Commit graph

15487 commits

Author SHA1 Message Date
Axel Huebl
bb2849002b
emacs: libxml2 deps (#16103)
emacs depends on libxml2.
2020-04-16 17:27:09 -05:00
Marc Allen
a704922c29
Bugfix: For spack buildcache check, Handle specs where only the hash is (#15663)
provided (#15662).

Prior to this fix, the checked Spec object would not be populated, and
concretization would fail.

Co-authored-by: Marc Allen <mrcall@amazon.com>
2020-04-16 14:06:13 -07:00
Glenn Johnson
07a4ac67b8
Add ncurses+termlib dependency to mesa (#16038)
Mesa links against libtinfo so needs to depend on ncurses. It also needs
a little help finding the library directory so an LDFLAGS configure
option is added.
2020-04-16 13:25:28 -05:00
Amjad Kotobi
2e4e34e6cc
New version xrootd-4.11.3 (#16092) 2020-04-16 12:53:20 -05:00
Carlos Arango Gutierrez
5d7f4db9ad
singularity: updated maintainer list (#16093) 2020-04-16 18:43:38 +02:00
athanasio
f912cce7ee
openbabel: fix compilation errors (#16090)
- Disable maeparser as it is broken with CMake
- Added missing dependencies
2020-04-16 10:49:43 -05:00
Amjad Kotobi
e1777c5708
New package bonniepp added (#16091) 2020-04-16 10:49:30 -05:00
Harmen Stoppels
7dcc8a5463
Add new version 1.1.1 (#16087) 2020-04-16 09:50:48 -05:00
Antonio Arena
fd3cdffb40
New matlab versions (#16086) 2020-04-16 09:50:14 -05:00
Axel Huebl
125fc2e611
MPark.Variant: GCC 7.3.1 Conflict (#16081)
* MPark.Variant: GCC 7.3.1 Conflict

Due to an ICE in this specific patch-release of GCC, compile
errors in downstream packages should be avoided with a clean
conflict.

* Fix superfluous spaces

Co-Authored-By: Adam J. Stewart <ajstewart426@gmail.com>

* Fix typo

Co-authored-by: Adam J. Stewart <ajstewart426@gmail.com>
2020-04-16 09:48:19 -05:00
Tiziano Müller
7c5fc6acea
dbcsr: expose all options, check openblas feats (#16034)
* dbcsr: expose all options, check openblas feats

* dbcsr: use Ninja to build, ensure serialized tests

* dbcsr: add myself as maintainer
2020-04-16 09:47:31 -05:00
asmaahassan90
7ac6f7fed9
Add Cubist (#16069)
* Add Cubist

* enhance recipe

* Not using OS module anymore

* remove white space

* Fix build shell

* make Flake8 happy

* use bash shell for build

* Convert it To MakefilePackage as per peer-review
2020-04-16 08:24:35 -05:00
ilbiondo
b0ec2788ab
HAL: added new package at v2.1 (#16085)
Co-authored-by: Massimiliano Culpo <massimiliano.culpo@gmail.com>
2020-04-16 12:19:20 +02:00
darmac
04c6a781b6
Add new package: zookeeper-benchmark (#16067)
* Add new package: zookeeper-benchmark

* refine zookeeper version

* refine zookeeper version variant

* remove unused variant
2020-04-15 23:33:45 -05:00
darmac
f66bd41d9a
Neo4j (#16068)
* Update var/spack/repos/builtin/packages/neo4j/package.py

Co-Authored-By: Adam J. Stewart <ajstewart426@gmail.com>

* Add new package: neo4j

* refine neo4j package

* fix flake8 warning

Co-authored-by: Adam J. Stewart <ajstewart426@gmail.com>
2020-04-15 20:45:46 -05:00
Harsh Bhatia
29e2475a68
update: memsurfer with python3 (#15636)
* update: memsurfer with python3

* flake8 compliance

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

Co-Authored-By: Adam J. Stewart <ajstewart426@gmail.com>

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

Co-Authored-By: Adam J. Stewart <ajstewart426@gmail.com>

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

Co-Authored-By: Adam J. Stewart <ajstewart426@gmail.com>

* removed build_type preferences at adamjstewart's suggestion

* Added build/run dependency on python3.7

as suggested by adam stewart

* more flake8 horror!

Co-authored-by: Adam J. Stewart <ajstewart426@gmail.com>
2020-04-15 20:11:48 -05:00
Rao Garimella
05afce85fa
Upgrade MSTK versions (#16079) 2020-04-15 18:13:47 -05:00
Carson Woods
a28c127043
netcdf-cxx4: bugfix (#16080)
* Add new variants

* Fix missing config_args variable
2020-04-15 18:05:42 -05:00
Todd Gamblin
bd3f24afe1 Merge branch 'releases/v0.14' into develop 2020-04-15 15:27:00 -07:00
Michael Kuhn
277350ceed Make tags case insensitive
Currently, tags are case sensitive, which is unintuitive:
```console
$ spack list -t hpc
==> 2 packages.
nek5000  nektools
$ spack list -t HPC
==> 1 packages.
mfem
$ spack list -t Hpc
==> 0 packages.
```

This change makes them case insensitive:
```console
$ spack list -t hpc
==> 3 packages.
mfem  nek5000  nektools
$ spack list -t HPC
==> 3 packages.
mfem  nek5000  nektools
$ spack list -t Hpc
==> 3 packages.
mfem  nek5000  nektools
```
2020-04-15 14:56:25 -07:00
Axel Huebl
d9630b572a x.org packages: mirror mixin
overhaul all x.org packages to use available mirrors.
2020-04-15 14:44:13 -07:00
Todd Gamblin
7a68a4d851 update CHANGELOG.md for 0.14.2 2020-04-15 14:32:01 -07:00
Todd Gamblin
a3bcd88f8d version bump: 0.14.2 2020-04-15 14:30:58 -07:00
Todd Gamblin
740f8fe1a9 bugfix: spack test should not output [+] for mock installs (#15609)
`spack test` has a spurious '[+] ' in the output:

```
lib/spack/spack/test/install.py .........[+] ......
```

Output is properly suppressed:

```
lib/spack/spack/test/install.py ...............
```
2020-04-15 14:30:58 -07:00
wspear
999c8e3a67
Added maintainers (#16078)
Co-authored-by: Wyatt Spear <wspear@cs.uoregon.edu>
2020-04-15 16:07:57 -05:00
ilbiondo
e41ac9af8a
Sonlib (#16060)
* sonLib package as required by the HAL toolkit

* cleanup

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

Co-Authored-By: Adam J. Stewart <ajstewart426@gmail.com>

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

Co-Authored-By: Adam J. Stewart <ajstewart426@gmail.com>

Co-authored-by: Adam J. Stewart <ajstewart426@gmail.com>
2020-04-15 16:04:06 -05:00
Kelly (KT) Thompson
fef4e80a6d
New package: py-cmake-format (#16055)
* New package py-cmake-format

* wrap long lines

* Fix package description formatting.
2020-04-15 16:01:50 -05:00
Harmen Stoppels
f072d24c98
Bump version of libtree (#16051) 2020-04-15 15:57:21 -05:00
Todd Gamblin
430ca7c7cf spack install terminal output handling in foreground/background (#15723)
Makes the following changes:

* (Fixes #15620) tty configuration was failing when stdout was 
  redirected. The implementation now creates a pseudo terminal for
  stdin and checks stdout properly, so redirections of stdin/out/err
  should be handled now.
* Handles terminal configuration when the Spack process moves between
  the foreground and background (possibly multiple times) during a
  build.
* Spack adjusts terminal settings to allow users to to enable/disable
  build process output to the terminal using a "v" toggle, abnormal
  exit cases (like CTRL-C) could leave the terminal in an unusable
  state. This is addressed here with a special-case handler which
  restores terminal settings.

Significantly extend testing of process output logger:

* New PseudoShell object for setting up a master and child process
  and configuring file descriptor inheritance between the two
* Tests for "v" verbosity toggle making use of the added PseudoShell
  object
* Added `uniq` function which takes a list of elements and replaces
  any consecutive sequence of duplicate elements with a single
  instance (e.g. "112211" -> "121")

Co-authored-by: Adam J. Stewart <ajstewart426@gmail.com>
2020-04-15 12:47:41 -07:00
Massimiliano Culpo
55f5afaf3c database: maintain in-memory consistency on remove (#15777)
The performance improvements done in #14693 where leaving the DB in an inconsistent state when specs were removed from it. This PR updates the DB internal state whenever the DB is written to a file.

Note that we still cannot properly enumerate installed dependents, so there is a TODO in this code. Fixing that will require the dependents dictionaries in specs to be re-keyed (either by hash, or not keyed at all -- a list would do).  See #11983 for details.
2020-04-15 12:47:16 -07:00
Andrew W Elble
6b559912c1 performance: add a verification file to the database (#14693)
Reading the database repeatedly can be quite slow.  We need a way to speed
up Spack when it reads the DB multiple times, but the DB has not been
modified between reads (which is nearly all the time).

- [x] Add a file containing a unique uuid that is regenerated at database
    write time. Use this uuid to suppress re-parsing the database
    contents if we know a previous uuid and the uuid has not changed.

- [x] Fix mutable_database fixture so that it resets the last seen
    verifier when it resets.

- [x] Enable not rereading the database immediately after a write. Make
    the tests reset the last seen verifier in between tests that use the
    database fixture.

- [x] make presence of uuid module optional
2020-04-15 12:47:00 -07:00
Peter Scheibel
9b5805a5cd Remove DB conversion of old index.yaml (#15298)
Removed the code that was converting the old index.yaml format into
index.json. Since the change happened in #2189 it should be
considered safe to drop this (untested) code.
2020-04-15 12:45:57 -07:00
Adam J. Stewart
c6c1d01ab6 Allow Spack Environments with '-h' in the name (#15429)
If a user invoked "spack env activate example-henv", Spack would
mistakenly interpret the "-h" from "example-henv" as the "-h" option.
This commit allows users to create and activate environments with
"-h" in the name.

This issue existed for bash shell support as well as csh support, and
this commit addresses both, along with some other unrelated csh
support issues.
2020-04-15 12:38:31 -07:00
Peter Scheibel
b9688a8c35 Environments/views: only override spec prefix for non-external packages (#15475)
* only override spec prefix for non-external packages

* add test that environment shell modifications respect explicitly-specified prefixes for external packages

* add clarifying comment
2020-04-15 12:37:37 -07:00
Jonathon Anderson
ed2781973c Source devnull in environment_after_sourcing_files (closes #15775) (#15791)
spack.util.environment_after_sourcing_files compares the local
environment against a shell environment after having sourced a
file; but this ends up including the default shell profile and
rc, which might differ from the local environment.

To change this, compare against the default shell environment,
expressed here as 'source /dev/null'.
2020-04-15 12:37:16 -07:00
Todd Gamblin
99bb88aead bugfix: TERM may not be in the environment on Cray (#15630) 2020-04-15 12:37:03 -07:00
Massimiliano Culpo
a85cce05a1 Blacklist Lmod variable modifications when sourcing files (#15778)
fixes #15775

Add all the variables listed here:

https://lmod.readthedocs.io/en/latest/090_configuring_lmod.html

to the list of those blacklisted when constructing environment
modifications by sourcing files.
2020-04-15 12:36:53 -07:00
Axel Huebl
e1e804168a Tests: Mirror Mixin Classes 2020-04-15 11:44:14 -07:00
Axel Huebl
7e5257e44a x.org: mirror mixin
According to my nightly CI/CD tests, x.org is another large provider
of software in common build chains that is often down.

Added a hand-selected amount of mirrors that is well up-to-sync.
Tested with `util-macros` that has a quite "recent" patch release.

Other packages to follow in an individual PR.
2020-04-15 11:44:14 -07:00
Todd Gamblin
a563884af3
spack install terminal output handling in foreground/background (#15723)
Makes the following changes:

* (Fixes #15620) tty configuration was failing when stdout was 
  redirected. The implementation now creates a pseudo terminal for
  stdin and checks stdout properly, so redirections of stdin/out/err
  should be handled now.
* Handles terminal configuration when the Spack process moves between
  the foreground and background (possibly multiple times) during a
  build.
* Spack adjusts terminal settings to allow users to to enable/disable
  build process output to the terminal using a "v" toggle, abnormal
  exit cases (like CTRL-C) could leave the terminal in an unusable
  state. This is addressed here with a special-case handler which
  restores terminal settings.

Significantly extend testing of process output logger:

* New PseudoShell object for setting up a master and child process
  and configuring file descriptor inheritance between the two
* Tests for "v" verbosity toggle making use of the added PseudoShell
  object
* Added `uniq` function which takes a list of elements and replaces
  any consecutive sequence of duplicate elements with a single
  instance (e.g. "112211" -> "121")

Co-authored-by: Adam J. Stewart <ajstewart426@gmail.com>
2020-04-15 11:05:41 -07:00
Federico Ficarelli
94aa368af8
Fix grcp@1.27.0: (#16052)
Current default version was missing a dependency.
2020-04-15 11:32:08 -05:00
darmac
6eee7b6bb8
Add new package: mrbench (#16062) 2020-04-15 11:25:49 -05:00
darmac
c470a8da6a
Add new package: kinesis (#16063) 2020-04-15 11:25:21 -05:00
Robert Pavel
8935406756
Added Laghos v3 to Proxy Apps v3 (#16070)
Also fixed upper bound for v2 apps
2020-04-15 11:13:07 -05:00
Michael Kuhn
a157b479c8
julea: New package (#16071) 2020-04-15 11:12:28 -05:00
ilbiondo
4afdaa5f4b
IQ-TREE: added new package at v1.6.12 (#16064) 2020-04-15 16:37:25 +02:00
ilbiondo
666bc844be
Phylobayes MPI: added new package at v1.8b (#16065) 2020-04-15 13:26:37 +02:00
Massimiliano Culpo
ff0ec9cf61
openfoam: set run environment by sourcing bashrc (#15949) 2020-04-15 12:21:02 +02:00
ilbiondo
d41e366d0d
py-sonlib: added new package (#16058)
Co-Authored-By: Massimiliano Culpo <massimiliano.culpo@gmail.com>
2020-04-15 10:35:01 +02:00
Dan Lipsa
fd2e6ee50f
Apply same patch to version 10. (#15963) 2020-04-14 22:30:45 -05:00