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
* 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
- 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`
* 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>
* 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
* Switch hdf5 package from autotools to cmake.
* Add variant for building with zlib, default to ON.
* Update for format requirements.
* Format change.
* Fix breakage from last merge from develop.
Switch szip to use libaec (unrestricted encryption).
Remove 'static' variant: static libs will only be installed when
~shared.
* Improve args based on suggestions from pull request.
* Update code URL to github.com
Add/modify 4 depends_on lines to fix running "spack graph --deptype=link hdf5".
* Remove trailing whitespace.
* Remove dependencies added solely to make "spack greph --type=link" work.
* Add new version HDF5 1.8.22.
* Remove unnecessary java_check.
* Fix whitespace for style checks.
* Reverted zlib version dependency to 1.1.2:.
zlib variant removed.
api version default renamed "default".
* Remove blank line.
* Whitespace corrections.
* iRemoved unnecessary 'debug' variant.
* Fix typo in version number in conflict for '+szip'.
* Set default for tools variant to True.
Remove patch functions dependent on 'libtool' file that cmake doesn't
produce.
* Remove line to set ONLY_SHARED_LIBS to true.
Add post_install code to install only one version of tools with shared
linkage and original tool names.
* Remove trailing white space and import of glob package not used.
* Leave BUILD_TESTING set to default which is ON.
* Remove post_install code to install only one version of tools because
some dependent packages running tests in e4s testing are using
h5diff-shared. Keep both tools versions for now.
* No longer need to import os.
This adds a package for `irep`, a tool for reading `lua` input decks from
Fortran, C, and C++.
`irep` can be built with either `lua` or `luajit`. To address this, we also add
a virtual package for lua called `lua-lang`. `luajit` isn't, by default, a drop-in
replacement for `lua`, but we add a `+lualinks` variant to it that adds symlinks
that make it behave like `lua@5.1`. With this variant enabled, it provides the
`lua-lang` virtual. `lua` always provides `lua-lang`.
- [x] add `irep` package
- [x] add `+lualinks` variant to `lua-luajit`
- [x] create `lua-lang` virtual, provided by `lua` and `luajit+lualinks`
Co-authored-by: Kayla Richarda Butler <butler59@quartz1148.llnl.gov>
Co-authored-by: Todd Gamblin <tgamblin@llnl.gov>
Currently, module configurations are inconsistent because modulefiles are generated with the configs for the active environment, but are shared among all environments (and spack outside any environment).
This PR fixes that by allowing Spack environments (or other spack config scopes) to define additional sets of modules to generate. Each set of modules can enable either lmod or tcl modules, and contains all of the previously available module configuration. The user defines the name of each module set -- the set configured in Spack by default is named "default", and is the one returned by module manipulation commands in the absence of user intervention.
As part of this change, the module roots configuration moved from the config section to inside each module configuration.
Additionally, it adds a feature that the modulefiles for an environment can be configured to be relative to an environment view rather than the underlying prefix. This will not be enabled by default, as it should only be enabled within an environment and for non-default views constructed with separate projections per-spec.
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
Currently, module configurations are inconsistent because modulefiles are generated with the configs for the active environment, but are shared among all environments (and spack outside any environment).
This PR fixes that by allowing Spack environments (or other spack config scopes) to define additional sets of modules to generate. Each set of modules can enable either lmod or tcl modules, and contains all of the previously available module configuration. The user defines the name of each module set -- the set configured in Spack by default is named "default", and is the one returned by module manipulation commands in the absence of user intervention.
As part of this change, the module roots configuration moved from the `config` section to inside each module configuration.
Additionally, it adds a feature that the modulefiles for an environment can be configured to be relative to an environment view rather than the underlying prefix. This will not be enabled by default, as it should only be enabled within an environment and for non-default views constructed with separate projections per-spec.
TODO:
- [x] code changes to support multiple module sets
- [x] code changes to support modules relative to a view
- [x] Tests for multiple module configurations
- [x] Tests for modules relative to a view
- [x] Backwards compatibility for module roots from config section
- [x] Backwards compatibility for default module set without the name specified
- [x] Tests for backwards compatibility
* Make -j flag less exceptional
The -j flag in spack behaves differently from make, ctest, ninja, etc,
because it caps the number of jobs to an arbitrary number 16.
Spack will behave like other tools if `spack install` uses a reasonable
default, and `spack install -j <num>` *overrides* that default.
This will be particularly useful for Spack usage outside of a traditional
HPC context and for HPC centers that encourage users to compile on
login nodes with many cores instead of on compute nodes, which has
become increasingly common as individual nodes have more cores.
This maintains the existing default value of min(num_cpus, 16). However,
as it is right now, Spack does a poor job at determining the number of
cpus on linux, since it doesn't take cgroups into account. This is
particularly problematic when using distributed builds with slurm. This PR
also introduces `spack.util.cpus.cpus_available()` to consolidate
knowledge on determining the number of available cores, and improves
core detection for linux. This should also improve core detection for Docker/
Kubernetes, which also use cgroups.
Drops:
* C_INCLUDE_PATH
* CPLUS_INCLUDE_PATH
* LIBRARY_PATH
* INCLUDE
We already decided to use C_INCLUDE_PATH, CPLUS_INCLUDE_PATH, INCLUDE over CPATH here:
https://github.com/spack/spack/pull/14749
However, none of these flags apply to Fortran on Linux. So for consistency it seems better to make the user use -I and -L flags by hand or through pkgconfig.
* Procedure to deprecate old versions of software
* Add documentation
* Fix bug in logic
* Update tab completion
* Deprecate legacy packages
* Deprecate old mxnet as well
* More explicit docs
libuuid is currently contained in util-linux, libuuid and uuid. This
change introduces a new virtual provider `uuid` and renames the existing
`uuid` package to `ossp-uuid`.
util-linux's libuuid is provided in the form of a separate package
util-linux-uuid to make sure that packages depending on uuid and
util-linux can use a separate uuid implementation, which the concretizer
does not allow if libuuid is contained in util-linux.
Users can add test() methods to their packages to run smoke tests on
installations with the new `spack test` command (the old `spack test` is
now `spack unit-test`). spack test is environment-aware, so you can
`spack install` an environment and then run `spack test run` to run smoke
tests on all of its packages. Historical test logs can be perused with
`spack test results`. Generic smoke tests for MPI implementations, C,
C++, and Fortran compilers as well as specific smoke tests for 18
packages.
Inside the test method, individual tests can be run separately (and
continue to run best-effort after a test failure) using the `run_test`
method. The `run_test` method encapsulates finding test executables,
running and checking return codes, checking output, and error handling.
This handles the following trickier aspects of testing with direct
support in Spack's package API:
- [x] Caching source or intermediate build files at build time for
use at test time.
- [x] Test dependencies,
- [x] packages that require a compiler for testing (such as library only
packages).
See the packaging guide for more details on using Spack testing support.
Included is support for package.py files for virtual packages. This does
not change the Spack interface, but is a major change in internals.
Co-authored-by: Tamara Dahlgren <dahlgren1@llnl.gov>
Co-authored-by: wspear <wjspear@gmail.com>
Co-authored-by: Adam J. Stewart <ajstewart426@gmail.com>
Since #11598 sbang has been installed within the install_tree. This doesn’t play
nicely with install_tree padding, since sbang can’t do its job if it is installed in a
long path (this is the whole point of sbang).
This PR changes the padding specification. Instead of $padding inside paths,
we now have a separate `padding:` field in the `install_tree` configuration.
Previously, the `install_tree` looked like this:
```
/path/to/opt/spack_padding_padding_padding_padding_padding/
bin/
sbang
.spack-db/
...
linux-rhel7-x86_64/
...
```
```
This PR updates things to look like this:
/path/to/opt/
bin/
sbang
spack_padding_padding_padding_padding_padding/
.spack-db/
...
linux-rhel7-x86_64/
...
So padding is added at the start of all install prefixes *within* the unpadded
root. The database and all installations still go under the padded root.
This ensures that `sbang` is in the shorted possible path while also allowing
us to make long paths for relocatable binaries.
* [NEW] Added amdfftw, amdlibflame and amdscalapack recipes
Updated base fftw, libflame and netlib-scalapack recipes
to accommodate the above listed AMD Optimizing CPU Libraries
which are a set of numerical routines optimized for AMD platforms.
Updated amdblis spack recipe
amdblis:
1. updated with amdblis 2.2 release
amdfftw:
1. "--enable-single" now work as synonym for "--enable-float"
amdlibflame:
1. Added enable_or_disable_threads() to set value for "--enable-multithreading" flag
Libflame:
1. Added enable_or_disable_threads() to set value for "--enable-multithreading" flag
2. Corrected invocation of "enable_or_disable('threads')"
Change-Id: I9da0a2c2c4e2075b7fa2776e7cfe6548a2e0b32f
* Added amd-toolchain-support as maintainers
Added team github account amd-toolchain-support
as maintainers for all the recipes owned by
AMD Optimizing CPU Libraries (AOCL) team
Change-Id: I9a7969bd48fc42cfbb88dd7bd93e0802c6138582
* Incorporated review comments
Updated packages.yaml with aocl components
Handled Flake8 test failures
Change-Id: I0a03f02d8c9f326b2434ec907958c3de3a8e18eb
* Readded accidental removal of stream recipe
amdfftw:
1. Updated the aocc clang selection as per spack standards
fftw:
1. Currently apple-clang section is redundant,
already it is handled in the conflict checks.
Change-Id: Idef4a3f61717eb81f321e0cd16e7ba9619eac846
* Fix for style and docs/validate (pull_request) test
unnumbered format placeholders from {} to {0}
Change-Id: If67a3374177ec067573e5504462d257712fafc05
* changed compiler references to Spack's compiler wrapper:spack_cc, spack_cxx, spack_fc
Change-Id: I7ae29c978fff16e37773913f14c84df232499763
* Removed 'single' variant from amdfftw recipe
Instead of conflict for apple-clang + openmp, handled this senario
via below available feature:
depends_on('llvm-openmp', when='%apple-clang +openmp')
Change-Id: I701b23d83e822a500ca3aaf2b60cc9ace09e13dc
* Added relevant info for users who prefers to use single precision
Change-Id: I3506e21da428ddef5fb7895b5aaed32c2a061ef6
* Minor changes on fftw, amdfftw and libflame
amdfftw:
1. Removed escape symbol to the single quotes
2. Rewording the conflict line from Recommended
to Required
fftw:
1. Reorded to following recommended sections:
versions, variants, dependencies, providers,
patches
libflame:
1. Added provides entry for 5.1.0 version
Change-Id: I21ebff99b6dfde031763154693ecb3f1fa47b476
* Removed single quote from amdfftw docstring to fix style failures
Change-Id: Ife939a5a2f5ccbc8879b730c7bebfe2fcfef9332
* Adding AOCC compiler to SPACK community
The AOCC compiler system offers a high level of advanced optimizations, multi-threading and processor support that includes global optimization, vectorization, inter-procedural analyses, loop transformations, and code generation. AMD also provides highly optimized libraries, which extract the optimal performance from each x86 processor core when utilized. The AOCC Compiler Suite simplifies and accelerates development and tuning for x86 applications.
* Added unit tests for detection and flags for AOCC
* Addressed reviewers comments w.r.t version checks and url,checksum related line lengths
Co-authored-by: Test User <spack@example.com>
The YAML config for paths and modules of external packages has
changed: the new format allows a single spec to load multiple
modules. Spack will automatically convert from the old format
when reading the configs (the updates do not add new essential
properties, so this change in Spack is backwards-compatible).
With this update, Spack cannot modify existing configs/environments
without updating them (e.g. “spack config add” will fail if the
configuration is in a format that predates this PR). The user is
prompted to do this explicitly and commands are provided. All
config scopes can be updated at once. Each environment must be
updated one at a time.
* Separate Apple Clang from LLVM Clang
Apple Clang is a compiler of its own. All places
referring to "-apple" suffix have been updated.
* Hack to use a dash in 'apple-clang'
To be able to use autodoc from Sphinx we need
a valid Python name for the module that contains
Apple's Clang code.
* Updated packages to account for the existence of apple-clang
Co-authored-by: Adam J. Stewart <ajstewart426@gmail.com>
* Added unit test for XCode related functions
Co-authored-by: Gregory Becker <becker33@llnl.gov>
Co-authored-by: Adam J. Stewart <ajstewart426@gmail.com>
This commit removes the DYLD_LIBRARY_PATH variable from the default
modules.yaml for darwin. The rationale behind deleting this
environment variable is that paths in this environment variable take
precedence over the default locations of libraries (usually the
install path of the library), which can lead to linking errors in some
circumstances. For example, executables intended to link with Apple's
system BLAS and LAPACK will instead link to a spack-installed
implementation (e.g., OpenBLAS), causing runtime errors.
These errors are resolved by instead relying on paths set in
DYLD_FALLBACK_LIBRARY_PATH, which is lower in precedence than default
locations of libraries.
Spack currently cannot run as a background process uninterrupted because some of the logging functions used in the install method (especially to create the dynamic verbosity toggle with the v key) cause the OS to issue a SIGTTOU to Spack when it's backgrounded.
This PR puts the necessary gatekeeping in place so that Spack doesn't do anything that will cause a signal to stop the process when operating as a background process.
fixes#11555
Every path in CPATH is equivalent to a -I path to the compiler,
while every path in *_INCLUDE_PATH is equivalent to -isystem.
The latter avoids the noise due to warnings coming from 3rd party
libraries that a project depends on.
Added INCLUDE env variable (Intel Fortran, .mod files)
connect_timeout can be used to increase the time Spack waits for the
server to answer. This can be used to work around slow connections or
servers.
Fixes#14700
Fixes#9394Closes#13217.
## Background
Spack provides the ability to enable/disable parallel builds through two options: package `parallel` and configuration `build_jobs`. This PR changes the algorithm to allow multiple, simultaneous processes to coordinate the installation of the same spec (and specs with overlapping dependencies.).
The `parallel` (boolean) property sets the default for its package though the value can be overridden in the `install` method.
Spack's current parallel builds are limited to build tools supporting `jobs` arguments (e.g., `Makefiles`). The number of jobs actually used is calculated as`min(config:build_jobs, # cores, 16)`, which can be overridden in the package or on the command line (i.e., `spack install -j <# jobs>`).
This PR adds support for distributed (single- and multi-node) parallel builds. The goals of this work include improving the efficiency of installing packages with many dependencies and reducing the repetition associated with concurrent installations of (dependency) packages.
## Approach
### File System Locks
Coordination between concurrent installs of overlapping packages to a Spack instance is accomplished through bottom-up dependency DAG processing and file system locks. The runs can be a combination of interactive and batch processes affecting the same file system. Exclusive prefix locks are required to install a package while shared prefix locks are required to check if the package is installed.
Failures are communicated through a separate exclusive prefix failure lock, for concurrent processes, combined with a persistent store, for separate, related build processes. The resulting file contains the failing spec to facilitate manual debugging.
### Priority Queue
Management of dependency builds changed from reliance on recursion to use of a priority queue where the priority of a spec is based on the number of its remaining uninstalled dependencies.
Using a queue required a change to dependency build exception handling with the most visible issue being that the `install` method *must* install something in the prefix. Consequently, packages can no longer get away with an install method consisting of `pass`, for example.
## Caveats
- This still only parallelizes a single-rooted build. Multi-rooted installs (e.g., for environments) are TBD in a future PR.
Tasks:
- [x] Adjust package lock timeout to correspond to value used in the demo
- [x] Adjust database lock timeout to reduce contention on startup of concurrent
`spack install <spec>` calls
- [x] Replace (test) package's `install: pass` methods with file creation since post-install
`sanity_check_prefix` will otherwise error out with `Install failed .. Nothing was installed!`
- [x] Resolve remaining existing test failures
- [x] Respond to alalazo's initial feedback
- [x] Remove `bin/demo-locks.py`
- [x] Add new tests to address new coverage issues
- [x] Replace built-in package's `def install(..): pass` to "install" something
(i.e., only `apple-libunwind`)
- [x] Increase code coverage
Add a configuration option to suppress gpg warnings during binary
package verification. This only suppresses warnings: a gpg failure
will still fail the install. This allows users who have already
explicitly trusted the gpg key they are using to avoid seeing
repeated warnings that it is self-signed.
