The error message was not updated when the behavior of Spack environments
was changed to not automatically activate the local environment in #17258.
The previous error message no longer makes sense.
When Spack installs a package, it stores repository package.py files
for it and all of its dependencies - any package with a Spack metadata
directory in its installation prefix.
It turns out this was too broad: this ends up including external
packages installed by Spack (e.g. installed by another Spack instance).
Currently Spack doesn't store the namespace properly for such packages,
so even though the package file could be fetched from the external,
Spack is unable to locate it.
This commit avoids the issue by skipping any attempt to locate and copy
from the package repository of externals, regardless of whether they
have a Spack repo directory.
On Cray platforms, we rely heavily on the module system to figure out
what targets, compilers, etc. are available. This unfortunately means
that we shell out to the `module` command as part of platform
initialization.
Because we run subcommands in a shell, we can get infinite recursion if
`setup-env.sh` and friends are in some init script like `.bashrc`.
This fixes the infinite loop by adding guards around `setup-env.sh`,
`setup-env.csh`, and `setup-env.fish`, to prevent recursive
initializations of Spack. This is safe because Spack never shells out to
itself, so we do not need it to be initialized in subshells.
- [x] add recursion guard around `setup-env.sh`
- [x] add recursion guard around `setup-env.csh`
- [x] add recursion guard around `setup-env.fish`
* fix binutils deptype for gcc
binutils needs to be a run dependency of gcc
* Fix gcc+binutils build on RHEL7+
static-libstdc++ is not available with system gcc.
Anyway, as it is for bootstraping, we do not really care depending on
a shared libstdc++.
Co-authored-by: Michael Kuhn <michael@ikkoku.de>
Spack was attempting to calculate abspath on the located config.guess
path even when it was not found (None); this commit skips the abspath
calculation when config.guess is not found.
* Activate environment in container file
This PR will ensure that the container recipes will build the spack
environment by first activating the environment.
* Deactivate environment before environment collection
For Singularity, the environment must be deactivated before running the
command to collect the environment variables. This is because the
environment collection uses `spack env activate`.
* share/spack/setup-env.fish file to setup environment in fish shell
* setup-env.fish testing script
* Update share/spack/setup-env.fish
Co-Authored-By: Elsa Gonsiorowski, PhD <gonsie@me.com>
* Update share/spack/qa/setup-env-test.fish
Co-Authored-By: Adam J. Stewart <ajstewart426@gmail.com>
* updates completions using `spack commands --update-completion`
* added stderr-nocaret warning
* added fish shell tests to CI system
Co-authored-by: becker33 <becker33@llnl.gov>
Co-authored-by: Adam J. Stewart <ajstewart426@gmail.com>
Co-authored-by: Elsa Gonsiorowski, PhD <gonsie@me.com>
* [py-mdanalysis] new version and added dependencies
Original commit message:
Author: Andrew Elble <aweits@rit.edu>
Date: Thu Nov 14 08:35:14 2019 -0500
mdanalysis
* [py-mdanalysis] python is type build/run
* [py-mdanalysis] updated numpy version requirement for all listed versions of py-mdanalysis
* [py-mdanalysis] updated biopython version requirement for all listed versions of py-mdanalysis
* [py-mdanalysis] updated py-griddataformats version requirement for all listed versions of py-mdanalysis
* [py-mdanalysis] gsd only required after version 1.17.0 and requires gsd@1.4.0
* [py-mdanalysis] only requires mmtf-python after version 0.16.0 and requires version 1.0.0
* [py-mdanalysis] has required py-joblib since version 0.16
* [py-mdanalysis] updated py-scipy version requirement for all listed versions of py-mdanalysis
* [py-mdanalysis] updated py-matplotlib version requirement for all listed versions of py-mdanalysis
* [py-mdanalysis] has required py-mock since version 0.18.0
* [py-mdanalysis] py-scikit-learn only required after version 0.16.0 and only for +analysis variant
* [py-mdanalysis] Reordered and reformatted for readability
* [py-mdanalysis] flake8 fixes
* [py-mdanalysis] proactively adding version 1.0.0 while I'm here since major release
* [py-mdanalysis] fixing some forgotten colons
* [ruby] fixing path to gcc such that users can use gem to install native gems to their home directory
* [ruby] working on making flake8 happier
* [ruby] Line can't really be split cleanly. Enhancing flake8's calm.
ya learn something new every day...
* [ruby] line break where requested
* [ruby] make raw string
* [ruby] only running for x86_64-linux everything else is untested
* [ruby] finding rbconfig.rb in a cross platform manner
* new package: GraphBlast
* polish
* add cuda_arch setup
* flake8
* the package requires cuda variant and dependency
* add comments
* define cuda_arch
* implement multiple and custom cuda arches
* tidy up, improve
* flake8
* improve style
* add variant description
* use patch method, add new version for latest commit building since master now fails
* remove gcc conflict, tidy up
* also indicate build range for boost
Co-authored-by: Sinan81 <sbulut@3vgeomatics.com>
Co-authored-by: Sinan81 <Sinan81@github>
py-mpi4py installs its header files at a difficult-to-predict location:
$prefix/lib/python-x.y/site-packages/mpi4py/include
With the new `headers` properties, dependent packages have now an easy
way to obtain this location:
spec['py-mpi4py'].headers.directories[0]
* cp2k: variant tuning `lmax` was broken
- `spack install cp2k lmax=6` now works
* Update var/spack/repos/builtin/packages/cp2k/package.py
Co-authored-by: Adam J. Stewart <ajstewart426@gmail.com>
* Update var/spack/repos/builtin/packages/cp2k/package.py
Co-authored-by: Adam J. Stewart <ajstewart426@gmail.com>
* Update var/spack/repos/builtin/packages/cp2k/package.py
Co-authored-by: Adam J. Stewart <ajstewart426@gmail.com>
* Update var/spack/repos/builtin/packages/cp2k/package.py
Co-authored-by: Adam J. Stewart <ajstewart426@gmail.com>
* Update var/spack/repos/builtin/packages/cp2k/package.py
Co-authored-by: Adam J. Stewart <ajstewart426@gmail.com>
* Update var/spack/repos/builtin/packages/cp2k/package.py
Co-authored-by: Adam J. Stewart <ajstewart426@gmail.com>
Co-authored-by: Adam J. Stewart <ajstewart426@gmail.com>
* New package: coin3d
* Update package.py
* Flake-8
* Update var/spack/repos/builtin/packages/coin3d/package.py
Co-authored-by: Adam J. Stewart <ajstewart426@gmail.com>
* Add link-time dependencies
* Add configure flags for boost; remove version 4.0.0 (doesn't compile)
Co-authored-by: iarspider <iarpsider@gmail.com>
Co-authored-by: Adam J. Stewart <ajstewart426@gmail.com>
* cray: detect frontend compilers automatically
This commit permits to detect frontend compilers
automatically, with the exception of cce.
Co-authored-by: Gregory Becker <becker33.llnl.gov>
* New package: fjcontrib + new variants for fastjet
* Flake-8
* Flake-8 once more
* Update package.py
* Allow choosing which plugins to build
Build all plugins by default.
* Flake-8
* Always build all plugins
* Update package.py
Co-authored-by: iarspider <iarpsider@gmail.com>
[george.hartzell@172-16-193-97 spack-explore-docker]$ spack containerize
Running `spack containerize` with the example `spack.yaml` file fails
with an error that ends like so:
```
[...]
File "/local_scratch/hartzell/tmp/spack-explore-docker/lib/spack/external/ruamel/yaml/scanner.py", line 165, in need_more_tokens
self.stale_possible_simple_keys()
File "/local_scratch/hartzell/tmp/spack-explore-docker/lib/spack/external/ruamel/yaml/scanner.py", line 309, in stale_possible_simple_keys
"could not find expected ':'", self.get_mark())
ruamel.yaml.scanner.ScannerError: while scanning a simple key
in "/local_scratch/hartzell/tmp/spack-explore-docker/spack.yaml", line 26, column 1
could not find expected ':'
in "/local_scratch/hartzell/tmp/spack-explore-docker/spack.yaml", line 28, column 5
```
Indenting the block string fixes the problem for me.
CentOS 7,
```
$ spack --version
0.14.2-1529-ec58f28c2
```
The Geant4 cmake check requires Qt5OpenGL_FOUND, so we must require
the Qt5 +opengl variant. If not, the cmake phase fall through to Qt4
and fails due to a missing Qt4::QtGui target.
In Geant4InterfaceOptions.cmake:
```
if(Qt5Core_FOUND
AND Qt5Gui_FOUND
AND Qt5Widgets_FOUND
AND Qt5OpenGL_FOUND
AND Qt5PrintSupport_FOUND)
```
Ref: https://github.com/Geant4/geant4/blob/master/cmake/Modules/Geant4InterfaceOptions.cmake#L90
(5baee230e93612916bcea11ebf822756cfa7282c, Import Geant4 10.6.0 source tree)
