On MacOS, brew installs /usr/local/bin/python but the Python prefix is not /usr/local/bin
Use the python command sys.exec to get the correct directory, instead of the ad hoc self.prefix
previously used
This was a bear to debug; been driving me nuts since I started using spack.
Since spack passes PYTHONHOME down to package builds in the environment
it was passing PYTHONHOME of /usr/local/bin to the PETSc build that uses Python so
the PETSc Python ./configure errored immediately with
ImportError: No module named site
since python could find no python modules. Todd Gamblin pointed out that my first try to fix
this was wrong since it assumed the spack python was the same python used to run spack. Elizabeth Fischer
suggested how to get it to work also with python3
Funded-by: IDEAS
Project: IDEAS/xSDK
Time: 7 hours
Thanks-to: Todd Gamblin, Elizabeth Fischer
* Update the krell institute products to use the latest features of spack for building on cluster platforms.
* Address travis error messages and resubmit the pull request.
* Update the contents of openspeedshop package.py so it passes the flake8 tests.
* Fix flake8 error-whitespack issue in mrnet package.py file.
* Add updates based on spack reviewer feedback.
* More fixes based on comments from reviewers. Switch using extend to using append, remove additional setting of PATH and LD_LIBRARY_PATH that should not be required due to RPATH.
* More review related changes. Update MPIOption.append lines and take out xercesc references.
* Create a base options function for common openspeedshop base cmake options to reduce redundencies.
* Add libxml2+python depends on to get around issues with the libxml2 package file.
Add a package that installed the pre-built maven distribution.
I've given up, for now, on building maven from source. That processed
stumbled on two points before I gave up:
1. It downloaded several hundred .{pop,jar} files and I despaired of
figuring out some way of mirroring and checksumming them; and
2. It exploded complaining about too many unacceptable license files,
which seems odd in its own source tree.
Perhaps someone with more Java fu that I admit to can figure it out.
In the meantime, this is useful.
* libsodium: add latest versions, fix old versions
older versions of libsodium were added to an "old" subdirectory
* zeromq: add 4.1.4
prerequiste for the latest develop version of flux
Pkg-config depends on glib which depends on pkg-config. As a result,
pkg-config used to build glib internally. However, this fails on Mac.
Building pkg-config with an internal glib is now a variant, turned on
by default, and required to build glib.
* Tells boost explictly about libraries and headers
Ideally, bjam would determine the libraries and headers from the
executable. But it doesn't. This rigs a best guess for python libraries
and headers.
* Move glob import to top of file
* variable name change: alllibs --> all_libs
* Use dso suffix rather than hard-coded string
* Use only MAJOR.MINOR when setting up python in bjam
* mumps: Add support for Intel compiler and insure both lapack and blas libraries are passed to the examples
Likely it was not discoverged before that the examples require both lapack and blas libraries because it
was tested with Openblas which is one large library containing everything.
Funded-by: IDEAS
Project: IDEAS/xSDK
Time: .3 hours
* flake8 fix.
* Created the initial version of the 'OpenSceneGraph' package.
* Added 'zlib' as a dependency and linked it during the build step.
* Fixed a few minor PEP8 style violations in the 'OpenSceneGraph' package.
* Added cmake as a build dependency and improved the build procedure.
* Made a few important argument updates to improve package compatibility.
* Fixed up a few remaining style issues in the 'openscenegraph' package.
* Added a description for the 'openscenegraph' package.
* Fixed a bug that was causing some 'openscenegraph@3.2.3%gcc' installs to fail.
* Fixed a number of small issues with the 'openscenegraph' package.
* Removed a number of superfluous flags from the 'openscenegraph' install.
* Add new version property to handle joined version numbers
* Add unit test for new joined property
* Add documentation on version.up_to() and version.joined
Things that accessed the cdd package, such as `spack info cdd run
tripped over a buglet in the *cdd* package, causing them to exit with
something like this:
```
Caused by:
TypeError: 'str' object is not callable
File "/rss/spack/lib/spack/spack/repository.py", line 584, in get
self._instances[key] = package_class(copy)
File "/rss/spack/lib/spack/spack/package.py", line 398, in __init__
f = fs.for_package_version(self, self.version)
File "/rss/spack/lib/spack/spack/fetch_strategy.py", line 852, in for_package_version
attrs['url'] = pkg.url_for_version(version)
File "/rss/spack/var/spack/repos/builtin/packages/cdd/package.py", line 40, in url_for_version
str(version.dotted()).replace('.', ''))
```
@tgamblin pointed out that `dotted` is a property, not a functin call
and that the parentheses are therefor inappropriate.
This deletes the parentheses. `spack info cdd` now works for me.
Add package for htop, an interactive text-mode process viewer for
Unix systems. Think top, with pretty colors and dyanmic bar graphs.
More info [here](https://github.com/hishamhm/htop).
* Update the krell institute products to use the latest features of spack for building on cluster platforms.
* Address travis error messages and resubmit the pull request.
* Update the contents of openspeedshop package.py so it passes the flake8 tests.
* Fix flake8 error-whitespack issue in mrnet package.py file.
* Add updates based on spack reviewer feedback.
* More fixes based on comments from reviewers. Switch using extend to using append, remove additional setting of PATH and LD_LIBRARY_PATH that should not be required due to RPATH.
* More review related changes. Update MPIOption.append lines and take out xercesc references.
* Create a base options function for common openspeedshop base cmake options to reduce redundencies.
* Made optional CGAL dependencies optional.
* cgal: Added note explaining that the CORE library is not the same as core CGAL functionality.
* Bug fix and flake8
* flake8
* build_environment: allow compilers to set up an environment
* clang: mock up a toolchain directory for xcode
Some projects ignore CC and CXX flags and instead use xcode to find the
toolchain. Clang on Apple should set up the environment properly.
Arguably, every compiler could do this on Apple, but let's see how this
works out just for AppleClang for now.
The Documentation directory is ~1.7G and the excluded platforms add up
to about 7G. Ignoring swift saves another 500M. The resulting Xcode.app
copy is in the 2G range.
* compiler: set member variables early
This is required so that later methods can query things such as the
version of the compiler.
* compiler: support finding the real path of the compiler
On Apple, the /usr/bin compilers are actually wrapping tools themselves
which query xcrun for the currently selected Xcode installation. Pierce
this veil and get the real, full path the to underlying compilers
instead.
* icu4c: install with rpath
On macOS, icu installs with a library ID of the library name. Enabling
rpath makes its ID its full installed path which lets Qt5 link against
it successfully.
* qt: no -no-gtkstyle flag on Qt5 on macOS
* First version of Abinit package
* Ignore *.swp files
* Add libxc, etsf_io packages
* AtomPaw package
* Make Abinit depend on mpi@2: and external version of libxc, netcdf, hdf5, etsf_io
* etsf_io: install Fortran modules in prefix.include
* Remove etsf_io from abinit requirements
* Add libxc2.2.1 (required by Abinit and atompaw)
* Cleanup
* Run make check
* Cleanup
* Use ld_flags instead of hard-coded libs, fix pep8, add copyright
* Put scalapack before lapackblas
* Added support for the 'maxdims' and 'maxvars' flags for 'NetCDF'.
* Added the '+mpi' variant and improved dependencies for 'exodusii'.
Improved the 'exodusii' package so that it's less reliant on patches.
* Added better type checking to variant values in the 'netcdf' package.
* Corrected the required CMake version for the 'exodusii' package.
* Fixed the dependencies of the '+mpi' variant of the 'exodusii' package.
* Updates to Mesa and other Xorg packages
* Add packages for all Xorg Protocol extensions
* Add packages for first half of Xorg libraries
* Add packages for remaining Xorg libraries
* Add packages for all Xorg utilities
* Add packages for Xorg documentation tools
* Add build deps to Xorg protocol headers
* Add packages for XCB
* Add build deps to Xorg libraries
* Add build deps to Xorg utilities
* Add packages for Xorg fonts and font-related utilities
* Change font deptype from build to default
I wasn't sure which deptype was appropriate at first since none of
the packages are actually linked together. I initially chose the
build deptype for this reason. However, the font packages don't
install into their own prefix. They install into font-config. If
font-config is a build dependency, that means you can uninstall it
without uninstalling the font packages, which wouldn't make sense
since they install into font-config. So I switched them back to
the default deptype.
* Minor formatting changes to ncview
* Add half-way done xorg-server package
* Add packages for Xorg test suites, not yet tested!
* Add packages for Xorg data
* Add first quarter of Xorg apps
* Add more packages for Xorg apps
* Add dependencies to mesa
* Remove comments from mesa package
* Flake8
* Add more packages for Xorg apps
* Add more packages for Xorg apps
* Add more packages for Xorg apps
* Add more packages for Xorg apps
* Add more packages for Xorg apps
* Add package for Sublime Text
* Add packages for remaining Xorg apps
* Revisit testing packages, add missing dependencies
* Add dependencies, clean up FIXMEs
+ This change fixes a problem that manifests when trilinos is built against a
MKL installation defined as an external package. In this scenario, the MKL
libraries are found one directory deeper than for the case where spack
provides MKL. The extra directory is a platform name like 'intel64'.
+ The changes in this PR were recommended by contributor @davydden. I
implemented and tested with intel@16.0.3. These changes fix the issue I
reported. I did not attempt building trilinos against other BLAS
implementations.
+ fixes#1923
* mfem: add tarball extension
Add tarball extension as a result of a feature added in PR#1926, which
fixes earlier issues in this PR (PR#1202). Prior to adding this feature,
Spack would not autodetect the extension of the tarball downloaded from
the redirected, shorted Google URL, requiring a messy hack. This hack
worked for mfem version 3.1, but led to errors when adding mfem version
3.2 because the files downloaded from Google did not contain the package
name, version number, or extension. Adding the extension enables Spack
to rename the tarball downloaded from Google to a sensible name that is
compatible with its filename parsing algorithms so that Spack "does the
right thing" (detects that the file is a GZipped tarball, decompresses
it, runs GNU Make) in fetching and staging the package.
* mfem: add linkage to KLU & BTF
Add linkage to the KLU & BTF solvers, which are now enabled in MFEM for
versions 3.2 and later.
* mfem: Add superlu-dist variant
Add linkage to SuperLU_DIST, which is a new linear solver interface for
MFEM versions 3.2 and later.
* mfem: add netcdf variant for cubit mesh support
Add NetCDF variant for MFEM versions 3.2 and later; installing the
NetCDF interfaces enables CUBIT mesh support.
+ Cray compile wrappers are MPI wrappers.
+ Packages that need to be compiled with MPI compile wrappers normally use
'mpicc', 'mpic++' and 'mpif90' provided by the MPI vendor. However, when using
cray-mpich as the MPI vendor, the compile wrappers 'CC', 'cc' and 'ftn' must
be used.
+ In this scenario, the mpich package is hijacked by specifying cray-mpich as an
external package under the 'mpich:' section of packages.yaml. For example:
packages:
mpich:
modules:
mpich@7.4.2%intel@16.0.3 arch=cray-CNL-haswell: cray-mpich/7.4.2
buildable: False
all:
providers:
mpi: [mpich]
+ This change allows packages like parmetis to be built using the Cray compile
wrappers. For example: 'spack install parmetis%intel@16.0.3 ^mpich@7.4.2 os=CNL'
+ This commit relies on the existence of the environment variable CRAYPE_VERSION
to determine if the current machine is running a Cray environment. This check is
insufficient, but I'm not sure how to improve this logic.
+ Fixes#1827
* fix blas-lapack in scipy and numpy
* py-numpy: do not set rpath on macOS
* py-scipy: do not set Blas/Lapack. This appears to be picked up from py-numpy
* py-numpy: don't write rpath= in Sierra only
* py-numpy: add a link to build notes
* Updated nettle to have m4 as an immediate dependency to match new PATH
construction logic which only includes immediate dependencies.
* Update package.py
* Added check for ppc64le because configure cant guess the build type for rhel on ppc64le
Expand/clarify description of dependency types
Refactored getting the arch so that its less verbose
* Fixed flake8 issues
* everytrace: New package
Everytrace ensures that stack trace is obtained every time a program exits, for whatever reason.
* everytrace: Change CMake to build dependency
* Renamed to everytrace-example, flake8 and copyright issues.
* flake8
* Missing type=build
* Warn user if flake8 can't find setuptools
* Add missing dependencies of flake8
* Updates to py-autopep8, make packages activateable
* Check for presence of setuptools for Sphinx too
* Fix bug in order of commands
* Adding last version of fenics and making trilinos not ambiguous on hdf5
* forcing fenics to ignore hdf5 cxx
* Adding deptypes and correcting the hdf5 patch
* flake8 corrections
* cleaning some useless code
* Provide new versions of llvm.
+ Provide file list and md5 hashes for 3.8.1 and 3.9.0.
+ Clean up indentation for the 'releases' data structure to improve
consistency.
* Adding a block of code to the 'resources' structure for cfe.
* Merge cfe and clang resources into single entity.
* Added hadoop, spark, and variant spark+hadoop
* Docstrings, dependency types, urls, copyright
* Flake8 fixes, link dependency for hadoop
* Build type for spark, env problem setting JAVA_HOME
* New package: libquo
libquo is a high-level, easy to use programming interface tailored specifically
for MPI/MPI+X codes that may benefit from evolving process binding policies
during their execution. QUO allows for arbitrary process binding policies to
be enacted and reverted during the execution of an MPI/MPI+X application as
different computational phases are entered and exited, respectively.
https://github.com/losalamos/libquo
* Remove use of 'which' and fix style non-conformance.
* Add libint package
* Add Intel optimization flags recommended by CP2K
* Add new version and Intel compiler optimization flags for libxc
* Add older version of libint
* Libint depends on GMP C++ library
Pro tips from @adamjstewart:
* line too long in package description
* name it grib-api instead of grib_api
* depend on netcdf without reference to unnecessary constraints
* py-pil: Does not build with Python3.
* Set py-pillow to be the default pil provider
* Update package.py
* Change to comments requested by adamjstewart
* Remove version constraint from extends(), avoid a Spack bug.
* dealii: add missing python dependency
* boost: fix a bug which broke it on macOS with clang+gfortran
Boost was using gcc compiler instead of clang++, which lead to
cryptic Undefined symbols linking errors for boost::python::objects::function_object()
when building other packages against boost+python.
* boost: add exceptions for intel
* boost: use spack_cxx
* Turned <provider>_libs into an iterable
Modifications :
- added class LibraryList + unit tests
- added convenience functions `find_libraries` and `dedupe`
- modifed non Intel blas/lapack providers
- modified packages using blas_shared_libs and similar functions
* atlas : added pthread variant
* intel packages : added lapack_libs and blas_libs
* find_library_path : removed unused function
* PR review : fixed last issues
* LibraryList : added test on __add__ return type
* LibraryList : added __radd__ fixed unit tests
fix : failing unit tests due to missing `self`
* cp2k and dependecies : fixed blas-lapack related statements in package.py
Python will look to link with libncursesw in preference to libncurses. Since
ncurses in spack is built without suffixes there is no libncursesw and
python will link to the system libncursesw for _curses.so and
_curses_panel.so, as well as libpanelw for _curses_panel.so.
This PR introduces a patch that simple removes the check for ncursesw in
setup.py and therefore sets `curses_library` to `ncurses`.
* Added missing libtiff dependency
* added dependency on fontconfig
* Added version 2.2.3
* use autotools rather than cmake
The cmake build was not producing a complete install.
* There was no versioning of the installed libraries.
* gdlib-config was missing
* pkgconfig directory was missing
These problems do not happen when built with autotools.
yt is a python package for analyzing and visualizing volumetric, multi-resolution data from astrophysical simulations, radio telescopes, and a burgeoning interdisciplinary community.
* Fixed a few small bugs in the 'git-lfs' install script.
* Fixed a bug in the '(go|go-bootstrap)@1.4.2+test' install scripts.
* Fixing a minor style issue in the 'git-lfs' install script.
I encountered an HPC system where PETSc's configure stage does not find a valid `cpp` (C preprocessor). Explicitly pointing to Spack's `cpp` wrapper resolves the problem.
* Fixed a bug that was causing post-install METIS tests to fail.
* Improved the patching procedure used in the 'metis' install script.
* Enabled patch skipping for the 'metis' and 'parmetis' packages.
* Fixed some minor style issues in the 'parmetis' package.
* Improved the 'metis' test fix and added 'run_tests' support.
* Refactored and reorganized the 'zoltan' install script.
* Fixed a few bugs with the '+mpi' and '+fortan' variants of 'zoltan'.
* Reintroduced and improved the '+shared' variant for the 'zoltan' package.
* Improved compatibility with different MPI providers for 'zoltan'.
Includes :
- treatment of a generic hierarchy (i.e. lapack + mpi + compiler)
- possibility to specify which compilers are to be considered Core
- correct treatment of the 'family' directive
- unit tests for most new features
- add new version 2.10.3
- explicitly require hdf5 variant ~mpi, since we don't know how to build with mpicc
- explicitly disable glew since it may not be installed
