Commit graph

17039 commits

Author SHA1 Message Date
Michael Kuhn
44681dbca5 autotools: Fix config.guess detection, take two (#17333)
The previous fix from #17149 contained a thinko that produced errors for
packages that overwrite configure_directory.
2020-07-10 13:05:49 -07:00
Greg Becker
f2889e698a
spack install: improve error message with no args (#17454)
The error message was not updated when the behavior of Spack environments
was changed to not automatically activate the local environment in #17258.
The previous error message no longer makes sense.
2020-07-10 10:45:11 -07:00
Rémi Lacroix
ea546425e8
Update the bbcp package (#17436)
* bbcp: Update the URLs to use HTTPS.

The HTTP URLs do not work anymore.

* bbcp: Add missing libnsl dependency.

* bbcp: Rename the git-based version to match the branch name.

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

Co-authored-by: Adam J. Stewart <ajstewart426@gmail.com>
2020-07-10 08:27:07 -05:00
ketsubouchi
7269a5bf51
py-pysam: add LDFLAGS to curl (#17434)
* py-pysam: add LDFLAGS to curl

* Update var/spack/repos/builtin/packages/py-pysam/package.py

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

Co-authored-by: Adam J. Stewart <ajstewart426@gmail.com>
2020-07-10 08:26:21 -05:00
figroc
00d7e817c6
grpc: add versions 1.28/1.29/1.30 (#17433) 2020-07-10 08:25:47 -05:00
iarspider
ed7d485b58
New packages: thepeg, herwig++ (2.x) (#17443)
* New packages: Rivet, Herwig++ 2

* Add patches for thepeg

* Flake-8

* Update package.py

* Delete thepeg-2.1.6.patch

* Delete thepeg-2.1.5.patch

* Delete thepeg-2.1.3.patch

* Delete thepeg-2.2.0.patch
2020-07-10 08:25:21 -05:00
iarspider
38d387c9a5
New packages: looptools + vbfnlo (#17446)
* New package: vbfnlo

* Add new package: vbfnlo

* Add recipe for looptools

* Add patch for looptools

* LoopTools: patch not needed (fixed by developers without changing version)

* Remove patch file as well

* Update package.py

* Update package.py

* Fix vbfnlo recipe for old version

Co-authored-by: iarspider <iarpsider@gmail.com>
2020-07-10 08:24:14 -05:00
Julius-Plehn
02dd90ebf9
New Package: ChaNGa (#17442)
* WIP: changa package

* changa cleanup

* flake8 format

* adds master branch to ChaNGa

* positional arguments

* use install instead of copy
2020-07-10 08:22:20 -05:00
Patrick Gartung
e72e2568dd
Relocation of sbang needs to be done when the spack prefix changes even if the install tree has not changed. (#17455) 2020-07-09 22:28:51 -05:00
Rémi Lacroix
d9923a05e0
ltrace: Disable "-Werror". (#17444)
Some functions used by ltrace have been deprecated in recent versions of glibc.
2020-07-09 22:27:30 -05:00
Rémi Lacroix
8c6fa66b2a
openslide: Add missing dependencies. (#17445) 2020-07-09 22:26:37 -05:00
Harmen Stoppels
84eae97f91
aspirin for buildaches (#17437) 2020-07-09 22:00:38 -05:00
Sajid Ali
12099ed55e
clear mpicc and friends before each build (#17450)
* clear mpi env vars
2020-07-09 16:14:49 -05:00
Greg Becker
d0f5b69a19
installation: skip repository metadata for externals (#16954)
When Spack installs a package, it stores repository package.py files
for it and all of its dependencies - any package with a Spack metadata
directory in its installation prefix.

It turns out this was too broad: this ends up including external
packages installed by Spack (e.g. installed by another Spack instance).
Currently Spack doesn't store the namespace properly for such packages,
so even though the package file could be fetched from the external,
Spack is unable to locate it.

This commit avoids the issue by skipping any attempt to locate and copy
from the package repository of externals, regardless of whether they
have a Spack repo directory.
2020-07-09 11:08:51 -07:00
Peter Scheibel
ce9d30f80f
add public spack mirror (#17077) 2020-07-08 15:59:24 -07:00
Sinan
e02d955aed
new package: ligra (#17425)
* new package: ligra

* setup run environment

* tidy up

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

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

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

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

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

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

* flake8

Co-authored-by: Sinan81 <sbulut@3vgeomatics.com>
Co-authored-by: Adam J. Stewart <ajstewart426@gmail.com>
2020-07-08 16:30:53 -05:00
Frank Willmore
b3fff20d1f
enable flatcc to be built with gcc@9.X.X (#17430)
`gcc` 9 and above have more warnings that break the `flatcc` build by default, because `-Werror` is enabled.  This loosens the build up so that we can build with more compilers in Spack.

- [x] Add `-DFLATCC_ALLOW_WERROR=OFF` to `flatcc` CMake arguments

Co-authored-by: Frank Willmore <willmore@anl.gov>
2020-07-08 13:57:09 -07:00
Patrick Gartung
8c41173678
Buildcache: bindist test without invoking spack compiler wrappers. (#15687)
* Buildcache:
   * Try mocking an install of quux, corge and garply using prebuilt binaries
   * Put patchelf install after ccache restore
   * Add script to install patchelf from source so it can be used on Ubuntu:Trusty which does not have a patchelf pat package. The script will skip building on macOS
   * Remove mirror at end of bindist test
   * Add patchelf to Ubuntu build env
   * Revert mock patchelf package to allow other tests to run.
   * Remove depends_on('patchelf', type='build') relying instead on
   * Test fixture to ensure patchelf is available.

* Call g++ command to build libraries directly during test build

* Flake8

* Install patchelf in before_install stage using apt unless on Trusty where a build is done.

* Add some symbolic links between packages

* Flake8

* Flake8:

* Update mock packages to write their own source files

* Create the stage because spec search does not create it any longer

* updates after change of list command arguments

* cleanup after merge

* flake8
2020-07-08 15:05:58 -05:00
iarspider
0bed621d0c
Add missing file (#17426)
Co-authored-by: Ivan Razumov <ivan.razumov@cern.ch>
2020-07-08 10:50:47 -05:00
Amjad Kotobi
1d2754c3f6
r-usethis: new version and dependencies (#17411)
* r-usethis: new version and dependencies

* r-usethis: fix in dependency
2020-07-08 08:44:47 -05:00
tcojean
ae2a867a7f
Ginkgo: new versions (#17413)
* Add new Ginkgo versions with HIP support.

* Drop HIP support until more ROCm packages are integrated.
2020-07-08 08:42:56 -05:00
Adam J. Stewart
207e496162
spack create: ask how many to download (#17373) 2020-07-08 09:38:42 +02:00
ketsubouchi
f0391db096
typhon: fix build with Fujitsu compilers (#17424) 2020-07-08 09:28:41 +02:00
TZ
084994db9c
ncl: fix compilation errors with Intel compilers (#17391)
The Intel compilers are more strict and require special command
line options (like -std=c99) to properly compile NCL.
2020-07-08 08:42:49 +02:00
Simon Byrne
f85da868ac
Improve Travis sample in the docs (#17420)
- printf is better than echo for multiline strings
- ** should be &&
- use line continuation
- Use multiline block
2020-07-08 07:25:37 +02:00
iarspider
f1f31e3dfe
Fix YODA and Rivet recipes (#17412)
* Fix Rivet recipe; restrict Yoda versions for a give Rivet version

* Fix YODA recipe

* More tweaks to YODA version requirements

* Flake-8
2020-07-07 22:24:48 -05:00
Patrick Gartung
7f8e827db8
Relocate rpaths for all binaries, then do text bin replacement if the rpaths still exist after running patchelf/otool (#17418) 2020-07-07 16:46:39 -05:00
Adam J. Stewart
a63761f875
oneDNN: add v1.5.1 (#17419) 2020-07-07 16:38:47 -05:00
Adam J. Stewart
3ce16c89b7
GDAL: add v3.1.2 (#17416) 2020-07-07 15:45:25 -05:00
Massimiliano Culpo
f4ac3770b4
CudaPackage: maintainers are listed in the docstring (#17409)
fixes #17396

This prevents the class attribute to be inherited and
saves current maintainers from becoming the default
maintainers of every Cuda package.
2020-07-07 20:45:41 +02:00
Todd Gamblin
b0506a722e
releases: document releases/latest tag (#17402)
We got rid of `master` after #17377, but users still want a way to get
the latest stable release without knowing its number.

We've added a `releases/latest` tag to replace what was once `master`.

Co-authored-by: Massimiliano Culpo <massimiliano.culpo@gmail.com>
2020-07-07 11:44:15 -07:00
Peter Scheibel
650ab563f4
Uninstall: tolerate hook failures when force=true (#16513)
Fixes #16478

This allows an uninstall to proceed even when encountering pre-uninstall
hook failures if the user chooses the --force option for the uninstall.

This also prevents post-uninstall hook failures from raising an exception,
which would terminate a sequence of uninstalls. This isn't likely essential
for #16478, but I think overall it will improve the user experience: if
the post-uninstall hook fails, there isn't much point in terminating a
sequence of spec uninstalls because at the point where the post-uninstall
hook is run, the spec has already been removed from the database (so it
will never have another chance to run).

Notes:

* When doing spack uninstall -a, certain pre/post-uninstall hooks aren't
  important to run, but this isn't easy to track with the current model.
  For example: if you are uninstalling a package and its extension, you
  do not have to do the activation check for the extension.
* This doesn't handle the uninstallation of specs that are not in the DB,
  so it may leave "dangling" specs in the installation prefix
2020-07-07 11:37:36 -07:00
Christoph Junghans
90285c7d61
votca-tools: fix build with mkl (#17414) 2020-07-07 13:27:10 -05:00
Frank Willmore
6c300ab717
snappy: added v1.1.8 (#17397) 2020-07-07 17:25:26 +02:00
g-mathias
05d8ba170b
jube: added v2.4.0 (#17404)
Co-authored-by: lu64bag3 <gerald.mathias@lrz.de>
2020-07-07 16:11:53 +02:00
figroc
51f65152a5
abseil-cpp: added v20200225.2 (#17383) 2020-07-07 14:02:21 +02:00
Harmen Stoppels
1113357e35
libtree: fixed checksums (#17393)
The hash was wrongly computed for the `tar.gz` 
that Github provides, not the custom tarball which 
includes submodules as well.
2020-07-07 12:56:57 +02:00
ketsubouchi
d65a076c0d
bliss: add spaces to __DATE__ (#17385)
C++11 requires a space between literal and string macro.
2020-07-07 11:28:55 +02:00
Glenn Johnson
845139740f
mumax: new package at v3.10beta (#17398)
This PR creates a new spack package for

mumax: GPU accelerated micromagnetic simulator.

This uses the current beta version because
- it is somewhat dated, ~2018
- it is the only one that supports recent GPU kernels
2020-07-07 11:01:59 +02:00
TZ
1f87b07689
nco: added v4.8.[0,1] and v4.9.[0-3] (#17389) 2020-07-07 10:18:27 +02:00
TZ
cbaa1bca1c
ncview: added v2.1.8 (#17388) 2020-07-07 10:09:27 +02:00
Sinan
5fb6a06c37
gunrock: improved package recipe (added variants for applications and others) (#17340)
Co-authored-by: Massimiliano Culpo <massimiliano.culpo@gmail.com>
Co-authored-by: Sinan81 <sbulut@3vgeomatics.com>
2020-07-07 10:02:37 +02:00
Adam Moody
6e38fc56f6 mpifileutils: add v0.10.1 2020-07-06 18:19:29 -07:00
Todd Gamblin
c00a05bfba bugfix: no infinite recursion in setup-env.sh on Cray
On Cray platforms, we rely heavily on the module system to figure out
what targets, compilers, etc. are available. This unfortunately means
that we shell out to the `module` command as part of platform
initialization.

Because we run subcommands in a shell, we can get infinite recursion if
`setup-env.sh` and friends are in some init script like `.bashrc`.

This fixes the infinite loop by adding guards around `setup-env.sh`,
`setup-env.csh`, and `setup-env.fish`, to prevent recursive
initializations of Spack. This is safe because Spack never shells out to
itself, so we do not need it to be initialized in subshells.

- [x] add recursion guard around `setup-env.sh`
- [x] add recursion guard around `setup-env.csh`
- [x] add recursion guard around `setup-env.fish`
2020-07-06 13:55:14 -07:00
Todd Gamblin
9ec9327f5a docs: document releases and branches in Spack
- [x] Remove references to `master` branch
- [x] Document how release branches are structured
- [x] Document how to make a major release
- [x] Document how to make a point release
- [x] Document how to do work in our release projects
2020-07-06 11:39:19 -07:00
Todd Gamblin
11088df402 Remove references to master from CI
- [x] remove master from github actions
- [x] remove master from .travis.yml
- [x] make `develop` the default branch for `spack ci`
2020-07-06 11:39:19 -07:00
Todd Gamblin
4ea76dc95c change master/child to controller/minion in pty docstrings
PTY support used the concept of 'master' and 'child' processes. 'master'
has been renamed to 'controller' and 'child' to 'minion'.
2020-07-06 11:39:19 -07:00
cedricchevalier19
f0275d7e1b
Fix gcc + binutils compilation. (#9024)
* fix binutils deptype for gcc

binutils needs to be a run dependency of gcc

* Fix gcc+binutils build on RHEL7+

static-libstdc++ is not available with system gcc.
Anyway, as it is for bootstraping, we do not really care depending on
a shared libstdc++.

Co-authored-by: Michael Kuhn <michael@ikkoku.de>
2020-07-06 13:02:35 -05:00
Michael Kuhn
516c3e659f
autotools bugfix: handle missing config.guess (#17356)
Spack was attempting to calculate abspath on the located config.guess
path even when it was not found (None); this commit skips the abspath
calculation when config.guess is not found.
2020-07-06 10:53:02 -07:00
iarspider
e62ddcb582
Add Rivet and YODA (#17372)
* Add Rivet and YODA

* Add patches

* Flake-8

* Set level for Rivet patches

* Syntax fix

* Fix dependencies of Rivet

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

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

Co-authored-by: Adam J. Stewart <ajstewart426@gmail.com>
2020-07-06 10:51:36 -05:00