Environments and environment views have taken over the role of `spack activate/deactivate`, and we should deprecate these commands for several reasons:
- Global activation is a really poor idea:
- Install prefixes should be immutable; since they can have multiple, unrelated dependents; see below
- Added complexity elsewhere: verification of installations, tarballs for build caches, creation of environment views of packages with unrelated extensions "globally activated"... by removing the feature, it gets easier for people to contribute, and we'd end up with fewer bugs due to edge cases.
- Environment accomplish the same thing for non-global "activation" i.e. `spack view`, but better.
Also we write in the docs:
```
However, Spack global activations have two potential drawbacks:
#. Activated packages that involve compiled C extensions may still
need their dependencies to be loaded manually. For example,
``spack load openblas`` might be required to make ``py-numpy``
work.
#. Global activations "break" a core feature of Spack, which is that
multiple versions of a package can co-exist side-by-side. For example,
suppose you wish to run a Python package in two different
environments but the same basic Python --- one with
``py-numpy@1.7`` and one with ``py-numpy@1.8``. Spack extensions
will not support this potential debugging use case.
```
Now that environments are established and views can take over the role of activation
non-destructively, we can remove global activation/deactivation.
Currently, external `PythonPackage`s cause install failures because the logic in `PythonPackage` assumes that it can ask for `spec["python"]`. Because we chop off externals' dependencies, an external Python extension may not have a `python` dependency.
This PR resolves the issue by guaranteeing that a `python` node is present in one of two ways:
1. If there is already a `python` node in the DAG, we wire the external up to it.
2. If there is no existing `python` node, we wire up a synthetic external `python` node, and we assume that it has the same prefix as the external.
The assumption in (2) isn't always valid, but it's better than leaving the user with a non-working `PythonPackage`.
The logic here is specific to `python`, but other types of extensions could take advantage of it. Packages need only define `update_external_dependencies(self)`, and this method will be called on externals after concretization. This likely needs to be fleshed out in the future so that any added nodes are included in concretization, but for now we only bolt on dependencies post-concretization.
Co-authored-by: Todd Gamblin <tgamblin@llnl.gov>
Spack currently creates a temporary sbang that is moved "atomically" in place,
but this temporary causes races when multiple processes start installing sbang.
Let's just stick to an idempotent approach. Notice that we only re-install sbang
if Spack updates it (since we do file compare), and sbang was only touched
18 times in the past 6 years, whereas we hit the sbang tempfile issue
frequently with parallel install on a fresh spack instance in CI.
Also fixes a bug where permissions weren't updated if config changed but
the latest version of the sbang file was already installed.
The `intel` compiler at versions > 20 is provided by the `intel-oneapi-compilers-classic`
package (a thin wrapper around the `intel-oneapi-compilers` package), and the `oneapi`
compiler is provided by the `intel-oneapi-compilers` package.
Prior to this work, neither of these compilers could be bootstrapped by Spack as part of
an install with `install_missing_compilers: True`.
Changes made to make these two packages bootstrappable:
1. The `intel-oneapi-compilers-classic` package includes a bin directory and symlinks
to the compiler executables, not just logical pointers in Spack.
2. Spack can look for bootstrapped compilers in directories other than `$prefix/bin`,
defined on a per-package basis
3. `intel-oneapi-compilers` specifies a non-default search directory for the
compiler executables.
4. The `spack.compilers` module now can make more advanced associations between
packages and compilers, not just simple name translations
5. Spack support for lmod hierarchies accounts for differences between package
names and the associated compiler names for `intel-oneapi-compilers/oneapi`,
`intel-oneapi-compilers-classic/intel@20:`, `llvm+clang/clang`, and
`llvm-amdgpu/rocmcc`.
- [x] full end-to-end testing
- [x] add unit tests
"spack install foo" no longer adds package "foo" to the environment
(i.e. to the list of root specs) by default: you must specify "--add".
Likewise "spack uninstall foo" no longer removes package "foo" from
the environment: you must specify --remove. Generally this means
that install/uninstall commands will no longer modify the users list
of root specs (which many users found problematic: they had to
deactivate an environment if they wanted to uninstall a spec without
changing their spack.yaml description).
In more detail: if you have environments e1 and e2, and specs [P, Q, R]
such that P depends on R, Q depends on R, [P, R] are in e1, and [Q, R]
are in e2:
* `spack uninstall --dependents --remove r` in e1: removes R from e1
(but does not uninstall it) and uninstalls (and removes) P
* `spack uninstall -f --dependents r` in e1: will uninstall P, Q, and
R (i.e. e2 will have dependent specs uninstalled as a side effect)
* `spack uninstall -f --dependents --remove r` in e1: this uninstalls
P, Q, and R, and removes [P, R] from e1
* `spack uninstall -f --remove r` in e1: uninstalls R (so it is
"missing" in both environments) and removes R from e1 (note that e1
would still install R as a dependency of P, but it would no longer
be listed as a root spec)
* `spack uninstall --dependents r` in e1: will fail because e2 needs R
Individual unit tests were created for each of these scenarios.
Somehow a network error when cloning the repo for ci gets
categorized by gitlab as a script failure. To make sure we retry
jobs that failed for that reason or a similar one, include
"script_failure" as one of the reasons for retrying service jobs
(which include "no specs to rebuild" jobs, update buildcache
index jobs, and temp storage cleanup jobs.
Add a `project` block to the toml config along with development and CI
dependencies and a minimal `build-system` block, doing basically
nothing, so that spack can be bootstrapped to a full development
environment with:
```shell
$ hatch -e dev shell
```
or for a minimal environment without hatch:
```shell
$ python3 -m venv venv
$ source venv/bin/activate
$ python3 -m pip install --upgrade pip
$ python3 -m pip install -e '.[dev]'
```
This means we can re-use the requirements list throughout the workflow
yaml files and otherwise maintain this list in *one place* rather than
several disparate ones. We may be stuck with a couple more temporarily
to continue supporting python2.7, but aside from that it's less places
to get out of sync and a couple new bootstrap options.
Co-authored-by: Adam J. Stewart <ajstewart426@gmail.com>
This change uses the aws cli, if available, to retrieve spec files
from the mirror to a local temp directory, then parallelizes the
reading of those files from disk using multiprocessing.ThreadPool.
If the aws cli is not available, then a ThreadPool is used to fetch
and read the spec files from the mirror.
Using aws cli results in ~16 times speed up to recreate the binary
mirror index, while just parallelizing the fetching and reading
results in ~3 speed up.
The compiler bootstrapping logic currently does not add a task when the compiler package is already in the install task queue. This causes failures when the compiler package is added without the additional metadata telling the task to update the compilers list.
Solution: requeue compilers for bootstrapping when needed, to update `task.compiler` metadata.
Currently, develop specs that are not roots and are not explicitly listed dependencies
of the roots are not applied.
- [x] ensure dev specs are applied.
Co-authored-by: Todd Gamblin <tgamblin@llnl.gov>
`spack env create` enables a view by default (in a weird hidden
directory, but well...). This is asking for trouble with the other
default of `concretizer:unify:false`, since having different flavors of
the same spec in an environment, leads to collision errors when
generating the view.
A change of defaults would improve user experience:
However, `unify:true` makes most sense, since any time the issue is
brought up in Slack, the user changes the concretization config, since
it wasn't the intention to have different flavors of the same spec, and
install times are decreased.
Further we improve the docs and drop the duplicate root spec limitation
Dependencies specified by hash are unique in Spack in that the abstract
specs are created with internal structure. In this case, the constraint
generation for spec matrices fails due to flattening the structure.
It turns out that the dep_difference method for Spec.constrain does not
need to operate on transitive deps to ensure correctness. Removing transitive
deps from this method resolves the bug.
- [x] Includes regression test
Without this, Meson will use its Wraps to automatically download and
install dependencies. We want to manage dependencies explicitly,
therefore disable this functionality.
Currently, Spack can fail for a valid spec if the spec is constructed from overlapping, but not conflicting, concrete specs via the hash.
For example, if abcdef and ghijkl are the hashes of specs that both depend on zlib/mnopqr, then foo ^/abcdef ^/ghijkl will fail to construct a spec, with the error message "Cannot depend on zlib... twice".
This PR changes this behavior to check whether the specs are compatible before failing.
With this PR, foo ^/abcdef ^/ghijkl will concretize.
As a side-effect, so will foo ^zlib ^zlib and other specs that are redundant on their dependencies.
Argparse started raising ArgumentError exceptions
when the same parser is added twice. Therefore, we
perform the addition only if the parser is not there
already
Port match syntax to our unparser
Compilers and linker optimize string constants for space by aliasing
them when one is a suffix of another. For gcc / binutils this happens
already at -O1, due to -fmerge-constants. This means that we have
to take care during relocation to always preserve a certain length
of the suffix of those prefixes that are C-strings.
In this commit we pick length 7 as a safe suffix length, assuming the
suffix is typically the 7 characters from the hash (i.e. random), so
it's unlikely to alias with any string constant used in the sources.
In general we now pad shortened strings from the left with leading
dir seperators, but in the case of C-strings that are much shorter
and don't share a common suffix (due to projections), we do allow
shrinking the C-string, appending a null, and retaining the old part
of the prefix.
Also when rewiring, we ensure that the new hash preserves the last
7 bytes of the old hash.
Co-authored-by: Harmen Stoppels <harmenstoppels@gmail.com>
A user may want to set some attributes on a package without actually modifying the package (e.g. if they want to git pull updates to the package without conflicts). This PR adds a per-package configuration section called "set", which is a dictionary of attribute names to desired values. For example:
packages:
openblas:
package_attributes:
submodules: true
git: "https://github.com/myfork/openblas"
in this case, the package will always retrieve git submodules, and will use an alternate location for the git repo.
While git, url, and submodules are the attributes for which we envision the most usage, this allows any attribute to be overridden, and the acceptable values are any value parseable from yaml.
Newer versions of the CrayPE for EX systems have standalone compiler executables for CCE and compiler wrappers for Cray MPICH. With those, we can treat the cray systems as part of the linux platform rather than having a separate cray platform.
This PR:
- [x] Changes cray platform detection to ignore EX systems with Craype version 21.10 or later
- [x] Changes the cce compiler to be detectable via paths
- [x] Changes the spack compiler wrapper to understand the executable names for the standalone cce compiler (`craycc`, `crayCC`, `crayftn`).
Whenever the rpath string actually _grows_, it falls back to patchelf,
when it stays the same length or gets shorter, we update it in-place,
padded with null bytes.
This PR only deals with absolute -> absolute rpath replacement. We don't
use `_build_tarball(relative=True)` in our CI. If `relative` then it falls
back to the old replacement code.
With this PR, relocation time goes down significantly, likely because patchelf
does some odd things with mmap, causing lots of overhead. Example:
- `binutils`: 700MB installed, goes from `1.91s` to `0.57s`, or `3.4x` faster.
Relocation time: 27% -> 10% of total install time
- `llvm`: 6.8GB installed, goes from `28.56s` to `5.38`, or `5.3x` faster.
Relocation time: 44% -> 13% of total install time
The bottleneck is now decompression.
Note: I'm somewhat confused about the "relative rpath" code paths. Right
now this PR only deals with absolute -> absolute replacement. As far as
I understand, if you embrace relative rpaths when uploading to the
buildcache, the whole point is you _don't_ want to patch rpaths on
install? So it seems fine to not expand `$ORIGIN` again imho.
When a package asks for non-parallel make, we need to force `make -j1` because just doing `make` will run in parallel under jobserver (e.g. `spack env depfile`).
We now always add `-j1` when asked for a non-parallel execution (even if there is no jobserver).
And each `MakeExecutable` can now ask for jobserver support or not. For example: the default `ninja` does not support jobserver so spack applies the default `-j`, but `ninja@kitware` or `ninja-fortran` does, so spack doesn't add `-j`.
Tips: you can run `SPACK_INSTALL_FLAGS=-j1 make -f spack-env-depfile.make -j8` to avoid massive job-spawning because of build tools that don't support jobserver (ninja).
We try to avoid non-default variant values in the concretizer, but this doesn't make
sense for variants forced to take some non-default value by variant propagation.
Counting this as a penalty effectively biases the concretizer for small specs dependency
graphs -- something we try very hard to avoid elsewhere because it can lead to very
strange decisions.
Example: with the penalty, `spack spec hdf5` will choose the default `openmpi` as its
`mpi` provider, but `spack spec hdf5 ~~shared` will choose `mpich` because it has to set
fewer non-default variant values because `mpich`'s DAG is smaller. That's not a good
reason to prefer a non-default virtual provider.
To fix this, if the user explicitly requests a non-default value to be propagated, there
shouldn't be a penalty. Variant values set on the CLI already don't count as default; we
just need to extend that to propagated values.
Adds another post install hook that loops over the install prefix, looking for shared libraries type of ELF files, and sets the soname to their own absolute paths.
The idea being, whenever somebody links against those libraries, the linker copies the soname (which is the absolute path to the library) as a "needed" library, so that at runtime the dynamic loader realizes the needed library is a path which should be loaded directly without searching.
As a result:
1. rpaths are not used for the fixed/static list of needed libraries in the dynamic section (only for _actually_ dynamically loaded libraries through `dlopen`), which largely solves the issue that Spack's rpaths are a heuristic (`<prefix>/lib` and `<prefix>/lib64` might not be where libraries really are...)
2. improved startup times (no library search required)
Untouched spec pruning was added to reduce the number of specs
developers see getting rebuilt in their PR pipelines that they
don't understand. Because the state of the develop mirror lags
quite far behind the tip of the develop branch, PRs often find
they need to rebuild things untouched by their PR.
Untouched spec pruning was previously implemented by finding all
specs in the environment with names of packages touched by the PR,
traversing in both directions the DAGS of those specs, and adding
all dependencies as well as dependents to a list of concrete specs
that should not be considered for pruning.
We found that this heuristic results in too many pruned specs, and
that dependents of touched specs must have all their dependencies
added to the list of specs that should not be considered for pruning.
This issue was introduced in #29761:
```
==> Installing ncurses-6.3-22hz6q6cvo3ep2uhrs3erpp2kogxncbn
==> No binary for ncurses-6.3-22hz6q6cvo3ep2uhrs3erpp2kogxncbn found: installing from source
==> Using cached archive: /spack/var/spack/cache/_source-cache/archive/97/97fc51ac2b085d4cde31ef4d2c3122c21abc217e9090a43a30fc5ec21684e059.tar.gz
==> No patches needed for ncurses
==> ncurses: Executing phase: 'autoreconf'
==> ncurses: Executing phase: 'configure'
==> ncurses: Executing phase: 'build'
==> ncurses: Executing phase: 'install'
==> Error: AttributeError: 'str' object has no attribute 'propagate'
The 'ncurses' package cannot find an attribute while trying to build from sources. This might be due to a change in Spack's package format to support multiple build-systems for a single package. You can fix this by updating the build recipe, and you can also report the issue as a bug. More information at https://spack.readthedocs.io/en/latest/packaging_guide.html#installation-procedure
/spack/lib/spack/spack/build_environment.py:1075, in _setup_pkg_and_run:
1072 tb_string = traceback.format_exc()
1073
1074 # build up some context from the offending package so we can
>> 1075 # show that, too.
1076 package_context = get_package_context(tb)
1077
1078 logfile = None
```
It turns out this was caused by a bug that had been around much longer, in which the flags were passed by reference to the flag_handler, and the flag_handler was modifying the spec object, not just the flags given to the build system. The scope of this bug was limited by the forking model in Spack, which is how it went under the radar for so long.
PR includes regression test.
* remove deptype_query remnants
* deptypes -> deptype
These arguments haven't existed since 2017, but `traverse` now fails on unknown **kwargs, so they have finally popped up.
This updates the propagation logic used in `concretize.lp` to avoid rules with `path()`
in the body and instead base propagation around `depends_on()`.
Currently, compiler flags and variants are inconsistent: compiler flags set for a
package are inherited by its dependencies, while variants are not. We should have these
be consistent by allowing for inheritance to be enabled or disabled for both variants
and compiler flags.
- [x] Make new (spec language) operators
- [x] Apply operators to variants and compiler flags
- [x] Conflicts currently result in an unsatisfiable spec
(i.e., you can't propagate two conflicting values)
What I propose is using two of the currently used sigils to symbolized that the variant
or compiler flag will be inherited:
Example syntax:
- `package ++variant`
enabled variant that will be propagated to dependencies
- `package +variant`
enabled variant that will NOT be propagated to dependencies
- `package ~~variant`
disabled variant that will be propagated to dependencies
- `package ~variant`
disabled variant that will NOT be propagated to dependencies
- `package cflags==True`
`cflags` will be propagated to dependencies
- `package cflags=True`
`cflags` will NOT be propagated to dependencies
Syntax for string-valued variants is similar to compiler flags.
Fixes an issue on the RHEL8 UBI container where this test would fail because `gr_mem`
was empty for every entry in the `grp` DB.
You have to check *both* the `pwd` database (which has primary groups) and `grp` (which
has other gorups) to do this correctly.
- [x] update `llnl.util.filesystem.group_ids()` to do this
- [x] use it in the `sbang` test
This PR introduces breadth-first traversal, and moves depth-first traversal
logic out of Spec's member functions, into `traverse.py`.
It introduces a high-level API with three main methods:
```python
spack.traverse.traverse_edges(specs, kwargs...)
spack.traverse.traverse_nodes(specs, kwags...)
spack.traverse.traverse_tree(specs, kwargs...)
```
with the usual `root`, `order`, `cover`, `direction`, `deptype`, `depth`, `key`,
`visited` kwargs for the first two.
What's new is that `order="breadth"` is added for breadth-first traversal.
The lower level API is not exported, but is certainly useful for advanced use
cases. The lower level API includes visitor classes for direction reversal and
edge pruning, which can be used to create more advanced traversal methods,
especially useful when the `deptype` is not constant but depends on the node
or depth.
---
There's a couple nice use-cases for breadth-first traversal:
- Sometimes roots have to be handled differently (e.g. follow build edges of
roots but not of deps). BFS ensures that root nodes are always discovered at
depth 0, instead of at any depth > 1 as a dep of another root.
- When printing a tree, it would be nice to reduce indent levels so it fits in the
terminal, and ensure that e.g. `zlib` is not printed at indent level 10 as a
dependency of a build dep of a build dep -- rather if it's a direct dep of my
package, I wanna see it at depth 1. This basically requires one breadth-first
traversal to construct a tree, which can then be printed with depth-first traversal.
- In environments in general, it's sometimes inconvenient to have a double
loop: first over the roots then over each root's deps, and maintain your own
`visited` set outside. With BFS, you can simply init the queue with the
environment root specs and it Just Works. [Example here](3ec7304699/lib/spack/spack/environment/environment.py (L1815-L1816))
Currently, many tests hardcode to older versions of gcc for comparisons of
concretization among compiler versions. Those versions are too old to concretize for
`aarch64`-family targets, which leads to failing tests on `aarch64`.
This PR fixes those tests by updating the compiler versions used for testing.
Currently, many tests hardcode the expected architecture result in concretization to the
`x86_64` family of architectures.
This PR generalizes the tests that can be generalized, to cover multiple architecture
families. For those that test specific relationships among `x86_64`-family targets, it
ensures that concretization uses the `x86_64`-family targets in those cases.
Currently, many tests rely on the fact that `AutotoolsPackage` imposes no dependencies
on the inheriting package. That is not true on `aarch64`-family architectures.
This PR ensures that the fact `AutotoolsPackage` on `aarch64` pulls in a dependency on
`gnuconfig` is ignored when testing for the appropriate relationships among dependencies
Additionally, 5 tests currently prompt the user for input when `gpg` is available in the
user's path. This PR fixes that issue. And 7 tests fail currently when the user has a
yubikey available. This PR fixes the incorrect gpg argument causing those issues.
The `spack info <package>` command does not show the `Virtual Packages:` output unless the `--virtuals` command option is passed. Before this changes, the information that the command is supposed to be illustrating is not shown in the example and is confusing.
Changes to improve locating shared libraries on Windows, which in
turn enables the use of Clingo. This PR attempts to establish a
proper distinction between linking on Windows vs. Linux/Mac: on
Windows, linking is always done with .lib files (never .dll files).
This somewhat complicates the model since the Spec.lib method could
return libraries that were used for both linking and loading, but
since these are not always the same on Windows, it was decided to
treat Spec.libs as being for link-time libraries. Additional functions
are added to help dependents locate run-time libraries.
* Clingo is now the default concretizer on Windows
* Clingo is now the concretizer used for unit tests on Windows
* Fix a permissions issue that can occur while moving Git files during
fetching/staging
* Packages can now implement "win_add_library_dependent" to register
files/directories that include libraries that would need to link
to dependency dlls
* Packages can now implement "win_add_rpath" to register the locations
of dlls that dependents would want to load
* "Spec.libs" on Windows is updated to return link-time libraries
(i.e. .lib files, rather than .dll files)
* PackageBase.rpath on Windows is now updated to return the most-likely
locations where .dlls will be found (which is generally in the bin/
directory)
Currently there's a slow sequential step in binary relocation where all
strings of a binary are collected, with rpaths removed, and then
filtered for the old install root.
This is completely unnecessary, and also incorrect, since we replace
more than just the old install root in the prefix to prefix mapping. And
in fact the prefix to prefix mapping is parallel, and a single pass. So
even as an optimization, this filter makes no sense anymore.
Therefor we remove it
- single pass over the binary data matching all prefixes
- collect offsets and replacement strings
- do in-place updates with `fseek` / `fwrite`, since typically our
replacement touch O(few bytes) while the file is O(many megabytes)
- be nice: leave the file untouched if some string can't be
replaced
* Add patches for building clingo with MSVC
* Help python find clingo DLL
* If an executable is located in "C:\Program Files", Executable was
running into issues with the extra space. This quotes the exe
to ensure that it is treated as a single value.
Signed-off-by: Kiruya Momochi <65301509+KiruyaMomochi@users.noreply.github.com>
This commit extends the DSL that can be used in packages
to allow declaring that a package uses different build-systems
under different conditions.
It requires each spec to have a `build_system` single valued
variant. The variant can be used in many context to query, manipulate
or select the build system associated with a concrete spec.
The knowledge to build a package has been moved out of the
PackageBase hierarchy, into a new Builder hierarchy. Customization
of the default behavior for a given builder can be obtained by
coding a new derived builder in package.py.
The "run_after" and "run_before" decorators are now applied to
methods on the builder. They can also incorporate a "when="
argument to specify that a method is run only when certain
conditions apply.
For packages that do not define their own builder, forwarding logic
is added between the builder and package (methods not found in one
will be retrieved from the other); this PR is expected to be fully
backwards compatible with unmodified packages that use a single
build system.
Instead of looping over multiple regexes and the entire text file
contents, create a giant regex with all literal prefixes and do a single
pass over files to detect prefixes. Not only is a single pass faster,
it's also likely that the regex is compiled better, given that most
prefixes share a common ... prefix.
In the dfs code, flip edges so that `parent` means `from` and
`spec` means `to` in the direction of traversal. This makes it slightly
easier to write generic/composable code. For example when using visitors
where one visitor reverses direction, and another only cares about
accepting particular edges or not depending on whether the target node
is seen before, it would be good if the second visitor didn't have to
know whether the order was changed or not.
Use the same compression level as `gzip` (6) instead of what Python uses
(9).
The LLVM tarball takes 4m instead of 12m to create, and is <1% larger.
That's not worth the wait...
#32137 added an option to update() a BinaryCacheIndex with a
cooldown: repeated attempts within this cooldown would not
actually retry. However, the cooldown was not properly
tracked for failures (which is common when the mirror
does not store any binaries and therefore has no index.json).
This commit ensures that update(..., with_cooldown=True) will
also skip the update even if a failure has occurred within the
cooldown period.
Due to reuse concretization, we may generate DAGs with two occurrences
of the same package corresponding to distinct specs. This happens when
build dependencies are reused, since their dependencies are ignored in
concretization.
This caused a regression, for example: `spec['openssl']` would take the
'openssl' of the build dep `cmake`, instead of the direct `openssl`
dependency, simply because the edge to `cmake` was traversed first and
we do depth first traversal.
One solution that was discussed is to limit `spec[name]` to just direct
deps, or direct deps + transitive link deps, but this is too breaking.
Instead, this PR simply prioritizes transitive link and direct
build/run/test deps, and then falls back to a full DAG traversal. So,
it's just about order of iteration.
Scan the text files for relocatable prefixes *before* creating a tarball,
to reduce the amount of work to be done during install from binary
cache.
Co-authored-by: Harmen Stoppels <harmenstoppels@gmail.com>
Instead of showing
```
==> Error: Timed out waiting for a write lock.
```
show
```
==> Error: Timed out waiting for a write lock after 1.200ms and 4 attempts on file: /some/file
```
s.t. we actually get to see where acquiring a lock failed even when not
running in debug mode.
And use pretty time units everywhere, so we don't get 1.45e-9 seconds
but 1.450ns etc.
* backtraces without --debug
Currently `--debug` is too verbose and not-`--debug` gives to little
context about where exceptions are coming from.
So, instead, it'd be nice to have `spack --backtrace` and
`SPACK_BACKTRACE=1` as methods to get something inbetween: no verbose
debug messages, but always a full backtrace.
This is useful for CI, where we don't want to drown in debug messages
when installing deps, but we do want to get details where something goes
wrong if it goes wrong.
* completion
Currently `relocate_text` and `relocate_text_bin` are unsafe in the
sense that they run in parallel, and lead to races when modifying
different items pointing to the same inode.
This leads to the issue observed in #33453.
This PR:
1. Renames those functions to `unsafe_*` so people are aware
2. Adds logic to deal with hardlinks in current binary packages
3. Adds logic to deal with hardlinks when creating new binary tarballs,
so the install side doesn't have to de-dupe hardlinks.
4. Adds a test for 3
The assumption is that all our relocation logic preserves inodes. That
is, we should never copy a file, modify it, and then move it back. I
quickly verified, and its seems like this is true for (binary) text
relocation, as well as rpath patching in patchelf (even when the file
grows) and mach-o fixes.
* gitlab: Do not use root_spec['pkg_name'] anymore
For a long time it was fine to index a concrete root spec with the name
of a dependency in order to access the concrete dependency spec. Since
pipelines started using `--use-buildcache dependencies:only,package:never`
though, it has exposed a scheduling issue in how pipelines are
generated. If a concrete root spec depends on two different hashes of
`openssl` for example, indexing that root with just the package name
is ambiguous, so we should no longer depend on that approach when
scheduling jobs.
* env: make sure exactly one spec in env matches hash
When installing some/all specs from a buildcache, build edges are pruned
from those specs. This can result in a much smaller effective DAG. Until
now, `spack env depfile` would always generate a full DAG.
Ths PR adds the `spack env depfile --use-buildcache` flag that was
introduced for `spack install` before. This way, not only can we drop
build edges, but also we can automatically set the right buildcache
related flags on the specific specs that are gonna get installed.
This way we get parallel installs of binary deps without redundancy,
which is useful for Gitlab CI.
When downloading from binary cache not only replace RPATHs to dependencies, but
also text references to dependencies.
Example:
`autoconf@2.69` contains a text reference to the executable of its dependency
`perl`:
```
$ grep perl-5 /shared/spack/opt/spack/linux-amzn2-x86_64_v3/gcc-7.3.1/autoconf-2.69-q3lo/bin/autoreconf
eval 'case $# in 0) exec /shared/spack/opt/spack/linux-amzn2-x86_64_v3/gcc-7.3.1/perl-5.34.1-yphg/bin/perl -S "$0";; *) exec /shared/spack/opt/spack/linux-amzn2-x86_64_v3/gcc-7.3.1/perl-5.34.1-yphg/bin/perl -S "$0" "$@";; esac'
```
These references need to be replace or any package using `autoreconf` will fail
as it cannot find the installed `perl`.
Co-authored-by: Stephen Sachs <stesachs@amazon.com>
"spack install" will not update the binary index if given a concrete
spec, which causes it to fall back to direct fetches when a simple
index update would have helped. For S3 buckets in particular, this
significantly and needlessly slows down the install process.
This commit alters the logic so that the binary index is updated
whenever a by-hash lookup fails. The lookup is attempted again with
the updated index before falling back to direct fetches. To avoid
updating too frequently (potentially once for each spec being
installed), BinaryCacheIndex.update now includes a "cooldown"
option, and when this option is enabled it will not update more
than once in a cooldown window (set in config.yaml).
Co-authored-by: Tamara Dahlgren <35777542+tldahlgren@users.noreply.github.com>
* Add libpressio and dependencies; some of these packages are
maintained as forks of the original repositories and in those
cases the docstring mentions this.
* Add optional dependency in adios2 on libpressio
* cub package: set CUB_DIR environment variable for dependent
installations
* Clear R_HOME/R_ENVIRON before Spack installation (avoid sources
outside of Spack from affecting the installation in Spack)
* Rename dlib to dorian3d-dlib and update dependents; add new dlib
implementation. Pending an official policy on how to handle
packages with short names, reviewer unilaterally decided that
the rename was acceptable given that the new Spack dlib package
is referenced more widely (by orders of magnitude) than the
original
Co-authored-by: Samuel Li <shaomeng@users.noreply.github.com>
When installing an individual spec `spack --only=package --cache-only /xyz`
from a buildcache, Spack currently issues tons of warnings about
missing build deps (and their deps) in the database.
This PR disables these warnings, since it's fine to have a spec without
its build deps in the db (they are just "missing").
Currently `traverse_dependencies` fixes deptypes to traverse once and
for all in the recursion, but this is incorrect, since deptypes depend
on the node (e.g. if it's a dependency and cache-only, don't follow
build type edges, even if the parent is build from sources and needs
build deps.)
Support spackbot rebuilding all specs from source when asked (with "rebuild everything")
- Allow overriding --prune-dag cli opt with env var
- Use job variable to optionally prevent rebuild jobs early exit behavior
- ci rebuild: Use new install argument to insist deps are always installed from binary, but
package is only installed from source.
- gitlab: fix bug w/ untouched pruning
- ci rebuild: install from hash rather than json file
- When doing a "rebuild everything" pipeline, make sure that each install job only consumes
binary dependencies from the mirror being populated by the current pipeline. This avoids
using, e.g. binaries from develop, when rebuilding everything on a PR.
- When running a pipeline to rebuild everything, do not die because we generated a hash on
the broken specs list. Instead only warn in that case.
- bugfix: Replace broken no-args tty.die() with sys.exit(1)
Print a message of the form
```
Fetch mm:ss. Build: mm:ss. Total: mm:ss
```
when installing from buildcache.
Previously this only happened for source builds.
Currently "spack ci generate" chooses the first matching entry in
gitlab-ci:mappings to fill attributes for a generated build-job,
requiring that the entire configuration matrix is listed out
explicitly. This unfortunately causes significant problems in
environments with large configuration spaces, for example the
environment in #31598 (spack.yaml) supports 5 operating systems,
3 architectures and 130 packages with explicit size requirements,
resulting in 1300 lines of configuration YAML.
This patch adds a configuraiton option to the gitlab-ci schema called
"match_behavior"; when it is set to "merge", all matching entries
are applied in order to the final build-job, allowing a few entries
to cover an entire matrix of configurations.
The default for "match_behavior" is "first", which behaves as before
this commit (only the runner attributes of the first match are used).
In addition, match entries may now include a "remove-attributes"
configuration, which allows matches to remove tags that have been
aggregated by prior matches. This only makes sense to use with
"match_behavior:merge". You can combine "runner-attributes" with
"remove-attributes" to effectively override prior tags.
When a pipeline generation job is automatically failed because it
generated jobs for specs known to be broken on develop, print better
information about the broken specs that were encountered. Include
at a minimum the hash and the url of the job whose failure caused it
to be put on the broken specs list in the first place.
* env depfile: allow deps only install
- Refactor `spack env depfile` to use a Jinja template, making it a bit
easier to follow as a human being.
- Add a layer of indirection in the generated Makefile through an
`<prefix>/.install-deps/<hash>` target, which allows one to specify
different options when installing dependencies. For example, only
verbose/debug mode on when installing some particular spec:
```
$ spack -e my_env env depfile -o Makefile --make-target-prefix example
$ make example/.install-deps/<hash> -j16
$ make example/.install/<hash> SPACK="spack -d" SPACK_INSTALL_FLAGS=--verbose -j16
```
This could be used to speed up `spack ci rebuild`:
- Parallel install of dependencies from buildcache
- Better readability of logs, e.g. reducing verbosity when installing
dependencies, and splitting logs into deps.log and current_spec.log
* Silence please!
* spack.compiler.Compiler: introduce prefix property
We currently don't really have something that gives the GCC install
path, which is used by many LLVM-based compilers (llvm, llvm-amdgpu,
nvhpc, ...) to fix the GCC toolchain once and for all.
This `prefix` property is dynamic in the sense that it queries the
compiler itself. This is necessary because it's not easy to deduce the
install path from the `cc` property (might be a symlink, might be a
filename like `gcc` which works by having the compiler load a module
that sets the PATH variable, might be a generic compiler wrapper based
on environment variables like on cray...).
With this property introduced, we can clean up some recipes that have
the logic repeated for GCC.
* intel-oneapi-compilers: set --gcc-sysroot to %gcc prefix
Caches used by repositories don't reference the global spack.repo.path instance
anymore, but get the repository they refer to during initialization.
Spec.virtual now use the index, and computation done to compute the index
use Repository.is_virtual_safe.
Code to construct mock packages and mock repository has been factored into
a unique MockRepositoryBuilder that is used throughout the codebase.
Add debug print for pushing and popping config scopes.
Changed spack.repo.use_repositories so that it can override or not previous repos
spack.repo.use_repositories updates spack.config.config according to the modifications done
Removed a peculiar behavior from spack.config.Configuration where push would always
bubble-up a scope named command_line if it existed
Resolves#31782
With this change, if a spec is concrete after parsing (e.g. spec.yaml
or /hash-based), then it is not disambiguated (a process which requires
(a) that the spec be installed and (b) that it be part of the
currently-active environment).
This commit allows you to:
* Diff specs from an environment regardless of whether they have
been installed (more useful for projection/matrix-based envs)
* Diff specs read from .yaml files which may or may not be entirely
different installations of Spack
Co-authored-by: Massimiliano Culpo <massimiliano.culpo@gmail.com>
* Docs: Getting Started Dependencies
Finally document what one needs to install to use Spack on
Linux and Mac :-)
With <3 for minimal container users and my colleagues with
their fancy Macs.
* Debian Update Packages: GCC, Python
- build-essential: includes gcc, g++ (thx Cory)
- Python: add python3-venv, python3-distutils (thx Pradyun)
* Add RHEL8 Dependencies
* filter_file: introduce argument 'start_at'
* autotools: extend patching of the libtool script
* autotools: refactor _patch_usr_bin_file
* autotools: improve readability of the filtering
* autotools: keep the modification time of the configure scripts
* autotools: do not try to patch directories
* autotools: explain libtool patching for posterity
Co-authored-by: Massimiliano Culpo <massimiliano.culpo@gmail.com>
Co-authored-by: Harmen Stoppels <harmenstoppels@gmail.com>
Remove `module-info mode load` condition that prevents auto-unloading when autoloading is enabled. It looks like this condition was added to work around an issue in environment-modules that is no longer necessary.
Add quotes to make is-loaded happy
When concurrent misc_cache provider index rebuilds happen, try to
rebuild it only once, so we don't exceed misc_cache lock timeout.
For example, when using `spack env depfile`, with no previous
misc_cache, running `make -f depfile -j8` could run at most 8 concurrent
`spack install` locking on misc_cache to rebuild the provider index. If
one rebuild takes 30s, before this fix, the "worst" lock could wait up
to 30s * 7, easily exceeding misc_cache lock timeout. Now, the "worst"
lock would take 30s * 1 + ~1s * 6.
Currently, module changes from `setup_dependent_package` are applied only to the module of the package class, but not to any parent classes' modules between the package class module and `spack.package_base`.
In this PR, we create a custom class to accumulate module changes, and apply those changes to each class that requires it. This design allows us to code for a single module, while applying the changes to multiple modules as needed under the hood, without requiring the user to reason about package inheritance.
* find/list: display package counts last
We have over 6,600 packages now, and `spack list` still displays the number of packages
before it lists them all. This is useless for large sets of results (e.g., with no args)
as the number has scrolled way off the screen before you can see it. The same is true
for `spack find` with large installations.
This PR changes `spack find` and `spack list` so that they display the package count
last.
* add some quick testing
Co-authored-by: Danny McClanahan <1305167+cosmicexplorer@users.noreply.github.com>
Allow environment variables and spack-specific path substitution variables (e.g. `$spack`) to be
used in the paths associated with develop specs, while maintaining the ability to keep those
paths relative to the environment rather than the working directory.
Install: Add use-buildcache option to install
* Allow differentiating between top level packages and dependencies when
determining whether to install from the cache or not.
* Add unit test for --use-buildcache
* Use metavar to display use-buildcache options.
* Update spack-completion
Make it possible to install the Clingo package on Windows; this
also provides a means to use Clingo with Spack on Windows.
This includes
* A new "winbison" package: Windows has a port of bison and flex where
the two packages are grouped together. Clingo dependencies have been
updated to use winbison on Windows and bison elsewhere (this avoids
complicating the existin bison/flex packages until we can add support
for implied virtuals).
* The CMake build system was incorrectly converting CMAKE_INSTALL_PREFIX
to POSIX format.
* The re2c package has been modified to use CMake on Windows; for now
this is done by overloading the configure/build/install methods to
perform CMake-appropriate operations; the package should be refactored
once support for multiple build systems in one Package is available.
This commit fixes#27027.
The root cause of the issue is that the `SPACK_OLD_PROMPT` variable
was evaluated in string interpolation regardless of whether the
guard condition above evaluates to true or false. This commit uses
the `eval` keyword to defer evaluation until the command is executed.
Co-authored-by: Alexander Hornburg <alexande@xilinx.com>
Spack currently depends on parsing filenames of downloaded files to
determine what type of archive they are and how to decompress them.
This commit adds a preliminary check based on magic numbers to
determine archive type (but falls back on name parsing if the
extension type cannot be determined).
As part of this work, this commit also enables decompression of
.tar.xz-compressed archives on Windows.
Include exception info related to url retrieval in debug messages
which otherwise would be swallowed. This is intended to be useful
for detecting if CA configuration interferes with downloads from
HTTPS links.
This fixes a bug where two installations that differ only by package hash will not show
up in `spack find`.
The bug arose because `_cmp_node` on `Spec` didn't include the package hash in its
yielded fields. So, any two `Spec` objects that were only different by package hash
would appear to be equal and would overwrite each other when inserted into the same
`dict`. Note that we could still *install* specs with different package hashes, and they
would appear in the database, but we code that needed to put them into data structures
that use `__hash__` would have issues.
This PR makes `Spec.__hash__` and `Spec.__eq__` include the `process_hash()`, and it
makes `Spec._cmp_node` include the package hash. All of these *should* include all
information in a spec so that we don't end up in a situation where we are blind to
particular field differences.
Eventually, we should unify the `_cmp_*` methods with `to_node_dict` so there aren't two
sources of truth, but this needs some thought, since the `_cmp_*` methods exist for
speed. We should benchmark whether it's really worth having two types of hashing now
that we use `json` instead of `yaml` for spec hashing.
- [x] Add `package_hash` to `Spec._cmp_node`
- [x] Add `package_hash` to `spack.solve.asp.spec_clauses` so that the `package_hash`
will show up in `spack diff`.
- [x] Add `package_hash` to the `process_hash` (which doesn't affect abstract specs
but will make concrete specs correct)
- [x] Make `_cmp_iter` report the dag_hash so that no two specs with different
process hashes will be considered equal.
53a7b49 created a reference error which broke `.libs` (and
`find_libraries`) for many packages. This fixes the reference
error and improves the testing for `find_libraries` by actually
checking the extension types of libraries that are retrieved by
the function.
* catch json schema errors and reraise as property of SpackError
* no need to catch subclass of given error
* Builtin json library for Python 2 uses more generic type
* Correct instantiation of SpackError (requires a string rather than an exception)
* Use exception chaining (where possible)
