Commit graph

15732 commits

Author SHA1 Message Date
Massimiliano Culpo
46bfcbbd3d hwloc: added 'master' version pointing at the HEAD of the master branch (#13734) 2019-11-15 12:38:30 -08:00
Adam J. Stewart
5510bba1fd
Document use of the maintainers field (#12270)
* Document use of the maintainers field

* Use fake GitHub usernames

* GitHub action is not automatic yet
2019-11-15 13:58:24 -06:00
Greg Becker
74e04b7e20 Config option to allow gpg warning suppression (#13744)
Add a configuration option to suppress gpg warnings during binary
package verification. This only suppresses warnings: a gpg failure
will still fail the install. This allows users who have already
explicitly trusted the gpg key they are using to avoid seeing
repeated warnings that it is self-signed.
2019-11-14 16:22:19 -08:00
Greg Becker
c587c76537 Config option to allow gpg warning suppression (#13743)
Add a configuration option to suppress gpg warnings during binary
package verification. This only suppresses warnings: a gpg failure
will still fail the install. This allows users who have already
explicitly trusted the gpg key they are using to avoid seeing
repeated warnings that it is self-signed.
2019-11-14 16:22:01 -08:00
Satish Balay
40c77bf158
xsdk@0.5.0 (#13682)
Update:
 hypre@2.18.2
 mfem@4.0.1-xsdk
 superlu-dist@6.1.1
 trilinos@12.18.1
 - dtk-3.1
 petsc@3.12.1
 dealii@9.1.1
 pflotran@xsdk-0.5.0
 alquimia@xsdk-0.5.0
 sundials@5.0.0
 plasma@19.8.1
 magma@2.5.1
 amrex@19.08
 slepc@3.12.0
 omega-h@9.29.0
 strumpack@3.3.0
 pumi@2.2.1
 tasmanian@7.0
 phist@1.8.0

New:
 ginkgo@1.1.0
 py-libensemble@0.5.2
 precice@1.6.1
 butterflypack@1.1.0

Add variants:
 ginkgo
 libensemble
 precice
 butterflypack
 strumpack
 trilinos

tasmanian:  use ~openmp only on OSX
precice: disable on OSX
enable sundials+superlu-dist
sundials+superlu-dist requires OpenMP 4.5+ (so enable only for gcc@6.1+)
enable mfem+sundials
enable sundials+petsc+superlu_dist
remove hypre~internal-superlu
petsc: build with +batch on cray
precice: use ~petsc on cray
libensemble: add as runtime dependency for PYTHONPATH
2019-11-14 16:36:51 -06:00
t-karatsu
94c9e5f9a0 z3: bugfix about python dependency and fallthrough annotation. (#13713)
* z3:

* Fixed python dependency to always be required.

* bugfix about fallthrough annotation.

* z3: Add patch for before ver.4.4.1.

* Update var/spack/repos/builtin/packages/z3/package.py

Co-Authored-By: Adam J. Stewart <ajstewart426@gmail.com>
2019-11-14 16:28:05 -06:00
Seth R. Johnson
e670476024 Mark conflicts between newer packages and Intel 14 compilers (#13729)
* Mark compiler/version conflict for CMake

Intel 14 lacks some C++11 features needed to compile new versions of
cmake.
```
/tmp/s3j/spack-stage/spack-stage-cmake-3.15.5-46lgp4ybhopy2p4rr66rxnew5iaddvmg/spack-src/Source/
cm_static_string_view.hxx(28): error: expected an operator
   friend static_string_view operator"" _s(const char* data, size_t
                                     ^
```

* Mark compiler/version conflict for icu4c

With Intel 14.0.4 on Linux for icu4c 60.1 and higher:
```
locid.cpp(1156): error #1140: a using-declaration may not name a constructor or destructor
        using KeywordEnumeration::KeywordEnumeration;
```

* Mark compiler/version conflict for nasm

Error installing `nasm@2.14.02%intel@14.0.4`:
```
In file included from nasmlib/crc64.c(35):
./include/nasmlib.h(116): error: expected a ";"
  fatal_func nasm_assert_failed(const char *, int, const char *);
```

* Mark compiler/version conflict for bison

Installing `bison@3.4.2%intel@14.0.4`:
```
In file included from /tmp/s3j/spack-stage/spack-stage-bison-3.4.2-
uzjszv4owvqsymjpxtxvvegfavc6k5my/spack-src/lib/quotearg.c(33):
/tmp/s3j/spack-stage/spack-stage-bison-3.4.2-uzjszv4owvqsymjpxtxvvegfavc6k5my/spack-src/lib/
xalloc.h(51): warning #303: explicit type is missing ("int" assumed)
  extern _Noreturn void xalloc_die (void);
```

* Mark compiler/version conflict for icu4c

With `icu4c@60.1%intel@16.0.4` and `icu4c@64.1%intel@16.0.4`:

```
In file included from ucurr.cpp(26):
static_unicode_sets.h(130): error #913: invalid multibyte character sequence
      {POUND_SIGN, u'£'},
                     ^
```

* Change conflict comments into messages
2019-11-14 16:27:36 -06:00
George Hartzell
7a6c7f23a0 py-matplotlib only needs backports when ^python@:2 (#13712)
* py-matplotlib only needs backports when ^python@:2

This implements @scheibelp's suggestion in #13711.

py-matplotlib should only depends_on py-backports-functools-lru-cache
when it's using a python that actually *needs* it.

See #13711 for details.

* Don't depend_ons py-enum34 unless python@:3.3

* Tighten up enum34 dependency

@adamjstewart cracked open the setup.py files and suggested a tighter
dependency for py-enum34.  1.4 and 1.5 only require it for pythons
before 3.4, 1.3 requires it unconditionally.  So...., we'll do the
same.

* Remove conflict on python 3.4 from enum34

at @adamjstewart's request see PR notes
2019-11-14 16:26:44 -06:00
Gregory Lee
8490587c76 add boost dependency to stat package (#13735) 2019-11-14 16:26:24 -06:00
xfzhao
2fb5df0284 update to v0.6.4 (#13737) 2019-11-14 16:26:08 -06:00
Emir İşman
46871416b1 Update DMTCP package to v2.6.0 (#13739) 2019-11-14 16:20:44 -06:00
Nicholas Sly
d79d11b6d4 Removed github repository and develop version from dataspaces package as it is no longer present/accessible. (#13740) 2019-11-14 16:20:13 -06:00
xfzhao
11e65661ac update vsearch (#13736) 2019-11-14 16:17:02 -06:00
Peter Scheibel
28163cb34f determine target relative to the link directory rather than the full link path (which includes the file name) (#13727) 2019-11-14 12:15:47 -08:00
Massimiliano Culpo
7e84fe966c hwloc: added 'master' version pointing at the HEAD of the master branch (#13731) 2019-11-14 12:06:07 -06:00
Sinan
00bf299e46 new package Qscintilla (with python bindings via py-pyqt ) (#12793)
* qscintilla_with_python_bindings_disabled

* pyqt5 with variant +qsci to compile qscintilla python bindings

* fix a dyn linking issue for Qsci python module

* fix a bug

* fix bug: use sip provided by py-pyqt5

* fix typo

* tidy up, make designer

* tidy up

* fix designer build issue, set env for designer plugin

* tidy up

* tidy up

* minor improvements

* improve style

* build Qscintilla python bindings here

* make qsci config option variant dependent

* get rid of commented out code

* improvements: add resource for qscintilla, improve config_args

* flake8: spaces, blank lines etc

* flake8: fix long lines

* Update var/spack/repos/builtin/packages/py-pyqt4/package.py

Co-Authored-By: Adam J. Stewart <ajstewart426@gmail.com>

* Update var/spack/repos/builtin/packages/py-pyqt4/package.py

Co-Authored-By: Adam J. Stewart <ajstewart426@gmail.com>

* Update var/spack/repos/builtin/packages/py-pyqt4/package.py

Co-Authored-By: Adam J. Stewart <ajstewart426@gmail.com>

* Update var/spack/repos/builtin/packages/qscintilla/package.py

Co-Authored-By: Adam J. Stewart <ajstewart426@gmail.com>

* dont install source tree under prefix

* remove duplicate line

* use os.path.join instead of +

* separate build and run environment setups

* flake8

* Update var/spack/repos/builtin/packages/py-pyqt5/package.py

Co-Authored-By: Adam J. Stewart <ajstewart426@gmail.com>

* Update var/spack/repos/builtin/packages/py-pyqt5/package.py

Co-Authored-By: Adam J. Stewart <ajstewart426@gmail.com>

* Update var/spack/repos/builtin/packages/py-pyqt5/package.py

Co-Authored-By: Adam J. Stewart <ajstewart426@gmail.com>

* fix rsrc path

* use python_include_dir

* use "with working_dir"

* Update var/spack/repos/builtin/packages/py-pyqt4/package.py

Co-Authored-By: Adam J. Stewart <ajstewart426@gmail.com>

* Update var/spack/repos/builtin/packages/py-pyqt5/package.py

Co-Authored-By: Adam J. Stewart <ajstewart426@gmail.com>

* Update var/spack/repos/builtin/packages/py-pyqt5/package.py

Co-Authored-By: Adam J. Stewart <ajstewart426@gmail.com>

* Update var/spack/repos/builtin/packages/py-pyqt5/package.py

Co-Authored-By: Adam J. Stewart <ajstewart426@gmail.com>

* Update var/spack/repos/builtin/packages/qscintilla/package.py

Co-Authored-By: Adam J. Stewart <ajstewart426@gmail.com>

* Update var/spack/repos/builtin/packages/py-pyqt4/package.py

Co-Authored-By: Adam J. Stewart <ajstewart426@gmail.com>

* Update var/spack/repos/builtin/packages/py-pyqt4/package.py

Co-Authored-By: Adam J. Stewart <ajstewart426@gmail.com>

* flake8
2019-11-14 12:01:49 -06:00
Matthias Maiterth
ab2b3f30a5 package/geopm: Added versions 1.0.0 and 1.1.0 (#13721)
* package/geopm: Added versions 1.0.0 and 1.1.0

Added changes for 1.1.0 and 1.0.0 in this patch.
Patch for 1.0.0 was previously not merged.
variant for hwloc removed since that is not a dependency since 0.5.1 and
variant('hwloc', when=:0.5.1 is not supported afaik.
made depends_on versions more explicit.

* package/geopm: removed 1.0.0 release candidates 1 and 2.
2019-11-14 12:01:03 -06:00
Hector Martinez-Seara
cd04538bb9 Adding final bug-releases for the gromacs-2016 and -2018 and Plumed (#13715)
* Adding final bug-releases for the gromacs-2016 and -2018

* Added newer versions of plumed and libmatheval not a dependency >v2.5

* plumed package: chamge name git branch to master
2019-11-14 12:00:36 -06:00
Seth R. Johnson
b8916ecc08 Fix libbsd on Intel compilers (#13720)
Libbsd assumes GCC-defined compiler macros:
```
In file included from nlist.c(44):
local-elf.h(238): catastrophic error: #error directive: Unknown ELF machine type
  #error Unknown ELF machine type
   ^
```
The `__amd64__` and `__x86_64__` macros should be equivalent, but the
latter is defined by intel.
2019-11-14 11:59:46 -06:00
Peter Scheibel
3f861e18b0 symlink relativization: determine target relative to the link directory (#13710)
when making a package relative, relocate links relative to link directory

rather than the full link path (which includes the file name) because `os.path.relpath` expects a directory.
2019-11-13 17:51:57 -08:00
sknigh
045e9c905f Added "file" package and added missing depenency to VIM (#13705)
* Added "file" package and added missing depenency to Vim

* added which and grep

* Added gzip

* added missing dependency to gmake
2019-11-13 18:12:10 -06:00
David Böhme
1ed8de8757 Add Caliper v2.2.0 and v2.1.1 (#13723)
* Add Caliper v2.2.0 and v2.1.1

* Add conflict for adiak when for versions <2.2

* Trim trailing whitespace
2019-11-13 18:11:09 -06:00
Greg Becker
43b0356e14 Allow binary relocation of strings in relative binaries (#13725)
Binaries with relative RPATHS currently do not relocate strings
hard-coded in binaries

This PR extends the best-effort relocation of strings hard-coded
in binaries to those whose RPATHs have been relativized.
2019-11-13 16:03:35 -08:00
Greg Becker
b280034380 Allow binary relocation of strings in relative binaries (#13724)
Binaries with relative RPATHS currently do not relocate strings
hard-coded in binaries

This PR extends the best-effort relocation of strings hard-coded
in binaries to those whose RPATHs have been relativized.
2019-11-13 16:03:16 -08:00
G-Ragghianti
dc36b4737d Papi components (#13706)
* Added support for papi components.

* Restored sha256 hashes to package files.
2019-11-13 15:49:06 -06:00
Justin S
a2ef7896b7 rnaz: new package at 2.1 (#13707) 2019-11-13 15:48:06 -06:00
thelfer
ff9b03edc3 Fix mgis package dependency on boost/numpy (#13717) 2019-11-13 15:35:09 -06:00
William F Godoy
d6274e1a1d Docs update for deprecated spack sha256 (#13701)
* Docs update for deprecated `spack sha256`

* Added macOS shasum

* Update lib/spack/docs/packaging_guide.rst

Co-Authored-By: Adam J. Stewart <ajstewart426@gmail.com>
2019-11-13 15:21:27 -06:00
Sinan
9ae4f42ab5 new package: sfcgal (#12624)
* new package: sfcgal

* improve meta information

* add variant and optional dependencies

* add cmake options for building with viewer

* improve dependency type

* improve viewer variant

* improve viewer variant

* specify dependency versions

* add ref

* remove depricated variant
2019-11-13 15:19:43 -06:00
Hari Subramoni
1a6bba1632 Update MVAPICH2 package for 2.3.2 release (#13236)
* Update MVAPICH2 package for 2.3.2 release
Update default build from psm to mrail

* Update different provides for older versions based on feedback from Todd Gamblin

* Simplify rule so one rule covers 2.1 and 2.2

* Add support for disabling rpath based on feedback from Dr. Shende

* Add colon based on comment

* Address review comment by Adam Stewart

* Add declaration of the wrapperpath variant.
    - Thanks to Massimiliano Culpo for the comment
2019-11-13 15:18:35 -06:00
Satish Balay
4d37db02da superlu_dist: fix build with xl compilers (#13702)
* superlu_dist: fix build with xl compilers

* fix link error  ../SRC/libsuperlu_dist.so.6.1.1: undefined reference to `ztrtri_'

* Fixed the ordering of the spec on the xl-611 patch.

* fix flake8 error
2019-11-13 15:03:24 -06:00
Chris Green
56de86dda6 root: relax libxml2 requirements when ~python. (#13657)
* Relax libxml2 requirements when ~python.

Per https://github.com/spack/spack/issues/13637#issuecomment-552026561

* Satisfy package_sanity.py::test_prs_update_old_api.
2019-11-12 23:33:47 -08:00
Satish Balay
53b2add34f
strumpack: revert default to ~shared [i.e behavior before this variant was added] as +shared fails on multiple builds (#13703) 2019-11-12 20:22:34 -06:00
Todd Gamblin
da386b560a docs: use nicer looking code blocks in docs (#13708)
- [x] Use higher contrast terminal output font
- [x] Use higher contrast code block background color than default
- [x] Use a noticeable prompt character

See also https://github.com/spack/spack-tutorial/pull/10.
2019-11-12 18:18:41 -08:00
Simon Pintarelli
d0de9f8d9d add new version for py-ranger-fm (formerly py-ranger) (#13681)
- download from pypi, drop 1.7.2
- drop 1.7.2, it is not available from pypi
2019-11-12 12:05:18 -06:00
sknigh
1ae824737e Add missing dependencies to flex. (#13692) 2019-11-12 12:01:15 -06:00
h-denpo
2b6c4245d0 Fixed url. url="https://sourceware.org/pub/libffi/libffi-3.2.1.tar.gz") (#13693) 2019-11-12 11:58:49 -06:00
t-karatsu
ca19fb86c1 damselfly: Add mpi dependency. (#13694) 2019-11-12 11:58:11 -06:00
Adrian Jackson
57aa7ba045 Fixing Fortran MPI compiler reference in mpt package (#13699) 2019-11-12 11:57:07 -06:00
Stephen Hudson
cea7403b67 Update nlopt package to add Python bindings to PYTHONPATH (#13688)
* Update nlopt package to add Python bindings to PYTHONPATH

* Use extends for nlopt/python fix

* nlopt - change develop to master and add python dep qualifiers
2019-11-12 11:46:12 -06:00
Massimiliano Culpo
826e8c6394 athena, mvapich2, spectrum-mpi: use new API to setup environment (#13677)
* athena: updated api call to setup build environment

* mvapich2: updated api call to setup build and run environment

* spectrum-mpi: updated api call to setup build and run environment
2019-11-12 11:44:12 -06:00
Frédéric Simonis
b1965fa913 precice: enable petsc by default (#13696) 2019-11-12 11:40:37 -06:00
Satish Balay
cbfdc85d26
trilinos: add version 12.18.1 with dtk-3.1 (#13690) 2019-11-12 07:52:24 -06:00
Satish Balay
9e12b4e95a
sundial: add patch for build failure on cori/theta (#13665) 2019-11-12 07:52:05 -06:00
Daryl W. Grunau
5a9389a528 verify.py: os.path.exists exception handling (#13656) 2019-11-11 17:47:47 -06:00
Simon Pintarelli
e5b38c525e SIRIUS: add new version, add magma support (#13680)
- depends on spfft starting from 6.4.0
- add magma variant
- avoid setting cuda_arch to none
- add python dependencies
- use release as default build type
2019-11-11 16:19:40 -06:00
sknigh
fdb85744e3 added lcov package (#13687) 2019-11-11 15:13:48 -06:00
Adrian Jackson
3eaa790efa Add HPE MPT package (#13616)
* Adding in HMPT package for HPE MPI libraries

* Updating copyright dates

* Renaming HPE MPI package

* Fixing error in package file

* Tidying up defintions and linting

* liniting

* Adding in library setup so packages that want to manually add mpi libraries can do so (i.e. npb)

* Linting

* Linting

* Investigating old API errors

* Investigating api errors

* Investigating api errors

* Investigating api errors

* Investigating api errors

* Investigating api errors: adding back in functions to see when the build fails

* Investigating api errors: adding back in functions to see when the build fails

* Investigating api errors: adding back in functions to see when the build fails

* Investigating api errors: adding back in functions to see when the build fails

* Investigating api errors: adding back in functions to see when the build fails

* Linting

* Linting

* Fixing

* Fixing
2019-11-11 13:22:20 -06:00
Adam J. Stewart
dc51d676a2
cuDNN: add new versions (#13668)
* cuDNN: add new versions

* cuDNN 9.0 can build against CUDA 9.1

* Undo version format change
2019-11-11 12:53:26 -06:00
Adam J. Stewart
03fb2d61c6
Add new version of Intel MKL-DNN (#13669)
* Add new version of Intel MKL-DNN

* Get OpenMP build working

* lomp is also needed for linking

* http -> https

* Add myself as maintainer
2019-11-11 12:52:53 -06:00