In an active concretize environment, support installing one or more
cli specs only if they are already present in the environment. The
`--no-add` option is the default for root specs, but optional for
dependency specs. I.e. if you `spack install <depspec>` in an
environment, the dependency-only spec `depspec` will be added as a
root of the environment before being installed. In addition,
`spack install --no-add <spec>` fails if it does not find an
unambiguous match for `spec`.
This is as much a question as it is a minor fine-tuning of the docs. I've been known to add things to an environment by editing the `spack.yaml` file directly. When I read the previous version of this sentence, I was afraid that `spack add` was actually doing *two* things, modifying the `spack.yaml` and updating something else that defined the roots of the Environment. A bit of experimentation suggests that editing the `spack.yaml` file is sufficient to change the roots.
Co-authored-by: Adam J. Stewart <ajstewart426@gmail.com>
- [x] add `concretize.lp`, `spack.yaml`, etc. to licensed files
- [x] update all licensed files to say 2013-2021 using
`spack license update-copyright-year`
- [x] appease mypy with some additions to package.py that needed
for oneapi.py
As of #18260, `spack load` and `spack env activate` now use
`prefix_inspections` from the modules configuration to decide
how to modify environment variables.
This updates the modules configuration documentation to describe
how to update environment variables with the `prefix_inspections`
section. This also updates the `spack load` and environments
documentation to refer to the new `prefix_inspections` documentation.
As of #13100, Spack installs the dependencies of a _single_ spec in parallel.
Environments, when installed, can only get parallelism from each individual
spec, as they're installed in order. This PR makes entire environments build
in parallel by extending Spack's package installer to accept multiple root
specs. The install command and Environment class have been updated to use
the new parallel install method.
The specs and kwargs for each *uninstalled* package (when not force-replacing
installations) of an environment are collected, passed to the `PackageInstaller`,
and processed using a single build queue.
This introduces a `BuildRequest` class to track install arguments, and it
significantly cleans up the code used to track package ids during installation.
Package ids in the build queue are now just DAG hashes as you would expect,
Other tasks:
- [x] Finish updating the unit tests based on `PackageInstaller`'s use of
`BuildRequest` and the associated changes
- [x] Change `environment.py`'s `install_all` to use the `PackageInstaller` directly
- [x] Change the `install` command to leverage the new installation process for multiple specs
- [x] Change install output messages for external packages, e.g.:
`[+] /usr` -> `[+] /usr (external bzip2-1.0.8-<dag-hash>`
- [x] Fix incomplete environment install's view setup/update and not confirming all
packages are installed (?)
- [x] Ensure externally installed package dependencies are properly accounted for in
remaining build tasks
- [x] Add tests for coverage (if insufficient and can identity the appropriate, uncovered non-comment lines)
- [x] Add documentation
- [x] Resolve multi-compiler environment install issues
- [x] Fix issue with environment installation reporting (restore CDash/JUnit reports)
* env: no automatic activation
* Ensure ci rebuild jobs activate the environment (no longer automagic)
Co-authored-by: Scott Wittenburg <scott.wittenburg@kitware.com>
To specify an environment for a comment, the user can specify
"spack -e <env>". The documentation incorrectly specified "-E" (which
is actually used to ignore any implicit use of environments).
This PR adds a new command to Spack:
```console
$ spack containerize -h
usage: spack containerize [-h] [--config CONFIG]
creates recipes to build images for different container runtimes
optional arguments:
-h, --help show this help message and exit
--config CONFIG configuration for the container recipe that will be generated
```
which takes an environment with an additional `container` section:
```yaml
spack:
specs:
- gromacs build_type=Release
- mpich
- fftw precision=float
packages:
all:
target: [broadwell]
container:
# Select the format of the recipe e.g. docker,
# singularity or anything else that is currently supported
format: docker
# Select from a valid list of images
base:
image: "ubuntu:18.04"
spack: prerelease
# Additional system packages that are needed at runtime
os_packages:
- libgomp1
```
and turns it into a `Dockerfile` or a Singularity definition file, for instance:
```Dockerfile
# Build stage with Spack pre-installed and ready to be used
FROM spack/ubuntu-bionic:prerelease as builder
# What we want to install and how we want to install it
# is specified in a manifest file (spack.yaml)
RUN mkdir /opt/spack-environment \
&& (echo "spack:" \
&& echo " specs:" \
&& echo " - gromacs build_type=Release" \
&& echo " - mpich" \
&& echo " - fftw precision=float" \
&& echo " packages:" \
&& echo " all:" \
&& echo " target:" \
&& echo " - broadwell" \
&& echo " config:" \
&& echo " install_tree: /opt/software" \
&& echo " concretization: together" \
&& echo " view: /opt/view") > /opt/spack-environment/spack.yaml
# Install the software, remove unecessary deps and strip executables
RUN cd /opt/spack-environment && spack install && spack autoremove -y
RUN find -L /opt/view/* -type f -exec readlink -f '{}' \; | \
xargs file -i | \
grep 'charset=binary' | \
grep 'x-executable\|x-archive\|x-sharedlib' | \
awk -F: '{print $1}' | xargs strip -s
# Modifications to the environment that are necessary to run
RUN cd /opt/spack-environment && \
spack env activate --sh -d . >> /etc/profile.d/z10_spack_environment.sh
# Bare OS image to run the installed executables
FROM ubuntu:18.04
COPY --from=builder /opt/spack-environment /opt/spack-environment
COPY --from=builder /opt/software /opt/software
COPY --from=builder /opt/view /opt/view
COPY --from=builder /etc/profile.d/z10_spack_environment.sh /etc/profile.d/z10_spack_environment.sh
RUN apt-get -yqq update && apt-get -yqq upgrade \
&& apt-get -yqq install libgomp1 \
&& rm -rf /var/lib/apt/lists/*
ENTRYPOINT ["/bin/bash", "--rcfile", "/etc/profile", "-l"]
```
This PR adds a 'concretize' entry to an environment's spec.yaml file
which controls how user specs are concretized. By default it is
set to 'separately' which means that each spec added by the user is
concretized separately (the behavior of environments before this PR).
If set to 'together', the environment will concretize all of the
added user specs together; this means that all specs and their
dependencies will be consistent with each other (for example, a
user could develop code linked against the set of libraries in the
environment without conflicts).
If the environment was previously concretized, this will re-concretize
all specs, in which case previously-installed specs may no longer be
used by the environment (in this sense, adding a new spec to an
environment with 'concretize: together' can be significantly more
expensive).
The 'concretize: together' setting is not compatible with Spec
matrices; this PR adds a check to look for multiple instances of the
same package added to the environment and fails early when
'concretize: together' is set (to avoid confusing messages about
conflicts later on).
While the build environment already takes share/pkgconfig into account,
the generated module files etc. only consider lib/pkgconfig and
lib64/pkgconfig.
Using "compilers" with the "s" is an invalid config section and throws an error.
Traceback (most recent call last):
File "spack/bin/spack", line 48, in <module>
sys.exit(spack.main.main())
File "/home/omsai/src/libkmap/spack/lib/spack/spack/main.py", line 633, in main
env = ev.find_environment(args)
File "/home/omsai/src/libkmap/spack/lib/spack/spack/environment.py", line 263, in find_environment
return Environment(env)
File "/home/omsai/src/libkmap/spack/lib/spack/spack/environment.py", line 534, in __init__
self._read_manifest(f)
File "/home/omsai/src/libkmap/spack/lib/spack/spack/environment.py", line 561, in _read_manifest
self.yaml = _read_yaml(f)
File "/home/omsai/src/libkmap/spack/lib/spack/spack/environment.py", line 402, in _read_yaml
validate(data, filename)
File "/home/omsai/src/libkmap/spack/lib/spack/spack/environment.py", line 395, in validate
e, data, filename, e.instance.lc.line + 1)
spack.config.ConfigFormatError: /home/omsai/src/libkmap/spack.yaml:15: Additional properties are not allowed ('compilers' was unexpected)
