* 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
* Add tests to mercurial package
* Add support for --insecure with mercurial fetching
* Install man pages and tab-completion scripts
* Add tests and latest version for all deps
* Flake8 fix
* Use certifi module to find CA certificate
* Flake8 fix
* Unset PYTHONPATH when running hg
* svn_fetch should use to svn-test, not hg-test
* Drop Python 3 support in Mercurial
Python 3 support is a work in progress and isn't currently
recommended:
https://www.mercurial-scm.org/wiki/SupportedPythonVersions
* Test both secure and insecure hg fetching
* Test both secure and insecure git and svn fetching
* Initial add of flac
* Initial add of id3lib
* Initial add of the opus codec
* Initial add of sox audio processing tools
* Cleanup spec files to be inline with current standard
* Fix pep8 compliance
* Remove un-needed configuration
* ncl: add depends_on statements for bison, flex and libiconv
* ncl: depends on flex for building and linking
* ncl: links with -ll, so requires flex with variant '+lex'
* ncl: depends on szip; external hdf5 may not provide it
* Disable parallel builds
The install step creates a bunch of links to the vim binary, e.g.
`view`. When run with -j greater than 1 there are silent failures.
Running w/out parallelism seems to fix it.
* Only constrain the install phase to be -j 1
Thanks @adamjstewart!
* Add package for nginx@1.12.0
Includes support for:
- zlib
- pcre (and pcre-jit)
- openssl (https support)
Built and basics tested on CentOS 7. I haven't tested the `https`
support [yet].
* Include final bit of doc string sentence.
I trimmed the docstring that I lifed from https://nginx.org/en a bit
too aggressively and left a '...' to remind me to fix it.
Apparently I need more obvious reminders.
Thanks @davydden!
* Install the shell completion scripts
Install the `git-completion.{bash,tcsh,zsh}` and `git-prompt.sh` into
`$(spack location -i git)/share/` (aka `prefix.share/`).
* Use copy_tree to copy all the files
The dest dir already exists, so install_tree()'s not an option.
* Added a package for the MDAnalysis toolkit.
* Added the dependency on setuptools.
* Added the rest of the dependencies to the py-mdanalysis package. Also
added the griddataformats and seaborn packages to satisfy requirements.
* Removed seaborn package since it has been recently added.
* Fixed flake8 error
* Removed inadvertent commits.
* Cleaned up reviewers feedback.
Update the package recipe w.r.t. AutotoolsPackage changes,
now builds "out of source".
Update the package with version info for 1.3.0.
> Mosh 1.3.0 released, with John Hood as release lead. The release includes broader platform compatibility, robustness improvements, better testing, and fixes for excess CPU consumption in some cases. We have switched to semver.org-style versioning and will increment the minor version number whenever we add new functionality. (In our previous practice, this release would probably have been called “1.2.7.”)
Tested on CentOS 7.
* adding 0.5.1 and variant for uint8 bit stream word type
* Revisions as per davydden
* fixing style (flake8) issues
* - switched to derive from MakefilePackage
- fixed typo in variant check
- Confirmed installs correctly with bswtuint8 variant
* added build method; changed zfp_incdir to incdir
* Add the rockstar package
* Add rockstar to yt.
* Correct signature of prep_yt.
* Correct rockstar package installation process
Needed to change the way the necessary prefixes are found as well as
how the completed package is copied.
There should probably be a way to do the copying in a more 'spack' way.
* Add license
* Add description.
* Set no hdf5 variant as default.
* Use copy_tree for copying files
* Use MakefilePackage
* Address concerns from @adamjstewart
* Fix flake8 errors.
Adds a package for mallocMC, a memory allocator for many core
architectures.
This project provides a framework for fast memory managers on
many core accelerators. Currently, it supports NVIDIA GPUs of
compute capability sm_20 or higher through the ScatterAlloc
algorithm. mallocMC is header-only.
Downstream Dependencies
PIConGPU and other projects of HZDR's
*Computational Radiation Physics* group
References
- Markus Steinberger, Michael Kenzel, Bernhard Kainz and Dieter Schmalstieg.
*ScatterAlloc: Massively parallel dynamic memory allocation for the GPU*,
Innovative Parallel Computing (InPar), 2012,
https://doi.org/10.1109/InPar.2012.6339604
- Carlchristian Eckert.
*Enhancements of the massively parallel memory allocator ScatterAlloc and its adaption to the general interface mallocMC*,
Junior Thesis (grosser Beleg), 2014,
http://dx.doi.org/10.5281/zenodo.34461
This adds a maintained version of the (since 2012)
stalled original project.
https://github.com/ComputationalRadiationPhysics/cuda_memtest
Nvidia's NVML (via the GPU deployment kit) could also be
added, providing serial number output of failing GPUs
for multi-GPU nodes.
* Fixes patch paths for earlier boost versions
The directory structure of boost changed at version 1.56.0, so the patch
being used for python support did not work on earlier versions. This
adds another patch that matches earlier versions.
* Removes commented out code
* Fixes needed to build htop
* Build libncursesw.so, not libncurses.so
* Remove htop hack now that it is picking up newer ncurses
* Tell packages to link to new ncursesw libraries
- clean up fetch urls
- inherit from AutotoolsPackage instead of Package
- explicit fPIC flags look suspicious, but leave them in there.
- in scalasca, use the cube version that is implicit from
the scorep dependency instead of specifying it twice.
* The beginnings of a package for shiny-server
Just stashing a WIP.
This doesn't work.
This goes for a while and/but blows up with some OpenSSL related issue.
* Make it work!
Yay!
* shiny-server needs R with X support
My environment gets this for "free" from my packages.yaml, but it
should be explicity.
* Address feedback
- python version
- gcc dependency
- Flake8 comment rules
* Richer caveats and warnings.
* Convert to CMakePackage and fix python version typo
* Fix typo: noqab -> noqa
* Ensure proper build location, clean up comments
* Update tinyxml
* url seems to have changed
* spack replaces "_2_6_2" with "_2.6.2" unless the url is explicitly
given
* copyfile is no longuer available by default
* URL version-parsing should work as of #2972
* Remove fake URLs from Spack
* Ignore long lines for URLs that start with ftp:
* Preliminary changes to version regexes
* New redesign of version regexes
* Allow letters in version-only
* Fix detection of versions that end in Final
* Rearrange a few regexes and add examples
* Add tests for common download repositories
* Add test cases for common tarball naming schemes
* Finalize version regexes
* spack url test -> spack url summary
* Clean up comments
* Rearrange suffix checks
* Use query strings for name detection
* Remove no longer necessary url_for_version functions
* Strip off extraneous information after package name
* Add one more test
* Dot in square brackets does not need to be escaped
* Move renaming outside of parse_name_offset
* Fix versions for a couple more packages
* Fix flake8 and doc tests
* Correctly parse Python, Lua, and Bio++ package names
* Use effective URLs for mfem
* Add checksummed version to mitos
* Remove url_for_version from STAR-CCM+ package
* Revert changes to version numbers with underscores and dashes
* Fix name detection for tbb
* Correctly parse Ruby gems
* Reverted mfem back to shortened URLs.
* Updated instructions for better security
* Remove preferred=True from newest version
* Add tests for new `spack url list` flags
* Add tests for strip_name_suffixes
* Add unit tests for version separators
* Fix bugs related to parseable name but in parseable version
* Remove dead code, update docstring
* Ignore 'binary' at end of version string
* Remove platform from version
* Flip libedit version numbers
* Re-support weird NCO alpha/beta versions
* Rebase and remove one new fake URL
* Add / to beginning of regex to avoid picking up similarly named packages
* Ignore weird tar versions
* Fix bug in url parse --spider when no versions found
* Less strict version matching for spack versions
* Don't rename Python packages
* Be a little more selective, version must begin with a digit
* Re-add fake URLs
* Fix up several other packages
* Ignore more file endings
* Add parsing support for Miniconda
* Update tab completion
* XFAILS are now PASSES for 2 web tests
- _spider in web.py was actually failing to spider deeper than a certain
point.
- Fixed multiprocessing pools to not use daemons and to allow recursive
spawning.
- Added detailed tests for spidering and for finding archive versions.
- left some xfail URL finding exercises for the reader.
- Fix noqa annotations for some @when decorators
* add packages for EasyBuild and dependencies
* fix remarks w.r.t. docstrings & download urls, make dependency specs stricter w.r.t. required versions
* fix easybuild-* dep specs, should be open-ended
* correct dep specs for easybuild and easybuild-easyconfigs using @3.1.2[:]
* Run python setup.py test if --run-tests
* Attempt to import the Python module after installation
* Add testing support to numpy and scipy
* Remove duplicated comments
* Update to new run-tests callback methodology
* Remove unrelated changes for another PR
* perl: make extendable and add Module::Build package
* perl: allow 'spack create' to identify perl packages from their contents
* perl-module-build: fix indenting of package docstring
* perl: split install() method for extensions into phases
* perl: auto-detect build method (Makefile.PL vs Build.PL) and define a 'check' method
* PerlPackage: use import statements similar to those in AutotoolsPackage
* PerlModule: fix detection of Build.PL
* PerlPackageTemplate: remove extraneous lines to avoid flake8 warnings
* PerlPackageTemplate: split into separate templates for Makefile.PL and Build.PL
* PerlPackage: add cross-references to docstrings
* AutotoolsPackage: fix ambiguous cross-references to avoid errors in doc tests
* PerlbuildPackageTemplate: depend on perl-module-build if Build.PL exists
* ENH: add package for building OpenFOAM (1612) from www.openfoam.com
- provide 'openfoam' as virtual package.
- package as openfoam-com to reflect the distribution point.
This initial spack packaging for OpenFOAM supports a number of possible
variants and should handle 64-bit labels properly now that the scotch
package has been updated accordingly.
* ENH: update package for foam-extend (extend-project.de)
- provide 'openfoam' as virtual package.
- much of the build is now aligned with how the openfoam-com package
looks, with the aim of future refactoring.
- avoid installing intermediate targets.
- contains its own environment sourcing script for the build, for more
flexibility and robustness (doesn't touch the python build environ)
* ENH: added package for building from openfoam.org
- provide 'openfoam' as a virtual package.
- this is largely a direct copy of the openfoam-com package.
It has been supplied as a courtesy for users and to ensure maximum
consistency in quality and naming between the foam-extend,
openfoam-com and openfoam-org packages.
* CONFIG: add openfoam into bash completion providers list
* ENH: have openfoam-com use spack as USERMPI
- also simplify the generation of mplib/compiler rules
* ENH: have openfoam-org use spack as SYSTEMMPI
- this setup requires more environment settings than USERMPI
(openfoam-com), but is currently the only means of integration
for openfoam-org
- simplify generation of mplib/compiler rules
* ENH: simplify generation of mplib/compiler rules (foam-extend)
- rename mpi rules from SPACK,SPACKMPI to USER,USERMPI for consistency
with openfoam-com and to generalize for any build system.
* STYLE: record spack tree as a log file (openfoam)
- can be useful for future diagnostics and general record keeping
* 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
* Add Blast+ package.
Adds support for NCBI's blast+@2.6.0. I'll be adding a few historical versions in the near future.
It's a fairly direct transliteration of the [Homebrew Science recipe][hbs].
I skipped the mysql support.
There is a problem with HDF5 support. Blast's configure script test program defines a macro 'HOST' to a string value and one of the HDF5 bits has an variable named 'HOST'. Fun things happen. I've disabled support for now.
I've run very very basic tests. I'll get this out to my users and ensure that it works and fine tune the options and etc....
[hbs]: https://github.com/Homebrew/homebrew-science/blob/master/blast.rb
* Flake8 fixes
* Update w.t.r. mamelara's PR and cleanup
Add paths to things in the --with-* config args
Add add'l config flags from #3394.
Update patch to no-op and add comment.
Add add'l dependencies after studying `configure --help`.
* Flake8 cleanup
* Add support for blast+@2.2.30
Need to work around a configure bug. See https://github.com/Homebrew/homebrew-science/issues/2337#issuecomment-170011511.
* Re-wrap comment, line length not a problem.
I'd broken a comment across to line in a fit of flake8
induced fear. Adam pointed out that it's ok.
* Remove explicit prefix config
Remove explicit prefix config, the autotools package does it for us.
* Added packages for Structural Simulation Toolkit and Dumpi trace
* sst-dumpi deps
Remove extraneous dependency from sst-dumpi
* Removed redundant function and fake-url from sst-dumpi package
* Fixed URL, Added git branches, requested changes
sst-dumpi version listed as 6.1, made an upstream change to 6.1.0
sst-macro and sst-dumpi can be installed as v6.1.0 and master branch
* Added bootstrap. Tweaked URLs and description
- drop old TCL support from paraview build.
- add +plugins variant to have include directories installed. This is
enabled by default since the additional diskspace for includes is
really minimal and since this also allows re-use of the VTK libraries
from ParaView without necessarily requiring a separate VTK
installation.
- +opengl2 is now the default. As per all newer VTK and paraview versions.
BUG: broken install for paraview-5.0.1 with includes and without python
- incorrect conditional for ui_pqExportStateWizard.h when python is
disabled and includes are to be installed.
gcc compiler detection patch.
These have both been fixed in paraview 5.3.0
ENH: refactor as a CMakePackage.
- Note that "spack install paraview" works as expected, but
"spack build paraview" fails in weird unrelated ways.
