spliced specs, we preserve the *full* provenance of how to build, and we can reproduce a spliced spec from the original builds that produced it.
**NOTE**: Because we have switched the spec format, this PR changes Spack's hashing algorithm. This means that after this commit, Spack will think a lot of things need rebuilds.
There are two major benefits this PR provides:
* The switch to JSON format speeds up Spack significantly, as Python's builtin JSON implementation is orders of magnitude faster than YAML.
* The new Spec format will soon allow us to represent DAGs with potentially multiple versions of the same dependency -- e.g., for build dependencies or for compilers-as-dependencies. This PR lays the necessary groundwork for those features.
The old `spec.yaml` format continues to be supported, but is now considered a legacy format, and Spack will opportunistically convert these to the new `spec.json` format.
* Added spackage to build Sina (https://github.com/LLNL/Sina).
* Improvements to sina/package.py
Made numerous simplifications and improvements to sina/package.py
based on PR feedback.
* Added licence info
* Added maintainers
* Changed maintainers to be Github IDs.
Added a dependency for mpip@3.5: when the libunwind is set to true (which is the default)
and '~setjmp' is set to False (which is also the default) to avoid a configure
time error from not finding libunwind.
Co-authored-by: Massimiliano Culpo <massimiliano.culpo@gmail.com>
This modification accounts for:
1. Bootstrapping from sources using system, non-standard Python
2. Using later an ABI compatible standard Python interpreter
* tests: make `spack url [stats|summary]` work on mock packages
Mock packages have historically had mock hashes, but this means they're also invalid
as far as Spack's hash detection is concerned.
- [x] convert all hashes in mock package to md5 or sha256
- [x] ensure that all mock packages have a URL
- [x] ignore some special cases with multiple VCS fetchers
* url stats: add `--show-issues` option
`spack url stats` tells us how many URLs are using what protocol, type of checksum,
etc., but it previously did not tell us which packages and URLs had the issues. This
adds a `--show-issues` option to show URLs with insecure (`http`) URLs or `md5` hashes
(which are now deprecated by NIST).
This allows to fix the compilation of gcc versions less than 11.1.0,
due to the remove of cyclades of libsanitizer as it is described in
the patch:
The Linux kernel has removed the interface to cyclades from the latest
kernel headers due to them being orphaned for the past 13
years. libsanitizer uses this header when compiling against glibc, but
glibcs itself doesn't seem to have any references to cyclades. Further
more it seems that the driver is broken in the kernel and the firmware
doesn't seem to be available anymore. As such since this is breaking
the build of libsanitizer (and so the GCC bootstrap) it is proposed to
remove this.
Co-authored-by: Arcesio Castaneda Medina <arcesio.castaneda.medina@itwm.fraunhofer.de>
By changing return values from C #defines to enums, gdbm-1.20 breaks a kludge:
#ifndef GDBM_ITEM_NOT_FOUND
# define GDBM_ITEM_NOT_FOUND GDBM_NO_ERROR
#endif
The absence of the #define causes perl to #define GDBM_ITEM_NOT_FOUND
as GDBM_NO_ERROR which incorrect for gdbm@1.20:
* Optionally enable ccmake in cmake
Renames ncurses variant to `ccmake` since that's how users know it, and
explicitly enable/disable `BUILD_CursesDialog`.
* Make cmake locate its dependencies with CMAKE_PREFIX_PATH, and set rpath flags too
* Undo variant name & defaults change
Fixes removal of SPACK_ENV_PATH from PATH in the presence of trailing
slashes in the elements of PATH:
The compiler wrapper has to ensure that it is not called nested like
it would happen when gcc's collect2 uses PATH to call the linker ld,
or else the compilation fails.
To prevent nested calls, the compiler wrapper removes the elements
of SPACK_ENV_PATH from PATH.
Sadly, the autotest framework appends a slash to each element
of PATH when adding AUTOTEST_PATH to the PATH for the tests,
and some tests like those of GNU bison run cc inside the test.
Thus, ensure that PATH cleanup works even with trailing slashes.
This fixes the autotest suite of bison, compiling hundreds of
bison-generated test cases in a autotest-generated testsuite.
Co-authored-by: Harmen Stoppels <harmenstoppels@gmail.com>
netlib-lapack: Version 3.9.0 and above no longer builds with the IBM XL
compiler (#25447). Ported some fixes from the old ibm-xl.patch and added
logic for detection of XL's -qrecur flag.
Apply stable-release fixes from 2017 to older autoconf releses:
- Fix the scripts autoheader and autoscan to pass the test suite
- Fix test case to passing when libtool 2.4.3+ is in use
autoconf-2.13 dates back to 1999. The build wasn't possible since
4 years: Since 2017, we patch autom4te which didn't exist in 2.13,
failing the build of it. 4 years of not being able to build 2.13
is a crystal clear indication that we can remove it safely.
* amrex: support sundials variant in newer amrex versions
* propagate cuda_arch to sundials
* change to old string formatting
* require sundials+rocm when amrex+rocm
Ensure that testsuite has py-anytree and py-parameterized
and finds gtk-doc's gitdocize.
Co-authored-by: Adam J. Stewart <ajstewart426@gmail.com>
Co-authored-by: Adam J. Stewart <ajstewart426@gmail.com>
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>
* py-jupyterhub: add version: 1.4.1
* dont need mako for latest release
* sort dependencies
* notebook isnt used for 1.4.1+
* add dependency on py-jupyter-telemetry; create new package py-jupyter-telemetry
* py-jupyter-telemetry: declare missing dependencies
* py-jupyterhub: need more specific depends_on before less specific
* add py-json-logger; py-jupyter-telemetry: add depends_on for py-json-logger
* Update var/spack/repos/builtin/packages/py-jupyter-telemetry/package.py
Co-authored-by: Adam J. Stewart <ajstewart426@gmail.com>
* remove py-json-logger erroneously and duplicatively added
* Update var/spack/repos/builtin/packages/py-jupyterhub/package.py
Co-authored-by: Adam J. Stewart <ajstewart426@gmail.com>
* need py-alembic@1.4: for newest py-jupyterhub
Co-authored-by: Adam J. Stewart <ajstewart426@gmail.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
By default, figlet looks for fonts in `/usr/local/share/figlet`, and if
it doesn't exist you get `figlet: standard: Unable to open font file`.
This fix changes the default font dir to the one installed in the
install prefix.
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
some of these are not resolvable in that there is only an http page
available, or a page reported as broken is actually ok, or a page has
an SSL error that does not prevent one from visiting (and no good replacement)
Signed-off-by: vsoch <vsoch@users.noreply.github.com>
Co-authored-by: vsoch <vsoch@users.noreply.github.com>
* Add intel-tbb-oneapi package that does the cmake configure and build.
Compare too the intel-oneapi-tbb package which only downloads a script that contains prebuilt binaries.
* Rename package intel-tbb-cmake
* Incorporate intel-tbb-cmake into intel-tbb package
* 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
Most of these are perl packages that need to point to the meta docs site,
and then a fair amount of http addresses that need to be https, and then
the rest are usually documentation sites that no longer exist or were
otherwise changes
Signed-off-by: vsoch <vsoch@users.noreply.github.com>
Co-authored-by: vsoch <vsoch@users.noreply.github.com>
* 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
- remove unneeded dependency on blas
- create external-lapack variant
- patch makefile to not build lapack if `+external-lapack`
Also:
- fix homepage link
- set parallel = False
- make references to `spec` consistent
- remove unneeded `build` method
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).
By default the number of parellel compiler processes launched by
py-grpcio equals the number of threads. This commit limit it to
spack config build_jobs.
* Provide new version of eospac.
+ Provide version 6.5.0beta.
+ Make version 6.4.2 the default
+ Also increment
* volunteer to be the maintainer (for now).
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.
* Added py-meshio package
* Added setuptools dependency to py-meshio package
* Update var/spack/repos/builtin/packages/py-meshio/package.py
Co-authored-by: Adam J. Stewart <ajstewart426@gmail.com>
* Update var/spack/repos/builtin/packages/py-meshio/package.py
Co-authored-by: Adam J. Stewart <ajstewart426@gmail.com>
* Update var/spack/repos/builtin/packages/py-meshio/package.py
Co-authored-by: Adam J. Stewart <ajstewart426@gmail.com>
* Update var/spack/repos/builtin/packages/py-meshio/package.py
Co-authored-by: Adam J. Stewart <ajstewart426@gmail.com>
* Update var/spack/repos/builtin/packages/py-meshio/package.py
Co-authored-by: Adam J. Stewart <ajstewart426@gmail.com>
* added missing py-importlib-metadata dependency in py-meshio
Co-authored-by: Adam J. Stewart <ajstewart426@gmail.com>
#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)
As of cray-mpich version 8.1.7, conventional MPI compiler wrappers are included in cray-mpich.
Co-authored-by: Luke Roskop <lroskop@cedar.head.cm.us.cray.com>
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.
Add HPDDM, MMG, ParMMG and Tetgen to PETSc.
Add mmg version 5.5.2 (compatible with PETSc).
Add parmmg, depending on mmg.
Add pic variant to tetgen for PETSc.
* Adding a heap of NOAA packages for UFS.
Adding the Unified Forecast System (UFS) and all of the packages
it depends on.
* Fixing style tests.
* Removing the package CMAKE_BUILD_TYPE override.
* Removing compiler specs from `cmake_args()`.
- provides the site packages fix
- excludes the hdf5 linking changes (which are fixed in conduit@develop's build system)
- relaxes constraints to allows building static ascent against shared python
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>
* ampl: Add missing ampl_lic install and improve look of resources
* ampl: Add myself as maintainer
* ampl: Remove unused variable and delete extra lines
Co-authored-by: Rob Groner <rug262@psu.edu>
* rct: new packages (core packages and some dependencies)
* rct: new packages (core packages and some dependencies)
* radical-entk: updated dependencies (according to comments)
* radical-gtod: updated version name
* radical-pilot: updated dependencies (according to comments)
* radical-saga: updated dependencies (according to comments)
* radical-utils: updated dependencies and set old versions deprecated
* saga-python: removed due to absence of packages (in PyPI, GitHub), this project was replaced by `radical-saga` and corresponding package `py-radical-saga` should be used
* saga-python: rolled back, but with deprecation status
* ntplib: removed maintainer
* pika: removed maintainer
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.
* Fix for building shared lib when enabling ROCm, for STRUMPACK 5.1.1.
* Update patch for shared lib with STRUMPACK 5.1.1 and ROCm, also update FindHIP.cmake
* update patch for shared libs with ROCm
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.
* elk package updated to handle 3 latest versions support for older
versions is dropped
* fixed typos
* openmp dependency handling added
* and for blis too
* Retain support for elk 3, deprecate
Co-authored-by: Adam J. Stewart <ajstewart426@gmail.com>
* cp2k: fix build with GCC-10+ and MPICH
* cp2k: update SIRIUS and ELPA dependencies
* elpa: add version 2021.05.001, add ROCm support, include SVE flags
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
These versions can cause weird concretizations, and it looks like the
old version of xsdk may not even work because of xsdktrilinos being
disabled. The hypre version tagged for xsdk@0.2 no longer exists at the
described location.
With the previous naming scheme, `trilinos@:10` concretizes to
`trilinos@xsdk-0.2.0`. Now, it's clear what the xsdk version is closest
to. Changed from tag to the corresponding commit SHA for safety.
* Do not allow cray build system patch for later version of otf2
* Modify flag_handler logic in the trilinos package
Modify flag_handler logic in the trilinos package to work better with compilers
other than CCE
Run CTest at build time with:
```
spack install --test=root openpmd-api@<version>
```
and run smoke-tests after install and loading of the package via
```
spack load -r /<spec>
spack test run /<spec>
```
This pull request adds a new workflow to build and deploy Spack Docker containers
from GitHub Actions. In comparison with our current system where we use Dockerhub's
CI to build our Docker containers, this workflow will allow us to now build for multiple
architectures and deploy to multiple registries. (At the moment x86_64 and Arm64 because
ppc64le is throwing an error within archspec.)
As currently set up, the PR will build all of the current containers (minus Centos6 because
those yum repositories are no longer available?) as both x86_64 and Arm64 variants. The
workflow is currently setup to build and deploy containers nightly from develop as well as
on tagged releases. The workflow will also build, but NOT deploy containers on a pull request
for the purposes of testing this PR. At the moment it is setup to deploy the built containers to
GitHub's Container Registry although, support for also uploading to Dockerhub/Quay can be
included easily if we decide to keep releasing on Dockerhub/want to begin releasing on Quay.
This is an attempt to fix "Missing base commit" messages in the codecov UI. Because we do not run
full tests on package PRs, package PRs' merge commits on `develop` don't have coverage info. It
appears that codecov will give you an error if the pseudo-base's coverage data doesn't all apply
properly to the real PR base, unless the `allow_coverage_offsets` option is set.
* See here for docs:
https://docs.codecov.com/docs/comparing-commits#pseudo-comparison
* See here for another potential solution:
https://community.codecov.com/t/2480/15
`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
* Bump py-boto3, add python constraints, bump deps
* Update var/spack/repos/builtin/packages/py-boto3/package.py
Co-authored-by: Adam J. Stewart <ajstewart426@gmail.com>
* Update var/spack/repos/builtin/packages/py-boto3/package.py
Co-authored-by: Adam J. Stewart <ajstewart426@gmail.com>
* Update var/spack/repos/builtin/packages/py-boto3/package.py
Co-authored-by: Adam J. Stewart <ajstewart426@gmail.com>
Co-authored-by: Adam J. Stewart <ajstewart426@gmail.com>
* Add py-os-service-types
* Update var/spack/repos/builtin/packages/py-os-service-types/package.py
Co-authored-by: Adam J. Stewart <ajstewart426@gmail.com>
Co-authored-by: Adam J. Stewart <ajstewart426@gmail.com>
* Add py-oslo-i18n
* Update var/spack/repos/builtin/packages/py-oslo-i18n/package.py
Co-authored-by: Adam J. Stewart <ajstewart426@gmail.com>
Co-authored-by: Adam J. Stewart <ajstewart426@gmail.com>
* Bump py-botocore and add python constraints
* Update var/spack/repos/builtin/packages/py-botocore/package.py
Co-authored-by: Adam J. Stewart <ajstewart426@gmail.com>
Co-authored-by: Adam J. Stewart <ajstewart426@gmail.com>
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.
These are the versions tested (and successfully patched) against
intel-tbb.nvhpc-remove-flags.2017.patch: @2017, @2017.8, @2018, @2018.6
intel-tbb.nvhpc-remove-flags.2019.patch: @2019
intel-tbb.nvhpc-remove-flags.2019.1.patch: @2019.[1-6]
intel-tbb.nvhpc-remove-flags.2019.7.patch: @2019.[7-8]
intel-tbb.nvhpc-remove-flags.2019.9.patch: @2019.9, 2020.[0-3]
The intel-tbb.nvhpc-version-script-fix.2017.patch was tested and
applied successfully against all of the versions above.
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.
* rnpletal: New package
RNPL is an old package that is still used today by my collaborators, but doesn't see any development any more. I'm creating a Spack package merely to make it easier to install it on various systems. The code is not modern (C without prototypes – yes, that used to be a thing), and a large diff modernizes the code to make it palatable to modern C and Fortran compilers.
RNPL contains several sub-package. The current Spack package builds only the main one.
* rnpletal: Remove unused import
* Convert into AutotoolsPackage
* Don't check for "shared" variant
* rnpletal: Change "version" to `develop`
* rnpletal: Use existing `configure` function
* adjust for erroneous detection of nvc as gcc
adjust for erroneous detection of nvc as gcc when it is built with gcc
* add missing parenthesis :/
* fix trailing whitespace
* re-work hdf5 patch for nvc to make it more general
* flake8 fixes
* Render as comment
Render intended note as a comment rather than logical constraint
Co-authored-by: Frank Willmore <willmore@anl.gov>
- 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`
* kadath: New package
* Update var/spack/repos/builtin/packages/kadath/package.py
Co-authored-by: Adam J. Stewart <ajstewart426@gmail.com>
* Update var/spack/repos/builtin/packages/kadath/package.py
Co-authored-by: Adam J. Stewart <ajstewart426@gmail.com>
* Update var/spack/repos/builtin/packages/kadath/package.py
Co-authored-by: Adam J. Stewart <ajstewart426@gmail.com>
* Update var/spack/repos/builtin/packages/kadath/package.py
Co-authored-by: Adam J. Stewart <ajstewart426@gmail.com>
* kadath: Add description to MPI variant
* kadath: Add empty line
* kadath: Add variant "codes=none" to avoid empty default
Co-authored-by: Adam J. Stewart <ajstewart426@gmail.com>
* add variant with compiler optimization
Update package.py to include variant with compiler optimization, benchmarked at A-HUG hackaton to improve major kernel time by roughly 3%.
* fix style
* Update var/spack/repos/builtin/packages/laghos/package.py
Co-authored-by: Adam J. Stewart <ajstewart426@gmail.com>
Co-authored-by: Adam J. Stewart <ajstewart426@gmail.com>
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.
* lorene: Install only executables, not unrelated files in the same directory
* lorene: Don't determine compile dependencies
The current way doesn't work (cpp misses C++ include paths), and we don't need dependencies anyway.
* lorene: Correct BLAS library names
* lorene: Remove comment
Gitlab truncates job trace output (even the complete raw output) at 4MB,
so this change captures it to a file under "user_data" artifacts as well,
to make sure we can debug output from the end of the rebuild job.
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()
* sst-elements: add optional support for flashdimmsim, dramsim3 and
add new packages for each
* sst-dumpi: add version 7.1.0
* sst-core: autotools dependencies are required for all versions
* new package: dtc
* add error message redirect for +dumpi, otf, and otf2: these are not
currently supported
Modifications:
- Remove the "build tests" workflow from GitHub Actions
- Setup a similar e2e test on Gitlab
In this way we'll reduce load on GitHub Actions workflows and for e2e tests will
benefit from the buildcache reuse granted by pipelines.
ENABLE_SPLASH configuration has been removed entirely after 21.06 so
patch is no longer necessary after #24931. (Versions between 0.90.1 and
21.06 will likely still need a patch, and while it's not clear if this
patch is the right one, seems better to leave something in.)
- add version 9.1.2
- set a license file
- set the license environment variable
- remove the download and license information out of the description so
it does not show up in environment modules
- extend python and set python version constraints
- build gurobipy to be used in any compatible python, used for more
extensive computations than the gurobi shell
- remove preexisting PYTHONPATH from gurobi.sh as the shell uses a
built-in python, which will likely be different from "system" python
- add maintainer
`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
* [py-lmfit] fixed py-asteval dependency requirements
* [py-lmfit] added version 1.0.2
* [py-lmfit] flake8
* [py-lmfit] 1.0.2 reqires python 3.6
* [py-lmfit] removed newer dependency requirements to be in line with setup.py not requirements.txt
* pbs: new virtual package
Some of our clusters have an older installation of
libtorque and tm.h that are *not* from OpenPBS. Using the current
openpbs dependency for openmpi causes concretization errors due to
restrictions on older python and hwloc requirements that don't apply,
even with an external non-buildable installation.
The new 'torque' bundle package allows users to point to that external
installation without problems.
Detailed description of torque by Sergey Kosukhin <skosukhin@gmail.com>
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.
* aws-parallelcluster: update maintainers list
Signed-off-by: Tim Lane <tilne@amazon.com>
* aws-parallelcluster: add v2.11.1
Signed-off-by: Tim Lane <tilne@amazon.com>
This PR fixes the tesseract package
- add missing dependencies
- build documentation
- build and install java component
- build and install training component
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>
* Adding package for omegaconf
* Update var/spack/repos/builtin/packages/py-omegaconf/package.py
Co-authored-by: Adam J. Stewart <ajstewart426@gmail.com>
* Changing py-omegaconf to use github source URL instead of pypi
* Style fix
Co-authored-by: Adam J. Stewart <ajstewart426@gmail.com>
Worked with flecsi developers to tighten, relax, and clarify
constraints and better understand how the flecsi project uses
legion. In the process, discovered that flecsi@1.4 cannot be
built with legion without heavy changes/reverts to the legion
and gasnet spackages.
Also, most importantly, fixed branding as to how flecsi is spelled
We add compilation flags when using %nvhpc to suppress warnings
(which due to global -Werror flag in the build get promoted to
errors) for the following:
Diagnostic 111: statement is unreachable
Diagnostic 177: variable "foo" was declared but never referenced
Diagnostic 188: enumerated type mixed with another type
Diagnostic 550: variable "foo" was set but never used
#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
z3 is a dependency of llvm and llvm-amdgpu, and when z3 python bindings
are enabled it depends on py-setuptools as a run dependency. That's
fine, except that py-setuptools now influences the hash of
llvm/llvm-amdgpu, which can be very annoying when another package
restricts the py-setuptools version -- you'll end up recompiling llvm
for no good reason :(.
* Updated the lbann package to not enabled OpenMP in BLAS package when
working on Darwin systems.
* Add the Sphinx RTD theme as an explicit dependency when building documentation
In some cases the FindHDF5.cmake returnd a wrong value for the HDF5 library names and path. For example it returns hdf5-shared as library name without a search path or checking if this is really an existing shared library. By HDF5_NO_FIND_PACKAGE_CONFIG_FILE=True/ON to the cmake options, the FindHDF5 module does not rely on a properly install hdf5-config.cmake and thus searches for the library and its paths. This results in a usable return value and fenics works afterwards.
* Updates for dependencies in main branch
* Add more depends
* Make CMake available at runtime for fenics-dolfinx
* Add maintainer
Co-authored-by: Garth N. Wells <gnw20@cam.ac.uk>
Although `cpio` is present in many environments, it may not be always
available.
The failure to build this package can be reproduced in a fresh Docker
image `debian:10`.
* trilinos: rename basker variant
The Basker solver is part of amesos2 but is clearer without the extra
scoping.
* trilinos: automatically enable teuchos and remove variant
Basically everything in trilinos needs teuchos
* trilinos: group top-level dependencies
* trilinos: update dependencies, removing unused
- GLM, X11 are unused (x11 lacks dependency specs too)
- Python variant is more like a TPL so rearrange that
- Gtest internal package shouldn't be compiled or exported
- Add MPI4PY requirement for pytrilinos
* trilinos: remove package meta-options
- XSDK settings and "all opt packages" are not used anywhere
- all optional packages are dangerous
* trilinos: Use hwloc iff kokkos
See #19119, also the HWLOC tpl name was misspelled so this was being ignored before.
* Flake
* Fix trilinos +netcdf~mpi
* trilinos: default to disabling external dependencies
* Remove teuchos from downstream dependencies
* fixup! trilinos: Use hwloc iff kokkos
* Add netcdf requirements to packages with ^trilinos+exodus
* trilinos: disable exodus by default
* fixup! Add netcdf requirements to packages with ^trilinos+exodus
* trilinos: only enable hwloc when @13: +kokkos
* xyce: propagate trilinos dependencies more simply
* dtk: fix missing boost dependency
* trilinos: remove explicit metis dependency
* trilinos: require metis/parmetis for zoltan
Disable zoltan by default to minimize default dependencies
* trilinos: mark mesquite disabled and fix kokkos arch
* xsdk: fix trilinos to also list zoltan [with zoltan2]
* ci: remove nonexistent variant from trilinos
* trilinos: add missing boost dependency
Co-authored-by: Satish Balay <balay@mcs.anl.gov>
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
* Change url and checksums for libpng to official sourceforge archives
* Update url scheme from http to https
* switch to .xz archives
Co-authored-by: Todd Gamblin <tgamblin@llnl.gov>
* Add py-h5py version 3.3.0
The mpi4py dependency was bumped to 3.0.2 in setup.py. I'm not sure if that's actually required or not, but nothing lower is still tested.
* Use environment variable to stop h5py using setuptools setup_requires feature
* Add myself as a maintainer for py-h5py
* [py-transformers] can now use newer versions of tokenizers
* [py-transformers] Added version 4.6.1
* [py-transformers] removing old patch
* [py-transformers] boto3 no longer needed
* first build of py-torchmeta
* updated versions for torchvision and torch
* [py-torchmeta] using pil provider
Co-authored-by: Sid Pendelberry <sid@rit.edu>
The Makefile for the MAGMA smoke tests uses pkg-config to find
the MAGMA compile flags, but the test() routine in the spack
package was not configured to provide the location of the
pkg-config file. This modification sets PKG_CONFIG_PATH correctly
to allow the smoketests to successfully compile. It also removes
the *_dir variables which were unused by the magma
examples/Makefile.
Using the original concretizer, trying to concretize py-jupyterlab fails
with
```
==> Error: Invalid Version range: 6.1.0:6.1
```
because py-tornado does not have a 6.1.0 version but only a 6.1 one.
Makefiles for libtirpc have hardcoded the -pipe flag to the compiler
nvhpc compilers do not recognize that flag.
This PR provides a patch to remove the -pipe flag from the Makefile.
Patch should work with libtirpc@1.2.6 and @1.1.4
jupyterlab was looking for its application directory inside the python
prefix instead its own one. This was fixed by setting the according
environment variable.
* 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.
Getting rid of another top-level file.
`coverage.py` has supported `pyproject.toml` since version 5.0, and
all versions of coverage so far work with python 2.7. We just need to
ensure that a version of coverage with the `toml` extra is installed
in the test environment.
I tested this with `coverage run`, `coverage report`, and `coverage html`.
* openPMD-api: rename develop
Rename to match known Spack version comparison schemes:
```
develop>main>master>head>trunk>9999>0>z>a
```
Currently, the hdf5 patch that is pre-0.14.0 is also applied to
`dev`, which naturally fails (already applied).
* fix dev in warpx
* py-markupsafe: add 2.0.1
* Update var/spack/repos/builtin/packages/py-markupsafe/package.py
Co-authored-by: Adam J. Stewart <ajstewart426@gmail.com>
Co-authored-by: Adam J. Stewart <ajstewart426@gmail.com>
This moves our `mypy` configuration from `.mypy.ini` to `.pyproject.toml`
and increases the minimum `mypy` version in the tests.
- [x] move `mypy` configuration to `pyproject.toml`
- [x] remove `.mypy.ini`
- [x] ensure that `mypy` version .900 or higher is used in tests
Ideally a test-only dependency won't be in the build, but until then
mark the requirement of gtest up to 1.10.
See e4s job failure at https://gitlab.spack.io/spack/spack/-/jobs/349959 .
Looks like 1.11 introduces some breaking incompatibilities, so perhaps
we should transition later.
about: Report a bug in the core of Spack (command not working as expected, etc.)
labels: "bug,triage"
---
<!-- Explain, in a clear and concise way, the command you ran and the result you were trying to achieve.
Example: "I ran `spack find` to list all the installed packages and ..." -->
### Steps to reproduce the issue
```console
$ spack <command1> <spec>
$ spack <command2> <spec>
...
```
### Error Message
<!-- If Spack reported an error, provide the error message. If it did not report an error but the output appears incorrect, provide the incorrect output. If there was no error message and no output but the result is incorrect, describe how it does not match what you expect. -->
```console
$ spack --debug --stacktrace <command>
```
### Information on your system
<!-- Please include the output of `spack debug report` -->
<!-- If you have any relevant configuration detail (custom `packages.yaml` or `modules.yaml`, etc.) you can add that here as well. -->
### Additional information
<!-- These boxes can be checked by replacing [ ] with [x] or by clicking them after submitting the issue. -->
- [ ] I have run `spack debug report` and reported the version of Spack/Python/Platform
- [ ] I have searched the issues of this repo and believe this is not a duplicate
- [ ] I have run the failing commands in debug mode and reported the output
<!-- We encourage you to try, as much as possible, to reduce your problem to the minimal example that still reproduces the issue. That would help us a lot in fixing it quickly and effectively!
If you want to ask a question about the tool (how to use it, what it can currently do, etc.), try the `#general` channel on our Slack first. We have a welcoming community and chances are you'll get your reply faster and without opening an issue.
Other than that, thanks for taking the time to contribute to Spack! -->
description:Report a bug in the core of Spack (command not working as expected, etc.)
labels:[bug, triage]
body:
- type:textarea
id:reproduce
attributes:
label:Steps to reproduce
description:|
Explain, in a clear and concise way, the command you ran and the result you were trying to achieve.
Example: "I ran `spack find` to list all the installed packages and ..."
placeholder:|
```console
$ spack <command1> <spec>
$ spack <command2> <spec>
...
```
validations:
required:true
- type:textarea
id:error
attributes:
label:Error message
description:|
If Spack reported an error, provide the error message. If it did not report an error but the output appears incorrect, provide the incorrect output. If there was no error message and no output but the result is incorrect, describe how it does not match what you expect.
placeholder:|
```console
$ spack --debug --stacktrace <command>
```
- type:textarea
id:information
attributes:
label:Information on your system
description:Please include the output of `spack debug report`
validations:
required:true
- type:markdown
attributes:
value:|
If you have any relevant configuration detail (custom `packages.yaml` or `modules.yaml`, etc.) you can add that here as well.
- type:checkboxes
id:checks
attributes:
label:General information
options:
- label:I have run `spack debug report` and reported the version of Spack/Python/Platform
required:true
- label:I have searched the issues of this repo and believe this is not a duplicate
required:true
- label:I have run the failing commands in debug mode and reported the output
required:true
- type:markdown
attributes:
value:|
We encourage you to try, as much as possible, to reduce your problem to the minimal example that still reproduces the issue. That would help us a lot in fixing it quickly and effectively!
If you want to ask a question about the tool (how to use it, what it can currently do, etc.), try the `#general` channel on [our Slack](https://slack.spack.io/) first. We have a welcoming community and chances are you'll get your reply faster and without opening an issue.
Other than that, thanks for taking the time to contribute to Spack!
about: Some package in Spack didn't build correctly
title: "Installation issue: "
labels: "build-error"
---
<!-- Thanks for taking the time to report this build failure. To proceed with the report please:
1. Title the issue "Installation issue: <name-of-the-package>".
2. Provide the information required below.
We encourage you to try, as much as possible, to reduce your problem to the minimal example that still reproduces the issue. That would help us a lot in fixing it quickly and effectively! -->
### Steps to reproduce the issue
<!-- Fill in the exact spec you are trying to build and the relevant part of the error message -->
```console
$ spack install <spec>
...
```
### Information on your system
<!-- Please include the output of `spack debug report` -->
<!-- If you have any relevant configuration detail (custom `packages.yaml` or `modules.yaml`, etc.) you can add that here as well. -->
### Additional information
<!-- Please upload the following files. They should be present in the stage directory of the failing build. Also upload any config.log or similar file if one exists. -->
* [spack-build-out.txt]()
* [spack-build-env.txt]()
<!-- Some packages have maintainers who have volunteered to debug build failures. Run `spack maintainers <name-of-the-package>` and @mention them here if they exist. -->
### General information
<!-- These boxes can be checked by replacing [ ] with [x] or by clicking them after submitting the issue. -->
- [ ] I have run `spack debug report` and reported the version of Spack/Python/Platform
- [ ] I have run `spack maintainers <name-of-the-package>` and @mentioned any maintainers
- [ ] I have uploaded the build log and environment files
- [ ] I have searched the issues of this repo and believe this is not a duplicate
description:Some package in Spack didn't build correctly
title:"Installation issue: "
labels:[build-error]
body:
- type:markdown
attributes:
value:|
Thanks for taking the time to report this build failure. To proceed with the report please:
1. Title the issue `Installation issue: <name-of-the-package>`.
2. Provide the information required below.
We encourage you to try, as much as possible, to reduce your problem to the minimal example that still reproduces the issue. That would help us a lot in fixing it quickly and effectively!
- type:textarea
id:reproduce
attributes:
label:Steps to reproduce the issue
description:|
Fill in the exact spec you are trying to build and the relevant part of the error message
placeholder:|
```console
$ spack install <spec>
...
```
validations:
required:true
- type:textarea
id:information
attributes:
label:Information on your system
description:Please include the output of `spack debug report`
validations:
required:true
- type:markdown
attributes:
value:|
If you have any relevant configuration detail (custom `packages.yaml` or `modules.yaml`, etc.) you can add that here as well.
- type:textarea
id:additional_information
attributes:
label:Additional information
description:|
Please upload the following files:
* **`spack-build-out.txt`**
* **`spack-build-env.txt`**
They should be present in the stage directory of the failing build. Also upload any `config.log` or similar file if one exists.
- type:markdown
attributes:
value:|
Some packages have maintainers who have volunteered to debug build failures. Run `spack maintainers <name-of-the-package>` and **@mention** them here if they exist.
- type:checkboxes
id:checks
attributes:
label:General information
options:
- label:I have run `spack debug report` and reported the version of Spack/Python/Platform
required:true
- label:I have run `spack maintainers <name-of-the-package>` and **@mentioned** any maintainers
required:true
- label:I have uploaded the build log and environment files
required:true
- label:I have searched the issues of this repo and believe this is not a duplicate
about: Suggest adding a feature that is not yet in Spack
labels: feature
---
<!--*Please add a concise summary of your suggestion here.*-->
### Rationale
<!--*Is your feature request related to a problem? Please describe it!*-->
### Description
<!--*Describe the solution you'd like and the alternatives you have considered.*-->
### Additional information
<!--*Add any other context about the feature request here.*-->
### General information
- [ ] I have run `spack --version` and reported the version of Spack
- [ ] I have searched the issues of this repo and believe this is not a duplicate
<!--If you want to ask a question about the tool (how to use it, what it can currently do, etc.), try the `#general` channel on our Slack first. We have a welcoming community and chances are you'll get your reply faster and without opening an issue.
Other than that, thanks for taking the time to contribute to Spack!
description:Suggest adding a feature that is not yet in Spack
labels:[feature]
body:
- type:textarea
id:summary
attributes:
label:Summary
description:Please add a concise summary of your suggestion here.
validations:
required:true
- type:textarea
id:rationale
attributes:
label:Rationale
description:Is your feature request related to a problem? Please describe it!
- type:textarea
id:description
attributes:
label:Description
description:Describe the solution you'd like and the alternatives you have considered.
- type:textarea
id:additional_information
attributes:
label:Additional information
description:Add any other context about the feature request here.
- type:checkboxes
id:checks
attributes:
label:General information
options:
- label:I have run `spack --version` and reported the version of Spack
required:true
- label:I have searched the issues of this repo and believe this is not a duplicate
required:true
- type:markdown
attributes:
value:|
If you want to ask a question about the tool (how to use it, what it can currently do, etc.), try the `#general` channel on [our Slack](https://slack.spack.io/) first. We have a welcoming community and chances are you'll get your reply faster and without opening an issue.
Other than that, thanks for taking the time to contribute to Spack!
A module folder with a :class:`AnalyzerBase <spack.analyzers.analyzer_base.AnalyzerBase>`
A module folder with a :class:`~spack.analyzers.analyzer_base.AnalyzerBase`
that provides base functions to run, save, and (optionally) upload analysis
results to a `Spack Monitor <https://github.com/spack/spack-monitor>`_ server.
@@ -286,7 +268,7 @@ Other Modules
tarball URLs.
:mod:`spack.error`
:class:`SpackError <spack.error.SpackError>`, the base class for
:class:`~spack.error.SpackError`, the base class for
Spack's exception hierarchy.
:mod:`llnl.util.tty`
@@ -335,8 +317,8 @@ Writing analyzers
To write an analyzer, you should add a new python file to the
analyzers module directory at ``lib/spack/spack/analyzers`` .
Your analyzer should be a subclass of the :class:`AnalyzerBase <spack.analyzers.analyzer_base.AnalyzerBase>`. For example, if you want
to add an analyzer class ``Myanalyzer`` you woul write to
``spack/analyzers/myanalyzer.py`` and import and
to add an analyzer class ``Myanalyzer`` you would write to
``spack/analyzers/myanalyzer.py`` and import and
use the base as follows:
..code-block::python
@@ -347,7 +329,7 @@ use the base as follows:
Note that the class name is your module file name, all lowercase
except for the first capital letter. You can look at other analyzers in
except for the first capital letter. You can look at other analyzers in
that analyzer directory for examples. The guide here will tell you about the basic functions needed.
^^^^^^^^^^^^^^^^^^^^^^^^^
@@ -356,13 +338,13 @@ Analyzer Output Directory
By default, when you run ``spack analyze run`` an analyzer output directory will
be created in your spack user directory in your ``$HOME``. The reason we output here
is because the install directory might not always be writable.
is because the install directory might not always be writable.
..code-block::console
~/.spack/
analyzers
Result files will be written here, organized in subfolders in the same structure
as the package, with each analyzer owning it's own subfolder. for example:
@@ -380,11 +362,11 @@ as the package, with each analyzer owning it's own subfolder. for example:
│ └── spack-analyzer-install-files.json
└── libabigail
└── lib
└── spack-analyzer-libabigail-libz.so.1.2.11.xml
└── spack-analyzer-libabigail-libz.so.1.2.11.xml
Notice that for the libabigail analyzer, since results are generated per object,
we honor the object's folder in case there are equivalently named files in
we honor the object's folder in case there are equivalently named files in
different folders. The result files are typically written as json so they can be easily read and uploaded in a future interaction with a monitor.
@@ -426,7 +408,7 @@ and then return the object with a key as the analyzer name. The result data
should be a list of objects, each with a name, ``analyzer_name``, ``install_file``,
and one of ``value`` or ``binary_value``. The install file should be for a relative
path, and not the absolute path. For example, let's say we extract a metric called
``metric`` for ``bin/wget`` using our analyzer ``thebest-analyzer``.
``metric`` for ``bin/wget`` using our analyzer ``thebest-analyzer``.
We might have data that looks like this:
..code-block::python
@@ -482,7 +464,7 @@ Saving Analyzer Results
The analyzer will have ``save_result`` called, with the result object generated
to save it to the filesystem, and if the user has added the ``--monitor`` flag
to upload it to a monitor server. If your result follows an accepted result
format and you don't need to parse it further, you don't need to add this
format and you don't need to parse it further, you don't need to add this
function to your class. However, if your result data is large or otherwise
needs additional parsing, you can define it. If you define the function, it
is useful to know about the ``output_dir`` property, which you can join
@@ -548,7 +530,7 @@ each one (separately) to the monitor:
Notice that this function, if you define it, requires a result object (generated by
``run()``, a monitor (if you want to send), and a boolean ``overwrite`` to be used
to check if a result exists first, and not write to it if the result exists and
to check if a result exists first, and not write to it if the result exists and
overwrite is False. Also notice that since we already saved these files to the analyzer metadata folder, we return early if a monitor isn't defined, because this function serves to send results to the monitor. If you haven't saved anything to the analyzer metadata folder
yet, you might want to do that here. You should also use ``tty.info`` to give
the user a message of "Writing result to $DIRNAME."
@@ -616,7 +598,7 @@ types of hooks in the ``__init__.py``, and then python files in that folder
can use hook functions. The files are automatically parsed, so if you write
a new file for some integration (e.g., ``lib/spack/spack/hooks/myintegration.py``
you can then write hook functions in that file that will be automatically detected,
and run whenever your hook is called. This section will cover the basic kind
and run whenever your hook is called. This section will cover the basic kind
of hooks, and how to write them.
^^^^^^^^^^^^^^
@@ -624,7 +606,7 @@ Types of Hooks
^^^^^^^^^^^^^^
The following hooks are currently implemented to make it easy for you,
the developer, to add hooks at different stages of a spack install or similar.
the developer, to add hooks at different stages of a spack install or similar.
If there is a hook that you would like and is missing, you can propose to add a new one.
"""""""""""""""""""""
@@ -632,9 +614,9 @@ If there is a hook that you would like and is missing, you can propose to add a
"""""""""""""""""""""
A ``pre_install`` hook is run within an install subprocess, directly before
the install starts. It expects a single argument of a spec, and is run in
the install starts. It expects a single argument of a spec, and is run in
a multiprocessing subprocess. Note that if you see ``pre_install`` functions associated with packages these are not hooks
as we have defined them here, but rather callback functions associated with
as we have defined them here, but rather callback functions associated with
a package install.
@@ -657,7 +639,7 @@ here.
This hook is run at the beginning of ``lib/spack/spack/installer.py``,
in the install function of a ``PackageInstaller``,
and importantly is not part of a build process, but before it. This is when
we have just newly grabbed the task, and are preparing to install. If you
we have just newly grabbed the task, and are preparing to install. If you
write a hook of this type, you should provide the spec to it.
..code-block::python
@@ -666,7 +648,7 @@ write a hook of this type, you should provide the spec to it.
"""On start of an install, we want to...
"""
print('on_install_start')
""""""""""""""""""""""""""""
``on_install_success(spec)``
@@ -744,8 +726,8 @@ to trigger after anything is written to a logger. You would add it as follows:
post_install=HookRunner('post_install')
# hooks related to logging
post_log_write=HookRunner('post_log_write')# <- here is my new hook!
post_log_write=HookRunner('post_log_write')# <- here is my new hook!
You then need to decide what arguments my hook would expect. Since this is
related to logging, let's say that you want a message and level. That means
@@ -775,7 +757,7 @@ In this example, we use it outside of a logger that is already defined:
This is not to say that this would be the best way to implement an integration
with the logger (you'd probably want to write a custom logger, or you could
have the hook defined within the logger) but serves as an example of writing a hook.
have the hook defined within the logger) but serves as an example of writing a hook.
----------
Unit tests
@@ -785,6 +767,38 @@ Unit tests
Unit testing
------------
---------------------
Developer environment
---------------------
..warning::
This is an experimental feature. It is expected to change and you should
not use it in a production environment.
When installing a package, we currently have support to export environment
variables to specify adding debug flags to the build. By default, a package
install will build without any debug flag. However, if you want to add them,
you can export:
..code-block::console
export SPACK_ADD_DEBUG_FLAGS=true
spack install zlib
If you want to add custom flags, you should export an additional variable:
..code-block::console
export SPACK_ADD_DEBUG_FLAGS=true
export SPACK_DEBUG_FLAGS="-g"
spack install zlib
These environment variables will eventually be integrated into spack so
they are set from the command line.
------------------
Developer commands
------------------
@@ -795,6 +809,29 @@ Developer commands
``spack doc``
^^^^^^^^^^^^^
.._cmd-spack-style:
^^^^^^^^^^^^^^^
``spack style``
^^^^^^^^^^^^^^^
spack style exists to help the developer user to check imports and style with
mypy, flake8, isort, and (soon) black. To run all style checks, simply do:
..code-block::console
$ spack style
To run automatic fixes for isort you can do:
..code-block::console
$ spack style --fix
You do not need any of these Python packages installed on your system for
the checks to work! Spack will bootstrap install them from packages for
your use.
^^^^^^^^^^^^^^^^^^^
``spack unit-test``
^^^^^^^^^^^^^^^^^^^
@@ -873,7 +910,7 @@ just like you would with the normal ``python`` command.
^^^^^^^^^^^^^^^
Spack blame is a way to quickly see contributors to packages or files
in the spack repository. You should provide a target package name or
in the spack repository. You should provide a target package name or
file name to the command. Here is an example asking to see contributions
for the package "python":
@@ -883,8 +920,8 @@ for the package "python":
LAST_COMMIT LINES % AUTHOR EMAIL
2 weeks ago 3 0.3 Mickey Mouse <cheddar@gmouse.org>
a month ago 927 99.7 Minnie Mouse <swiss@mouse.org>
2 weeks ago 930 100.0
2 weeks ago 930 100.0
By default, you will get a table view (shown above) sorted by date of contribution,
@@ -1255,7 +1292,7 @@ Publishing a release on GitHub
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