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2022-10-18intel-oneapi-compilers: do not pass -Wno-unused-command-line-argument to icc ↵Robert Cohn1-27/+21
+ refactor (#33389)
2022-10-18go,gcc: Support external go compilers for Go bootstrap (#27769)Bernhard Kaindl3-10/+54
For ARM64, fallback to gccgo. (go-bootstrap@1.4 can't support ARM64)
2022-10-18papi: fix for Intel OneAPI compiler (#33225)Howard Pritchard1-0/+5
Without this patch one hits this error trying to compiler papi with Intel OneAPI: icx: error: Note that use of '-g' without any optimization-level option will turn off most compiler optimizations similar to use of '-O0' [-Werror,-Wdebug-disables-optimization] Signed-off-by: Howard Pritchard <howardp@lanl.gov> Signed-off-by: Howard Pritchard <howardp@lanl.gov>
2022-10-18vsearch: add v2.22.1 (#33327)snehring1-0/+4
2022-10-18mothur: add v1.48.0 and variants (#33326)snehring1-20/+63
2022-10-18intel-oneapi-compilers: fix Python 2.7 compliance (#33383)Massimiliano Culpo1-2/+2
2022-10-17py-fiona: add v1.8.22 (#33372)Adam J. Stewart1-1/+2
2022-10-17lz4: add 1.9.4 (#33334)Michael Kuhn1-0/+1
2022-10-17Bugfix HIP and aluminum rocm build (#33344)Brian Van Essen2-7/+31
* Fixed two bugs in the HIP package recipe. The first is that the HIP_PATH was being set to the actual spec, and not the spec prefix. The second bug is that HIP is expected to be in /opt/rocm-x.y.z/hip but it's libraries can exist at both /opt/rocm-x.y.z/hip/lib and /opt/rocm-x.y.z/lib. This means that the external detection logic may find it in either and it turns out that some modules only expose one of those two locations. Logic is added to ensure that the internal HIP_PATH and associated ROCM_PATH are correctly set in both cases. * Added support for Aluminum to use the libfabric plugin with either RCCL or NCCL.
2022-10-17grid: reference `fftw-api` instead of `fftw` (#33374)Mosè Giordano1-1/+1
This makes it possible to compile with, e.g., `cray-fftw`, not just `fftw`.
2022-10-17New packages: libbigwig, methyldackel (#33273)snehring2-0/+66
* libbigwig: adding new package libbigwig * methyldackel: adding new package methyldackel * libbigwig: tighten up curl variant
2022-10-17Initial contribution of LibPressio ecosystem (#32630)Robert Underwood34-26/+1408
* Add libpressio and dependencies; some of these packages are maintained as forks of the original repositories and in those cases the docstring mentions this. * Add optional dependency in adios2 on libpressio * cub package: set CUB_DIR environment variable for dependent installations * Clear R_HOME/R_ENVIRON before Spack installation (avoid sources outside of Spack from affecting the installation in Spack) * Rename dlib to dorian3d-dlib and update dependents; add new dlib implementation. Pending an official policy on how to handle packages with short names, reviewer unilaterally decided that the rename was acceptable given that the new Spack dlib package is referenced more widely (by orders of magnitude) than the original Co-authored-by: Samuel Li <shaomeng@users.noreply.github.com>
2022-10-17py-xopen: version bump to 1.6.0 (#33231)Luke Diorio-Toth2-1/+28
* version bump to 1.6.0 * added py-isal, updated URL
2022-10-17Classic Intel compilers do not support gcc-toolchain (#33281)Stephen Sachs1-15/+26
* Classic Intel compilers do not support gcc-toolchain This fix removes `--gcc-toolchain=` from the ~.fcg` files for the classic Intel compilers. AFAIK this option is only supported for Clang based compilers. This lead to an issue when installing cmake. Reproducer: ``` spack install cmake@3.24.2%intel@2021.7.0~doc+ncurses+ownlibs~qt build_type=Release arch=linux-amzn2-skylake_avx512 ``` Tagging maintainer @rscohn2 * Add `-gcc-name` for icc .. and `-gxx-name` for icpc. AFAIK this is used for modern C++ support, so we can ignore `ifort`. Co-authored-by: Stephen Sachs <stesachs@amazon.com>
2022-10-17py-horovod: add v0.26 (#33311)Adam J. Stewart2-0/+6
* py-horovod: add v0.26 * py-petastorm: add v0.12.0
2022-10-17GnuPG: add v2.3.8 and update stack (#33368)Massimiliano Culpo6-1/+12
2022-10-17Add checksum for py-ipykernel 6.15.2 (#33360)iarspider1-0/+1
2022-10-17Add checksum for py-secretstorage 3.3.3 (#33366)iarspider1-0/+1
2022-10-17python: add 3.10.7, 3.9.14, 3.8.14, 3.7.14 (#32623)Carlos Bederián1-2/+6
2022-10-17hypre 2.26.0 (#33299)Rui Peng Li1-0/+1
2022-10-17Add checksum for py-prompt-toolkit 3.0.31 (#33362)iarspider1-0/+1
2022-10-17Add checksum for py-grpcio-tools 1.48.1 (#33358)iarspider1-2/+5
2022-10-17Add checksum for py-astroid 2.12.7, py-astroid 2.12.10, py-setuptools ↵iarspider4-30/+46
62.6.0, py-wrapt 1.14.1, py-pylint 2.15.0 (#32976) * Add checksum for py-astroid 2.12.7, py-setuptools 62.6.0 * Also add checksum for py-wrapt * Update package.py * Update package.py (#57) * Update package.py * Update package.py * Update package.py
2022-10-17py-jupyterlab-pygments: install from wheel to avoid cyclic dependency (#33278)iarspider1-7/+21
* py-jupyterlab-pygments: avoid cyclic dependency * Fix style * Update package.py * Update package.py * [@spackbot] updating style on behalf of iarspider * Update package.py * Flake-8 * fix Co-authored-by: iarspider <iarspider@users.noreply.github.com>
2022-10-17py-numpy: add v1.23.4 (#33260)Adam J. Stewart1-0/+1
2022-10-17Add checksum for py-sniffio 1.3.0 (#32975)iarspider1-0/+2
2022-10-17py-tensorflow-hub: zlib, again. (#33359)Harmen Stoppels2-5/+31
2022-10-17mariadb-c-client: add 3.3.2, 3.2.7, 3.1.18, 3.0.10 (#33335)Michael Kuhn1-0/+4
2022-10-17sdl2: add v2.0.22 and v2.24.1 (#33351)Wouter Deconinck1-0/+4
2022-10-17nextflow: add v20.10.0 (#33354)Diego Alvarez1-0/+5
2022-10-17libblastrampoline: Add versions 5.1.1, 5.2.0 (#33352)Mosè Giordano1-0/+2
2022-10-17py-setuptools: add v65.5.0 (#33353)Adam J. Stewart1-0/+5
2022-10-16py-sphinx: add v5.3 and v5.2 (#33356)Adam J. Stewart1-0/+4
2022-10-16octopus: upgrade to 12.1 (#33343)Hans Fangohr1-0/+1
2022-10-16tasmanian: disable openmp by default (#33345)Miroslav Stoyanov1-2/+1
2022-10-16py-meson-python: add new versions (#33294)Adam J. Stewart1-1/+10
2022-10-16py-tensorflow: fix zlib (#33349)Harmen Stoppels2-1/+16
* py-tensorflow: fix zlib * [@spackbot] updating style on behalf of haampie Co-authored-by: haampie <haampie@users.noreply.github.com>
2022-10-16meson: update OneAPI compiler support patch (#33293)Adam J. Stewart2-6/+163
2022-10-15Add checksum for py-seaborn 0.12.0 (#33145)iarspider1-5/+19
* Add checksum for py-seaborn 0.12.0 * Update package.py * Update package.py * [@spackbot] updating style on behalf of iarspider * Update package.py Co-authored-by: iarspider <iarspider@users.noreply.github.com>
2022-10-14rocksdb: add 7.7.3 (#33341)Michael Kuhn1-0/+1
2022-10-14glib: add 2.74.0 and 2.72.4 (#33332)Michael Kuhn1-2/+6
2022-10-14gptl: new version 8.1.1; use the correct mpi fortran compiler (#33235)WuK1-0/+5
* gptl: new version 8.1.1; use the correct `mpifc` * add `F90` and `$F77`
2022-10-14seacas: update to latest release (#33330)Greg Sjaardema1-0/+3
Add checksum for latest tag/release
2022-10-14ninja: New version 1.11.1 (#33215)Erik Schnetter1-0/+1
2022-10-14Add checksum for py-oauthlib 3.2.1 (#33201)iarspider1-2/+21
* Add checksum for py-oauthlib 3.2.1 * Update package.py * [@spackbot] updating style on behalf of iarspider * Update package.py * Update package.py Co-authored-by: iarspider <iarspider@users.noreply.github.com>
2022-10-14py-libensemble: updating package for v0.9.3 (#33298)John-Luke Navarro1-5/+3
* commit updating py-libensemble package for 0.9.3 * removed commented-out lines
2022-10-14 petsc,py-petsc4py,slepc,py-slepc4py: add version 3.18.0 (#32938)Satish Balay7-1/+94
* petsc,py-petsc4py,slepc,py-slepc4py: add version 3.18.0 * workaround for dealii build failure [with petsc version check] * pism: add compatibility fix to for petsc@3.18 * add in hipsolver dependency
2022-10-14hip@5.2.0 onwards: set prefix properly (#33257)eugeneswalker1-4/+6
* hip-set-prefix-rocm5.2.0-onwards * Update var/spack/repos/builtin/packages/hip/package.py Update description Co-authored-by: Satish Balay <balay@mcs.anl.gov>
2022-10-14Fix pika@0.9.0 sha (#33307)Auriane R1-1/+1
2022-10-13UPC++/GASNet-EX 2022.9.0 update (#33277)Dan Bonachea2-4/+10
* gasnet: Add new release hash * upcxx: Add new release hash * gasnet: misc updates * upcxx: misc updates
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