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2021-09-24Remove centos:6 image references (#26095)Harmen Stoppels4-86/+1
This was EOL November 30th, 2020. I believe the "builds" are failing on develop because of it.
2021-09-24opencascade: add v7.5.3; added VTK INCLUDE cmake flag (#26209)Wouter Deconinck1-0/+6
2021-09-24Use Leap instead of Tumbleweed for e2e bootstrapping test (#26205)Massimiliano Culpo1-1/+1
Tumbleweed has been broken for a couple of days. The attempt to fix it in #26170 didn't really work. Let's try to move to a more stable release series for OpenSuse.
2021-09-24radical cybertools: add v1.8.0 (#26215)Mikhail Titov4-4/+9
2021-09-24g2: add maintainers and version 3.4.5 (#26105)Edward Hartnett1-2/+5
* added new release, added noaa software maintainers to maintainer list * updated comment * removed trailing whitespace
2021-09-23fontconfig: add dependency python (#25960)kjrstory1-0/+1
2021-09-23gperftools package: add variants (#26032)iarspider1-1/+16
* Make libunwind optional * Add support for sized_delete and debugalloc Co-authored-by: Seth R. Johnson <johnsonsr@ornl.gov> Co-authored-by: Harmen Stoppels <harmenstoppels@gmail.com>
2021-09-23h5py: new version 3.4 (#25935)Thomas Kluyver1-0/+1
No changes to dependencies or supported Python versions. https://docs.h5py.org/en/stable/whatsnew/3.4.html
2021-09-23python: Fix regression in python-2.7.17+-distutils-C++.patch (#25821)bernhardkaindl3-0/+260
2021-09-23SQLite: make variants discoverable (#25885)Christoph Conrads1-0/+49
Co-authored-by: Harmen Stoppels <harmenstoppels@gmail.com>
2021-09-23Pin opensuse image in bootstrap tests (#26170)Harmen Stoppels1-1/+1
Currently zypper in opensuse containers throws 'not permitted' Temporarily fix the digest until they fixed their upstream package manager issues
2021-09-22Merge tag 'v0.16.3' into developGregory Becker0-0/+0
2021-09-22dihydrogen package: add missing dependency (#25896)Brian Van Essen1-0/+1
2021-09-22added NOAA software maintainers to maintainer list (#26112)Edward Hartnett1-1/+1
2021-09-22pango: Fix build: restore autotools-based versions (#26084)bernhardkaindl1-6/+2
Fix the build of pango and it's 20 dependents: Only provide the versions which support the build using autotools (conversion to MesonPackage didn't progress) This only restores the list of versions of August 10, before the build broke.
2021-09-22Add Rclone v1.56.1 (#26124)Alec Scott1-1/+2
2021-09-22add conflict (#26028)albestro1-0/+3
2021-09-22Add Picard v2.26.2 (#26125)Alec Scott1-1/+2
2021-09-22su2: add version 7.0.4-7.2.0 (#25956)kjrstory1-0/+9
2021-09-21Add Slepc v3.15.2 (#26123)Alec Scott1-1/+2
2021-09-21gfsio: add NOAA software maintainers (#26106)Edward Hartnett1-2/+4
* added NOAA software maintainers to maintainer list * added comment about NCEPLIBS
2021-09-21Bump version and update changelogv0.16.3Harmen Stoppels2-1/+13
2021-09-21Fix style testsHarmen Stoppels1-1/+1
2021-09-21Remove centos:6 image referencesHarmen Stoppels4-86/+1
This was EOL November 30th, 2020. I believe the "builds" are failing on develop because of it.
2021-09-21docker: remove boto3 from CentOS 6 since it requires and updated pip (#24813)Massimiliano Culpo1-1/+0
2021-09-21docker: Fix CentOS 6 build on Docker Hub (#24804)Massimiliano Culpo1-0/+3
This change make yum usable again on CentOS 6
2021-09-21Ensure all roots of an installed environment are marked explicit in db (#24277)Greg Becker2-0/+28
2021-09-21locks: only open lockfiles once instead of for every lock held (#24794)Todd Gamblin1-20/+127
This adds lockfile tracking to Spack's lock mechanism, so that we ensure that there is only one open file descriptor per inode. The `fcntl` locks that Spack uses are associated with an inode and a process. This is convenient, because if a process exits, it releases its locks. Unfortunately, this also means that if you close a file, *all* locks associated with that file's inode are released, regardless of whether the process has any other open file descriptors on it. Because of this, we need to track open lock files so that we only close them when a process no longer needs them. We do this by tracking each lockfile by its inode and process id. This has several nice properties: 1. Tracking by pid ensures that, if we fork, we don't inadvertently track the parent process's lockfiles. `fcntl` locks are not inherited across forks, so we'll just track new lockfiles in the child. 2. Tracking by inode ensures that referencs are counted per inode, and that we don't inadvertently close a file whose inode still has open locks. 3. Tracking by both pid and inode ensures that we only open lockfiles the minimum number of times necessary for the locks we have. Note: as mentioned elsewhere, these locks aren't thread safe -- they're designed to work in Python and assume the GIL. Tasks: - [x] Introduce an `OpenFileTracker` class to track open file descriptors by inode. - [x] Reference-count open file descriptors and only close them if they're no longer needed (this avoids inadvertently releasing locks that should not be released).
2021-09-21Use AWS CloudFront for source mirror (#23978)Todd Gamblin1-1/+1
Spack's source mirror was previously in a plain old S3 bucket. That will still work, but we can do better. This switches to AWS's CloudFront CDN for hosting the mirror. CloudFront is 16x faster (or more) than the old bucket. - [x] change mirror to https://mirror.spack.io
2021-09-21Cray: fix extracting paths from module files (#23472)Harmen Stoppels2-3/+13
Co-authored-by: Tiziano Müller <tm@dev-zero.ch>
2021-09-21Fix use of quotes in Python build system (#22279)Adam J. Stewart1-1/+1
2021-09-21clang/llvm: fix version detection (#19978)Michael Kuhn3-7/+11
This PR fixes two problems with clang/llvm's version detection. clang's version output looks like this: ``` clang version 11.0.0 Target: x86_64-unknown-linux-gnu ``` This caused clang's version to be misdetected as: ``` clang@11.0.0 Target: ``` This resulted in errors when trying to actually use it as a compiler. When using `spack external find`, we couldn't determine the compiler version, resulting in errors like this: ``` ==> Warning: "llvm@11.0.0+clang+lld+lldb" has been detected on the system but will not be added to packages.yaml [reason=c compiler not found for llvm@11.0.0+clang+lld+lldb] ``` Changing the regex to only match until the end of the line fixes these problems. Fixes: #19473
2021-09-21Fix fetching for Python 3.9.6 (#24686)Adam J. Stewart1-6/+6
When using Python 3.9.6, Spack is no longer able to fetch anything. Commands like `spack fetch` and `spack install` all break. Python 3.9.6 includes a [new change](https://github.com/python/cpython/pull/25853/files#diff-b3712475a413ec972134c0260c8f1eb1deefb66184f740ef00c37b4487ef873eR462) that means that `scheme` must be a string, it cannot be None. The solution is to use an empty string like the method default. Fixes #24644. Also see https://github.com/Homebrew/homebrew-core/pull/80175 where this issue was discovered by CI. Thanks @branchvincent for reporting such a serious issue before any actual users encountered it! Co-authored-by: Todd Gamblin <tgamblin@llnl.gov>
2021-09-21w3emc: add NOAA software maintainers (#26110)Edward Hartnett1-2/+4
2021-09-21boost: fix for @1.77.0%intel (#25965)Tiziano Müller1-0/+6
Add patch for build script from boost repo.
2021-09-22spack/build_environment.py: Clean MAKEFLAGS, DISPLAY and TERM (#26092)bernhardkaindl1-0/+7
clean_environment(): Unset three more environment variables: MAKEFLAGS: Affects make, can eg indirectly inhibit enabling parallel build DISPLAY: Tests of GUI widget libraries might try to connect to an X server TERM: Could make testsuites attempt to color their output
2021-09-21added NOAA software maintainers to the maintainers list (#26102)Edward Hartnett1-1/+1
2021-09-21sfcio: add NOAA software maintainers (#26108)Edward Hartnett1-2/+4
* added NOAA software maintainers to maintainer list * added comment about NCEPLIBS project
2021-09-21ip2: add NOAA software maintainers and deprecation note (#26107)Edward Hartnett1-4/+7
* added NOAA software maintainers to maintainer list, added comment about library being deprecated * deleted trailing whitespace
2021-09-21libtool: fix running the unit-tests with spack install --test root (#25707)bernhardkaindl1-1/+22
Besides adding autoconf and automake as needed for tests of 2.4.6, skip Fortran test cases when Fortran compilers are not provided.
2021-09-21Feature: Add deprecated versions section to spack info output (#25972)Tamara Dahlgren1-5/+20
2021-09-21Fix for - Installation issue: amdlibflame #25878 (#25987)AMD Toolchain Support1-0/+2
* Fix for - Installation issue: amdlibflame #25878 * Updated with python+pythoncmd - Symlink 'python3' executable to 'python'
2021-09-21w3nco: add NOAA software maintainers (#26111)Edward Hartnett1-2/+5
2021-09-21packages/phist new version 1.9.5 (#26114)Jonas Thies1-0/+1
2021-09-21added noaa software maintainers to maintainer list (#26103)Edward Hartnett1-1/+1
2021-09-21Fix FORM recipe (#26104)iarspider1-2/+3
2021-09-21sigio: add NOAA software maintainers (#26109)Edward Hartnett1-2/+4
2021-09-21ddd,debuild,flux-sched: add missing dependencies (#26090)bernhardkaindl3-0/+6
2021-09-21petsc: fix for enabling openmp (#25942)Melven Roehrig-Zoellner1-1/+1
* petsc: fix for enabling openmp * petsc: shorten comment (style guidelines) * petsc: move flag to make code more clear
2021-09-21mvapich2-gdr: add v2.3.6 (#26076)natshineman1-11/+12
Co-authored-by: Nick Contini <contini.26@buckeyemail.osu.edu>