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2020-06-25mpich: Allow building with external hwloc library (#15305)Erik Schnetter1-1/+20
This is in principle supported already, but requires a patch to avoid build errors. Closes #15302 Co-authored-by: Michael Kuhn <michael.kuhn@informatik.uni-hamburg.de>
2020-06-25Separate Apple Clang from LLVM Clang (#17110)Massimiliano Culpo62-94/+136
* Separate Apple Clang from LLVM Clang Apple Clang is a compiler of its own. All places referring to "-apple" suffix have been updated. * Hack to use a dash in 'apple-clang' To be able to use autodoc from Sphinx we need a valid Python name for the module that contains Apple's Clang code. * Updated packages to account for the existence of apple-clang Co-authored-by: Adam J. Stewart <ajstewart426@gmail.com> * Added unit test for XCode related functions Co-authored-by: Gregory Becker <becker33@llnl.gov> Co-authored-by: Adam J. Stewart <ajstewart426@gmail.com>
2020-06-25msmc2: added package at v2.1.2 (#17170)manifest1-0/+43
Co-authored-by: Adam J. Stewart <ajstewart426@gmail.com>
2020-06-24Update the version of Cereal. (#17244)Brian Van Essen1-0/+1
2020-06-24chill: Patch to include gmp, isl, and libquadmath (#16996)John Jolly4-1/+150
The rose library uses the `strtoflt128` and `quadmath_snprintf` functions. In order to successfully link the rose library, chill must also link the GCC libquadmath library to resolve the two functions. This patch changes the chill build to include this library. Chill will also not compile unless headers from the gmp and isl libraries are found in the includes path. Two patches - one each for gmp and isl - modify the chill build process to add options to specify those paths. These options follow the similar pattern as seen with BOOSTHOME and ROSEHOME options which already exist in the chill build process. Because of the addition of GMPHOME and ISLHOME options, build requirements for gmp and isl are also added.
2020-06-24vtk: Add patch for finding Fujitsu-MPI wrapper commands. (#17069)Tomoki, Karatsu2-0/+21
2020-06-24mvapich2: Fix build with gcc@10: (#17114)Michael Kuhn1-0/+10
2020-06-24openjdk and jdk: extend the list of provided versions of java (#17151)Sergey Kosukhin2-1/+4
2020-06-24[podio] patch to correctly load dictionaries in v00-10 (#17157)vvolkl2-0/+21
2020-06-24New package: py-mmtf-python (#17201)Jen Herting1-0/+19
* mdanalysis * [py-mmtf-python] fixed copyright Co-authored-by: Andrew Elble <aweits@rit.edu>
2020-06-24Update a supported package 'user-meamc' for lammps (#17207)oracleLee1-2/+4
* Update package.py * edit confliction when add package 'meam' The USER-MEAMC fully replaces the MEAM package, which has been removed from LAMMPS after the 12 December 2018 version.
2020-06-24Fix missing dependency in Mono (#17208)cedricchevalier191-0/+3
* Add missing dependency on Python for Mono. At build time * Adding version 6.8.0.123 for mono
2020-06-24add cond py-mpi4py dep to conduit (#17211)Cyrus Harrison1-0/+1
2020-06-24ecp-io-sdk: remove deprecated numa variant from unify-fs (#17212)Chuck Atkins1-1/+1
2020-06-24The lapack-0.3.9-xerbl patch is no longer needed (#17217)Glenn Johnson1-1/+1
The lapack-0.3.9-xerbl patch is not needed for versions 0.3.10 and above.
2020-06-24timemory: Updated nearly all options to default to OFF (#17221)Jonathan R. Madsen1-18/+15
* Updated nearly all options to default to OFF * Fixed imported but unused module flake error
2020-06-24Updated MUMPS(5.3.3) (#17223)Michio Ogawa1-2/+3
* Updated MUMPS-5.3.3 * fixed E741 error(l -> ltr)
2020-06-24NCCL: add latest version (#17234)Adam J. Stewart1-3/+7
2020-06-24py-horovod: add latest version (#17235)Adam J. Stewart1-0/+1
2020-06-24GPyTorch: add new package (#17237)Adam J. Stewart1-0/+21
2020-06-24dtcmp: add v1.1.1 (#17240)Adam Moody1-0/+1
Signed-off-by: Adam Moody <moody20@llnl.gov>
2020-06-24lwgrp: add v1.0.3 (#17242)Adam Moody1-0/+1
2020-06-24quantum-espresso: fix for scalapack with openmpi (#17179)Nichols A. Romero1-1/+7
2020-06-24gromacs: fix fftw and update cmake dependencies (#17226)Gilles Gouaillardet1-1/+4
* gromacs: fix fftw dependency Only depend on fftw+mpi when gromacs is built with mpi, and depend on fftw~mpi otherwise. * gromacs: fix cmake dependency master branch depends on cmake 3.11 (as specified in CMakeLists.txt cmake dependency is also bumped to 3.11 when fj compilers are used in order to fix OpenMP detection.
2020-06-24perl: added v5.30.3 and v5.32.0 (#17220)Michael Kuhn1-1/+5
perl.org still recommends 5.30.3, so keep it as the preferred version.
2020-06-24quantum-espresso: correctly cross-compile code for Cray and BG/Q (#17180)Nichols A. Romero1-0/+13
2020-06-23Enable mysql for macos (#17177)victorusu1-1/+7
I get the following error message, if I do not use editline from the system. ``` >> 3090 Undefined symbols for architecture x86_64: 3091 "_tgetent", referenced from: 3092 _terminal_set in libedit.a(terminal.c.o) 3093 "_tgetflag", referenced from: 3094 _terminal_set in libedit.a(terminal.c.o) 3095 "_tgetnum", referenced from: 3096 _terminal_set in libedit.a(terminal.c.o) ... 3110 _terminal_insertwrite in libedit.a(terminal.c.o) 3111 _terminal_clear_EOL in libedit.a(terminal.c.o) 3112 _terminal_clear_screen in libedit.a(terminal.c.o) 3113 _terminal_beep in libedit.a(terminal.c.o) 3114 ... 3115 ld: symbol(s) not found for architecture x86_64 ```
2020-06-23revocap-refiner: updated package (#17192)Michio Ogawa1-22/+17
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
2020-06-22swig: fix older builds on newer platforms by updating config files (#16854)Joseph Ciurej1-0/+3
* 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
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