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Author SHA1 Message Date
snehring
f77a38a96b
mash: fix compilation for aarch64 (#40218) 2023-09-28 10:16:11 -06:00
Harmen Stoppels
6d55066b94
Use st_nlink in hardlink tracking (#39328) 
Only add potential hardlinks to a set/dict, instead of each file. This
should be much cheaper, since hardlinks are very rare.
 2023-09-28 13:24:56 +00:00
Harmen Stoppels
78132f2d6b
glibc: dont link libgcc_eh.a pre 2.17, and backport at_random auxval patch (#40013) 
This resolves an interesting circular dependency between gcc and glibc:

1. glibc < 2.17 depends on libgcc.a and libgcc_eh.a
2. libgcc_eh.a is only built when gcc is configured with
   --enable-shared
3. but building shared libraries requires crt*.o and libc.so

Backport AT_RANDOM auxval changes to avoid dealing with wrong inline 
assembly (fallback code fails on ubuntu 23.04)
 2023-09-28 13:30:43 +02:00
Brian Vanderwende
fba47e87d7
Support optional vars script arguments (#40064) 2023-09-28 06:52:22 -04:00
Massimiliano Culpo
bf8e8d9f5f
cmake: add v3.27.6 (#40037) 
Co-authored-by: Harmen Stoppels <me@harmenstoppels.nl>
 2023-09-28 11:06:28 +02:00
Sam Gillingham
ebc0e9be19
kealib: add 1.5.1 and 1.5.2 versions (#40202) 
* add recent kealib versions
* udpdate depends_on so hl not required for latest version
 2023-09-27 19:08:28 -06:00
Vicente Bolea
b6f08f1d4e
vtk-m: add VTK-m 2.1.0-rc1 (#39581) 2023-09-27 10:13:18 -06:00
Jared Popelar
d9724597ed
Trilinos package: build on Windows (#34622) 
Update Trilinos and dependencies to build a limited version of Trilinos
on Windows.

* Support trilinos~mpi~shared on Windows
* superlu: force CMake build on Windows
* boost: update to build on Windows (proper option formatting and
  build tool names)
* pcre, openblas: add CMake-based build (keep prior build system
  as default on platforms other than Windows)
* openblas: add patch when using Intel Fortran compiler (currently
  this is included as part of the hybrid %msvc compiler in Spack)

Co-authored-by: John Parent <john.parent@kitware.com>
 2023-09-27 09:58:12 -06:00
kwryankrattiger
c90c946d52
ParaView: Add versio 5.11.2 (#40213) 2023-09-27 10:20:13 -05:00
Martin Aumüller
bb66d15d08
ffmpeg: fix build with XCode 15 (#40187) 
As reported in #40159, a shared library build of ffmpeg 6.0 fails with the linker that was added with XCode 15:
ld: building exports trie: duplicate symbol '_av_ac3_parse_header'
clang: error: linker command failed with exit code 1 (use -v to see invocation)

Forcing the old linker with -Wl,-ld_classic works around this.
 2023-09-27 16:41:32 +02:00
snehring
1cd2d07f0b
last: add new version, fix build on aarch64 (#40216) 
Co-authored-by: Bernhard Kaindl <bernhardkaindl7@gmail.com>
 2023-09-27 16:32:18 +02:00
Garth N. Wells
43cb49d87a
py-nanonbind: add new versions (#40161) 2023-09-27 16:28:26 +02:00
eugeneswalker
5165524ca6
e4s cray sles: suspend ci until machine issues resolved (#40219) 2023-09-27 04:51:34 +02:00
Martin Aumüller
38dc3a6896
vtk: @9.2 need seacas@2022-10-14, fix macos (#39896) 
Co-authored-by: Bernhard Kaindl <bernhardkaindl7@gmail.com>
 2023-09-26 13:48:44 -06:00
John W. Parent
115e448bd3
Paraview package: update freetype find patch for shared libs (#40085) 
VTK's (and therefore Paraview's) FindFreetype module required patching to
handle static import libraries from Freetype. However it did not cover
shared libraries. This adds support for importing shared freetype into the VTK build
 2023-09-26 10:41:24 -07:00
Harmen Stoppels
5c25437c9f
spack --profile: dump to stderr (#40209) 2023-09-26 16:18:47 +02:00
Christoph Weber
0e72ff4a0d
ploticus: new package (#39881) 
Co-authored-by: Bernhard Kaindl <contact@bernhard.kaindl.dev>
 2023-09-26 08:15:12 -05:00
Matt Fraser
90edd18d1f
Add NCCL v2.18.5-1 release to recipe (#40201) 2023-09-26 08:05:23 -05:00
Massimiliano Culpo
40dbadb868
crosstool-ng: add v1.26.0 (#40204) 2023-09-26 11:17:39 +02:00
Martin Aumüller
c16546bd4c
libressl: fix package & new versions (#39741) 2023-09-26 10:39:29 +02:00
Dom Heinzeller
143e6a4fbb
Always apply Python unixcompilers.py rpath fix, not just on cray (#39929) 
* Rename var/spack/repos/builtin/packages/python/cray-rpath-3.1.patch as var/spack/repos/builtin/packages/python/rpath-non-gcc.patch and apply unconditionally

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

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

---------

Co-authored-by: Adam J. Stewart <ajstewart426@gmail.com>
 2023-09-26 02:38:20 -06:00
Martin Aumüller
13816f19fd
opencv: add 4.7.0 and 4.8.0 and fix ffmpeg dependency (#39013) 2023-09-26 10:28:29 +02:00
Martin Aumüller
34ff3b408b
seacas: correctly limit fmt dependency (#39756) 
versions older than 2022-10-14 do not build with fmt@10, either:
fmt/core.h:1579:3: error: static_assert failed due to requirement 'formattable'
 2023-09-26 06:35:38 +02:00
Victor A. P. Magri
aec88ef3e6
hypre: add support for magma (#40121) 2023-09-26 06:27:14 +02:00
snehring
9fda22d942
bcl2fastq2: patch for compiling on aarch64 (#40195) 2023-09-26 06:26:19 +02:00
snehring
550613ee3a
gmap-gsnap: add v2023-07-20 and aarch64 support (#40200) 2023-09-26 05:59:31 +02:00
Ethan Williams
5341834ebe
Elbencho: add elbencho package (#40193) 
* add elbencho package
* pep8 compliant
* add description
* depends on boost
* boost options
* dependencies
* fix ncurses not linking properly missing tinfo
* pep8 fix
* fix style of boost variants
* final style fix - spack style is happy
* correct cufile env variable name

---------

Co-authored-by: Ethan W <mail@ethanwilliams.xyz>
 2023-09-25 18:53:28 -06:00
Alberto Invernizzi
fc027e34d1
apex: add new version 2.6.3 + deal with ompt build problem (#40073) 
* add new version 2.6.3
* add conflict for openmp when using gcc
 2023-09-25 16:00:58 -07:00
Harmen Stoppels
aef58776b4
openssl: new versions (#40194) 
apparently there was still a 1.1.1 release
 2023-09-25 21:54:05 +02:00
Cameron Smith
4e17a40d09
omegah: new version (#40192) 2023-09-25 13:53:36 -06:00
Matthieu Dorier
d97251a4c6
spdlog: add version 1.12.0 (#40186) 2023-09-25 12:23:02 -07:00
snehring
2a66a67132
subread: removing mtune arg to compiler (#40197) 2023-09-25 12:19:25 -07:00
eugeneswalker
10fd69ec74
new package: gsibec (#40137) 2023-09-25 11:28:04 -06:00
Harmen Stoppels
9889a0cac6
py-numcodecs: drop upperbound, add new version, avoid native compilation (#40183) 
* py-numcodecs: drop upperbound, add new version, avoid native compilation

* py-numcodecs: add entrypoints

* Remove another upperbound on python

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

---------

Co-authored-by: Adam J. Stewart <ajstewart426@gmail.com>
 2023-09-25 07:28:32 -06:00
Harmen Stoppels
65ffd0dd63
jsoncpp: add meson build system, update package, update cmake ~ownlibs (#39639) 2023-09-25 10:13:30 +02:00
Bernhard Kaindl
3d2c779b87
openssh: add version 9.4p1 and fix compile issue with new zlib-1.3 (#40174) 
The fix for the compile issue was improved by Bernhard Kaindl.
He also added to fix two classes of other build fails:
- add missing openssl dependency version limit to older openssh versions
- add missing -fcommon for new compilers building old openssh versions

Co-authored-by: snehring <snehring@iastate.edu>
 2023-09-25 08:30:10 +02:00
Harmen Stoppels
b57c2a10d4
phist: remove python 3.10 upperbound (#40175) 2023-09-25 08:28:13 +02:00
Diego Alvarez S
849a0a5eeb
Add opendjk 11.0.20.1+1, 17.0.8.1+1 (#40035) 2023-09-25 05:09:30 +02:00
Rocco Meli
7e4a6160b9
namd: Add NAMD 3.0b3 and ARM support (#40134) 2023-09-25 05:04:17 +02:00
dependabot[bot]
646e7b4b00
build(deps): bump black in /.github/workflows/style (#40165) 
Bumps [black](https://github.com/psf/black) from 23.1.0 to 23.9.1.
- [Release notes](https://github.com/psf/black/releases)
- [Changelog](https://github.com/psf/black/blob/main/CHANGES.md)
- [Commits](https://github.com/psf/black/compare/23.1.0...23.9.1)

---
updated-dependencies:
- dependency-name: black
  dependency-type: direct:production
  update-type: version-update:semver-minor
...

Signed-off-by: dependabot[bot] <support@github.com>
Co-authored-by: dependabot[bot] <49699333+dependabot[bot]@users.noreply.github.com>
 2023-09-24 17:48:02 +00:00
eugeneswalker
eea86c3981
new package: ecmwf-atlas (#40136) 2023-09-24 10:43:09 -06:00
dependabot[bot]
37c48fc82c
build(deps): bump urllib3 from 2.0.4 to 2.0.5 in /lib/spack/docs (#40119) 
Bumps [urllib3](https://github.com/urllib3/urllib3) from 2.0.4 to 2.0.5.
- [Release notes](https://github.com/urllib3/urllib3/releases)
- [Changelog](https://github.com/urllib3/urllib3/blob/main/CHANGES.rst)
- [Commits](https://github.com/urllib3/urllib3/compare/2.0.4...v2.0.5)

---
updated-dependencies:
- dependency-name: urllib3
  dependency-type: direct:production
  update-type: version-update:semver-patch
...

Signed-off-by: dependabot[bot] <support@github.com>
Co-authored-by: dependabot[bot] <49699333+dependabot[bot]@users.noreply.github.com>
 2023-09-24 17:35:48 +02:00
George Young
47daba3dc1
blast-plus: add 2.14.1 (#40179) 
Co-authored-by: LMS Bioinformatics <bioinformatics@lms.mrc.ac.uk>
 2023-09-24 09:33:38 -06:00
Brian Vanderwende
46062d98fd
visit: Add NetCDF format support (#40065) 2023-09-24 17:26:34 +02:00
François Trahay
4e37084ed4
EZTrace: add v2.1 (#39748) 2023-09-24 17:12:32 +02:00
Thomas Madlener
e7c229393d
garfieldpp: Fix the signature of setup_dependent_build_environment (#40133) 2023-09-24 17:04:41 +02:00
Houjun Tang
87fd9c3e93
sw4: add v3.0 (#40146) 2023-09-24 16:54:32 +02:00
snehring
676f2a3175
hmmer: adding new version 3.4 (#40148) 2023-09-24 16:53:18 +02:00
Adam J. Stewart
5fe7f5329b
py-torchvision: minimize dependencies (#40163) 2023-09-24 16:27:09 +02:00
Adam J. Stewart
c6a3dd03ab
py-torchmetrics: add v1.2.0 (#40164) 2023-09-24 16:25:34 +02:00