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2021-06-22adding save of build times on install (#24350)Vanessasaurus7-44/+153
Here we are adding an install_times.json into the spack install metadata folder. We record a total, global time, along with the times for each phase. The type of phase or install start / end is included (e.g., build or fail) Signed-off-by: vsoch <vsoch@users.noreply.github.com> Co-authored-by: vsoch <vsoch@users.noreply.github.com>
2021-06-22py-beniget: add new package (#24439)Adam J. Stewart1-0/+19
2021-06-22py-gast: add v0.4.0 (#24437)Adam J. Stewart1-0/+1
2021-06-21hdf5: fix compiler detection in flag_handler (#24451)Paul Henning1-1/+1
The original implementation of `flag_handler` searched the `self.compiler.cc` string for `clang` or `gcc` in order to add a flag for those compilers. This approach fails when using a spack-installed compiler that was itself built with gcc or clang, as those strings will appear in the fully-qualified compiler executable paths. This commit switches to searching for `%gcc` or `%clang` in `self.spec`. Co-authored-by: Paul Henning <phenning@lanl.gov>
2021-06-21open mpi: remove preferred for 4.0.5 release (#24433)Howard Pritchard1-1/+1
the 4.1.1 release has fixes for problems that kept 4.1.0 from being the default open mpi version to build using spack. related to #24396 Signed-off-by: Howard Pritchard <hppritcha@gmail.com>
2021-06-21MAGMA: add patch to build with CUDA sm_37 (#24442)Adam J. Stewart2-0/+28
2021-06-22Axom: Remove blueos check on cuda variant (#24349)Chris White2-65/+68
* remove blueos check on cuda variant, fix typo * restore necessary compiler guard * remove axom+cuda from testing because it only partially works outside ppc systems
2021-06-21Fetching: git on Mac OS (#24247)Peter Scheibel4-6/+17
Extend the changes in #24163 to unit tests.
2021-06-19psimd: add new package (#24406)Adam J. Stewart1-0/+24
2021-06-19cpuinfo: add new versions (#24402)Adam J. Stewart1-0/+7
2021-06-19FP16: add new versions, prevent downloads (#24403)Adam J. Stewart1-4/+42
2021-06-19pthreadpool: add new versions (#24404)Adam J. Stewart1-0/+6
2021-06-19FXdiv: add new package (#24405)Adam J. Stewart1-0/+47
2021-06-19singularity: add v3.8.0 (#24407)snehring1-0/+1
2021-06-19Beast2: add v2.6.4 (#24410)Alec Scott1-1/+3
2021-06-19bedtools2: add v2.30.0 (#24412)Alec Scott1-1/+2
2021-06-19benchmark: add v1.5.5 (#24413)Alec Scott1-2/+3
2021-06-19Bismarck: add v0.23.0 (#24414)Alec Scott1-1/+2
2021-06-19cantera: add v2.5.1 (#24415)Alec Scott1-1/+3
2021-06-19coreset: add v1.09 (#24419)Alec Scott1-1/+2
2021-06-19diamond: add v2.0.9 (#24421)Alec Scott1-1/+3
2021-06-18reditools: update and add features (#24370)Glenn Johnson5-944/+236
This PR does the following: - adds version corresponding to commit at 08/03/2020 - adds missing get_DE_events.py script - adds dependencies needed by get_DE_events.py - removes REDItoolDenovo.py.patch and python2to3.patch in favor of running 2to3 and reindent pre-build - add batch_sort.patch to handle differences in string/char handling betweeen python2 and python3 - adds a variant for the Nature Protocol - adds dependencies for the nature_protocol variant - added myself as maintainer This PR adds a new version of reditools from git.
2021-06-18Add LIKWID 5.2.0 and a patch for LIKWID 5.1.0 (#24399)Thomas Gruber1-3/+27
2021-06-18abi-dumper: add v1.2 (#24392)Alec Scott1-3/+4
2021-06-18SLATE: Add e4s testsuite-inspired smoke test (#23376)Sergei Shudler1-0/+28
2021-06-18Heffte: Add e4s testsuite-inspired smoke test (#23652)Sergei Shudler1-0/+61
2021-06-18Removed unofficial MAGMA release and enabled MAGMA in e4s (#24400)G-Ragghianti3-31/+2
2021-06-18spla: add version 1.5.0 and fix compilation with amdblis (#24374)Simon Frasch2-0/+18
2021-06-18Checksum update for NAGCompiler download , Version 7.0 (Build 7048) (#24360)Themos Tsikas1-1/+1
2021-06-18petsc, petsc4py: add version 3.15.1 (#24397)Satish Balay2-0/+2
2021-06-18double-conversion: New versions 3.1.5, 2.0.2 (#24385)Erik Schnetter1-0/+2
A version 2.0.3 is also advertised, but doesn't download.
2021-06-18Fixes for opencv (#24361)Glenn Johnson2-4/+28
This PR fixes a couple of issues with the opencv package, mostly in relation to cuda. This is only focused on cuda, not any of the other variants. - Added versions to the contrib_vers list. Added for all that can be retrieved from github. The one for the latest version was missing. - Added a cmake patch for v3.2.0. - Deprecated versions 3.1.0 and 3.2.0 as neither of those could be built, with or without cuda. - Adjusted constraints on applying initial cmake patch. - Added cudnn dependency when +cuda. - Set constraints for cudnn and cuda for older versions of opencv.
2021-06-18Add an audit system to Spack (#23053)Massimiliano Culpo6-1/+652
Add a new "spack audit" command. This command can check for issues with configuration or with packages and is intended to help a user debug a failed Spack build. In some cases the reported issues are always errors but are too costly to check for (e.g. packages that specify missing variants on dependencies). In other cases the issues may be legitimate but uncommon usage of Spack and we want to be sure the user intended the behavior (e.g. duplicate compiler definitions). Audits are grouped by theme, and for now the two themes are packages and configuration. For example you can run all available audits on packages with "spack audit packages". It is intended that in the future users will be able to define their own audits. The package audits are good candidates for running in package_sanity (i.e. they could catch bugs in user-submitted packages before they are merged) but that is left for a later PR.
2021-06-18FBGEMM: GCC 5+ and AVX2 required (#24356)Adam J. Stewart1-0/+8
2021-06-18Disable magma in the E4S pipeline (#24395)Massimiliano Culpo1-1/+1
Building magma has been failing consistently and is currently blocking PRs from being merged. Disable that spec while we investigate the failure and work on a fix.
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>