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Author SHA1 Message Date
Howard Pritchard
07b6834ec5
OpenMPI: added v4.0.4 (#17202) 
Bug fix release:

4.0.4 -- June, 2020
-----------------------
- Fix a memory patcher issue intercepting shmat and shmdt.  This was
  observed on RHEL 8.x ppc64le (see README for more info).
- Fix an illegal access issue caught using gcc's address sanitizer.
  Thanks to  Georg Geiser for reporting.
- Add checks to avoid conflicts with a libevent library shipped with LSF.
- Switch to linking against libevent_core rather than libevent, if present.
- Add improved support for UCX 1.9 and later.
- Fix an ABI compatibility issue with the Fortran 2008 bindings.
  Thanks to Alastair McKinstry for reporting.
- Fix an issue with rpath of /usr/lib64 when building OMPI on
  systems with Lustre.  Thanks to David Shrader for reporting.
- Fix a memory leak occurring with certain MPI RMA operations.
- Fix an issue with ORTE's mapping of MPI processes to resources.
  Thanks to Alex Margolin for reporting and providing a fix.
- Correct a problem with incorrect error codes being returned
  by OMPI MPI_T functions.
- Fix an issue with debugger tools not being able to attach
  to mpirun more than once.  Thanks to Gregory Lee for reporting.
- Fix an issue with the Fortran compiler wrappers when using
  NAG compilers.  Thanks to Peter Brady for reporting.
- Fix an issue with the ORTE ssh based process launcher at scale.
  Thanks to Benjamín Hernández for reporting.
- Address an issue when using shared MPI I/O operations.  OMPIO will
  now successfully return from the file open statement but will
  raise an error if the file system does not supported shared I/O
  operations.  Thanks to Romain Hild for reporting.
- Fix an issue with MPI_WIN_DETACH.  Thanks to Thomas Naughton for reporting.

Signed-off-by: Howard Pritchard <howardp@lanl.gov>
 2020-06-23 09:46:50 +02:00
Adam J. Stewart
f8e3e8289d
py-torchvision: added v0.6.1 (#17203) 2020-06-23 09:45:36 +02:00
Wouter Deconinck
0ffbd79bd0
[hepmc3] gcc@9.3.0 patch for @3.1.2:3.2.1, conflicts for earlier @:3.1.1 (#17182) 
See ba38f14d8f, which is included in master and released as of hepmc3@3.2.2
 2020-06-23 09:44:44 +02:00
vvolkl
36e603c7d6
whizard: added zlib as a dependency (#17205) 2020-06-23 08:56:23 +02:00
Tomoki, Karatsu
1d10c6c730
caffe: use MPI compiler when using hdf5+mpi (#17125) 2020-06-23 08:54:54 +02:00
Michael Kuhn
55f26b0ccb
lua: fix linking to ncurses (#17206) 
PR #17108 broke the build. Spack's ncurses package does not provide a
libtermcap, so we need to use libtinfow.
 2020-06-23 08:30:45 +02:00
vvolkl
735416dbf4
HEP generator update: evtgen, tauola, photos, pythia8, lhapdf, whizard (#16880) 
* add package evtgen

fix formatting

add evtgen dependencies and update pythia8

fix formatting

* [evtgen] update versions

* [pythia8] add 'without-PACKAGE' args

* fix formatting

* Add LHAPDF

Co-authored-by: iarspider

* Add package whizard

fix formatting

* [pyhtia8, evtgen] add conflict msg re: circular dependencies

* [pyhtia8, evtgen] fix conflicts

* [pyhtia8, evtgen] fix msg string

* Set pythia8 default to ~evtgen
 2020-06-22 13:16:06 -05:00
Jen Herting
985c5c7792
[py-macs2] new version and dependency (#16817) 
* [py-macs2] Combined commit

- Added version 2.1.3.3
- added dependency py-cython

Author: Jen Herting <jen@herting.cc>
Date:   Tue May 26 16:41:28 2020 -0400

[py-macs2] added sha256=

Author: Andrew Elble <aweits@rit.edu>
Date:   Tue Oct 29 10:34:33 2019 -0400

migrated repos

* [py-macs2] fixed copyright

* [py-macs2] py-cython is build dependency
 2020-06-22 13:15:46 -05:00
Omar Padron
224dc95159
Pre ci optimization (#16372) 
* add initial optimization script

* integrate optimization in spack ci

* make optimization opt-in

* fix import error

* flake8 fixes

* update command completion

* work around vermin errors

* fix sphynx errors
 2020-06-22 13:19:47 -04:00
Joseph Ciurej
42f2c168d2
swig: fix older builds on newer platforms by updating config files (#16854) 
* swig: revise 'autotools' automated 'config.*' update mechanism to support 'config.sub' and adapt 'swig' accordingly
 2020-06-22 10:44:29 -05:00
Brian Van Essen
4e9a98997a
Added 8.0 RC to the versions (#17176) 2020-06-22 08:22:14 -05:00
G-Ragghianti
54cfec025f
blaspp: moved to new git repo (#17184) 
Extended the list of maintainers
 2020-06-22 14:21:46 +02:00
darmac
a76545b813
dos2unix: add build dependency on gettext (#17191) 2020-06-22 13:37:26 +02:00
Brian Van Essen
0d08e18df5
Minor cleanup for conduit and hydrogen (#17136) 
* Fix how the Conduit detects that the MPI compiler is the same as the
CC compiler and is more careful when it sets the MPI compilers to be
the Cray PE system compilers.

* Remove unnecessary push of the MPI compilers to the C compilers for Hydrogen.
 2020-06-22 09:32:55 +02:00
Wouter Deconinck
3fc963b1f9
delphes: better specify the dependency on root (#17175) 
Compiling delphes with default root cxxstd=11 fails, see e.g. https://sft.its.cern.ch/jira/si/jira.issueviews:issue-html/ROOT-9492/ROOT-9492.html
 2020-06-22 09:31:57 +02:00
iarspider
0b74285a14
py-pyheadtail: added new package at v1.14.1 (#17159) 
Co-authored-by: iarspider <iarpsider@gmail.com>
 2020-06-22 08:52:19 +02:00
Hans Pabst
73b3bbbd22
libxsmm: added v1.16 (#17185) 2020-06-22 08:36:46 +02:00
Christoph Junghans
e91d7988e5
votca-*: added v1.6.1 (#17186) 2020-06-22 08:36:01 +02:00
Michael Kuhn
0cddfb9d8a
meson: added v0.54.3 (#17190) 2020-06-22 08:30:17 +02:00
Adam J. Stewart
4bfa844de0
SciPy: add v1.5.0 (#17189) 2020-06-22 08:20:04 +02:00
Adam J. Stewart
c7f6608f5e
NumPy: add v1.19.0 (#17183) 2020-06-20 17:46:10 -05:00
Chris White
a20ba315f5
Axom/Conduit: Fix error when fortran is not defined (#17171) 
* Fix error when fortran is not defined

* Guard more ~fortran cases
 2020-06-19 14:31:09 -05:00
G-Ragghianti
844312f213
Updated slate package to use new git repo. Added maintainer. (#17165) 
* Updated slate package to use new git repo.  Added maintainer.
 2020-06-19 11:10:03 -05:00
Alexander Knieps
b73536b4ad
Update to swipl package (#17173) 
* Added version 8.2.0, added dependency for documentation build, added variants for documentations

* Renamed variant '+man' to '+html'

Co-authored-by: Alexander Knieps <a.knieps@fz-juelich.de>
 2020-06-19 11:03:25 -05:00
Adam J. Stewart
b80d5e74e5
PyTorch: add v1.5.1 (#17167) 2020-06-18 17:24:38 -05:00
Adam J. Stewart
5a0c5de50b
py-pandas: add v1.0.5 (#17161) 2020-06-18 17:24:27 -05:00
Adam J. Stewart
33e6d0f378
py-matplotlib: add v3.2.2 (#17160) 2020-06-18 17:24:14 -05:00
Massimiliano Culpo
6d9f0262de
libjpeg-turbo: fixed sha256 (#17154) 2020-06-18 14:44:32 +02:00
lorddavidiii
68c13d76f9
arpack-ng: fix build with gcc@10: (#17131) 2020-06-18 14:43:52 +02:00
darmac
2a13bad8eb
atop: fix ld error (#17150) 2020-06-18 14:42:52 +02:00
Sinan
1de20f00b6
arrayfire: added cudnn as a dependency when +cuda (#17146) 
Co-authored-by: Sinan81 <sbulut@3vgeomatics.com>
 2020-06-18 11:20:17 +02:00
Omar Padron
82eb71cb95
Explicitly install setuptools in docker images (#17143) 2020-06-18 11:16:24 +02:00
Shintaro Iwasaki
910d258706
argobots, bolt: updates to package.py (#17117) 2020-06-18 11:11:59 +02:00
Itaru Kitayama
4fe78bceaa
cube and libjpeg-turbo: added cube v4.5 and libjpeg-turbo v2.0.4 (#17132) 2020-06-18 10:40:54 +02:00
Axel Huebl
2fd3ab3c9c
Fetching from urls: Error Message (#16434) 
* Fetching from urls: Error Message

Fix the error message when fetching from consecutive `urls` of a
package version. Each fail should show the currently failing URL,
not the first url.

Example multi-problem run that occured in real life:
```
==> 5821: Installing util-macros
curl: (28) Connection timed out after 10000 milliseconds
curl: (16) Error in the HTTP2 framing layer
curl: (22) The requested URL returned error: 403 Forbidden
==> Fetching https://www.x.org/archive/individual/util/util-macros-1.19.1.tar.bz2
==> Failed to fetch file from URL: https://www.x.org/archive/individual/util/util-macros-1.19.1.tar.bz2
    Curl failed with error 28
==> Fetching https://mirrors.ircam.fr/pub/x.org/individual/util/util-macros-1.19.1.tar.bz2
==> Failed to fetch file from URL: https://www.x.org/archive/individual/util/util-macros-1.19.1.tar.bz2
    Curl failed with error 16
==> Fetching http://xorg.mirrors.pair.com/individual/util/util-macros-1.19.1.tar.bz2
==> Failed to fetch file from URL: https://www.x.org/archive/individual/util/util-macros-1.19.1.tar.bz2
    URL https://www.x.org/archive/individual/util/util-macros-1.19.1.tar.bz2 was not found!
==> Fetching from https://www.x.org/archive/individual/util/util-macros-1.19.1.tar.bz2 failed.
==> Error: FetchError: All fetchers failed for spack-stage-util-macros-1.19.1-se2a2e74oyusj2r4esgcb7pr3qhh45ef
```

- `urls[0]`: HTTP2 layer error
- `urls[1]`: timeout
- `urls[2]`: missing file on mirror

* x.org: two more mirrors

x.org mirrors are a bit tricky, since many are out-of-sync or off.
A good package to test with is `util-macros`, which had a "recent"
release.
 2020-06-18 10:37:32 +02:00
Adam J. Stewart
1f85d6eceb
Docs: fix rst link to spack ci (#17147) 2020-06-18 09:44:03 +02:00
Toyohisa Kameyama
58e20430b1
minimap2: fix a typo in the recipe (#17148) 2020-06-18 09:43:06 +02:00
Seth R. Johnson
1bb94f2913
glib: fix 2.56 build with python@2 (#17144) 
* glib: fix 2.56 build with python@2

* flake8
 2020-06-17 23:32:25 -05:00
Joseph Ciurej
c8199ece65
python: fix patch issue for 2.7.X, 3.7.X (#17140) 
* python: fixing patch issue for 2.7.X, 3.7.X versions (#17128)

* python: fixing the C/C++ 'distutils' patching for @3.7.0:3.7.1
 2020-06-17 23:30:41 -05:00
Greg Becker
5b59e883c1
cray module do not work without CRAY_LD_LIBRARY_PATH (#17031) 
Co-authored-by: Gregory Becker <becker33.llnl.gov>
 2020-06-17 15:53:30 -07:00
Adam J. Stewart
c0cdc00409
oneDNN: add v1.5.0 (#17137) 2020-06-17 16:01:46 -05:00
Michael Kuhn
f7008f37d4 slurm: Fix build with gcc@10: 
gcc@10: defaults to -fno-common, which breaks slurm up to version
20-02-1. For more details, see https://gcc.gnu.org/gcc-10/porting_to.html
 2020-06-17 13:42:00 -07:00
Sergey Kosukhin
01b277ad0f
openmpi: options for local transport (#16831) 2020-06-17 14:41:24 -05:00
Chris White
506f31b7a7
axom conduit mfem build fixes (#17121) 
* honor global compiler flags

* Honor debug variant when using global compiler flags

* Add cppflags to c/cxx flags, clarify flag handling
 2020-06-17 12:43:47 -05:00
vvolkl
03880f5413
Split hepmc Into hepmc and hepmc3 (#16892) 2020-06-17 12:13:27 -05:00
Michio Ogawa
ad18933ef4
FrontISTR: various updates to the package (#17089) 
* Added maintainers
* Refined dependencies
* Changed git url
 2020-06-17 17:45:51 +02:00
Sergey Kosukhin
eca08c77e3
openmpi: fixes for NAG compiler (#17073) 
* openmpi: fixes for NAG compiler

* openmpi: more fixes
 2020-06-17 10:32:08 -05:00
Seth R. Johnson
e90c229dab
Fix/clarify some trilinos variants/dependencies (#17006) 
- Parallel HDF5 isn't required -- the comment seems to be about a
  transitive dependency with pnetcdf.
- Boost usage should respect the variant, not automatically be reenabled
  when choosing DTK.
 2020-06-17 09:34:53 -05:00
takanori-ihara
eb5f1886b7
py-tensorflow: Update for use with Fujitsu compiler (#17088) 
* py-tensorflow: Update for use with Fujitsu compiler

* py-tensorflow: remove -march option

* fix flake8 error
 2020-06-17 08:00:36 -05:00
darmac
dc0dfe9220
New package: lynx (#17099) 2020-06-16 23:04:00 -07:00