Commit graph

28263 commits

Author SHA1 Message Date
Vicente Bolea
328addd43d
ParaView: add v5.11.0-RC2 (#33486)
Co-authored-by: eugeneswalker <38933153+eugeneswalker@users.noreply.github.com>
2022-11-01 15:49:57 -07:00
Greg Becker
f696f02a46
Unit tests: make unit tests work for aarch64 machines (#33625)
Currently, many tests hardcode to older versions of gcc for comparisons of
concretization among compiler versions. Those versions are too old to concretize for
`aarch64`-family targets, which leads to failing tests on `aarch64`.

This PR fixes those tests by updating the compiler versions used for testing.

Currently, many tests hardcode the expected architecture result in concretization to the
`x86_64` family of architectures.

This PR generalizes the tests that can be generalized, to cover multiple architecture
families. For those that test specific relationships among `x86_64`-family targets, it
ensures that concretization uses the `x86_64`-family targets in those cases.

Currently, many tests rely on the fact that `AutotoolsPackage` imposes no dependencies
on the inheriting package. That is not true on `aarch64`-family architectures.

This PR ensures that the fact `AutotoolsPackage` on `aarch64` pulls in a dependency on
`gnuconfig` is ignored when testing for the appropriate relationships among dependencies

Additionally, 5 tests currently prompt the user for input when `gpg` is available in the
user's path. This PR fixes that issue. And 7 tests fail currently when the user has a
yubikey available. This PR fixes the incorrect gpg argument causing those issues.
2022-11-01 16:25:55 -06:00
Greg Sjaardema
e0265745bc
Update command option for example (#33321)
The `spack info <package>` command does not show the `Virtual Packages:` output unless the `--virtuals` command option is passed.  Before this changes, the information that the command is supposed to be illustrating is not shown in the example and is confusing.
2022-11-01 15:29:50 -06:00
Massimiliano Culpo
75360bdc21
Allow target requirements in packages.yaml (#32528)
This PR solves the issue reported in #32471 specifically for targets and operating systems, 
by avoiding to add a default platform to anonymous specs.
2022-11-01 22:11:49 +01:00
Harmen Stoppels
230e96fbb8
Add elf parsing utility function (#33628)
Introduces `spack.util.elf.parse_elf(file_handle)`
2022-11-01 19:42:06 +00:00
Michael Kuhn
6b3ea94630
perl: add 5.36.0 (#33336) 2022-11-01 12:13:53 -07:00
Michael Kuhn
6dd2bb258c
xz: add 5.2.7 (#33338) 2022-11-01 20:02:11 +01:00
Cody Balos
1abcc8caf7
sundials: add v6.4.1, new ginkgo and kokkos variants, plus some fixes (#33644)
* sundials: add v6.4.1, new ginkgo and kokkos variants, plus some fixes
* add missing kokkos/kokkos-kernels variant
* add v6.4.0
2022-11-01 12:45:53 -06:00
Massimiliano Culpo
23aef6bb94
Let pytest-cov create the xml directly (#33619)
`coverage` sometimes failed to combine, even if there were multiple reports.
2022-11-01 19:04:45 +01:00
liuyangzhuan
973b43b1c1
superlu-dist: fix rocm variant for the master branch (#33624)
* superlu-dist: fix rocm variant for the master branch
* simplify superlu-dist
* add mpi include to HIP_HIPCC_FLAGS

Co-authored-by: liuyangzhuan <liuyangzhuan@users.noreply.github.com>
2022-11-01 10:28:01 -07:00
Mikael Simberg
d925ba9bc6
Add tracy 0.9 (#33638)
* Add tracy 0.9
* Add conflict for pika and tracy@0.9:
2022-11-01 09:22:34 -07:00
Adam J. Stewart
1780f3ab3c
py-pytorch-lightning: add v1.8.0 (#33643) 2022-11-01 09:13:12 -07:00
Qian Jianhua
d6f25becdb
py-ilmbase: add dependency to py-numpy (#33633)
* py-ilmbase: add dependency to py-numpy

* fix style
2022-11-01 10:36:50 -05:00
Sinan
f2c84efed2
package/py-simplekml_add_new_versions (#33632)
Co-authored-by: sbulut <sbulut@3vgeomatics.com>
2022-11-01 10:30:02 -05:00
Harmen Stoppels
156dd5848e
Relocate links using prefix to prefix map (#33636)
Previously symlinks were not relocated when they pointed across packages
2022-11-01 16:00:51 +01:00
Mark W. Krentel
cd40d02214
hpctoolkit: adjust rocm dependency types (#33627)
Drop the link dependency type for the rocm packages.  We don't
actually link, and that adds rpaths that conflict with the app.
2022-10-31 21:38:04 -07:00
Adam J. Stewart
3187d4e7b1
py-torchmetrics: add v0.10.2 (#33630) 2022-10-31 20:01:23 -07:00
kwryankrattiger
6b86a8562f
ParaView: ParaView needs to set the HDF5 API (#33617)
When building ParaView with a newer HDf5 than 1.10, it needs to select the 1.10 API using flags.
2022-10-31 20:58:02 -06:00
Adam J. Stewart
df6cdcf6c7
GDAL: add v3.5.3 (#33623) 2022-10-31 19:53:52 -06:00
Luke Diorio-Toth
02097b1856
new package: polypolish (#33601)
* added polypolish package, comfirmed builds
* added bwa dep
2022-10-31 15:07:40 -07:00
downloadico
a83456dd7b
julia: don't look for the openlibm libraries when unneeded (#33626)
* julia: don't look for the openlibm libraries when unneeded
Cause spack to *not* check for the existence of the openlibm libraries (by adding it to the pkgs list) when ~openlibm is specified.
* [@spackbot] updating style on behalf of downloadico

Co-authored-by: downloadico <downloadico@users.noreply.github.com>
2022-10-31 16:05:49 -06:00
SoniaScard
269304a7ac
ophidia-server: new package at v1.7 (#33581)
Co-authored-by: SoniaScard <SoniaScard@users.noreply.github.com>
2022-10-31 14:20:56 -07:00
Massimiliano Culpo
ace8c74e20
Revert "gitlab: when_possible -> false (#33443)" (#33552)
This reverts commit b1559cc831.
2022-10-31 13:31:57 -07:00
Michael Kuhn
fc2d5d2311
Fix pkgconfig dependencies (#33614)
Packages should depend on the virtual provider, pkgconfig, not on its implementations pkg-config or pkgconf.
2022-10-31 11:44:07 -07:00
Mark Olesen
ef3cd6d6ca
openfoam: update mechanism for creating spack-specific wmake rules (#33615)
- the updated OpenFOAM wmake rules now allow multiple locations for
  compiler flags:
  * wmake/General/common/c++Opt  [central]
  * wmake/linux64Gcc/c++Opt      [traditional]
- match both '=' and ':=' make rule lines

Co-authored-by: Mark Olesen <Mark.Olesen@esi-group.com>
2022-10-31 09:43:58 -07:00
John W. Parent
222cef9b7c
Windows: fix library loading and enable Clingo bootstrapping (#33400)
Changes to improve locating shared libraries on Windows, which in
turn enables the use of Clingo. This PR attempts to establish a
proper distinction between linking on Windows vs. Linux/Mac: on
Windows, linking is always done with .lib files (never .dll files).
This somewhat complicates the model since the Spec.lib method could
return libraries that were used for both linking and loading, but
since these are not always the same on Windows, it was decided to
treat Spec.libs as being for link-time libraries. Additional functions
are added to help dependents locate run-time libraries.

* Clingo is now the default concretizer on Windows
* Clingo is now the concretizer used for unit tests on Windows
* Fix a permissions issue that can occur while moving Git files during
  fetching/staging
* Packages can now implement "win_add_library_dependent" to register
  files/directories that include libraries that would need to link
  to dependency dlls
* Packages can now implement "win_add_rpath" to register the locations
  of dlls that dependents would want to load
* "Spec.libs" on Windows is updated to return link-time libraries
  (i.e. .lib files, rather than .dll files)
* PackageBase.rpath on Windows is now updated to return the most-likely
  locations where .dlls will be found (which is generally in the bin/
  directory)
2022-10-31 09:36:52 -07:00
Erik
214890c026
Enable Cuda for AMReX smoke test. (#28576)
* Enable Cuda for AMReX smoke test.

* style fix

* more style fixes

* change /... to join_path

Co-authored-by: Tamara Dahlgren <35777542+tldahlgren@users.noreply.github.com>
2022-10-31 09:33:55 -07:00
Erik Schnetter
30d84a2716
rsync: New version 3.2.7 (#33618) 2022-10-31 09:26:45 -07:00
psakievich
6990cf76a0
Nalu-Wind: Allow for standard versions of trilinos (#33620)
* Nalu-Wind: Allow for standard versions of trilinos

This will allow us to utilize custom numeric versions for trilinos in `spack-manager` while we continue to develop `nalu-wind`.
Pinging @eugeneswalker @jrood-nrel @tasmith4

* Update var/spack/repos/builtin/packages/nalu-wind/package.py
2022-10-31 08:37:38 -07:00
Harmen Stoppels
7db38433e2
gmake: add a patch so dirs are not executed (#33578) 2022-10-31 08:17:40 -06:00
Satish Balay
a93b3643c6
exago: query and use MPI compilers from spack (#33598)
* exago: query and use MPI compilers from spack

* exago: requires explicit location of mpi.h for nvcc
2022-10-31 07:03:26 -07:00
Harmen Stoppels
a4930c74cb
Make --backtrace show non-SpackError backtraces (#33540) 2022-10-31 12:49:19 +00:00
Harmen Stoppels
1ab888cdc1
remove sequential filter in binary relo (#33608)
Currently there's a slow sequential step in binary relocation where all
strings of a binary are collected, with rpaths removed, and then
filtered for the old install root.

This is completely unnecessary, and also incorrect, since we replace
more than just the old install root in the prefix to prefix mapping. And
in fact the prefix to prefix mapping is parallel, and a single pass. So
even as an optimization, this filter makes no sense anymore.

Therefor we remove it
2022-10-31 10:41:59 +01:00
Harmen Stoppels
616d5a89d4
_replace_prefix_bin performance improvements (#33590)
- single pass over the binary data matching all prefixes
- collect offsets and replacement strings
- do in-place updates with `fseek` / `fwrite`, since typically our
  replacement touch O(few bytes) while the file is O(many megabytes)
- be nice: leave the file untouched if some string can't be
  replaced
2022-10-31 10:08:16 +01:00
Mosè Giordano
fb4be98f26
utf8proc: add v2.8.0 (#33611) 2022-10-31 00:47:20 +01:00
Diego Alvarez
20fafe6a46
openjdk: add 11.0.16.1+1, 11.0.17+8, 17.0.4.1+1, 17.0.5+8 (#33355) 2022-10-30 13:25:41 -06:00
Mosè Giordano
7d5446740c
libgit2: add v1.4.4 and v1.5.0 (#33604) 2022-10-30 12:13:47 +01:00
eugeneswalker
999c460b1e
e4s ci: add mfem +rocm (#31604) 2022-10-29 23:32:46 +00:00
Veselin Dobrev
82470f880a
New MFEM version: 4.5 (#33480)
* New MFEM version: 4.5

Add new MFEM variants: ginkgo, hiop

* mfem: small tweaks

* mfem: tweak testing script

* mfem: try to resolve issue #30483

* mfem: fix style

* mfem: tweak for Spack-built hipsparse

Co-authored-by: eugeneswalker <38933153+eugeneswalker@users.noreply.github.com>
2022-10-29 13:22:25 -07:00
eugeneswalker
e5274de7ec
unifyfs %oneapi: -Wno-error=deprecated-non-prototype,unused-function (#33602) 2022-10-29 13:19:27 -07:00
eugeneswalker
23aada1d24
gettext: constrain nvhpc patch to @:0.20.0 (#33489) 2022-10-29 21:41:10 +02:00
Massimiliano Culpo
7e645f54c5
Deprecate spack bootstrap trust/untrust (#33600)
* Deprecate spack bootstrap trust/untrust
* Update CI
* Update tests
2022-10-29 12:24:26 -07:00
Sergey Kosukhin
29f1e8395c
mpich: fix rpath flags in mpif90 when building with oneapi (#33319)
Co-authored-by: eugeneswalker <38933153+eugeneswalker@users.noreply.github.com>
2022-10-29 12:17:43 -06:00
Jonas Thies
83b49070e6
phist: add/update conflicts with cray-libsci and/or python@3.11: for … (#33587)
* phist: add/update conflicts with cray-libsci and/or python@3.11: for versions <1.11.2

* phist: style fix
2022-10-29 10:12:26 -07:00
eugeneswalker
ef8c15c5ef
czmq %oneapi: -Wno-error: gnu-null-pointer-arithmetic, strict-prototypes (#33586) 2022-10-29 06:14:15 -06:00
eugeneswalker
c10d525956
json-c %oneapi: add -Wno-error=implicit-function-declaration (#33585) 2022-10-29 06:13:54 -06:00
Satish Balay
6edb20c7a6
mumps: update URLs, and add versions 5.5.0, 5.5.1 (#33597) 2022-10-29 11:34:45 +02:00
Axel Huebl
b06c5a43d9
WarpX 22.10 & PICMI-Standard (#33594)
Update `warpx` & `py-warpx` to the latest release, `22.10`.
Update `py-picmistandard` accordingly.
2022-10-29 11:27:46 +02:00
Adam J. Stewart
06bac4a487
libtiff: CMake support, internal codecs variants (#33591) 2022-10-29 06:36:14 +02:00
Brian Van Essen
6c5a7fefd6
Fixed a bad variant when statement for including cuDNN. (#33595) 2022-10-28 13:21:50 -06:00