Commit graph

11277 commits

Author SHA1 Message Date
Reid Priedhorsky
ed9a1b7a45 add Charliecloud 0.9.1 (#8902) 2018-08-06 17:43:00 -05:00
Adam J. Stewart
5f10d9239b Remove default variant bug from list of known issues (#8900) 2018-08-06 16:56:45 -04:00
George Hartzell
4e985051c0 Docstring typo: builing -> building (#8896) 2018-08-06 13:36:57 -04:00
健美猞猁
a816397322 Bump R to v3.5.1. (#8895) 2018-08-06 11:16:27 -05:00
Sergey Kosukhin
7cc11debdd Libtool: version 'develop' (#8894)
* libtool: add version 'develop'.

* libtool: patch: correct parsing of compiler output when collecting predeps and postdeps.
2018-08-06 10:43:26 -05:00
Sajid Ali
3fc1a65867 modified: var/spack/repos/builtin/packages/py-pytest/package.py (#8890) 2018-08-06 09:21:49 -05:00
Thomas Roehl
377e957f3b LIKWID: Switch to perf_event backend to allow user installations but with limited features (#8886)
* Switch to perf_event backend to allow user installations but with limited features.

* Fix flake8 issues

* Fix flake8 issues remove filter for INSTALL_CHOWN

* Incorporate the comments
2018-08-06 09:21:30 -05:00
健美猞猁
4dc8936b63 Bump mvapich2 to the latest v2.3 release. (#8892) 2018-08-06 12:03:33 +02:00
George Hartzell
9c2c6c7f7e Add unzip runtime dependency to lua package (#8831)
* Add unzip to lua-luaposix

I ended up on an [Ubuntu] system that hadn't had unzip employed
and discovered lua-luaposix requires it (while buildig Lmod).

Closes #8533

* Move unzip prereq to lua, type=run

Rather than touching up each of the lua rocks (packages)
that need unzip, make it available as a run dependency in
lua.

Tested by building lmod on a minimal Ubuntu system.
2018-08-05 13:26:22 -05:00
Adam J. Stewart
7e0bd152b7 Generate coverage reports for all unit and build tests 2018-08-04 21:18:49 -07:00
Todd Gamblin
5cc2309330 revert cd9691de5 (#4692) while we work on a fix. 2018-08-04 20:31:55 -07:00
Christoph Junghans
abd1dfc333 kim-api: initial commit (#8873)
* kim-api: initial commit

* Update package.py
2018-08-04 16:47:35 -05:00
Tin Huynh
eb39d0c729 Package/flang: Updated to use own version of llvm (#8766)
Flang now uses its own version of llvm and clang (called flang-driver). This is
handled by adding flang-specific versions of the LLVM package and updates flang
to depend on those versions.
2018-08-03 20:35:09 -04:00
Todd Gamblin
b5071312c4 spack spec: no extra newline with --yaml; error with no specs
- `spack spec` now returns an error if given no specs

- removed superfluous trailing newline from `spack spec --yaml` output
  (only one newline now)
2018-08-03 15:18:34 -05:00
Christoph Junghans
c73d237d08 simplemoc: version bump (#8884) 2018-08-03 14:31:06 -05:00
Mark W. Krentel
69641851ea libmonitor: update version and add variant to configure (#8834)
* libmonitor: update to version 2018.07.18 and add variant to configure
for hpctoolkit.

* Specify the @2013.02.18 version in cbtf-argonavis and cbtf-krell,
since this is no longer the default version.  These are the only
other packages that use libmonitor.
2018-08-03 14:00:12 -04:00
Adam J. Stewart
4de301ebf2 Update bash completion with new spack arch flags 2018-08-03 11:32:08 -05:00
Adam J. Stewart
4f76e80925 Add spack arch --operating-system and --target flags 2018-08-03 11:32:08 -05:00
Abhinav Bhatele
febfa60935 Update broken codesign.llnl.gov urls (#8880)
* amg2013: fix homepage and url

* kripke: fix homepage and url

* lcals: fix homepage and url

* lulesh: fix homepage and move to git

* urls on single line
2018-08-03 10:25:10 -05:00
Geoffrey Oxberry
0c01f42a9f arpack: add version 3.6.2 (#8881) 2018-08-03 09:53:44 -05:00
健美猞猁
8e1cc26be7 dmd: a new package. (#8826)
* dmd: a new package.

* Install src for dmd.

* Install src to prefix.src.

* Replace copy_tree with install_tree.
2018-08-02 22:07:01 -05:00
Todd Gamblin
43c77ac3cb libdwarf: remove use of hide_files()
- This was a nasty workaround due to the way our compiler wrappers used
  to work.  We don't want to have to modify our elfutils installation to
  install libdwarf.

- Since cd9691de5, we no longer need this because the package will always
  come before dependencies in our include order.
2018-08-02 19:00:52 -07:00
dorier
1ec06e6111 new package: XSD (#8784) 2018-08-02 16:28:19 -04:00
Stephen Herbein
3b0983a217 flux: update flux-core package and add a flux-sched package (#8818)
Renames the flux package to flux-core and updates its dependencies, versions,
and variants. Adds a flux-sched package.

This also updates two flux-core dependencies: lua and czmq.
2018-08-02 16:20:55 -04:00
Dan FitzGerald
e554add64b Change MUMPS to allow it to build with clang+xlf compiler combination (#8388)
The mumps package was unable to build using the llvm clang compiler
suite, as it defaulted to using mpif90 for linking and mpif90 cannot
be used for linking shared library code. This PR modifies the MUMPS
package.py to allow it to use IBM XL Fortran for linking. It also
eliminates the need for the existing MUMPS IBM XL patches by having
package.py specify the compiler-dependent "shared" flag to the
linker, and always using the compiler suite's Fortran compiler
for linking.
2018-08-02 14:23:37 -04:00
Tom Merrick
51aa604ed2 Fix openmpi to work with slurm/pmi and mxm (#8427)
* Add binutils+libiberty for mxm fabric
* Help find the pmi library when using the slurm scheduler
2018-08-02 14:06:39 -04:00
Levi Baber
c94109c34c Package py-biom-format fixes (#8727)
* py-biom-format: needs py-setuptools at runtime
* py-biom-format: needs py-pyqi
2018-08-02 13:51:51 -04:00
Yifan Zhu
6f2a739053 New package: GRNBoost (#8763) 2018-08-02 13:46:36 -04:00
Michael Kuhn
12fb1cdbe5 Replace pkg-config dependencies with virtual (#8783)
Several packages specified pkg-config as a dependency, which is
a specific implementation of the pkgconfig virtual. Most packages
do not request a specific implementation. The current concretizer
may choose a different implentation of pkgconfig for the nonspecific
dependents, which conflicts with the request for pkg-config. This
replaces all requests for a specific implementation of pkgconfig
with the virtual package as a temporary solution to the issue.
2018-08-02 13:29:04 -04:00
Matthias Wolf
b1c35e1e13 package neovim: add info for version 0.3.1 (#8866) 2018-08-02 13:04:59 -04:00
Adam J. Stewart
d07e9e13ab Update homepage for laghos (#8864) 2018-08-02 13:03:52 -04:00
Matthias Wolf
1aa01873c7 Adding lazy property python module (#47) (#8867) 2018-08-02 11:44:16 -05:00
Michael Kuhn
ec3ffd9d28 sz: fix checksum for 2.0.2.0 (#8868) 2018-08-02 11:43:59 -05:00
Kelly (KT) Thompson
d68338cc8c Trilinos: Update rules for superlu-dist version compatibility. (#8851) 2018-08-02 11:25:30 -05:00
Takayuki Kobayashi
3a919c6abb Update and Bugfix for pexsi/package.py (#8822)
* Update and Bugfix for pexsi/package.py

1. pexsi@0.10.2 is not compatible with superlu-dist@5.4.0 due to [Change LargeDiag to LargeDiag_MC64; Add LargeDiag_AWPM](d7dce5a348).
2. In the 'edit' phase, '@MPICXX_LIB' must be substituted before '@MPICXX' is substituted.

* change dict to list of tuples

Use a list of tuples to remember the order of `substitutions`.

* Update package.py

* Update package.py
2018-08-02 11:24:57 -05:00
Douglas Duckworth
da959ba220 added py-setuptools as dependency (#8843)
* added py-setuptools as dependency

* more changes
2018-08-02 11:24:26 -05:00
Sergey Kosukhin
ec174dae69 CMake: patch for NAG. (#8869) 2018-08-02 11:17:15 -05:00
Michael Kuhn
4a6a19be85 adios2: add 2.2.0 (#8871)
This also enables the bzip2 and zfp variants. The sz variant is
currently broken.
2018-08-02 11:16:17 -05:00
Sergey Kosukhin
03dc78a894 netcdf-fortran: enforce autoreconf when building with NAG. (#8844)
* netcdf-fortran: enforce autoreconf when building with NAG.

* netcdf-fortran: patch the configure script instead of running autoreconf to get rid of additional dependencies.

* netcdf-fortran: add comment for the patch.
2018-08-02 08:32:20 -05:00
Geoffrey Oxberry
c79cd5fe51 suite-sparse: add version 5.3.0 (#8837) 2018-08-02 07:25:57 +02:00
Geoffrey Oxberry
e793f29173 openblas: add version 0.3.2 (#8833) 2018-08-01 19:14:48 -05:00
Kelly (KT) Thompson
432a5ecd36 Dia needs access to gettext and pkg-config. (#8840)
When using spack on a ubuntu baseline system, I was unable to build dia with
adding these build dependencies on gettext and pkg-config.
2018-08-01 19:12:17 -05:00
Sergey Kosukhin
abfb16af78 Small patch for netlib-lapack. (#8854) 2018-08-01 18:55:07 -05:00
Sergey Kosukhin
23b6850849 Conflict for cmake 3.11.x and Intel. (#8855) 2018-08-01 18:53:53 -05:00
becker33
cd9691de53 cc: package search paths come before dependency paths (#4692)
Spack currently prepends include paths, library paths, and rpaths to the compile line.  This causes problems when a header or library in the package has the same name as one exported by one of its dependencies.  The *dependency's* header will be preferred over the package's, which is not what most builds expect.  This also breaks some of our production codes.

This restores the original cc behavior (from *very* early Spack) of parsing compiler arguments out by type (`-L`, `-I`, `-Wl,-rpath`) and reconstituting the full command at the end.

`<includes> <other_args> <library dirs> <rpaths>`

This differs from the original behavior in one significant way, though: it *appends* the library arguments so that dependency libraries do not shadow those in the build. 

This is safe because semantics aren't affected by *interleaving* `-I`, `-L`, and `-Wl,-rpath` arguments with others, only with each other (so the order fo two `-L` args affects the search path, but we search for all libraries on the command line using the same search path).

We preserve the following:
1. Any system directory in the paths will be listed last.
2. The root package's include/library/RPATH flags come before flags of the same type for any dependency.
3. Order will be preserved within flags passed by the build (except system paths, which are moved to be last)
4. Flags for dependencies will appear between the root flags and the system flags, and the flags for any dependency will come before those for *its* dependencies (this is for completeness -- we already guarantee this in `build_environment.py`)
2018-08-01 15:48:00 -07:00
Holly
38062a8abc docs: minor text changes (#8858) 2018-08-01 13:59:51 -07:00
Stephen Herbein
de60e9d582 lmod: fix use of custom separator in prepend_path etc. (#8737)
fixes #8736
2018-08-01 12:58:54 +02:00
Geoffrey Oxberry
db79c86ed6 lmod: add version 7.8 (#8838) 2018-07-31 23:19:41 -07:00
Stephen Herbein
cdbc545793 docs: update spack view argument synatx (#8839)
The `--dependencies` and `--exclude` flags are now arguments to the `spack view`
comand rather than the `spack view symlink` command.
2018-07-31 10:41:41 -07:00
Geoffrey Oxberry
f7761d1081 slepc: add blopex variant (#8820) 2018-07-30 18:18:36 -05:00