Commit graph

21179 commits

Author SHA1 Message Date
Alexander Baumgarten
c0486f6768
Feature/r tximportdata (#19902)
* # FIXME: Add a list of GitHub accounts to
    # FIXME: Add a list of GitHub accounts to
Package for r-tximportData

* Fixed file format / flake8 errors
2020-11-13 14:14:36 -06:00
fodinabor
472c365b58
binutils: Fix checksum for 2.35.1 (#19901)
As noted in #19899 and introduced by #19827
2020-11-13 12:55:58 -06:00
Thomas Madlener
d5b89b422d
Add sio and add it as possible dependency for podio (#19875)
Newest podio can use SIO as backend
2020-11-13 12:43:43 -06:00
arjun-raj-kuppala
fbde1abc8c
AMD ROCm - HIP update and bump up version to 3.9.0 for rccl,debug agent, hip-rocclr and atmi (#19832)
* AMD - Bumped up version for hip-rocclr, rocm-opencl, rocm-smi-lib

* AMD ROCm - HIP update and bump up version to 3.9.0 for rccl,debug agent, hip-rocclr and atmi

* Update package.py

* Update package.py

* Update package.py

* Update var/spack/repos/builtin/packages/hip/package.py

Co-authored-by: Adam J. Stewart <ajstewart426@gmail.com>

Co-authored-by: Adam J. Stewart <ajstewart426@gmail.com>
2020-11-13 12:25:57 -06:00
eugeneswalker
3a3bf5387e
suite-sparse: mpfr, gmp needed for @5.8.0: (#19898) 2020-11-13 10:12:02 -08:00
Sreenivasa Murthy Kolam
b08744566d
bump up version for 3.9.0 (#19894) 2020-11-13 10:59:18 -06:00
t-nojiri
d2673ac56c
openfoam: Fix for aarch64 (#19803)
* openfoam: Fix for aarch64

* openfoam: Add comment for openfoam-org
2020-11-13 10:45:42 -06:00
Ganesh Kumar
d40a35e8d7
ROCm 3.9 Stage2 recipe (#19838)
Co-authored-by: root <root@mlseqa-hyd-virt-srv-07.amd.com>
2020-11-12 23:04:19 -06:00
Joseph Schoonover
d346e877ef
Add feq-parse package (#19891)
Co-authored-by: Joe Schoonover <joe@fluidnumerics.com>
2020-11-12 22:31:04 -06:00
Tim Haines
a1e9d584e1
binutils: add version 2.35.1 (#19827) 2020-11-12 19:05:24 -06:00
Greg Becker
fafff0c6c0
move sbang to unpadded install tree root (#19640)
Since #11598 sbang has been installed within the install_tree. This doesn’t play
nicely with install_tree padding, since sbang can’t do its job if it is installed in a
long path (this is the whole point of sbang).

This PR changes the padding specification.  Instead of $padding inside paths,
we now have a separate `padding:` field in the `install_tree` configuration.

Previously, the `install_tree` looked like this:

```
    /path/to/opt/spack_padding_padding_padding_padding_padding/
        bin/
            sbang
        .spack-db/
            ...
        linux-rhel7-x86_64/
            ...
```

```
This PR updates things to look like this:

    /path/to/opt/
        bin/
            sbang
        spack_padding_padding_padding_padding_padding/
            .spack-db/
                ...
            linux-rhel7-x86_64/
                ...

So padding is added at the start of all install prefixes *within* the unpadded
root.  The database and all installations still go under the padded root.

This ensures that `sbang` is in the shorted possible path while also allowing
us to make long paths for relocatable binaries.
2020-11-12 16:08:55 -08:00
Peter Scheibel
32bfe0a001
Testing: ensure that all packages can be pickled (#19890)
As of #18205, all packages must be pickle-able to be installed by
Spack.

This adds a test to check that each package can be pickled. If any
package fails to pickle, the test keeps going and collects the names
of all failed packages; it then takes the first one that failed and
attempts to re-pickle it, generating the full stack trace for the
failed pickle attempt.
2020-11-12 15:55:34 -08:00
Peter Scheibel
ca3b912703
run unit tests on 3.8 only for Mac OS vs. both 3.8 and 3.9 (#19889) 2020-11-12 13:22:41 -08:00
Robert Blake
aeafe18b49
openmpi: external detection support (#18600) 2020-11-12 13:03:35 -08:00
Adam J. Stewart
02281a891d
MavenPackage: allow additional build args (#19676) 2020-11-12 12:57:49 -08:00
Adam J. Stewart
f46bd411f4
py-cython: python is a link dep (#19768) 2020-11-12 12:53:13 -08:00
Adam J. Stewart
2fc2a4cd2a
py-matplotlib: set LIBRARY_PATH to locate link deps (#19855)
* py-matplotlib: set LIBRARY_PATH to locate link deps

* py-matplotlib: add v3.3.3
2020-11-12 12:50:44 -08:00
Adam J. Stewart
37e51eb2a5
OpenSSL: libs may be in lib64 directory (#19862) 2020-11-12 12:45:45 -08:00
vvolkl
72e66bd01f
[gaudi] v35r0 (#19878)
* [gaudi] v35r0

* [gaudi] format

* [gaudi] comments from #19878
2020-11-12 14:43:06 -06:00
tcojean
978e85d669
Add smoke tests to Ginkgo. (#19888) 2020-11-12 14:42:34 -06:00
Peter Scheibel
bb42470211
macos: update build process to use spawn instead of fork (#18205)
Spack creates a separate process to do package installation. Different
operating systems and Python versions use different methods to create
it but up until Python 3.8 both Linux and Mac OS used "fork" (which
duplicates process memory, file descriptor table, etc.).

Python >= 3.8 on Mac OS prefers creating an entirely new process
(referred to as the "spawn" start method) because "fork" was found to
cause issues (in other words "spawn" is the default start method used
by multiprocessing.Process). Spack was dependent on the particular
behavior of fork to replicate process memory and transmit file
descriptors.

This PR refactors the Spack internals to support starting a child
process with the "spawn" method. To achieve this, it makes the
following changes:

- ensure that the package repository and other global state are
  transmitted to the child process
- ensure that file descriptors are transmitted to the child process in
  a way that works with multiprocessing and spawn
- make all the state needed for the build process and tests picklable
  (package, stage, etc.)
- move a number of locally-defined functions into global scope so that
  they can be pickled
- rework tests where needed to avoid using local functions

This PR also reworks sbang tests to work on macOS, where temporary
directories are deeper than the Linux sbang limit. We make the limit
platform-dependent (macOS supports 512-character shebangs)

See: #14102
2020-11-12 12:26:23 -08:00
eugeneswalker
81cab3b271
suite-sparse: add deps: mpfr, gmp (#19883) 2020-11-12 11:29:07 -08:00
Morten Kristensen
8cf2806f00
py-vermin: add latest version 1.0.3 (#19886) 2020-11-12 13:23:38 -06:00
Wouter Deconinck
b0d2586f52
[acts] conflicts with %gcc@:7 since @0.23: due to c++17 <charconv> (#19881) 2020-11-12 13:08:12 -06:00
Scott Wittenburg
fbbd71d3d7
Pipelines: Compare target family instead of architecture (#19884)
In compiler bootstrapping pipelines, we add an artificial dependency
between jobs for packages to be built with a bootstrapped compiler
and the job building the compiler.  To find the right bootstrapped
compiler for each spec, we compared not only the compiler spec to
that required by the package spec, but also the architectures of
the compiler and package spec.

But this prevented us from finding the bootstrapped compiler for a
spec in cases where the architecture of the compiler wasn't exactly
the same as the spec.  For example, a gcc@4.8.5 might have 
bootstrapped a compiler with haswell as the architecture, while the 
spec had broadwell.  By comparing the families instead of the architecture
 itself, we know that we can build the zlib for broadwell with the gcc for 
haswell.
2020-11-12 10:46:15 -08:00
Brian Spilner
2a8dba48da
new release: cdo-1.9.9 (#19876) 2020-11-12 11:29:57 -06:00
t-nojiri
301b94d338
elpa: Fix for aarch64 (#19872) 2020-11-12 11:24:45 -06:00
Satish Balay
757b74aeff
xsdk@0.6.0 (#19846)
Update:
 hypre@2.20.0
 mfem@4.2.0
 superlu-dist@6.4.0
 trilinos@13.0.1
 datatransferkit@3.1-rc2
 petsc@3.14.1
 dealii@9.2.0
 pflotran@xsdk-0.6.0
 alquimia@xsdk-0.6.0
 sundials@5.5.0
 plasma@20.9.20
 magma@2.5.4
 amrex@20.10
 slepc@3.14.0
 omega-h@9.32.5
 strumpack@5.0.0
 pumi@2.2.5
 tasmanian@7.3
 phist@1.9.3
 ginkgo@1.3.0
 py-libensemble@0.7.1
 precice@2.1.1
 butterflypack@1.2.1

New:
 heffte@2.0.0
 slate@2020.10.00

Variants:
 datatransferkit
 heffte
 slate

petsc: enable +cuda
sundials: enable +cuda +trilinos
strumpack: enable +cuda
2020-11-12 11:15:29 -06:00
Desmond
9f7ad82665
Package/r bigalgebra (#19826)
* py-json-get: new package at 1.1.1

* py-json-get: new package at 1.1.1

* r-bigalgebra: new package at 0.8.4

* r-bigalgebra: new package at 0.8.4 with corrections

* Added an additional change to tarball and dependencies

* removing accidentally added file

* Added tarball that uses mirror and removed redundant dependencies

* Fixed version and added dep.

* Updated checksum

* Fixed urls

* Added list_url

Co-authored-by: las_djorton <las_djorton@build.las.iastate.edu>
2020-11-12 11:13:20 -06:00
Pieter Ghysels
d1493fb3d8
SuperLU-Dist: Add CUDA variant (#19847)
* Add CUDA support to superlu-dist

* Use spec['cuda'].libs.directories[0] iso spec['cuda'].prefix.lib
so it works for both lib and lib64

The suggested:
args.append('-DTPL_CUDA_LIBRARIES=' +
            spec['cuda'].libs.ld_flags)
did not work because it does not link with cuBLAS.
2020-11-12 08:57:44 -06:00
Jean-Paul Pelteret
821b195ba4
Fix scalapack build error (#19824) 2020-11-12 08:55:58 -06:00
Satish Balay
a99cc0fac0
kokkos add "graviton" to spack_micro_arch_map (#19869)
* kokkos add "graviton" to spack_micro_arch_map

* also add "graviton2"
2020-11-12 08:55:37 -06:00
Greg Becker
527a81b469
Keep output machine readable using spack find --format in an env (#19698)
Currently, full JSON output is the only machine readable option for `spack find`
in an environment.

`spack find --format` is also designed to be machine readable, but we print extra
headers in environments.

-[x] don't print headers in `spack find` output when in an environment
2020-11-11 22:13:51 -08:00
Dr. Christian Tacke
b9f20c2351
yaml-cpp: Improve shared library building (#19866)
* No version of yaml-cpp in spack can build shared AND
  static libraries at the same time.  So drop the "static"
  variant and let "shared" handle that alone.

  Or in other words: No version handles the
  BUILD_STATIC_LIBS flag.

* The flag for building shared libraries changed from
  BUILD_SHARED_LIBS to YAML_BUILD_SHARED_LIBS at some
  point. So just pass both flags.

* Use the newer define_from_variant.
2020-11-11 20:05:58 -06:00
Satish Balay
33469414a5
fix typo wrt target=graviton (#19865)
* fix typo wrt target=graviton

This fixes spack build on aarch64 box

* update archspec hash
2020-11-11 19:29:13 -06:00
Massimiliano Culpo
e80276cd14
spack env deactivate/spack unload: demote warning message to debug message (#19864) 2020-11-11 12:02:03 -08:00
Dr. Christian Tacke
2929f59c03
msgpack-c: Add Version 3.1.1 (#19863) 2020-11-11 12:27:28 -06:00
Jen Herting
3dab441986
New package: py-cuml (#19474)
* [py-cuml] created template

* [py-cuml] setup phases and added build_directory

* [py-cuml] added dependencies

* [py-cuml] depends on libcumlprims

* [py-cuml] requiring multigpu version

* [py-cuml] figuring out the best way to get concretization to happen cleanly

* [py-cuml] removed singlegpu variat from libcuml

* [py-cuml] depends on py-cudf

* [py-cuml] depends on cupy

* [py-cuml] fixed typoo

* [py-cuml] depends on py-scipy

* [py-cuml] depends on py-treelite

* [py-cuml] py-treelite is now a variant of treelite

* [py-cuml] depends on joblib

* [py-cuml] depends on py-scikit-learn

* [py-cuml] flake8

* [py-cuml] added homepage and description. removed fixmes

* [py-cuml] updated checksum
2020-11-11 12:27:12 -06:00
Adam J. Stewart
d1ca322aef
Restore spack checksum verbosity (#19480) 2020-11-11 11:26:17 -06:00
Filippo Spiga
e828641d80
Adding support to build ucx development branch (#18089)
* Enabling build of v1.9.x development branch.

* v1.8.1 is the preferred (stable) version.

* Fixing code style

Co-authored-by: Filippo Spiga <fspiga@nvidia.com>
Co-authored-by: Adam J. Stewart <ajstewart426@gmail.com>
2020-11-11 10:58:29 -06:00
Jen Herting
b660a2112f
New package: libcuml (#19471)
* [libcuml] created template

* [libcuml] set cmake list dir

* [libcuml] added some dependencies

* [libcuml] adding some default cmake args

* [libcuml] depends on nccl

* [libcuml] temporarily disabling cuml prims building

* [libcuml] building internal faiss?

* [libcuml] added dependency treelite

* [libcuml] depends on google_test

* [libcuml] forcing single gpu per: https://github.com/rapidsai/cuml/issues/2528#issuecomment-657675957

* [libcuml] added prims?

* [libcuml] adding libcumlcomms ?

* Revert "[libcuml] adding libcumlcomms ?"

This reverts commit 0e0765b7d4d27bdc01d54d24e8c2f9eac1cb4eb2.

* Revert "[libcuml] added prims?"

This reverts commit d0b1f868ea5e425cc7d1a5ce7adc642258dfc38e.

* [libcuml] added varient single gpu

* [libcuml] removed variant singlegpu

* [libcuml] added homepage and description. removed fixmes

* [libcuml] flake8

* [libcuml] cleaning up leftover commented out code

* [libcuml] updated checksum added ucx dependency
2020-11-11 10:55:57 -06:00
Sreenivasa Murthy Kolam
f5c7a3619a
add spack recipe for rocm version of the tensile (#19669)
* add spack recipe for rocm version of the tensile

* fix flake8 error
2020-11-11 10:55:23 -06:00
Greg Becker
229fc11fdb
axom: devtools require llvm clang-format (#19740)
* follow-up to previous PR

* build type
2020-11-11 10:54:24 -06:00
vvolkl
2c55d47c1e
[podio] set pythonpath correctly (#19779)
* [podio] put python dir in python path

* Update var/spack/repos/builtin/packages/podio/package.py

Co-authored-by: Adam J. Stewart <ajstewart426@gmail.com>

Co-authored-by: Adam J. Stewart <ajstewart426@gmail.com>
2020-11-11 10:53:56 -06:00
Kai Torben Ohlhus
a6011ccbb7
suite-sparse: add versions 5.8.0 and 5.8.1 (#19812)
Update homepage URL and see release notes:
- https://github.com/DrTimothyAldenDavis/SuiteSparse/releases/tag/v5.8.1
- https://github.com/DrTimothyAldenDavis/SuiteSparse/releases/tag/v5.8.0
2020-11-11 10:53:27 -06:00
t-nojiri
48093350c6
arbor: Add version 0.4 (#19839) 2020-11-11 10:50:32 -06:00
Stephen Hudson
56df3fcbaa
Add optional deps mpmath and deap to py-libensemble (#19852) 2020-11-11 10:45:16 -06:00
Keita Iwabuchi
8edd245bb3
Metall package: add v0.6 (#19854)
* Metall: add version 0.2

* Add Metall v0.3

* Update Metall package to v0.4 and v0.5.

* Metall package: add v0.6
2020-11-11 10:43:00 -06:00
t-nojiri
3167aec0ab
ace: Add version 6.5.12 (#19856) 2020-11-11 10:42:30 -06:00
Mark Olesen
a90324a5b2
openfoam: remove mplibUSER provisioning (#19861)
- has never been used by the spack package or by the upstream package

Co-authored-by: Mark Olesen <Mark.Olesen@esi-group.com>
2020-11-11 10:38:50 -06:00