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2022-03-29cmake: use CMAKE_INSTALL_RPATH_USE_LINK_PATH (#29703)Harmen Stoppels2-31/+80
* cmake: use CMAKE_INSTALL_RPATH_USE_LINK_PATH Spack has a heuristic to add rpaths for packages it knows are required, but it's really a heuristic, and it does not work when the dependencies put their libraries in a different folder than `<prefix>/lib{64,}`. CMake patches binaries after install with the "install rpaths", which by default are provided by Spack and its heuristic through `CMAKE_INSTALL_RPATH`. CMake however knows better what libraries are effectively being linked to, and has an option to include those in the install rpath too, through `CMAKE_INSTALL_RPATH_USE_LINK_PATH`. These two CMake options are complementary, repeated rpaths seem to be filtered, and the "use link path" paths are appended to Spack's heuristic "install rpath". So, it seems like a good idea to enable "use link path" by default, so that: - `dlopen` by library name uses Spack's heuristic search paths - linked libraries in non-standard locations within a prefix get an rpath thanks to CMake. * docs
2022-03-29cgns: add v4.3.0 (#29773)Greg Sjaardema1-0/+1
2022-03-29mochi-margo: add v0.9.8 (#29771)Matthieu Dorier1-0/+1
2022-03-29SUNDIALS: refactor CMake recipe (#29585)Seth R. Johnson1-181/+95
- Use define/define_from_variant - Remove unused "fortran_flags" - Fix CUDA architectures when using multiple (needs semicolon not comma separators) - Add `when=` variant restrictions to simplify logic
2022-03-28cuda: add 11.6.2 (#29756)Carlos Bederián1-0/+4
2022-03-28spack info: make sections optional; add build/stand-alone test information ↵Tamara Dahlgren4-49/+191
(#22097) Add output of build- and install-time tests to info command Enable dependencies, variants, and versions by default (i.e., provide --no* options; add gcc to test_info_fields to increase coverage for c_names->v_names
2022-03-28Convert git-over-ssh package URLs to canonical format (#29754)Thomas Dickerson3-3/+3
Use canonical SSH urls for git-over-ssh package urls. See also: discussion on #29706, #29749, and https://forum.gitlab.com/t/provided-ssh-url-is-in-the-wrong-format/14320
2022-03-28spiner: fix +cuda (#29758)Richard Berger1-2/+2
2022-03-28Add ssh to filter of valid urls (#29749)John W. Parent1-1/+1
2022-03-28e4s ci spack.yaml: add h5bench (#29755)eugeneswalker1-0/+1
2022-03-28New package: spiner (#29719)Richard Berger1-0/+77
* New package: spiner * Update dependencies for spiner package * Update var/spack/repos/builtin/packages/spiner/package.py Co-authored-by: Seth R. Johnson <johnsonsr@ornl.gov> * Update var/spack/repos/builtin/packages/spiner/package.py Co-authored-by: Seth R. Johnson <johnsonsr@ornl.gov> * Remove versions that can't be installed and use ports-of-call@1.1.0 Co-authored-by: Seth R. Johnson <johnsonsr@ornl.gov>
2022-03-28Removed unneeded conflicts in CudaPackage and RocmPackage (#29699)Massimiliano Culpo2-8/+0
Since the variant is conditional there's no need to add conflicts too.
2022-03-28survey package: add versions 1.0.2/1.0.3; add tls model variant (#29375)Jim Galarowicz1-3/+16
2022-03-28ports-of-call: new version 1.1.0 (#29723)Richard Berger1-2/+2
Version 1.0.0 was uninstallable.
2022-03-28batchedblas: new package (#29028)FJ-NaokiMatsumura2-0/+52
2022-03-28gpi-space: add v22.03 (#29736)Max Zeyen1-0/+1
2022-03-28Adding NVIDIA HPC SDK 22.3 (#29737)Filippo Spiga1-0/+4
Co-authored-by: Filippo Spiga <fspiga@nvidia.com>
2022-03-28julia: add patch reverting llvm rpath changes (#29731)Harmen Stoppels2-0/+35
2022-03-28julia 1.6/1.7: constrain libgit2, libssh2 (#29728)Harmen Stoppels1-4/+8
2022-03-27py-torch: fix to build with fujitsu-ssl2 (#29283)FJ-NaokiMatsumura8-0/+544
* py-torch: fix build with fujitsu-ssl2 * fix to use fujitsu-ssl2 in py-torch v1.5.0 to v1.11.0 * fix to use fujitsu-ssl2 in py-torch v1.2.0 to v1.11.0 * Delete fj-ssl2.patch * renamed the patches * Rename fj-ssl2.1.5.patch to fj-ssl2_1.5.patch * Delete fj-ssl2_1.5.patch
2022-03-27mochi-thallium: new package (#29722)Matthieu Dorier1-0/+60
2022-03-27autotools doc: add missing right quote (#29734)百地 希留耶1-1/+1
2022-03-27h5z-zfp: fix build when ^hdf5+mpi (#29733)David M. Rogers1-3/+9
2022-03-27openmpi: switch to using main (#29725)Howard Pritchard1-8/+8
The Open MPI project has elected to name our development branch - main. Signed-off-by: Howard Pritchard <howardp@lanl.gov>
2022-03-26py-torchvision: adjust jpeg dependency (#29614)Glenn Johnson1-1/+1
2022-03-26llvm: add @14.0.0 (#29732)eugeneswalker1-0/+2
* llvm: add @14.0.0 * llvm@14 provides virtual
2022-03-25r-rsqlite: add v2.2.10 (#29624)Glenn Johnson1-0/+2
2022-03-25[julia] gfortran patch required for 1.7.2 (#29720)Jen Herting1-1/+1
2022-03-25Update rocm recipes for rocm-5.0.0 release (#29269)Sreenivasa Murthy Kolam48-109/+529
* update rocm recipes for ROCm-5.0.0 release * revert address sanitizer changes * fix style errors * update to the rocm recipes for 5.0.2 release * fix review comments inside the rocfft recipe * update the rocfft recipe for sqlite dependency
2022-03-25New package: ports-of-call (#29696)Richard Berger1-0/+35
2022-03-25Use the appropriate function to remove files in the stage directory (#29690)Massimiliano Culpo3-4/+29
We shouldn't be using "remove_linked_tree" to remove the lock file, since that function expects to receive a directory path as an argument. Also, as a further measure to avoid regression, this commit restores the "ignore_errors=True" argument on linux and adds a unit test checking that "remove_linked_tree" doesn't change file permissions as a side effect of a failure to remove.
2022-03-24Sherpa: add several new variants used by CMS (#29338)iarspider2-22/+85
2022-03-24vecgeom: fix install error when ~cuda (#29716)Valentin Volkl1-9/+11
2022-03-24PDC: add version 0.2 and branches (#29572)Jean Luca Bez1-1/+7
* Update package.py * Update package.py * Fixes on versions * Fix style * Remove code * Include latest version and removed code * Remove unecessary cmake dependency * Apply suggestions
2022-03-24environment.py: ensure view dir does not exist (#29641)Harmen Stoppels4-0/+101
2022-03-24Fix py-onnx-runtime recipe (#29646)iarspider2-11/+24
* Fix py-onnx-runtime recipe * Add missing dependencies * Update var/spack/repos/builtin/packages/py-cerberus/package.py Co-authored-by: Adam J. Stewart <ajstewart426@gmail.com> * Update package.py * Better fix for py-onnx-runtime Co-authored-by: Adam J. Stewart <ajstewart426@gmail.com>
2022-03-24omega-h: add v10.1.0 from fork (#29528)Cameron Smith1-0/+1
* omegah: v10.1.0 this version is from the SCOREC fork of Omega_h * prefix version with scorec Co-authored-by: Seth R. Johnson <johnsonsr@ornl.gov> Co-authored-by: Seth R. Johnson <johnsonsr@ornl.gov>
2022-03-24add_files_to_view: flip incorrect default (#29700)Harmen Stoppels4-4/+4
2022-03-24environment.py: concrete root specs to view (#29634)Harmen Stoppels1-5/+6
Slight simplification of the code: just pass the list of concrete root specs to the view
2022-03-24fix --reuse w/ upstreams in env (#29680)Harmen Stoppels1-3/+5
2022-03-24environment views: single pass view generation (#29443)Harmen Stoppels14-25/+950
Reduces the number of stat calls to a bare minimum: - Single pass over src prefixes - Handle projection clashes in memory Symlinked directories in the src prefixes are now conditionally transformed into directories with symlinks in the dst dir. Notably `intel-mkl`, `cuda` and `qt` has top-level symlinked directories that previously resulted in empty directories in the view. We now avoid cycles and possible exponential blowup by only expanding symlinks that: - point to dirs deeper in the folder structure; - are a fixed depth of 2.
2022-03-24environment.py: clean up broken views on failure (#29643)Harmen Stoppels2-13/+46
When view creation fails for some reason, remove it, so that the next time around it can start from scratch.
2022-03-23Update py-numpy dependency on Python to avoid build failures (#29682)Ralf Gommers1-6/+6
2022-03-23py-cffi: add compiler flags to fix build with clang (#29679)Valentin Volkl1-0/+10
* py-cffi: add compiler flags to fix build with clang For %clang@13.0.1, this avoids the ``` clang-13: warning: optimization flag '-ffat-lto-objects' is not supported [-Wignored-optimization-argument] ``` warning being turned into an error, and fixes this link error: ``` build/temp.linux-x86_64-3.10/c/_cffi_backend.o: file not recognized: file format not recognized ``` * style
2022-03-23environment: be more defensive when deleting roots for old views (#29636)Harmen Stoppels2-2/+19
Currently `old_root` is computed by reading the symlink at `self.root`. We should be more defensive in removing it by checking that it is in the same directory as the new root. Otherwise, in the worst case, when someone runs `spack env create --with-view=./view -d .` and `view` already exists and is a symlink to `/`, Spack effectively runs `rm -rf /`.
2022-03-23tetgen: add v1.5.1 and v1.6.0 (#29630)Ce Qin1-1/+3
2022-03-23python: drop dependency on `file` for script check (#29513)Harmen Stoppels4-4/+55
`file` was used to detect Python scripts with shebangs, so that the interpreter could be changed from <python prefix> to <view path>. With this change, we detect shebangs using Python instead, so that `file` is no longer required.
2022-03-23kahip: add v3.12, v3.13 and v3.14 (#29648)Matthew Archer1-2/+13
Co-authored-by: cleathart <c.leathart@hotmail.co.uk>
2022-03-23variorum: update package for CCE (#29656)luker1-0/+5
CCE needs additional compiler flags.
2022-03-23libgit2: add versions 1.2.0, 1.3.0, 1.4.0, 1.4.1, 1.4.2, 1.4.3 (#29675)eugeneswalker1-0/+5