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2020-07-21hpcviewer, ibm-java: new versions (#17612)Mark W. Krentel2-0/+8
Add hpcviewer version 2020.07 and ibm-java 8.0.6.11.
2020-07-20Bugfix: Do not raise InstallError for ascent_ver (#17578)Tamara Dahlgren1-3/+3
2020-07-20bugfix: ignore Apple's "gcc" by default (#17589)Todd Gamblin3-29/+51
Apple's gcc is really clang. We previously ignored it by default but there was a regression in #17110. Originally we checked for all clang versions with this, but I know of none other than `gcc` on macos that actually do this, so limiting to `apple-clang` should be ok. - [x] Fix check for `apple-clang` in `gcc.py` to use version detection from `spack.compilers.apple_clang`
2020-07-20Fix MacOS build tests (#17542)Massimiliano Culpo2-11/+35
* MacOS build tests - Run on PR that modify the YAML file of the workflow - Don't clone Spack, since we are in the Spack repo now * Try to add opengl to configuration to build jupyter * fixup
2020-07-20Configuration: allow usage of command-line scopes with environments (#14608)Dr. Christian Tacke1-4/+4
Spack did not support usage of the `--config-scope` option in combination with an environment: In `lib/spack/spack/main.py`, `spack.config.command_line_scopes` is set equal to any config scopes passed by the `--config-scope` option. However, this is done after activating an environment. In the process of activating an environment, the `spack.config.config` singleton is instantiated, so later setting of `spack.config.command_line_scopes` is ignored. This commit sets command line scopes before activating an environment to ensure that they are included in the configuration. Co-authored-by: Tim Fuller <tjfulle@sandia.gov>
2020-07-20py-dp-gp-cluster: new package at 2019-09-22 (#17549)Justin S1-0/+33
* py-dp-gp-cluster: new package * py-dp-gp-cluster: remove master, add 2019-09-22 * py-dp-gp-cluster: require python2, older gpy, sklearn * py-dp-gp-cluster: remove cython runtime dep
2020-07-18update ascent package with recent ver dep logic, and dray support (#17502)Cyrus Harrison1-19/+66
* update ascent package with recent ver dep logic, and dray support * update pmt name, make babelflow logic dep on mpi
2020-07-18Add texlive 2020 version (#17559)Jon Rood3-4/+21
* Add new versions of texlive and poppler. * Add new versions of harfbuzz which also relocated source location to github. * Update var/spack/repos/builtin/packages/harfbuzz/package.py Co-authored-by: Adam J. Stewart <ajstewart426@gmail.com> * Restore deleted url line in harfbuzz. Co-authored-by: Adam J. Stewart <ajstewart426@gmail.com>
2020-07-17allow GNUPGHOME to come from SPACK_GNUPGHOME in env, if set (#17139)eugeneswalker1-1/+1
2020-07-17r-devtools: add version 2.3.0; update dependencies (#17408)Amjad Kotobi1-8/+31
2020-07-17libint (package): add tuning options for MOLGW (#17329)Fabien Bruneval1-0/+23
2020-07-17New package: parallelmergetree (#17501)Cyrus Harrison1-0/+34
2020-07-17Bugfix/install missing compiler from buildcache (#17536)Scott Wittenburg2-0/+40
Ensure compilers installed from buildcache are registered.
2020-07-17py-matplotlib: add v3.3.0Adam J. Stewart1-5/+7
2020-07-17buildcache: list all mirrors even if one failsScott Wittenburg1-2/+2
2020-07-17subversion: added v1.14.0 amd v1.13.0, added new url (#17519)Amjad Kotobi1-1/+6
2020-07-16add devil ray package (#17495)Cyrus Harrison1-0/+318
* add dray with mid-review changes * remove env import since its impliclity included
2020-07-16Updates to maestrowf package (#17470)Francesco Di Natale2-18/+46
* Addition of Chainmap to satisfy Maestro dependency. * Additional versions and dependencies for Maestro. * Updated URL to point to pypi. * Updates to chainmap hashes. * Updates to pull version from PyPi. * Corrections to flake8 errors. * Stricter restrictions on Python versioning. Maestro actually supports Python 3.5 and later. Co-authored-by: Adam J. Stewart <ajstewart426@gmail.com> * Only install chainmap for Python2 versions. Co-authored-by: Adam J. Stewart <ajstewart426@gmail.com> * Removal of setuptools python cond. * Removal of version constaints on setuptools. Co-authored-by: Adam J. Stewart <ajstewart426@gmail.com>
2020-07-16Version 1.13.2 still needs the XL patch. (#17561)Kelly (KT) Thompson2-0/+14
2020-07-16adept-utils: 1.0.1 does not build w/ boost 1.73.0 or newer (#17560)Scott Wittenburg1-1/+1
2020-07-16Mark old icu4c as conflicting (#17562)Seth R. Johnson1-0/+2
GCC 4.8.5 on rhel6: ``` utext.cpp:572:5: error: 'max_align_t' in namespace 'std' does not name a type std::max_align_t extension; ^ utext.cpp: In function 'UText* utext_setup_67(UText*, int32_t, UErrorCode*)': utext.cpp:587:73: error: 'max_align_t' is not a member of 'std' spaceRequired = sizeof(ExtendedUText) + extraSpace - sizeof(std::max_align_t); ^ utext.cpp:587:73: note: suggested alternative: In file included from /projects/spack/opt/spack/gcc-4.4.7/gcc/6ln2t7b/include/c++/4.8.5/cstddef:42:0, from utext.cpp:19: /projects/spack/opt/spack/gcc-4.4.7/gcc/6ln2t7b/lib/gcc/x86_64-unknown-linux-gnu/4.8.5/include/stddef.h: 425:3: note: 'max_align_t' } max_align_t; ^ utext.cpp:598:57: error: 'struct ExtendedUText' has no member named 'extension' ut->pExtra = &((ExtendedUText *)ut)->extension; ^ g++ ... loadednormalizer2impl.cpp g++ ... chariter.cpp ```
2020-07-16Fix security issue in CI (#17545)Harmen Stoppels2-9/+1
The `spack-build-env.txt` file may contains many secrets, but the obvious one is the private signing key in `SPACK_SIGNING_KEY`. This file is nonetheless uploaded as a build artifact to gitlab. For anyone running CI on a public version of Gitlab this is a major security problem. Even for private Gitlab instances it can be very problematic. Co-authored-by: Scott Wittenburg <scott.wittenburg@kitware.com>
2020-07-16Add new dependencies required in latest rsync. (#17558)Jon Rood2-0/+5
2020-07-16PySCF new package (#17474)Nichols A. Romero2-0/+45
* Initial version of PySCF. * Add master branch to xcfun library * PySCF only compatible with specific commit of xcfun library * Update var/spack/repos/builtin/packages/py-pyscf/package.py Co-authored-by: Adam J. Stewart <ajstewart426@gmail.com> * Update var/spack/repos/builtin/packages/py-pyscf/package.py Co-authored-by: Adam J. Stewart <ajstewart426@gmail.com> * Revert "PySCF only compatible with specific commit of xcfun library" This reverts commit 8296005400fbe76d0c8339b7ca06e71a801f0a22. * Revert "Add master branch to xcfun library" This reverts commit f2b69989316a6bece6530d5d63f1d120ab4c14a8. * Issues conflict for xcfun library version rather than relying on a random commit. * Add version xcfun 2.0.0a2 which is needed by PySCF. * Remove xcfun conflict and express dependency more explictly. Add comment as to why this is necessary. Co-authored-by: Adam J. Stewart <ajstewart426@gmail.com>
2020-07-16Abinit+wannier90 fix (#17417)downloadico2-20/+134
* wannier90: add versions 3.0.0 and 3.1.0 and 'shared variant' Added versions 3.0.0 and 3.1.0 Added shared variant Added url_for_version function as versions less than 3 are from the wannier.org site and versions 3 and up are from github.com Added the MPI libraries to the list of libs substituted into the make.sys file in place of @LIBS Made it possible to build a shared object version of the library for versions < 3 by filtering the src/Makefile.2 file (based off of the patch from a src rpm from RHEL for version 2.0.1) Create a modules directory in the install prefix root directory and copy the Fortran .mod files there. Set the MPIFC variable to the Spack Fortran MPI compiler wrapper. * abinit: added 'wannier90' variant which enables building abinit with wannier90 Added wannier90 variant Made abinit depend on the shared object ('shared') variant of wannier90 if the wannier90 variant is selected Add configure args for wannier90 libs, includes, and binaries and to set MPIFC set the dft-flavor to wannier90 when wannier90 is enabled and only set the dft flavor to 'atompaw+libxc' if wannier90 is not selected * Update var/spack/repos/builtin/packages/abinit/package.py Co-authored-by: Greg Becker <becker33@llnl.gov> * Update var/spack/repos/builtin/packages/wannier90/package.py Co-authored-by: Greg Becker <becker33@llnl.gov> * Update var/spack/repos/builtin/packages/wannier90/package.py Co-authored-by: Greg Becker <becker33@llnl.gov> * incorporated bbecker's suggestion for making the strings less ugly! * incorporated bbecker's suggestion to fix the logic for picking which "DFT flavor" configure argument. If the wannier variant is enabled, it passes --with-dft-flavor=wannier90 to configure, otherwise it passes --with-dft-flavor=atompaw+libxc to configure * Changed to using plain strings * Fixed version tests * incorporated @adamjstewart's fix for testing if the major version is > 2 * incorporated @adamjstewart's fix to check if mpi is enabled and only set the MPIFC variable if it is. * Update var/spack/repos/builtin/packages/wannier90/package.py Co-authored-by: Adam J. Stewart <ajstewart426@gmail.com> * Only set MPIFC if '+mpi' is set * incorporated fixes from @adamjstewart including: - using the string=True argument to filter_file (and removed the unneeded escapes) - changing the url to the github location - fixing the version checks - building a libwannier.dylib on darwin * incorporated fixes suggested by @adamjstewart including: - using the string=True argument to filter_file and cleaned up the escapes - only pass the MPIFC argument to configure when '+mpi' is set - chaned the url to the github site for Wannier090 - fixed the version checks - build a 'libwannier.dylib' file when building the shared variant on darwin * Update var/spack/repos/builtin/packages/wannier90/package.py Co-authored-by: Greg Becker <becker33@llnl.gov> * moved a configure argument from it's own '+mpi' check to under the lower one * Update var/spack/repos/builtin/packages/wannier90/package.py Co-authored-by: Adam J. Stewart <ajstewart426@gmail.com> * Cleaned up syntax as suggested by @adamjstewart It looks *so much better* now! Thanks! * removed unneeded import of 'find' from 'llnl.util.filesystem' package as suggested by @adamjstewart * Update var/spack/repos/builtin/packages/wannier90/package.py Co-authored-by: Adam J. Stewart <ajstewart426@gmail.com> * incorporated changes from @adamjstewart changed check to "if '@:2 +shared' in spec:" instead of a nested check of '@:2' and '+shared' removed unneeded joins used in filter_file and spliced the list of objs directly into the filter_file call used the dso_suffix instead of testing for darwin to determine the name of the shared library * removed whitespace from blank line * fixed bug with '../../wannier90.x: .*' not being treated as a regexp. Thanks Adam! * fixed missing whitespace when modifying Makefile.2 Co-authored-by: Greg Becker <becker33@llnl.gov> Co-authored-by: Adam J. Stewart <ajstewart426@gmail.com>
2020-07-16Make the largest layer of the docker image cacheable (#17553)Harmen Stoppels4-56/+56
2020-07-16Update for Build 7020 of nagfor compiler (#17555)Themos Tsikas1-1/+1
2020-07-16Add new package: hibench (#17552)darmac1-0/+35
2020-07-16New package: openloops (#17520)iarspider3-0/+225
* New package: OpenLoops * install() for openloops * Working OpenLoops recipe * Flake-8 * Only copy collection file if required; add clarification to num_jobs * Add __future__ import just in case * Fix missing space * Remove __future__ import * Changes from review, pt. 1 Co-authored-by: Adam J. Stewart <ajstewart426@gmail.com> * Replace print() with write() * Flake-8 Co-authored-by: iarspider <iarpsider@gmail.com> Co-authored-by: Adam J. Stewart <ajstewart426@gmail.com>
2020-07-16kallisto: remove mpich dependency (#17551)Tom Payerle1-1/+0
kallisto does not depend on mpich or MPI, except possibly indirectly through hdf5 (but that should be handled by hdf5).
2020-07-15Add new package: prometheus (#17541)darmac1-0/+34
2020-07-15storm: update url, version & runtime depends (#17523)darmac1-5/+7
* storm: update url, version & runtime depends * fix list_url error
2020-07-15vasp: New package. (#15187)fcannini1-0/+138
* vasp: New package. * Remove unneeded `#noqa` Co-authored-by: Adam J. Stewart <ajstewart426@gmail.com> * Removed a completely needless tty.debug() * Add compiler conflicts() and minute fixes Co-authored-by: Adam J. Stewart <ajstewart426@gmail.com>
2020-07-15add apcomp package (#17494)Cyrus Harrison1-0/+182
* add apcomp package * add maintainers * fake8 * Update var/spack/repos/builtin/packages/apcomp/package.py Co-authored-by: Adam J. Stewart <ajstewart426@gmail.com> * review suggestions Co-authored-by: Adam J. Stewart <ajstewart426@gmail.com>
2020-07-15Update icu4c package (#17461)Rémi Lacroix1-6/+11
* icu4c: Add new versions for older releases. The old URLs for versions 60.1, 58.2 and 57.1 do not work anymore so add the versions available on Github. The old versions are kept for reference (cf. #15896). * icu4c: Add versions 66.1 and 67.1. * icu4c: Fix compilation of versions 58 and 59 with recent glibc.
2020-07-15changes to py-torch recipe to enable rocm build (#17410)kolamsrinivas2-1/+112
* changes to recipe to enable rocm build * fixing flake8 issue * addressed the review comment
2020-07-15Adds new R package: GSODR (#17529)Julius-Plehn3-0/+44
* R GSODR package * use cloud mirror
2020-07-15[root] fix cmake args for r variant (#17487)vvolkl1-1/+2
* [root] fix cmake args for r variant * [root] add readline dependency to +r
2020-07-15spack containerize: added --fail-fast argument to containerize install. (#17533)Paul2-2/+2
2020-07-15Go: added v1.14.5 and v1.13.13. (#17539)Paul1-0/+2
2020-07-15visit package update, add glu as a linux dep (#17537)Cyrus Harrison1-0/+6
* visit: add glu as a dep for linux * add note to suggested install command about mesa
2020-07-15curl: add dependency on libidn2 (#17526)Dr. Christian Tacke1-0/+3
If the system has libidn2 installed, then curl will use it. spack has a libidn2 package, so let's use that! Related: #16514
2020-07-15namd: added v2.14b2 (#17395)yellowhat1-1/+2
Co-authored-by: Adam J. Stewart <ajstewart426@gmail.com>
2020-07-15cantera: better specify dependency on sundials (#17540)ketsubouchi1-1/+1
2020-07-14New Package: GrADS (#17476)Julius-Plehn3-0/+85
* grads minimal package * udpt template * grads minima * grads & shapelib package * hdf4 * cleanup * hdf5, netcdf variants * updates environment function * updating paths and pkgconfig * cleanup
2020-07-14[acts] Add 0.25.x series (#17485)Hadrien G1-1/+9
* Add Acts v0.25 support * Add Acts v0.25.1 * Add acts v0.25.2
2020-07-14[acts] remove false dependency (#17511)vvolkl1-2/+2
2020-07-14r-glue: new version (#17517)Amjad Kotobi1-0/+1
2020-07-14gpdb: fix runtime issue (#17521)darmac1-1/+12
2020-07-14zsh (package): add versions; switch to .xz archives (#17489)Jon Rood1-5/+8
* Add new versions including 5.8 * Download .xz archives for existing versions (this requires updating the associated checksums)
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