* perl: provide +gdbm variant for use when system dbm is missing or buggy
* perl: remove gdbm variant; always depends on gdbm
* perl: pass gdbm paths as Configure arguments
The blast+ configure script supports building
--with-{python,perl}=path and --without-{python,perl}.
This commit makes the use of those two languages configurable via
variants and adds dependencies and explicit --with-... or
--without-... flags to configure.
Python was a non-optional dependency, now it is a variant that
defaults to `True`.
Perl was not previously an explicit dependency but the configure
script was likely to discover one on your system (`/usr/bin/perl`).
It is now a variant that defaults to `True`.
I am unable to accurately determine what these flags to the configure
script enable. My users are frustrated by the dependency on Python in
particular because it constrains the other modules that they can have
loaded for new discernible benefit.
* 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
* Properly ignore flake8 F811 redefinition errors
* Add unit tests for flake8 command
* Allow spack flake8 to work on systems with older git
* Skip flake8 unit tests for Python 2.6 and 3.3
* Added a package for the MDAnalysis toolkit.
* Added the hash for the 1.0 release of caffe and put in a conflict
statemet indicating that protobuf requires a c++11 compiler.
* Changed minimum version number.
* Tweaked the minimum version number.
* Fixed flake8 error.
* grib-api: add version 1.21.0
* libemos: add version 4.4.7 and allow choice of eccodes or grib-api
* magics: add version 2.32.0
* libemos: add description for eccodes variant
* eccodes: new package for encoding and decoding meteorological data
* eccodes: remove line breaks from package docstring
* eccodes: simplify names of variants
* eccodes: give a description for each variant
* eccodes: use succinct code for cmake_args
* eccodes: found extra dependency for python variant
* eccodes: add URL for a list of available releases
- py-setuptools is required by py-yt for importing yt in jupyter notebooks.
- add two dependencies needed for python 2.7
- add the py-subprocess32 package
- Spack doesn't need eggs -- it manages its own directories
- Simplify install layout and reduce sys.path searches by installing all
packages flat (eggs are deprecated for wheels, and this is also what
wheels do).
- We now supply the --single-version-externally-managed argument to
`setup.py install` for setuptools packages and setuptools.
- modify packages to only use setuptools args if setuptools is an
immediate dependency
- Remove setuptools from packages that do not need it.
- Some packages use setuptools *only* when certain args (likeb
'develop' or 'bdist') are supplied to setup.py, and they specifically
do not use setuptools for installation.
- Spack never calls setup.py this way, so just removing the setuptools
dependency works for these packages.
* Checksum code wasn't opening binary files as binary.
- Fixes Python 3 issue where files are opened as unicode text by default,
and decoding fails for binary blobs.
* Simplify fetch test parametrization.
* - add tests for URL fetching and checksumming.
- fix coverage on interface functions in FetchStrategy superclass
- add some extra crypto tests.
* Fix for llvm 4.0.0 on centos
This addresses https://github.com/LLNL/spack/issues/3791
* Only enable this option if on linux
* Change condition to satisfy standard
* Package install remove prior unfinished installs
Depending on how spack is terminated in the middle of building a
package it may leave a partially installed package in the install
prefix. Originally Spack treated the package as being installed if
the prefix was present, in which case the user would have to
manually remove the installation prefix before restarting an
install. This commit adds a more thorough check to ensure that a
package is actually installed. If the installation prefix is present
but Spack determines that the install did not complete, it removes
the installation prefix and starts a new install; if the user has
enabled --keep-prefix, then Spack reverts to its old behavior.
* Added test for partial install handling
* Added test for restoring DB
* Style fixes
* Restoring 2.6 compatibility
* Relocated repair logic to separate function
* If --keep-prefix is set, package installs will continue an install from an existing prefix if one is present
* check metadata consistency when continuing partial install
* Added --force option to make spack reinstall a package (and all dependencies) from scratch
* Updated bash completion; removed '-f' shorthand for '--force' for install command
* dont use multiple write modes for completion file
