Commit graph

6516 commits

Author SHA1 Message Date
Todd Gamblin
f082d26ddd Fixes #1098: spack graph crashes for large graphs.
- Fixed logic for collapsing backward edges

- Last collapse now depends on whether prior step in left collapse
  sequence alrady did the collapse.
2016-09-27 23:28:51 -04:00
Todd Gamblin
0d3d74e5c2 Improvements to the Spack graph command.
- Distinguish between static (package) and dynamic (spec) graphs.

  - static graphs ignore conditions and multiple instances (hashes) and
    plot raw dependencies among packages.

  - dynamic graphs include information from particular specs (instances of
    packages) and can have multiple instances with hashes.

- Allow graphing all packages in the install DB.

  - useful for debugging.
2016-09-27 11:00:50 -04:00
Todd Gamblin
43ca805248 Factor out canonical_deptype function, cleanup spec.py 2016-09-27 11:00:50 -04:00
Todd Gamblin
cd960caf8d Clean up Exceptions in spec.py 2016-09-27 11:00:45 -04:00
Adam J. Stewart
9b575dd976 Various updates to scipy and numpy (#1856) 2016-09-27 10:56:24 -04:00
Michael Kuhn
00b3aa77ae Update cdo to 1.7.2 (#1858) 2016-09-27 10:56:04 -04:00
Erik Schnetter
88af9f783d Make PETSc build on Darwin (#1835)
Don't set cpp when building on Darwin.
2016-09-26 10:38:02 -07:00
Erik Schnetter
3282eaea8d Update OpenSSL (#1853) 2016-09-26 10:37:40 -07:00
Denis Davydov
1e10309ff7 some fixes to blas/lapack usage in packages (#1852)
* atlas: fix unit test

* openblas: remove symlinks; use lapack_libs.ld_flags in the test

* mkl: fix openmp variant of blas/lapack libs

* intel-parallel-studio: fix openmp variant of blas/lapack libs

* netlib-scalapack: fix blas/lapack for multilib case (e.g. mkl)

* arpack-ng: fix blas/lapack for multilib case (e.g. mkl)

* petsc: explicitly specify blas/lapack

* minor

* cantera: fix blas/lapack usage

* ipopt: fix blas/lapack usage

* netlib-lapack: fix external blas usage

* mfem: fix lapack/blas usage

* superlu-mt: fix blas usage

* flake8 fixes
2016-09-26 10:37:23 -07:00
Todd Gamblin
cb36aadaf6 Fix doc bugs, widen columns in the package list 2016-09-23 18:07:33 -07:00
Patrick Gartung
ec91152a36 a few package used in HEP including ROOT6 2016-09-23 18:07:22 -07:00
Adam J. Stewart
64194a823a Remove duplicate ICU package (#1837)
* Remove duplicate ICU package

* Ignore deleted files during flake8 tests

* Rename Boost ICU variant
2016-09-23 14:16:59 -07:00
Denis Davydov
6ef6428331 m4: fix compilation on Sierra with GCC (#1844)
* m4: fix compilation on Sierra with GCC

* m4: check macOS version
2016-09-23 13:38:29 -07:00
Bruno Turcksin
98d54182d3 Add Trilinos 12.8.1 (#1843) 2016-09-23 13:36:21 -07:00
Erik Schnetter
73ec2a27d0 Don't require git for Julia @0.5: (#1834) 2016-09-23 13:35:12 -07:00
Erik Schnetter
8147a09489 Update jemalloc to 4.2.1 (#1839) 2016-09-23 13:32:57 -07:00
Robert D. French
3d282b9239 Add libmesh, needed for some FEM applications (#1846) 2016-09-23 13:26:27 -07:00
Denis Davydov
df5e151049 hypre: fix a bug with blas/lapack names (#1841) 2016-09-23 10:06:18 -07:00
Erik Schnetter
c0ebbc97c9 Update OpenSSL (#1836)
This is a security update with priority "HIGH".
2016-09-23 08:21:15 -07:00
Denis Davydov
462a4a1353 boost: fix a bug which broke it on macOS with clang+gfortran (#1816)
* dealii: add missing python dependency

* boost: fix a bug which  broke it on macOS with clang+gfortran

Boost was using gcc compiler instead of clang++, which lead to
cryptic Undefined symbols linking errors for boost::python::objects::function_object()
when building other packages against boost+python.

* boost: add exceptions for intel

* boost: use spack_cxx
2016-09-22 13:47:22 -07:00
Adam J. Stewart
a638b62ab1 Updates to CGAL and ICU4C packages (#1828) 2016-09-22 11:50:50 -07:00
Ben Boeckel
c7860322f5 package: fix variable name usage (#1829) 2016-09-22 11:47:25 -07:00
Adam J. Stewart
f1f301ad3b Fix spack checksum output indentation (#1826) 2016-09-22 11:33:29 -07:00
Elizabeth Fischer
64c3b11478 suitesparse: Added +fpic (for linking with shared libraries) (#1542) 2016-09-22 11:03:49 -07:00
Erik Schnetter
7ad6c35627 New package "charm" for the Charm++ parallel programming framework (#1766) 2016-09-22 00:48:00 -07:00
Eric
025b779a30 Fix sbang for perl (#1802)
* Perform shebang fix for all files

* Fix sbang for perl scripts

Otherwise perl would look at the #! line and call sbang again, resulting
in an infinite loop.
2016-09-22 00:43:47 -07:00
Elizabeth Fischer
98f9dd266f Remove SPACK_DIRTY env var (#1818)
* Removed SPACK_DIRTY env var support.

* Finished removing SPACK_DIRTY support.

* Minor changes.
2016-09-22 00:43:33 -07:00
Massimiliano Culpo
1db2552644 fix : stops infinite recursion for python 2.6 (#1823) 2016-09-22 00:31:28 -07:00
Massimiliano Culpo
d848559f70 Reworking of lapack_shared_libs and similar properties (#1682)
* Turned <provider>_libs into an iterable

Modifications :
- added class LibraryList + unit tests
- added convenience functions `find_libraries` and `dedupe`
- modifed non Intel blas/lapack providers
- modified packages using blas_shared_libs and similar functions

* atlas : added pthread variant

* intel packages : added lapack_libs and blas_libs

* find_library_path : removed unused function

* PR review : fixed last issues

* LibraryList : added test on __add__ return type

* LibraryList : added __radd__ fixed unit tests

fix : failing unit tests due to missing `self`

* cp2k and dependecies : fixed blas-lapack related statements in package.py
2016-09-21 12:27:59 -07:00
Todd Gamblin
6b6f868f2a Flake8 fixes. 2016-09-21 04:35:15 -07:00
Todd Gamblin
786ab114b7 Merge branch 'qt-osx' of git://github.com/mathstuf/spack into mathstuf-qt-osx 2016-09-21 04:32:03 -07:00
George Hartzell
51d869493a Add package for bedtools2 (#1572)
Add package for bedtools2, with support for v2.25.0 and v2.26.0.
2016-09-21 04:23:03 -07:00
George Hartzell
db0baaafe3 Add package for bamtools (#1571)
bamtools provides a C++ API & command-line toolkit for working with BAM
data.
2016-09-21 04:22:55 -07:00
Mayeul d'Avezac
3d1c92e22c Update espresso recipe to track change in spack internals (#1734) 2016-09-21 04:18:35 -07:00
Adam J. Stewart
cf925ddc97 Add missing build dependencies to hdf package (#1812) 2016-09-21 04:16:57 -07:00
Kelly Thompson
3d3614e522 Update to allow netlib-scalapack to build against netlib-lapack. (#1539) 2016-09-21 04:10:30 -07:00
Glenn Johnson
c1284a9046 Stop python from linking with system ncurses (#1672)
Python will look to link with libncursesw in preference to libncurses. Since
ncurses in spack is built without suffixes there is no libncursesw and
python will link to the system libncursesw for _curses.so and
_curses_panel.so, as well as libpanelw for _curses_panel.so.

This PR introduces a patch that simple removes the check for ncursesw in
setup.py and therefore sets `curses_library` to `ncurses`.
2016-09-21 04:02:28 -07:00
Glenn Johnson
851b58248d Build pkg-config files for ncurses (#1673) 2016-09-21 04:02:07 -07:00
Elizabeth Fischer
899f3a7e37 Fixed bug propagating --dirty flag to sub-installs. (#1625)
* Fixed bug propagating --dirty flag to sub-installs.

* Fix syntax error

* Allow --dirty flag to be set with SPACK_DIRTY env var.

* Added dirty flag to `spack diy` and `spack setup`, as is currently in `spack install`

* flake8
2016-09-21 03:56:56 -07:00
Glenn Johnson
73012ec4c8 Rework libgd package (#1679)
* Added missing libtiff dependency
* added dependency on fontconfig
* Added version 2.2.3
* use autotools rather than cmake

The cmake build was not producing a complete install.
* There was no versioning of the installed libraries.
* gdlib-config was missing
* pkgconfig directory was missing

These problems do not happen when built with autotools.
2016-09-21 01:56:20 -07:00
Matt Belhorn
94b24e8893 Adds all available CrayPE CPU targets to platform by default. (#1745) 2016-09-21 01:48:33 -07:00
Todd Gamblin
ae6252ca5f Merge branch 'efischer/160914-FixBinutils226Question' of git://github.com/citibeth/spack into bugfix/efischer-160914-FixBinutils226Question 2016-09-21 01:45:38 -07:00
Axel Huebl
d3e04b3daf Close #1683 Apply ADIOS 1.10.0 Patch (HDF5 1.10+) (#1699)
* Close #1683 Apply ADIOS 1.10.0 Patch

Also correct version dependencies and comments.

* Clean Up ADIOS

- add develop
- simplify HDF5 options (parallel only)
- remove optional netCDF (not fully v4)
2016-09-21 00:55:54 -07:00
Massimiliano Culpo
3254d2f8f9 cp2k : added dependencies (#1724)
* wannier90 : added package (#24)

* wannier90 : added package

* cp2k : added dependency on wannier90

* elpa : updated package, added cp2k dependency (#26)

Conflicts:
	var/spack/repos/builtin/packages/elpa/package.py
2016-09-21 00:53:06 -07:00
Alfredo Adolfo Gimenez
02307cf7ce Set JAVA_HOME on module load and on dependent installs. (#1716)
* Set JAVA_HOME on module load and on dependent installs.

* Include environment setup from dependencies in dependee module (#1714)
2016-09-21 00:52:09 -07:00
Massimiliano Culpo
1cc48bf7d7 grackle : added package (#1725)
Modifications :

* grackle : added package
* grackle : added version 2.2
2016-09-21 00:51:49 -07:00
Erik Schnetter
3c7ea3000a Wrap yt package (#1751)
yt is a python package for analyzing and visualizing volumetric, multi-resolution data from astrophysical simulations, radio telescopes, and a burgeoning interdisciplinary community.
2016-09-21 00:37:46 -07:00
Sergey Kosukhin
746495896c Qt library: added variant to enable/disable compilation of examples (#1763) 2016-09-21 00:25:14 -07:00
Patrick Gartung
e6dc448f18 Compiling python with gnu c++ on macos fails with toolboxglue enabled. 2016-09-20 23:34:15 -07:00
Denis Davydov
27801c354b fix MacOs class for Sierra (#1811) 2016-09-20 17:25:23 -07:00