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2020-06-23Added unit tests to Github Actions (#16610)Massimiliano Culpo4-35/+67
* Added unit tests to Github Actions * Set user e-mail and name for git tests to succeed * Simplify setup.sh logic * Replicate Travis script on Github Actions * Update flags since '.' is not allowed * Added badge, simplified workflow * Remove pinning of coverage * Remove unit tests run on Github Actions from Travis
2020-06-23dock: new package at 6.9 (#17138)Justin S1-0/+59
2020-06-23strace: added v5.3 to v5.7 (#17193)darmac1-0/+5
2020-06-23r-spatialEco: added v1.3-2 (#17194)Amjad Kotobi1-0/+1
2020-06-23parallel-netcdf: add missing perl dependency (#17156)Michael Kuhn1-0/+2
parallel-netcdf's buildiface script needs perl during build.
2020-06-23swfft: Add patch to make it build (#17196)Mosè Giordano2-0/+15
2020-06-23py-gsd: new package at v1.9.3 (#17200)Jen Herting1-0/+25
Co-authored-by: Andrew Elble <aweits@rit.edu>
2020-06-23OpenMPI: added v4.0.4 (#17202)Howard Pritchard1-1/+2
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>
2020-06-23py-torchvision: added v0.6.1 (#17203)Adam J. Stewart1-1/+2
2020-06-23[hepmc3] gcc@9.3.0 patch for @3.1.2:3.2.1, conflicts for earlier @:3.1.1 ↵Wouter Deconinck2-0/+16
(#17182) See https://gitlab.cern.ch/hepmc/HepMC3/-/commit/ba38f14d8f56c16cc4105d98f6d4540c928c6150, which is included in master and released as of hepmc3@3.2.2
2020-06-23whizard: added zlib as a dependency (#17205)vvolkl1-0/+1
2020-06-23caffe: use MPI compiler when using hdf5+mpi (#17125)Tomoki, Karatsu1-0/+6
2020-06-23lua: fix linking to ncurses (#17206)Michael Kuhn1-1/+1
PR #17108 broke the build. Spack's ncurses package does not provide a libtermcap, so we need to use libtinfow.
2020-06-22HEP generator update: evtgen, tauola, photos, pythia8, lhapdf, whizard (#16880)vvolkl7-0/+279
* 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[py-macs2] new version and dependency (#16817)Jen Herting1-0/+2
* [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
2020-06-22Pre ci optimization (#16372)Omar Padron4-3/+393
* 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
2020-06-22swig: fix older builds on newer platforms by updating config files (#16854)Joseph Ciurej2-61/+85
* swig: revise 'autotools' automated 'config.*' update mechanism to support 'config.sub' and adapt 'swig' accordingly
2020-06-22Added 8.0 RC to the versions (#17176)Brian Van Essen1-0/+10
2020-06-22blaspp: moved to new git repo (#17184)G-Ragghianti1-5/+6
Extended the list of maintainers
2020-06-22dos2unix: add build dependency on gettext (#17191)darmac1-0/+2
2020-06-22Minor cleanup for conduit and hydrogen (#17136)Brian Van Essen2-4/+1
* 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.
2020-06-22delphes: better specify the dependency on root (#17175)Wouter Deconinck1-1/+2
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
2020-06-22py-pyheadtail: added new package at v1.14.1 (#17159)iarspider1-0/+24
Co-authored-by: iarspider <iarpsider@gmail.com>
2020-06-22libxsmm: added v1.16 (#17185)Hans Pabst1-1/+2
2020-06-22votca-*: added v1.6.1 (#17186)Christoph Junghans5-4/+13
2020-06-22meson: added v0.54.3 (#17190)Michael Kuhn1-0/+1
2020-06-22SciPy: add v1.5.0 (#17189)Adam J. Stewart1-2/+6
2020-06-20NumPy: add v1.19.0 (#17183)Adam J. Stewart1-1/+4
2020-06-19Axom/Conduit: Fix error when fortran is not defined (#17171)Chris White2-4/+8
* Fix error when fortran is not defined * Guard more ~fortran cases
2020-06-19Updated slate package to use new git repo. Added maintainer. (#17165)G-Ragghianti1-4/+3
* Updated slate package to use new git repo. Added maintainer.
2020-06-19Update to swipl package (#17173)Alexander Knieps1-0/+7
* 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>
2020-06-18PyTorch: add v1.5.1 (#17167)Adam J. Stewart1-1/+2
2020-06-18py-pandas: add v1.0.5 (#17161)Adam J. Stewart1-1/+2
2020-06-18py-matplotlib: add v3.2.2 (#17160)Adam J. Stewart1-2/+6
2020-06-18libjpeg-turbo: fixed sha256 (#17154)Massimiliano Culpo1-5/+7
2020-06-18arpack-ng: fix build with gcc@10: (#17131)lorddavidiii1-0/+6
2020-06-18atop: fix ld error (#17150)darmac1-0/+3
2020-06-18arrayfire: added cudnn as a dependency when +cuda (#17146)Sinan1-0/+1
Co-authored-by: Sinan81 <sbulut@3vgeomatics.com>
2020-06-18Explicitly install setuptools in docker images (#17143)Omar Padron4-0/+4
2020-06-18argobots, bolt: updates to package.py (#17117)Shintaro Iwasaki2-12/+7
2020-06-18cube and libjpeg-turbo: added cube v4.5 and libjpeg-turbo v2.0.4 (#17132)Itaru Kitayama2-0/+2
2020-06-18Fetching from urls: Error Message (#16434)Axel Huebl2-4/+10
* 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.
2020-06-18Docs: fix rst link to spack ci (#17147)Adam J. Stewart1-3/+3
2020-06-18minimap2: fix a typo in the recipe (#17148)Toyohisa Kameyama1-1/+1
2020-06-17glib: fix 2.56 build with python@2 (#17144)Seth R. Johnson1-3/+11
* glib: fix 2.56 build with python@2 * flake8
2020-06-17python: fix patch issue for 2.7.X, 3.7.X (#17140)Joseph Ciurej6-3/+539
* 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
2020-06-17cray module do not work without CRAY_LD_LIBRARY_PATH (#17031)Greg Becker2-5/+9
Co-authored-by: Gregory Becker <becker33.llnl.gov>
2020-06-17oneDNN: add v1.5.0 (#17137)Adam J. Stewart1-1/+2
2020-06-17slurm: Fix build with gcc@10:Michael Kuhn1-0/+9
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
2020-06-17openmpi: options for local transport (#16831)Sergey Kosukhin5-30/+309
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