Commit graph

11713 commits

Author SHA1 Message Date
健美猞猁
c1daedfdbf Gromacs conflicts with cmake@3.10: . (#8956) 2018-08-11 08:37:51 -05:00
Levi Baber
c2b913d709 r-biasedurn: new package (#8937)
* r-biasedurn: new package

* r-biasedurn: add list_url
2018-08-10 16:08:31 -05:00
Levi Baber
7e1e689e4c r-amap: new package (#8935)
* r-amap: new package

* r-amap: add list_url

* r-amap: dep type
2018-08-10 15:21:22 -05:00
Levi Baber
b78c198b62 r-fastcluster: new package (#8934)
* r-fastcluster: new package

* r-fastcluster: add list_url
2018-08-10 15:01:12 -05:00
jthies
14f6b13a7b Phist 1.6.1 (#8933)
* packages/phist: new version 1.6.1

* packages/phist: depends on Python 3.x for generating Fortran and C++ bindings

* packages/phist: new version 1.7.2

* phist: depend on python@3 only for versions later than 1.7

* packages/phist: depend on python@3: rather than 3

* phist: python dependency is type='build', thans @adamjstewart
2018-08-10 12:53:18 -05:00
Tom Merrick
b1182741d4 Branch with the meson build-system (#8467)
* Branch with the meson build-system

* Fix build_environment for dual loads and add create code

* Add documentation

* Fixed option list

* Update build_system_guess for meson

* Fixed documentation errors

* Added meson to build and configure and updated documentation

* fix typos
2018-08-10 12:52:09 -05:00
Denis Davydov
2a94d59433 boost: add 1.68.0 (#8931) 2018-08-09 17:08:20 -05:00
Scott Wittenburg
2278c65d0a spec: make full_hash look like dag_hash (#8911) 2018-08-09 09:00:49 -07:00
Gregory Lee
bbcb2bb8ca add fgfs variant to stat and develop version (#8919) 2018-08-09 10:56:08 -05:00
Levi Baber
a4d0e62dbd perl6-slurp: new package (#8672)
* perl6-slurp: new package

* perl-perl6-slurp: changing perl version dependency
2018-08-09 10:35:54 -05:00
Hadrien G
9e981fc73f Remove duplicate variant in Boost package (#8923) 2018-08-09 10:29:57 -05:00
Todd Gamblin
ed79d6a11b bugfix: cc handles spaces in flag variables properly
- cc cleanup caused a parsing regression in flag handling

- We added proper quoting to array expansions, but flag variables were
  never actually converted to arrays. Old code relied on this.

This commit:
- Adds reads to convert flags to arrays.
- Makes the cc test check for improper space handling to prevent future
  regressions.
2018-08-09 08:00:22 -07:00
Mark W. Krentel
393d3c64fc libiberty: new package (#8912)
* libiberty: new package

The libiberty.a library from GNU binutils.  Libiberty provides
demangling and support functions for the GNU toolchain.

This package uses the binutils tarfile but only builds the libiberty
subdirectory.  This is useful for other packages that want the
demangling functions without the rest of binutils.

Add variant 'fpic' to compile with -fPIC.

Addresses some issues raised in PR #8806.

* libiberty: change variant name to 'pic'.

Allow libiberty to install the library in lib64 and don't try to copy
it to lib.
2018-08-09 08:19:09 -05:00
Elsa Gonsiorowski, PhD
1cd33e7052 ECP VELOC Package update (#8910)
* update of veloc & dep versions (replace old non-working versions)

* veloc doesn't work with gcc <= 4.9.3

* explicitly pass MPI to CMake for veloc build
2018-08-08 21:40:38 -04:00
Satish Balay
2e891a6312 superlu_dist should be built with 'HAVE_PARMETIS=TRUE'. (#8917) 2018-08-08 20:50:48 -04:00
Todd Gamblin
bb5d83890d cc: refactor flag adding so that it's not in reverse order
- flags were prepended in reverse order to args, but this makes it hard
  to see what order they'll be in on the final command line.

- add them in the order they'll appear to make cc easier to maintain.

- simplify code for assembling the command line

- fix separator used in SPACK_SYSTEM_DIRS test
2018-08-08 01:51:51 -07:00
Todd Gamblin
4210f839e2 cc: restore ccache support in the wrapper, add a regression test
- Add back ccache support to the wrapper.
- Add a regression test to make sure ccache is working properly.
2018-08-08 01:51:51 -07:00
Todd Gamblin
62089d43ef cc: run shellcheck linter on the cc compiler script, minor cleanup
- This corrects most of the issues found by shellcheck

- This also uses ':' as the delimiter for SPACK_SYSTEM_DIRS, for
  consistency with other variables.
2018-08-08 01:51:51 -07:00
Todd Gamblin
b84067f6db cc: don't use sed to filter system directories
- filtering using sed causes most builds to slow down quite a bit, as the
  compiler wrapper has to run sed many times, and *it* runs many times

- do the system directory parsing directly in bash
2018-08-08 01:51:51 -07:00
Todd Gamblin
0e81f6cba5 refactor: clean up and fix the cc test
- Add tests to ensure that RPATHs are not added in cc mode, which can
  cause some builds to fail.

- Change cc.py to use pytest style

- Instead of writing out all the flags, break the flags down into
  variables so that it's easy to read what each test is supposed to
  check. This should make cc.py more maintainable in the future.
2018-08-08 01:51:51 -07:00
Todd Gamblin
c8fb9b5479 bugfix: cc should not add -L or -Wl,-rpath in compile-only mode
- Adding -L and -Wl,-rpath to compile-only command lines ("cc mode" or
  "-c") causes clang (if not also other compilers) to emit warnings that
  confuse configure systems.

- Clang will print warnings about unused command-line arguments.

- This fix ensures that -L and -Wl,-rpath are not added if the compile
  line is just building an object file with -c

- This also cleans up the cc script in several places.
2018-08-08 01:51:51 -07:00
Gregory Becker
683c7fbf3b Restore 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 of
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`)
2018-08-08 01:51:51 -07:00
Mark W. Krentel
f152063898 elfutils: update version and add variants (#8891)
* elfutils: update version and add variants

Add latest version 0.173.

Add variants bzip2, xz and zlib to support reading compressed DWARF
sections, default True.

Move maintainer-mode to a variant with default False.  This is only
useful for developers who want to modify the source for generated
files.

* Add dependency on zlib for reading compressed DWARF sections.

Add variants to use bzip2 and xz for compressed sections.

Remove maintainer mode and the dependencies on flex and bison.
These are not used for one-time builds.

Be sure to squash both the commits and the commit messages.
2018-08-07 14:04:05 -05:00
Micheal Quinn
203bd555a4 Fixing the addition curly brackets to conform to the rest of the templates usage of a literal curly bracket 2018-08-07 19:56:11 +02:00
Micheal Quinn
d163be6a13 Adding logic to the autoload if statement so it only fire if the module is being loaded. 2018-08-07 19:56:11 +02:00
cedricchevalier19
3301e21f06 Fix performance issue when compiling. (#8828)
* Fix performance issue when compiling.

Spack was doing active wait when compiling, spoiling one core.
My fix consists in not setting any timeout for select, instead of
the previous 0 second.

* Fix comments about select.select timeout
2018-08-07 09:13:07 -07:00
Adam J. Stewart
79e7359f4d Add libs attribute to mesa and mesa-glu packages (#8904)
Also fix dependency version in glvis package.
Fixes build errors mentioned in #8454.
2018-08-07 10:18:05 +02:00
Paul Chelarescu
6ef2eb8f7e libstdc++ detection uses os.path.realpath instead of os.readlink (#8865) 2018-08-06 22:30:29 -07:00
Geoffrey Malcolm Oxberry
e380b08bab spack general packages.yaml defaults: add unwind
This commit adds 'libunwind' as the default 'unwind' provider in
spack. This preference should be overridden by the
darwin/packages.yaml file on macOS. Continues the changes discussed in
2018-08-06 22:01:50 -07:00
Geoffrey Malcolm Oxberry
4f251345fb caliper: update to use unwind virtual package 2018-08-06 22:01:50 -07:00
Geoffrey Malcolm Oxberry
6d92a88eb4 gperftools: use unwind virtual package 2018-08-06 22:01:50 -07:00
Geoffrey Malcolm Oxberry
f395aaa71d mfem+libunwind: use "unwind" virtual package 2018-08-06 22:01:50 -07:00
Geoffrey Malcolm Oxberry
ec0050a1bb darwin packages.yaml defaults: add unwind provider
This commit adds default unwind providers to the default packages.yaml
for darwin. Compiler versions are supplied with the apple-unwind
package so that apple-unwind is only used with Apple's clang fork, and
not with LLVM's clang.
2018-08-06 22:01:50 -07:00
Geoffrey Malcolm Oxberry
163fc4cd18 apple-libunwind: new package, provides unwind
This commit continues the changes discussed in #8823 by creating a new
"apple-libunwind" placeholder package that supplies instructions for
how to configure packages.yaml to register Apple's libunwind
implementation with spack. This package also provides the "unwind"
virtual package representing the libunwind base API. The clang-apple
compiler version should be specified in packages.yaml so that
apple-unwind is only used with Apple's clang compiler, not the stock
LLVM compiler.
2018-08-06 22:01:50 -07:00
Geoffrey Malcolm Oxberry
853a3f14c7 Make libunwind provider of unwind virtual pkg
This commit begins addressing the ideas discussed in #8823. The
libunwind library now provides the "unwind" virtual package, which
represents the "libunwind base API" common to LLVM libunwind, Apple's
LLVM libunwind, and non-GNU libunwind.
2018-08-06 22:01:50 -07:00
Levi Baber
ea6918c1bf py-crossmap: needs py-setuptools (#8898)
* py-crossmap: needs py-setuptools

* py-crossmap: additional deps

* py-crossmap: make bx build/run
2018-08-06 17:43:14 -05:00
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