Commit graph

11258 commits

Author SHA1 Message Date
sknigh
a76c50d1ee Allow tty output to be timestamped (#10554)
* Spack debug output now includes microsecond-granularity timestamps.
* Timestamps can also be enabled with the `--timestamp` command line argument.
2019-02-13 10:14:35 -08:00
健美猞猁
2202579685 Cnvnator: a new package. (#8959) 2019-02-13 11:15:00 +01:00
Matthias Wolf
861dd06bd1 enh: allow time like HH:MM in date strings. (#10034) 2019-02-13 11:05:00 +01:00
George Hartzell
f65a1155e1 Enhancement to module autoload documentation (#10310)
* Note that `none` is the default for lmod autoload

Save a bit of confusion by *explicitly* pointing out that `none` is
the default value for autoload in the lmod module file generator.

* Add a tip re building software externally

Add a tip about using `autoload: all` when building packages outside
of the tree that use artifacts (e.g. libraries, includes) within the
tree.
2019-02-12 22:02:13 +01:00
Chris Green
05f565356f Allow secondary generators when building with CMake. (#9324)
CMake supports the notion of secondary generators which provide extra
information to (e.g.) IDEs over and above that normally provided by
the primary generator. Spack only supports the 'Unix Makefiles' and
'Ninja' primary generators but was not parsing out the primary
generator when a secondary generator was also included (e.g. for
a generator attribute like 'Codeblocks - Ninja'). This adds a regex
for extracting the primary generator for validation.

Since the secondary generator is irrelevant to a Spack build, it is
passed on to CMake without further validation.
2019-02-12 12:39:19 -06:00
健美猞猁
f9c27f52bd casacore: new package (#7471) 2019-02-12 17:22:48 +01:00
Ben Morgan
8fd4e9a9fa xerces-c: Add cxxstd variant (#10561)
Add variant to support compiling against main C++ standards if needed
for ABI compatibility. Use 'default' value as Xerces-C autoconf system
does not enforce a minimum, or set a default, C++ standard.
2019-02-12 09:40:59 +01:00
Brian Van Essen
dc12ca5c76 lbann: updated versions (#10568) 2019-02-12 09:05:32 +01:00
Matthias Diener
068eefb4f5 remove remaining lzma dependencies (#10553) 2019-02-12 09:03:50 +01:00
Matthias Diener
6e38423d1c openssl: add version 1.1.1a (#10562) 2019-02-12 08:58:50 +01:00
Omar Padron
0ef139ac4d work around an issue with docker/dockerhub (#10547)
* try to workaround an issue with docker/dockerhub
* apply workaround only when running in travis
2019-02-08 16:39:40 -08:00
Javier Cervantes
36ebd7462c root package major update (#8428)
* Extend current recipe for root package
* Add removed old version
* Add dependency type for Python and R packages
* Add compiler variants
* Adding new root version: 6.14.00
* Add back the minimum cmake version required
* LZ4 and xxhash support for old (using builtin options) and new versions (external packages)
* Set PYTHONPATH in setup_environment
* Address typos and issues pointed by HadrienG2
* Add newer ROOT versions
* Solve support for asimage
* Define incompatible variants
* Organize old dependencies
* Add support for minuit
* Add support for pythia6
* Remove unneeded list_url
* Update license header
* Remove block of commented old dependencies
* Contrain Qt version
* Comment pythia8 variant/dependency, not supported by spack
* Force not to build pythia8
2019-02-08 09:17:07 -08:00
Matthias Diener
ff67009161 libarchive: remove lzma dependency (#10517)
lzma was last updated in 2008 and has compilation
issues on some platforms. The format has been superceded
by xz (see e.g. https://tukaani.org/xz/).
2019-02-08 16:33:13 +01:00
Denis Davydov
5623ac3d6b CudaPackage: fix wrong version range (#10551) 2019-02-08 16:32:43 +01:00
Robert Blake
a55fc5b963 Adding a package for cardioid. (#10448)
* Adding a package for cardioid.

* Changing package to pass flake8

* Removing template leftovers per @ax3l 's advice

* Adding a homepage so tests pass.

* Removing whitespace for flake8

* Changing the name of master branch to match spack standards.
2019-02-08 11:17:26 +01:00
Michael Kuhn
84bc2a4215 meson: add 0.49.1 and disable rpath stripping (#10463)
rpath stripping breaks (at least) the gtkplus build because at-spi2-atk's
dependencies can not be found.
2019-02-08 11:15:49 +01:00
Peter Scheibel
d8746d596e
bug report template: suggest --stacktrace instead of -s (#10548)
1137b18 removed the -s option from spack such that to see a stack
trace you must pass the --stacktrace option. The bug report templates
were not updated accordingly.
2019-02-07 21:06:57 -06:00
Piotr Luszczek
f093515002 netlib-scalapack package: add CMake test patch (#10452)
Add patch to fix Fortran mangling in CMake test

This is a fix for builds with GCC 6/7/8 and CMake 2/3. It includes
a link to the issue where this is reported. For now, the Spack
package applies the patch to all releases >= 2.0.2
2019-02-07 20:58:27 -06:00
Justin Stanley
ec6de8326e repeatmasker package: add variant for cross_match engine (#10534) 2019-02-07 16:53:30 -06:00
wspear
76feb0205d New package: py-jupyterhub (#10461)
This package depends on both python 3.5+ and node-js which depends on
python 2.7/2.8 to build. Currently it can only be installed if the
node-js package's python dependency is manually removed, so node-js
will build with python found on the system rather than provided by
spack. Upcoming commits may allow spack to reconcile this
automatically.
2019-02-07 16:47:46 -06:00
Justin Stanley
ef89ae03bc mirdeep2 package: make sure bins are executable (#10515) 2019-02-07 13:05:19 -06:00
mathsen
570af0c313 Trilinos package: update superlu-dist dependency (#10511)
Trilinos master branch gets the latest superlu-dist (currently 6.1.0)
2019-02-07 12:58:45 -06:00
Massimiliano Culpo
58f1dc037a log-parse: fix error message when no error lines are found (#10543) 2019-02-07 12:19:19 -06:00
Satish Balay
b8684b318c
petsc: petscvariables is used from user makefiles - so it should not have spack compilers listed (#10365) 2019-02-07 09:09:23 -06:00
Satish Balay
1d71a5ea57
petsc4py and libensemble: add @develop dependencies (#10539)
* py-petsc4py: add @develop

* py-libensemble: add @develop dependency on py-petsc4py@develop
2019-02-07 09:06:31 -06:00
Satish Balay
0ad1b2a2c8
petsc@xsdk-0.2.0: fix sowing dependency (#10535) 2019-02-07 09:05:43 -06:00
Satish Balay
753fec39ae
xsdk@develop fixes (#10521)
* xsdk@develop: switch trilinos from @master to @develop

* xsdk@develop: dtk - fix trilinos dependency on dtk.
 - dkt-3.0 should be used with trilinos-12.4*
 - dtk/master should be used with trilinos@develop
2019-02-07 09:05:14 -06:00
Justin Stanley
09a884322f orthofiller: new package at 1.1.4 (#10373) 2019-02-07 10:22:36 +01:00
Gregory Lee
f0cb4580d1 fixed checksum (#10393) 2019-02-07 10:20:45 +01:00
Levi Baber
af7f1bb3ca new package: perl logger simple (#10509) 2019-02-07 10:19:07 +01:00
Levi Baber
07b5a6a512 perl-file-homedir: new package (#10533) 2019-02-07 10:09:20 +01:00
Levi Baber
4679c11098 py-biopython: new version (#10532) 2019-02-07 10:08:45 +01:00
Matthias Diener
d4d402586c cmake: add version 3.13.4 (#10538) 2019-02-07 09:15:32 +01:00
Justin Stanley
401d305f4e phrap-crossmatch-swat: new package at 1.090518 (#10529) 2019-02-06 19:13:44 -06:00
Mario Melara
5bc71f07dd Add x86_64 as target to cray platform (#10369)
Add x86_64 as a target for the Cray platform, and also designate it
as the default front_end target.
2019-02-06 17:49:00 -06:00
Owen Solberg
cdbaf8dfc5 mafft package: add version 7.407 (#10488) 2019-02-06 13:55:16 -06:00
Matthias Diener
6dbc1afe45 jdk package: add version 1.8.0_202 (#10536) 2019-02-06 13:54:02 -06:00
Levi Baber
0cf0fd47c8 New package: perl-object-insideout (#10508) 2019-02-06 13:53:33 -06:00
Matthias Wolf
5281403fb2 fmt package: fix cmake arguments (#10500) 2019-02-06 13:52:49 -06:00
Stephen Herbein
b028e99cac py-black: add new package 2019-02-06 13:50:04 -06:00
Stephen Herbein
4e92974ed1 py-toml: add latest version and update checksums to sha256
A version >= 0.9.4 required for py-black.  Added latest, which is
0.10.0.  Manually verified that the .tar.gz for v0.9.3 used to generate
the sha256 matched the previous md5.
2019-02-06 13:50:04 -06:00
Matthias Diener
bdabdb85ed curl package: add version 7.63.0 (#10516) 2019-02-06 13:48:36 -06:00
Douglas Duckworth
d053eac538 py-multiqc: add version 1.7 (#10520)
Added sha256 for py-multiqc as well as require py-matplotlib < v 3.0
2019-02-06 13:47:59 -06:00
Levi Baber
1a34bebe79 genemark et package: add version 4.38 (#10519)
Also add heu_dir to bin/
2019-02-06 13:46:35 -06:00
Jon Rood
11c52c3bf7 Paraview package: update PYTHONPATH for dependents (#10501)
Add vtkmodules directory to PYTHONPATH in Paraview for Trilinos
2019-02-06 12:45:14 -06:00
Daniel Topa
d9d75635c7 Add Python 3.7.2 updated (#10531)
Also add versions 3.7.1, 3.6.8, 3.6.7, 3.6.6. Does NOT alter preferred version (2.7.15).

Supplants PR 10491 "Add Python 3.7.2" (https://github.com/spack/spack/pull/10491).

Verification builds on LANL Darwin:

**Intel Xeon**
[+] /scratch/users/dantopa/new-spack/pr.new.python-3.7.2/general/opt/spack/linux-centos7-x86_64/gcc-4.8.5/python-3.7.2-d3p7vg6w2r563cpmwsmbgjbsiqc4j4fq
[+] /scratch/users/dantopa/new-spack/pr.new.python-3.7.2/general/opt/spack/linux-centos7-x86_64/gcc-4.8.5/python-3.7.1-ibom6qj2z64egyaqz5htkwp5tr362il6
[+] /scratch/users/dantopa/new-spack/pr.new.python-3.7.2/general/opt/spack/linux-centos7-x86_64/gcc-4.8.5/python-3.6.8-rkifc3c7mjgdglw27upiap767ut4wpkz
[+] /scratch/users/dantopa/new-spack/pr.new.python-3.7.2/general/opt/spack/linux-centos7-x86_64/gcc-4.8.5/python-3.6.7-meuesn43twttt756exyzqgdhohjgipjq
[+] /scratch/users/dantopa/new-spack/pr.new.python-3.7.2/general/opt/spack/linux-centos7-x86_64/gcc-4.8.5/python-3.6.6-qwnwme7otyuoqqudcglfmfy75t5npywl

**Arm**
[+] /scratch/users/dantopa/new-spack/pr.new.python-3.7.2/arm/opt/spack/linux-rhel7-aarch64/gcc-4.8.5/python-3.7.2-qj27kzs4ttdqudm3hsi3pt57kv7lshco
[+] /scratch/users/dantopa/new-spack/pr.new.python-3.7.2/arm/opt/spack/linux-rhel7-aarch64/gcc-4.8.5/python-3.7.1-io5eneirgvpegy3tosvp6wq5ndf7yjis
[+] /scratch/users/dantopa/new-spack/pr.new.python-3.7.2/arm/opt/spack/linux-rhel7-aarch64/gcc-4.8.5/python-3.6.8-ej3vnvta2hbtrh7p5hokfqkuewxeqgsa
[+] /scratch/users/dantopa/new-spack/pr.new.python-3.7.2/arm/opt/spack/linux-rhel7-aarch64/gcc-4.8.5/python-3.6.7-l3qnue72ewppn2wxza3w6l62l7ijlque
[+] /scratch/users/dantopa/new-spack/pr.new.python-3.7.2/arm/opt/spack/linux-rhel7-aarch64/gcc-4.8.5/python-3.6.6-b55pdoqsr5bie4k5djd4vokm3nywhm45

**Power9**
[+] /scratch/users/dantopa/new-spack/pr.new.python-3.7.2/power9/opt/spack/linux-rhel7-ppc64le/gcc-4.8.5/python-3.7.2-cicayvl7ki4tswoqlljsmcetwqcnoh3x
[+] /scratch/users/dantopa/new-spack/pr.new.python-3.7.2/power9/opt/spack/linux-rhel7-ppc64le/gcc-4.8.5/python-3.7.1-7vej3zvnvyj2jvz5lnxhnts3ok2fcxbp
[+] /scratch/users/dantopa/new-spack/pr.new.python-3.7.2/power9/opt/spack/linux-rhel7-ppc64le/gcc-4.8.5/python-3.6.8-xijljmdanyrybcx2rv65qshycmbrfv6c
[+] /scratch/users/dantopa/new-spack/pr.new.python-3.7.2/power9/opt/spack/linux-rhel7-ppc64le/gcc-4.8.5/python-3.6.7-vqdhzg7c3xxxregqmzxsqqfzxt2hajvq
[+] /scratch/users/dantopa/new-spack/pr.new.python-3.7.2/power9/opt/spack/linux-rhel7-ppc64le/gcc-4.8.5/python-3.6.6-jf4bnsdwk3qjhtmvjjhblnrcz5dztfdq

2019-02-05
Signed-off-by: Daniel Topa <dantopa@lanl.gov>

Signed-off-by: Daniel Topa <dantopa@lanl.gov>
2019-02-06 12:03:25 -06:00
Nichols A. Romero
5394f0016a CUDA compiler conflicts for Linux (#10460)
* CUDA compiler conflicts for Linux.

* Add Volta and Turing GPUs.

* Add mandatory conflict for Volta and Turing GPUs.

* Revert "CUDA compiler conflicts for Linux."

This reverts commit 7d4ff654ac53aad272c59e9f7f8bb3fbb32bcec4.

* Compiler conflicts introduced from previous commit into CUDA packaged moved and integrated into CUDA build system.

* More conversative with compiler conflicts for cuda 10.0.130, since I don't know what will happen with future cuda 10.x releases.

* Correct off-by-one errors in clang conflicts for x86_64 Linux.

* No restrictions on Apple Clang compiler until we are able to distinguish Xcode clang from github clang more easily. Note to fix this in the future.

* Change comment to clarify that github clang refers to LLVM clang.

* Fix and simplify index range.

* Fix overlapping conflicts for CUDA 10.0.130

* Removed extra ^cuda from conflict.
2019-02-06 17:09:52 +01:00
Valentin Clement (バレンタイン クレメン)
548e6736c4 Update CLAW package with version 1.2.1 (#10528) 2019-02-06 15:51:52 +01:00
Levi Baber
881ce3a5c2 perl-yaml: new package (#10514) 2019-02-06 15:47:54 +01:00
simo-tuomisto
1be258a587 wordnet: new package (#10526) 2019-02-06 15:38:48 +01:00