* Remove variants disabling blas and lapack for py-numpy, issues
building these have been resolved
* For CMake greater than 3.10, FindMPI changed, so use
MPIEXE_EXECUTABLE instead of MPIEXE for 3.10 and newer
fixes#7128
Before this PR packages that were indirectly dependent on python might
have failed due to inconsistency between the python found in the
environment and the standard libraries set in PYTHONHOME
This adds a static version of hpgmg (up to now only the latest commit
from the master branch was available). This also adds a debug variant
and sets optimization flags for ~debug when the compiler is gcc,
intel, or clang
Adds the latest release of libSplash (1.7.0) and newly learned
CMake flags for explicit dependency control.
Modifies HDF5 dependency: non-MPI splash does (and did) never run
with a parallel HDF5, due to it's internal cross-dependencies on
MPI.
* libdwarf: fix linker flags
* libdwarf: fix header install names
* libdwarf: add zlib dependency
Prior to this commit, libdwarf was linked to the system zlib. This
commit links it to spack-installed zlib.
* libdwarf: fix dynamic library suffix for Darwin
* Adding support for the Accelerate library on OS X
* Fixed guard on variable and added another depends_on statement to make sure that openblas gets selected even when openmp_blas variant is not turned on.
* Added a package for the MDAnalysis toolkit.
* Added some flags to fix the build RPATHs and OpenMP for LBANN on OS X.
* Fixed Hydrogen branch of Elemental to find OpenMP on OS X.
* Cleaned up JUnit report generation on install
The generation of a JUnit report was previously part of the install
command. This commit factors the logic into its own module, and uses
a template for the generation of the report.
It also improves report generation, that now can deal with multiple
specs installed at once. Finally, extending the list of supported
formats is much easier than before, as it entails just writing a
new template.
* Polished report generation + added tests for failures and errors
The generation of a JUnit report has been polished, so that the
stacktrace is correctly displayed with Jenkins JUnit plugin. Standard
error is still not used.
Added unit tests to cover for installation failures and installation
errors.
* libtool: fix linking of libtool on darwin
* binutils, libtool: fix conflicts w/ BSD tools, v2
Fix namespace conflicts with BSD tools in a more elegant fashion,
using a program prefix, similar to Homebrew.
* Tell R's configure about tcltk config
Add configure arguments that specify the location of
the tcl and tk config scripts.
Fixes#7072
* Flake8 cleanup
Looking at build logs, it seems that prior to this commit bzip2 was
using 'cc', and relying on the PATH to be set correctly to find Spack
wrappers. This commit improves the robustness of the recipe, by using
the absolute path of the wrapper.
On Darwin and other BSD systems, the system 'libtool' and 'libtoolize'
are BSD libtool and libtoolize, respectively. Some build systems
require the GNU versions of these commands, so BSD package systems
tend to name the GNU versions 'glibtool' and 'glibtoolize',
respectively, to avoid namespace collisions.
A problem with the current libtool package is that it installs the GNU
libtool commands as 'libtool' and 'libtoolize', respectively, but
build systems on BSD platforms will attempt to run 'glibtool' and
'glibtoolize'. The expedient solution to this problem is to symlink
'libtool' to 'glibtool' and 'libtoolize' to 'glibtoolize', because
attempting to patch the detection logic one build system at a time
seems impractical.
* Added new link line flag
* Refactored some of the common components out of the different
version's build commands. Also corrected the when commands to
properly capture non-numeric names such as local.
* Added support to the Elemental package for the Hydrogen branch.
* Turning off default Qt support. Restricting Qt version to <= 4.9 else geant4 won't build
* Making vecgeom optional
* Differentiating between cxx11 and cxx14 support
* Making vecgeom optional. Part 2. forgot to move usolids option
* Adding explicit CXX11 and CXX14 support
* Adding more clhep version to support newer GEANT4 versions
* Adding GEANT4 versions 10.03.p03 and 10.04
* Checkpoint. Adding opengl and x11 variant. Lead up to more changes to enable X11 support
* Adding dependency on fixesproto for newer versions
* Making the X11 dependent pieces work without requiring X11 on the system
* Adding motif
This provides options for hardware and software rendering with the
gl API and updates the vtk package to make use of those options:
* Create new "gl" virtual package, provided by mesa
* Add external-only "opengl" package, which represents a system
install that provides gl
* For vtk: prefer system gl implementation by default to get speed
up from hardware rendering. When software rendering is specifically
requested (+osmesa), try to use the llvmpipe approach, as it is
much faster.
* Make qt dependency optional for vtk
* Add basic support for VTK on osx
* qt: Depend on virtual gl package, rather than mesa impl
* visit: add version 2.12.3
* visit: add version 2.13.0
* visit: enable building with hdf5+mpi
* visit: add qwt dependency
Building VisIt requires Qwt, which is not part of Qt. Prior to this
commit, this dependency was not included in the VisIt spack package,
resulting in a configure-time bug with an error message indicating a
missing Qwt dependency.
This commit fixes this bug by adding Qwt dependency information.
Update the qt4 CoreWLAN patch to apply to macOS/OS X 10.12 and 10.13,
which both still use the CoreWLAN framework in their SDKs (although
it's apparently deprecated?!). Without this patch update, `spack
install qt@4.8.6` fails on macOS/OS X 10.12 because the linker
cannot find headers from the CoreWLAN framework.
Apple removed support for Objective-C garbage collection in binaries
in XCode 5.1, but VTK 6.1.0 and earlier set flags for garbage
collection, resulting in a compile-time bug when compiling VTK using
any recent version of XCode (i.e., Apple Clang).
This commit fixes this bug by removing the garbage collection flags
via setting the variable `VTK_REQUIRED_OBJCXX_FLAGS` to the empty
string. This variable has the same value (i.e., the empty string) in
the root-level CMakeLists.txt file for VTK 6.2.0 and later.
VTK 6.1.0 and earlier do not use paths stored in `NETCDF_CXX_ROOT` to
detect the presence of NetCDF C++ headers and libraries. Consequently,
VTK 6.1.0 does not build.
This commit fixes this bug by setting the advanced variables
`NETCDF_CXX_INCLUDE_DIR` and `NETCDF_CXX_LIBRARY` at the command line
to specify the directory containing headers and the full library path
for the NetCDF C++ bindings.
The flag_handlers method was being set as a bound method, but when
reset in the package.py file it was being set as an unbound method
(all python2 issues). This gets the underlying function information,
which is the same in either case.
The bug was uncovered for parmetis in #6858. This is a partial fix.
Included are changes to the parmetis package.py file to make use of
flag_handlers.
This makes use of the new flag_handler logic from 28d8784a to set
compiler flags for ipopt by passing them as arguments to the build
system rather than injecting them into the compiler wrappers. This
avoids conflicts between flags that are chosen by the build system
and flags that are set by the user.
* ruby: fix +openssl & +readline variants
Fix "unqualified variable spec['openssl']" error in the ruby package
that arises when trying to install the `+openssl` variant by
referencing the `spec` field in the `Ruby` class. A similar error
arises when trying to install the `+readline` variant; this error is
also fixed by this patch.
* ruby: make +openssl variant default to on
Ruby's gem command will fetch gems from HTTPS resources by default
(e.g., gem install bundler). Without openssl, request to fetch gems
bounce back with the error
```
ERROR: While executing gem ... (Gem::Exception)
Unable to require openssl, install OpenSSL and rebuild ruby (preferred) or use non-HTTPS sources
```
Without the ability to install gems -- required for some spack
packages -- the ruby installation has limited utility for many users.
* ruby: update rubygems ssl cert to fix ssl errors
The SSL certificate bundled with Ruby 2.2.0 is outdated, so e.g., `gem
install erubis` will fail with an SSL certificate error. This commit
installs the updated SSL certificate to the proper directory so that
gems can be downloaded and installed from RubyGems.
The url in graphviz has been fixed and its version has been
updated to the latest available (2.40.1). Added variants for
expat, qt, gtk+ and ghostscript.
* py-fparser: parser for Fortran 77..2003 code
* py-fparser: guard against external pytest.ini
* py-fparser: define 'develop' version as latest master branch
* py-fparser: fetch tagged versions from git repo
* py-fparser: add latest release 0.0.6
* py-fparser: whitespace adjustments for flake8
* py-fparser: inherit python dependency from PythonPackage
* py-fparser: rely on spack to resolve sub-dependencies
* py-fparser: try type='test' for py-pytest
* py-fparser: fetch release tarballs instead of git commits
* py-fparser: test deptype is available, remove comment
* py-fparser: limit versions that use py-six
* py-fparser: version ranges do not need a lower bound
* qt: move licence acceptance from qt3krell.patch to qt3accept.patch
* qt: ensure that ptrdiff_t is defined for qt@3.3.8b
* qt: disable webglplugin for qt@5.10~opengl
* qt: depend on libxext (for qt@3 and @4)
* qt: avoid X dependencies on darwin platforms
* Revert "qt: avoid X dependencies on darwin platforms"
This reverts commit 05ce08de94be1e02d7e2f2dae0c1ae59baa3f65a.
* qt: limit range of versions depending on libxext
See #6794
This fixes cases where test-only dependencies were omitted from
consideration when modifying the environment at build time. This
includes an update to the python package definition to add
testing-related python extensions to its specialized environment
setup.
* coinhsl: add version 2014.01.10 (stable)
* coinhsl: make 2014.01.10 preferred version
Make Harwell Subroutines Library for IPOPT version 2014.01.10 the
preferred version because it is the latest stable version released.
* coinhsl: add option to link w/ BLAS libraries
Building emacs on darwin throws an error when trying to build an Emacs
app in the nextstep/Emacs.app path of the build tree. For now, disable
building this app.
It's possible to enable building the app also; Homebrew offers options
to this effect, and also adds Mac-specific options for starting the
emacs daemon. However, for the sake of simplicity and getting a
workable up-to-date emacs installation on my machine as quickly as
possible, this commit focuses on a minimal viable modification.
* Add a new package: unblur.
* Add a new package: unblur.
* Add a new package: unblur.
* Add a new package: unblur.
Conflicts:
var/spack/repos/builtin/packages/unblur/package.py
* Add a new package: unblur.
* Fix git on ubuntu, first cut
Spack needs to pass information about where the linker
can find `libintl`. We're currently using `LDFLAGS` to do so.
The `LDFLAGS` info is pasted into the command line upstream
of the a file (`libgit.a`) that includes unresolved symbols that
need that library. This fails on Ubuntu, although it seems to
work on CentOS (see #6841).
This change allows git to build on a Ubuntu 16.04.3 droplet.
TODO: test on other platforms...
* Add a bit of useful commentary
* Upgrade recipe for parmetis to be a CMakePackage
+ Eliminate `install` method (use the one from CMakePackage).
+ Move configure options to new method `cmake_args`
+ Move special install instructions for DarwinOS to a `run_after` method.
* Fix run_after section; Remove variant +debug.
Control the find_package of the PNG variant explicitly.
This avoids picking up an "external" PNGwriter install in
case `~png` is picked by changing the default "AUTO" search
to explicit "ON" (required) of "OFF" (ignore if exists).
* py-psyclone: Code generation for the PSyKAl framework from the GungHo project
* py-psyclone: add installation tests based on py.test
* py-psyclone: define 'develop' version as latest master branch
* py-psyclone: extract tagged version 1.5.1 from git repo
* py-psyclone: whitespace adjustments for flake8
* py-psyclone: use compatible versions of py-fparser
* py-psyclone: use type='test' for selected dependencies
* Updating OpenFAST to use explicit lapack and blas libraries from Spack.
* Simplifying openfast blas lib logic and fixes flake8 errors.
* Changing order of blas and lapack libs in openfast package.
* py-pybedtools: Create new package
* py-pybedtools: add py-six requirement
* py-pybedtools: remove py-cython dependency for release version
* py-pybedtools: include minimum version of py-pysam
* Provide build_type variant for Metis.
+ Ideally, we would make Metis a CMakePackage, but `metis@:5` doesn't use CMake.
+ For now, provide a `build_type=` variant similar what is found in
CMakePackage.
+ There is a potential for duplicate specification of `CMAKE_BUILD_TYPE` if both
variants `+debug` and `build_type=` are specified. I am looking for advice on
how this can be resolved.
* Update metis recipe in response to flake8 and user comments.
+ Wrap comment lines that used more than 80 columns.
+ Change `+debug` variant to avoid potential for multiple `-DCMAKE_BUID_TYPE=`
arguments provided to cmake. Specifying this variant no longer appends this
configure option. However, if `+debug` is specified, require
`build_type=Debug` to maintain expected behavior.
* For metis, remove +debug variant; use build_type= instead.
+ Update recipe for metis@4 to extract `build_type=` values and set `OPTFLAGS`
accordingly.
+ For metis@5:, the behavior from the previously supported variant `+debug` can
be obtained with the options `+gdb build_type=Debug`
* Conflicts added for metis@4 when build_type != Release|Debug.
* Use spack function conflicts instead of 'raise InstallError'.
* Create a symbolic link for MotionCor2.
* Create a symbolic link for MotionCor2.
* Create a symbolic link for MotionCor2.
* Create a symbolic link for MotionCor2.
* Adding NEURON package widely used in computational neuroscience community
* flake8 fixes
* Add rx3d variant
* Addressed review comments from Adam
* Addressed 2nd review comments
* Added check for +mpi on bg-q
* Filter spack compiler wrappers in NEURON scripts
Add gcc march=native flag to make front-end build robust
* Make develop as preferred version due to bug in long filename handlings in <= v7.4
* Avoid use of gcc in cross compiling environment
Use arch specific options on cray and bg-q arch
* Simplify cross compiling build:
- v7.5 added and no longer need develop as preferred version
- legacy cray related options removed
- cross compiling args reduced
- python arguments reduced as neuron finds proper libraries
* Simplify bg-q configurations
* Cleanup and unify arch options
* Make sure to add commonly available packages as dependency
* Arch path added to dependent_environment as nrniv needed at runtime
* Support for Power 8 architecture
* Fix python3 on OS X
* flake8 fix
* remove unnecessary conflcist directives
* Added a package for the MDAnalysis toolkit.
* Added a patch file to get rid of compiler warnings with intel compiler
and inlining. Added checksum values for other versions of protobuf.
* Added dependency on Intel compiler for intel patch
* added variant examples to paraview package.py
* qt: added libxt dependency
* add variant to use external hdf5, this is needed when compiling with gcc@4.8.5
* paraview: added python dependecies to PYTHONPATH
* Start adding Nek5000 package
* Add tools to install: genmap, prenek, postnek
* Address comments by @davydden
* Use install_tree (thanks @junghans) and polish
* Update url
* Fix flake formatting errors
* Change F77 and CC compilers
Apparently spack compilers can't be called outside spack and we
have an underscore test in our Nek5000/core/makenek.inc file which
calls F77 compiler.
* Add support for visit and profiling options
* Fix a typo
* Fix a typo
* Remove the C check
* Add visit variant
* Update the install of int_tp tool
* Let MAXNEL to be set during installation
* Added magma package
* Incorporated Serban's change
* Remove deleted files
* argparse.py
* Sync forked Spack repo in github
* Add spectrum-mpi lib path to LD_LIBRAY_PATH in spack_env.
As a result of supporting alternate installation directories, spectrum-mpi does
not use rpath anymore, so we need to set LD_LIBRARY_PATH in spack_env to allow
MPI programs to run during dependent package configuration.
* Fix flake8 error (blank line at EOF)
* xios: XML-IO-SERVER library for IO management of climate models
* xios: install to prefix directory
* xios: add a test case
* xios: define versions to use cache and mirror directories
* xios: use proper svn URL for version 910
* xios: package url must be defined, otherwise uninstall fails
* xios: add trunk version to allow building latest revision
* xios: enable parallel build
* xios: allow installation with mpif90 compiler wrappers
* xios: use mpi variants of dependencies
* xios: allow user to specify MPI launcher via MPIRUN environment variable
* xios: prefer spack versions of blitz and boost (needed for gcc@7)
* xios: enable builds with clang+gfortran on OSX
* xios: use numeric versions for releases, @develop for trunk
* xios: different patches required for @1.0 and @develop
* xios: patch function for clang works across revisions
* xios: link blitz library
* xios: workaround bug 17782 in llvm
* xios: whitespace adjustments for flake8
* xios: avoid bare except clause
* xios: netcdf-fortran inherits ^netcdf+mpi from xios dependencies
* combine all patches for 1612 into a single file, with additional
comments to explain the rational.
* Add kahip decomposition variant.
* Add support for ARM64 architecture.
* filter instead of patching etc/config.*/settings. This eliminates
patch files for 1706, perhaps for the future as well.
* URLs at or before version 1612 have a different structure, so
provide a url_for_version implementation to handle this
* singularity - added master branch as this has latest fixes - 2.4 does not compile on centos 6 without use of this branch
* renamed to develop
* added master branch properly
* add OctavePackage
1. remove import CudaPackage which is not needed anymore
2. mention CudaPackage and OctavePackage in packaging guide
3. adjust OctavePackageTemplate
4. add clue file for Octave build
5. sanity check on self.prefix
* use setup_environment
* esmf: put .mod files in the spack compiler search path
* esmf: allow building with Cray mpi
* esmf: create run-path dependent libraries on osx
* esmf: link fortran interface libraries when building with mpich
* Fix detection of blas and lapack: provide libraries/includes as
arguments to CMake rather than using CMake's auto-detection.
This includes a patch to QMCPACK's CMake files to refer to
Spack-built blas/lapack implementations. This also includes
special-case logic for the intel-mkl implementation of blas/lapack
* Break up unit tests and short tests. Only hard failure if the unit
tests fail, if short tests fail issue a warning only.
* Add QMCPACK 3.3.0, get rid of 3.0.0
- define MPICH_SKIP_MPICXX, link libmpich instead of libmpi
(as per disussion in PR #4990)
ENH: more flexible editing/patching of openfoam env files
CONFIG: comment out requirement for openmpi+thread_multiple
- was originally slated for the 1712 release and beyond, but there are
reportedly unstable version/network combinations.
Leave as comment for future reference, since it may be arise again.
STYLE: renamed openfoam-site.patch as 1706-site.patch (and reformatted)
- to preserve against impending changes in the layout of
config.{csh,sh}/settings
