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2021-09-13Avoid hidden circular dependencies in spack.architecture (#25873)Massimiliano Culpo1-5/+2
* Refactor platform etc. to avoid circular dependencies All the base classes in spack.architecture have been moved to the corresponding specialized subpackages, e.g. Platform is now defined within spack.platforms. This resolves a circular dependency where spack.architecture was both: - Defining the base classes for spack.platforms, etc. - Collecting derived classes from spack.platforms, etc. Now it dopes only the latter. * Move a few platform related functions to "spack.platforms" * Removed spack.architecture.sys_type() * Fixup for docs * Rename Python modules according to review
2021-09-13Disable dvsdk variants (#25889)Chuck Atkins1-11/+14
* dvsdk: Turn off variants by default This allows an install to more easily be explicit about which pieces to turn on as more variants are added * dvsdk: effectively disable the broken variants
2021-09-13kokkos: fail gracefully on missing microarch (#25910)Seth R. Johnson2-26/+19
Fall back on known parent microarches (as determined by spack's built-in archspec knowledge). Clsoes spack/spack#25907 .
2021-09-13Switch http to https where latter exists (#25672)Tamara Dahlgren339-537/+537
* Switch http to https where latter exists * Hopefully restore original permissions * Add URL updates after include the -L curl option * Manual corrections to select URL format strings
2021-09-13New Version: mothur@1.46.1 (#25850)Desmond Orton1-0/+1
2021-09-13trilinos: add conflicts for fortran (#25911)Seth R. Johnson1-0/+4
2021-09-13Add a master branch for gnuconfig (#25866)Harmen Stoppels1-0/+2
2021-09-13Log4cxx add v0.12.0, convert to CMakePackage (#25875)Nic McDonald1-13/+10
2021-09-13ravel: fix missing header file (#25906)Tim Gymnich2-1/+12
Co-authored-by: Massimiliano Culpo <massimiliano.culpo@gmail.com>
2021-09-13Make sure perl doesn't run into recompile with fPIC linker errors (#25834)Harmen Stoppels1-2/+6
2021-09-13draco: add v7.11.0 (#24631)Kelly (KT) Thompson1-4/+7
2021-09-13py-kornia: add new package (#25844)Adam J. Stewart1-0/+20
2021-09-13Add SYCL build option to ArborX (#25736)Daniel Arndt1-1/+2
2021-09-13py-glmnet: new package (#25711)Harmen Stoppels1-0/+26
2021-09-13hpx, kokkos: add consistent variants for C++ std (#25535)Mikael Simberg2-4/+13
* Add cuda_constexpr variant to Kokkos package * Don't require nvcc_wrapper in Kokkos package when using Cray compiler
2021-09-13HiPACE: Update openPMD dep, add v21.09 (#25698)Axel Huebl2-5/+4
2021-09-13Tell gtk-doc where the XML catalog is (#25569)Glenn Johnson1-0/+6
* Tell gtk-doc where the XML catalog is The gtk-doc configure script has an option for specifying the path to the XML catalog. If this is not set the configure script will search a defined set of directories for a catalog file and will set `with_xml_catalog` based on that. Only if no system catalog is found will the XML_CATALOG_FILES be looked at. In order to make sure that the spack provided catalog is used, pass the `--with-xml-catalog` option. * Use the property from docbook-xml
2021-09-13httpie: add v2.5.0 (#25888)Mickaël Schoentgen1-4/+7
2021-09-13nmap: overhaul of the package recipe (#25656)gpotter21-0/+34
2021-09-13environment-modules: add version 5.0.0 (#25904)Xavier Delaruelle1-12/+22
Adapt configure arguments to only keep useful ones for this new major release version.
2021-09-13py-pandas: add v1.3.3 (#25905)Adam J. Stewart1-0/+1
2021-09-10openssh: Fix parallel install issue, add test suite (#25790)bernhardkaindl1-3/+42
- Parallel install was failing to generate a config file. - OpenSSH has an extensive test suite, run it if requested. - 'executables' wrongly had 'rsh', replaced the openssh tools.
2021-09-09SQLite: fix rtree, add version, make discoverable (#25554)Christoph Conrads1-2/+16
There are two ways to build SQLite: With the Autotools setup or the so-called "amalgamation" which is a single large C file containing the SQLite implementation. The amalgamation build is controlled by pre-processor flags and the Spack setup was using an amalgamation pre-processor flag for a feature that is controlled by an option of the configure script. As a consequence, until now Spack has always built SQLite with the rtree feature enabled.
2021-09-09Have GROMACS log files indicate spack was used (#25869)Mark Abraham1-0/+6
Knowing that spack has patched the code and organized the build is potentially valuable information for GROMACS users and developers troubleshooting their builds. PLUMED does further patches to GROMACS, so that is expressed directly also.
2021-09-09openssl: link system openssl.conf after installation (#25807)acastanedam1-0/+6
Co-authored-by: Arcesio Castaneda Medina <arcesio.castaneda.medina@itwm.fraunhofer.de>
2021-09-09libfabric: Adds v1.13.1 (#25827)Raghu Raja1-11/+15
This commit adds the 1.13.1 release. There was an update to the release tarball on 9/7/21, so using the latest sha256 sum here.
2021-09-09specs: move to new spec.json format with build provenance (#22845)Nathan Hanford2-0/+68
This is a major rework of Spack's core core `spec.yaml` metadata format. It moves from `spec.yaml` to `spec.json` for speed, and it changes the format in several ways. Specifically: 1. The spec format now has a `_meta` section with a version (now set to version `2`). This will simplify major changes like this one in the future. 2. The node list in spec dictionaries is no longer keyed by name. Instead, it is a list of records with no required key. The name, hash, etc. are fields in the dictionary records like any other. 3. Dependencies can be keyed by any hash (`hash`, `full_hash`, `build_hash`). 4. `build_spec` provenance from #20262 is included in the spec format. This means that, for spliced specs, we preserve the *full* provenance of how to build, and we can reproduce a spliced spec from the original builds that produced it. **NOTE**: Because we have switched the spec format, this PR changes Spack's hashing algorithm. This means that after this commit, Spack will think a lot of things need rebuilds. There are two major benefits this PR provides: * The switch to JSON format speeds up Spack significantly, as Python's builtin JSON implementation is orders of magnitude faster than YAML. * The new Spec format will soon allow us to represent DAGs with potentially multiple versions of the same dependency -- e.g., for build dependencies or for compilers-as-dependencies. This PR lays the necessary groundwork for those features. The old `spec.yaml` format continues to be supported, but is now considered a legacy format, and Spack will opportunistically convert these to the new `spec.json` format.
2021-09-09Add new package gnuconfig (#25849)Harmen Stoppels1-0/+26
2021-09-09Fix python/packages.py's config_vars for python2 packages (#25839)bernhardkaindl1-9/+11
Analysis mostly by me, fix updated after suggestion by Adam J. Steward Co-authored-by: Bernhard Kaindl <bernhard.kaindl@ait.ac.at>
2021-09-09py-torchmetrics: add v0.5.1 (#25855)Adam J. Stewart1-0/+1
2021-09-08sina: new package (#25448)Esteban Pauli1-0/+78
* Added spackage to build Sina (https://github.com/LLNL/Sina). * Improvements to sina/package.py Made numerous simplifications and improvements to sina/package.py based on PR feedback. * Added licence info * Added maintainers * Changed maintainers to be Github IDs.
2021-09-08root: Add Version 6.24.06 (#25822)Dr. Christian Tacke1-0/+1
2021-09-08conduit: changes related to hdf5 builds that use cmake (#25719)Cyrus Harrison1-0/+4
2021-09-08mpip: fix package to depends on libunwind when +libunwind (#24007)lukebroskop1-3/+2
Added a dependency for mpip@3.5: when the libunwind is set to true (which is the default) and '~setjmp' is set to False (which is also the default) to avoid a configure time error from not finding libunwind. Co-authored-by: Massimiliano Culpo <massimiliano.culpo@gmail.com>
2021-09-08url stats: add `--show-issues` option (#25792)Todd Gamblin65-132/+174
* tests: make `spack url [stats|summary]` work on mock packages Mock packages have historically had mock hashes, but this means they're also invalid as far as Spack's hash detection is concerned. - [x] convert all hashes in mock package to md5 or sha256 - [x] ensure that all mock packages have a URL - [x] ignore some special cases with multiple VCS fetchers * url stats: add `--show-issues` option `spack url stats` tells us how many URLs are using what protocol, type of checksum, etc., but it previously did not tell us which packages and URLs had the issues. This adds a `--show-issues` option to show URLs with insecure (`http`) URLs or `md5` hashes (which are now deprecated by NIST).
2021-09-08trilinos: Gather teko requirements in one place and add conflict for muelu ↵Paul Kuberry1-7/+10
(#25703)
2021-09-08gcc: add patch for sanitizer in gcc<11.1.0 (#25804)acastanedam1-0/+3
This allows to fix the compilation of gcc versions less than 11.1.0, due to the remove of cyclades of libsanitizer as it is described in the patch: The Linux kernel has removed the interface to cyclades from the latest kernel headers due to them being orphaned for the past 13 years. libsanitizer uses this header when compiling against glibc, but glibcs itself doesn't seem to have any references to cyclades. Further more it seems that the driver is broken in the kernel and the firmware doesn't seem to be available anymore. As such since this is breaking the build of libsanitizer (and so the GCC bootstrap) it is proposed to remove this. Co-authored-by: Arcesio Castaneda Medina <arcesio.castaneda.medina@itwm.fraunhofer.de>
2021-09-08perl: Bind us to @gdbm:1.19 due to API change in gdbm@1.20: (#25819)bernhardkaindl1-1/+2
By changing return values from C #defines to enums, gdbm-1.20 breaks a kludge: #ifndef GDBM_ITEM_NOT_FOUND # define GDBM_ITEM_NOT_FOUND GDBM_NO_ERROR #endif The absence of the #define causes perl to #define GDBM_ITEM_NOT_FOUND as GDBM_NO_ERROR which incorrect for gdbm@1.20:
2021-09-08systemc: new package (#25761)Nic McDonald1-0/+28
2021-09-08ParaView: disable externals for fmt and exprtk (#25462)Ethan Stam1-1/+3
2021-09-08trilinos: yak shaving (#25549)Seth R. Johnson1-311/+192
* trilinos: yak shaving - use flags instead of manually adding cxxflags - rearrange defines more sensibly - use conflicts instead of inline package disables - fix some inapplicable definitions such as OpenMP instantiation - disable "broken" leaf packages(FEI, Panzer) by default - rely on upstream libraries 'libs' rather than manual names * flake8 * Fix executable call * Address reviewer feedback
2021-09-08Cmake: improve ncurses detection (#25776)Harmen Stoppels1-0/+13
* Optionally enable ccmake in cmake Renames ncurses variant to `ccmake` since that's how users know it, and explicitly enable/disable `BUILD_CursesDialog`. * Make cmake locate its dependencies with CMAKE_PREFIX_PATH, and set rpath flags too * Undo variant name & defaults change
2021-09-08Add new version of Alpaka, set minimal CMake version (#25835)iarspider1-0/+2
2021-09-08Make sure we only pull in openssl w/ +ownlibs (#25559)Harmen Stoppels1-3/+3
2021-09-08Update catch2 (#25838)iarspider1-1/+4
2021-09-08mbedtls: trun into a MakefilePackage (#25558)Harmen Stoppels1-34/+49
This is a step towards building cmake with curl using mbedtls instead of openssl; building mbedtls shouldn't require cmake then.
2021-09-08Add new versions of nlopt (#25836)Sebastian Ehlert1-2/+6
2021-09-08netlib-lapack: Fixes for IBM XL builds (#25793)QuellynSnead2-2/+99
netlib-lapack: Version 3.9.0 and above no longer builds with the IBM XL compiler (#25447). Ported some fixes from the old ibm-xl.patch and added logic for detection of XL's -qrecur flag.
2021-09-07autoconf package: Fix 2.69 and 2.62 to pass the testsuite (#25701)bernhardkaindl1-1/+21
Apply stable-release fixes from 2017 to older autoconf releses: - Fix the scripts autoheader and autoscan to pass the test suite - Fix test case to passing when libtool 2.4.3+ is in use autoconf-2.13 dates back to 1999. The build wasn't possible since 4 years: Since 2017, we patch autom4te which didn't exist in 2.13, failing the build of it. 4 years of not being able to build 2.13 is a crystal clear indication that we can remove it safely.
2021-09-07amrex: support sundials variant in newer amrex versions (#25745)Cody Balos1-6/+12
* amrex: support sundials variant in newer amrex versions * propagate cuda_arch to sundials * change to old string formatting * require sundials+rocm when amrex+rocm
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