Commit graph

27616 commits

Author SHA1 Message Date
dlkuehn
cd2b2898a1
kallisto: add v0.48.0 (#29689)
Co-authored-by: David Kuehn <las_dkuehn@iastate.edu>
2022-03-30 10:48:44 +02:00
dlkuehn
4c437a8683
freebayes: add v1.3.6 (#29692)
Co-authored-by: David Kuehn <las_dkuehn@iastate.edu>
2022-03-30 10:45:31 +02:00
Tom Scogland
4898759eab
gcc: add missing dependencies (#29671)
Co-authored-by: Adam J. Stewart <ajstewart426@gmail.com>
2022-03-30 10:42:38 +02:00
Cameron Smith
295507129b
simmetrix-simmodsuite: add opencascade variant and version 16.0-220312 (#29759)
Co-authored-by: Massimiliano Culpo <massimiliano.culpo@gmail.com>
2022-03-30 02:33:45 -06:00
Matthieu Dorier
eba0997521
ftxui: add new package (#29724) 2022-03-30 10:10:45 +02:00
Glenn Johnson
acb982f7fa
py-m2r: constrain py-mistune to version 0.8.1 (#29608)
* py-m2r: constrain py-mistune to version 0.8.1

* Remove lower half of py-mistune version constraint
2022-03-30 08:00:39 +00:00
Greg Sjaardema
ef1e96def4
cgns: add maintainer (#29775) 2022-03-30 09:42:18 +02:00
Niclas Jansson
fdab17a4d4
neko: add new package (#28791)
Co-authored-by: Massimiliano Culpo <massimiliano.culpo@gmail.com>
2022-03-30 09:34:10 +02:00
Thomas Dickerson
8806f9f826
proj: add v8.2.1, v8.2.0 and v8.1.1 (#29774)
Version 9.0.0 drops Autotools support in favor of CMake and will presumably require larger changes to package.py
2022-03-30 01:31:56 -06:00
Robert Pavel
54d738ff9c
Flecsi: updated version semantic (#29780)
Updated flecsi spackage to better support changes in control variables
in post 2.1.0 releases while also making legacy versions clearer as to
what is a tagged release and what is a rolling-ish development branch
2022-03-30 09:21:17 +02:00
Mikael Simberg
e58ac0705d
Add patch to fix compilation of boost with compilers not in path (#29718)
Co-authored-by: Mikael Simberg <mikael.simberg@iki.if>
2022-03-30 09:14:03 +02:00
Glenn Johnson
0182e39d44
r-quantreg: add v5.88 (#29621) 2022-03-29 21:02:41 -06:00
Glenn Johnson
7cfe626e21
py-reportlab: add missing dependency on freetype (#29611)
* py-reportlab: add missing dependency on freetype

* Add missing dependencies

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

Use pil virtual.

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

Co-authored-by: Adam J. Stewart <ajstewart426@gmail.com>
2022-03-29 20:43:12 -05:00
Seth R. Johnson
0367b73ed5
Trilinos: add linker flags to improve behavior (#29492) 2022-03-29 18:13:09 -04:00
Nichols A. Romero
f66e7aea94
Support DASK backend in XARRAY. (#29726)
* Support DASK backend in XARRAY.

* Create XARRAY parallel variant with correct py-dask dependency.
2022-03-29 14:02:40 -06:00
MicK7
ef23c3b122
Update cgns for new release (#29709)
Add CGNS 4.3.0 version
2022-03-29 20:36:05 +02:00
Asher Mancinelli
078ee48c4b
ExaGO: add v1.4.0 and v1.4.1 (#29712)
* ExaGO: Handling of cuda architectures and amdgpu targets changed
  to effectively handle multiple targets. See #28441.
* Add ROCm support to ExaGO and update ROCm support in HiOp
* ExaGO+rocm requires HiOp+rocm
* Newer versions of CMake may set HIP_CLANG_INCLUDE_PATH incorrectly:
  add comments to the ExaGO/HiOp packages explaining how to address
  this problem if it occurs.
2022-03-29 10:01:30 -07:00
Harmen Stoppels
9516fa9447
cmake: use CMAKE_INSTALL_RPATH_USE_LINK_PATH (#29703)
* cmake: use CMAKE_INSTALL_RPATH_USE_LINK_PATH

Spack has a heuristic to add rpaths for packages it knows are required,
but it's really a heuristic, and it does not work when the dependencies
put their libraries in a different folder than `<prefix>/lib{64,}`.

CMake patches binaries after install with the "install rpaths", which by
default are provided by Spack and its heuristic through
`CMAKE_INSTALL_RPATH`.

CMake however knows better what libraries are effectively being linked
to, and has an option to include those in the install rpath too, through
`CMAKE_INSTALL_RPATH_USE_LINK_PATH`.

These two CMake options are complementary, repeated rpaths seem to be
filtered, and the "use link path" paths are appended to Spack's
heuristic "install rpath".

So, it seems like a good idea to enable "use link path" by default, so
that:
- `dlopen` by library name uses Spack's heuristic search paths
- linked libraries in non-standard locations within a prefix get an
rpath thanks to CMake.

* docs
2022-03-29 12:24:10 -04:00
Greg Sjaardema
c0b400c422
cgns: add v4.3.0 (#29773) 2022-03-29 09:46:55 -06:00
Matthieu Dorier
134debc518
mochi-margo: add v0.9.8 (#29771) 2022-03-29 17:39:14 +02:00
Seth R. Johnson
ed1a48f50a
SUNDIALS: refactor CMake recipe (#29585)
- Use define/define_from_variant
- Remove unused "fortran_flags"
- Fix CUDA architectures when using multiple (needs semicolon not comma
  separators)
- Add `when=` variant restrictions to simplify logic
2022-03-29 17:09:02 +02:00
Carlos Bederián
02cbb8ffaa
cuda: add 11.6.2 (#29756) 2022-03-28 17:38:38 -06:00
Tamara Dahlgren
fd055d4678
spack info: make sections optional; add build/stand-alone test information (#22097)
Add output of build- and install-time tests to info command

Enable dependencies, variants, and versions by default (i.e., provide --no* 
options; add gcc to test_info_fields to increase coverage for c_names->v_names
2022-03-28 22:15:38 +00:00
Thomas Dickerson
40fad1472a
Convert git-over-ssh package URLs to canonical format (#29754)
Use canonical SSH urls for git-over-ssh package urls. See also: discussion on #29706, #29749, and https://forum.gitlab.com/t/provided-ssh-url-is-in-the-wrong-format/14320
2022-03-28 14:48:20 -07:00
Richard Berger
00469d84e7
spiner: fix +cuda (#29758) 2022-03-28 15:30:44 -06:00
John W. Parent
1c2fff2cb7
Add ssh to filter of valid urls (#29749) 2022-03-28 14:13:55 -07:00
eugeneswalker
5424e4bdc1
e4s ci spack.yaml: add h5bench (#29755) 2022-03-28 20:55:14 +00:00
Richard Berger
5fe20b462c
New package: spiner (#29719)
* New package: spiner

* Update dependencies for spiner package

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

Co-authored-by: Seth R. Johnson <johnsonsr@ornl.gov>

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

Co-authored-by: Seth R. Johnson <johnsonsr@ornl.gov>

* Remove versions that can't be installed and use ports-of-call@1.1.0

Co-authored-by: Seth R. Johnson <johnsonsr@ornl.gov>
2022-03-28 13:22:46 -06:00
Massimiliano Culpo
2856b29740
Removed unneeded conflicts in CudaPackage and RocmPackage (#29699)
Since the variant is conditional there's no need to add
conflicts too.
2022-03-28 10:58:56 -06:00
Jim Galarowicz
a7e365536b
survey package: add versions 1.0.2/1.0.3; add tls model variant (#29375) 2022-03-28 09:20:14 -07:00
Richard Berger
6aedbb32da
ports-of-call: new version 1.1.0 (#29723)
Version 1.0.0 was uninstallable.
2022-03-28 11:30:57 -04:00
FJ-NaokiMatsumura
9e169ae243
batchedblas: new package (#29028) 2022-03-28 17:16:03 +02:00
Max Zeyen
1dbab78db1
gpi-space: add v22.03 (#29736) 2022-03-28 14:50:21 +02:00
Filippo Spiga
8228ac7d62
Adding NVIDIA HPC SDK 22.3 (#29737)
Co-authored-by: Filippo Spiga <fspiga@nvidia.com>
2022-03-28 05:18:29 -06:00
Harmen Stoppels
3f41f8d093
julia: add patch reverting llvm rpath changes (#29731) 2022-03-28 02:34:27 -06:00
Harmen Stoppels
1ac7f2b02b
julia 1.6/1.7: constrain libgit2, libssh2 (#29728) 2022-03-28 10:28:09 +02:00
FJ-NaokiMatsumura
26f94b24e8
py-torch: fix to build with fujitsu-ssl2 (#29283)
* py-torch: fix build with fujitsu-ssl2

* fix to use fujitsu-ssl2 in py-torch v1.5.0 to v1.11.0

* fix to use fujitsu-ssl2 in py-torch v1.2.0 to v1.11.0

* Delete fj-ssl2.patch

* renamed the patches

* Rename fj-ssl2.1.5.patch to fj-ssl2_1.5.patch

* Delete fj-ssl2_1.5.patch
2022-03-27 19:22:18 -06:00
Matthieu Dorier
c75fb4da20
mochi-thallium: new package (#29722) 2022-03-27 18:18:24 -06:00
百地 希留耶
cd00eba9d6
autotools doc: add missing right quote (#29734) 2022-03-27 22:42:29 +00:00
David M. Rogers
073330e893
h5z-zfp: fix build when ^hdf5+mpi (#29733) 2022-03-27 13:50:53 -04:00
Howard Pritchard
bb9ac2be9c
openmpi: switch to using main (#29725)
The Open MPI project has elected to name our development branch - main.

Signed-off-by: Howard Pritchard <howardp@lanl.gov>
2022-03-27 13:01:33 +02:00
Glenn Johnson
b1f38f6fa2
py-torchvision: adjust jpeg dependency (#29614) 2022-03-26 21:21:37 -05:00
eugeneswalker
8e4e69e91d
llvm: add @14.0.0 (#29732)
* llvm: add @14.0.0

* llvm@14 provides virtual
2022-03-26 15:42:24 -06:00
Glenn Johnson
a785eeb896
r-rsqlite: add v2.2.10 (#29624) 2022-03-25 21:06:19 -06:00
Jen Herting
1b41e7408d
[julia] gfortran patch required for 1.7.2 (#29720) 2022-03-25 19:20:22 +01:00
Sreenivasa Murthy Kolam
15bdc6b3e1
Update rocm recipes for rocm-5.0.0 release (#29269)
* update rocm recipes for ROCm-5.0.0 release

* revert address sanitizer changes

* fix style errors

* update to the rocm recipes for 5.0.2 release

* fix review comments inside the rocfft recipe

* update the rocfft recipe for sqlite dependency
2022-03-25 10:56:52 -07:00
Richard Berger
56717e8b85
New package: ports-of-call (#29696) 2022-03-25 09:13:06 -06:00
Massimiliano Culpo
048a0de35b
Use the appropriate function to remove files in the stage directory (#29690)
We shouldn't be using "remove_linked_tree" to remove the lock file,
since that function expects to receive a directory path as an
argument.

Also, as a further measure to avoid regression, this commit restores
the "ignore_errors=True" argument on linux and adds a unit test
checking that "remove_linked_tree" doesn't change file permissions
as a side effect of a failure to remove.
2022-03-25 08:39:09 +01:00
iarspider
4702b49094
Sherpa: add several new variants used by CMS (#29338) 2022-03-24 19:30:33 -06:00
Valentin Volkl
0168047429
vecgeom: fix install error when ~cuda (#29716) 2022-03-24 18:38:56 -06:00