- 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
* superlu-dist: Update package.py for superlu-dist v6.0.0 using CMake
* superlu_dist: Update the header of package.py
* Specify lapack_blas and DCMAKE_INSTALL_LIBDIR
disable support for superlu-dist before v5
## 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.
* xSDK: a bundle/meta package that simple installs a series of packages with suitable specs
This is based on struggles with previous attempts at such a bundler
Funded-by: IDEAS
Project: IDEAS/xSDK
Time: 12 hours
* PETSc needs c++11 when built with Trilinos
* Added alquimia package
* remove direct setting of cpp in petsc/package.py since it doesn't work on some systems.
Funded-by: IDEAS
Project: IDEAS/xSDK
Time: .3 hours
Reported-by: Mark A. Berrill <berrillma@ornl.gov>
* provide the MPI compilers to PETSc configure with --with-cc etc instead of --with-mpi-dir
Funded-by: IDEAS
Project: IDEAS/xSDK
* Spack bug fix issue #3144
String could contain /n which resulting in spack generating warning message to stderr on each
use of compiler which configure interpreted as failing compiler
Thanks-to: Mark A. Berrill <berrillma@ornl.gov>
* Fixed alquimia package
Alquimia expects PETSC_DIR and PETSC_ARCH to be defined, and
refuses to install if they are not. Spack does not define PETSC_
ARCH, so Alquimia will not install. This patch does two things
to fix the alquimia build:
1. A patch has been added to remove the dependency on PETSC_ARCH.
2. Alquimia currently depends on old versions of PETSc and pflotran.
@ghammond86 updated the alquimia interfaces to use more recent
versions, but his patch is still sitting in an alquimia pull
request. As a result, the spack installer now uses his fork
of alquimia. This is a temporary fix until his pull request is
accepted.
* Need to pass to Alquimia the MPI compilers, not the raw compilers
Otherwise the PETSc tests do not produce executables that can run because they are not
linked against MPI libraries
Funded-by: IDEAS
Project: IDEAS/xSDK
Time: .5 hours
* Add alquimia to xSDK build
Funded-by: IDEAS
Project: IDEAS/xSDK
* Fix flake8 errors for xsdk packages
* Add xsdk support for xsdk version xsdk-0.2.0
Note that currently it is just dummy code, but will eventually use
a xsdk-0.2.0 tag for each package it installs.
Funded-by: IDEAS
Project: IDEAS/xSDK
Time: .7 hours
* Do not build Mumps by default for PETSc since it is not portable, for example to Cray
Allow alquimia to accept PETSc even if the PETSc test executable cannot run since this is a problem on Cray.
Reported-by: Alicia Marie Klinvex <amklinv@sandia.gov>
* Add xsdk-0.2.0-rc1 tag for xsdk-0.2.0 installs
* Switch alquimia download site back to standard location
since they have incorporated Glenn Hammond's fixes
Also it no longer needs the patch to the Alquimia cmake
Funded-by: IDEAS
Project: IDEAS/xSDK
Reported-by: Sergi Molins Rafa <smolins@lbl.gov>
* update hypre to use the latest release candidate for xsdk 0.2.0
Funded-by: IDEAS
Project: IDEAS/xSDK
Reported-by: Ulrike Meier Yang <yang11@llnl.gov>
* Re-added patch to alquimia
The patch was out of date and has been updated accordingly.
* Added Tpetra-free option to Trilinos
The Tpetra stack takes forever to build and is not used by any of the
IDEAS teams, so there should be an option to disable it. I have added
this option and updated the xSDK accordingly. I also disabled
xSDKTrilinos in the xSDK, since none of the apps teams currently use it,
and it's largely Tpetra-based.
* Removed alquimia patch from develop version
The patch has been incorporated into alquimia and is no longer
necessary for the develop version. The tagged version has not
been updated accordingly and still needs the patch for now.
(When the tagged version gets updated, the patch does need to be
removed from spack altogether, or it will break the build.)
* Removed patch from alquimia
It has been incorporated into alquimia, both the develop and
rc2 tagged versions. The 0.2.0 version of alquimia has been updated
to tag rc2 rather than rc1.
* update xsdk-0.2.0 to depend on PETSc xsdk-0.2.0-rc2 which fixes for Apple xcode 8.3
Commit-type: bug-fix
Funded-by: IDEAS
Project: IDEAS/xSDK
* import sys got lost in merge with develop
* Update xsdk packages to use xsdk-0.2.0 tag
Commit-type: feature
Funded-by: IDEAS
Project: ECP
* Fixes for Flake8
note, had to ignore some long lines due to a single string
* simple improvements to XDK packages as suggested by Spack pull request reviewers
Commit-type: style-fix
Funded-by: IDEAS
Project: xSDK
* Removed unneeded : after develop as requested by Denis Davydov in pull request review
Commit-type: style-fix
Funded-by: IDEAS
Project: xSDK
Thanks-to: Denis Davydov
* Removed change that may not be needed due to updates in PETSc spack file such as using mpicc etc directly
Commit-type: bug-fix
Funded-by: IDEAS
Project: xSDK
Thanks-to: Adam J. Stewart
* Do not turn on xSDKTrilinos for xSDK builds since it requires tpetra
Commit-type: bug-fix
Funded-by: IDEAS
Project: xSDK
* comment why MUMPS is disabled by default for PETSc so that others won't try to enable it when modifying petsc package next time
Commit-type: documentation
Funded-by: IDEAS
Project: xSDK
Thanks-to: Denis Davydov
- 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
* petsc: add 64bit variant
* hypre: add int64 variant
* superlu-dist: add int64 variant
* petsc: add int64 variant
* metis: rename idx64 to int64 to make it consistent with other packages
* mumps: rename idx64 to int64 to make it consistent with other packages
* dealii: rename 64bit to int64 to make it consistent with other packages
* 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
Add version 4.0.3 to metis package. Attempted to implement reasonable
versions of all variants declared for metis@5.1.0; some of these do
not have analogues in metis@4.0.3, and errors are raised accordingly.
Also updated dependencies of packages with depends_on('metis') to
depends_on('metis@5:') to ensure that these packages still build.
