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manifestoso merged 1840 commits intoDeepThoughtHPC:bcolzfrom
spack:develop
Oct 16, 2020
Merged

branch sync#3
manifestoso merged 1840 commits intoDeepThoughtHPC:bcolzfrom
spack:develop

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koning and others added 30 commits October 2, 2020 12:14
It looks like intel compilers generate warnings for omp pragmas when
openmp flag is not given, which due to other flags set get promoted to
errors.

This adds a flag to ignore the pragma omp warnings (icc diagnostic
number 3180 on %intel@14:).
SuperLU v6.3.0 changes the name of numerous structures, causing errors
in Amesos up through Trilinos 13.
When we attempt to determine whether a remote spec (in a binary mirror)
is up-to-date or needs to be rebuilt, we compare the full_hash stored in
the remote spec.yaml file against the full_hash computed from the local
concrete spec.  Since the full_hash moved into the spec (and is no longer
at the top level of the spec.yaml), we need to look there for it.  This
oversight from #18359 was causing all specs to get rebuilt when the
full_hash wasn't fouhd at the expected location.
alalazo and others added 28 commits October 13, 2020 09:15
* autotools: add attribute to delete libtool archives .la files

According to Autotools Mythbuster (https://autotools.io/libtool/lafiles.html)
libtool archive files are mostly vestigial, but they might create issues
when relocating binary packages as shown in #18694.

For GCC specifically, most distributions remove these files with
explicit commands:

https://git.stg.centos.org/rpms/gcc/blob/master/f/gcc.spec#_1303

Considered all of that, this commit adds an easy way for each
AutotoolsPackage to remove every .la file that has been installed.
The default, for the time being, is to maintain them - to be consistent
with what Spack was doing previously.

* autotools: delete libtool archive files by default

Following review this commit changes the default for
libtool archive files deletion and adds test to verify
the behavior.
* Fixed wrong link to version 0.0.0 and add hash for version 0.1.4

* Fix failing build for neovim@master and neovim@stable and add hash for version 0.4.0

* Fix flake8 issues

* Removed unnecessary newline

* Depedency conditions restriction to neovim >= 0.2.0 as previous versions fail to compile

* Removed build dependency on git

* Removed master from all conditions
* Make release_90 preferred version.

* Be more explicity about CUDA dependencies.

* Remove duplicate CUDA dependency in Flang package and introduce nvptx variant.

* Fix nvptx variant message.
* uqtk: Add version and fixes for Fujitsu compiler.

* Fixed order of versions.

* Add condition to execute function.
* amrex: Add CUDA variant

* amrex: require at least cuda 9
Added non standard paths to LD_LIBRARY_PATH
* Add new package: bdii

* bdii: refine dependents
* update to migraphx for rocm_3.7.0 and rocm_3.8.0

* fix flake8 errors

* address review comments

* review changes

* removed the msgpack,mentioned twice
* make opengl and spectrum-mpi set has_code = False
* allow environments to specify dev-build packages

* spack develop and spack undevelop commands

* never pull dev-build packges from bincache

* reinstall dev_specs when code has changed; reinstall dependents too

* preserve dev info paths and versions in concretization as special variant

* move install overwrite transaction into installer

* move dev-build argument handling to package.do_install

now that specs are dev-aware, package.do_install can add
necessary args (keep_stage=True, use_cache=False) to dev
builds. This simplifies driving logic in cmd and env._install

* allow 'any' as wildcard for variants

* spec: allow anonymous dependencies

raise an error when constraining by or normalizing an anonymous dep
refactor concretize_develop to remove dev_build variant
refactor tests to check for ^dev_path=any instead of +dev_build

* fix variant class hierarchy
@manifestoso manifestoso merged commit 0dcdb99 into DeepThoughtHPC:bcolz Oct 16, 2020
manifestoso pushed a commit that referenced this pull request Oct 16, 2020
* Add Collier and SysCalc recipes

* Remove extra syscalc version

* Build collier with -j1 for @:1.2.4

* Add recipe for gosam-contrib

* Update gosam-contrib recipe with 'provides'

* Madgraph recipe, first version

* Finalize madgraph recipe + flake8

* Make py2 version of madgraph default; fix hash for syscalc; fix patch

* Handle virtual packages (#3)

* Update package.py

* Update packages.yaml

* Remove virtual packages - pt. 1

* Remove virtual packages - pt. 2

* Changes from review - pt. 1

* Changes from code review - pt. 2

* Update var/spack/repos/builtin/packages/collier/package.py

Co-authored-by: Adam J. Stewart <[email protected]>

* Update var/spack/repos/builtin/packages/madgraph5amc/package.py

Co-authored-by: Adam J. Stewart <[email protected]>

* Add hash for version 2.7.2 (available in our private mirror)

* Fixes for 2.7.3 family

* Patches for 2.7.3{.py3,}{.atlas,}

* Fix hash of syscalc

* Hack to fix concretization (2.7.3 matches 2.7.3.py3)

* Add conflict statement (reported to devs)

* Apply suggestions from code review

Co-authored-by: Adam J. Stewart <[email protected]>

* Update package.py

* Delete madgraph5amc-2.7.2.atlas.patch

* Delete madgraph5amc-2.7.2.patch

* Update package.py

* Apply suggestions from code review

Co-authored-by: Adam J. Stewart <[email protected]>

Co-authored-by: iarspider <[email protected]>
Co-authored-by: Adam J. Stewart <[email protected]>
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