Commit graph

16316 commits

Author SHA1 Message Date
Harmen Stoppels
24dff9cf20 Fix security issue in CI (#17545)
The `spack-build-env.txt` file may contains many secrets, but the obvious one is the private signing key in `SPACK_SIGNING_KEY`. This file is nonetheless uploaded as a build artifact to gitlab. For anyone running CI on a public version of Gitlab this is a major security problem. Even for private Gitlab instances it can be very problematic.

Co-authored-by: Scott Wittenburg <scott.wittenburg@kitware.com>
2020-07-23 13:52:09 -07:00
Dr Owain Kenway
e4265d3135 llvm-flang: Only build offload code if cuda enabled (#17466)
* llvm-flang Only build offload code if cuda enabled

The current version executes `cmake(*args)` always as part of the post install.  If device offload is not part of the build, this results in referencing `args` without it being set and the error:

```
==> Error: UnboundLocalError: local variable 'args' referenced before assignment

```

Looking at prevoous version of `llvm-package.py` this whole routine appears to be only required for offload, some indent `cmake/make/install` to be under the `if`.

* Update package.py

Add comment
2020-07-23 13:51:35 -07:00
Sajid Ali
5e5cc99147 clear mpicc and friends before each build (#17450)
* clear mpi env vars
2020-07-23 13:48:47 -07:00
Greg Becker
44bc176d08
cray: detect shasta os properly (#17467)
Fixes #17299

Cray Shasta systems appear to use an unmodified Sles or other Linux operating system on the backend (like Cray "Cluster" systems and unlike Cray "XC40" systems that use CNL).

This updates the CNL version detection to properly note that this is the underlying OS instead of CNL and delegate to LinuxDistro.
2020-07-23 13:20:03 -07:00
robo-wylder
3c145b42bc
environment-views: fix bug where missing recipe/repo breaks env commands (#17608)
* environment-views: fix bug where missing recipe/repo breaks env commands

When a recipe or a repo has been removed from Spack and an environment
is active, it causes the view activation to crash Spack before any
commands can be executed. Further, the error message it not at all clear
in explaining the issue.

This forces view regeneration to always start from scratch to avoid the
missing package recipes, and defaults add_view=False in main for views activated
by the `spack -e` option.

* add messages to env status and deactivate

Warn users that a view may be corrupt when deactivating an environment
or checking its status while active. Updated message for activate.

* tests for view checking

Co-authored-by: Gregory Becker <becker33@llnl.gov>
2020-07-23 11:00:58 -07:00
Peter Scheibel
ae82650174
Update fetch order to match iteration order of MirrorReference (#17572) 2020-07-23 10:58:59 -07:00
Greg Becker
e8aa737b09
util.executable.which: handle path separators like /bin/which (#17668)
* util.executable.which: handle path separators like /bin/which

Co-authored-by: Massimiliano Culpo <massimiliano.culpo@gmail.com>
2020-07-23 10:54:25 -07:00
ilbiondo
f42394daf5
csa-c: added new package at master (#17676)
Co-authored-by: Massimiliano Culpo <massimiliano.culpo@gmail.com>
2020-07-23 17:07:48 +02:00
ilbiondo
10dacc2588
nn-c: added new package at v1.86.2 (#17675)
Co-authored-by: Massimiliano Culpo <massimiliano.culpo@gmail.com>
2020-07-23 17:06:35 +02:00
ilbiondo
5067b956f4
Shapeit4: added new package at v4.1.3 (#17674) 2020-07-23 13:22:58 +02:00
Tamara Dahlgren
605c1a76e0
Reduce output verbosity with debug levels (#17546)
* switch from bool to int debug levels

* Added debug options and changed lock logging to use more detailed values

* Limit installer and timestamp PIDs to standard debug output

* Reduced verbosity of fetch/stage/install output, changing most to debug level 1

* Combine lock log methods; change build process install to debug

* Changed binary cache install messages to extraction messages
2020-07-23 00:49:57 -07:00
Nick Robison
39cfa9630c
[M4] Add missing compiler flag on Cray Compiler (#17604)
* [M4] Add missing compiler flag on Cray Compiler

The new version of the Cray Compiler are based on Clang, which means we
need to add the same LDFLAG as other clang environments.
2020-07-22 23:55:03 -07:00
Adam J. Stewart
4b33558707
Cython: add v0.29.21 (#17650) 2020-07-22 18:36:55 -07:00
Jen Herting
48e8072b26
New Package: py-boto (#17639)
Added py-boto package
2020-07-22 17:52:36 -07:00
Frédéric Simonis
37fa6fe343
precice: Add version 2.1.0 (#17644) 2020-07-22 16:49:36 -07:00
eugeneswalker
f1eec05d0e
bugfix: use getattr for variation.prefix/suffix (#17669) 2020-07-22 16:15:25 -07:00
Mark W. Krentel
4c7e52adaa
hpctoolkit: add version 2020.07.21 (#17645) 2020-07-22 13:53:41 -07:00
Ben Bergen
4ca6d1f0f7
Added variant to enable Legion SPY logging. (#17637) 2020-07-22 11:41:20 -06:00
Hadrien G
b8135bd205
[acts] Add version 0.28.0 (#17622)
Add acts v0.28.0
2020-07-22 09:14:51 -07:00
Justin S
dedadcd2ea
hisat2 (package): add version 2.2.0, update homepage (#17600) 2020-07-21 19:29:18 -07:00
Adam J. Stewart
983aeea850
New packages: py-azure-cli and dependencies (#17585) 2020-07-21 19:21:29 -07:00
Todd Gamblin
0c44a9a504
bugfix: make compiler preferences slightly saner (#17590)
* bugfix: make compiler preferences slightly saner

This fixes two issues with the way we currently select compilers.

If multiple compilers have the same "id" (os/arch/compiler/version), we
currently prefer them by picking this one with the most supported
languages.  This can have some surprising effects:

* If you have no `gfortran` but you have `gfortran-8`, you can detect
  `clang` that has no configured C compiler -- just `f77` and `f90`. This
  happens frequently on macOS with homebrew. The bug is due to some
  kludginess about the way we detect mixed `clang`/`gfortran`.

* We can prefer suffixed versions of compilers to non-suffixed versions,
  which means we may select `clang-gpu` over `clang` at LLNL. But,
  `clang-gpu` is not actually clang, and it can break builds. We should
  prefer `clang` if it's available.

- [x] prefer compilers that have C compilers and prefer no name variation
  to variation.

* tests: add test for which()
2020-07-21 18:48:37 -07:00
Hadrien G
b81339cf80
[acts] Add 0.27.x series (#17621)
Add acts v0.27 and v0.27.1
2020-07-21 10:56:18 -07:00
Harmen Stoppels
6c69b8a4d4
ci pipelines: activate environment without view (#17440) 2020-07-21 10:15:43 -07:00
Tiziano Müller
ec1237479e
cp2k: make libint optional (#17618) 2020-07-21 09:13:59 -07:00
t-nojiri
40e2a41477
aegean (package): remove -m64 on aarch64 (#17615) 2020-07-20 23:57:09 -07:00
Hadrien G
f168d63586
acts: added v0.26 (#17602) 2020-07-21 08:37:21 +02:00
Nick Robison
78a84efb4b
flatbuffers: added v0.12.0 (#17603) 2020-07-21 08:30:44 +02:00
Seth R. Johnson
c6891376f4
qt4: add missing libSM dependency (#17611)
See https://github.com/spack/spack/issues/15082 and
https://github.com/spack/spack/pull/16226
2020-07-21 08:12:36 +02:00
Mark W. Krentel
83b281f36b
hpcviewer, ibm-java: new versions (#17612)
Add hpcviewer version 2020.07 and ibm-java 8.0.6.11.
2020-07-21 08:09:53 +02:00
Tamara Dahlgren
86ec698a33
Bugfix: Do not raise InstallError for ascent_ver (#17578) 2020-07-20 18:32:56 -07:00
Todd Gamblin
897e80e596
bugfix: ignore Apple's "gcc" by default (#17589)
Apple's gcc is really clang. We previously ignored it by default but
there was a regression in #17110.

Originally we checked for all clang versions with this, but I know of
none other than `gcc` on macos that actually do this, so limiting to
`apple-clang` should be ok.

- [x] Fix check for `apple-clang` in `gcc.py` to use version detection
  from `spack.compilers.apple_clang`
2020-07-20 18:24:18 -07:00
Massimiliano Culpo
ab32799b52
Fix MacOS build tests (#17542)
* MacOS build tests

- Run on PR that modify the YAML file of the workflow
- Don't clone Spack, since we are in the Spack repo now

* Try to add opengl to configuration to build jupyter

* fixup
2020-07-20 17:25:42 -07:00
Dr. Christian Tacke
bd236918dd
Configuration: allow usage of command-line scopes with environments (#14608)
Spack did not support usage of the `--config-scope` option in
combination with an environment: In `lib/spack/spack/main.py`,
`spack.config.command_line_scopes` is set equal to any config scopes
passed by the `--config-scope` option. However, this is done after
activating an environment. In the process of activating an environment,
the `spack.config.config` singleton is instantiated, so later setting of
`spack.config.command_line_scopes` is ignored.

This commit sets command line scopes before activating an environment to
ensure that they are included in the configuration.

Co-authored-by: Tim Fuller <tjfulle@sandia.gov>
2020-07-20 13:58:06 -07:00
Justin S
3949a85f9a
py-dp-gp-cluster: new package at 2019-09-22 (#17549)
* py-dp-gp-cluster: new package

* py-dp-gp-cluster: remove master, add 2019-09-22

* py-dp-gp-cluster: require python2, older gpy, sklearn

* py-dp-gp-cluster: remove cython runtime dep
2020-07-20 10:48:17 -05:00
Cyrus Harrison
bab1852340
update ascent package with recent ver dep logic, and dray support (#17502)
* update ascent package with recent ver dep logic, and dray support

* update pmt name, make babelflow logic dep on mpi
2020-07-18 08:53:48 -05:00
Jon Rood
ef814b7a32
Add texlive 2020 version (#17559)
* Add new versions of texlive and poppler.

* Add new versions of harfbuzz which also relocated source location to github.

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

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

* Restore deleted url line in harfbuzz.

Co-authored-by: Adam J. Stewart <ajstewart426@gmail.com>
2020-07-18 08:49:32 -05:00
eugeneswalker
96fa6f0c1b
allow GNUPGHOME to come from SPACK_GNUPGHOME in env, if set (#17139) 2020-07-17 13:29:30 -07:00
Amjad Kotobi
e4ba1c1daf
r-devtools: add version 2.3.0; update dependencies (#17408) 2020-07-17 12:11:29 -07:00
Fabien Bruneval
bbbf0466dc
libint (package): add tuning options for MOLGW (#17329) 2020-07-17 12:10:05 -07:00
Cyrus Harrison
dc18b3e3d4
New package: parallelmergetree (#17501) 2020-07-17 12:03:11 -07:00
Scott Wittenburg
b5f82696e2
Bugfix/install missing compiler from buildcache (#17536)
Ensure compilers installed from buildcache are registered.
2020-07-17 11:13:36 -07:00
Adam J. Stewart
a5aa150a98 py-matplotlib: add v3.3.0 2020-07-17 11:05:41 -07:00
Scott Wittenburg
ae03782032 buildcache: list all mirrors even if one fails 2020-07-17 10:04:05 -06:00
Amjad Kotobi
c729c6b93c
subversion: added v1.14.0 amd v1.13.0, added new url (#17519) 2020-07-17 16:33:46 +02:00
Cyrus Harrison
324c383d8e
add devil ray package (#17495)
* add dray with mid-review changes

* remove env import since its impliclity included
2020-07-16 19:51:41 -07:00
Francesco Di Natale
35b7a69456
Updates to maestrowf package (#17470)
* Addition of Chainmap to satisfy Maestro dependency.

* Additional versions and dependencies for Maestro.

* Updated URL to point to pypi.

* Updates to chainmap hashes.

* Updates to pull version from PyPi.

* Corrections to flake8 errors.

* Stricter restrictions on Python versioning.

Maestro actually supports Python 3.5 and later.

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

* Only install chainmap for Python2 versions.

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

* Removal of setuptools python cond.

* Removal of version constaints on setuptools.

Co-authored-by: Adam J. Stewart <ajstewart426@gmail.com>
2020-07-16 19:38:45 -05:00
Kelly (KT) Thompson
d69c32d7ef
Version 1.13.2 still needs the XL patch. (#17561) 2020-07-16 19:35:33 -05:00
Scott Wittenburg
27aaff3dc2
adept-utils: 1.0.1 does not build w/ boost 1.73.0 or newer (#17560) 2020-07-16 19:34:47 -05:00
Seth R. Johnson
fc8847cf4e
Mark old icu4c as conflicting (#17562)
GCC 4.8.5 on rhel6:
```
utext.cpp:572:5: error: 'max_align_t' in namespace 'std' does not name a
type
     std::max_align_t    extension;
     ^
utext.cpp: In function 'UText* utext_setup_67(UText*, int32_t,
UErrorCode*)':
utext.cpp:587:73: error: 'max_align_t' is not a member of 'std'
             spaceRequired = sizeof(ExtendedUText) + extraSpace -
sizeof(std::max_align_t);
                                                                         ^
utext.cpp:587:73: note: suggested alternative:
In file included from
/projects/spack/opt/spack/gcc-4.4.7/gcc/6ln2t7b/include/c++/4.8.5/cstddef:42:0,
                 from utext.cpp:19:
/projects/spack/opt/spack/gcc-4.4.7/gcc/6ln2t7b/lib/gcc/x86_64-unknown-linux-gnu/4.8.5/include/stddef.h:
425:3: note:   'max_align_t'
 } max_align_t;
   ^
utext.cpp:598:57: error: 'struct ExtendedUText' has no member named
'extension'
                 ut->pExtra    = &((ExtendedUText *)ut)->extension;
                                                         ^
   g++   ...  loadednormalizer2impl.cpp
   g++   ...  chariter.cpp
```
2020-07-16 19:34:02 -05:00