Commit graph

6762 commits

Author SHA1 Message Date
Alicia Klinvex
44653fa488 Fix xsdk build broken by petsc and trilinos (#4893)
* Fix xsdk build broken by petsc and trilinos

See #4891 for details

* Fix version conflict in trilinos package

Trilinos version 11 may conflict with superlu-dist.
The version "xsdk-0.2.0" was conflicting with superlu-dist,
even though it shouldn't.  I added a lower bound to the
comparison to fix this problem.

Thanks for the help @davydden!
2017-08-01 12:05:15 -05:00
Adam J. Stewart
82735deafd Clarify docs on using a hash in a spec (#4908) 2017-07-31 13:13:39 -07:00
scheibelp
69a6c8ef78 Fix preference for X.Y version when mixed with X.Y.Z versions (#4922)
For packages which contain a mix of versions with formats X.Y and
X.Y.Z, if the user entered an X.Y version as a preference in
packages.yaml, Spack would get confused and favor any version A.B.Z
where X=A and Y=B. In the case where there is a mix of these version
types, this commit updates preferences so Spack will favor an exact
match.
2017-07-31 13:11:08 -07:00
paulhopkins
1c7e5724d9 Add --color=[always|never|auto] argument; fix color when piping (#3013)
* Disable spec colorization when redirecting stdout and add command line flag to re-enable
* Add command line `--color` flag to control output colorization
* Add options to `llnl.util.tty.color` to allow color to be auto/always/never
* Add `Spec.cformat()` function to be used when `format()` should have auto-coloring
2017-07-31 12:57:47 -07:00
Adam J. Stewart
f3c70c235c Add latest version of SCons (#4929) 2017-07-31 19:57:56 +02:00
Axel Huebl
751f1d4fca ZeroMQ: C++ Headers (cppzmq) (#4841)
Adds the cppzmq library, adding a C++ API to ZeroMQ (libzmq). In order to find the autotools-build libzmq, this requires the upcoming cppzmq release (or development branch).
2017-07-31 19:54:06 +02:00
Adam J. Stewart
1f5ca90929 Add missing dependencies to unixodbc (#4928) 2017-07-31 19:44:33 +02:00
Adam J. Stewart
0aaab9bc8c Add latest version of expat (#4930) 2017-07-31 19:36:18 +02:00
Adam J. Stewart
a9efae271b Add latest version of apr (#4931) 2017-07-31 19:35:48 +02:00
George Hartzell
c126c5553c zsh: add variant that skips tcsetpgrp test (#4923)
zsh's configure script fails if there's it tries to test for terminal
functionality if there's not a terminal (e.g. in a Jenkins build).

The configure script has a switch that asserts that tcsetpgrp works
and thereby avoids running that test.

This commit adds a variant that invokes that switch, defaulting to
True.
2017-07-31 11:17:04 -05:00
Axel Huebl
6d97397ab0 gBenchmark: v1.2.0 (#4935)
Adds a the latest version of gBenchmark, release 1.2.0.

This is the first gBenchmark version with proper
[CMake config package installs](https://github.com/google/benchmark/issues/363).
This is important for dependencies building against it, such as gRPC.
2017-07-31 10:06:17 -05:00
Robert Pavel
f7c24289e5 Initial Spackage for qmd-progress library (#4924)
* Initial Spackage for qmd-progress library

PROGRESS is a library is focused on the development of general solvers
that are commonly used in quantum chemistry packages.

* Removed LA-CC from description to fix formatting

* Added Additional Formatting Requests

Added requested formatting changes and also ensured that graphlib and
mpi are disabled if not enabled
2017-07-28 17:10:24 -05:00
sknigh
92ea7c4337 Fix for m4%clang (#4912)
* Fix for m4%clang

* Restricted condition to not subsitute rtlib on OSX
2017-07-28 11:32:53 -05:00
Jon Rood
c5d2206206 Adding QWT package. (#4911)
* Adding QWT package.

* Using builtin file filtering.

* Formatting.
2017-07-27 16:22:29 -05:00
Christoph Junghans
78d7587c93 bml: fix homepage (#4918) 2017-07-27 16:07:47 -05:00
Akhil Reddy Patlolla
6bdc373100 Added Proxy App tag (#4917)
* Added Proxy App tag

*  NO changes except proxy app tag
2017-07-27 15:56:59 -05:00
pkondamudi
ce601a9304 New Package: lcals (#4792)
* New Pacakge: lcals

* added logic for arch detection and compiler choice.

* fixes for comments.

* addressed comments.

* removed LCALS_ARCH and added flags though spack.

* addressed comments.

* flake 8 fix.

* reerted the changes along with comments.
2017-07-27 14:24:28 -05:00
Jim Galarowicz
99cac0bf94 Fix for Krell openspeedshop spack package bug. New multi-value variant for GUI build. (#4880)
* Update the krell institute products to use the latest features of spack for building on cluster platforms.

* Address travis error messages and resubmit the pull request.

* Update the contents of openspeedshop package.py so it passes the flake8 tests.

* Fix flake8 error-whitespack issue in mrnet package.py file.

* Add updates based on spack reviewer feedback.

* More fixes based on comments from reviewers.  Switch using extend to using append, remove additional setting of PATH and LD_LIBRARY_PATH that should not be required due to RPATH.

* More review related changes.  Update MPIOption.append lines and take out xercesc references.

* Create a base options function for common openspeedshop base cmake options to reduce redundencies.

* Add libxml2+python depends on to get around issues with the libxml2 package file.

* Using boost over 1.60.0 causes compile errors.  This is a known boost bug. Also, dyninst-9.2.0 is set to be the vesrion of dyninst to use with OSS, as of now. The newer version fails to build.

* Fix bad syntax in specifying the boost version range.

* Update the version numbers for the krell institute components and tools: cbtf and openspeedshop.

* Do not build glib for qt3, it is not needed and causes build problems at this time anyway.

* A fix was added for setting LD_LIBRARY_PATH in the qt3 build, but if LD_LIBRARY_PATH is not set the qt build fails. So so check and set LD_LIBRARY_PATH if not set, update if it is set.

* Update the fix for qt3 build by setting LD_LIBRARY_PATH instead of checking for whether it is set or not per Adams comment that spack clears LD_LIBRARY_PATH.

* A fix was added for setting LD_LIBRARY_PATH in the qt3 build, but if LD_LIBRARY_PATH is not set the qt build fails. So so check and set LD_LIBRARY_PATH if not set, update if it is set.

* Trim comments to fit more concisely.

* Fix tabs versus spaces and swap if and else clause check from a negative to a positive check.

* Fix issues with the cbtf-argonavis build, update to use dyninst-9.3.2, fixes to openspeedshop package build.

* Fix issues with the cbtf-argonavis package.py files related to comments.

* Add changes for changing the krell packages from Package to CMakePackage.

* Add better changes for changing the krell packages from Package to CMakePackage.

* Add more modifications for changing the krell packages from Package to CMakePackage.

* Add additional modifications for changing the krell packages from Package to CMakePackage and fixing Travis erros

* Fix new travis errors.

* Fix new travis errors.

* Add more changes for PR 4765.

* Add more refinements to the conversion from Package to CMakePackage.

* Fix new travis errors.

* Add dependencies for MPI to be passed to cbtf-krell, so it can build the MPI collectors requested by the builder of openspeedshop.

* Remove extra unnecessary routine to adjust build arguments. Fix if-else clause issue.

* Fix more flake issues caused by last changes.

* Fix a bug where openspeedshop will not build when no mpi variants are specified.  Also switch to a multiple level variant for building the gui(s).  Use none, qt3, and qt4 as the variants with qt3 being the default.

* Add fix for spack issue #4843, where LTDL include files were not found.

* Add the build_type variant back into the openspeedshop package file.
2017-07-27 11:06:44 -05:00
pkondamudi
31a329d237 New Package: RSbench (#4752)
* New Package: RSbench

* minor change

* removed tags as per PR# 4749

* addressed comments and added gcc compiler.

* added proxy app tags to description.

* removed setting CC to pgicc through spec.

* removed compiler as depedency

* removed pgi variant.

* flake 8 fix.

* added mpi depedency with pgi compiler

* added  pgi compiler

* removed PGI compiler as depedency.

* added tags and addressed other code formattings.

* added tags and addressed other code formattings.

* addressed comments.
2017-07-27 10:59:30 -05:00
Denis Davydov
ddc1dcd084 openblas: add 0.2.20 (#4915) 2017-07-27 08:51:39 -05:00
Audrey Thoma
70a089287e snptest: new package (#4900)
* snptest: new package

* fixed version things

* fixed install phase
2017-07-26 17:44:15 -05:00
Adam J. Stewart
b33f92da34 Improve version detection for URLs with dynamic after version (#4902) 2017-07-26 17:43:54 -05:00
Robert Pavel
6e99e2c58e Updated Namespace of BML Repository (#4910) 2017-07-26 17:42:26 -05:00
pkondamudi
4ab12fb503 added MPI dependency to Nekbone package (#4903)
* removed the tags as per comment in PR# 4749

* addressed above comments

* changed fortran compiler.

* added proxy application tags.

* added tags by removing them from description.

* addressed comments

* used join_path instead of path concat.

* removed the tags as per comment in PR# 4749

* addressed above comments

* changed fortran compiler.

* added proxy application tags.

* added tags by removing them from description.

* addressed comments

* used join_path instead of path concat.

* added tags.

* changes to use MPI as depedency.

* removed MPI as variant.

* changed pointer to filtered makenek file.

* flake 8 fix.
2017-07-26 14:27:29 -05:00
Audrey Thoma
b62f0962b0 shortstack: new package (#4905) 2017-07-26 10:14:55 -05:00
Adam J. Stewart
07aec4366f Add universal build_type variant to CMakePackage (#4797)
* Add universal build_type variant to CMakePackage
* Override build_type in some packages with different possible values
* Remove reference to no longer existent debug variant
* Update CBTF packages with new build_type variant
* Keep note on build size of LLVM
2017-07-25 16:34:43 -07:00
Sam Bateman
4b996e9f49 tmux should not set PKG_CONFIG_PATH (#4901)
* fixes #967

* Version bump to 0.9.1

- Bugfixes for spack find
- 0.9.1 can read specs from current develop.

* Don't assume spack is in the path when building docs.

* Remove PKG_CONFIG_PATH from tmux configure

* Change tmux to AutotoolsPackage

* Correct link to libtinfo in tmux
2017-07-25 17:08:34 -05:00
becker33
30f6d2ab90 fix callpath bug (#4659)
* fix callpath bug I found while testing env/cc

* fix hanging indent for flake
2017-07-25 13:51:56 -07:00
Audrey Thoma
6693dc1092 transdecoder: new package (#4895)
* transdecoder: new package

* fixed package structure
2017-07-25 15:51:14 -05:00
Audrey Thoma
402233ecc8 transposome: new package (#4896) 2017-07-25 15:50:42 -05:00
Audrey Thoma
668233a819 trimgalore: new package (#4899) 2017-07-25 15:50:23 -05:00
Gregory Lee
42717bd8e8 fix config.guess patch for ppc64le (#4858)
* fix config.guess patch for ppc64le

* explicit patch for config.guess not required
2017-07-25 13:44:51 -07:00
Audrey Thoma
71991cd9c9 cleaveland4: new package (#4894)
* cleaveland4: new package

* fixing return line in viennarna url_for_version
2017-07-25 13:18:34 -05:00
Audrey Thoma
20ab66a2e9 tabix: new package (#4886)
* tabix: new package

* fixed docs location
2017-07-25 13:02:08 -05:00
Audrey Thoma
5184dda309 sumaclust: new package (#4884)
* sumaclust: new package

* tweaking url and make specs
2017-07-25 08:04:25 -05:00
Jimmy Tang
1d1a0e3d63 Update zstd version (#4873)
* Update zstd version

* Change order of versions

* Use MakefilePackage
2017-07-25 07:55:02 -05:00
Jimmy Tang
2b792f943f Rename the gpu variant to cuda, this is to be consistent with other (#4890)
packages.
2017-07-25 07:53:33 -05:00
Denis Davydov
b0b86e5ffe fix GobjectIntrospection on Darwin (#4872)
* fix GobjectIntrospection on Darwin

* minor
2017-07-24 19:51:17 -05:00
Audrey Thoma
4237e5fffd stacks: new package (#4875) 2017-07-24 19:50:40 -05:00
Stas Sergienko
07e60bc26b added new version of jdk 8u141-b15 (#4876) 2017-07-24 19:50:16 -05:00
Audrey Thoma
d2f08c95d9 swarm: new package (#4885) 2017-07-24 19:49:59 -05:00
Audrey Thoma
8038945145 structure: new package (#4879)
* structure: new pacakge

* fixing package structure (not a pun)
2017-07-24 18:02:20 -05:00
Audrey Thoma
0c96c330ec subread: new package (#4882) 2017-07-24 18:01:56 -05:00
Stas Sergienko
9aa3749787 added new version of cdo (#4877) 2017-07-24 15:50:44 -05:00
Audrey Thoma
bd0699b026 stringtie: new package (#4878) 2017-07-24 15:50:32 -05:00
Adam J. Stewart
250ee413e9 Change Version formatting properties and functions to return Version objects (#4834)
* Change version.up_to() to return Version() object
* Add unit tests for Version.up_to()
* Fix packages that expected up_to() to return a string
* Ensure that up_to() preserves separator characters
* Use version indexing instead of up_to
* Make all Version formatting properties return Version objects
* Update docs
* Tests need to test string representation
2017-07-24 13:02:13 -07:00
Jimmy Tang
df2fc25ddf Add a py-theano version from git repo (#4871) 2017-07-24 08:56:54 -05:00
健美猫
8a06e3d867 Add cuda variant for mvapich2. (#4800)
* Add cuda variant for mvapich2.

* Disable cuda for mvapich2 by default.
2017-07-23 12:18:05 -05:00
Stephen McDowell
1cdb3c61ca fix sphinx dependencies, add v1.6.3 (#4870) 2017-07-23 09:44:12 -05:00
Milton Woods
4044e9f918 Perl - allow package activation without PERL5LIB variable (#4540)
* perl: prepend default perl @INC path to support package activation

* perl: remove stray comma from list of configure arguments

* perl: final comma in configure arguments makes adding arguments safer

This reverts commit fdc10cd611f525ebc31ca1953e048095b1c75350.

* perl: add comment about modified @INC (thanks to George Hartzell)

* perl: use self.prefix.lib and self.prefix.bin for clarity

* perl: convert tabs added by editor to spaces for flake8

* perl: use new path syntax: prefix.lib.perl5

* perl: avoid line break before binary operator

* perl: use compact spack syntax for perl executable
2017-07-23 09:41:45 -05:00