sbang: convert sbang script to POSIX shell #19529

tgamblin · 2020-10-26T20:21:10Z

sbang was previously a bash script but did not need to be. This converts it to a plain old POSIX shell script and adds some options. This also allows us to simplify sbang shebangs to #!/bin/sh /path/to/sbang instead of #!/bin/bash /path/to/sbang.

The new script passes shellcheck (with a few exceptions noted in the file)

SBANG_DEBUG env var enables printing what would be executed
sbang checks whether it has been passed an option and fails gracefully
sbang will now fail if it can't find a second shebang line, or if
the second line happens to be sbang (avoid infinite loops)
add more rigorous tests for sbang behavior using SBANG_DEBUG

adamjstewart · 2020-10-26T21:19:22Z

Yay testing! Also see #18299, maybe you can review this at the same time while you're at it.

tgamblin · 2020-10-26T22:39:08Z

@adamjstewart addressed. I'll rebase on that when it's done.

alalazo

Typo, due to a wrongly resolved conflict?

bin/sbang

alalazo

LGTM

bin/sbang

lib/spack/spack/test/sbang.py

`sbang` was previously a bash script but did not need to be. This converts it to a plain old POSIX shell script and adds some options. This also allows us to simplify sbang shebangs to `#!/bin/sh /path/to/sbang` instead of `#!/bin/bash /path/to/sbang`. The new script passes shellcheck (with a few exceptions noted in the file) - [x] `SBANG_DEBUG` env var enables printing what *would* be executed - [x] `sbang` checks whether it has been passed an option and fails gracefully - [x] `sbang` will now fail if it can't find a second shebang line, or if the second line happens to be sbang (avoid infinite loops) - [x] add more rigorous tests for `sbang` behavior using `SBANG_DEBUG`

`sbang` now lives at https://github.com/spack/sbang, and it has its own test suite that's more extensive than what's in Spack. We'll leave sbang tests to sbang from now on, and just vendor `bin/sbang` directly. Remaining `sbang` tests have to do with patching files, not with `sbang`'s functionality. This update also fixes a bug with `sbang` and multiple command line arguments that was introduced in #19529. See: * spack/sbang#1 * spack/sbang#2 - [x] include latest `sbang` from https://github.com/spack/sbang - [x] remove old `sbang` tests from Spack - [x] update `COPYRIGHT`

`sbang` now lives at https://github.com/spack/sbang, and it has its own test suite that's more extensive than what's in Spack. We'll leave sbang tests to sbang from now on, and just vendor `bin/sbang` directly. Remaining `sbang` tests have to do with patching files, not with `sbang`'s functionality. This update also fixes a bug with `sbang` and multiple command line arguments that was introduced in #19529. See: * spack/sbang#1 * spack/sbang#2 - [x] include latest `sbang` from https://github.com/spack/sbang - [x] remove old `sbang` tests from Spack - [x] update `COPYRIGHT` and `cmd/license.py`

commit 65f3155500b33d29917d948052c7594653343bca Merge: c43a284009 8b96e10ecc Author: Tamara Dahlgren <dahlgren1@llnl.gov> Date: Thu Nov 5 10:22:10 2020 -0800 Merge remote-tracking branch 'origin/develop' into features/parallel-env-builds commit 8b96e10ecc6052c53e5296a56947b9072693acff Author: Greg Becker <becker33@llnl.gov> Date: Thu Nov 5 09:59:44 2020 -0800 Remove hardcoded version numbers from container logic (#19716) Previously, we hardcoded a list of Spack versions which could be used by the containerize command. This PR removes that list. It's a maintenance burden when cutting a release, and prevents older versions of Spack from creating containers to be used by newer versions. commit dcd514c3215d4760e154b194cfe9f187720e5476 Author: ilbiondo <61497728+ilbiondo@users.noreply.github.com> Date: Thu Nov 5 18:04:24 2020 +0100 filtlong package (#19732) * filtlong package * Update var/spack/repos/builtin/packages/filtlong/package.py Co-authored-by: Adam J. Stewart <ajstewart426@gmail.com> Co-authored-by: Adam J. Stewart <ajstewart426@gmail.com> commit 4c254c6c9f67a43247c0be5c3da256e057c958d8 Author: ilbiondo <61497728+ilbiondo@users.noreply.github.com> Date: Thu Nov 5 18:02:43 2020 +0100 bamaddrg package (#19729) * bamaddrg package * Change version to URL rather than git commit 08e825f47433972ddcdb35f1187d41be91f6318a Author: Andrew W Elble <aweits@rit.edu> Date: Thu Nov 5 11:31:11 2020 -0500 kokkos-legacy: fix host_arch/gpu_arch variants (#19754) 'default' specifies a value that is not present in 'values'. commit 6dc25e7dbf5ad5a6dd5a1c1ba7c2ef34aa37986a Author: Andrew W Elble <aweits@rit.edu> Date: Thu Nov 5 11:30:32 2020 -0500 py-pykwalify: fix conflict directive (missing '^') (#19753) commit fa7ba11d1acf5b1f3835948f037521603ad7375b Author: Andrew W Elble <aweits@rit.edu> Date: Thu Nov 5 11:30:08 2020 -0500 py-quantities: fix conflict directive (missing '^') (#19752) commit 9bca9611c5566ed4b28d55060c6cbd2c84eb8bbc Author: Andrew W Elble <aweits@rit.edu> Date: Thu Nov 5 10:53:24 2020 -0500 py-flye: fix conflict directive (missing '%') (#19751) commit 9908e7a5906219a9d775f855c7075d2e6ee41424 Author: Andrew W Elble <aweits@rit.edu> Date: Thu Nov 5 10:26:26 2020 -0500 pfunit: fix conflict directive (missing '+') (#19750) commit d7335185e3e2d26b6596b8f74b49f5697d802aff Author: Andrew W Elble <aweits@rit.edu> Date: Thu Nov 5 10:26:03 2020 -0500 heffte: fix conflict directive (missing '^') (#19749) commit 09ec3e926891d0216d308bae047680aef677204f Author: Adam J. Stewart <ajstewart426@gmail.com> Date: Thu Nov 5 08:44:00 2020 -0600 Update packages.yaml format references in packages (#19741) commit 619eb6c08bc693f5c843c37d613b8fd68226d19f Author: Tamara Dahlgren <35777542+tldahlgren@users.noreply.github.com> Date: Wed Nov 4 15:47:08 2020 -0800 bug fix: Display error when curl is missing even in non-debug mode (#19695) commit c4b4cd497313d12121585b9996e2d8b02987e16f Author: Andrew W Elble <aweits@rit.edu> Date: Wed Nov 4 16:17:19 2020 -0500 py-llvmlite: fix llvm compatibility version (#19739) won't build with llvm 11 commit 4cd711cb790c1eaa1dc2be5f41fad74aed24113a Author: Chris White <white238@llnl.gov> Date: Wed Nov 4 12:37:24 2020 -0800 Axom: update package (#19717) * update spack package from axom's main repo * flake8, plus loop over possible clangformat paths commit 6f4e2e58c3e7542f99ce50db02f3cbf9860bbbe5 Author: Jeremy <jjwilke@users.noreply.github.com> Date: Wed Nov 4 10:47:41 2020 -0800 10.1 release and various bug fixes for SST packages (#19719) commit cc0a58581699303704a3df1e4fc80c9f00fe7fe3 Author: arjun-raj-kuppala <60718144+arjun-raj-kuppala@users.noreply.github.com> Date: Wed Nov 4 10:44:59 2020 -0800 AMD - Bumped up version for hip-rocclr, rocm-opencl, rocm-smi-lib (#19721) commit 3daa7b7b40181b16dbd0ef5e03a63a264f1ddd7f Author: Sreenivasa Murthy Kolam <67086238+srekolam@users.noreply.github.com> Date: Thu Nov 5 00:13:40 2020 +0530 update rocm-bandwidth-test,rocm-dbgapi,rocprofiler for rocm 3.9.0 (#19724) * update rocm-bandwidth-test,rocm-dbgapi,rocprofiler for rocm 3.9.0 * bump up rocm-gdb for rocm-3.9.0 commit ab046403f66e9fd833f9293624cec967882725b1 Author: ilbiondo <61497728+ilbiondo@users.noreply.github.com> Date: Wed Nov 4 19:37:15 2020 +0100 admixtools package (#19727) commit 5b02910e9cbc351d9ddd78ebba98bda5bdb9c058 Author: Satish Balay <balay@mcs.anl.gov> Date: Wed Nov 4 12:27:11 2020 -0600 petsc add version 3.14.1 (#19730) commit 5511c29869ade026c0f0cdce90f674d4e69900c1 Author: Veselin Dobrev <v-dobrev@users.noreply.github.com> Date: Wed Nov 4 10:26:39 2020 -0800 New MFEM version: 4.2 (#19684) commit 823a3fa646489789834804480e55f8d0b1b12542 Author: Robert Maynard <robert.maynard@kitware.com> Date: Wed Nov 4 13:25:17 2020 -0500 Added HIP support to VTK-m package (#19523) commit c2b943c2096d066b0e54a4bec3ba34dad77a8fb4 Author: Satish Balay <balay@mcs.anl.gov> Date: Wed Nov 4 10:28:14 2020 -0600 Trilinos: fix error when configuring downstream dependency commit 44d406a1aa5f661f4a334f7e4c4861058772c65b Author: darmac <xiaojun2@hisilicon.com> Date: Wed Nov 4 21:37:24 2020 +0800 Add new package: abi-compliance-checker (#18737) * Add new package: abi-compliance-checker * refine dependencies * change exuberant-ctags to universal-ctags commit efb26bb14ff70c4dcf789240c2e6b21b2323c010 Author: Andrew W Elble <aweits@rit.edu> Date: Tue Nov 3 17:47:38 2020 -0500 libusb: disable udev (#19713) * libusb: disable udev spack has no libudev/systemd package currently * convert to AutotoolsPackage * remove spack import commit ddd2aa0ffc7ad7aecff55b39c7cb23dfc05d0dae Author: Andrew W Elble <aweits@rit.edu> Date: Tue Nov 3 13:43:16 2020 -0500 sirius,spfft: fix defaults for amdgpu_target to be str, not tuple (#19660) commit 6bcb7128e6e8c886eead23768ac040d84d4a4ae7 Author: Glenn Johnson <glenn-johnson@uiowa.edu> Date: Tue Nov 3 12:42:40 2020 -0600 Regenerate patch for gate to include SGE script (#19663) The previous patch left out the SGE.script file. commit 4ba7ad5162571c34a41ba8d738e65c4c1ddc7c87 Author: Glenn Johnson <glenn-johnson@uiowa.edu> Date: Tue Nov 3 12:41:47 2020 -0600 New package - gatepet2stir (#19664) commit e93ac1a8bdcbb4b0155e6463508923d52615ba8b Author: Sreenivasa Murthy Kolam <67086238+srekolam@users.noreply.github.com> Date: Wed Nov 4 00:09:40 2020 +0530 bump up hsakmt-roct ,hsa-rocr-dev,llvm-amdgpu version for 3.9.0 release (#19668) * bump up version for 3.9.0 release * update version of rocminfo for rocm-3.9.0 * bump up rocm-cmake version for rocm-3.9.0 * bump up rocm-smi and rocmdevice-libs for 3.9.0 * bumpup comgr version for rocm_ 3.9.0 * bump rocm-clang-ocl for rocm-3.9.0 * bump hipify-clang for rocm-3.9.0 commit 886ae9a83f13e521707697ad6b9338244ffd09eb Author: Andrew W Elble <aweits@rit.edu> Date: Tue Nov 3 13:36:24 2020 -0500 speexdsp: fix link dependency on FFT library (#19714) without this, the library does not have a dependency on the fft lib it was built with. commit 95d63afa58e0a4ab8fd89fd33075862b4cfdcff6 Author: Desmond <odesmond21@gmail.com> Date: Tue Nov 3 12:35:26 2020 -0600 Package/py json get (#19689) * py-json-get: new package at 1.1.1 * py-json-get: new package at 1.1.1 Co-authored-by: las_djorton <las_djorton@build.las.iastate.edu> commit b9d12c93efcf42e6b9e8b439ea14c20e721d1cc4 Author: Andrew W Elble <aweits@rit.edu> Date: Tue Nov 3 13:34:17 2020 -0500 disable tests to fix build. (#19697) commit 001f90f411c0f13beb978c27b9ff2546a31777e0 Author: mic84 <mrosso@lbl.gov> Date: Tue Nov 3 10:33:45 2020 -0800 amrex: new version 20.11 (#19691) * amrex: new version 20.11 * Fix formatting issues commit 2c511a7dd05a5c5c9efad8bb166f11bcbd3670bf Author: Geoffrey Oxberry <goxberry@gmail.com> Date: Tue Nov 3 10:31:29 2020 -0800 new package: fprettify 0.3.6 (#19699) commit 11fb0e17b0b923c999b060e4c3f4023f201f8c76 Author: Andrew W Elble <aweits@rit.edu> Date: Tue Nov 3 13:29:59 2020 -0500 py-pygobject: new version 3.38.0 (#19709) fix to allow Gtk and others work from 'import gi' etc. commit cefbc39356266cbec6e4f8ac1b6ef4c4c007dfc5 Author: darmac <xiaojun2@hisilicon.com> Date: Wed Nov 4 02:27:45 2020 +0800 Add new package: libbinio (#19706) commit ffec64ce30157ab1c11902306226a22d4a1ea17e Author: darmac <xiaojun2@hisilicon.com> Date: Wed Nov 4 02:27:22 2020 +0800 Add new package: jose (#19707) commit b7421c1476039b8b9b567025bab039069cc988e4 Author: darmac <xiaojun2@hisilicon.com> Date: Wed Nov 4 02:26:54 2020 +0800 Add new package: libdatrie (#19708) commit 6492b9a84ee1137f18b361998c16f018a6ba40cb Author: Daniel Arndt <arndtd@ornl.gov> Date: Tue Nov 3 13:25:26 2020 -0500 Use commit instead of branch as version for dtk 3.1-rc2 (#19712) commit 859fbae4fa20f9d5d96b312538c1e34de84016c5 Author: Char Aznable <32589713+Char-Aznable@users.noreply.github.com> Date: Tue Nov 3 10:07:20 2020 -0800 Trilinos: support cuda, hwloc, Kokkos_ARCH_* and c++ std (#19119) commit 771e8b62943a82c3572b2a73aad8521c8043d080 Author: Elliot Saba <staticfloat@gmail.com> Date: Tue Nov 3 10:04:29 2020 -0800 [julia]: CPU names are LLVM-style, must map across (#19549) In this case, the `zen2` architecture is unknown; Spack must use the LLVM-style `znver2` target instead. commit 8cc08bd88b9eb0d6f8c2947ac86d668100b9b9ee Author: Pieter Ghysels <pghysels@lbl.gov> Date: Tue Nov 3 10:04:12 2020 -0800 Trilinos: Add STRUMPACK dependency (#19560) * Trilinos: Add STRUMPACK dependency * break long lines, flake8 cleanup * Use spec['strumpack'].libs.directories[0] instead of spec['strumpack'].prefix.lib because libraries may be in lib or lib64. Likewise use headers.directories[0] iso prefix.include. Suggested by adamjstewart commit cd625e597463ad6bd5880d740504bb4f49895a90 Author: Wouter Deconinck <wdconinc@gmail.com> Date: Tue Nov 3 12:03:48 2020 -0600 [dire] dire is included in pythia8@8300: so dire depends_on adjusted (#19628) commit 125b80d193828ad95d6b8bd8a61c93e391e9e99a Author: Geoffrey Gunter <12984092+gmgunter@users.noreply.github.com> Date: Tue Nov 3 10:03:19 2020 -0800 range-v3: add version 0.11.0 (#19639) * range-v3: add version 0.11.0 This release drops support for llvm-3.9 per the release notes. https://github.com/ericniebler/range-v3/releases/tag/0.11.0 * range-v3: rename 'develop' version to 'master' Co-authored-by: Adam J. Stewart <ajstewart426@gmail.com> Co-authored-by: Adam J. Stewart <ajstewart426@gmail.com> commit dc3d03ed30db822b558cb4927d4ba62a20ffa2fd Author: Satish Balay <balay@mcs.anl.gov> Date: Tue Nov 3 12:02:53 2020 -0600 superlu-dist: update to version 6.4.0 (#19682) commit 5b33157a459bce18ff7ec559f74c90ce8be13a3c Author: Satish Balay <balay@mcs.anl.gov> Date: Tue Nov 3 12:01:14 2020 -0600 petsc@3.14 update superlu-dist dependency [keep it open-ended for both petsc and superlu-dist future versions] (#19686) commit 294715282a87feee9358639a30614d207c4ae9c0 Author: Satish Balay <balay@mcs.anl.gov> Date: Tue Nov 3 12:00:50 2020 -0600 py-petsc4py: add version 3.14.0 (#19681) commit 76491869887b8ce99903e727029e37e38aab1efe Author: Tim Haines <thaines.astro@gmail.com> Date: Tue Nov 3 09:37:35 2020 -0600 Elfutils: added v0.182 (#19700) commit a920ef50dd7ccacaac6735b50460d414434faab2 Author: darmac <xiaojun2@hisilicon.com> Date: Tue Nov 3 22:19:43 2020 +0800 Add new package: istio (#17829) commit 5a54e39d71ff3a9ae6f65b931dd7101ec47d6117 Author: darmac <xiaojun2@hisilicon.com> Date: Tue Nov 3 22:18:28 2020 +0800 Add new package: py-boom (#18811) * Add new package: py-boom * change name to py-boom-boot-manager commit 75e73d7fcc57d5cc41e0302905a396c7f3ab8e29 Author: Shahzeb Siddiqui <shahzebmsiddiqui@gmail.com> Date: Tue Nov 3 06:15:46 2020 -0500 documentation: fix formatting of code-block section (#19693) commit 4637d97d41a0269a977d257327ab98d956c0530b Author: dunatotatos <contact@dunatotatos.com> Date: Tue Nov 3 12:13:00 2020 +0100 snakemake: add upper limit to allowed python versions (#19705) Running v3.1.2 with Python 3.7 returns a SyntaxError close to `async=True`. commit 03b740431616b35fe1bbe70ac69fe9508390389c Author: darmac <xiaojun2@hisilicon.com> Date: Tue Nov 3 18:20:06 2020 +0800 Add new package: abi-dumper (#18738) * Add new package: abi-dumper * refine dependencies commit d38fdb3854cbcada368efd48c3faf44dea960e2f Author: Brian Van Essen <vanessen1@llnl.gov> Date: Mon Nov 2 18:08:44 2020 -0800 Update cuDNN packages to check Power installation (#19620) * Updated cuDNN package to check to make sure that target directory exists before linking it. * Fixed flake8 * Fixed Flake8 commit b4ea74c11bf6e444dda1b93f3b2c934fdde74a60 Author: Hervé Yviquel <hyviquel@gmail.com> Date: Mon Nov 2 18:53:11 2020 -0300 allow ucx to build with more recent version of gdrcopy (#19606) * allows UCX since v1.7 to build with more recent version of gdrcopy (v2.X) * Update var/spack/repos/builtin/packages/ucx/package.py Co-authored-by: Adam J. Stewart <ajstewart426@gmail.com> Co-authored-by: Adam J. Stewart <ajstewart426@gmail.com> commit ecc3bfd48471035ec260c37e82a045e079addb64 Author: Todd Gamblin <tgamblin@llnl.gov> Date: Mon Nov 2 13:21:11 2020 -0800 Bugfix - hashing: don't recompute full_hash or build_hash (#19672) There was an error introduced in #19209 where `full_hash()` and `build_hash()` are called on older specs that we've read in from the DB; older specs may not be able to compute these hashes (e.g. if they have removed patches used in computing the full_hash). When serializing a Spec, we want to generate the full/build hash when possible, but we need a mechanism to skip it for Specs that have themselves been read from YAML (and may not support this). To get around this ambiguity and to fix the issue, we: - Add an attribute to the spec called `_hashes_final`, that is `True` if we can't lazily compute `build_hash` and `full_hash`. - Set `_hashes_final` to `False` for new specs (i.e., lazily computing hashes is ok) - Set `_hashes_final` to `True` for concrete specs read in via `from_node_dict`, as it may be too late to recompute hashes. - Compute and write out all hashes in `node_dict_with_hashes` *if possible*. Effectively what this means is that we can round-trip specs that are missing `_build_hash` and `_full_hash` without recomputing them, but for all new specs, we'll compute them and store them. So Spack should work fine with old DBs now. commit 2ca894bd1ea847d7226c7b4479d26cd645071f4e Author: Satish Balay <balay@mcs.anl.gov> Date: Mon Nov 2 14:02:50 2020 -0600 pumi add version 2.2.5 (#19680) commit 4d6c9a8f2907639bf3c9c4b3ccfeb413186c12de Author: Satish Balay <balay@mcs.anl.gov> Date: Mon Nov 2 12:50:10 2020 -0600 omega-h: add version 9.32.5 (#19679) commit 62eab8923e8cf182c67c10b6162777d19e2d55b0 Author: Seth R. Johnson <johnsonsr@ornl.gov> Date: Mon Nov 2 11:21:44 2020 -0500 ROOT: use native CMakePackage functions in packages.py (#19642) * root: update to built-in CMakePackage functions * root: Disable options from missing variants * Remove modification of CMAKE_PROGRAM_PATH commit f621e97f473b7a55dac140e6aa76201f00f9b077 Author: Scott McMillan <scott.andrew.mcmillan@gmail.com> Date: Mon Nov 2 10:12:15 2020 -0600 Fix issue with NAMD patch not applying cleanly (#19675) Co-authored-by: Scott McMillan <smcmillan@nvidia.com> commit acc075d79d009bfa1e9b1a67a4a559c9fa9772e3 Author: Tiziano Müller <tiziano.mueller@chem.uzh.ch> Date: Mon Nov 2 14:39:21 2020 +0100 llvm: fix +lldb build with external ncurses on openSUSE (#19627) fixes #19625 commit 4fe56de72ebfe09b81419663064331fb5770aab0 Author: Harmen Stoppels <harmenstoppels@gmail.com> Date: Mon Nov 2 09:54:29 2020 +0100 hip: revert using libs.directories[0] instead of prefix.lib (#19671) Currently fails with: Error: NoLibrariesError: Unable to recursively locate rocm-device-libs libraries commit b2d6c634216a0ee2f0532372456ad389dd6fb427 Author: eugeneswalker <38933153+eugeneswalker@users.noreply.github.com> Date: Sun Nov 1 19:52:06 2020 -0800 hip: setup run environments (#19637) * hip: rocminfo is a runtime requirement * hip: +setup_run_environment, +setup_dependent_run_environment * hip: run environment: get lib dir using libs.directories[0], not prefix.lib Co-authored-by: Adam J. Stewart <ajstewart426@gmail.com> Co-authored-by: Adam J. Stewart <ajstewart426@gmail.com> commit a80d221bfa1c9be4b2b9eff9f057edf62c34e50b Author: Todd Gamblin <tgamblin@llnl.gov> Date: Fri Oct 30 17:06:05 2020 -0700 sbang: fixes for sbang relocation This fixes sbang relocation when using old binary packages, and updates code in `relocate.py`. There are really two places where we would want to handle an `sbang` relocation: 1. Installing an old package that uses `sbang` with shebang lines like `#!/bin/bash $spack_prefix/sbang` 2. Installing a *new* package that uses `sbang` with shebang lines like `#!/bin/sh $install_tree/sbang` The second case is actually handled automatically by our text relocation; we don't need any special relocation logic for new shebangs, as our relocation logic already changes references to the build-time `install_tree` to point to the `install_tree` at intall-time. Case 1 was not properly handled -- we would not take an old binary package and point its shebangs at the new `sbang` location. This PR fixes that and updates the code in `relocation.py` with some notes. There is one more case we don't currently handle: if a binary package is created from an installation in a short prefix that does *not* need `sbang` and is installed to a long prefix that *does* need `sbang`, we won't do anything. We should just patch the file as we would for a normal install. In some upcoming PR we should probably change *all* `sbang` relocation logic to be idempotent and to apply to any sort of shebang'd file. Then we'd only have to worry about which files to `sbang`-ify at install time and wouldn't need to care about these special cases. commit a4dd8d5582d3d4bae74c4a8d500a950f2237500a Author: Adam J. Stewart <ajstewart426@gmail.com> Date: Sun Nov 1 17:15:04 2020 -0600 Scalapack: don't apply patches twice (#19662) commit ea8ba48a327e6bae85ed22f45214933b02acaebb Author: Adam J. Stewart <ajstewart426@gmail.com> Date: Sun Nov 1 15:33:14 2020 -0600 meson: add new version, external find support (#19658) commit 750027e80f04419a97928f427be10cfc747803b8 Author: Adam J. Stewart <ajstewart426@gmail.com> Date: Sun Nov 1 15:11:46 2020 -0600 libepoxy: remove meson dependency (#19659) commit 854aed25714b823820f0135322b6f0b6be9322d9 Author: Adam J. Stewart <ajstewart426@gmail.com> Date: Sun Nov 1 15:11:40 2020 -0600 krb5: fix build with Apple Clang 12 (#19657) commit f62efe5e2eb73a4fb45d99a6e73d834bc9af8b56 Author: Hervé Yviquel <hyviquel@gmail.com> Date: Sun Nov 1 13:08:06 2020 -0300 Fix rdma-core package installation (#19643) * add python-docutils dependency * adds symlink to script for better compatibility if py-docutils installation * Improve post_install phase of py-docutils Co-authored-by: Adam J. Stewart <ajstewart426@gmail.com> * fix review of rdma-core package * improve formating of py-docutils package Co-authored-by: Adam J. Stewart <ajstewart426@gmail.com> commit ffd5f6b19614da9862a28a4b772a74bae84f161c Author: Andrew W Elble <aweits@rit.edu> Date: Sun Nov 1 11:07:45 2020 -0500 arborx: fix depends_on conditional (missing '+') (#19655) commit 68ab6b252a832721ee2ad0aaae285c65659e1a25 Author: Andrew W Elble <aweits@rit.edu> Date: Sun Nov 1 11:07:08 2020 -0500 hpl: fix conflict directive (missing '^') (#19656) commit 3630a8a87aeffed3973d6334d81d419bd23b9c06 Author: Andrew W Elble <aweits@rit.edu> Date: Sun Nov 1 09:11:38 2020 -0500 root: conflict is with a dependency (#19654) commit e4a5a06e87c2176077c405d2ddb59e3783ae6518 Author: Massimiliano Culpo <massimiliano.culpo@gmail.com> Date: Sun Nov 1 13:16:59 2020 +0100 gromacs: simplified use of targets (#19646) commit 77fc458d2964490c83863d667df10b9a740ce05e Author: Massimiliano Culpo <massimiliano.culpo@gmail.com> Date: Sun Nov 1 01:05:13 2020 +0100 opencv: fixed conflict firectives (missing '^') (#19645) See https://github.com/spack/spack/pull/19501#issuecomment-718406357 commit 6b35324cf35cf655c2342c8ecd8a17fdb4ce86c4 Author: Tim Haines <thaines.astro@gmail.com> Date: Sat Oct 31 13:03:04 2020 -0500 elfutils: add support for version 0.181 (#19634) This also includes handling of the new libdebuginfod flags. commit 2cf160689646b8ee681b88860adfef821d3bb280 Author: Jerome Soumagne <jsoumagne@hdfgroup.org> Date: Sat Oct 31 13:02:03 2020 -0500 mercury: update to v2.0.0 (#19635) Remove deprecated selfforward option, on by default Rename verbose option to debug option commit 826ed5ff24f3c2ca0270defb9819952f269393d9 Author: Geoffrey Gunter <12984092+gmgunter@users.noreply.github.com> Date: Sat Oct 31 10:58:37 2020 -0700 fmt: add version 7.1.0 (#19638) commit 51a9473bf867af3e5f8f024d124c71b5b03384a0 Author: vijay kallesh <Vijay-teekinavar.Kallesh@amd.com> Date: Sat Oct 31 22:27:17 2020 +0530 [NEW] Added amdfftw, amdlibflame and amdscalapack recipes (#19457) * [NEW] Added amdfftw, amdlibflame and amdscalapack recipes Updated base fftw, libflame and netlib-scalapack recipes to accommodate the above listed AMD Optimizing CPU Libraries which are a set of numerical routines optimized for AMD platforms. Updated amdblis spack recipe amdblis: 1. updated with amdblis 2.2 release amdfftw: 1. "--enable-single" now work as synonym for "--enable-float" amdlibflame: 1. Added enable_or_disable_threads() to set value for "--enable-multithreading" flag Libflame: 1. Added enable_or_disable_threads() to set value for "--enable-multithreading" flag 2. Corrected invocation of "enable_or_disable('threads')" Change-Id: I9da0a2c2c4e2075b7fa2776e7cfe6548a2e0b32f * Added amd-toolchain-support as maintainers Added team github account amd-toolchain-support as maintainers for all the recipes owned by AMD Optimizing CPU Libraries (AOCL) team Change-Id: I9a7969bd48fc42cfbb88dd7bd93e0802c6138582 * Incorporated review comments Updated packages.yaml with aocl components Handled Flake8 test failures Change-Id: I0a03f02d8c9f326b2434ec907958c3de3a8e18eb * Readded accidental removal of stream recipe amdfftw: 1. Updated the aocc clang selection as per spack standards fftw: 1. Currently apple-clang section is redundant, already it is handled in the conflict checks. Change-Id: Idef4a3f61717eb81f321e0cd16e7ba9619eac846 * Fix for style and docs/validate (pull_request) test unnumbered format placeholders from {} to {0} Change-Id: If67a3374177ec067573e5504462d257712fafc05 * changed compiler references to Spack's compiler wrapper:spack_cc, spack_cxx, spack_fc Change-Id: I7ae29c978fff16e37773913f14c84df232499763 * Removed 'single' variant from amdfftw recipe Instead of conflict for apple-clang + openmp, handled this senario via below available feature: depends_on('llvm-openmp', when='%apple-clang +openmp') Change-Id: I701b23d83e822a500ca3aaf2b60cc9ace09e13dc * Added relevant info for users who prefers to use single precision Change-Id: I3506e21da428ddef5fb7895b5aaed32c2a061ef6 * Minor changes on fftw, amdfftw and libflame amdfftw: 1. Removed escape symbol to the single quotes 2. Rewording the conflict line from Recommended to Required fftw: 1. Reorded to following recommended sections: versions, variants, dependencies, providers, patches libflame: 1. Added provides entry for 5.1.0 version Change-Id: I21ebff99b6dfde031763154693ecb3f1fa47b476 * Removed single quote from amdfftw docstring to fix style failures Change-Id: Ife939a5a2f5ccbc8879b730c7bebfe2fcfef9332 commit 08f4ba0c986162f91398d4f6ded01e51dc0b2995 Author: Morten Kristensen <me@mortens.dev> Date: Sat Oct 31 17:55:32 2020 +0100 py-vermin: add latest version 1.0.1 (#19641) commit d855ad2abb379ce8344f720a9a623edb511c21c8 Author: Adam J. Stewart <ajstewart426@gmail.com> Date: Fri Oct 30 19:12:47 2020 -0500 py-pandas: add v1.1.4 (#19632) commit dee92f9b4247b1fe42a9a6aa69026069f71131f6 Author: Andrew W Elble <aweits@rit.edu> Date: Fri Oct 30 20:01:29 2020 -0400 New package: gqrx (#19633) * gqrx and dependencies * changes * forgot log4cpp * misc dep fixes commit 9fb2d5521de3f24f970ebf9cb5384ba43f471564 Author: Danny Taller <66029857+dtaller@users.noreply.github.com> Date: Fri Oct 30 13:33:54 2020 -0700 changes to support hip build of camp (#19502) * camp: changes to support hip build * hip: add fallback path for external hip to detect other rocm components Co-authored-by: Greg Becker <becker33@llnl.gov> commit c4aa5cb5bcc72bf5f3ba4e78338cca35394043f2 Author: Massimiliano Culpo <massimiliano.culpo@gmail.com> Date: Fri Oct 30 21:17:15 2020 +0100 Update documentation on containers (#19631) fixes #15183 - Moved the container related content from workflows.rst into containers.rst - Deleted the docker_for_developers.rst file, since it describes an outdated procedure Co-authored-by: Axel Huebl <a.huebl@hzdr.de> Co-authored-by: Omar Padron <omar.padron@kitware.com> commit 33c3c3c700cf0acd458389526974945e62fe895e Author: Massimiliano Culpo <massimiliano.culpo@gmail.com> Date: Fri Oct 30 21:10:45 2020 +0100 Config: cache results of get_config (#19605) `config.get_config` now caches the results and returns the same configuration if called multiple times with the same arguments (i.e. the same section and scope). As a consequence, it is expected that users will always call update methods provided in the `config` module after changing the configuration (even if manipulating it as a Python nested dictionary). The following two examples should cover most scenarios: * Most configuration update logic in the core (e.g. relating to adding new compiler) should call `Configuration.update_config` * Tests that need to change the global configuration should use the newly-provided `config.replace_config` function. (if neither of these methods apply, then the essential requirement is to use a method marked as `_config_mutator`) Failure to call such a function after modifying the configuration will lead to unexpected results (e.g. calling `get_config` after changing the configuration will not reflect the changes since the first call to get_config). commit 458d88eaad3c4e93210915ffa9b3bb64cc52d007 Author: Massimiliano Culpo <massimiliano.culpo@gmail.com> Date: Fri Oct 30 21:02:14 2020 +0100 Make archspec a vendored dependency (#19600) - Added archspec to the list of vendored dependencies - Removed every reference to llnl.util.cpu - Removed tests from Spack code base commit f82e858238c5d03ad3ec358886962fab627f07aa Author: Mathew Cleveland <clevelam@lanl.gov> Date: Fri Oct 30 13:58:09 2020 -0600 update to OPPPY-0_1_4 release (#17716) Co-authored-by: Cleveland <cleveland@lanl.gov> commit d0ad622272839f002461f844647b957b654c2336 Author: darmac <xiaojun2@hisilicon.com> Date: Sat Oct 31 03:56:31 2020 +0800 Add new package: wayland (#18826) * Add new package: wayland * remove duplicated dependency commit d6f0cb04611737055d5caf91a5b0a9a5874d9952 Author: David M. Rogers <predictivestatmech@gmail.com> Date: Fri Oct 30 15:55:21 2020 -0400 Patched hypre to better add flags based on compiler. (#19498) * Patched hypre to better add flags based on compiler. * Update package.py This file seems to have lots of edits, so the patch may succeed with offsets. Has anyone checked with spack patch to be sure it'll work with versions 2.15 - 2.20? commit ae3178f4ebd083127aaba005b8f4505026a70dc0 Author: t-nojiri <68096132+t-nojiri@users.noreply.github.com> Date: Sat Oct 31 04:54:04 2020 +0900 py-pycbc: Fix for aarch64 (#19563) * py-pycbc: Fix for aarch64 * py-pycbc: Change patch application conditions commit 31f57e56bb3c71f03d2ea2d265d0fa4713f0baa6 Author: Scott Wittenburg <scott.wittenburg@kitware.com> Date: Fri Oct 30 13:53:33 2020 -0600 Binary caching: use full hashes (#19209) * "spack install" now has a "--require-full-hash-match" option, which forces Spack to skip an available binary package when the full hash doesn't match. Normally only a DAG-hash match is required, which ensures equivalent Specs, but does not account for changing logic inside the associated package. * Add a local binary cache index which tracks specs that have a binary install available in a remote binary cache. It is updated with "spack buildcache list" or for a given spec when a binary package is retrieved for that Spec. commit 124d6543374b4446942c8dc8aa6b9a22ac0b7b00 Author: Dr. Christian Tacke <58549698+ChristianTackeGSI@users.noreply.github.com> Date: Fri Oct 30 20:52:15 2020 +0100 glew: Refactor as CMakePackage (#19588) In #18394 it was noted, that this package should be changed from a generic "Package" to a "CMakePackage". It makes a bunch of things easier. And it uses all the common cmake code. commit e1c1967b548f5244a23c2ef8d881d5e8e8c50b9a Author: t-nojiri <68096132+t-nojiri@users.noreply.github.com> Date: Sat Oct 31 04:51:57 2020 +0900 diamond: The version 2.0.4 file name has been changed. (#19595) * diamond: The version 2.0.4 file name has been changed. * diamond: Removed v2.0.4 URL. commit 7dea225fcefd33266438e1c9d403d6139a45215c Author: Brian Van Essen <vanessen1@llnl.gov> Date: Fri Oct 30 12:51:10 2020 -0700 Update lbann version and simplify installation (#19579) * Added hash values for LBANN v0.101 and Hydrogen v1.5.0. Updated the LBANN package to be more successful in resolving a legal configuration of MPI and HWLOC packages. This required the removal of the MPI virtual package since it is unable to resolve dependencies with minimum version requirements. As a result to enable a reasonable install line for LBANN this requires explicit forwarding of MPI variants to Hydrogen and Aluminum. Due to the lack of variant forwarding, there are many explicitly replicated dependencies for both LBANN and Hydrogen. Fixed the error in LBANN where gpu variant was replaced by the cuda variant, but not all dependencies were fixed. * Fixed the minumum cuDNN version for newer versions of LBANN. * Added explicit versioning of the MPI libraries for DiHydrogen to avoid all of the conflicts with minimum required versions of the OpenMPI library. * Removed explicit MPI versions and went back to using the MPI virtual dependency. Updated construction of variant forwarding to use iterative construction of constraints and variants. This exacerbates the challenges with backtracking in the current concretizer, but should be fixed in the new concretizer. * Added support for including the DiHydrogen library in LBANN as well as support for the distributed convolution (DistConv) parallel algorithms. Also include support for building with half precision. * Moving dependencies around * Added conflict statement to ensure that the variant dihydrogen is required for distconv. * Removed the preferred field * Fixed Flake8 and cuDNN version bounds commit a04e7686f80f9e14388e79570de436a62cead284 Author: Hervé Yviquel <hyviquel@gmail.com> Date: Fri Oct 30 16:50:20 2020 -0300 add recent versions of rdma-core package (#19604) commit c3630ed26e83151729e2f650fd7517ec2d601ce8 Author: Dr. Christian Tacke <58549698+ChristianTackeGSI@users.noreply.github.com> Date: Fri Oct 30 20:46:19 2020 +0100 hepmc: Add variants for length and momemtum (#19609) commit 5a5c220d0afa8048631422f18bc5ef992e5ecbae Author: Toyohisa Kameyama <kameyama@riken.jp> Date: Sat Oct 31 04:44:15 2020 +0900 py-dotnetcore2: Add conflict non x86_64 targets. (#19623) commit f2318d80d2296713ce60f8e7f3ca836487f997cb Author: Robert Underwood <robertu94@users.noreply.github.com> Date: Fri Oct 30 15:41:21 2020 -0400 sz: version bump 2.1.11 (#19613) commit 05cd3c43801dc07c1807695082ada63a37040156 Author: Jen Herting <jen@herting.cc> Date: Fri Oct 30 15:36:49 2020 -0400 New package: py-cudf (#19111) * [py-cudf] created template * [py-cudf] set build directory * [py-cudf] adding dependencies * [py-cudf] fixed phases * [py-cudf] added cmake to fetch some third party dependencies * [py-cudf] flake8 * [py-cudf] added homepage and description. removed fixmes * [py-cudf] added dependency of py-cupy * [py-cudf] depends on py-fsspec * [py-cudf] py-pyarrow requires +orc * [py-cudf] py-pyarrow requires +parquet * [py-cudf] removed upper python limit * [py-cudf] checksum changed commit 724325f789abf109d9de31bf22403e98f77585cf Author: Tiziano Müller <tiziano.mueller@chem.uzh.ch> Date: Fri Oct 30 20:35:24 2020 +0100 molden: adding the package (#19626) commit fef20524f968c759d596eca5ad9d6be92edcbb3f Author: Teodor Nikolov <teodor.nikolov22@gmail.com> Date: Fri Oct 30 19:36:53 2020 +0100 clingo: compilation error - needs a patch (#19624) * Add a patch to clingo Co-authored-by: Adam J. Stewart <ajstewart426@gmail.com> commit 3d7e8ff39906262c0b9cb6b9230739495e9d08f9 Author: Adam J. Stewart <ajstewart426@gmail.com> Date: Fri Oct 30 12:42:15 2020 -0500 PyTorch: add v1.7.0 (#19555) commit cb877e2a28717501528f7b6195164b8b0c989fa8 Author: Adam J. Stewart <ajstewart426@gmail.com> Date: Fri Oct 30 12:23:12 2020 -0500 py-pillow-simd: add older version (#19500) commit be146797199bf0976bbc4a3e75b2bc684dbd0779 Author: Adam J. Stewart <ajstewart426@gmail.com> Date: Fri Oct 30 12:22:53 2020 -0500 GDAL: add new version (#19504) commit bea65aacdad9c35e6332ee1d20ca80c65bca1f04 Author: Adam J. Stewart <ajstewart426@gmail.com> Date: Fri Oct 30 12:22:38 2020 -0500 py-torchvision: add v0.8.0 (#19556) * py-torchvision: add v0.8.0 * py-torchvision: add v0.8.1 commit bfab98d41ef752cfda6d1ae737357c18c569d7ee Author: Adam J. Stewart <ajstewart426@gmail.com> Date: Fri Oct 30 12:22:07 2020 -0500 oneDNN: add v1.6.5 (#19557) commit 9dd2ddb7db9f3b422331a5cd30cb8f88db8256fc Author: Adam J. Stewart <ajstewart426@gmail.com> Date: Fri Oct 30 12:21:52 2020 -0500 py-numpy: add v1.19.3 (#19593) commit f6189031b9227c5bc90ba80355405ed7de23f891 Author: Seth R. Johnson <johnsonsr@ornl.gov> Date: Fri Oct 30 12:53:30 2020 -0400 ninja: support spack find external (#19616) commit fc1d39dedcac23412d2be5c1c640021440a36e19 Author: manifest <robqiao@users.noreply.github.com> Date: Sat Oct 31 03:13:03 2020 +1030 gemini dep cyordereddict + (#19333) * gemini dep py-cyordereddict + * dep ipyparallel + * py-ipython-cluster + * py-cyordereddict URL+dep fix * Update var/spack/repos/builtin/packages/py-cyordereddict/package.py Co-authored-by: Adam J. Stewart <ajstewart426@gmail.com> * py-ipython-cluster-helper dep fix * py-ipyparallel dep fix * ipython-cluster-helper debug * ipython-cluster-helper debug * ipyparallel dep fix * ipython-cluster-helper dep fix Co-authored-by: Adam J. Stewart <ajstewart426@gmail.com> commit e4851d1a893f2ae79f7b4a8df0c973cc3ccbb553 Author: ajaust <alexander.jaust@ipvs.uni-stuttgart.de> Date: Fri Oct 30 17:39:59 2020 +0100 New package: py-pyprecice (#19558) * added initial version of package and patch for precice-bindings * updated package name * cleanup in script; added version requirement to cython * Remove unnecessary part of patch * cleanup package * added initial version of package and patch for precice-bindings * updated package name * cleanup in script; added version requirement to cython * Remove unnecessary part of patch * cleanup package * update style of package * reformatting to fullfil style requirements * reformatting again * fixing some of the issues mention in PR; working on fixing install stage * readded py-wheel as dependency Co-authored-by: Benjamin Rüth <benjamin.rueth@tum.de> commit aaa1afe9ec624fc86259ef817c059a5247770575 Author: Chuck Atkins <chuck.atkins@kitware.com> Date: Fri Oct 30 11:16:17 2020 -0400 mesa: Retire older autotools mesa as mesa18 and create current meson mesa (#19528) commit 6a381940ae461236dbf19c59c341c56f5f5b60f4 Author: Morten Kristensen <me@mortens.dev> Date: Fri Oct 30 10:26:56 2020 +0100 py-vermin: added v1.0.0 (#19618) commit 11ea2be74ab56dbc0f444308e389940c4eb9f55a Author: t-nojiri <68096132+t-nojiri@users.noreply.github.com> Date: Fri Oct 30 18:19:40 2020 +0900 openfoam-org: added v8.0 (#19622) openfoam: fixed build on aarch64 commit aa14a0aec7cac860a33c395128acf3d4684f4f13 Author: Michael Kuhn <michael.kuhn@ovgu.de> Date: Fri Oct 30 10:16:40 2020 +0100 graphviz: fix implicit patch (#19621) The patch seems to be included in version 2.44.1 already. Moreover, it is necessary to specify `level=0` to make it apply. commit 3a863020f0043c49c02b6b8eb35200e1dc078308 Author: Peter Scheibel <scheibel1@llnl.gov> Date: Thu Oct 29 22:23:36 2020 -0700 CI: disable vermin check for deprecated hash (#19612) Spack has a fallback for hash checking with m55sums that may not be supported in earlier versions of Python 3.x. The comments in the Spack code acknowledge that this is best effort and may fail, but recent vermin checks (running as part of our CI) reject this. This disables vermin checks for that fallback. commit 52379d87fe7cf1db7389e1f00bde1c6563dae36f Author: t-nojiri <68096132+t-nojiri@users.noreply.github.com> Date: Fri Oct 30 12:01:05 2020 +0900 caliper: Fix for aarch64 (#19564) commit ebe1c6badd0053096b002d4621047e9dec971c00 Author: Chris Chambreau <chambreau1@llnl.gov> Date: Thu Oct 29 18:56:54 2020 -0500 mpip: add v3.5 release (#19559) * Update for mpip-3.5 release * Additional changes to support 3.5 and 3.4.1 releases * Specify python deptype commit c954d50998f6a223027d864c5e4f161e5b2e27f1 Author: Frank Willmore <frankwillmore@gmail.com> Date: Thu Oct 29 16:52:54 2020 -0500 Oneapi add compiler (#19330) * enable flatcc to be built with gcc/9.X.X * add static option for building libyogrt * cleanup * Initial working version * rework new oneapi wrappers * tested and removed my initials from source * cleanup * Update __init__.py * remove whitespace * working now with mods for testing, detection. Detection for oneapi is working, but entry needs to be modified to add link path for libimf.so. Cleared cruft for old Intel versions * fixed some formatting * cleanup * flake8 cleanup * flake8 * fixed syntax of compiler version detection tests * fixed syntax of compiler version detection tests modified: detection.py * fix typo * fixes for compilers tests * remove erroneous tests for outdated -std= flags, remove ifx version check (output won't parse) Co-authored-by: Frank Willmore <willmore@anl.gov> commit 52959528a2cb7e7e9b213efd1243a078502ac708 Author: Jean-Paul Pelteret <jppelteret@gmail.com> Date: Thu Oct 29 21:29:39 2020 +0100 Suite-sparse: Fix Darwin install name (#19507) commit af057e0196967f0ba34410d0e1dbceba7ad01396 Author: Geoffrey Oxberry <goxberry@gmail.com> Date: Thu Oct 29 12:14:55 2020 -0700 yapf: add version 0.30.0 (#19598) commit 305d8d9b1bb28ec326427f2de6f11e7c2e55828d Author: Ben Corbett <32752943+corbett5@users.noreply.github.com> Date: Thu Oct 29 11:52:10 2020 -0700 Adds a package for LvArray (#19221) * RAJA and CHAI changes. * Added LvArray package. commit e2a720930a2cfe28e2f77df6e8447cfafdc6a720 Author: David Beckingsale <davidbeckingsale@gmail.com> Date: Thu Oct 29 11:32:56 2020 -0700 Patch CMake version check in Umpire (#19590) * Patch CMake version check in Umpire * Update version constraint for cmake_version_check patch Co-authored-by: Adam J. Stewart <ajstewart426@gmail.com> * Add maintainers to Umpire Co-authored-by: Adam J. Stewart <ajstewart426@gmail.com> commit 518124c14aacf84cec9e2b7941493df510d2a838 Author: Jen Herting <jen@herting.cc> Date: Thu Oct 29 12:20:18 2020 -0400 [py-torch-nvidia-apex] added version 201019 and added dependency on p… (#19548) * [py-torch-nvidia-apex] added version 201019 and added dependency on py-pybind11 * [py-torch-nvidia-apex] changed versioning format * [py-torch-nvidia-apex] removed redundent version condition * [py-torch-nvidia-apex] removed condition on dependency commit 0fc79293c6ec14d70334ff318a24a7e798ef673c Author: Jen Herting <jen@herting.cc> Date: Thu Oct 29 12:17:14 2020 -0400 New package: py-cupy (#19468) * [py-cupy] created template * [py-cupy] added dependencies * [py-cupy] switched to git based download for submodules * [py-cupy] added dependencies * [py-cupy] added homepage and description. removed fixmes * [py-cupy] updated to tarball from pypi commit c2e66109480fa38cf5045f05e28b23ff4f7aa08e Author: h-denpo <57649496+h-denpo@users.noreply.github.com> Date: Fri Oct 30 01:10:57 2020 +0900 plplot:fix:　add: depends_on('libsm', type='link') (#19594) commit a4a64e1fbd8c1050b406b4031cbe062fb28ab507 Author: Rémi Lacroix <remi.lacroix@idris.fr> Date: Thu Oct 29 17:08:13 2020 +0100 Gromacs: Remove a dependency that could never be enabled. (#19599) The `fft` variant was removed but not the associated dependency. commit 71cb46afde6a42e7fc84a7ae70062be2d18a5c8a Author: Greg Becker <becker33@llnl.gov> Date: Thu Oct 29 08:38:17 2020 -0700 clingo+python extends python (#19585) commit 09b63ae3d101d2889a7bbf8e393068abdc93312b Author: AMD Toolchain Support <73240730+amd-toolchain-support@users.noreply.github.com> Date: Thu Oct 29 20:43:30 2020 +0530 Adding AOCC support for M4 (#19572) * Adding AOCC support for M4 * combining 4 if-statements into a single if-statement with or conditions * keeping parentheses around the or expressions * fixing flake8 test failures Co-authored-by: mohan babu <mohbabul@amd.com> commit 0bed9a1990893178c45bd0e89133187ff0ce52bd Author: G-Ragghianti <33492707+G-Ragghianti@users.noreply.github.com> Date: Thu Oct 29 11:13:02 2020 -0400 SLATE package: New versions of slate, blaspp, and lapackpp with CMake build support (#19587) * New versions of slate, blaspp, and lapackpp with CMake build support * Fixing formatting commit ad87eece17dd7dbdfe39fd9c28ff65d52f1ac6e6 Author: t-nojiri <68096132+t-nojiri@users.noreply.github.com> Date: Thu Oct 29 11:11:36 2020 +0900 launchmon: Fix for aarch64 (#19562) commit ef9c80de233cb5491c11b39c7c261fbfb9d48e92 Author: Seth R. Johnson <johnsonsr@ornl.gov> Date: Wed Oct 28 21:47:16 2020 -0400 qt: Silence build and force `xmlpatterns` library on for Qt4 (#19591) For some mysterious reason Qt4 stopped building the xmlpatterns component, needed by some downstream packages. With this patch, the component successfully builds with ``` qt@4.8.7~dbus~debug~examples~framework~gtk~opengl~phonon+shared~sql~ssl~tools~webkit freetype=none arch=linux-rhel7-haswell %gcc@10.2.0 ``` commit f7269ffd0a4ecd875cfef6ee959babbc181ff98f Author: manifest <robqiao@users.noreply.github.com> Date: Thu Oct 29 12:16:04 2020 +1030 pest suit + (#19458) * pestpp + * build -f default commit b4a0a43d980f23623101ca5bbaf34d3791d239df Author: manifest <robqiao@users.noreply.github.com> Date: Thu Oct 29 12:15:24 2020 +1030 PopLDdecay package + (#17802) * poplddecay bio * flake8 debug * bin PATH correction * build step opt * BUILD_PATH fix * retro implementation + style fix commit 3243e904a84042522d1b298ec7ddd75574eddf4b Author: manifest <robqiao@users.noreply.github.com> Date: Thu Oct 29 12:14:38 2020 +1030 Pbbam debug (#17803) * pbbam path fix * pbbam flake8 fix * sys var build_directory sub * pbbam flake8 fix commit aebf20ebdc0f5d1ea03956681e0b16ffaffa9568 Author: Todd Gamblin <tgamblin@llnl.gov> Date: Wed Oct 28 14:07:05 2020 -0700 sbang: vendor sbang `sbang` now lives at https://github.com/spack/sbang, and it has its own test suite that's more extensive than what's in Spack. We'll leave sbang tests to sbang from now on, and just vendor `bin/sbang` directly. Remaining `sbang` tests have to do with patching files, not with `sbang`'s functionality. This update also fixes a bug with `sbang` and multiple command line arguments that was introduced in #19529. See: * https://github.com/spack/sbang/pull/1 * https://github.com/spack/sbang/pull/2 - [x] include latest `sbang` from https://github.com/spack/sbang - [x] remove old `sbang` tests from Spack - [x] update `COPYRIGHT` and `cmd/license.py` commit 44bacefb27675aaed22d77c768fb18a627e678eb Author: David Beckingsale <davidbeckingsale@gmail.com> Date: Wed Oct 28 16:54:23 2020 -0700 RAJA package: Don't set both CUDA_ARCH and CMAKE_CUDA_FLAGS (#19589) commit f028079564275ba1207d9df673b02220cfb49acf Author: dunatotatos <contact@dunatotatos.com> Date: Wed Oct 28 16:58:30 2020 +0100 Update strelka (#19565) * Update package.py Remove breaking patch. Patching the shebang is useless is the dependencies are properly loaded before execution. Furthermore, the long paths which can be generated when installing with Spack can exceed the maximum length of the shebang. * Add newer versions of strelka. commit 1dd7370885df69a1bcdc40fcb6a0ae9b430e76f1 Author: dunatotatos <contact@dunatotatos.com> Date: Wed Oct 28 16:57:19 2020 +0100 Remove unused dependency. (#19566) Boost is not used to build Manta. commit f320a650d853acf036ce067631a5874a4a331b8f Author: Toyohisa Kameyama <kameyama@riken.jp> Date: Thu Oct 29 00:56:52 2020 +0900 py-mmcv: fix Opencv detection. (#19567) commit 98a17715903b3385d46b4716675bd7aea997246d Author: Roberto Di Remigio <robertodr@users.noreply.github.com> Date: Wed Oct 28 16:56:11 2020 +0100 Do not build XCFun tests (#19568) commit f4b63db78f5d4d10891a69a28bc0ed7a0b4ab2f8 Author: Roberto Di Remigio <robertodr@users.noreply.github.com> Date: Wed Oct 28 16:55:46 2020 +0100 Do not build MRCPP tests (#19569) commit 85e6334d6fee497064bacf62aed8a6b745ea2175 Author: Roberto Di Remigio <robertodr@users.noreply.github.com> Date: Wed Oct 28 16:55:19 2020 +0100 Add new package: mrchem (#19571) commit 674fb16828f08767235cbefaa1d90832b083f594 Author: Dr. Christian Tacke <58549698+ChristianTackeGSI@users.noreply.github.com> Date: Wed Oct 28 16:53:33 2020 +0100 openssl: Add version 1.1.1h (#19574) commit 9b809e01b47d48f01b3d257912fe1b752943cd3d Author: Pieter Ghysels <pghysels@lbl.gov> Date: Tue Oct 27 18:28:24 2020 -0700 Add new minor version 1.2.1 for ButterflyPACK (#19554) commit 6a5d399f55f09c0447f37c5cd14425203681225a Author: lorddavidiii <maximillian.bensch@aei.mpg.de> Date: Wed Oct 28 02:11:37 2020 +0100 asciidoc-py3 add docbook dependency and fix a enviroment variable problem for docbook-{xml,xsl} (#19547) * asciidoc-py3: add docbook-{xml,xsl} dependency * docbook-{xsl,xml}: fix XML_CATALOG_FILES enviroment variable commit 79b0eab2afda9ff61b36668503942a00fb6c0e89 Author: Jen Herting <jen@herting.cc> Date: Tue Oct 27 21:11:06 2020 -0400 New package: libcudf (#19110) * [libcudf] created template * [libcudf] depends on cuda * [libcudf] set cmake dir * [libcudf] depends on boost * [libcudf] depends on py-pyarrow * [libcudf] depends on librmm * [libcudf] depends on dlpack * [libcudf] added more dependency information from https://github.com/rapidsai/libcudf/blob/v0.15.0/CONTRIBUTING.md#customizing-the-build * [libcudf] removed python dependencies * [libcudf] fixed url that got mangled in package renaming * [libcudf] added default build options from build.sh * [libcudf] added version 0.16.0a * [libcudf] removed version 0.16.0a as it's an alpha version * [libcudf] added homepage and description. removed fixmes * [libcudf] flake8 * [libcudf] arrow requires +orc * [libcudf] requires +parquet * [libcudf] checksum changed commit 7bd5397aca5f003168f4b99d06471542bb70215f Author: Jen Herting <jen@herting.cc> Date: Tue Oct 27 21:10:40 2020 -0400 New Package: py-rmm (#19104) * [py-rmm] created template * [py-rmm] added dependencies * [py-rmm] setting build_directory * [py-rmm] added dependencies cuda and spdlog * [py-rmm] added homepage and description. removed fixmes * [py-rmm] added for loop for dependency versions * [py-rmm] flake8 * [py-rmm] updating upper range of python version * [py-rmm] removing python upper limit commit 429f49a1e4ab1fcd1f93048c0ebe46afe1905b22 Author: t-nojiri <68096132+t-nojiri@users.noreply.github.com> Date: Wed Oct 28 10:09:05 2020 +0900 bowtie2: Add version 2.4.2 (#19537) commit 965ccb78cf5064780f606fc3da9f4af26be05807 Author: Todd Gamblin <tgamblin@llnl.gov> Date: Tue Oct 27 00:13:09 2020 -0700 sbang: use bashcov in sbang on Linux commit ec9456feb8f14c173a8786c136a1bc496579231b Author: Todd Gamblin <tgamblin@llnl.gov> Date: Mon Oct 26 11:06:03 2020 -0700 sbang: convert sbang script to POSIX shell `sbang` was previously a bash script but did not need to be. This converts it to a plain old POSIX shell script and adds some options. This also allows us to simplify sbang shebangs to `#!/bin/sh /path/to/sbang` instead of `#!/bin/bash /path/to/sbang`. The new script passes shellcheck (with a few exceptions noted in the file) - [x] `SBANG_DEBUG` env var enables printing what *would* be executed - [x] `sbang` checks whether it has been passed an option and fails gracefully - [x] `sbang` will now fail if it can't find a second shebang line, or if the second line happens to be sbang (avoid infinite loops) - [x] add more rigorous tests for `sbang` behavior using `SBANG_DEBUG` commit 9f89a7e9f7ce279e4b47ec06a9ffb90a453b2f7a Author: adityakavalur <33232772+adityakavalur@users.noreply.github.com> Date: Tue Oct 27 14:24:09 2020 -0400 Update package.py (#19513) On Cori(Cray-XC40), I need to pass the entire path for the compilers, this is what is saved in c_compiler, cpp_compiler, f_compiler. Therefore, when for the MPI wrappers only the binary name is provided I run into the same issue. There is no drawback of passing the entire path, this is set by the user through the compiler path anyways. commit 7313cf5ea5df6d4c35277b4bcd1853ee91948e8a Author: Roberto Di Remigio <robertodr@users.noreply.github.com> Date: Tue Oct 27 15:58:24 2020 +0100 Update MRCPP package.py (#19541) commit 78a759129aab6079a2c9435cb9c77a52c29e4626 Author: h-denpo <57649496+h-denpo@users.noreply.github.com> Date: Tue Oct 27 23:54:33 2020 +0900 ghostscript: fix: add: depends_on('krb5', type='link') (#19536) commit f6c51efa852e6e346f898b257b98f18b6759d1ee Author: t-nojiri <68096132+t-nojiri@users.noreply.github.com> Date: Tue Oct 27 23:53:38 2020 +0900 diamond: Add version 2.0.4 (#19535) commit 64974c43c7ec1912028b7e86c7dab63e60441839 Author: Jungwon Kim <iarapre@gmail.com> Date: Tue Oct 27 10:53:22 2020 -0400 added -lpthread flag in kv/tests/CMakeLists.txt (#19533) * added -lpthread flag in kv/tests/CMakeLists.txt * Update var/spack/repos/builtin/packages/papyrus/package.py Co-authored-by: Adam J. Stewart <ajstewart426@gmail.com> Co-authored-by: Adam J. Stewart <ajstewart426@gmail.com> commit e214deec5b9a0fa6c2521229b99606fb5862ba97 Author: daichi-nishi <70185009+daichi-nishi@users.noreply.github.com> Date: Tue Oct 27 23:53:04 2020 +0900 modified:var/spack/repos/builtin/packages/ppopen-appl-bem-at/package.py (#19538) commit 57200f01fd027a9691491e744c458532740efe82 Author: Chuck Atkins <chuck.atkins@kitware.com> Date: Tue Oct 27 10:52:28 2020 -0400 camp: Add missing checksum (#19543) commit bb00b1a7c9eae3d307f0a22dcccae9e33a5885d0 Author: Toyohisa Kameyama <kameyama@riken.jp> Date: Tue Oct 27 14:11:43 2020 +0900 sbang: add support for php (#18299) PHP supports an initial shebang, but its comment syntax can't handle our 2-line shebangs. So, we need to embed the 2nd-line shebang comment to look like a PHP comment: <?php #!/path/to/php ?> This adds patching support to the sbang hook and support for instrumenting php shebangs. This also patches `phar`, which is a tool used to create php packages. `phar` itself has to add sbangs to those packages (as phar archives apparently contain UTF-8, as well as binary blobs), and `phar` sets a checksum based on the contents of the package. Co-authored-by: Todd Gamblin <tgamblin@llnl.gov> commit cb07d9ddb1e744c8e0f1aded64ab3f5bf9e5bae3 Author: t-nojiri <68096132+t-nojiri@users.noreply.github.com> Date: Tue Oct 27 10:20:18 2020 +0900 netgauge: Fix for aarch64 (#19462) * netgauge: Fix for aarch64 * netgauge: Revise the points indicated by the review. commit e9223062a8f4f74f6bcf24849753f798d5e168cf Author: Geoffrey Gunter <12984092+gmgunter@users.noreply.github.com> Date: Mon Oct 26 18:18:34 2020 -0700 New package: date (#19515) * Add new package: date * date: resolve style conformance issues * date: explicitly disable some cmake options Explicitly disable CMake options corresponding to variant 'tzdb=download' * date: make more cmake options explicit * date: simplify defining cmake cli args commit bc4e7eabfec37df50911b63aa2f53c14e7ddfa70 Author: Todd Gamblin <tgamblin@llnl.gov> Date: Mon Oct 26 16:23:22 2020 -0700 coverage: add bin directory to coverage (#19530) commit 93c985e5a92a4f6350199b04559ffc0d487b1c40 Author: iarspider <iarspider@gmail.com> Date: Mon Oct 26 22:20:45 2020 +0100 New package: py-minrpc (#19524) * New package: py-minrpc * Delete package.py.save * Update var/spack/repos/builtin/packages/py-minrpc/package.py Co-authored-by: Adam J. Stewart <ajstewart426@gmail.com> Co-authored-by: Adam J. Stewart <ajstewart426@gmail.com> commit 5d5711621a54616775b0ae397833af90dea1a674 Author: jthies <jonas.thies@dlr.de> Date: Mon Oct 26 22:19:53 2020 +0100 packages/phist: fix incorrect git url (#19527) Co-authored-by: Thies <thie_jo@fe-store01.sc.bs.dlr.de> commit 4f720fb9ba014d73fcb4ad9a4d67caef9e537c8c Author: Sinan <sbulutw@gmail.com> Date: Mon Oct 26 14:17:27 2020 -0700 package/gunrock add v1.2 (#19516) * package/gunrock add v1.2 * Update var/spack/repos/builtin/packages/gunrock/package.py Co-authored-by: Adam J. Stewart <ajstewart426@gmail.com> Co-authored-by: sbulut <sbulut@3vgeomatics.com> Co-authored-by: Adam J. Stewart <ajstewart426@gmail.com> commit 4f9c621284ce1890e2e37976b567fd1082b701a9 Author: David Beckingsale <davidbeckingsale@gmail.com> Date: Mon Oct 26 14:12:03 2020 -0700 Add camp & BLT dependencies to Umpire (#19411) * Add camp & BLT dependencies to Umpire * Remove tests variant commit 1c2c30a139296d53a7474a6f53e542a05b5e685d Author: Patrick Gartung <gartung@fnal.gov> Date: Mon Oct 26 14:37:54 2020 -0500 sbang: put sbang in the install_tree (#11598) `sbang` is not always accessible to users of packages, e.g., if Spack is installed in someone's home directory and they deploy software for others. Avoid this by: 1. Always installing the `sbang` script in the `install_tree` 2. Relocating binaries to point to the copy in the `install_tree` and not the one in the Spack installation. This PR also: - ensures that `sbang` is reinstalled if it is modified in Spack - adds tests - updates the way `gobject-introspection` patches Makefiles to support `sbang` Co-authored-by: Todd Gamblin <tgamblin@llnl.gov> commit 718150b99766a8fa0193ae589c38bf16e0060eca Author: dunatotatos <contact@dunatotatos.com> Date: Mon Oct 26 19:32:35 2020 +0100 Update GATK versions. (#19521) commit b9d3d668d9457a1a6dfa86d1869ffa0350807f30 Author: takanori-ihara <62980219+takanori-ihara@users.noreply.github.com> Date: Tue Oct 27 03:31:45 2020 +0900 fujitsu-ssl2: update package.py (#19519) commit 7ce4518cc0f01772d071fe135c352c2f674c5c2e Author: Geoffrey Gunter <12984092+gmgunter@users.noreply.github.com> Date: Mon Oct 26 11:29:16 2020 -0700 abseil-cpp: add versions 20200923.{1,2} (#19517) commit 7649c652c0bab3654caca9928ee608fb7eb16864 Author: Jen Herting <jen@herting.cc> Date: Mon Oct 26 14:24:30 2020 -0400 New package: py-visdom (#19479) * [py-visdom] created template * [py-visdom] added dependencies * [py-visdom] added homepage and description. removed fixmes * [py-visdom] added dependency on py-torchfile * [py-visdom] py-pillow -> pil * [py-visdom] fixed url format * [py-visdom] fixed url format commit 7ca1f6c5d51f5e2fc582603012c3ca5a053ee4eb Author: David Beckingsale <davidbeckingsale@gmail.com> Date: Mon Oct 26 10:15:55 2020 -0700 Add BLT package (#19410) * Add BLT package * Switch install function Co-authored-by: Adam J. Stewart <ajstewart426@gmail.com> * Add type='run' to cmake dependency Co-authored-by: Adam J. Stewart <ajstewart426@gmail.com> * Add git attribute to BLT Co-authored-by: Adam J. Stewart <ajstewart426@gmail.com> commit f921bcbe0b01f63acfc692f9b6cc6751ffc1fbd1 Author: Tiziano Müller <tiziano.mueller@chem.uzh.ch> Date: Mon Oct 26 16:32:15 2020 +0100 cp2k, libxc, libint: fix builds with %intel, resp. intel-parallel-studio+mkl (#19522) * cp2k: locate correct include dir when using intel-parallel-studio+mkl for fftw-api * libxc: drop arch-specific intel opt. flags fixes #17794 * libint: drop arch-specific intel opt. flags, always build Fortran example with FC fixes #17509 commit fd6c163e0279b69206cb24b605b4ca275e39020c Author: Todd Gamblin <tgamblin@llnl.gov> Date: Mon Oct 26 07:24:49 2020 -0700 bugfix: test_push_and_fetch_keys should be skipped w/o gpg (#19511) - [x] add a `@pytest.skipif` decorator commit 2e3355d2f9d7f62979fcf7b5f7736c37a1e264b9 Author: Sinan <sbulutw@gmail.com> Date: Sun Oct 25 18:39:44 2020 -0700 package/pmdk add variants, version 1.9 (#19512) * package/pmdk add variants, version 1.9 * add dependency * Update var/spack/repos/builtin/packages/pmdk/package.py Co-authored-by: Adam J. Stewart <ajstewart426@gmail.com> Co-authored-by: sbulut <sbulut@3vgeomatics.com> Co-authored-by: Adam J. Stewart <ajstewart426@gmail.com> commit 182ca4cb688f8fa6e6d232a4c85eab044f3da52b Author: jthies <jonas.thies@dlr.de> Date: Sun Oct 25 22:35:43 2020 +0100 phist: two new versions and disable ccache because we don't have a dependency on ccache. (#19510) Otherwise, phist would look for ccache via cmake, which is not the spack way to do it. Co-authored-by: Thies <thie_jo@be-cpu03.sc.bs.dlr.de> commit 01953dc5134643995db0f769eddab8868b62b1ae Author: Todd Gamblin <tgamblin@llnl.gov> Date: Sat Oct 24 16:48:04 2020 -0700 bugfix: fix config merge order for OrderdDicts (#18482) The logic in `config.py` merges lists correctly so that list elements from higher-precedence config files come first, but the way we merge `dict` elements reverses the precedence. Since `mirrors.yaml` relies on `OrderedDict` for precedence, this bug causes mirrors in lower-precedence config scopes to be checked before higher-precedence scopes. We should probably convert `mirrors.yaml` to use a list at some point, but in the meantie here's a fix for `OrderedDict`. - [x] ensuring that keys are ordered correctly in `OrderedDict` by re-inserting keys from the destination `dict` after adding the keys from the source `dict`. - [x] also simplify the logic in `merge_yaml` by always reinserting common keys -- this preserves mark information without all the special cases, and makes it simpler to preserve insertion order. Assuming a default spack configuration, if we run this: ```console $ spack mirror add foo https://bar.com ``` Results before this change: ```console $ spack config blame mirrors --- mirrors: /Users/gamblin2/src/spack/etc/spack/defaults/mirrors.yaml:2 spack-public: https://spack-llnl-mirror.s3-us-west-2.amazonaws.com/ /Users/gamblin2/.spack/mirrors.yaml:2 foo: https://bar.com ``` Results after: ```console $ spack config blame mirrors --- mirrors: /Users/gamblin2/.spack/mirrors.yaml:2 foo: https://bar.com /Users/gamblin2/src/spack/etc/spack/defaults/mirrors.yaml:2 spack-public: https://spack-llnl-mirror.s3-us-west-2.amazonaws.com/ ``` commit 6752a39629be9fb9362e35ffdcce9bcb5cf40f2d Author: Massimiliano Culpo <massimiliano.culpo@gmail.com> Date: Sat Oct 24 22:29:48 2020 +0200 py-coverage: added v5.3 (#19509) commit 2893c23e7c8caa611d03a2e9558577cc2473d917 Author: Todd Gamblin <tgamblin@llnl.gov> Date: Fri Oct 23 22:16:01 2020 -0700 docs: update docs on shell support and using packages (#19486) Shell integration no longer requires setting `SPACK_ROOT`, so we can simplify the documentation on it. The docs on shell support and using packages are getting a bit old, and information on `spack load` (which seems to be everyone's most common way of using packages) is hard to find. This PR simplifies the shell documentation to remove SPACK_ROOT, and also moves some sections around for clearer organization. - [x] make docs on sourcing setup scripts clearer and simpler - [x] introduce `spack load` early in the basic usage guide instead of burying it in the module docs - [x] clean up module docs so that spack module tcl loads comes later - [x] be clear about the different ways to use packages so that the users can find the docs better. Co-authored-by: Massimiliano Culpo <massimiliano.culpo@gmail.com> commit 560beb098efdd5b13f02692317fa5460c9b81141 Author: Todd Gamblin <tgamblin@llnl.gov> Date: Fri Oct 23 18:54:34 2020 -0700 csh: don't require SPACK_ROOT for sourcing setup-env.csh (#18225) Don't require SPACK_ROOT for sourcing setup-env.csh and make output more consistent commit 4cf85ed5f715fc93fe88cabeed08f8dc94fc8e68 Author: Marty Kandes <mkandes@sdsc.edu> Date: Fri Oct 23 16:58:13 2020 -0700 Fix GROMACS to require FFTW when using cuda (#19505) GROMACS still requires a version of FFTW when compiling it to utilize NVIDIA GPUs. In fact, the type of calculation that depends on FFTW -- Particle-Mesh Ewald (PME) -- is generally run on the host system's CPUs, even when GPUs are available. commit 978d8ad0af3958f74b5c61e8cc4fa22c3ff0d622 Author: iarspider <iarspider@gmail.com> Date: Fri Oct 23 21:59:52 2020 +0200 New package: py-rise (#19496) * New package: py-rise * Fix URL and add description * Update var/spack/repos/builtin/packages/py-rise/package.py Co-authored-by: Adam J. Stewart <ajstewart426@gmail.com> Co-authored-by: Adam J. Stewart <ajstewart426@gmail.com> commit bbc048e615f5043234c55130511322f723b67e87 Author: Tiziano Müller <tiziano.mueller@chem.uzh.ch> Date: Fri Oct 23 18:02:56 2020 +0200 let intel-parallel-studio provide fftw-api for +mkl (#19497) commit ccc331af2633f611ad7fc84ff5ee6dd3e9ef7639 Author: Scott McMillan <scott.andrew.mcmillan@gmail.com> Date: Fri Oct 23 11:00:16 2020 -0500 CMake fix: narrow versions that the PGI patch is applied to (#19495) Co-authored-by: Scott McMillan <…

tgamblin added tests General test capability(ies) sbang and removed tests General test capability(ies) labels Oct 26, 2020

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sbang: use bashcov in sbang on Linux

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autoreconf fails on all packages since sbang rework #19580

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Fix sbang to properly quote command line arguments #19581

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sbang: vendor sbang #19582

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sbang: fixes for sbang relocation #19636

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sbang: convert sbang script to POSIX shell #19529

sbang: convert sbang script to POSIX shell #19529

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sbang: convert sbang script to POSIX shell #19529

sbang: convert sbang script to POSIX shell #19529

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