Commit graph

8813 commits

Author SHA1 Message Date
Sinan81
08e389cb7d new package: py-humanize 2019-08-21 16:10:51 -07:00
Chuck Atkins
77e4e3d87e
mercury: Fix CMake 3.15 configure error (#12504) 2019-08-21 13:28:20 -04:00
Jeffrey Salmond
a41014ed9e mvapich2 depends on slurm when built with process_managers=slurm (#12489) 2019-08-20 16:43:28 -05:00
Daryl W. Grunau
dbbccd1303 prefix -> self.prefix (#12487) 2019-08-20 16:41:41 -05:00
Cameron Stanavige
11c0a7882d UnifyFS: new package - rename from UnifyCR (#12439)
UnifyCR has been renamed to UnifyFS. Renaming the Spack package is
the last step in this process.

This renames the package and changes any UnifyCRs to UnifyFS within
the package.
2019-08-20 11:13:22 -05:00
Ryan S. Elliott
7737d623b0 kim-api: added version 2.1.3 (#12457) 2019-08-20 16:29:17 +02:00
Teodor Nikolov
118e20a087 Add Kokkos 2.9.0 (#12466) 2019-08-20 13:07:11 +02:00
健美猞猁
6d959494d4 r: added version 3.6.1. (#12470) 2019-08-20 11:13:18 +02:00
Pariksheet Nanda
64de824cf6 py-pyfaidx: tweak dependencies; fixes #12445 (#12446)
* py-pyfaidx: tweak dependencies; fixes #12445

* py-pyfaidx: add suggestions for #12446
2019-08-16 22:41:32 -05:00
Dan Lipsa
39ad0efb9a Solve compilation error on summit. (#12305)
* This constexpr does not compile on summit.

I tried gcc6.4 and gcc7.4

* Add link the the llvm bug report.
2019-08-16 15:27:35 -04:00
Frédéric Simonis
7bb08b6ecb preCICE: Fix Eigen include directory (#12441) 2019-08-16 09:00:01 -05:00
Sinan
46e8de914a new package: laszip (#12432) 2019-08-15 19:07:40 -05:00
Pariksheet Nanda
862b3b00df camx: add version 6.50 (#12437)
* camx: add version 6.50

* camx: remove unpredictable download URL

* camx: install manual and data files
2019-08-15 19:07:22 -05:00
Adam J. Stewart
f568f19b13
Overhaul PyTorch package (#12420)
* Overhaul PyTorch package

* Flake8

* Distributed requires MPI, NCCL not specified correctly

* Binary was being specified incorrectly

* Run tests at install time

* Disable GLOO in addition to GLOO_IBVERBS
2019-08-15 17:54:09 -05:00
Mark W. Krentel
3a78f0e0fd hpctoolkit: add version 2019.08.14 (#12435)
Add version 2019.08.14 and rename 'develop' to 'master' to match the
git branch name (now that master is also a special name).
2019-08-15 17:53:41 -05:00
Michael Kuhn
0cdcee92fb go: Add 1.12.8 and 1.11.13 (#12433)
Both address security issues:
https://groups.google.com/forum/#!topic/golang-nuts/fCQWxqxP8aA
2019-08-15 17:01:43 -05:00
Seth R. Johnson
4b400d5032 Update VisIt to version 3.0.1 and fix on mac (#12396)
* Add option to disable QTDesigner plugin for qwt

Qt designer shouldn't be necessary to build downstream GUI code.
Currently `qwt^qt~tools` fails to build:

(darwin clang@10.0.1)
```
compiling qwt_designer_plugin.cpp
compiling qwt_designer_plotdialog.cpp
moc qwt_designer_plugin.h
moc qwt_designer_plotdialog.h
rcc qwt_designer_plugin.qrc
qwt_designer_plugin.h:23: Error: Undefined interface
make[1]: *** [moc/moc_qwt_designer_plugin.cpp] Error 1
make[1]: *** Waiting for unfinished jobs....
qwt_designer_plugin.cpp:17:10: fatal error: 'QDesignerFormEditorInterface' file not found
         ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
1 error generated.
make[1]: *** [obj/qwt_designer_plugin.o] Error 1
make: *** [sub-designer-make_default-ordered] Error 2
```

* Update VTK for newer VisIt and compiler versions

Several changes/enhancements to VTK package

---

Add version 8.1.0 (default version for VisIt 3.x)

---

Tweak VTK options for version 8 and VisIt:

- only add mpi4py version option when mpi4py is enabled
- Require object factory for downstream packages
- Remove OpenGL preference for VTK 8

---

Combine +python3 into +python

The spec for using python3 should just be `+python^python@3:`.

---

Remove unused VTK cmake argument on newer version

---

Patch for Python 3 fails on VTK 6.1 (needed for VisIt 2.x):
```
==> Patch /rnsdhpc/code/spack/var/spack/repos/builtin/packages/vtk/python3.7-const-char.patch failed.
==> Error: ProcessError: Command exited with status 1:
    '/usr/bin/patch' '-s' '-p' '1' '-i' '/rnsdhpc/code/spack/var/spack/repos/builtin/packages/vtk/python3.7-const-char.patch' '-d' '.'
```

and as it happens, VisIt 2.13 is incompatible with Python 3 anyway.

---

Fix compiler error:

As spack's configuration warning says, double-quotes can cause trouble:
```
==> [2019-07-29-11:47:55.269653] Warning: Quotes in command arguments can confuse scripts like configure.
  The following arguments may cause problems when executed:
      -DVTK_REQUIRED_OBJCXX_FLAGS=""
  Quotes aren't needed because spack doesn't use a shell.
  Consider removing them
```
They were being added to the compile line, causing clang to think it was
asked to compile an empty file:
```
cd /private/var/folders/fy/x2xtwh1n7fn0_0q2kk29xkv9vvmbqb/T/s3j/spack-stage/spack-stage-3nk9bwe_/spack-build/Rendering/OpenGL && /rnsdhpc/code/spack/lib/spack/env/clang/clang++  -DVTK_IN_VTK -DvtkRenderingOpenGL_EXPORTS -F/Applications/Xcode.app/Contents/Developer/Platforms/MacOSX.platform/Developer/SDKs/MacOSX10.14.sdk/System/Library/Frameworks  -DGLX_GLXEXT_LEGACY  -O2 -g -DNDEBUG -isysroot /Applications/Xcode.app/Contents/Developer/Platforms/MacOSX.platform/Developer/SDKs/MacOSX10.14.sdk -fPIC   -fvisibility=hidden -fvisibility-inlines-hidden "" -o CMakeFiles/vtkRenderingOpenGL.dir/vtkCocoaGLView.mm.o -c /rnsdhpc/code/spack/var/spack/stage/vtk-6.1.0-b2mj276iz77fadisv2me365qe27t3gxt/spack-src/Rendering/OpenGL/vtkCocoaGLView.mm
clang: error: no input files
make[2]: *** [Rendering/OpenGL/CMakeFiles/vtkRenderingOpenGL.dir/vtkCocoaGLView.mm.o] Error 1
```

* Modernize/PEP-8 visit package statements

* Add new VisIt version and patches for building on Mac

- VisIt's cmake assumes a 'vtk(tiff|jpeg|png)' *library* target exported by
  VTK, but VTK 8.1.x on my configuration seems to have these as header-only
  targets with library dependencies.
- Explicitly add QT path to visit configure: Without this, somehow
  `${VISIT_QT_DIR}` was being set to empty, so that the build failed with
  `missing /bin/moc`.
- VisIt assumes that if it isn't being built statically, QWT has been built as
  a mac Framework. QWT actually is built as a framework based on whether QT
  itself is.

Error message:
```
-- Looking for QWT
CMake Error at CMake/SetUpThirdParty.cmake:131 (MESSAGE):
    Include Directory for QWT (/rnsdhpc/code/spack/opt/spack/darwin-mojave-x86_64/clang-10.0.1-apple/qwt-6.1.3-bmfxirweplzhjoiil4rw632evkyteuwk/lib/qwt.framework/Versions/Current/Headers) does not exist.
Call Stack (most recent call first):
  CMake/FindQwt.cmake:57 (SET_UP_THIRD_PARTY)
  CMakeLists.txt:1251 (INCLUDE)
```
2019-08-15 10:13:45 -05:00
Axel Huebl
ce15510566 ADIOS 2.4.0: Add new Deps (#12414)
* ADIOS 2.4.0: Add new Deps

Version 2.4.0 of ADIOS2 added new dependencies that are not
yet listed as `depends_on` and/or disabled otherwise. Add them
now to avoid picking them up from system paths, e.g. `libpng`.

* ADIOS2: Variant Defaults Change

* Python: False by default
* ADIOS1: only used prior to 2.3.0
2019-08-15 10:11:35 -05:00
Seth R. Johnson
283f355b10 Update icu4c to version 64.1 (#12429)
Version 60.1 fails to build on linux with clang@7.0.1 and clang@8.0.0:

```
digitlst.cpp:508:9: error: use of undeclared identifier 'freelocale'
        freelocale(gCLocale);
        ^
   clang++     ...  coll.cpp
digitlst.cpp:520:26: error: use of undeclared identifier 'LC_ALL_MASK'
    gCLocale = newlocale(LC_ALL_MASK, "C", (locale_t)0);
                         ^
   clang++     ...  sortkey.cpp
   clang++     ...  bocsu.cpp
   clang++     ...  ucoleitr.cpp
   clang++     ...  ucol.cpp
   clang++     ...  ucol_res.cpp
2 errors generated.
   clang++     ...  ucol_sit.cpp
   clang++     ...  collation.cpp
*** Failed compilation command follows:
----------------------------------------------------------
/projects/spack/lib/spack/env/clang/clang++ -D_REENTRANT
-DU_HAVE_ELF_H=1 -DU_HAVE_ATOMIC=1 -DU_HAVE_STRTOD_L=1
-DU_HAVE_XLOCALE_H=1 -I. -I../common -DU_ATTRIBUTE_DEPRECATED=
-DU_I18N_IMPLEMENTATION -std=c++11 -W -Wall -pedantic -Wpointer-arith
-Wwrite-strings -Wno-long-long -c -DPIC -fPIC -o digitlst.o digitlst.cpp
--- ( rebuild with "make VERBOSE=1 all" to show all parameters )
--------
make[1]: *** [digitlst.o] Error 1
make[1]: *** Waiting for unfinished jobs....
   clang++     ...  collationsettings.cpp
make[1]: Leaving directory
`/build/s3j-spack/spack-stage/spack-stage-k9ba3gqo/spack-src/source/i18n'
make: *** [all-recursive] Error 2
```
2019-08-14 22:54:37 -05:00
Shintaro Iwasaki
ae2ab920fb Update BOLT package (#12423)
* bolt: add new versions

* bolt: add argobots dependency

From this version, BOLT uses an external Argobots, not a builtin one.
2019-08-14 21:40:51 -05:00
Daryl W. Grunau
5346d5e966 Fix skopeo dependencies (#12425) 2019-08-14 19:14:33 -05:00
Daryl W. Grunau
b8ffb1cf7f Fix charliecloud dependencies (#12427) 2019-08-14 19:14:00 -05:00
Cameron Stanavige
226f23bc43 UnifyCR: update dependencies and build options (#12216)
* UnifyCR: update dependencies and build options

This adds some specifics about dependencies and conflicts and adds
additional build options and variants. UnifyCR now also has limited
fortran support.

* Remove debug statements condition on Spack debug

Change debug print statements to now be turned on when the -g cflag
is found in the flags the user sets.
2019-08-14 15:50:10 -07:00
Daryl W. Grunau
9e08c7ff47 Package umoci dependency (#12422)
* bump eospac version

* Revert "bump eospac version"

This reverts commit 835b1f822d8c083f6ab9eb17222c00409e8eb3da.

* umoci depends on go-md2man
2019-08-14 17:35:52 -05:00
Christoph Junghans
41c917b6e6 lammps: add version 20190807 (#12424) 2019-08-14 17:35:24 -05:00
Daryl W. Grunau
0c5f5d4d0d New package: device-mapper (#12406)
* bump eospac version

* Revert "bump eospac version"

This reverts commit 835b1f822d8c083f6ab9eb17222c00409e8eb3da.

* new package: device-mapper

* address comments by @hartzell

* extraneous whitespace

* capitalization

* device-mapper -> lvm2

* unprovide device-mapper

* address comments by @adamjstewart

* address comments by @adamjstewart
2019-08-14 14:54:15 -05:00
Justin S
da21d27712 r-rmutil: new package at 1.1.3 (#12417)
* r-rmutil: new package at 1.1.3

* r-rmutil: use cloud.r-project.org
2019-08-14 14:53:57 -05:00
Daryl W. Grunau
a9845da15f New package: go-md2man (#12397)
* bump eospac version

* Revert "bump eospac version"

This reverts commit 835b1f822d8c083f6ab9eb17222c00409e8eb3da.

* new package: go-md2man

* address comments by @adamjstewart
2019-08-14 12:56:51 -05:00
Adam J. Stewart
0f075b0cc8
NCCL: fix build on older Linux systems (#12415) 2019-08-14 12:34:00 -05:00
Toyohisa Kameyama
e620883a3c masurca: build on arm. (#12416)
* remove -minline-all-stringops when target is arm.
* change int3 to raise(SIGTRAP) when target is arm.
2019-08-14 10:38:50 -05:00
Sinan
3a4a513bed add new package: py-python-magic (#12409)
* add new package: py-python-magic

* tidy up

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

Co-Authored-By: Adam J. Stewart <ajstewart426@gmail.com>
2019-08-14 10:37:06 -05:00
Adam J. Stewart
2e6b44328a
zstd: fix build linking error (#12413) 2019-08-13 21:09:25 -05:00
Toyohisa Kameyama
c52f8478b2 starce: new version and build on ARM. (#12401)
1. souce URL change to github.
2. Add version 5.1 and 5.2
3. enable build on ARM.
2019-08-13 19:38:45 -05:00
Jordan Ogas
4119886cbc add charliecloud master branch; add dependencies (#12327)
* add master and dependencies

* remove gcc and make

* add variants, make doc and ch-grow dependencies optional

* capitalize description sentence

* move dependencies and variants below version block

* fix typos
2019-08-13 19:37:58 -05:00
Daryl W. Grunau
2c68b7f006 packages/umoci (#12346)
* bump eospac version

* Revert "bump eospac version"

This reverts commit 835b1f822d8c083f6ab9eb17222c00409e8eb3da.

* new package: umoci

* Package -> MakefilePackage

* add missing build phase

* relax expand=False requirement
2019-08-13 19:37:34 -05:00
Sinan
fcf6bb8f45 add new versions (#12393) 2019-08-13 19:35:02 -05:00
Sinan
53e12f66cf add new version (#12394) 2019-08-13 19:34:34 -05:00
Sinan
bb5663701e add new version (#12395) 2019-08-13 19:33:12 -05:00
Toyohisa Kameyama
d752ef38c9 subread: build on ARM. (#12400) 2019-08-13 19:23:52 -05:00
Ricardo Silva
5116312ca2 package/gromacs: simd optimizations autodetection for more versions (#12402)
* gromacs: fix simd detection for pre 2018 versions

* pre 2018 the cmake file was named differently
* fixed up post 2018 patch file which was non pretty

* Trim patch
2019-08-13 19:21:59 -05:00
健美猞猁
5429713eef Add version 2.4.0 for cantera. (#12405) 2019-08-13 19:18:38 -05:00
Gregory Lee
aabdeb9b63 patch opa-psm2 to build with spack wrappers (#12407) 2019-08-13 19:13:21 -05:00
Daryl W. Grunau
c931757d02 Fix package gpgme dependency (#12410)
* bump eospac version

* Revert "bump eospac version"

This reverts commit 835b1f822d8c083f6ab9eb17222c00409e8eb3da.

* build depends on gnupg which provides gpgsm binary
2019-08-13 19:08:50 -05:00
Michael Kuhn
384281bf94 gcc: Add 9.2.0 (#12411) 2019-08-13 19:08:12 -05:00
Tiziano Müller
95fec7adfc CP2K/SIRIUS: add support for building with CUDA, fix CP2K build with MKL (#11418)
* cp2k/sirius: add CUDA support

* cp2k: fix building with MKL

* sirius: make sure to link against Spacks blas/lapack/scalapack
2019-08-13 19:59:08 +02:00
brietzke
68c176998a new package: asagi: create package.py (#11931)
* Create package.py

* applied reviewer suggestions

* Update package.py

* remove CamelCase from variant names

* add comment on why fetching package via git

* found typo in variant to cmake-argumentlist translation

* rename variants to ~nonuma ~nompi to be in sync with cmake-args, refine mpi@3-dependency definition

* Revert "rename variants to ~nonuma ~nompi to be in sync with cmake-args, refine mpi@3-dependency definition"

This reverts commit 58e8cf7d93c5665f0b4b50228946857734716cef.

* remove version-preference
2019-08-13 11:13:41 -05:00
Sinan
bb6ec7fb40 Package/grass: fix iconv linking issue (#12165)
* fix iconv linking issue, package_grass fix linking iconv, add more comments
2019-08-12 13:45:05 -07:00
Owen Solberg
230678367c singularity: update version to 3.3.0 (#12295)
* add checksum for singularity release 3.3.0

* update singularity doc URL

URL at the lbl.gov domain has message saying:
"This website is going away soon! Update your bookmarks!"

* add note about build log file for post-install step

* provide links to both 2.x and 3.x security docs

* remove whitespace.  Passing flake8 confirmed locally this time :)

* add TODO comment for fakeroot support
2019-08-12 15:38:15 -05:00
Jean-Paul Pelteret
2cc89fbf69 New package: TexStudio (#12301)
* Poppler library: Add new versions

* Poppler library: Allow building with QT4

* Poppler library: Install header files

* Add patch to Poppler package

* Add new package: TexStudio
2019-08-12 14:48:28 -05:00
Russell J. Hewett
31f9135cbc blaze: converted to CMakePackage (#12357)
The previous version does not properly install the required cmake
configuration files for blaze-lib, so find_package does not work
correctly.

This patch converts the blaze-lib package to use CMakePackage,
adds the required cmake dependency, and removes the install()
member function, which is not working correctly and is no longer
needed.
2019-08-12 14:47:54 -05:00
Geoffrey Oxberry
6de750d860 gtksourceview: new package (#12387) 2019-08-12 14:44:54 -05:00
Janne Blomqvist
490168be4d openblas: fix target detection for cross-compiling (#12390)
In a review of a previous pull request (
https://github.com/spack/spack/pull/10713 ) it was mentioned that the
proper way to figure out the target architecture is via
spec.architecture.target.  This patch fixes this for the openblas
package.

Signed-off-by: Janne Blomqvist <janne.blomqvist@aalto.fi>
2019-08-12 14:43:04 -05:00
Janne Blomqvist
820b220b22 openblas@0.3.7: New version (#12391)
This adds OpenBLAS 0.3.7 (released 2019-08-11).
2019-08-12 14:41:26 -05:00
Kelly (KT) Thompson
5b84d6dff1 Apply xl patch for cce@9: to fix cmake. (#12392) 2019-08-12 14:41:00 -05:00
Daryl W. Grunau
9538889f1c packages/skopeo (#12348)
* bump eospac version

* Revert "bump eospac version"

This reverts commit 835b1f822d8c083f6ab9eb17222c00409e8eb3da.

* new package: skopeo

* address flake8 issues

* address adamjstewart's comments

* use the Executable class and undocumented 'str' feature for output

* Package -> MakefilePackage

* add missing build phase

* patch -> edit phase
2019-08-12 11:28:05 -05:00
Seth R. Johnson
172fcb0225 Update SWIG versions and add Fortran fork (#12185)
* Add git repositories for SWIG and SWIG-Fortran

* Fix typo in documentation

* Move 'master' to top of SWIG version list
2019-08-11 12:58:12 -05:00
Glenn Johnson
30cf665d16 Fix py-matplotlib build with Intel compiler (#12144)
Not sure what happened between #5321 and now but the CC=CXX fix now
prevents py-matplotlib from building with the Intel compiler. I verified
with versions of py-matplotlib from 2.0.2 to 3.0.2 and intel-17.0.4 and
19.0.4 that py-matplotlib successfully builds with the Intel compiler
without that code.
2019-08-11 12:57:31 -05:00
Seth R. Johnson
52a737affe Use correct GCC installation when installing clang with GCC (#12381) 2019-08-11 12:40:12 -05:00
Sinan
5532b8e617 new package: qwtpolar (#12382)
* create qwtpolar package

* patch config files so that qwtpolar successfully builds

* make flake8 happy
2019-08-11 12:39:58 -05:00
Frédéric Simonis
33bec18cc2 Add preCICE xSDK support (#12356)
* Add preCICE xSDK support

* Cleanup generation of cmake arguments

* Generalize numpy include

* Fix python spec

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

* Fix numpy spec

Co-Authored-By: Adam J. Stewart <ajstewart426@gmail.com>
2019-08-11 12:19:44 -05:00
Adam J. Stewart
0d4114b095
Add NCCL 2.4.8-1 (#12362) 2019-08-10 11:53:29 -05:00
Adam J. Stewart
c5c1d1db43
Port py-poster to Python 3 (#12363)
* Port py-poster to Python 3

* Forgot the patch
2019-08-10 11:53:15 -05:00
Adam J. Stewart
e69456bde2
Add py-clipboard package (#12364) 2019-08-10 11:52:52 -05:00
Adam J. Stewart
6e14e74014
Add py-gee-asset-manager package (#12365) 2019-08-10 11:52:38 -05:00
Adam J. Stewart
889b625452
Add py-geeadd package (#12366) 2019-08-10 11:52:24 -05:00
Adam J. Stewart
8e4d60645f
Add py-geeup package (#12367) 2019-08-10 11:52:10 -05:00
Adam J. Stewart
706d57bd23
Add py-google-api-core package (#12368) 2019-08-10 11:51:56 -05:00
Adam J. Stewart
09e0f1ad4e
Add py-google-cloud-core package (#12369) 2019-08-10 11:51:41 -05:00
Adam J. Stewart
3c54e55546
Add py-google-cloud-storage package (#12370) 2019-08-10 11:51:27 -05:00
Adam J. Stewart
a3cc7eb4f7
Add py-google-resumable-media package (#12371) 2019-08-10 11:51:12 -05:00
Adam J. Stewart
b329d5f27f
Add py-googleapis-common-protos package (#12372) 2019-08-10 11:50:58 -05:00
Adam J. Stewart
fbf386328c
Add py-oauth2client package (#12373) 2019-08-10 11:50:43 -05:00
Adam J. Stewart
1d0f61816a
Add py-pathlib package (#12374) 2019-08-10 11:50:24 -05:00
Adam J. Stewart
37e59cbd7e
Add py-pyperclip package (#12375) 2019-08-10 11:50:10 -05:00
Adam J. Stewart
572bc5cc77
Add py-pysmartdl package (#12376) 2019-08-10 11:49:55 -05:00
Adam J. Stewart
3601f1c825
Add py-retrying package (#12377) 2019-08-10 11:49:41 -05:00
Adam J. Stewart
25b3946e0b
Add py-selenium package (#12378) 2019-08-10 11:49:25 -05:00
Sajid Ali
48016366c8 modified: var/spack/repos/builtin/packages/libflame/package.py (#12379) 2019-08-10 11:48:58 -05:00
Cameron Smith
a4a30de8a1 libconfig: add version 1.7.1 (#12324)
* libconfig: add version 1.7.1

* move 1.7.1 above 1.6, latest version is preferred
2019-08-10 11:08:53 -05:00
Seth R. Johnson
54018b488a Fix build for moab 4.9.2 on gcc8 (#12328)
```
5 errors found in build log:
     609      CXX      mbpart.o
     610      CXX      quality.o
     611      CXX      umr.o
     612      CXX      merge.o
     613      CXX      parread.o
     614    mbpart.cpp: In function 'int main(int, char**)':
  >> 615    mbpart.cpp:494:19: error: no match for 'operator<<' (operand types
            are 'std::ostream' {aka 'std::basic_ostream<char>'} and 'std::ostri
            ngstream' {aka 'std::__cxx11::basic_ostringstream<char>'})
     616             std::cerr << tmp_output_file << " : failed to write file."
             << std::endl;
     617             ~~~~~~~~~~^~~~~~~~~~~~~~~~~~
     618    mbpart.cpp:494:19: note: candidate: 'operator<<(int, int)' <built-i
            n>
     619    mbpart.cpp:494:19: note:   no known conversion for argument 2 from
            'std::ostringstream' {aka 'std::__cxx11::basic_ostringstream<char>'
            } to 'int'
     620    In file included from /software/user_tools/centos-7.2.1511/cades-ns
            ed-spack/opt/spack/linux-centos7-x86_64/gcc-4.8.5/gcc-8.2.0-uc6sbum
            ioobdbkw4rwfyn2givi4nyvwq/include/c++/8.2.0/iterator:64,
     621                     from /software/user_tools/centos-7.2.1511/cades-ns
            ed-spack/var/spack/stage/moab-4.9.2-77uuzmj4ofb7z7vz6m25sftyks7p5do
            7/spack-src/src/moab/Range.hpp:167,

     ...

     886    /software/user_tools/centos-7.2.1511/cades-nsed-spack/opt/spack/lin
            ux-centos7-x86_64/gcc-4.8.5/gcc-8.2.0-uc6sbumioobdbkw4rwfyn2givi4ny
            vwq/include/c++/8.2.0/ostream:682:5: note: candidate: 'template<cla
            ss _Ostream, class _Tp> typename std::enable_if<std::__and_<std::__
            not_<std::is_lvalue_reference<_Tp> >, std::__is_convertible_to_basi
            c_ostream<_Ostream>, std::__is_insertable<typename std::__is_conver
            tible_to_basic_ostream<_Tp>::__ostream_type, const _Tp&, void> >::v
            alue, typename std::__is_convertible_to_basic_ostream<_Tp>::__ostre
            am_type>::type std::operator<<(_Ostream&&, const _Tp&)'
     887         operator<<(_Ostream&& __os, const _Tp& __x)
     888         ^~~~~~~~
     889    /software/user_tools/centos-7.2.1511/cades-nsed-spack/opt/spack/lin
            ux-centos7-x86_64/gcc-4.8.5/gcc-8.2.0-uc6sbumioobdbkw4rwfyn2givi4ny
            vwq/include/c++/8.2.0/ostream:682:5: note:   template argument dedu
            ction/substitution failed:
     890    /software/user_tools/centos-7.2.1511/cades-nsed-spack/opt/spack/lin
            ux-centos7-x86_64/gcc-4.8.5/gcc-8.2.0-uc6sbumioobdbkw4rwfyn2givi4ny
            vwq/include/c++/8.2.0/ostream: In substitution of 'template<class _
            Ostream, class _Tp> typename std::enable_if<std::__and_<std::__not_
            <std::is_lvalue_reference<_Tp> >, std::__is_convertible_to_basic_os
            tream<_Ostream>, std::__is_insertable<typename std::__is_convertibl
            e_to_basic_ostream<_Tp>::__ostream_type, const _Tp&, void> >::value
            , typename std::__is_convertible_to_basic_ostream<_Tp>::__ostream_t
            ype>::type std::operator<<(_Ostream&&, const _Tp&) [with _Ostream =
             std::basic_ostream<char>&; _Tp = std::__cxx11::basic_ostringstream
            <char>]':
     891    mbpart.cpp:494:22:   required from here
  >> 892    /software/user_tools/centos-7.2.1511/cades-nsed-spack/opt/spack/lin
            ux-centos7-x86_64/gcc-4.8.5/gcc-8.2.0-uc6sbumioobdbkw4rwfyn2givi4ny
            vwq/include/c++/8.2.0/ostream:682:5: error: no type named 'type' in
             'struct std::enable_if<false, std::basic_ostream<char>&>'
     893      CXXLD    mbdepth
     894      CXXLD    hexmodops
  >> 895    make[2]: *** [mbpart.o] Error 1
     896    make[2]: *** Waiting for unfinished jobs....
     897    make[2]: Leaving directory `/localscratch/tmp/s3j-spack/spack-stage
            /spack-stage-NT13kT/spack-src/tools'
  >> 898    make[1]: *** [all-recursive] Error 1
     899    make[1]: Leaving directory `/localscratch/tmp/s3j-spack/spack-stage
            /spack-stage-NT13kT/spack-src/tools'
  >> 900    make: *** [all-recursive] Error 1
```
2019-08-10 11:08:13 -05:00
Adam J. Stewart
f9e6f0fb62
py-numexpr: switch from PyPI to GitHub download (#12360) 2019-08-09 22:27:34 -05:00
Ricardo Silva
c5849ce04f gromacs: fix CPU optimizations detection (simd=auto) (#12354)
* SL-637
* https://redmine.gromacs.org/issues/2927
* tested with cmake 3.14.4 and 3.15.1
2019-08-09 21:38:16 -05:00
Russell J. Hewett
7cc57d74e4 Updated Blaze version 3.5 and added access to master branch (#12341)
* blaze: added version 3.5

* blaze: added access to bleeding edge
2019-08-09 21:32:54 -05:00
Cameron Stanavige
13112d6b1c flatcc: add version 0.5.3 (#12358)
This updates the flatcc package to have the latest version.
2019-08-09 21:32:10 -05:00
Geoffrey Oxberry
28ffc1a4b9 gnome-common: new package (#12359) 2019-08-09 21:31:47 -05:00
Geoffrey Oxberry
92c65f3150 Add new package: libfive@master (#12334) 2019-08-09 18:10:00 -05:00
Toyohisa Kameyama
b54576abaf sdl2: fix dependency for libxext and build on ARM (#12351)
1. add dependency for libxext2.
2. SSEMATH is off is aarch64.
3. reformat comment for flake8.
2019-08-09 10:24:16 -05:00
Sean McGrath
74fe729be2 New Plink beta version (#12352)
* Plink 1.9 Beta 6.10 added

* Typo Fix
2019-08-09 10:22:18 -05:00
Sinan
a999092a93 newpackage/tippecanoe (#12319)
* newpackage/tippecanoe

* make flake8 happy

* add "r" for raw text
2019-08-09 10:18:26 -05:00
Geoffrey Oxberry
7b47178a53 bugfix: hunspell: add missing gettext dependency (#12347)
* hunspell: write autoreconf method to triage error

This commit fixes the error described in GitHub issue
`AutotoolsPackage` class attempts to call `libtoolize`, which doesn't
exist on macOS systems that externally install `libtool` in Spack via
Homebrew -- Homebrew installzes GNU libtoolize as `glibtoolize`.

The fix is to call `autoreconf` only, and GitHub pull request #12344
makes this change in
AutotoolsPackage (https://github.com/spack/spack/pull/12344). However,
while waiting for that pull request to be merged, overriding the
`autoreconf` method achieves the same result for a self-contained
fix. This self-contained fix is necessary to fix a dependency bug in
the `hunspell` package.

* hunspell: add missing gettext dependency

* hunspell: add version 1.7.0
2019-08-09 10:17:57 -05:00
Derick Huth
850b2ad42e Fixed broken iegenlib package (#12229)
* Fixed broken iegenlib package

* [IEGenLib] fixed for style

* [IEGenLib] style fixes

* [IEGenLib] removed CMAKE_BUILD_TYPE option from config_args
2019-08-09 10:14:17 -05:00
angel-devicente
e203068125 Added checksum for binutils@2.32 (#12350) 2019-08-08 23:56:41 -05:00
Geoffrey Oxberry
9336a8be38 enchant@2.2.5: new package (#12349) 2019-08-08 22:50:06 -05:00
Toyohisa Kameyama
14bdd56004 hisea: build on ARM. (#12302) 2019-08-08 22:45:23 -05:00
Marc-Andre Hermanns
606246572a Add new releases of Cube Tools, Opari2, OTF2, and Score-P (#12303) 2019-08-08 22:44:33 -05:00
Owen Solberg
178476d8c8 new package: Cromwell (#12309)
* add new package cromwell

* fix flake8 errors, add cromwell-womtool package

* change name of cromwell to cromwell-server

* renamed cromwell-server to just cromwell

* update description to what is in the project docs

* fixing format call for python2.6 compatibility
2019-08-08 22:39:00 -05:00
Sinan
d1e8ea302f new package: aria2 (#12318)
* new package: aria2

* tidy up
2019-08-08 22:36:13 -05:00
Cameron Smith
51adb6a4ef netcdf-cxx4: add m4 dep for call to autoreconf (#12325) 2019-08-08 22:29:42 -05:00
Geoffrey Oxberry
1a432fb213 guile: add versions 2.2.1 through 2.2.6 (#12333) 2019-08-08 22:22:17 -05:00
Adam J. Stewart
89af88aa02
Re-add py-cython dependency to py-tables (#12338) 2019-08-08 21:57:16 -05:00
Adam J. Stewart
b409283ad5
Add py-certifi 2019.6.16 (#12339) 2019-08-08 21:57:01 -05:00
Adam J. Stewart
0b4e13c034 openssl package: add versions including 1.1.1c (#12342)
* Add comment that 1.0.1 versions are no longer supported
* Add comment that 1.0.2 versions are only supported up to
  December 2019
* Add versions 1.0.2s, 1.0.2r, and 1.0.2p
* Add versions 1.1.0k, 1.1.0j, and 1.1.0i
* Add version 1.1.1c
* Add comment that 1.1.0 versions are only supported up to
  September 2019
2019-08-08 17:04:53 -07:00
Jon Rood
941eb5d756 Generalize STK package settings in Trilinos (#11917)
* Making STK package in Trilinos more general.

* Remove comment about seacas exodus settings.
2019-08-07 16:11:15 -05:00
Pariksheet Nanda
0c9bc8da86 ncbi-toolkit: add version 22_0_0 (#12278)
* ncbi-toolkit: fix compiler+version restriction (spack/spack#12276)

* ncbi-toolkit: update urls for current and archive releases

* ncbi-toolkit: add compatibility for boost@1.69:

* ncbi-toolkit: add compatibility for boost@1.70:

* ENH: Add debug variant to significantly reduce install size

* ncbi-toolkit: add archive url for 22_0_0 (spack/spack#12278)
2019-08-07 14:18:36 -05:00
Piotr Luszczek
f7026a058b Version 19.8.1 of PLASMA (#12299)
* Remove unnecessary setting with buggy prefix

Spack adds installation prefix by default and the "self." is missing

* Add version 19.8.1 of PLASMA
2019-08-07 00:08:59 -05:00
Daryl W. Grunau
4f6916261c new package: py-exodus (#12291) 2019-08-06 23:11:56 -05:00
Mark W. Krentel
2f84db881b ncurses: fix pic and opt flags (#12272)
Resolves #11932.

Move the PIC flags from CFLAGS on the configure line to the spack
compiler wrapper for ncurses.  The problem with the configure line for
autotools is that specifying CFLAGS sets the entire flags, thus
deleting the flags that configure would add itself.

By default, if CFLAGS is unspecified, then configure picks a sensible
default of `-g -O2`.  But adding `-fPIC` erases these and it ends up
building unoptimized.
2019-08-06 22:21:25 -05:00
Cameron Smith
e077532baf pumi: new version 2.2.1 (#12282) 2019-08-06 22:09:46 -05:00
Tamara Dahlgren
951d42596b tests: explain and test dependency flattening routines (#11993)
- Add comments to explain that `install_dependency_symlinks` and `flatten_dependencies` are actually used.
- Add a test that exercises the routines.
2019-08-06 17:11:23 -07:00
Seth R. Johnson
09d4fcc6ad graphviz package: add MacOS fixes and quartz support (#11128)
* Add patch to detect newer versions of MacOS and to fix a typo in
  configure.ac (AM_LIBTOOLSFLAGS should be AM_LIBTOOLFLAGS)
* Remove variant declarations for unsupported languages
* Add support for quartz on MacOS
* Add optional X Window support
* Specifically build against qt@4 when building QT support
* Point to appropriate C++ standard libraries when building with
  Clang on MacOS
* Disable parallel build (for all platforms)
* Increase verbosity of configure script by adding
  --disable-silent-rules
2019-08-06 16:26:45 -07:00
Adam J. Stewart
66e9b1279a
Overhaul numpy package (#12170)
* Add numpy 1.17.0

* Overhaul numpy package

* Flake8 fixes

* Undefined reference fix

* HeaderList and LibraryList need an arg

* veclibfort has no headers

* Add patch for older versions of py-numpy

* Remove py-meep hack from py-numpy package

* libflame: always add max arg hack flag

* Fix build with GCC 4.8

* Compiler flags come from self.compiler

* Only apply -std=c99 to cflags

* Try to fix libflame package

* Fix ATLAS build on macOS

* --force-clang flag added in 3.10.3
2019-08-06 18:20:23 -05:00
t-karatsu
d488d04ed3 fltk: fix about variable types (#12292)
* fltk: fix about variable types
2019-08-06 11:07:27 -07:00
Daryl W. Grunau
cb7e9c155e Packages/musl (#12288)
* bump eospac version

* Revert "bump eospac version"

This reverts commit 835b1f822d8c083f6ab9eb17222c00409e8eb3da.

* fix-up musl-gcc wrapper script

* address adamjstewart's comments
2019-08-05 20:16:14 -05:00
Toyohisa Kameyama
567cef7ae3 c-blosc package: Add -std=gnu99 flag for gcc (#11959)
When building with GCC, c-blosc requires the -std=gnu99 flag.
Before this patch, the build would only add -std=gnu99 for GCC when
building on specific architectures; this adds -std=gnu99 in all cases
when using GCC.
2019-08-05 18:04:16 -07:00
Adam J. Stewart
2e14cdb8fd
Move new packages from tutorial to builtin (#12289)
* Move new packages from tutorial to builtin

* Remove unicode character from docstring
2019-08-05 19:55:39 -05:00
Satish Balay
0db3d6ca37 Balay/amrex 19.08 (#12287)
* amrex: add version 19.08

* amrex: update sundials dependency for @19.08
2019-08-05 17:34:01 -05:00
Axel Huebl
3457dffdca
openPMD-api: pre-load depend libs (#12279)
When loading `openpmd-api` as a lib to build outside of
spack or to build depending spack packages, the "CMake-PUBLIC"
header-only library MPark.Variant must be available. Also,
the `*Config.cmake` package must be able to find dependent
libs if used.
2019-08-05 14:02:23 -05:00
Satish Balay
5560d5b601
Add version 19.8.0 of PLASMA (#12275) 2019-08-04 20:37:46 -05:00
Satish Balay
480cd9344f
Add version 2.5.1 of MAGMA released today (#12274) 2019-08-04 20:36:48 -05:00
Satish Balay
47aa08081a
ginkgo: add maintainers (#12273) 2019-08-04 20:36:04 -05:00
Sinan
3ad61441f1 new package: py-backports-tempfile (#12261)
* new package: py-backports-tempfile

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

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

* remove rc version

* fix single quote
2019-08-04 16:10:24 -05:00
Sinan
7ee56c2f36 package/py-apipkg add new version, add sha256 sums (#12260)
* add new version, add sha256 sums

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

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

* add python dependencies
2019-08-03 18:38:34 -05:00
Sinan
0b606f7c46 new package: py-backports-weakref (#12262)
* new package: py-backports-weakref

* use the version at pypi.org
2019-08-03 18:37:10 -05:00
Sinan
fcfdfb86c7 new package: py-usgs (#12263)
* new package: py-usgs

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

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

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

Co-Authored-By: Adam J. Stewart <ajstewart426@gmail.com>
2019-08-03 18:36:55 -05:00
Sinan
cc54d910a6 new package: py-requests-futures (#12264)
* new package: py-requests-futures

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

Co-Authored-By: Adam J. Stewart <ajstewart426@gmail.com>
2019-08-03 18:36:42 -05:00
Sinan
9432b1f789 new package: py-colorlog (#12265)
* new package: py-colorlog

* improve styling.

* remove spaces
2019-08-03 18:36:29 -05:00
Sinan
5bb73d4ad3 new package: py-colorpy (#12266)
* new package: py-colorpy

* remove incorrect dependency
2019-08-03 18:36:17 -05:00
Adam J. Stewart
36558dc262
Add py-uritemplate package (#12259) 2019-08-03 10:44:13 -05:00
Adam J. Stewart
5e2af206d3
Add py-earthengine-api package (#12253) 2019-08-02 23:37:59 -05:00
Adam J. Stewart
c36c7f2bab
Add py-google-api-python-client package (#12254) 2019-08-02 23:35:21 -05:00
Adam J. Stewart
ccfaeecfeb
Add py-google-auth-httplib2 package (#12255) 2019-08-02 23:35:00 -05:00
Adam J. Stewart
ccc4af4bec
Add py-google-auth package (#12256) 2019-08-02 23:34:32 -05:00
Adam J. Stewart
8b270290c4
Add py-httplib2 package (#12257) 2019-08-02 23:34:04 -05:00
Adam J. Stewart
958d385e09
Add py-pyasn1-modules package (#12258) 2019-08-02 23:33:37 -05:00
Adam J. Stewart
0de42519cf
Add py-cachetools package (#12252) 2019-08-02 20:47:46 -05:00
Adam J. Stewart
eb528f89a7
Add py-pyasn1 0.4.6 (#12251) 2019-08-02 20:09:15 -05:00
Reinhard Prix
7845d91fda swig: add latest version, 4.0.0 (#12243) 2019-08-02 20:08:26 -05:00
Satish Balay
8010965a3d slepc: update python dependencies to be in sync with petsc (#12250) 2019-08-02 20:07:29 -05:00
Daryl W. Grunau
b4f8294408 packages/musl (#12247)
* new musl package
2019-08-02 20:06:59 -05:00
Marc-Andre Hermanns
0290170935 Set default resource manager to 'none' (#12092) 2019-08-02 19:23:14 -05:00
Toyohisa Kameyama
50b90ed2bf minimap2, py-mappy: change dependency and build on ARM (#12127)
* minimap2: remove py-mappy dependency and build on ARM
py-mappy: Change URL and new version.

* merge py-mappy to minimap2.

* 1. add type in depends_on.
2. remove unneeded which.
2019-08-02 19:21:33 -05:00
Chris Green
0c1496896d Resolves #11487. (#12136)
* Incorporate as a patch upstream commit 0c20dbf059 (diff-acb9169b4ccbac494ced5140d285a015) resolving problems with `-Wno-...` options not being understood by GCC.
* Incorporate as a patch upstream PR https://github.com/ericniebler/range-v3/pull/1202 fixing upstream issue https://github.com/ericniebler/range-v3/issues/1196.
* Compile tests only if we actually want to run them.
* Optionally compile documentation with a `+doc` variant.
* Add `+examples` and `+perf` variants to avoid unnecessary compilation of components usually not required for install.
* Add conditional build-only dependency on Boost when appropriate.
* Install docs, examples and performance tests if built (not part of upstream build instructions).
* Add @chissg as a maintainer.
2019-08-02 19:19:39 -05:00
Toyohisa Kameyama
b6789b2ba3 py-flye: change to build ARM. (#12176) 2019-08-02 19:15:49 -05:00
Todd Kordenbrock
a54687ead9 FAODEL: Add 1.1906.1 (#12180) 2019-08-02 19:14:21 -05:00
Toyohisa Kameyama
dbeee34829 vdt: add simd variant (#12188)
1. add simd variant and check target.
2. build on source directory before 0.3.8.
2019-08-02 19:10:39 -05:00
TiffanyAnn
ff15f61443 py-mpi4py: Added build argument for mpicc path (#12191)
* added build arguments to resolve error with Cray-MPICH

* fixed indentation
2019-08-02 19:09:37 -05:00
Hironori-Yamaji
53bd964a59 ermod: new package (#12192) 2019-08-02 19:08:35 -05:00
Toyohisa Kameyama
53b1a92f69 parsimonator: Enable build on non x86_64 hosts. (#12194) 2019-08-02 19:07:43 -05:00
Glenn Johnson
6278ba43e9 Update c-blosc and fix building tests with icc (#12204)
- Update c-blosc to 1.17.0
- Add patch to build test_forksafe for versions 1.15.0 through 1.17.0
  when compiled with the Intel compiler.
- Remove code that turned off building the test with the Intel compiler
2019-08-02 19:05:43 -05:00
Toyohisa Kameyama
93f6833990 raxml: compile n non-x86 hosts. (#12208)
1. xmmintrrin.h is included x86 only.
2. Add makefiles for non-x86 hosts.
3. mpicc in Makefiles is replaced spacks mpi compile command.
4. variant check is rewite with satisfies.
2019-08-02 19:04:25 -05:00
Toyohisa Kameyama
3fc5a08f5b dialign-tx: build on ARM. (#12210) 2019-08-02 19:02:36 -05:00
liuyangzhuan
474bf18853 added a package butterflypack (#12222)
* added a package butterflypack

* remove one line in the python script
2019-08-02 18:58:30 -05:00
Mark W. Krentel
45d852b87d hpcviewer: update sha sums for version 2019.07 (#12236)
We (Rice HPCToolkit) issued a re-release of hpcviewer 2019.07 due to
some serious bugs.
2019-08-02 18:55:46 -05:00
Satish Balay
4ee260d3e3 ginkgo: fix branch -> commit for @1.0.0. Also add variant: develtools (#12248)
This fixes error with multiple builds - when they use the cached tarball.
2019-08-02 18:54:15 -05:00
dbs8842
2529b753da liggghts: added version 3.8.0 (#12242) 2019-08-02 18:53:06 -05:00
Gregory Lee
214b67066e glib: fix glib dependency build fixes #9992 (#12153)
add rpaths for glib config and py-pygobject build
2019-08-02 15:18:04 -05:00
wspear
9dd61f5313 Fixed arch setting variants. Activate cray arch automatically. (#11203) 2019-08-02 15:14:43 -05:00
Chuck Atkins
0e532d324c
adios2: Fix backwards compatibility version logic for FindMPI (#12241) 2019-08-02 15:27:47 -04:00
Tamara Dahlgren
574c13837f
packages: Add autotools dependencies to bolt (#12246)
Fixes #12060 (per wspear).

This change is needed for minimal container environments.
2019-08-02 12:22:51 -07:00
Patrick Gartung
9cf6aece85
Geant4 data packages: Set the install path name explicitly. (#12244)
* Geant4 data packages: Set the install path name explicitly.

* Use the correct directory name for g4photonevaporation,g4radioactivedecay,g4realsurface
2019-08-02 13:48:35 -05:00
Chris Green
023de09134 mysql package: New versions, add conflicts, cope with use of dtrace. (#11356)
* Add versions 8.0.16, 5.7.26, and 5.6.44
* Update boost dependency for versions 8.0.16, 8.0.15, and 8.0.14
* Update dtrace script when building for versions before 8 as is done
  for the glib package
* Set perl as a build dependency for versions before 8
* cxxstd=17 conflicts with version 8 when server code is built
  (~client_only)
* Add -Wno-deprecated-declarations for cxxstd > 11
* Add -Wno-error=register for cxxstd > 14
2019-08-02 10:51:02 -07:00
Axel Huebl
46f03074ef openPMD-api: Increase ADIOS2 Minimum (#12169)
The minimum required version of ADIOS2 is v2.4.0 .
2019-08-02 15:31:29 +02:00
MikeG
d384025df7 valgrind: added version 3.15.0 (#12239) 2019-08-02 15:10:37 +02:00
Seth R. Johnson
68d78c0dbe Fix py-matplotlib build (#12230) (#12234) 2019-08-01 17:58:06 -05:00
Seth R. Johnson
46027bea13 Fix QT4 build for mac (#10944)
This updates the Spack QT package to enable building qt version 4 on
MacOS. 

This includes the following changes to the qt package:

* add version 4.8.7
* add option to build with or without shared libs
* add options to disable tools, ssl, sql, and freetype support
* add qt4-tools patch when building qt@4+tools
* add option to build as a framework (only available on MacOS)
* replace qt4-el-capitan patch with qt4-mac patch (which includes the
  edits from qt4-el-capitan)
* apply qt4-pcre-include-conflict.patch only for version 4.8.6
  (rather than all 4.x versions)
* apply qt4-gcc-and-webkit.patch for 4.x versions before 4.8.7 and
  create a separate qt4-gcc-and-webkit-487.patch for version 4.8.7
* update patch function for qt@4 on MacOS to update configure
  variables relevant to Spack (e.g. PREFIX)
* add option to build freetype with Spack, as a vendored dependency
  of QT, or not at all (default is to build with Spack)

This includes the following edits outside of the qt package:

* Update MacOS version utility function to return all parts of the
  Mac version (rather than just the first two)
* gettext package: implement "libs"
* python package: add gettext as a dependency
2019-08-01 10:22:35 -07:00
Ben Bergen
8922c1f666 Add HDF5 variant to Legion package (#12221) 2019-08-01 10:33:29 -06:00
Sajid Ali
e21e10837f modified: var/spack/repos/builtin/packages/blis/package.py (#12225) 2019-08-01 09:37:23 -05:00
Sajid Ali
f30b717744 Add libflame (#12193)
* Add libflame

	new file:   var/spack/repos/builtin/packages/libflame/Makefile_5.1.0.patch
	new file:   var/spack/repos/builtin/packages/libflame/package.py

* 	modified:   var/spack/repos/builtin/packages/libflame/package.py
2019-08-01 09:33:24 -05:00
Adam J. Stewart
61b824580e py-pyqt5: add missing py-enum34 dependency (#12224) 2019-08-01 13:30:35 +02:00
t-karatsu
9b03ab43ed bdw-gc: add variant for Multithreading (#12223) 2019-08-01 13:29:41 +02:00
Mark W. Krentel
e628f1b4eb unzip: fix build for cray back-end
Fixes #12007.

The Cray cc wrappers don't handle the -s flag (strip) cleanly, It's
not essential to strip the binary, so just remove the flag on Cray.

Note: the default build on Cray is for the back end and the unzip
binary won't run on the front end.  To build for FE, use something
like arch=cray-fe-x86_64.
2019-07-31 20:44:40 -07:00
Gregory Lee
2c2abb454c fix mpa package build error with a patch (#12217) 2019-07-31 16:48:06 -05:00
Gregory Lee
162f1338d9 patch launchmon to fix char * conversion error (#12219) 2019-07-31 16:47:35 -05:00
Rémi Lacroix
5c970613b6 Magma: fix prefix (#12220)
`prefix` is not available in `cmake_args` method, use `self.prefix`.
Fixes #12214.
2019-07-31 16:43:47 -05:00
Adam J. Stewart
f7d1df4d3a
Update Package Creation Tutorial for PEARC19 (#12209)
* Update Package Creation Tutorial for PEARC19

* A few remaining fixes

* Fix section link
2019-07-31 12:54:09 -05:00
Matthieu Dorier
65a1db87f8 Preventing jsoncpp from building tests (#11948)
* Preventing jsoncpp from building tests
jsoncpp: making -DJSONCPP_WITH_TESTS=OFF conditioned by self.run_tests
2019-07-31 12:18:25 -05:00
Ondřej Čertík
7e61527f9e F18: Fix the location to the f18 binary (#12186) 2019-07-31 15:43:08 +02:00
jthies
ae1524821e phist: added version 1.8.0 (#12201) 2019-07-31 15:35:59 +02:00
t-karatsu
b744accaf6 igvtools: fixed query on jdk instead of java (#12195) 2019-07-31 14:49:51 +02:00
Ryan S. Elliott
86ff5baed7 kim-api: added version 2.1.2 (#12189) 2019-07-31 09:13:13 +02:00
t-karatsu
268c806111 genomefinisher: fixed query on jdk instead of java (#12196) 2019-07-31 08:55:56 +02:00
Adam J. Stewart
db2bbbcecf
Add pandas 0.25.0 (#12173) 2019-07-30 17:16:32 -05:00
Adam J. Stewart
59e9541386
Add tables 3.5.2 (#12172) 2019-07-30 17:16:15 -05:00
Adam J. Stewart
60da9303c6
Update numexpr dependency version (#12168) 2019-07-30 17:15:38 -05:00
Adam J. Stewart
70512b8ba2
Add py-matplotlib 3.1.1 (#12164) 2019-07-30 17:15:20 -05:00
Adam J. Stewart
482152e092
Add py-wxpython package (#12163) 2019-07-30 17:13:32 -05:00
Adam J. Stewart
c1c5f58d12
Add py-cairocffi package (#12161) 2019-07-30 17:13:02 -05:00
Adam J. Stewart
b34da4e108
Add SIPPackage base class (#12157) 2019-07-30 17:12:48 -05:00
Adam J. Stewart
f487f87e3e
Add Magics 4.1.0 (#12078) 2019-07-30 17:11:47 -05:00
Adam J. Stewart
e728883c71
Add eccodes 2.13.0 (#12077) 2019-07-30 17:11:29 -05:00
Adam J. Stewart
354ef2f9ca
Allow bsseeker to build with Python 3 (#12075) 2019-07-30 17:11:14 -05:00
Adam J. Stewart
e13bc0212c
Add py-pipits 2.4 (#12074)
* Add py-pipits 2.4

* Flake8 fix
2019-07-30 17:10:57 -05:00
Justin S
175abecc0b mii: new package at 1.0.2 (#12184)
* mii: new package at 1.0.2

* mii: fix improper formatting in description

* mii: add 1.0.3
2019-07-30 16:16:41 -05:00
健美猞猁
544914f34b gromacs: added version 4.5.5 (#12197) 2019-07-30 16:07:07 +02:00
Ben Bergen
73a9d6556e New package: cgdb (#12154) 2019-07-29 17:19:53 -07:00
Hans Pabst
6db873532c LIBXSMM package: add version 1.13 and optional shared libs (#11998)
* Add +shared variant, which builds shared library in addition to the
  static library.
* Install libraries even when specifying the header-only option
  (header-only is just about installing an additional folder).
* An additional make call is not required to build generator
  executables (they are built by default).
* Streamlined help-line of each variant.
2019-07-29 17:14:41 -07:00
Toyohisa Kameyama
5f716b7ffa hpgmp package: Don't add cpu=native on ARM when using gcc 5.x or before (#12034) 2019-07-29 16:53:59 -07:00
Adam J. Stewart
b8b2fa226e CMOR package: add version 3.4.0 (Python3-compatible) (#12076) 2019-07-29 16:12:37 -07:00
Nick Forrington
6e9f51d1d2 Quantum Espresso package: Specify F90 compiler (#12119) 2019-07-29 15:53:39 -07:00
Adam J. Stewart
c9e5de85fd SimulationIO package: add version 9.0.1 (#12079) 2019-07-29 15:40:57 -07:00
Chuck Atkins
f18c9e0ba5 catalyst package: Fix paths used for intermediate code generation (#12082)
Fixes #12065
2019-07-29 15:31:07 -07:00
Adam J. Stewart
f88636b090 PISM package: add version 1.1.4 (#12083) 2019-07-29 15:26:03 -07:00
Adam J. Stewart
9af155f0f6 Fix some Mac constraint checks (#12138)
* Fix Mac platform check for dependency in py-ipython package: 'when'
  constraints in Spack directives must be Specs (either a Spec
  object or a Spec in string format)
* Fix Mac version check in py-numpy: platform.mac_ver() returns a
  3-part string as its first tuple item so the check as written would
  never pass; use Spack Version object to simplify check.
* Fix Mac version check in qt package (the check was incorrectly
  comparing ints and strings) and use Spack version object to
  simplify check.
2019-07-29 15:05:02 -07:00
Glenn P Johnson
e7d9a6f426 Add conflicts statement for Python-3.6.7+ and Intel compiler
Python-3.6.7 and up do not build with the Intel compiler

- https://bugs.python.org/issue35473
- https://bugs.python.org/issue37415
2019-07-29 14:38:05 -07:00
Federico Ficarelli
dbd294c204 zeromq package: choose URL based on version; add versions (#12149)
* Add versions 4.3.0, 4.3.1, and 4.3.2
* The URL format changed after 4.1.4, so this adds a url_for_version
  function to choose the URL format based on the version
2019-07-29 14:36:33 -07:00
Hironori-Yamaji
43dd6b3418 Gromacs package: add openmp, mdrun_only, double_precision options (#12150) 2019-07-29 14:29:04 -07:00
Adam J. Stewart
c3dc63ce8f New package: py-pytest-isort (#12160) 2019-07-29 14:02:06 -07:00
Jon Rood
3e02dc258b LLVM package: add optional libomp_tsan support (#11793)
This is only available for LLVM version 6 or greater. So this also
adds a conflict statement for earlier versions of LLVM.
2019-07-29 12:23:15 -07:00
Owen Solberg
ee1c36a2b0 update cmake 3.15.1 checksum (#12182) 2019-07-29 15:13:52 -04:00
Adam J. Stewart
0d0a02b230 OpenGL package: always provides gl (#12158)
With this PR, a user can designate older versions of OpenGL as an
external Spack package, and dependents can use that installation
as long as they do not have version requirements.

MacOS currently comes with OpenGL 2.1; there is currently no
'provides' directive in the OpenGL Spack package which specifies a
gl version provided for versions earlier than OpenGL 3.3, so earlier
versions of OpenGL are not considered to provide any version of gl.
This PR records that any version of OpenGL provides 'gl' (which is
sufficient for any package that does not require a specific version
of gl).
2019-07-29 12:11:53 -07:00
Adam J. Stewart
d1752d8640 py-scipy package: add version 1.3.0 (#12171)
* Version 1.3.0 requires python 3.5 or later (no Python 2 support)
* Remove test of scipy.weave import (not available since 1.0)
* Add more-sensitive py-numpy constraints based on py-scipy version
* Replace py-nose dependency with py-pytest
* Add adamjstewart as maintainer
2019-07-29 11:57:59 -07:00
Adam J. Stewart
249f571556 New package: py-torchvision (#12175) 2019-07-29 11:42:08 -07:00
Adam J. Stewart
18bd189876 PyTorch package: add version 1.1.0 (#12174)
* Rename py-pytorch to py-torch
* Add versions 1.1.0 and 1.0.1
* Define modules to test import of after installation (import_modules)
* py-typing dependency is only needed for older versions of Python
  (3.4 or before)
* Newer versions of py-torch depend on newer versions of CUDA
* Add adamjstewart as maintainer
2019-07-29 11:39:05 -07:00
Seth R. Johnson
3d0b5bd541 Change dependencies to use virtual jpeg package (#12179)
This prevents conflicts between descendents that depend on an unintentional
arbitrary jpeg implementation.
2019-07-29 12:08:55 -05:00
Kelly (KT) Thompson
a3f6f52622 Add a new version (7.2) of draco. (#11852)
This change also
+ Makes the `build_type` user settable and
+ Adds support for running tests.
+ Provide depends_on('cmake') for versions prior to 7.0.
2019-07-28 22:15:21 -05:00
Jeongseok Lee
e23d613ee6 Update checksum of fmt 5.3.0 (#12037) 2019-07-28 22:07:51 -05:00
Seth R. Johnson
95985e0798 Prevent conflicts between libuuid and Apple Cocoa Framework on Mac (#12166)
* Remove libuuid dependency for python on Darwin

Python 2.7 includes Carbon, which requires a proprietary typedef defined in
the system `/usr/include/uuid/uuid.h`:
```
In file included from /rnsdhpc/code/spack/var/spack/stage/python-2.7.16-chgwvgls4ezgujsknn27vlmkhwbzpqik/Python-2.7.16/Python/mactoolboxglue.c:27:
In file included from /rnsdhpc/code/spack/var/spack/stage/python-2.7.16-chgwvgls4ezgujsknn27vlmkhwbzpqik/Python-2.7.16/Include/pymactoolbox.h:10:
In file included from /System/Library/Frameworks/Carbon.framework/Headers/Carbon.h:20:
In file included from /System/Library/Frameworks/CoreServices.framework/Headers/CoreServices.h:23:
In file included from /System/Library/Frameworks/CoreServices.framework/Frameworks/AE.framework/Headers/AE.h:20:
In file included from /System/Library/Frameworks/CoreServices.framework/Frameworks/CarbonCore.framework/Headers/CarbonCore.h:208:
In file included from /System/Library/Frameworks/CoreServices.framework/Frameworks/CarbonCore.framework/Headers/HFSVolumes.h:25:
/usr/include/hfs/hfs_format.h:794:2: error: unknown type name 'uuid_string_t'; did you mean 'io_string_t'?
```

Similarly, even with Python 3, having Spack's libuuid in the toolchain
causes matplotlib to fail to build downstream because its `osx` backend
links against Carbon:
```
building 'matplotlib.backends._macosx' extension
/rnsdhpc/code/spack/lib/spack/env/clang/clang -Wno-unused-result -Wsign-compare -Wunreachable-code -DNDEBUG -g -fwrapv -O3 -Wall -fPIC -I/usr/local/include -I/usr/X11/include -I/opt/X11/include -I. -I/rnsdhpc/code/spack/opt/spack/darwin-mojave-x86_64/clang-10.0.1-apple/python-3.7.2-bipx24oyxqxowqc75o5vfih7dljiaohz/include/python3.7m -c src/_macosx.m -o build/temp.macosx-10.14.5-x86_64-3.7/src/_macosx.o
In file included from src/_macosx.m:1:
In file included from /Applications/Xcode.app/Contents/Developer/Platforms/MacOSX.platform/Developer/SDKs/MacOSX10.14.sdk/System/Library/Frameworks/Cocoa.framework/Headers/Cocoa.h:12:
In file included from /Applications/Xcode.app/Contents/Developer/Platforms/MacOSX.platform/Developer/SDKs/MacOSX10.14.sdk/System/Library/Frameworks/Foundation.framework/Headers/Foundation.h:87:
In file included from /Applications/Xcode.app/Contents/Developer/Platforms/MacOSX.platform/Developer/SDKs/MacOSX10.14.sdk/System/Library/Frameworks/Foundation.framework/Headers/NSURLError.h:15:
In file included from /Applications/Xcode.app/Contents/Developer/Platforms/MacOSX.platform/Developer/SDKs/MacOSX10.14.sdk/System/Library/Frameworks/CoreServices.framework/Headers/CoreServices.h:24:
In file included from /Applications/Xcode.app/Contents/Developer/Platforms/MacOSX.platform/Developer/SDKs/MacOSX10.14.sdk/System/Library/Frameworks/CoreServices.framework/Frameworks/AE.framework/Headers/AE.h:20:
In file included from /Applications/Xcode.app/Contents/Developer/Platforms/MacOSX.platform/Developer/SDKs/MacOSX10.14.sdk/System/Library/Frameworks/CoreServices.framework/Frameworks/CarbonCore.framework/Headers/CarbonCore.h:208:
In file included from /Applications/Xcode.app/Contents/Developer/Platforms/MacOSX.platform/Developer/SDKs/MacOSX10.14.sdk/System/Library/Frameworks/CoreServices.framework/Frameworks/CarbonCore.framework/Headers/HFSVolumes.h:25:
/Applications/Xcode.app/Contents/Developer/Platforms/MacOSX.platform/Developer/SDKs/MacOSX10.14.sdk/usr/include/hfs/hfs_format.h:794:2: error: unknown type name 'uuid_string_t'; did you mean 'io_string_t'?
        uuid_string_t   ext_jnl_uuid;
        ^
/Applications/Xcode.app/Contents/Developer/Platforms/MacOSX.platform/Developer/SDKs/MacOSX10.14.sdk/usr/include/device/device_types.h:89:33: note: 'io_string_t' declared here
typedef char                    io_string_t[512];
```

MacOS version 10.14.5
Xcode 10.2.1
Apple LLVM version 10.0.1 (clang-1001.0.46.4)

* Mark libuuid as conflicting with Darwin due to framework

If Spack's libuuid is included by any other package that tests for or
requires the Cocoa or Carbon frameworks, the build will *fail* becuse it
appears that Apple's libraries require a special version of libuuid and
uuid.h.

```
In file included from /Applications/Xcode.app/Contents/Developer/Platforms/MacOSX.platform/Developer/SDKs/MacOSX10.14.sdk/System/Library/Frameworks/Cocoa.framework/Headers/Cocoa.h:12:
In file included from /Applications/Xcode.app/Contents/Developer/Platforms/MacOSX.platform/Developer/SDKs/MacOSX10.14.sdk/System/Library/Frameworks/Foundation.framework/Headers/Foundation.h:87:
In file included from /Applications/Xcode.app/Contents/Developer/Platforms/MacOSX.platform/Developer/SDKs/MacOSX10.14.sdk/System/Library/Frameworks/Foundation.framework/Headers/NSURLError.h:15:
In file included from /Applications/Xcode.app/Contents/Developer/Platforms/MacOSX.platform/Developer/SDKs/MacOSX10.14.sdk/System/Library/Frameworks/CoreServices.framework/Headers/CoreServices.h:24:
In file included from /Applications/Xcode.app/Contents/Developer/Platforms/MacOSX.platform/Developer/SDKs/MacOSX10.14.sdk/System/Library/Frameworks/CoreServices.framework/Frameworks/AE.framework/Headers/AE.h:20:
In file included from /Applications/Xcode.app/Contents/Developer/Platforms/MacOSX.platform/Developer/SDKs/MacOSX10.14.sdk/System/Library/Frameworks/CoreServices.framework/Frameworks/CarbonCore.framework/Headers/CarbonCore.h:208:
In file included from /Applications/Xcode.app/Contents/Developer/Platforms/MacOSX.platform/Developer/SDKs/MacOSX10.14.sdk/System/Library/Frameworks/CoreServices.framework/Frameworks/CarbonCore.framework/Headers/HFSVolumes.h:25:
/Applications/Xcode.app/Contents/Developer/Platforms/MacOSX.platform/Developer/SDKs/MacOSX10.14.sdk/usr/include/hfs/hfs_format.h:794:2: error: unknown type name 'uuid_string_t'; did you mean 'io_string_t'?
        uuid_string_t   ext_jnl_uuid;
        ^
/Applications/Xcode.app/Contents/Developer/Platforms/MacOSX.platform/Developer/SDKs/MacOSX10.14.sdk/usr/include/device/device_types.h:89:33: note: 'io_string_t' declared here
typedef char                    io_string_t[512];
```

* Revert "Mark libuuid as conflicting with Darwin due to framework"

This reverts commit 9a68b75202005fc265abe2033e4ad36312a9a34d.

* Document libuuid exception in python package
2019-07-28 14:58:09 -05:00
Sajid Ali
9afd5113bc Bump version for BLIS (#12162)
modified:   var/spack/repos/builtin/packages/blis/package.py
2019-07-27 18:32:06 -05:00
Chuck Atkins
8d0c3e482f cmake: Bump to 3.15.1 (#12151) 2019-07-27 12:21:03 -05:00
Xavier Delaruelle
398c53eaa2 environment-modules package: add version 4.3.0 (#12155) 2019-07-27 12:20:39 -05:00
Chuck Atkins
18e41f9959 adios2: Patch findmpi for downstream issues. (#12152) 2019-07-26 13:17:31 -07:00
Sinan
511f84dd8c kealib: fix incorrect md5sum for v1.4.11 (#12126)
* fix incorrect md5sum for v1.4.11

* fix url and replace md5 with sha256

* add mainter
2019-07-26 15:14:46 -05:00
Ryan S. Elliott
12055acccc update to kim-api-2.1.1 and openkim-models-2019-07-25 (#12137)
* update to kim-api-2.1.1 and openkim-models-2019-07-25

* openkim-models provide needed dependency constraints and settings

* add maintainers and fixup flake8 errors
2019-07-26 13:06:10 -05:00
Adam J. Stewart
fbb04ece43
Add flake8 3.7.8 (#12141) 2019-07-26 12:11:07 -05:00
t-karatsu
21daa41dd6 libxc: Make configure recognize Fujitsu compiler (#12147) 2019-07-26 12:09:52 -05:00
Justin S
e2d16429ae py-pyomo: new package at 5.6.6 (#12134)
* py-pyomo: new package at 5.6.6

* py-pyomo: add missing deps, python constraint
2019-07-26 10:38:25 -05:00
Rémi Lacroix
9caba3e072 Small fixes for font-util package (#12148)
* font-util: Remove duplicated dependencies.

* font-util: Fix path handling for font resources.

The "join_path" call made no sense but still managed to work somehow most of the times.
2019-07-26 10:32:39 -05:00
Adam J. Stewart
0babdab8f0 Add GDAL 3.0.1 (#12140) 2019-07-26 09:25:35 +02:00
Adam J. Stewart
07fefea52d Add Python 3.7.4 (#12142) 2019-07-26 09:18:46 +02:00
Oliver Breitwieser
867ba9d7fe googletest: Fix reversed +pthreads option (#12128)
If +pthreads is specified, googletest actually gets build without
pthreads support and vice versa.

If pthreads is not available, googletest should detect it itself which
is why "enabling" pthreads in case of ~pthreads does not seem to cause
any error.

Change-Id: I29de8c4a23dc3901124b27a1ead3354949b7e65b
2019-07-25 19:50:23 -05:00
Justin S
94af6cad5f interproscan: new package at 5.36-75.0 (#12130) 2019-07-25 19:49:42 -05:00
Matthias Diener
7cc1292202 git-lfs: add version 2.8.0 (#12131) 2019-07-25 19:46:03 -05:00
Glenn Johnson
7ad8061cbb Patches for graphviz (#12133)
- patch to build with qt5, enabling gvedit to build
- two patches to compile graphviz with icc
2019-07-25 19:45:10 -05:00
Satish Balay
7bd3b66f6e
xsdk: phist has a conflict with gcc version <= gcc-4.9.1 (#11946)
* xsdk: phist has a conflict with gcc version <= gcc-4.9.1 - so add a variant to disable it on older compiler builds

This is triggered by #11677

* fix typo
2019-07-25 14:01:00 -05:00
Chuck Atkins
e614d4b481 cmake: Add a patch to revert a findmpi regression (#12129) 2019-07-25 10:23:01 -07:00
Chris Green
c20c153d16
catch: more versions, new and older. (#12123)
New versions 2.9.0, 2.9.1, older versions 2.2.2, 2.2.3, 2.4.1, 2.4.2, 2.7.0, 2.7.1, 2.7.2.
2019-07-25 11:33:03 -05:00
simo-tuomisto
4c7ee8b7c8 lame & libmad: Added two new packages for sox mp3 support. (#11964)
* Added a new package for LAME and a variant in sox for it.

* Fixed download url for LAME

* libmad: Added new package libmad for mp3 decoding. Changed sox variant from lame to mp3.

* libmad: Added m4 as a requirement

* libmad: Added comment on patch origins

* libmad: Added a list_url for alternate download location

* libmad: Fixing libmad download url
2019-07-25 10:40:50 -05:00
Sinan
9ace419aa5 gdal: added versions 2.4.2 and 3.0.1 (#12125) 2019-07-25 17:14:37 +02:00
Chris Green
4190f302e5 geant4: improvements with respect to building against CLHEP. (#12124) 2019-07-25 08:58:13 -05:00
Todd Gamblin
b0abbfecb8 new command: spack maintainers queries package maintainers
- We don't currently make enough use of the maintainers field on
  packages, though we could use it to assign reviews.

- add a command that allows maintainers to be queried
  - can ask who is maintaining a package or packages
  - can ask what packages users are maintaining
  - can list all maintained or unmaintained packages

- add tests for the command
2019-07-24 14:10:08 -07:00
Glenn Johnson
8bb745325d Add py-setuptools as a build dependency for py-absl-py (#12109)
I needed to add py-setuptools to get py-absl-py to build.
2019-07-24 12:33:45 -05:00
Glenn Johnson
642d3345f6 Add conflicts statement to freetype for icc (#12111)
Freetype-2.8 and above use __builtin_shuffle which is not supported by
icc.
2019-07-24 12:33:24 -05:00
t-karatsu
0f98cf0398 Perl take in flags (#12112)
* perl: perl package takes in spack cflags.

* fix for flake8 test.
2019-07-24 12:32:49 -05:00
Toyohisa Kameyama
bbc689ae38 nnvm: cmake bug is fixed. (#12113) 2019-07-24 12:31:49 -05:00
Toyohisa Kameyama
cb62b1ff85 rapidjson: Don't add -march=native on ARM and gcc 5.x or before. (#12117) 2019-07-24 12:30:32 -05:00
Nichols A. Romero
63813fa9c0 QMCPACK Update July 2019 (#12097)
* Add QMCPACK v. 3.8.0

* Remove QE variant conflict for serial QMCPACK installations.

* Add support for QE 6.4.1 converter.

* FindLibxml2QMC patch function only needed prior to QMCPACK 3.8.0
2019-07-24 12:28:35 -05:00
Glenn Johnson
42c3782f7e Do not build c-blosc test if intel in spec (#12110)
While the c-blosc library compiles with icc some of the c-blosc tests do
not. Disable the tests so that the spack build can continue.
2019-07-24 11:17:11 -05:00
t-karatsu
0d690edfb2 cmake: fix cxx98flag's name (#12114) 2019-07-24 11:28:22 -04:00
Toyohisa Kameyama
a8b12f0cb6 rocksdb: Don't add -march=native on ARM and gcc 5.x or before. (#12108) 2019-07-23 22:33:05 -05:00
Douglas Duckworth
ec29461632 added relion 3.0.7 - removed deprecated versions (#12101)
* relion - added v 3.0.7 and removed deprecated versions that have inferior performance

* relion 3.0.7 does require cuda 9 or above
2019-07-23 18:13:00 -05:00