Commit graph

27447 commits

Author SHA1 Message Date
Wouter Deconinck
c75c27c95c
gdk-pixbuf: only build tests when requested (#32452)
The building of tests is optional [as of 2.42.9](801eef111d). This applies this option in the build.

The reason the option was added was to deal with test build failures in sandboxed environments and with certain glibc versions (caused by glib gresources). For example, with the latest version glibc and in the latest version of docker these tests [cannot be built](https://github.com/moby/moby/issues/43595).
2022-08-31 16:16:22 -07:00
Adam J. Stewart
f1f831edef
py-pandas: add v1.4.4 (#32459) 2022-08-31 14:27:15 -07:00
Satish Balay
60f37e8c88
llvm: fix 15.0.0rc builds on MacOS with command-line-tools (#32397)
* llvm: fix 15.0.0rc builds on MacOS with command-line-tools

Ref: https://github.com/llvm/llvm-project/issues/57037

i.e use -DBUILTINS_CMAKE_ARGS=-DCOMPILER_RT_ENABLE_IOS=OFF. But this needs switching "compiler-rt" from "projects" to "runtimes".

Also fixing the warnings below fixes compile errors

CMake Warning at CMakeLists.txt:101 (message):
  Using LLVM_ENABLE_PROJECTS=libcxx is deprecated now, please use
  -DLLVM_ENABLE_RUNTIMES=libcxx or see the instructions at
  https://libcxx.llvm.org/BuildingLibcxx.html for building the runtimes.


CMake Warning at CMakeLists.txt:101 (message):
  Using LLVM_ENABLE_PROJECTS=libcxxabi is deprecated now, please use
  -DLLVM_ENABLE_RUNTIMES=libcxxabi or see the instructions at
  https://libcxx.llvm.org/BuildingLibcxx.html for building the runtimes.


CMake Warning at CMakeLists.txt:101 (message):
  Using LLVM_ENABLE_PROJECTS=libunwind is deprecated now, please use
  -DLLVM_ENABLE_RUNTIMES=libunwind or see the instructions at
  https://libcxx.llvm.org/BuildingLibcxx.html for building the runtimes.


/private/var/folders/nt/_m1t_x7j76q6sl3xt91tqgs00000gn/T/balay/spack-stage/spack-stage-llvm-15.0.0-rc2-h2t5bohzyy7exz2ub3m42pfycjcmbndk/spack-build-h2t5boh/include/c++/v1/cstdlib:135:9: error: no member named 'at_quick_exit' in the global namespace
using ::at_quick_exit _LIBCPP_USING_IF_EXISTS;
      ~~^

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

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

Co-authored-by: Tamara Dahlgren <35777542+tldahlgren@users.noreply.github.com>
2022-08-31 13:29:07 -07:00
Massimiliano Culpo
0c6e3188ac
ASP-based solver: allow to reuse installed externals (#31558)
fixes #31484

Before this change if anything was matching an external
condition, it was considered "external" and thus something
to be "built".

This was happening in particular to external packages
that were re-read from the DB, which then couldn't be
reused, causing the problems shown in #31484.

This PR fixes the issue by excluding specs with a
"hash" from being considered "external"

* Test that users have a way to select a virtual

This ought to be solved by extending the "require"
attribute to virtual packages, so that one can:
```yaml
mpi:
  require: 'multi-provider-mpi'
```

* Prevent conflicts to be enforced on specs that can be reused.

* Rename the "external_only" fact to "buildable_false", to better reflect its origin
2022-08-31 20:05:55 +00:00
Seth R. Johnson
08261af4ab
py-breathe: add new version and improve version constraints (#31857)
* py-breathe: add new version and improve version constraints

* py-breathe: everyone loves versions

```
py-breathe, py-breathe in the air
don't be afraid to care
````

* Update var/spack/repos/builtin/packages/py-breathe/package.py

Co-authored-by: Adam J. Stewart <ajstewart426@gmail.com>

* add comment

Co-authored-by: Adam J. Stewart <ajstewart426@gmail.com>
2022-08-31 17:23:19 +00:00
Larry Knox
62e4177e44
hdf5-vol-log: Update package versions and update HDF5 dependency to version 1.13.2 (#32448)
* Add HDF5 version 1.13.2.
Remove HDF5 versions 1.13.0 and 1.13.1.

* Correct formatting.

* Update vol-log-based versions and HDF5 dependency version.
2022-08-31 06:29:15 -07:00
Ivan Maidanski
74506a2a83
bdw-gc: add v8.2.2 (#32453) 2022-08-31 06:18:49 -07:00
Adam J. Stewart
5fcfce18fd
py-gpytorch: add v1.9.0 (#32445) 2022-08-30 11:34:06 -07:00
Adam J. Stewart
c07c4629ff
py-kornia: add v0.6.7 (#32447) 2022-08-30 11:33:49 -07:00
Tamara Dahlgren
3894ceebc9
Environments: Add support for include URLs (#29026)
* Preliminary support for include URLs in spack.yaml (environment) files

This commit adds support in environments for external configuration files obtained from a URL with a preference for grabbing raw text from GitHub and gitlab for efficient downloads of the relevant files. The URL can also be a link to a directory that contains multiple configuration files.

Remote configuration files are retrieved and cached for the environment. Configuration files with the same name will not be overwritten once cached.
2022-08-30 11:13:23 -07:00
Ryan Marcellino
b35a0b1b40
New package: py-mkdocstrings-python (#32421) 2022-08-30 10:27:02 -07:00
Gregory Lee
543a797d1a
added STAT 4.2.0 and updated deps (#32385)
* added STAT 4.2.0 and updated deps

* launchmon package fix and style fixes

* launchmon package fix

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

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

Co-authored-by: Tamara Dahlgren <35777542+tldahlgren@users.noreply.github.com>
2022-08-30 09:25:55 -06:00
Ivan Maidanski
08c67302fc
libatomic_ops: add v7.6.14 (#32418)
Co-authored-by: Tamara Dahlgren <35777542+tldahlgren@users.noreply.github.com>
2022-08-30 06:00:09 -07:00
Harmen Stoppels
33cb61afb9
libxml2: fix building with nvhpc (#32440) 2022-08-30 06:13:47 -06:00
Wouter Deconinck
43ae15a887
root: new bugfix version 6.26.06 (#32230) 2022-08-30 10:31:17 +02:00
Toyohisa Kameyama
a735dc027d
oprnmx: fix to build with Fujitsu compiler. (#32389) 2022-08-30 10:26:15 +02:00
Olivier Cessenat
5be9f4dfef
coreutils: add support for external find (#32414) 2022-08-30 02:26:02 -06:00
David M. Rogers
d75234b675
hipsycl: fix building on OSX. Patch boost to be backward-compatible. (#31311)
Co-authored-by: frobnitzem <frobnitzem@users.noreply.github.com>
2022-08-30 10:22:34 +02:00
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