- [x] add `concretize.lp`, `spack.yaml`, etc. to licensed files
- [x] update all licensed files to say 2013-2021 using
`spack license update-copyright-year`
- [x] appease mypy with some additions to package.py that needed
for oneapi.py
* cp2k: locate correct include dir when using intel-parallel-studio+mkl for fftw-api
* libxc: drop arch-specific intel opt. flags
fixes#17794
* libint: drop arch-specific intel opt. flags, always build Fortran example with FC
fixes#17509
* libvdwxc: unbreak concretization, request fftw-api
mixing both fftw and fftw-api in a dependency tree can trigger the
following:
```
$ spack spec cp2k@master +sirius
==> [2020-09-16-12:36:06.552981] sirius applying constraint gsl
==> [2020-09-16-12:36:06.554270] sirius applying constraint openblas@0.3.10%gcc@7.5.0~consistent_fpcsr~ilp64+pic+shared threads=none arch=linux-opensuse_leap15-sandybridge
Traceback (most recent call last):
File "./bin/spack", line 64, in <module>
sys.exit(spack.main.main())
File "/data/tiziano/debug-spack/spack2/lib/spack/spack/main.py", line 762, in main
return _invoke_command(command, parser, args, unknown)
File "/data/tiziano/debug-spack/spack2/lib/spack/spack/main.py", line 490, in _invoke_command
return_val = command(parser, args)
File "/data/tiziano/debug-spack/spack2/lib/spack/spack/cmd/spec.py", line 103, in spec
spec.concretize()
File "/data/tiziano/debug-spack/spack2/lib/spack/spack/spec.py", line 2228, in concretize
user_spec_deps=user_spec_deps),
File "/data/tiziano/debug-spack/spack2/lib/spack/spack/spec.py", line 2716, in normalize
visited, all_spec_deps, provider_index, tests)
File "/data/tiziano/debug-spack/spack2/lib/spack/spack/spec.py", line 2654, in _normalize_helper
dep, visited, spec_deps, provider_index, tests)
File "/data/tiziano/debug-spack/spack2/lib/spack/spack/spec.py", line 2613, in _merge_dependency
visited, spec_deps, provider_index, tests)
File "/data/tiziano/debug-spack/spack2/lib/spack/spack/spec.py", line 2654, in _normalize_helper
dep, visited, spec_deps, provider_index, tests)
File "/data/tiziano/debug-spack/spack2/lib/spack/spack/spec.py", line 2554, in _merge_dependency
provider = self._find_provider(dep, provider_index)
File "/data/tiziano/debug-spack/spack2/lib/spack/spack/spec.py", line 2489, in _find_provider
providers = provider_index.providers_for(vdep)
File "/data/tiziano/debug-spack/spack2/lib/spack/spack/provider_index.py", line 80, in providers_for
return sorted(s.copy() for s in result)
File "/data/tiziano/debug-spack/spack2/lib/spack/llnl/util/lang.py", line 249, in <lambda>
lambda s, o: o is not None and s._cmp_key() < o._cmp_key())
TypeError: '<' not supported between instances of 'str' and 'NoneType'
```
while at the same point disallowing MKL as a fftw provider.
Solving both issues by depending on `fftw-api@3` instead and adding a
conflict on `^fftw~mpi` when using `+mpi` (thanks to alalazo).
* cp2k: use conflicts instead of runtime checks for fftw/openblas variants
* cp2k: do not support ~openmp for v8+
* sirius: version bump
* cp2k: fix overlapping deps for elpa
fixes#18029
* cp2k: update SIRIUS dependency for v8+
* spfft: requires CMake 3.11+
* cp2k: fix build with +sirius
* cp2k: variant tuning `lmax` was broken
- `spack install cp2k lmax=6` now works
* Update var/spack/repos/builtin/packages/cp2k/package.py
Co-authored-by: Adam J. Stewart <ajstewart426@gmail.com>
* Update var/spack/repos/builtin/packages/cp2k/package.py
Co-authored-by: Adam J. Stewart <ajstewart426@gmail.com>
* Update var/spack/repos/builtin/packages/cp2k/package.py
Co-authored-by: Adam J. Stewart <ajstewart426@gmail.com>
* Update var/spack/repos/builtin/packages/cp2k/package.py
Co-authored-by: Adam J. Stewart <ajstewart426@gmail.com>
* Update var/spack/repos/builtin/packages/cp2k/package.py
Co-authored-by: Adam J. Stewart <ajstewart426@gmail.com>
* Update var/spack/repos/builtin/packages/cp2k/package.py
Co-authored-by: Adam J. Stewart <ajstewart426@gmail.com>
Co-authored-by: Adam J. Stewart <ajstewart426@gmail.com>
* Separate Apple Clang from LLVM Clang
Apple Clang is a compiler of its own. All places
referring to "-apple" suffix have been updated.
* Hack to use a dash in 'apple-clang'
To be able to use autodoc from Sphinx we need
a valid Python name for the module that contains
Apple's Clang code.
* Updated packages to account for the existence of apple-clang
Co-authored-by: Adam J. Stewart <ajstewart426@gmail.com>
* Added unit test for XCode related functions
Co-authored-by: Gregory Becker <becker33@llnl.gov>
Co-authored-by: Adam J. Stewart <ajstewart426@gmail.com>
* cp2k: prettify arch-file, call pkg-config directly
this allows to re-use the arch-file without having to load the complete
Spack environment, for example after a dev-build
* cp2k: use consistency check instead of blas lib enum
this makes using other BLAS/LAPACK implementations possible without
explicitly adding support for them
* cp2k: add basic support for Cray and XL Compilers, correct Intel fp mode
* cp2k: add myself as maintainer
* cp2k: use "master" to denote the git version
* cp2k: use spack_cc/fc/cxx when possible, set CXX explicitly
* cp2k: set __MKL when using the MKL, not just the Intel compiler
* cp2k: drop self. when referencing spec where possible
* cp2k: add forgotten elpa+openmp dep
* cp2k: set C++14 for recent versions
* libint: switch to 2-stage build for 2.6.0+
* libint: add tune and fortran variants
* cp2k: add support for libint >= 2.0
* cp2k: use pkg-config for linking libxc
Now that Spack injects microarchitecture specific optimizations for
the selected target, packages should avoid adding flags that could
step over those.
* Remove -ffast-math optimization flag
* Add 'develop' version which points to git repo
* Depend on libint for all versions >= 3.0
* Build directory is different for versions >= 7 (including develop)
* Add "make test" as post install check
* cp2k: archive the Makefile after a successful installation
* cp2k: all checksums are now sha256
* libint: all checksums are now sha256 + added versions 2.4.X
* libxc: all checksums are now sha256 + added version 4.3.2
* cp2k: os.path.join instead of join_path + simplified openmp flags
* cp2k: turned into a MakefilePackage
* cp2k: refactored edit method so that Makefile writing happens last
* openblas: enable parallel builds
* cp2k: enable parallel builds
* cp2k: fix building on multilib/Suse distros
use the actual directory path where files where installed to instead of
the default prefix+'/lib'
* cp2k: ensure we have a non-header-only libxsmm
* openblas: disable max num CPU detection on virtualized build
* cp2k: install data and set compiled-in DATA_DIR
* cp2k: make libxc an optional dependency (enabled by default)
* cp2k: link libint statically
* cp2k: declare statically linked library deps as type=build
* cp2k: add support for PGI compiler
* cp2k: rename smm=none to smm=blas for clarification
* cp2k: blacklist unsupported compilers
* cp2k: mark wannier90 a build-time dep since statically linked
* cp2k: make pexsi and elpa optional
* cp2k: add support for v6.1
* libxc: add version 4.2.3
* cp2k: use pkg-config to link properly to libxsmm
* cp2k: fix OpenMP support by making it explicit
Previously, CP2K accepted threaded ELPA or BLAS, leading to #(CPU) processes
being spawned even though no explicit OpenMP was requested. Now the
`popt` variant should truly be thread free while the `psmp` variant uses
threads also internally.
* cp2k: source tarballs moved to GitHub
- remove the old LGPL license headers from all files in Spack
- add SPDX headers to all files
- core and most packages are (Apache-2.0 OR MIT)
- a very small number of remaining packages are LGPL-2.1-only
Replace use of `shutil.copytree` with `copy_tree` and `install_tree` functions in `llnl.util.filesystem`.
- `copy_tree` copies without setting permissions. It should be used to copy files around in the build directory.
- `install_tree` copies files and sets permissions. It should be used to copy files into the installation directory.
- `install` and `copy` are analogous single-file functions.
- add more extensive tests for these functions
- update packages to use these functions.
Added DFLAGS to the `make.inc` file being written.
These macros are also added to the language specific variables
like CFLAGS, CXXFLAGS and FCFLAGS. Changed `spec.satisfies('foo')`
with `'foo' in spec` in `intel-mkl`, see #4135. Added a basic
build interface to `intel-mpi`.
## Motivation
Python installations are both important and unfortunately inconsistent. Depending on the Python version, OS, and the strength of the Earth's magnetic field when it was installed, the name of the Python executable, directory containing its libraries, library names, and the directory containing its headers can vary drastically.
I originally got into this mess with #3274, where I discovered that Boost could not be built with Python 3 because the executable is called `python3` and we were telling it to use `python`. I got deeper into this mess when I started hacking on #3140, where I discovered just how difficult it is to find the location and name of the Python libraries and headers.
Currently, half of the packages that depend on Python and need to know this information jump through hoops to determine the correct information. The other half are hard-coded to use `python`, `spec['python'].prefix.lib`, and `spec['python'].prefix.include`. Obviously, none of these packages would work for Python 3, and there's no reason to duplicate the effort. The Python package itself should contain all of the information necessary to use it properly. This is in line with the recent work by @alalazo and @davydden with respect to `spec['blas'].libs` and friends.
## Prefix
For most packages in Spack, we assume that the installation directory is `spec['python'].prefix`. This generally works for anything installed with Spack, but gets complicated when we include external packages. Python is a commonly used external package (it needs to be installed just to run Spack). If it was installed with Homebrew, `which python` would return `/usr/local/bin/python`, and most users would erroneously assume that `/usr/local` is the installation directory. If you peruse through #2173, you'll immediately see why this is not the case. Homebrew actually installs Python in `/usr/local/Cellar/python/2.7.12_2` and symlinks the executable to `/usr/local/bin/python`. `PYTHONHOME` (and presumably most things that need to know where Python is installed) needs to be set to the actual installation directory, not `/usr/local`.
Normally I would say, "sounds like user error, make sure to use the real installation directory in your `packages.yaml`". But I think we can make a special case for Python. That's what we decided in #2173 anyway. If we change our minds, I would be more than happy to simplify things.
To solve this problem, I created a `spec['python'].home` attribute that works the same way as `spec['python'].prefix` but queries Python to figure out where it was actually installed. @tgamblin Is there any way to overwrite `spec['python'].prefix`? I think it's currently immutable.
## Command
In general, Python 2 comes with both `python` and `python2` commands, while Python 3 only comes with a `python3` command. But this is up to the OS developers. For example, `/usr/bin/python` on Gentoo is actually Python 3. Worse yet, if someone is using an externally installed Python, all 3 commands may exist in the same directory! Here's what I'm thinking:
If the spec is for Python 3, try searching for the `python3` command.
If the spec is for Python 2, try searching for the `python2` command.
If neither are found, try searching for the `python` command.
## Libraries
Spack installs Python libraries in `spec['python'].prefix.lib`. Except on openSUSE 13, where it installs to `spec['python'].prefix.lib64` (see #2295 and #2253). On my CentOS 6 machine, the Python libraries are installed in `/usr/lib64`. Both need to work.
The libraries themselves change name depending on OS and Python version. For Python 2.7 on macOS, I'm seeing:
```
lib/libpython2.7.dylib
```
For Python 3.6 on CentOS 6, I'm seeing:
```
lib/libpython3.so
lib/libpython3.6m.so.1.0
lib/libpython3.6m.so -> lib/libpython3.6m.so.1.0
```
Notice the `m` after the version number. Yeah, that's a thing.
## Headers
In Python 2.7, I'm seeing:
```
include/python2.7/pyconfig.h
```
In Python 3.6, I'm seeing:
```
include/python3.6m/pyconfig.h
```
It looks like all Python 3 installations have this `m`. Tested with Python 3.2 and 3.6 on macOS and CentOS 6
Spack has really nice support for libraries (`find_libraries` and `LibraryList`), but nothing for headers. Fixed.
* libint: updated version, ported to AutotoolsPackage
* elpa: updated version, ported to AutotoolsPackage
* wannier90: updated version, ported to MakefilePackage
* pexsi: updated version, ported to MakefilePackage
* cp2k: updated version, removed wannier 90 from dependencies if cp2k@4.1
* plumed: updated version
Modifications:
* modules has been turned into a single variant, as different versions
have different modules available
* added dictionaries for patches
* netlib-scalapack: ported to CMakePackage
- Added a new interface for Specs to pass build information
- Calls forwarded from Spec to Package are now explicit
- Added descriptor within Spec to manage forwarding
- Added state in Spec to maintain query information
- Modified a few packages (the one involved in spack install pexsi) to showcase changes
- This uses an object wrapper to `spec` to implement the `libs` sub-calls.
- wrapper is returned from `__getitem__` only if spec is concrete
- allows packagers to access build information easily
* 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
