`spack test` has a spurious '[+] ' in the output:
```
lib/spack/spack/test/install.py .........[+] ......
```
Output is properly suppressed:
```
lib/spack/spack/test/install.py ...............
```
Reading the database repeatedly can be quite slow. We need a way to speed
up Spack when it reads the DB multiple times, but the DB has not been
modified between reads (which is nearly all the time).
- [x] Add a file containing a unique uuid that is regenerated at database
write time. Use this uuid to suppress re-parsing the database
contents if we know a previous uuid and the uuid has not changed.
- [x] Fix mutable_database fixture so that it resets the last seen
verifier when it resets.
- [x] Enable not rereading the database immediately after a write. Make
the tests reset the last seen verifier in between tests that use the
database fixture.
- [x] make presence of uuid module optional
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.
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.
This makes sure that a package's fetch_options are used when fetching
new versions to checksum. This allows working around problems with
slow servers or those requiring a cookie to be set.
Bug: Spack hangs on some Cray machines
Reason: The TERM environment variable is necessary to run bash -lc "echo $CRAY_CPU_TARGET", but we run that command within env -i, which wipes the environment.
Fix: Manually forward the TERM environment variable to env -i /bin/bash -lc "echo $CRAY_CPU_TARGET"
When trying to use an upstream Spack repository, as of f2aca86 Spack
was attempting to write to the upstream DB based on a new metadata
directory added in that commit. Upstream DBs are read-only, so this
should not occur.
This adds a check to prevent Spack from writing to the upstream DB
fixes#15449
Before this PR a call to pkg.url_for_version was modifying
class attributes determining different results for subsequents
calls and an error when the urls was empty.
This recovers the old behavior of replace_prefix_bin that was
modified to work with elf binaries by prefixing os.sep to new prefix
until length is the same as old prefix.
Testing the install StopIteration exception resulted in an attribute error:
AttributeError: 'StopIteration' object has no attribute 'message'
This PR adds a unit test and resolves that error.
The new build process, introduced in #13100 , relies on a spec's dependents in addition to their dependencies. Loading a spec from a yaml file was not initializing the dependents.
- [x] populate dependents when loading from yaml
The distributed build PR (#13100) -- did not check the install status of dependencies when using the `--only package` option so would refuse to install a package with the claim that it had uninstalled dependencies whether that was the case or not.
- [x] add install status checks for the `--only package` case.
- [x] add initial set of tests
This change stores packages' configure arguments during build and makes
use of them while refreshing module files. This fixes problems such as in
#10716.
Bug: Spack hangs on some Cray machines
Reason: The TERM environment variable is necessary to run bash -lc "echo $CRAY_CPU_TARGET", but we run that command within env -i, which wipes the environment.
Fix: Manually forward the TERM environment variable to env -i /bin/bash -lc "echo $CRAY_CPU_TARGET"
- [x] move some logic for handling virtual packages from the `spack
dependencies` command into `spack.package.possible_dependencies()`
- [x] rework possible dependencies tests so that expected and actual
output are on the left/right respectively
When trying to use an upstream Spack repository, as of f2aca86 Spack
was attempting to write to the upstream DB based on a new metadata
directory added in that commit. Upstream DBs are read-only, so this
should not occur.
This adds a check to prevent Spack from writing to the upstream DB
* try extend path to solve PyQt5.sip not found issue
* disable private sip installation in sippackage class
* undo manual PyQt5 dir creation in py-sip site-packages dir
* fix typo
* fix typo
* also apply fix to PyQt4
* tidy up
* flake8 and tidy up
* tidy and undo hardcoding of python_include_dir
* replace hardcoded python inc dir
* fix minor issues
* rethink include dir variable name
* improve style
* add new versions
* implement new sip setup to qsci installation
* set sip-incdir correctly for the new setup
* setup extend_path thing before qsci python bindings
* take care of conflict
* flake8
* also extend for PyQt4
* improve style
* improve style
* SipPackage build sys should depend on py-sip
* consolidate extend_path fixes into SipPackage
* fix typo
* fix bugs
* flake8
* revert sip doc to pre-resource setup
* import os module
* flake8
Co-authored-by: Sinan81 <sbulut@3vgeomatics.com>
Add a 'define_from_variant` helper function to CMake-based Spack
packages to convert package variants into CMake arguments. For
example:
args.append('-DFOO=%s' % ('ON' if '+foo' in self.spec else 'OFF'))
can be replaced with:
args.append(self.define_from_variant('foo'))
The following conversions are handled automatically:
* Flag variants will be converted to CMake booleans
* Multivalued variants will be converted to semicolon-separated strings
* Other variant values are converted to CMake string arguments
This also adds a 'define' helper method to convert any variable to
a CMake argument. It has the same conversion rules as
'define_from_variant' (but operates directly on values rather than
requiring the user to supply the name of a package variant).
* Buildcache: Install into non-default directory layouts
Store a dictionary mapping of original dependency prefixes to dependency hashes
Use the loaded spec to grab the new dependency prefixes in the new directory layout.
Map the original dependency prefixes to the new dependency prefixes using the dependency hashes.
Use the dependency prefixes map to replace original rpaths with new rpaths preserving the order.
For mach-o binaries, use the dependency prefixes map to replace the dependency library entires for libraries and executables and the replace the library id for libraries.
On Linux, patchelf is used to replace the rpaths of elf binaries.
On macOS, install_name_tool is used to replace the rpaths and dependency libraries of mach-o binaries and the id of mach-o libraries.
On Linux, macholib is used to replace the dependency libraries of mach-o binaries and the id of mach-o libraries.
Binary text with padding replacement is attempted for all binaries for the following paths:
spack layout root
spack prefix
sbang script location
dependency prefixes
package prefix
Text replacement is attempted for all text files using the paths above.
Symbolic links to the absolute path of the package install prefix are replaced, all others produce warnings.
PR #15212 added a new connect_timeout option that can be overridden
using fetch_options but had to specified per-version. This adds a new
per-package variable that can be used to override fetch_options for
all versions in the package. This includes connect_timeout as well
as 'cookie' (e.g. for the jdk package).
Packages can combine package-level fetch_options with per-version
fetch_options, in which case the version fetch_options completely
override the package-level fetch_options.
This commit includes tests for the added behavior.
fixes#15449
Before this PR a call to pkg.url_for_version was modifying
class attributes determining different results for subsequents
calls and an error when the urls was empty.
* add --skip-unstable-versions option to 'spack mirror create' which skips sources/resource for packages if their version is not stable (i.e. if they are the head of a git branch rather than a fixed commit)
* '--skip-unstable-versions' should skip all VCS sources/resources, not just those which are not cachable
Allows spack.config InternalConfigScope and Configuration.set() to
handle keys with trailing ':' to indicate replacement vs merge
behavior with respect to lower priority scopes.
Lists may now be replaced rather than merged (this behavior was
previously only available for dictionaries).
This commit adds tests for the new behavior.
Testing the install StopIteration exception resulted in an attribute error:
AttributeError: 'StopIteration' object has no attribute 'message'
This PR adds a unit test and resolves that error.
This recovers the old behavior of replace_prefix_bin that was
modified to work with elf binaries by prefixing os.sep to new prefix
until length is the same as old prefix.
Removed the code that was converting the old index.yaml format into
index.json. Since the change happened in #2189 it should be
considered safe to drop this (untested) code.
Spack's fflags are meant for both f77 and fc. Therefore, they must
be passed as FFLAGS and FCFLAGS to the configure scripts of
Autotools-based packages.
The distributed build PR (#13100) -- did not check the install status of dependencies when using the `--only package` option so would refuse to install a package with the claim that it had uninstalled dependencies whether that was the case or not.
- [x] add install status checks for the `--only package` case.
- [x] add initial set of tests
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
* CudaPackage: add support for Tesla K80 and older CUDA
* Flake8 fixes
* Fix cuda_arch when no arch is set
* Fine-tune cuda_arch=37,50 supported CUDA versions
* CUDA 6.5+ supports SM_37
* Add @svenevs as a maintainer
The new build process, introduced in #13100 , relies on a spec's dependents in addition to their dependencies. Loading a spec from a yaml file was not initializing the dependents.
- [x] populate dependents when loading from yaml
* Buildcache command: add install option -o/--otherarch
This will allow matching specs from other archs, for example
installing macOS buildcaches on linux hosts.
* spack commands --update-completion
args.specs is a list, which results in output like this:
```
eval `spack load --sh ['libxml2', 'xz']`
```
We want this instead:
```
eval `spack load --sh libxml2 xz`
```
This change stores packages' configure arguments during build and makes
use of them while refreshing module files. This fixes problems such as in
#10716.
* Emit a sensible error message if compiler's target is overly specific
fixes#14798fixes#13733
Compiler specifications require a generic architecture family as
their target. This commit improves the error message that is
displayed to users if they edit compilers.yaml and use an overly
specific name.
The hashing logic looks for function calls that are Spack directives.
It expects that when a Spack directive is used that it is referenced
directly by name, and that the directive function is not itself
retrieved by calling another function. When the hashing logic
encountered a function call where the function was determined
dynamically, it would fail (attempting to access a name attribute
that does not happen to exist in this case).
This updates the hashing logic to filter out function calls where the
function is determined dynamically when looking for uses of Spack
directives.
Spack now requires an exact match of the compiler version
requested by the user. A loose constraint can be given to
Spack by using a version range instead of a concrete version
(e.g. 4.5: instead of 4.5).
Sometimes one needs to preserve the (relative order) of
mtimes on installed files. So it's better to just copy
over all the metadata from the source tree to the install
tree. If permissions need fixing, that will be done anyway
afterwards.
One major use case are resource()s:
They're unpacked in one place and then copied to their
final place using install_tree(). If the resource is a
source tree using autoconf/automake, resetting mtimes
uncorrectly might force unwanted autoconf/etc calls.
If the mimetype returned from `file -h -b --mime-type` contains slashes
in its subtype, the tuple returned from `spack.relocate.mime_type` will
have a size larger than two, which leads to errors.
Change-Id: I31de477e69f114ffdc9ae122d00c573f5f749dbb
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
* Buildcache creation change the way prefix is copied to workdir.
* install_tree copies hardlinked files
* tarfile creates hardlinked files on extraction.
* create a temporary tarfile from prefix and extract it to workdir
* Use temp tarfile to move workdir to prefix to preserve hardlinks instead of copying
