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2021-06-17gsl package: update patch for later version (#22968)Glenn Johnson2-0/+324
Old patch is still provided for older versions.
2021-06-17oneAPI compiler: update openmp flag (#23771)Frank Willmore2-2/+2
2021-06-17Adding support for spack monitor with containerize (#23777)Vanessasaurus9-4/+420
This should get us most of the way there to support using monitor during a spack container build, for both Singularity and Docker. Some quick notes: ### Docker Docker works by way of BUILDKIT and being able to specify --secret. What this means is that you can prefix a line with a mount of type secret as follows: ```bash # Install the software, remove unnecessary deps RUN --mount=type=secret,id=su --mount=type=secret,id=st cd /opt/spack-environment && spack env activate . && export SPACKMON_USER=$(cat /run/secrets/su) && export SPACKMON_TOKEN=$(cat /run/secrets/st) && spack install --monitor --fail-fast && spack gc -y ``` Where the id for one or more secrets corresponds to the file mounted at `/run/secrets/<name>`. So, for example, to build this container with su (spackmon user) and sv (spackmon token) defined I would export them on my host and do: ```bash $ DOCKER_BUILDKIT=1 docker build --network="host" --secret id=st,env=SPACKMON_TOKEN --secret id=su,env=SPACKMON_USER -t spack/container . ``` And when we add `env` to the secret definition that tells the build to look for the secret with id "st" in the environment variable `SPACKMON_TOKEN` for example. If the user is building locally with a local spack monitor, we also need to set the `--network` to be the host, otherwise you can't connect to it (a la isolation of course.) ## Singularity Singularity doesn't have as nice an ability to clearly specify secrets, so (hoping this eventually gets implemented) what I'm doing now is providing the user instructions to write the credentials to a file, add it to the container to source, and remove when done. ## Tags Note that the tags PR https://github.com/spack/spack/pull/23712 will need to be merged before `--monitor-tags` will actually work because I'm checking for the attribute (that doesn't exist yet): ```bash "tags": getattr(args, "monitor_tags", None) ``` So when that PR is merged to update the argument group, it will work here, and I can either update the PR here to not check if the attribute is there (it will be) or open another one in the case this PR is already merged. Finally, I added a bunch of documetation for how to use monitor with containerize. I say "mostly working" because I can't do a full test run with this new version until the container base is built with the updated spack (the request to the monitor server for an env install was missing so I had to add it here). Signed-off-by: vsoch <vsoch@users.noreply.github.com> Co-authored-by: vsoch <vsoch@users.noreply.github.com>
2021-06-17e4s ci env: package preferences: use newer versions (#24371)eugeneswalker1-14/+14
2021-06-17vtk: Limit freetype versions (#24389)Erik Schnetter1-0/+3
freetype 2.0.3 introduces an incompatible change Co-authored-by: Tamara Dahlgren <35777542+tldahlgren@users.noreply.github.com>
2021-06-17gloo: add +cuda variant (#24390)Adam J. Stewart1-1/+4
2021-06-17hwloc: New version 2.5.0 (#24387)Erik Schnetter1-0/+1
2021-06-17freetype: Add version 2.0.2 (#24386)Erik Schnetter1-0/+1
2021-06-17codecov: disable inline annotations on PRs (#24362)Todd Gamblin1-0/+5
Inline codecov annotations make the code hard to read, and they add annotations in files that seemingly have nothing to do with the PR. Sadly, they add a whole lot of noise and not a lot of benefit over looking at the PR on codecov. We should just have people look at the coverage on codecov itself.
2021-06-17MAGMA: add v2.6.0, sm_37 support (#24383)Adam J. Stewart2-0/+29
2021-06-17ONNX: add new package (#24384)Adam J. Stewart1-0/+26
2021-06-17arm-forge: add v21.0.2 and variant to detect PMU counters (#24298)Nick Forrington1-3/+14
2021-06-17Fix an issue where cray module files may not have CRAY_MPICH_DIR set (#24267)Harmen Stoppels1-0/+7
2021-06-17vtk: patch to replace use of FT_CALLBACK_DEF (#24238)Tom Payerle1-0/+6
2021-06-17New package: py-pyusb (#23733)Andreas Baumbach1-0/+20
* New package: py-pyusb Change-Id: I606127858b961b5841c60befc5a8353df0f9f38c * fixup dependencies Change-Id: I0c9b0ccee693d2c4e847717950d4ce64cb319794 * fixup 2 Change-Id: Ibaccbdafd865e363564f491054e4e4ceb778727b * Update var/spack/repos/builtin/packages/py-pyusb/package.py Co-authored-by: Adam J. Stewart <ajstewart426@gmail.com> Co-authored-by: Adam J. Stewart <ajstewart426@gmail.com>
2021-06-17Break llvm-amdgpu circular dependency with rocm-device-libs (#23859)Harmen Stoppels38-335/+349
2021-06-17add -fallow-argument-mismatch flag for gcc10 (#24354)Anton Kozhevnikov1-0/+5
2021-06-17ci: add all locally computed hashes as job variables (#24359)Scott Wittenburg1-4/+9
2021-06-17New package: py-pyscreeze (#24251)Jen Herting1-0/+23
* [py-pyscreeze] created template * [py-pyscreeze] added dependencies * [py-pyscreeze] depends on scrot * [py-pyscreeze] Final cleanup - added homepage - added description - removed fixmes * [py-pyscreeze] using pil provider
2021-06-17open mpi: add v4.0.6 and fix a bug (#24344)Howard Pritchard1-1/+2
A patch no longer applies cleanly as its fixed in v4.0.6 - fix it here ==> Installing openmpi-4.0.6-in47f6rxspbnyibkdx6x4ekg6piujobd ==> No binary for openmpi-4.0.6-in47f6rxspbnyibkdx6x4ekg6piujobd found: installing from source ==> Fetching https://download.open-mpi.org/release/open-mpi/v4.0/openmpi-4.0.6.tar.bz2 Reversed (or previously applied) patch detected! Assume -R? [n] Apply anyway? [n] 2 out of 2 hunks ignored -- saving rejects to file opal/include/opal/sys/gcc_builtin/atomic.h.rej Signed-off-by: Howard Pritchard <howardp@lanl.gov>
2021-06-17Unset LD_PRELOAD and DYLD_INSERT_LIBRARIES (#24177)Harmen Stoppels1-0/+4
When running executables from build dependencies, we want to avoid that `LD_PRELOAD` and `DYLD_INSERT_LIBRARIES` any of their shared libs build by spack with system libraries.
2021-06-17nss: add nssutil3 library to pkg-config (#24364)Manuela Kuhn1-1/+1
This is needed for qt+webkit to build correctly. As reference the debian package was taken: https://salsa.debian.org/mozilla-team/nss/-/blob/master/debian/nss.pc.in
2021-06-17bowtie2: add constraints for the simde dependency (#24226)snehring1-6/+9
2021-06-17hiop: add v0.4.4, use commits for tags (#24365)Asher Mancinelli1-9/+12
2021-06-17NNPACK: add new package (#24333)Adam J. Stewart1-0/+118
2021-06-16py-peachpy: add new package (#24373)Adam J. Stewart1-0/+20
2021-06-17py-opcodes: add new package (#24372)Adam J. Stewart1-0/+17
2021-06-17z3: update package to use CMake build system (#24337)John Jolly1-24/+13
The Z3 solver provides a Z3Config.cmake file when built using the CMake build system. This submission changes the package build system to inherit the CMakePackage type. In addition to changing the build system, this submission: - Adds the GMP variant - Removes v4.4.0 and v4.4.1 as CMake was implemented starting with v4.5.0
2021-06-16TensorPipe: add new package (#24335)Adam J. Stewart1-0/+26
* TensorPipe: add new package * Add libuv dependency * Add min supported version of libuv
2021-06-16XNNPACK: add new package (#24334)Adam J. Stewart1-0/+104
* XNNPACK: add new package * XNNPACK: add resources
2021-06-16gloo: add py-torch submodule commits (#24330)Adam J. Stewart1-1/+16
* gloo: add py-torch submodule commits * gloo: add new version * gloo: add master branch * gloo: use Ninja generator
2021-06-16openssl: architecture check is now based on spec target (#24228)OliverPerks1-2/+1
2021-06-16eigen: fix build with nvhpc (#24253)Nicolas Cornu1-0/+4
2021-06-16kineto: add new package (#24319)Adam J. Stewart1-0/+28
2021-06-16FBGEMM: add new package (#24318)Adam J. Stewart1-0/+38
2021-06-16Dyninst: add v11.0.1 (#24322)Tim Haines1-0/+1
2021-06-16Set r-chipseq to bioconductor format (#24315)Glenn Johnson1-3/+5
- added description - converted to git from url - set commit rather than sha256
2021-06-16QNNPACK: add py-torch submodule commits (#24329)Adam J. Stewart1-14/+21
2021-06-16ParFlow: add new package (#24331)Steven Smith1-0/+81
2021-06-16r-effects: new package (#24342)Glenn Johnson1-0/+27
2021-06-16kaldi: fix building with mkl (#24338)archxlith1-1/+1
2021-06-16openfst: add v1.7.3 (#24339)archxlith1-0/+1
It's the highest version allowed in kaldi package
2021-06-16openmolcas: add v21.02, add mpi variant (#24343)snehring1-2/+21
2021-06-16cpuinfo: prevent downloads during build (#24345)Adam J. Stewart1-1/+29
2021-06-16pthreadpool: more specific resource destination (#24346)Adam J. Stewart1-6/+12
2021-06-15p4est: add v2.3.2 (#24311)Marc Fehling1-1/+2
2021-06-15openPMD-api: Build with Legacy API (#24341)Axel Huebl2-18/+34
Allow to build with `^hdf5@1.12.0 api=v110` and `v18`.
2021-06-15e4s ci: specs: add datatransferkit (#24325)eugeneswalker1-0/+1
2021-06-15add irep and lua-lang virtual dependency (#22492)Richarda Butler4-0/+50
This adds a package for `irep`, a tool for reading `lua` input decks from Fortran, C, and C++. `irep` can be built with either `lua` or `luajit`. To address this, we also add a virtual package for lua called `lua-lang`. `luajit` isn't, by default, a drop-in replacement for `lua`, but we add a `+lualinks` variant to it that adds symlinks that make it behave like `lua@5.1`. With this variant enabled, it provides the `lua-lang` virtual. `lua` always provides `lua-lang`. - [x] add `irep` package - [x] add `+lualinks` variant to `lua-luajit` - [x] create `lua-lang` virtual, provided by `lua` and `luajit+lualinks` Co-authored-by: Kayla Richarda Butler <butler59@quartz1148.llnl.gov> Co-authored-by: Todd Gamblin <tgamblin@llnl.gov>
2021-06-15cairo: fix gtkdocize patch (#24332)Seth R. Johnson1-3/+3
Patch in #23971 was not correct