Commit graph

27279 commits

Author SHA1 Message Date
luker
3779e645b8
scorep: modify configure flags for Cray platforms (#32201) 2022-08-30 00:25:35 -07:00
Olivier Cessenat
7f4799a4a2
visit: actually set the dev env for plugins again (#32427) 2022-08-30 08:02:23 +02:00
Jim Edwards
a09d4ffb4e
esmf: update package for cce (cray) compiler (#32433) 2022-08-30 07:53:45 +02:00
robgics
0c9b4bc3d2
Initial commit for freesurfer package (#32395)
* Initial commit for freesurfer package

* Add myself as maintainer

* Change URLs to https and move url function to proper place.
2022-08-29 14:35:34 -07:00
snehring
778af070f0
snphylo: update to new version (#32425) 2022-08-29 11:56:57 -07:00
Brian Van Essen
bd815fbada
Switched LBANN to using an explicit variant to enable unit testing (#32429)
support rather than relying on the spack install --test root option,
because it doesn't play nice in environments.
2022-08-29 12:53:45 -06:00
Luca Heltai
1c22af8ef4
dealii:: fixed application of stdcxx variant (#32413)
* Fixed imposition of stdcxx.

* Fixed style.
2022-08-29 08:41:17 -07:00
Seth R. Johnson
9687d91d72
celeritas: new version 0.1.1 (#32412) 2022-08-29 08:34:16 -07:00
Wouter Deconinck
a14d228e8b
gdk-pixbuf: new bugfix version 2.42.9 (#32420)
No changes of note. Just bugfixes. Full diff at https://gitlab.gnome.org/GNOME/gdk-pixbuf/-/compare/2.42.6...2.42.9?from_project_id=1548
2022-08-29 07:48:48 -07:00
Ryan Marcellino
b64d2393ea
New package: py-mkdocstrings (#32417) 2022-08-28 14:34:02 -07:00
Ryan Marcellino
d0173a486f
New package: py-mkdocs-jupyter (#32416) 2022-08-28 14:32:50 -07:00
Sergey Kosukhin
215379cc27
libxml2: add new versions (#32394)
* libxml2: add new versions

* libxml2: apply patch preventing SIGFPE
2022-08-27 02:29:49 -06:00
Adam J. Stewart
a7cc58d42c
py-radiant-mlhub: add v0.5 (#32406) 2022-08-26 18:02:02 -06:00
downloadico
430b8ca362
add sra-tools and NCBI-VDT packages (#32403)
* ncbi-vdb: add ncbi-vdb package to spack
ncbi-vdb provides the interface to the NCBI VDB

* sra-tools: add sra-tools to spack
2022-08-26 17:38:27 -06:00
Richard Berger
e6f6de406d
py-sphinx-rtd-theme: add version 1.0.0 (#32379) 2022-08-26 17:38:14 -06:00
Betsy McPhail
ad95719a1d
Use threading.TIMEOUT_MAX when available (#32399)
This value was introduced in Python 3.2. Specifying a timeout greater than
this value will raise an OverflowError.
2022-08-26 17:37:56 -06:00
Jen Herting
59bfa6bcd3
[py-pybedtools] added version 0.9.0 (#32401) 2022-08-26 21:44:53 +00:00
dlkuehn
c7acda0062
New packages: roary plus 5 new perl-* (#32217)
* New package: roary
2022-08-26 14:29:44 -06:00
Massimiliano Culpo
51244abee9
Configuration: Allow requirements for virtual packages (#32369)
Extend the semantics of package requirements to
allow using them also under a virtual package
attribute in packages.yaml

These requirements are enforced whenever that
virtual spec is present in the DAG.
2022-08-26 13:17:40 -07:00
kwryankrattiger
eb1c9c1583
SDK: Option to disable fortran support. (#32319)
This option was requested to support MacOS systems that do not have
fortran installed.
2022-08-26 11:12:13 -07:00
Ryan Marcellino
c227e7ab13
New package: py-mkdocs-material (#32387) 2022-08-26 10:32:03 -07:00
Ryan Marcellino
987c067f68
New package: py-mkdocs-autorefs (#32386) 2022-08-26 10:30:28 -07:00
Dom Heinzeller
26a16dc5bb
Add pic variant to bacio (#32388)
* Add pic variant to bacio

* Fix black style error
2022-08-26 09:24:34 -07:00
François Trahay
e41f9aad38
add eztrace 2.0 release (#32350)
* [EZTrace] Version uptate to 2.0

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

Co-authored-by: Tamara Dahlgren <35777542+tldahlgren@users.noreply.github.com>

Co-authored-by: Tamara Dahlgren <35777542+tldahlgren@users.noreply.github.com>
2022-08-26 08:45:05 -07:00
Massimiliano Culpo
b6ea2a46d1
Update archspec to latest commit (#32368)
Modifications:

- [x] Add graviton3
- [x] Optimize __eq__ for microarchitectures
2022-08-26 12:58:20 +02:00
Tom Scogland
a2f0588004
calculate make_jobs in ninja (#32384)
This is in case ninja's setup_dependent_package is called before its
module is initialized by build_environment
2022-08-26 03:37:53 -06:00
Chris White
b31cd189a7
Improve error message for yaml config file (#32382)
* improve error message

* Update lib/spack/spack/config.py

Co-authored-by: Tamara Dahlgren <35777542+tldahlgren@users.noreply.github.com>

Co-authored-by: Tamara Dahlgren <35777542+tldahlgren@users.noreply.github.com>
2022-08-26 02:43:03 +00:00
Wouter Deconinck
3ba58d85e2
libzmq: add patch for gcc-12; conflict for older gcc-11 versions (#32381)
Per #32214, the existing patch `92b2c...` for `gcc@11:` only applies
cleanly for `libzmq@4.3.3:4.3.4`. This PR adds a conflict for earlier
versions, as they cannot be patched due to different context.

For `gcc@11`, this leaves the most recent two versions available (a
satisfactory compromise).

For `gcc@12`, however, there is another existing conflict that makes
these most recent two versions unavailable. This PR adds an upstream
patch for the single most recent version that allows compilation with
`gcc@12` for that most recent version.

Starting point:
- `gcc@11` concretizes on all versions, attempts to apply patch on
`@4.2.3:4.3.4`, and only succeeds to apply patch on `@4.3.3:4.3.4`,
- `gcc@12` concretizes on `@:4.3.1` (and `@master`), attempts to apply
patch on `@4.2.3:4.3.1`, fails to apply patch on all.

Ending point:
- `gcc@11` concretizes on `@4.3.3:4.3.4` (and `@master`), attempts and
succeeds to apply patch on `@4.3.3:4.3.4`,
- `gcc@12` concretizes on `@4.3.4` (and `@master`), attempts and
succeeds to apply patch on `@4.3.4`.

Verified with environment build:
```yaml
spack:
  specs:
  - libzmq@4.3.4%gcc@12.1.0
  - libzmq@4.3.4%gcc@11.3.0
  - libzmq@4.3.3%gcc@11.3.0
  view: false
```
which returns the following:
```console
16:14:47 wdconinc@menelaos ~/git/spack (libzmq-patch-gcc12 *+$%=) $
spack install --fresh
==> Installing environment libzmq
[+]
/opt/software/linux-ubuntu22.04-skylake/gcc-12.1.0/libmd-1.0.4-egpgd6eoaqtsl5fja2iwsl6gyc4o32p5
[+]
/opt/software/linux-ubuntu22.04-skylake/gcc-12.1.0/libsodium-1.0.18-af3rsfnvck6anxf7eeog3f2bph44tjia
[+]
/opt/software/linux-ubuntu22.04-skylake/gcc-12.1.0/pkgconf-1.8.0-z5of2hj2c6ygd3kxr4cwv7u7t42sxair
[+]
/opt/software/linux-ubuntu22.04-skylake/gcc-11.3.0/libmd-1.0.4-tec234gco2sd7n52dkwbrad43sdhaw4o
[+]
/opt/software/linux-ubuntu22.04-skylake/gcc-11.3.0/libsodium-1.0.18-uljf675u3yrn5c7fdjdpa5c7qnnkynke
[+]
/opt/software/linux-ubuntu22.04-skylake/gcc-11.3.0/pkgconf-1.8.0-l4hzc2g4pnn7dwyttphmxivt3xghvpoq
[+]
/opt/software/linux-ubuntu22.04-skylake/gcc-12.1.0/libbsd-0.11.5-fi3ri64moy45ksr4sf5pcwd6k23dsa4o
[+]
/opt/software/linux-ubuntu22.04-skylake/gcc-11.3.0/libbsd-0.11.5-2matmm7im7oygrr77k7wznttv4rbupfz
==> Installing libzmq-4.3.4-t7ad54q3atrnte4rzq7g7cfjcw5227pr
==> No binary for libzmq-4.3.4-t7ad54q3atrnte4rzq7g7cfjcw5227pr found:
installing from source
==> Fetching
c593001a89.tar.gz
==> Fetching
310b8aa57a
==> Fetching
https://github.com/zeromq/libzmq/pull/4334.patch?full_index=1
==> Applied patch
92b2c38a2c.patch?full_index=1
==> Applied patch
https://github.com/zeromq/libzmq/pull/4334.patch?full_index=1
==> libzmq: Executing phase: 'autoreconf'
==> libzmq: Executing phase: 'configure'
==> libzmq: Executing phase: 'build'
==> libzmq: Executing phase: 'install'
==> libzmq: Successfully installed
libzmq-4.3.4-t7ad54q3atrnte4rzq7g7cfjcw5227pr
  Fetch: 0.61s.  Build: 1m 31.57s.  Total: 1m 32.18s.
[+]
/opt/software/linux-ubuntu22.04-skylake/gcc-12.1.0/libzmq-4.3.4-t7ad54q3atrnte4rzq7g7cfjcw5227pr
==> Installing libzmq-4.3.3-pxrd6piprucu65bkro2ixms6d3x2eudz
==> No binary for libzmq-4.3.3-pxrd6piprucu65bkro2ixms6d3x2eudz found:
installing from source
==> Fetching
9d9285db37.tar.gz
==> Using cached archive:
/home/wdconinc/.spack/cache/_source-cache/archive/31/310b8aa57a8ea77b7ac74debb3bf928cbafdef5e7ca35beaac5d9c61c7edd239
==> Applied patch
92b2c38a2c.patch?full_index=1
==> libzmq: Executing phase: 'autoreconf'
==> libzmq: Executing phase: 'configure'
==> libzmq: Executing phase: 'build'
==> libzmq: Executing phase: 'install'
==> libzmq: Successfully installed
libzmq-4.3.3-pxrd6piprucu65bkro2ixms6d3x2eudz
  Fetch: 0.93s.  Build: 11.55s.  Total: 12.48s.
[+]
/opt/software/linux-ubuntu22.04-skylake/gcc-11.3.0/libzmq-4.3.3-pxrd6piprucu65bkro2ixms6d3x2eudz
==> Installing libzmq-4.3.4-hiil6dzy2reb4nk555zztwh44rpbyv4h
==> No binary for libzmq-4.3.4-hiil6dzy2reb4nk555zztwh44rpbyv4h found:
installing from source
==> Using cached archive:
/home/wdconinc/.spack/cache/_source-cache/archive/c5/c593001a89f5a85dd2ddf564805deb860e02471171b3f204944857336295c3e5.tar.gz
==> Using cached archive:
/home/wdconinc/.spack/cache/_source-cache/archive/31/310b8aa57a8ea77b7ac74debb3bf928cbafdef5e7ca35beaac5d9c61c7edd239
==> Applied patch
92b2c38a2c.patch?full_index=1
==> libzmq: Executing phase: 'autoreconf'
==> libzmq: Executing phase: 'configure'
==> libzmq: Executing phase: 'build'
==> libzmq: Executing phase: 'install'
==> libzmq: Successfully installed
libzmq-4.3.4-hiil6dzy2reb4nk555zztwh44rpbyv4h
  Fetch: 0.01s.  Build: 10.77s.  Total: 10.78s.
[+]
/opt/software/linux-ubuntu22.04-skylake/gcc-11.3.0/libzmq-4.3.4-hiil6dzy2reb4nk555zztwh44rpbyv4h
```
2022-08-25 19:13:41 -06:00
Adam J. Stewart
c6842605ac
py-pytorch-lightning: add v1.7.3 (#32383) 2022-08-25 18:01:50 -06:00
snehring
4d10cdb7e8
phylip: adding workarounds for gcc10+ (#32376)
* phylip: adding workarounds for gcc10+

* phylip: switch to spec.satisfies
2022-08-25 16:29:40 -06:00
Massimiliano Culpo
1bffa46d4d
zig: add v0.9.1 (#32380) 2022-08-25 14:38:26 -07:00
Richard Berger
6e420c3556
charliecloud: add versions 0.28 and 0.29 (#32378) 2022-08-25 13:21:27 -07:00
Ryan Marcellino
a476f0fa59
New package: py-mkdocs (#32363) 2022-08-25 12:37:20 -07:00
AMD Toolchain Support
6fb13c0fc5
fixed cp2k libcp2k.pc (#32349)
Co-authored-by: Prasanthi <pdonthir@amd.com>
2022-08-25 12:01:02 -07:00
Glenn Johnson
c2291f7eb3
new packages: r-cmdstanr and cmdstan (#32364) 2022-08-25 11:58:31 -07:00
Glenn Johnson
925a99a043
new package: r-glmgampoi (#32366)
* new package: r-glmgampoi

* Remove duplicate depends_on directive
2022-08-25 11:50:11 -07:00
Glenn Johnson
883b96aeb5
new packages: r-scdblfinder and dependencies (#32367)
- r-bluster
- r-metapod
- r-scran
2022-08-25 11:47:12 -07:00
Matthieu Dorier
9204bd6204
[ycsb] fixes build process and installation of YCSB (#32213)
* [ycsb] fixes build process and installation of YCSB

* [ycsb] fixing style

* [ycsb] removed extra newline
2022-08-25 11:26:08 -07:00
Wileam Y. Phan
b482c71b43
New package: glab (#32251) 2022-08-25 11:23:15 -07:00
robgics
ff2874333d
ddt: Initial commit (#32338)
* ddt: Initial commit

* ddt: Minor change to license date to appease the CI gods

* Get rid of unattractive extra line

* Switch to sha256 instead of md5
2022-08-25 11:03:07 -07:00
Robert Pavel
7214a438dc
Adding e3sm-kernels to Spack (#32341)
* Initial Draft of E3SM-Kernels Spackage

Initial draft of E3SM-Kernels. Currently no support for nested_loops due
to build system limitations

* Style Check and Fixed gfortran Check

Fixed style issues and changed gnu toolchain check to a gfortran check
due to hybrid compilers (e.g. clang+gfortran)

* Fixed Style Issues
2022-08-25 11:01:07 -07:00
Lucas Frérot
06ba4d5c28
lammps: added build dependency to py-setuptools (#32351)
LAMMPS' setup.py uses setuptools as of lammps/lammps@2ed8e5cf02
2022-08-25 10:40:07 -07:00
Mikael Simberg
1c3979dcfa
Add patch for missing template instantiation in pika 0.7.0 on macOS (#32370) 2022-08-25 11:30:00 -06:00
Melven Roehrig-Zoellner
f0925e1823
tixi: new variants (fortran,shared) (#32356)
* tixi: new variants (fortran,shared)

Since some tixi 3 versions, additional CMake flags are needed to build
tixi with shared libraries, respectively with Fortran support.

* tixi: fix style
2022-08-25 10:27:00 -07:00
snehring
ba87413eeb
snap-berkeley: update to version 2.0.1 (#32358) 2022-08-25 10:21:53 -07:00
Tyler Funnell
a4cbdba388
fish: adding v3.5.1 (#32362) 2022-08-25 10:18:39 -07:00
snehring
70388da974
libfabric: adding missing dep for opx fabric (#32377) 2022-08-25 10:10:30 -07:00
Sreenivasa Murthy Kolam
f0df4b653d
Changes for ROCm-5.2.0 changes and new recipe rocwmma (#31667)
* Changes for ROCm-5.2.0 changes and new recipe rocwmma

* modify the maintainers for hipify-clang

* address review comments

* update the rocwmma new recipe as per latest syntax

* fix style errors

* modify the patch file to provide the details about the patch

* fix style errors
2022-08-25 10:00:02 -07:00
Adam J. Stewart
507e06b5d2
Python: add new maintainer (#31755) 2022-08-25 09:46:09 -07:00
H. Joe Lee
c8f8b6957d
libfabric: Match main version. (#32342)
* Match main version.

`develop` no loger exists.

* Change develop to main.
2022-08-25 09:25:43 -07:00