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Fixes #9394
Closes #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
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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.
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Add a new entry in `config.yaml`:
config:
shared_linking: 'rpath'
If this variable is set to `rpath` (the default) Spack will set RPATH in ELF binaries. If set to `runpath` it will set RUNPATH.
Details:
* Spack cc wrapper explicitly adds `--disable-new-dtags` when linking
* cc wrapper also strips `--enable-new-dtags` from the compile line
when disabling (and vice versa)
* We specifically do *not* add any dtags flags on macOS, which uses
Mach-O binaries, not ELF, so there's no RUNPATH)
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While the build environment already takes share/pkgconfig into account,
the generated module files etc. only consider lib/pkgconfig and
lib64/pkgconfig.
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Dotkit is being used only at a few sites and has been deprecated on new
machines. This commit removes all the code that provide support for the
generation of dotkit module files.
A new validator named "deprecatedProperties" has been added to the
jsonschema validators. It permits to prompt a warning message or exit
with an error if a property that has been marked as deprecated is
encountered.
* Removed references to dotkit in the docs
* Removed references to dotkit in setup-env-test.sh
* Added a unit test for the 'deprecatedProperties' schema validator
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* When cleaning the stage root, only remove directories that appear
to be used for staging Spack packages. Previously Spack was clearing
all directories in the stage root, which could remove content not
related to Spack if the user chose a staging root which contains
files/directories not managed by Spack.
* The documentation is updated with warnings about choosing a stage
directory that is only managed by Spack (although generally the
check added in this PR for "spack clean" should avoid removing
content that was not created by Spack)
* The default stage directory (in config.yaml) is now
$tempdir/$user/spack-stage and the logic is updated to omit the
$user portion of this path if $tempdir already contains a $user
directory.
* When creating stage root assign user read/write permissions to all
directories in the path under $user. Previously Spack was assigning
the permissions of the first existing parent directory
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Fixes #11163
The goal of this work is to simplify stage directory structures by eliminating use of symbolic links. This means, among other things, that` $spack/var/spack/stage` will no longer be the core staging directory. Instead, the first accessible `config:build_stage` path will be used.
Spack will no longer automatically append `spack-stage` (or the like) to configured build stage directories so the onus of distinguishing the directory from other work -- so the other work is not automatically removed with a `spack clean` operation -- falls on the user.
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The original packaging, with openfoam as a virtual and with
openfoam-com, openfoam-org and openfoam-extend as
providers, adds an obfuscation layer without any benefit.
- Rename `openfoam-com` to `openfoam`, and remove the
`openfoam` virtual package.
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* config:build_jobs now controls the number of parallel jobs to spawn during
builds, but cannot ever exceed the number of cores on the machine.
* The default is set to 16 or the number of available cores, whatever
is lowest.
* Updated docs to reflect the changes done to limit parallel builds
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* Add Fujitsu compiler to Spack.
* Fixes for flake8
* Chenges location of FCC to subdirectory called case-insensitive
* Add compiler tests for Fujitsu compiler
* Modify the logic of taking compiler version for new version of Fujitsu compiler
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* ninja: Make python a build-only dependency
* ninja, ninja-fortran: allow the packages to provide eachother
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* mesa: re-writen to new meson build system
* xorg-server: Remove unneeded mesa dependency
* glx: provide the virtual GLX package
* Convert most "mesa" dependencies to use virtual gl and glx dependencies
* mesa: Switch to always building from the git repo instead of a tarball
* Use gl and glx version ranges instead of exact versions
* glx: provide a default package
* add auto to swr variant
* Revert "add auto to swr variant"
This reverts commit 2e7cd8a8aca07767c00657d0d09985ddd6306883.
* update mesa package to version 19.0
* set +glx by default only when running on linux
* fix style issues in geant4 package
* remove virtual package "egl"
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* add cxxstd variant
* add CMake constraints based on platform/version
* add older versions
* update boost dependency version constraints (which are closely
tied to mysql version) and update boost cxxstd choice to be
the same as the cxxstd chosen for mysql
* add client-only support (including a patch for 5.5.x)
* record the mysql package as a provider of the mysql-client virtual
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* mariadb-c-client is a new package using the distinct, LGPL,
MySQL-compatible client library from mariadb.com. It provides the
virtual package mariadb-client
* mariadb is recorded as a provider of the mariadb-client virtual
* The mysql-client virtual package is also added, and mariadb-c-client
is recorded as a provider for it
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* Add binary package of the IBM Java SDK for big and little-endian
powerpc (power7, 8 and 9). The jdk and openjdk packages only install
on x86_64.
* Add ibm-java as a java provider
* The jdk and openjdk packages only install on x86_64. Add conflicts
for ppc64 and ppc64le to jdk and openjdk.
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* Create option to build missing compilers and add them to config before installing packages that use them
* Clean up kwarg passing for do_install, put compiler bootstrapping in separate method
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This spack command adds a new schema for a file which describes the
builder containers available, along with the compilers availabe on
each builder. The release-jobs command then generates the .gitlab-ci.yml
file by first expanding the release spec set, concretizing each spec
(in an appropriate docker container if --this-machine-only argument is
not provided on command line), and then combining and staging all the
concrete specs as jobs to be run by gitlab.
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* Remove /nfs/tmp2 from default configuration
* /nfs/tmp2 is going away from LC... and doesn’t exist for the rest of the world.
* update documentation to remove /nfs/tmp2 as well
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Grammar/spelling issues
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* Introduce FFTW2 and FFT3 providers for Intel-MKL and FFTW Spack packages.
* make fftw default package for fftw-api virtual package
* virtual package test assertion now provides location of default virtual packages.
* Change name of virtual package to fftw-api and used versioned interface.
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* Add a build_language config.yaml option which controls the language
of compiler messages
* build_language defaults to "C", in which case the compiler messages
will be in English. This allows Spack log parsing to detect and
highlight error messages (since the regular expressions to find
error messages are in English)
* The user can use the default language in their environment by setting
the build_language config variable to null or ''
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Spack can now be configured to assign permissions to the files installed by a package.
In the `packages.yaml` file under `permissions`, the attributes `read`, `write`, and `group` control the package permissions. These attributes can be set per-package, or for all packages under `all`. If permissions are set under `all` and for a specific package, the package-specific settings take precedence. The `read` and `write` attributes take one of `user`, `group`, and `world`.
packages:
all:
permissions:
write: group
group: spack
my_app:
permissions:
read: group
group: my_team
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Default config.yaml mis-named `install_path_scheme` as `directory_layout`.
This commit corrects the error.
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Fixes #9166
This is intended to reduce errors related to lock timeouts by making
the following changes:
* Improves error reporting when acquiring a lock fails (addressing
#9166) - there is no longer an attempt to release the lock if an
acquire fails
* By default locks taken on individual packages no longer have a
timeout. This allows multiple spack instances to install overlapping
dependency DAGs. For debugging purposes, a timeout can be added by
setting 'package_lock_timeout' in config.yaml
* Reduces the polling frequency when trying to acquire a lock, to
reduce impact in the case where NFS is overtaxed. A simple
adaptive strategy is implemented, which starts with a polling
interval of .1 seconds and quickly increases to .5 seconds
(originally it would poll up to 10^5 times per second).
A test is added to check the polling interval generation logic.
* The timeout for Spack's whole-database lock (e.g. for managing
information about installed packages) is increased from 60s to
120s
* Users can configure the whole-database lock timeout using the
'db_lock_timout' setting in config.yaml
Generally, Spack locks (those created using spack.llnl.util.lock.Lock)
now have no timeout by default
This does not address implementations of NFS that do not support file
locking, or detect cases where services that may be required
(nfslock/statd) aren't running.
Users may want to be able to more-aggressively release locks when
they know they are the only one using their Spack instance, and they
encounter lock errors after a crash (e.g. a remote terminal disconnect
mentioned in #8915).
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This commit adds 'libunwind' as the default 'unwind' provider in
spack. This preference should be overridden by the
darwin/packages.yaml file on macOS. Continues the changes discussed in
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This commit adds default unwind providers to the default packages.yaml
for darwin. Compiler versions are supplied with the apple-unwind
package so that apple-unwind is only used with Apple's clang fork, and
not with LLVM's clang.
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If the user sets "ccache: true" in spack's config.yaml, Spack will use an available
ccache executable when compiling c/c++ code. This feature is disabled by default
(i.e. "ccache: false") and the documentation is updated with how to enable
ccache support
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- This complies with the unix directory hierarchy standard (which Spack
attempts to follow)
- Also unclutters the repo root directory.
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(#7692)
- spack.util.lock behaves the same as llnl.util.lock, but Lock._lock and
Lock._unlock do nothing.
- can be disabled with a control variable.
- configuration options can enable/disable locking:
- `locks` option in spack configuration controls whether Spack will use filesystem locks or not.
- `-l` and `-L` command-line options can force-disable or force-enable locking.
- Spack will check for group- and world-writability before disabling
locks, and it will not allow a group- or world-writable instance to
have locks disabled.
- update documentation
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* Set default provider for every virtual package
* Add unit test to ensure that every virtual package has a default provider explicitly set
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* `spack purge` now is `spack clean`
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* Add format to separate target and os for path
spec format can now handle separations of target and os for setting
up the path.
* Added ${PLATFORM} et al to spec.format()
${PLATFORM}, ${OS}, ${TARGET}
* Update tests
Updated tests and got rid of unnecessary code.
* Also update documentation to reflect this new ability.
* Add default path scheme to config.yaml
Added default path scheme to config.yaml. Users can overwrite this
section if they want.
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This provides options for hardware and software rendering with the
gl API and updates the vtk package to make use of those options:
* Create new "gl" virtual package, provided by mesa
* Add external-only "opengl" package, which represents a system
install that provides gl
* For vtk: prefer system gl implementation by default to get speed
up from hardware rendering. When software rendering is specifically
requested (+osmesa), try to use the llvmpipe approach, as it is
much faster.
* Make qt dependency optional for vtk
* Add basic support for VTK on osx
* qt: Depend on virtual gl package, rather than mesa impl
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There are two providers, pkgconf and pkg-config, with the former being
the default provider.
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* Module files now are generated using a template engine refers #2902 #3173
jinja2 has been hooked into Spack.
The python module `modules.py` has been splitted into several modules
under the python package `spack/modules`. Unit tests stressing module
file generation have been refactored accordingly.
The module file generator for Lmod has been extended to multi-providers
and deeper hierarchies.
* Improved the support for templates in module files.
Added an entry in `config.yaml` (`template_dirs`) to list all the
directories where Spack could find templates for `jinja2`.
Module file generators have a simple override mechanism to override
template selection ('modules.yaml' beats 'package.py' beats 'default').
* Added jinja2 and MarkupSafe to vendored packages.
* Spec.concretize() sets mutual spec-package references
The correct place to set the mutual references between spec and package
objects at the end of concretization. After a call to concretize we
should now be ensured that spec is the same object as spec.package.spec.
Code in `build_environment.py` that was performing the same operation
has been turned into an assertion to be defensive on the new behavior.
* Improved code and data layout for modules and related tests.
Common fixtures related to module file generation have been extracted
in `conftest.py`. All the mock configurations for module files have been
extracted from python code and have been put into their own yaml file.
Added a `context_property` decorator for the template engine, to make
it easy to define dictionaries out of properties.
The default for `verbose` in `modules.yaml` is now False instead of True.
* Extendable module file contexts + short description from docstring
The contexts that are used in conjunction with `jinja2` templates to
generate module files can now be extended from package.py and
modules.yaml.
Module files generators now infer the short description from package.py
docstring (and as you may expect it's the first paragraph)
* 'module refresh' regenerates all modules by default
`module refresh` without `--module-type` specified tries to
regenerate all known module types. The same holds true for `module rm`
Configure options used at build time are extracted and written into the
module files where possible.
* Fixed python3 compatibility, tests for Lmod and Tcl.
Added test for exceptional paths of execution when generating Lmod
module files.
Fixed a few compatibility issues with python3.
Fixed a bug in Tcl with naming_scheme and autoload + unit tests
* Updated module file tutorial docs. Fixed a few typos in docstrings.
The reference section for module files has been reorganized. The idea is
to have only three topics at the highest level:
- shell support + spack load/unload use/unuse
- module file generation (a.k.a. APIs + modules.yaml)
- module file maintenance (spack module refresh/rm)
Module file generation will cover the entries in modules.yaml
Also:
- Licenses have been updated to include NOTICE and extended to 2017
- docstrings have been reformatted according to Google style
* Removed redundant arguments to RPackage and WafPackage.
All the callbacks in `RPackage` and `WafPackage` that are not build
phases have been modified not to accept a `spec` and a `prefix`
argument. This permits to leverage the common `configure_args` signature
to insert by default the configuration arguments into the generated
module files. I think it's preferable to handling those packages
differently than `AutotoolsPackage`. Besides only one package seems
to override one of these methods.
* Fixed broken indentation + improved resiliency of refresh
Fixed broken indentation in `spack module refresh` (probably a rebase
gone silently wrong?). Filter the writers for blacklisted specs before
searching for name clashes. An error with a single writer will not
stop regeneration, but instead will print a warning and continue
the command.
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* Make jpeg a virtual dependency.
* Make 'libjpeg-turbo' the default implementation of 'jpeg'.
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* Refactor IntelInstaller into IntelPackage base class
* Move license attributes from __init__ to class-level
* Flake8 fixes: remove unused imports
* Fix logic that writes the silent.cfg file
* More specific version numbers for Intel MPI
* Rework logic that selects components to install
* Final changes necessary to get intel package working
* Various updates to intel-parallel-studio
* Add latest version of every Intel package
* Add environment variables for Intel packages
* Update env vars for intel package
* Finalize components for intel-parallel-studio package
Adds a +tbb variant to intel-parallel-studio.
The tbb package was renamed to intel-tbb.
Now both intel-tbb and intel-parallel-studio+tbb
provide tbb.
* Overhaul environment variables set by intel-parallel-studio
* Point dependent packages to the correct MPI wrappers
* Never default to intel-parallel-studio
* Gather env vars by sourcing setup scripts
* Use mpiicc instead of mpicc when using Intel compiler
* Undo change to ARCH
* Add changes from intel-mpi to intel-parallel-studio
* Add comment explaining mpicc vs mpiicc
* Prepend env vars containing 'PATH' or separators
* Flake8 fix
* Fix bugs in from_sourcing_file
* Indentation fix
* Prepend, not set if contains separator
* Fix license symlinking broken by changes to intel-parallel-studio
* Use comments instead of docstrings to document attributes
* Flake8 fixes
* Use a set instead of a list to prevent duplicate components
* Fix MKL and MPI library linking directories
* Remove +all variant from intel-parallel-studio
* It is not possible to build with MKL, GCC, and OpenMP at this time
* Found a workaround for locating GCC libraries
* Typos and variable names
* Fix initialization of empty LibraryList
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* alsa-lib: new package
* cups: new package
* icedtea: new package
* icedtea: adding JAVA_HOME variable
* alsa: removing placeholder
* icedtea: typo fix
* alsa: fixing formattting
* icedtea: formatting fixes and cleanup
* icedtea: additional cleanup
* jdk: adding provides('java') to jdk, setting jdk to default java.
* icedtea: adding jdk as a dependency
* java: changing depends_on('jdk') and similar entries to depends_on('java')
* icedtea: removing unused imports, trying to placate flake8.
* fastqc: fixing flake8 error
* bazel: fixing typo in java dependency
* jdk: changing provides java to a range
* icedtea: cleaning up. Splitting up checksums.
* icedtea: jdk dependency is build only
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* Added package for 'libaec'.
* New version for package 'libaec'.
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* Several improvements for the openfoam packages
--
Refactor openfoam packages by adding an OpenfoamArch class
Use separate configure, build, install phases.
Provide FOAM_PROJECT_DIR dependent env for openfoam packages
- easier way to locate
Eliminate intermediate installation directories
- unneeded clutter.
- makes it less than easy to find the etc/bashrc file
Add versioning for all openfoam patches
- no certainty which parts (if any) will be needed in future versions,
especially if we strive to ensure that the upstream version builds
well with spack to begin with.
Support build of develop branches
- helps track build regressions for future openfoam releases
STYLE: use common/ and assets/ to provide additional (build) resources ...
* - adjust OpenFOAM provider
Move openfoam-com up front since this is the one being used as a base
for the others
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* Allow users to set parallel jobs in config.yaml
* Undo change from endash to emdash
* Remove parallel config, rename jobs to build_jobs
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* Set default providers for everything
* Add default OpenFOAM provider
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* Add missing dependencies to gawk
* Fix make check
* Add mawk packages and awk virtual dependency
* Use mawk instead of gawk to build ncurses
* Rearrange order of patches and dependencies
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