Commit graph

26982 commits

Author SHA1 Message Date
snehring
885a7a1979
gdal: fixing typo for libxml2 (#31734) 2022-07-25 14:05:45 -06:00
psakievich
8cde20997d
GCC: Add bootstrap conflict for M1 (#31189) 2022-07-25 15:12:54 -04:00
Paul Ferrell
babb0edf07
LLVM requires swig version > 3 (#31625) 2022-07-25 15:50:22 +02:00
haralmha
bf838fe15f
llvm: Add missing include for version range 8 to 11 (#31639) 2022-07-25 11:39:12 +02:00
Harmen Stoppels
b56871dd9c
Fix stage with uri params (#31618)
* don't determine extension of a url

* parse url to drop query params from filename
2022-07-25 10:31:13 +02:00
snehring
fe0643a14e
wget: replacing prior workaround with proper fix (#31699)
Co-authored-by: Harmen Stoppels <harmenstoppels@gmail.com>
2022-07-25 10:29:28 +02:00
Adam J. Stewart
cd4d657c2f
py-torchdata: add new package (#31704)
* py-torchdata: add new package

* third_party deps only in 0.4+
2022-07-25 10:22:53 +02:00
Adam J. Stewart
afbb4dbc88
py-torchmetrics: add v0.9.3 (#31707) 2022-07-25 10:22:25 +02:00
Adam J. Stewart
24869fd469
py-geopandas: add v0.11.1 (#31710) 2022-07-25 10:22:15 +02:00
Adam J. Stewart
d46e81798a
py-sphinx: add v5.1.0 (#31711) 2022-07-25 10:21:52 +02:00
Adam J. Stewart
5850afc9dc
Sphinx 5.1.0 breaks doc builds (#31709) 2022-07-24 21:45:01 +00:00
Ishaan Desai
241c7f7914
[py-pyprecice] add v2.4.0.0 (#31697)
* Add py-pyprecice v2.4.0.0

* Adding lower bound to pip dependency

* Removing when=@:2.1 from dependencies packaging and pip
2022-07-24 15:31:51 -05:00
Morten Kristensen
85b3c1d812
py-vermin: add latest version 1.4.1 (#31708) 2022-07-24 16:21:40 +02:00
Harmen Stoppels
215a99cbc3
clingo patch fixed in patch release (#31690) 2022-07-22 10:34:04 -07:00
Harmen Stoppels
517293efe0
llvm: fix patch already applied on main branch (#31694) 2022-07-22 09:46:03 -07:00
Harmen Stoppels
5cf7d8e9ef
coreutils: gnulib patch (#31693)
Co-authored-by: snehring <snehring@iastate.edu>
2022-07-22 15:36:14 +02:00
Harmen Stoppels
fce861d2ac
Mark external as explicit only when installing explicitly (#31665) 2022-07-22 15:20:17 +02:00
Hector Martinez-Seara
cfdfdf77e0
gromacs: Added version 2021.6 (#31692) 2022-07-22 15:18:59 +02:00
Harmen Stoppels
799553d302
autotools: add -I flag when non-standard libtool (#31677)
When
1. Spack installs libtool,
2. system libtool is installed too, and
3. system automake is used

Spack passes system automake's `-I <prefix>` flag to itself, even though
it's a default search path. This takes precedence over spack's libtool
prefix dir. This causes the wrong `libtool.m4` file to be used (since
system libtool is in the same prefix as system automake).

And that leads to error messages about incompatible libtool, something
something LT_INIT.
2022-07-22 15:11:38 +02:00
Massimiliano Culpo
5cf7bf3770
Use pkg_cls in spack.mirror.get_all_versions (#31636)
fixes #31627

spack.mirror.get_all_versions now uses the package class
instead of the package object in its implementation.

Ensure spec is concrete before staging for mirrors
2022-07-22 10:04:17 +02:00
Erik Schnetter
2b0b573827
mpitrampoline: New version 4.2.0 (#31683) 2022-07-22 09:22:24 +02:00
Nicholas Sly
0e6b57e953
py-torch: use immutable URLs for open-ce patches (#31672)
* Update open-ce patches for py-torch to us immutable URLs.  Update magma dependency specs to be more explicit.

* Address comments for PR regarding URLs and conflicting variants.

Co-authored-by: Nicholas Cameron Sly <sly1@llnl.gov>
2022-07-21 18:02:34 -06:00
Stephen Sachs
ee39fab226
[py-numpy] Newer versions do not build with icc (#31637)
* [py-numpy] Newer versions do not build with `icc`

Workaround until https://github.com/numpy/numpy/issues/22011 is solved.

* [py-numpy] Remove whitespaces
2022-07-21 12:33:41 -06:00
AMD Toolchain Support
5ffc095f63
Add version 3.2 of AMD libraries (#31538) 2022-07-21 13:32:28 +02:00
Adam J. Stewart
f85c4ec288
py-torch: ~caffe2 by default (#31656) 2022-07-21 09:43:02 +02:00
Adam J. Stewart
1af76946a4
py-torchvision: fix __version__ for stable releases (#31657) 2022-07-21 09:36:11 +02:00
Adam J. Stewart
609bc89fd9
py-gpytorch: add v1.8.0 (#31649) 2022-07-21 09:35:22 +02:00
Adam J. Stewart
de5a12c366
py-nbmake: add v1.3.3 (#31651) 2022-07-21 09:34:59 +02:00
Richard Berger
7d9c517c88
flecsi: correct version 2.x depends_on (#31658)
Propagate +shared to legion
2022-07-21 09:34:36 +02:00
Hadrien G
aa68f23177
root does not actually install libraries in /lib but in /lib/root (#31624) 2022-07-21 01:33:52 -06:00
Johannes Blaschke
15d50d81db
ncdu: add v1.16 and v1.17 (#31659) 2022-07-21 09:24:25 +02:00
shanedsnyder
56f5492fc0
darshan: add v3.4.0 to runtime/util packages (#31666) 2022-07-21 09:16:41 +02:00
snehring
d8983497f7
giflib: restrict patch to darwin (#31670) 2022-07-21 08:52:50 +02:00
psakievich
22798d7540
Don't restage develop specs when a patch fails (#31593)
* make develop specs not restage when a patch fails
* add a unit test
2022-07-20 13:55:16 -07:00
Harmen Stoppels
bf8c2b05b3
py-wheel: 0.37.1 (#31619) 2022-07-20 09:05:39 -06:00
haralmha
cf3774aa46
xgboost: Add version 1.6.1 and make openmp variant compatible with clang (#31557) 2022-07-20 07:45:01 -07:00
Harmen Stoppels
e7be8dbbcf
spack stage: add missing --fresh and --reuse (#31626) 2022-07-20 13:50:56 +02:00
Harmen Stoppels
e3aca44601
installer.py: require "explicit: True" in the install arguments to mark a package "explicit" (#31646) 2022-07-20 12:09:45 +02:00
Harmen Stoppels
43673fee80
py-pip: 22.x (#31621) 2022-07-18 19:13:42 -06:00
Servesh Muralidharan
918637b943
Update py-xdot to use python_purelib #31616 (#31628)
Issue discussed in https://github.com/spack/spack/issues/31616
2022-07-18 12:56:19 -07:00
Cory Bloor
5c59e9746a
rocblas: tighten tensile dependencies (#31414)
* rocblas: make tensile dependencies conditional

* Remove rocm-smi from the rocblas dependency list

rocm-smi was added to the rocblas dependency list because Tensile was a
dependency of rocBLAS and rocm-smi was a dependency of Tensile. However,
that reasoning was not correct.

Tensile is composed of three components:

  1. A command-line tool for generating kernels, benchmarking them, and
     saving the parameters used for generating the best kernels
     (a.k.a. "Solutions") in YAML files.
  2. A build system component that reads YAML solution files, generates
     kernel source files, and invokes the compiler to compile then into
     code object files (*.co, *.hsco). An index of the kernels and their
     associated parameters is also generated and stored in either YAML
     or MessagePack format (TensileLibrary.yaml or TensileLibrary.dat).
  3. A runtime library that will load the TensileLibrary and code object
     files when asked to execute a GEMM and choose the ideal kernel for
     your specific input parameters.

rocBLAS developers use (1) during rocBLAS development. This is when
Tensile depends on rocm-smi. The GPU clock speed and temperature must be
controlled to ensure consistency when doing the solution benchmarking.
That control is provided by rocm-smi. When building rocBLAS, Tensile is
used for (2). However, there is no need for control of the GPU at that
point and rocm-smi is not a dependency. At runtime, the rocBLAS library
uses Tensile for (3), but there is again no dependency on rocm-smi.

tl;dr: rocm-smi is a dependency of the tensile benchmarking tool,
which is not a build dependency or runtime dependency of rocblas.
2022-07-18 12:21:40 -07:00
eugeneswalker
b065d69136
e4s ci: add ginkgo +rocm (#31603) 2022-07-18 14:19:31 +02:00
Luke Diorio-Toth
710ec58df0
kraken2: add v2.1.2 (#31613) 2022-07-18 02:45:48 -06:00
Massimiliano Culpo
70be612f43
containerize: fix missing environment activation (#31596) 2022-07-18 10:31:16 +02:00
haralmha
c589f97cf0
lhapdf: add gettext libs explicitly (#31555)
Co-authored-by: Valentin Volkl <valentin.volkl@cern.ch>
2022-07-18 10:25:08 +02:00
Adam J. Stewart
ad4f551c22
py-pyarrow: aarch64 patch no longer applies/required (#31609) 2022-07-18 09:44:58 +02:00
Adam J. Stewart
37134aa331
py-kornia: add v0.6.6 (#31611) 2022-07-18 09:43:41 +02:00
Glenn Johnson
bb1632c99d
Fixes for kallisto package (#31617)
This PR contains several fixes for the kallisto package.

- create hdf5 variant as hdf5 is optional beginning with 0.46.2
- provide patch for 0.43 to link against libz
- provide patch for older versions to build again gcc-11 and up
- patch and code to use autoconf-2.70 and up
2022-07-18 09:37:21 +02:00
Jonathon Anderson
117c7cc3db
Only hack botocore when needed (#31610)
Newer versions of botocore (>=1.23.47) support the full IOBase
interface, so the hacks added to supplement the missing attributes are
no longer needed. Conditionally disable the hacks if they appear to be
unnecessary based on the class hierarchy found at runtime.
2022-07-18 08:40:13 +02:00
Luke Diorio-Toth
7b95e2f050
py-phydms, py-pypdf2, and py-pyvolve: new packages (#31540)
* py-panaroo: new package

* moving panaroo to branch

* py-phydms: new package

* added dependencies and new packages

* fixed py-pypdf2 dependencies
2022-07-16 17:24:29 -07:00