* 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
* github releases are not released versions, but from-source
releases
* they lack the mimification of the JS/CSS components and as
such require node-js and npm, this conflicts with python@3:
* this commit
* drops the from-source dependencies on node-js and npm and
* updates the checksums to the correct sha256 hashes of the
pypi releases. The pypi-tarballs are different
* ZFP: CMake Package
ZFP is primarily build via CMake, which will have all install logic
and configuration files generated.
The 0.5.0 release did not support this yet, so we toss it.
* Patch ADIOS1: ZFP 0.5.1+ support
* ZFP: Expose all CMake variants
* new package: py-python-ldap
* fix dependency types
* improvements
* Update var/spack/repos/builtin/packages/py-python-ldap/package.py
Co-Authored-By: Adam J. Stewart <ajstewart426@gmail.com>
* Update var/spack/repos/builtin/packages/py-python-ldap/package.py
Co-Authored-By: Adam J. Stewart <ajstewart426@gmail.com>
* add openldap dependency
* go-md2man: disable module-mode
* Update var/spack/repos/builtin/packages/go-md2man/package.py
Co-Authored-By: Adam J. Stewart <ajstewart426@gmail.com>
* add singularity 3.4.1
Signed-off-by: ArangoGutierrez <eduardo@sylabs.io>
* revert some changes
Signed-off-by: ArangoGutierrez <eduardo@sylabs.io>
* add maintainers list to pkg singularity
Add @alalazo and me to the Singularity maintainers list
* Update var/spack/repos/builtin/packages/singularity/package.py
Co-Authored-By: Adam J. Stewart <ajstewart426@gmail.com>
* Update var/spack/repos/builtin/packages/singularity/package.py
Co-Authored-By: Adam J. Stewart <ajstewart426@gmail.com>
* Update var/spack/repos/builtin/packages/singularity/package.py
Co-Authored-By: Adam J. Stewart <ajstewart426@gmail.com>
7bcb306 updated setup_environment in the GCC package to examine the
bin/ directory to find alternatively-named instances of CC, but this
failed to account for when GCC was being installed and failed when
it attempted to list the not-yet-existing installation prefix. This
commit updates the logic to skip this search if the bin/ directory
doesn't exist.
* libaio: fixed a condition that checks whether we are running on OS X
* libaio: simplified package by adding an explicit conflict for darwin
* libaio: added information to the docstring
* fio: added version 3.16, added conflict when using libaio, docstring
* lvm2: conflict due to libaio dep, improved docstring, simpler install
* mariadb: conflict due to libaio dep, improved docstring, version 10.4.7
* mariadb: the dependency on libaio is now conditional, removed conflict
* mariadb: fixed a typo in previous commit
Co-Authored-By: Adam J. Stewart <ajstewart426@gmail.com>
* libaio: turned into a MakefilePackage
Unlike the compiler binary name search logic, the `setup_environment` in
GCC's package assumes the compiler names are *exactly* `gcc`, `g++`,
etc. In many external installations (Homebrew, Macports) the
installation includes only *suffixed* versions such as `gcc-9`.
This patch uses the GCC compiler search suffixes to actually locate the
correct filenames for the installed compilers, allowing the
Spack-generated module file to have useful definitions of CC, CXX, etc.
It also allows for the possibility that the user's external installation
of GCC is compiled without Fortran support, in which case the `FC`
environment variables are not defined.
* The perl-uri-escape package duplicates perl-uri
The Perl URI::Escape module is in the Perl URI package so the Spack
perl-uri-escape package is a duplicate of the perl-uri package. This PR
does the following:
- replace `depends_on('perl-uri-escape')` with `depends_on('perl-uri')`
in packages that dependend on perl-uri-escape
- add the version from perl-uri-escape to perl-uri
- remove the unneeded dependency from perl-uri
- remove the perl-uri-escape package
* Reinstated perl-test-needs dependency
Put the perl-test-needs dependency for perl-uri back in but set it to
type='test'.
* For tests to succeed the type must be ('build', 'test')
Now that Spack injects microarchitecture specific optimizations for
the selected target, packages should avoid adding flags that could
step over those.
This PR adds interproscan-4.8, which has a completely different build
system than version 5. Note that this builds for running on a host as
opposed to a queue system. I am fairly certain that a queue system can
be configured later.
This PR also adds a patch for intrproscan-5 to build when the user
building the packages has a large GID by setting posix mode for tar.
* llvm: fixed issues with syntax and formatting
* use spec.architecture.target.family
* use spec.target instead of spec.architecture.target
* mesa: use == instead of __contains__
A function added to this package ran as part of importing it and
printed a warning for most Spack invocations, this removes the
warning message.
Also:
* Use compilers directly instead of Spack compiler wrappers (since
references to the compiler are embedded in text and binary files
of the installation)
* Add 'cross' variant for setting CROSS environment variable for
build
* Set UPCXX_INSTALL for generated module files
* Set UPCXX_GASNET_CONDUIT/UPCXX_NETWORK in generated module files
on Cray systems
* Also set UPCXX_NETWORK in build environment for Cray systems
The following dependencies were added:
+ depends_on('perl-exporter-tiny', type=('build', 'run'))
+ depends_on('perl-list-moreutils-xs', type=('build', 'run'))
Seamless translation from 'target=<generic>' to either
- target.family == <generic> (in methods)
- 'target=<generic>:' (in directives)
Also updated docs to show ranges in directives.
Fixes#12829
This adds a variant to the util-linux package that controls whether it
builds its own libuuid. Variant defaults to True. It enables other
packages to choose to get libuuid from the libuuid package instead.
This also changes the cryptsetup package to build util-linux with
~libuuid (so it uses an explicitly-Spack-built instance of libuuid
instead).
- add missing perl dependency
- only filter Makefile if referred to dependency is in the spec
- rewrite the shebang line of scripts to use spack perl
- remove tabix dependency as tabix and bgzip are part of htslib
* cuda: New version 10.1.243
Adds CUDA 10.1.243. The installer command-line arguments have slightly
changed, hence in the install method the version needs to be inspected
in order to give the correct arguments for the new installer.
* cuda: Combine common command-line arguments
The CUDA 10.1+ installer has slightly different command-line arguments
than previous versions. Keep the common parts together and only split
where they are different.
* Make flake8 happy
* update py-bokeh: new version & dependencies
* Revert "update py-bokeh: new version & dependencies"
This reverts commit 5e191a0b20a89f09630b4d223a28b19db715603f.
* update py-bokeh: new version & dependencies
* trigger travis-ci
* adjust python dependency-type to br
* update py-bokeh: new version & dependencies
* Revert "update py-bokeh: new version & dependencies"
This reverts commit 5e191a0b20a89f09630b4d223a28b19db715603f.
* new package: py-fsspec: add package.py
* trigger travis-ci
* adjust python dependency-type to br
* CGNS: Add setting of RPATH on Darwin
This should go in the CGNS CMakeLists.txt, but it isn't there yet and won't be in previous versions, so best to handle it here.
If building on darwin/MacOSX, need to set the RPATH so applications can find shared library correctly.
* Restrict MACOSX_RPATH setting
This has now been added to the CGNS distribution, so the setting of `CMAKE_MACOSX_RPATH` should be restricted to current and previous releases and not upcoming releases.
* new package: py-configojb
* add version 4.7.2
* improve dependencies
* fix url for versions > 5.0.0
* Update var/spack/repos/builtin/packages/py-configobj/package.py
Co-Authored-By: Adam J. Stewart <ajstewart426@gmail.com>
* Update var/spack/repos/builtin/packages/py-configobj/package.py
Co-Authored-By: Adam J. Stewart <ajstewart426@gmail.com>
* use format to create url strings
* fix typo
* improve style
* Update var/spack/repos/builtin/packages/py-configobj/package.py
Co-Authored-By: Adam J. Stewart <ajstewart426@gmail.com>
* py-gpaw: Fixing missing numpy include path, adding newer version of py-gpaw and fixing a bug with libxc.c in older py-gpaw
* py-gpaw: Fix Python and ASE version dependencies
- GPAW 19.8.1 requires Python 3.x, add dependency on python@3.5:
- GPAW releases are associated with a corresponding ASE release, add
matching ASE version dependencies.
* py-gpaw: Enable the scalapack variant by default
GPAW installation instructions say scalapack is optional but "highly
recommended". Thus enable it by default.
* add new cutadapt release 2.5, and adjust dependencies conditional on version
* use https, not ssh, for git url
Co-Authored-By: Adam J. Stewart <ajstewart426@gmail.com>
* update py-xopen (add 0.8.2 checksum)
* refine version specific dependencies
add py-bz2file, which needs to be created
* create py-bz2file
* Revert "refine version specific dependencies"
This reverts commit 70649da98851fefb2f936ca99a012fe6bef07b70.
* Revert "update py-xopen (add 0.8.2 checksum)"
This reverts commit 7400f44caa6e98419eb4bc3107704b91e8a2018b.
* update py-xopen (add 0.8.2 checksum)
* refine version specific dependencies
add py-bz2file, which needs to be created
* py-bz2file needed when built with python 2.7
Co-Authored-By: Adam J. Stewart <ajstewart426@gmail.com>
* space after comma
- Fix trailing whitespace missed by the bug described in #12755.
- Fix other style issues that have crept in over time (this can happen
when flake8 adds new checks with new versions)
There are problems with libunwind for arm and trying to use it with mesa.
See for example:
https://github.com/grate-driver/mesa/issues/6
disabling use of libunwind for arm, allows the package to be built
Signed-off-by: Howard Pritchard <hppritcha@gmail.com>
- Use of symbol testing macro requires explicit include()
- CMake policies are not version-portable and the support has to queried
based on CMake version
* libpeas@1.22.0: new package
* libpeas: note more build dependencies
Build and link dependencies were obtained through a combination of
examining the `config.log` file from `configure` and looking at the
pkg-config files of `libpeas`.
* libpeas: add search path for GIR/typelib files
* Use spec.architecture.target insted of platform.
* remove default in simd variant value.
simd variant change to archtecture independent values.
* Add check simd values.
* rewrite check simd values.
* * flake8
* change aarch64 to arm (neon support only 32 bit arm.)
* py-ase: New version 3.18
Add ASE version 3.18. ASE 3.18 has dropped support for python 2.x,
hence add a dependency on python@3.5: for it.
* Add more ASE dependencies
Address review comments, add dependencies on py-scipy, py-matplotlib,
py-flask, and also add type=('build', 'run') dependency specifiers.
While debugging this package on our Cray machine, tmux was throwing an
error involving the ncurses headers. Tmux would look for headers in
system locations rather than where spack installed ncurses. Tested only
on a Cray.
* Install the newest version of ncbi-rmblastn
Version ncbi-rmblastn 2.2.28 coonfiguration fails for gcc compiler on ubuntu 16.04 due to some compatibility issues that requires manual intervention to keep the installation going. However you still stumble upon other issues while compiling it.
Using Intel compiler passes the configuration step but fails for the compilation process as well.
Here I'm using the latest version and patch, and the recommended configuration option as mention in http://www.repeatmasker.org/RMBlast.html
* uploading ncbi-blast patch
The mariadb-5.5 series can not be compiled with gcc-9.1.0 and above. Add
a conflicts statement to reflect that.
The error is due to -Werror=address-of-packed-member, a warning that is
new in gcc-9.
* Update R CRAN packages
This PR update R CRAN packages. It also ensures that spack built
packages that correspond to R recommended packages are specified in the
dependency list. This is needed for #12015.
* Add more updates to packages
* Updated dependencies of CRAN R packages
Also, use cloud.r-project.org rather than cran.r-project.org to use
automatic redirection to mirrors. This minimizes the load on the cran
server.
* Update to latest versions of CRAN R packages
* Fix flake8 issues
Some blank lines at the end of a coupple of package files crept in.
* Adjust r-animation dependencies
The r-magick package depends on image-magick, so r-animation should as
well. Also, add in texlive for LaTeX support.
* New package: r-magick
* Adjust line spaces in r-magick
* Add swftools dependenct to r-animation
* New package: swftools
This is needed bt r-animation
* Add 'when' clause to some package dependencies
- r-animation
- r-coin
- r-dt
- r-openssl
* New package: r-ellipsis
* New package: r-vctrs
* New package: r-zeallot
* New package: r-generics
* New package: r-cardata
* Add r-progress dependency to r-readxl
* New package: r-askpass
* New package: r-openxlsx
* New package: r-rio
* New package: r-sys
* New package: r-zip
* Add more updated packages
These are updates that have happened while working on this PR as well as
catching the ones from the cran.rstudio.com URL that were missed before.
* New package: r-gower
* New package: r-recipes
* New package: r-squarem
* New package: r-libcoin
* New package: r-rcmdcheck
* New package: r-remotes
* New package: r-sessioninfo
* New package: r-xopen
* New package: r-rgexf
* New package: r-rook
* New package: r-later
* New package: r-promises
* New package: r-xfun
* New package: r-urca
* New package: r-ggsignif
* New package: r-polynom
* New package: r-ucminf
* New package: r-ordinal
* New package: r-inum
* New package: r-debugme
* New package: r-fs
* New package: r-shinyfiles
* New package: r-gsa
* New package: r-nmof
* New package: r-dosnow
* New package: r-rann
* New package: r-reticulate
* New package: r-future
* New package: r-globals
* New package: r-listenv
* New package: r-future-apply
* New package: r-rsvd
* New package: r-sctransform
* New package: r-mitools
* Remove a stray FIXME line
* Fix typo in dependency for r-rcmdcheck
* Remove the dependency on r-splines
The r-splines package never existed in spack, but it does not exist on
CRAN either. There is an archive version from 1999 but it does not have
the proper extension format for modern R packages. The latest version
does not depend on r-splines, and apparently previous versions at least
built without it. Also, bump the required R version.
* Fix typo in r-rcpp dependency
* Fix typos in dependencies
- r-diagrammer
- r-janitor
- r-seurat
Also, bump minimum R version for r-rngtools.
* New package: r-clisymbols
* New package: r-fitdistrplus
* New package: r-gbrd
* New package: r-gh
* New package: r-ini
* New package: r-metap
* New package: r-npsurv
* New package: r-rdpack
* New package: r-snakecase
* New package: r-tinytex
* New package: r-usethis
* Make recommended changes
Made the changes that were recommended in the initial review.
- change cran.rstudio.com to cloud.r-project.org
- change R-project to r-project
- for packages with no listed homepage use the canonical link to the
package page
- for packages with a dependency constraint on R itself, specify the
dependency type
- add `list_url` where missing from package
* New package: r-hdf5r
This is needed for some older versions of r-seurat.
* Set R versions in packages
If the R version is specified in the DESCRIPTION file then set it in the
respective spack package.py file.
* Update var/spack/repos/builtin/packages/r-aer/package.py
Change dependency version of r-car.
Co-Authored-By: Adam J. Stewart <ajstewart426@gmail.com>
* Set constraint of mlbench dependency of r-adabag
* Set constraint on r-rcpp dependency of r-ape
* Removed "suggested" r-testthat from r-bibtex
* Update var/spack/repos/builtin/packages/r-bindrcpp/package.py
Fix dependency spec of r-bindr in r-bindrcpp.
Co-Authored-By: Adam J. Stewart <ajstewart426@gmail.com>
* Update var/spack/repos/builtin/packages/r-blob/package.py
Add r-vctrs version constraint.
Co-Authored-By: Adam J. Stewart <ajstewart426@gmail.com>
* Remove r-base64enc dependency from r-callr
* Update var/spack/repos/builtin/packages/r-car/package.py
Set constraint on r-cardata dependency.
Co-Authored-By: Adam J. Stewart <ajstewart426@gmail.com>
* Remove unneeded dependencies from r-clipr
* Add gmake dependency to r-construct
* Set the proper homepage for r-crayon
* Add r-jsonlite as a dependency for r-crul
The jsonlite package moved from "suggests" to "imports" with 0.8.4.
* Remove accidental colon after package name
* Add version constraint to r-fpc dependency in r-dendextend
* Additional constraints for R version with r-digest
* Add r-jsonlite dependency for latest verion of r-dt
* Add r-htmltools dependency in r-dygraphs package
* Removed unneeded dependencies from r-fnn
* Remove unneeded dependencies from r-formatr
* Add version constraint for r-mvtnorm dependency in r-fpc
* Added gmake dependency to r-fs
* Add r-globals dependency in r-future-apply
* Add perl dependency to r-gdata
* Add openssl dependency for r-ggally
* Removed unneeded dependencies from r-globaloptions
* Update r-haven
- Add version constraint on r-forcats
- Add gmake build dependency
* Fixed gmake dependency
Gmake is a build only dependency.
* Apply suggestions from code review
Apply a batch of suggestions from Adam Stewart.
Co-Authored-By: Adam J. Stewart <ajstewart426@gmail.com>
* Remove unneeded dependencies from r-hoardr
* Fix r-htmlwidgets homepage
* Add gmake build dependency to r-httpuv
* Remove unneeded dependency from r-log4r
* Remove unneeded dependency from r-maldiquant
* Add gmake build dependency to r-minqa
* Remove unneeded dependency from r-mlbench
* Set constraint on R6 dependenvy of r-pbdzmq
* Set constraints on r-callr dependency of r-pkgbuild
* Remove unneeded dependency from r-nloptr
* Remove unneeded dependencies from r-pkgmaker
* Set R version constraint for r-raster
* Set version constraint on rcpp for r-rcppprorgess
* Added gmake build dependency
* Remove unneeded dependencies from r-rematch
* Remove unneeded dependency from r-plogr
* Add gmake build dependency for r-rcurl
* Apply suggestions from code review
Bring in more suggestions from Adam Stewart.
Co-Authored-By: Adam J. Stewart <ajstewart426@gmail.com>
* Remove cnpy dependency from r-rcppcnpy
The r-rcppcnpy package has its own modified copy of the cnpy source and
will build from that internal source. The cnpy dependency is therefore
unnecessary.
* Add comment to reconcile dependencies
The CRAN site lists Perl, Getopt::Long as a dependency. The Spack Perl
will have the Getopt::Long package installed so just depend on Perl.
* Add dependency on udunits2 with newer versions of r-units
* Set additional proj constraint for r-sf
Support for PROJ6 was added in r-sf-0.7-4.
* New package: pandoc
This package installs the pandoc and pandoc-citeproc binaries in order
to satisfy dependencies on pandoc until the Haskell framework is in
Spack.
* Add pandoc dependency to r-bookdown
* Add comment about MPI in r-ergm
* Add pandoc dependency for r-reprex
* Add proj constraints to r-rgdal dependencies
Support for PROJ6 was added in version 1.4-2.
* Modifications to r-rgl
- Rearranged the dependencies to be more consistent with other packages
- put the type last on the depends_on lines to be consistent with other
packages
- Added version constraints for some dependencies
- Added pandoc build dependency
* Be more accurate with rjsonio constraint for r-rgooglemaps
* Remove unneeded dependencies from r-rhmmer
* Tweak constraints for r-rjava
- Set java version constraint
- add gmake build dependency
* Add pandoc dependency to r-markdown
* Remove unneeded dependencies from r-rrcov
* Tweak r-rstan package
- remove duplicate specifications
- remove unneeded when conditions
- add version constraints
- arrange to follow order on CRAN page more closely
- add gmake build dependency
- add pandoc build dependency
* Add pandoc build dependency for r-rstantools
* Remove unneeded dependency from r-runit
* Remove unneeded dependencies from r-selectr
* Remove example R code from description
The example would module loading to break, at least in the case of Lmod
using TCL module files. It could be during the TCL to Lua conversion but
the module fails due to interpreting ipart of the example as a command.
* Update r-seurat
New version of r-seurat with new dependencies.
* New package: r-dqrng
* New package: r-leiden
* New package: r-rcppannoy
* New package: r-rcppparallel
* New package: r-rspectra
* New package: r-sitmo
* New package: r-uwot
* Remove unneeded dependency from r-snow
* Remove unneeded dependency from r-sourcetools
* Added pandoc build dependency for r-stanheaders
* Remove unneeded dependencies from r-taxizedb
* Remove unneeded dependencies from r-tclust
* Add dependency constraints for r-threejs
The following are needed for version 0.2.2:
- r-matrix
- r-jsonlite
* Remove unneeded dependencies from r-vfs
* Remove unneeded dependencies from r-vgam
* Remove unneeded dependency from r-xlconnectjars
* Remove unneeded dependency from r-xlsxjars
* Remove unneeded dependency from r-xnomial
* Remove ~mpi from fftw dependency of swftools
* Apply suggestions from code review
Add latest round of suggestions from Adam Stewart.
Co-Authored-By: Adam J. Stewart <ajstewart426@gmail.com>
* Fix rjsonio spec for r-rgooglemaps
The r-rjsonio spec is a when conditional.
* Rename 3 R.* packages
- r-utils --> r-r-utils (R.utils)
- r-oo --> r-r-oo (R.oo)
- r-methodss3 --> r-r-methodss3 (R.methodsS3)
Also, renamed dependencies in packages that depend on these three.
* Loosen version constraint on mariadb for r-rmysql
Make the mariadb constraint on mariadb-5.5 rather than the more
specific, and limiting, mariadb-5.5.56. This will allow an external
mariadb, such as mariadb-5.5.60 on CentOS-7.5 to be used. It also allows
for r-rmysql to be built against newer versions of the mariadb-5.5
series that might be added to spack.
* Convert to Autotools package
* dyninst and papi are now optional (off by default)
* limit dyninst version to < 10 (see
https://github.com/bsc-performance-tools/extrae/issues/30)
* Add numactl dependency
* Enable parallel installs for 3.7 and later
* Set EXTRAE_HOME in module files and for dependent package installs
* Generalize cxx11 support flag (previously it was using a specific
syntax and this updates it to use the cxx11 support flag for the
compiler in use).
* The install for kaldi was copying library symlinks but not the
actual library files, this makes sure to copy the libraries
* All libraries are installed to 'prefix.lib' (the original
library directory structure is no longer maintained)
* The install step for executables did not account for the different
dynamic library suffix on MacOS
e891cc4 updated the cairo package to make gobject support optional
and disabled it by default. gtkplus requires gobject support so this
explicitly enables +gobject on the cairo dependency of gtkplus.
Change the depends_on type from default (build + link) to just 'link'
for binutils and a few other packages. We don't use the binutils
utilities (only libs). On cori at NERSC (Cray), this was breaking the
build by covering up the system ld.
* Only apply issue-87.patch for versions before 1.2.3
* 1.2.3 builds fine with gcc@8:, but 1.2.2 and 1.2.2_p1 both fail
(with or without the patch) so the conflict is updated to exclude
only these two versions.
* Make mpi, scipy, petsc4py, and nlopt support optional
* Later versions depend on python@3.5:
* Versions before 0.4.1 must build with MPI: add a conflict for
@:0.4.1~mpi
Before this commit, CMake would still attempt to detect OpenMP, even
if RAJA were being installed with `spack install raja~openmp`, because
the option `ENABLE_OPENMP` is set to "On" by default. This commit
explicitly disables OpenMP when the Spack install spec contains
'~openmp`, ensuring that CMake does not attempt to detect and link
with OpenMP.
* esmf: add patch when building with intel for 7.0.x
* esmf: set Makefile variables required to propagate CXX/F90 flags
* ncl: add ymake patch for @6.4.0:
* ncl: add pixman, bzip2, freetype dependencies
* Add version 6.3.2 (which does not require patches like 6.1.5)
* Add +python variant to build Python bindings
* Option to build shared libraries does not exist for newer
versions including 6.3.2
* Update 'libs' property (library names are different for newer
versions)
* Add support to detect and build with MKL as blas provider
SEACAS is now using versions instead of just relying on always
installing master. There are now tagged versions.
The most recent version is the first that can be used with a
non-patched develop version of the CGNS package; previously, seacas
required that the CGNS library have some internally-developed patch
applied, but this is no longer needed.
Also, added support for adios2 package with the adios2 variant.
This currently defaults to off.
This variant (off by default) adds support for the kdreg option in
the GNI provider. It is disabled by default in order to avoid
potential runtime conflicts with the cray-mpich library. Only one
library at a time can use this feature.
This patch allows the libfabric package to work correctly out of
the box on systems like Cori at NERSC (since it's CLE7 update).
Otherwise the spack build may autodetect kdreg headers on the system
and enable this problematic feature.
* nlohmann-json: 3.7.0
The version 3.6.0 fix compile issues with GCC 9.0.
* nlohmann-json: proper test handling
tests are controlled via `spack install --test root|all ...`
instead of a variant.
This adds a special package type to Spack which is used to aggregate
a set of packages that a user might commonly install together; it
does not include any source code itself and does not require a
download URL like other Spack packages. It may include an 'install'
method to generate scripts, and Spack will run post-install hooks
(including module generation).
* Add new BundlePackage type
* Update the Xsdk package to be a BundlePackage and remove the
'install' method (previously it had a noop install method)
* "spack create --template" now takes "bundle" as an option
* Rename cmd_create_repo fixture to "mock_test_repo" and relocate it
to shared pytest fixtures
* Add unit tests for BundlePackage behavior
* new package: libglvnd
* remove virtual provides from libglvnd
libglvnd does not provide them directly, but
through implementations that depend on it.
* fix flake8 errors
* libglvnd: fix style/remove unecessary variants
* remove older libglvnd version
* explicitly enable all libglvnd stubs
* libglvnd: conflict with non-linux platform
* Choose a specific commit as a version (before, the only version was
the master branch)
* Add CMake patch which allows for building the version added here
(this replaces the existing patches for percept in Spack)
* Update trilinos dependency
Also update dependencies to build latest py-deeptools versions and
add a patch to run tests:
* Replace pypi URL with github URL to download tests
* Update dependency versions of py-pysam, py-matplotlib
* Add new py-deeptoolsintervals package as a dependency
* Add py-plotly and py-nose dependencies
* Patch setup.py to collect and run tests
UnifyCR has been renamed to UnifyFS. Renaming the Spack package is
the last step in this process.
This renames the package and changes any UnifyCRs to UnifyFS within
the package.
* Overhaul PyTorch package
* Flake8
* Distributed requires MPI, NCCL not specified correctly
* Binary was being specified incorrectly
* Run tests at install time
* Disable GLOO in addition to GLOO_IBVERBS
* Add option to disable QTDesigner plugin for qwt
Qt designer shouldn't be necessary to build downstream GUI code.
Currently `qwt^qt~tools` fails to build:
(darwin clang@10.0.1)
```
compiling qwt_designer_plugin.cpp
compiling qwt_designer_plotdialog.cpp
moc qwt_designer_plugin.h
moc qwt_designer_plotdialog.h
rcc qwt_designer_plugin.qrc
qwt_designer_plugin.h:23: Error: Undefined interface
make[1]: *** [moc/moc_qwt_designer_plugin.cpp] Error 1
make[1]: *** Waiting for unfinished jobs....
qwt_designer_plugin.cpp:17:10: fatal error: 'QDesignerFormEditorInterface' file not found
^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
1 error generated.
make[1]: *** [obj/qwt_designer_plugin.o] Error 1
make: *** [sub-designer-make_default-ordered] Error 2
```
* Update VTK for newer VisIt and compiler versions
Several changes/enhancements to VTK package
---
Add version 8.1.0 (default version for VisIt 3.x)
---
Tweak VTK options for version 8 and VisIt:
- only add mpi4py version option when mpi4py is enabled
- Require object factory for downstream packages
- Remove OpenGL preference for VTK 8
---
Combine +python3 into +python
The spec for using python3 should just be `+python^python@3:`.
---
Remove unused VTK cmake argument on newer version
---
Patch for Python 3 fails on VTK 6.1 (needed for VisIt 2.x):
```
==> Patch /rnsdhpc/code/spack/var/spack/repos/builtin/packages/vtk/python3.7-const-char.patch failed.
==> Error: ProcessError: Command exited with status 1:
'/usr/bin/patch' '-s' '-p' '1' '-i' '/rnsdhpc/code/spack/var/spack/repos/builtin/packages/vtk/python3.7-const-char.patch' '-d' '.'
```
and as it happens, VisIt 2.13 is incompatible with Python 3 anyway.
---
Fix compiler error:
As spack's configuration warning says, double-quotes can cause trouble:
```
==> [2019-07-29-11:47:55.269653] Warning: Quotes in command arguments can confuse scripts like configure.
The following arguments may cause problems when executed:
-DVTK_REQUIRED_OBJCXX_FLAGS=""
Quotes aren't needed because spack doesn't use a shell.
Consider removing them
```
They were being added to the compile line, causing clang to think it was
asked to compile an empty file:
```
cd /private/var/folders/fy/x2xtwh1n7fn0_0q2kk29xkv9vvmbqb/T/s3j/spack-stage/spack-stage-3nk9bwe_/spack-build/Rendering/OpenGL && /rnsdhpc/code/spack/lib/spack/env/clang/clang++ -DVTK_IN_VTK -DvtkRenderingOpenGL_EXPORTS -F/Applications/Xcode.app/Contents/Developer/Platforms/MacOSX.platform/Developer/SDKs/MacOSX10.14.sdk/System/Library/Frameworks -DGLX_GLXEXT_LEGACY -O2 -g -DNDEBUG -isysroot /Applications/Xcode.app/Contents/Developer/Platforms/MacOSX.platform/Developer/SDKs/MacOSX10.14.sdk -fPIC -fvisibility=hidden -fvisibility-inlines-hidden "" -o CMakeFiles/vtkRenderingOpenGL.dir/vtkCocoaGLView.mm.o -c /rnsdhpc/code/spack/var/spack/stage/vtk-6.1.0-b2mj276iz77fadisv2me365qe27t3gxt/spack-src/Rendering/OpenGL/vtkCocoaGLView.mm
clang: error: no input files
make[2]: *** [Rendering/OpenGL/CMakeFiles/vtkRenderingOpenGL.dir/vtkCocoaGLView.mm.o] Error 1
```
* Modernize/PEP-8 visit package statements
* Add new VisIt version and patches for building on Mac
- VisIt's cmake assumes a 'vtk(tiff|jpeg|png)' *library* target exported by
VTK, but VTK 8.1.x on my configuration seems to have these as header-only
targets with library dependencies.
- Explicitly add QT path to visit configure: Without this, somehow
`${VISIT_QT_DIR}` was being set to empty, so that the build failed with
`missing /bin/moc`.
- VisIt assumes that if it isn't being built statically, QWT has been built as
a mac Framework. QWT actually is built as a framework based on whether QT
itself is.
Error message:
```
-- Looking for QWT
CMake Error at CMake/SetUpThirdParty.cmake:131 (MESSAGE):
Include Directory for QWT (/rnsdhpc/code/spack/opt/spack/darwin-mojave-x86_64/clang-10.0.1-apple/qwt-6.1.3-bmfxirweplzhjoiil4rw632evkyteuwk/lib/qwt.framework/Versions/Current/Headers) does not exist.
Call Stack (most recent call first):
CMake/FindQwt.cmake:57 (SET_UP_THIRD_PARTY)
CMakeLists.txt:1251 (INCLUDE)
```
* ADIOS 2.4.0: Add new Deps
Version 2.4.0 of ADIOS2 added new dependencies that are not
yet listed as `depends_on` and/or disabled otherwise. Add them
now to avoid picking them up from system paths, e.g. `libpng`.
* ADIOS2: Variant Defaults Change
* Python: False by default
* ADIOS1: only used prior to 2.3.0
* UnifyCR: update dependencies and build options
This adds some specifics about dependencies and conflicts and adds
additional build options and variants. UnifyCR now also has limited
fortran support.
* Remove debug statements condition on Spack debug
Change debug print statements to now be turned on when the -g cflag
is found in the flags the user sets.
* add new package: py-python-magic
* tidy up
* Update var/spack/repos/builtin/packages/py-python-magic/package.py
Co-Authored-By: Adam J. Stewart <ajstewart426@gmail.com>
* add master and dependencies
* remove gcc and make
* add variants, make doc and ch-grow dependencies optional
* capitalize description sentence
* move dependencies and variants below version block
* fix typos
* gromacs: fix simd detection for pre 2018 versions
* pre 2018 the cmake file was named differently
* fixed up post 2018 patch file which was non pretty
* Trim patch
* Create package.py
* applied reviewer suggestions
* Update package.py
* remove CamelCase from variant names
* add comment on why fetching package via git
* found typo in variant to cmake-argumentlist translation
* rename variants to ~nonuma ~nompi to be in sync with cmake-args, refine mpi@3-dependency definition
* Revert "rename variants to ~nonuma ~nompi to be in sync with cmake-args, refine mpi@3-dependency definition"
This reverts commit 58e8cf7d93c5665f0b4b50228946857734716cef.
* remove version-preference
* add checksum for singularity release 3.3.0
* update singularity doc URL
URL at the lbl.gov domain has message saying:
"This website is going away soon! Update your bookmarks!"
* add note about build log file for post-install step
* provide links to both 2.x and 3.x security docs
* remove whitespace. Passing flake8 confirmed locally this time :)
* add TODO comment for fakeroot support
The previous version does not properly install the required cmake
configuration files for blaze-lib, so find_package does not work
correctly.
This patch converts the blaze-lib package to use CMakePackage,
adds the required cmake dependency, and removes the install()
member function, which is not working correctly and is no longer
needed.
In a review of a previous pull request (
https://github.com/spack/spack/pull/10713 ) it was mentioned that the
proper way to figure out the target architecture is via
spec.architecture.target. This patch fixes this for the openblas
package.
Signed-off-by: Janne Blomqvist <janne.blomqvist@aalto.fi>
Not sure what happened between #5321 and now but the CC=CXX fix now
prevents py-matplotlib from building with the Intel compiler. I verified
with versions of py-matplotlib from 2.0.2 to 3.0.2 and intel-17.0.4 and
19.0.4 that py-matplotlib successfully builds with the Intel compiler
without that code.
* Add preCICE xSDK support
* Cleanup generation of cmake arguments
* Generalize numpy include
* Fix python spec
Co-Authored-By: Adam J. Stewart <ajstewart426@gmail.com>
* Fix numpy spec
Co-Authored-By: Adam J. Stewart <ajstewart426@gmail.com>
* hunspell: write autoreconf method to triage error
This commit fixes the error described in GitHub issue
`AutotoolsPackage` class attempts to call `libtoolize`, which doesn't
exist on macOS systems that externally install `libtool` in Spack via
Homebrew -- Homebrew installzes GNU libtoolize as `glibtoolize`.
The fix is to call `autoreconf` only, and GitHub pull request #12344
makes this change in
AutotoolsPackage (https://github.com/spack/spack/pull/12344). However,
while waiting for that pull request to be merged, overriding the
`autoreconf` method achieves the same result for a self-contained
fix. This self-contained fix is necessary to fix a dependency bug in
the `hunspell` package.
* hunspell: add missing gettext dependency
* hunspell: add version 1.7.0
* add new package cromwell
* fix flake8 errors, add cromwell-womtool package
* change name of cromwell to cromwell-server
* renamed cromwell-server to just cromwell
* update description to what is in the project docs
* fixing format call for python2.6 compatibility
* Add comment that 1.0.1 versions are no longer supported
* Add comment that 1.0.2 versions are only supported up to
December 2019
* Add versions 1.0.2s, 1.0.2r, and 1.0.2p
* Add versions 1.1.0k, 1.1.0j, and 1.1.0i
* Add version 1.1.1c
* Add comment that 1.1.0 versions are only supported up to
September 2019
Resolves#11932.
Move the PIC flags from CFLAGS on the configure line to the spack
compiler wrapper for ncurses. The problem with the configure line for
autotools is that specifying CFLAGS sets the entire flags, thus
deleting the flags that configure would add itself.
By default, if CFLAGS is unspecified, then configure picks a sensible
default of `-g -O2`. But adding `-fPIC` erases these and it ends up
building unoptimized.
* Add patch to detect newer versions of MacOS and to fix a typo in
configure.ac (AM_LIBTOOLSFLAGS should be AM_LIBTOOLFLAGS)
* Remove variant declarations for unsupported languages
* Add support for quartz on MacOS
* Add optional X Window support
* Specifically build against qt@4 when building QT support
* Point to appropriate C++ standard libraries when building with
Clang on MacOS
* Disable parallel build (for all platforms)
* Increase verbosity of configure script by adding
--disable-silent-rules
* Add numpy 1.17.0
* Overhaul numpy package
* Flake8 fixes
* Undefined reference fix
* HeaderList and LibraryList need an arg
* veclibfort has no headers
* Add patch for older versions of py-numpy
* Remove py-meep hack from py-numpy package
* libflame: always add max arg hack flag
* Fix build with GCC 4.8
* Compiler flags come from self.compiler
* Only apply -std=c99 to cflags
* Try to fix libflame package
* Fix ATLAS build on macOS
* --force-clang flag added in 3.10.3
When building with GCC, c-blosc requires the -std=gnu99 flag.
Before this patch, the build would only add -std=gnu99 for GCC when
building on specific architectures; this adds -std=gnu99 in all cases
when using GCC.
When loading `openpmd-api` as a lib to build outside of
spack or to build depending spack packages, the "CMake-PUBLIC"
header-only library MPark.Variant must be available. Also,
the `*Config.cmake` package must be able to find dependent
libs if used.
* new package: py-backports-tempfile
* Update var/spack/repos/builtin/packages/py-backports-tempfile/package.py
Co-Authored-By: Adam J. Stewart <ajstewart426@gmail.com>
* remove rc version
* fix single quote
* add new version, add sha256 sums
* Update var/spack/repos/builtin/packages/py-apipkg/package.py
Co-Authored-By: Adam J. Stewart <ajstewart426@gmail.com>
* add python dependencies
* new package: py-usgs
* Update var/spack/repos/builtin/packages/py-usgs/package.py
Co-Authored-By: Adam J. Stewart <ajstewart426@gmail.com>
* Update var/spack/repos/builtin/packages/py-usgs/package.py
Co-Authored-By: Adam J. Stewart <ajstewart426@gmail.com>
* new package: py-requests-futures
* Update var/spack/repos/builtin/packages/py-requests-futures/package.py
Co-Authored-By: Adam J. Stewart <ajstewart426@gmail.com>
* minimap2: remove py-mappy dependency and build on ARM
py-mappy: Change URL and new version.
* merge py-mappy to minimap2.
* 1. add type in depends_on.
2. remove unneeded which.
* Incorporate as a patch upstream commit 0c20dbf059 (diff-acb9169b4ccbac494ced5140d285a015) resolving problems with `-Wno-...` options not being understood by GCC.
* Incorporate as a patch upstream PR https://github.com/ericniebler/range-v3/pull/1202 fixing upstream issue https://github.com/ericniebler/range-v3/issues/1196.
* Compile tests only if we actually want to run them.
* Optionally compile documentation with a `+doc` variant.
* Add `+examples` and `+perf` variants to avoid unnecessary compilation of components usually not required for install.
* Add conditional build-only dependency on Boost when appropriate.
* Install docs, examples and performance tests if built (not part of upstream build instructions).
* Add @chissg as a maintainer.
- Update c-blosc to 1.17.0
- Add patch to build test_forksafe for versions 1.15.0 through 1.17.0
when compiled with the Intel compiler.
- Remove code that turned off building the test with the Intel compiler
1. xmmintrrin.h is included x86 only.
2. Add makefiles for non-x86 hosts.
3. mpicc in Makefiles is replaced spacks mpi compile command.
4. variant check is rewite with satisfies.
* Geant4 data packages: Set the install path name explicitly.
* Use the correct directory name for g4photonevaporation,g4radioactivedecay,g4realsurface
* Add versions 8.0.16, 5.7.26, and 5.6.44
* Update boost dependency for versions 8.0.16, 8.0.15, and 8.0.14
* Update dtrace script when building for versions before 8 as is done
for the glib package
* Set perl as a build dependency for versions before 8
* cxxstd=17 conflicts with version 8 when server code is built
(~client_only)
* Add -Wno-deprecated-declarations for cxxstd > 11
* Add -Wno-error=register for cxxstd > 14
This updates the Spack QT package to enable building qt version 4 on
MacOS.
This includes the following changes to the qt package:
* add version 4.8.7
* add option to build with or without shared libs
* add options to disable tools, ssl, sql, and freetype support
* add qt4-tools patch when building qt@4+tools
* add option to build as a framework (only available on MacOS)
* replace qt4-el-capitan patch with qt4-mac patch (which includes the
edits from qt4-el-capitan)
* apply qt4-pcre-include-conflict.patch only for version 4.8.6
(rather than all 4.x versions)
* apply qt4-gcc-and-webkit.patch for 4.x versions before 4.8.7 and
create a separate qt4-gcc-and-webkit-487.patch for version 4.8.7
* update patch function for qt@4 on MacOS to update configure
variables relevant to Spack (e.g. PREFIX)
* add option to build freetype with Spack, as a vendored dependency
of QT, or not at all (default is to build with Spack)
This includes the following edits outside of the qt package:
* Update MacOS version utility function to return all parts of the
Mac version (rather than just the first two)
* gettext package: implement "libs"
* python package: add gettext as a dependency
Fixes#12007.
The Cray cc wrappers don't handle the -s flag (strip) cleanly, It's
not essential to strip the binary, so just remove the flag on Cray.
Note: the default build on Cray is for the back end and the unzip
binary won't run on the front end. To build for FE, use something
like arch=cray-fe-x86_64.
* Add +shared variant, which builds shared library in addition to the
static library.
* Install libraries even when specifying the header-only option
(header-only is just about installing an additional folder).
* An additional make call is not required to build generator
executables (they are built by default).
* Streamlined help-line of each variant.
* Fix Mac platform check for dependency in py-ipython package: 'when'
constraints in Spack directives must be Specs (either a Spec
object or a Spec in string format)
* Fix Mac version check in py-numpy: platform.mac_ver() returns a
3-part string as its first tuple item so the check as written would
never pass; use Spack Version object to simplify check.
* Fix Mac version check in qt package (the check was incorrectly
comparing ints and strings) and use Spack version object to
simplify check.
* Add versions 4.3.0, 4.3.1, and 4.3.2
* The URL format changed after 4.1.4, so this adds a url_for_version
function to choose the URL format based on the version
With this PR, a user can designate older versions of OpenGL as an
external Spack package, and dependents can use that installation
as long as they do not have version requirements.
MacOS currently comes with OpenGL 2.1; there is currently no
'provides' directive in the OpenGL Spack package which specifies a
gl version provided for versions earlier than OpenGL 3.3, so earlier
versions of OpenGL are not considered to provide any version of gl.
This PR records that any version of OpenGL provides 'gl' (which is
sufficient for any package that does not require a specific version
of gl).
* Version 1.3.0 requires python 3.5 or later (no Python 2 support)
* Remove test of scipy.weave import (not available since 1.0)
* Add more-sensitive py-numpy constraints based on py-scipy version
* Replace py-nose dependency with py-pytest
* Add adamjstewart as maintainer
* Rename py-pytorch to py-torch
* Add versions 1.1.0 and 1.0.1
* Define modules to test import of after installation (import_modules)
* py-typing dependency is only needed for older versions of Python
(3.4 or before)
* Newer versions of py-torch depend on newer versions of CUDA
* Add adamjstewart as maintainer
* Remove libuuid dependency for python on Darwin
Python 2.7 includes Carbon, which requires a proprietary typedef defined in
the system `/usr/include/uuid/uuid.h`:
```
In file included from /rnsdhpc/code/spack/var/spack/stage/python-2.7.16-chgwvgls4ezgujsknn27vlmkhwbzpqik/Python-2.7.16/Python/mactoolboxglue.c:27:
In file included from /rnsdhpc/code/spack/var/spack/stage/python-2.7.16-chgwvgls4ezgujsknn27vlmkhwbzpqik/Python-2.7.16/Include/pymactoolbox.h:10:
In file included from /System/Library/Frameworks/Carbon.framework/Headers/Carbon.h:20:
In file included from /System/Library/Frameworks/CoreServices.framework/Headers/CoreServices.h:23:
In file included from /System/Library/Frameworks/CoreServices.framework/Frameworks/AE.framework/Headers/AE.h:20:
In file included from /System/Library/Frameworks/CoreServices.framework/Frameworks/CarbonCore.framework/Headers/CarbonCore.h:208:
In file included from /System/Library/Frameworks/CoreServices.framework/Frameworks/CarbonCore.framework/Headers/HFSVolumes.h:25:
/usr/include/hfs/hfs_format.h:794:2: error: unknown type name 'uuid_string_t'; did you mean 'io_string_t'?
```
Similarly, even with Python 3, having Spack's libuuid in the toolchain
causes matplotlib to fail to build downstream because its `osx` backend
links against Carbon:
```
building 'matplotlib.backends._macosx' extension
/rnsdhpc/code/spack/lib/spack/env/clang/clang -Wno-unused-result -Wsign-compare -Wunreachable-code -DNDEBUG -g -fwrapv -O3 -Wall -fPIC -I/usr/local/include -I/usr/X11/include -I/opt/X11/include -I. -I/rnsdhpc/code/spack/opt/spack/darwin-mojave-x86_64/clang-10.0.1-apple/python-3.7.2-bipx24oyxqxowqc75o5vfih7dljiaohz/include/python3.7m -c src/_macosx.m -o build/temp.macosx-10.14.5-x86_64-3.7/src/_macosx.o
In file included from src/_macosx.m:1:
In file included from /Applications/Xcode.app/Contents/Developer/Platforms/MacOSX.platform/Developer/SDKs/MacOSX10.14.sdk/System/Library/Frameworks/Cocoa.framework/Headers/Cocoa.h:12:
In file included from /Applications/Xcode.app/Contents/Developer/Platforms/MacOSX.platform/Developer/SDKs/MacOSX10.14.sdk/System/Library/Frameworks/Foundation.framework/Headers/Foundation.h:87:
In file included from /Applications/Xcode.app/Contents/Developer/Platforms/MacOSX.platform/Developer/SDKs/MacOSX10.14.sdk/System/Library/Frameworks/Foundation.framework/Headers/NSURLError.h:15:
In file included from /Applications/Xcode.app/Contents/Developer/Platforms/MacOSX.platform/Developer/SDKs/MacOSX10.14.sdk/System/Library/Frameworks/CoreServices.framework/Headers/CoreServices.h:24:
In file included from /Applications/Xcode.app/Contents/Developer/Platforms/MacOSX.platform/Developer/SDKs/MacOSX10.14.sdk/System/Library/Frameworks/CoreServices.framework/Frameworks/AE.framework/Headers/AE.h:20:
In file included from /Applications/Xcode.app/Contents/Developer/Platforms/MacOSX.platform/Developer/SDKs/MacOSX10.14.sdk/System/Library/Frameworks/CoreServices.framework/Frameworks/CarbonCore.framework/Headers/CarbonCore.h:208:
In file included from /Applications/Xcode.app/Contents/Developer/Platforms/MacOSX.platform/Developer/SDKs/MacOSX10.14.sdk/System/Library/Frameworks/CoreServices.framework/Frameworks/CarbonCore.framework/Headers/HFSVolumes.h:25:
/Applications/Xcode.app/Contents/Developer/Platforms/MacOSX.platform/Developer/SDKs/MacOSX10.14.sdk/usr/include/hfs/hfs_format.h:794:2: error: unknown type name 'uuid_string_t'; did you mean 'io_string_t'?
uuid_string_t ext_jnl_uuid;
^
/Applications/Xcode.app/Contents/Developer/Platforms/MacOSX.platform/Developer/SDKs/MacOSX10.14.sdk/usr/include/device/device_types.h:89:33: note: 'io_string_t' declared here
typedef char io_string_t[512];
```
MacOS version 10.14.5
Xcode 10.2.1
Apple LLVM version 10.0.1 (clang-1001.0.46.4)
* Mark libuuid as conflicting with Darwin due to framework
If Spack's libuuid is included by any other package that tests for or
requires the Cocoa or Carbon frameworks, the build will *fail* becuse it
appears that Apple's libraries require a special version of libuuid and
uuid.h.
```
In file included from /Applications/Xcode.app/Contents/Developer/Platforms/MacOSX.platform/Developer/SDKs/MacOSX10.14.sdk/System/Library/Frameworks/Cocoa.framework/Headers/Cocoa.h:12:
In file included from /Applications/Xcode.app/Contents/Developer/Platforms/MacOSX.platform/Developer/SDKs/MacOSX10.14.sdk/System/Library/Frameworks/Foundation.framework/Headers/Foundation.h:87:
In file included from /Applications/Xcode.app/Contents/Developer/Platforms/MacOSX.platform/Developer/SDKs/MacOSX10.14.sdk/System/Library/Frameworks/Foundation.framework/Headers/NSURLError.h:15:
In file included from /Applications/Xcode.app/Contents/Developer/Platforms/MacOSX.platform/Developer/SDKs/MacOSX10.14.sdk/System/Library/Frameworks/CoreServices.framework/Headers/CoreServices.h:24:
In file included from /Applications/Xcode.app/Contents/Developer/Platforms/MacOSX.platform/Developer/SDKs/MacOSX10.14.sdk/System/Library/Frameworks/CoreServices.framework/Frameworks/AE.framework/Headers/AE.h:20:
In file included from /Applications/Xcode.app/Contents/Developer/Platforms/MacOSX.platform/Developer/SDKs/MacOSX10.14.sdk/System/Library/Frameworks/CoreServices.framework/Frameworks/CarbonCore.framework/Headers/CarbonCore.h:208:
In file included from /Applications/Xcode.app/Contents/Developer/Platforms/MacOSX.platform/Developer/SDKs/MacOSX10.14.sdk/System/Library/Frameworks/CoreServices.framework/Frameworks/CarbonCore.framework/Headers/HFSVolumes.h:25:
/Applications/Xcode.app/Contents/Developer/Platforms/MacOSX.platform/Developer/SDKs/MacOSX10.14.sdk/usr/include/hfs/hfs_format.h:794:2: error: unknown type name 'uuid_string_t'; did you mean 'io_string_t'?
uuid_string_t ext_jnl_uuid;
^
/Applications/Xcode.app/Contents/Developer/Platforms/MacOSX.platform/Developer/SDKs/MacOSX10.14.sdk/usr/include/device/device_types.h:89:33: note: 'io_string_t' declared here
typedef char io_string_t[512];
```
* Revert "Mark libuuid as conflicting with Darwin due to framework"
This reverts commit 9a68b75202005fc265abe2033e4ad36312a9a34d.
* Document libuuid exception in python package
* update to kim-api-2.1.1 and openkim-models-2019-07-25
* openkim-models provide needed dependency constraints and settings
* add maintainers and fixup flake8 errors
* font-util: Remove duplicated dependencies.
* font-util: Fix path handling for font resources.
The "join_path" call made no sense but still managed to work somehow most of the times.
If +pthreads is specified, googletest actually gets build without
pthreads support and vice versa.
If pthreads is not available, googletest should detect it itself which
is why "enabling" pthreads in case of ~pthreads does not seem to cause
any error.
Change-Id: I29de8c4a23dc3901124b27a1ead3354949b7e65b
* xsdk: phist has a conflict with gcc version <= gcc-4.9.1 - so add a variant to disable it on older compiler builds
This is triggered by #11677
* fix typo
* Added a new package for LAME and a variant in sox for it.
* Fixed download url for LAME
* libmad: Added new package libmad for mp3 decoding. Changed sox variant from lame to mp3.
* libmad: Added m4 as a requirement
* libmad: Added comment on patch origins
* libmad: Added a list_url for alternate download location
* libmad: Fixing libmad download url
- We don't currently make enough use of the maintainers field on
packages, though we could use it to assign reviews.
- add a command that allows maintainers to be queried
- can ask who is maintaining a package or packages
- can ask what packages users are maintaining
- can list all maintained or unmaintained packages
- add tests for the command
* Add QMCPACK v. 3.8.0
* Remove QE variant conflict for serial QMCPACK installations.
* Add support for QE 6.4.1 converter.
* FindLibxml2QMC patch function only needed prior to QMCPACK 3.8.0
* ioapi: add version 3.2
* ioapi: unwrap version checksum; it's exempt from line length QA
* ioapi: drop overridden build(); it's the same as the default
* cmake: Move cxx11 flags for fujitsu into the flag_handler method
* cmake: sanitization and error checking in flag_handler
* cmake: Fix fujitsu flag check from 'fc' to 'fj'
* openjdk
* Removing preferred from latest and adding a few lines for readability.
* Remove bad whitesapce
* removing formatting changes
* stable url for openjdk 1.8
* remove extra blank line
* actual binary
Add version for 'gpu' and variant for 'cuda'. These are currently available from the 'master-gpu' branch.
* hpctoolkit: add version gpu and variant cuda
* The gcc >= 4.8.x requirement only applies for dyninst >= 10.x.
ibm-java: fix the URL to only use a machine type that ibm-java
supports so that 'spack info' doesn't report a non-existent URL on
platforms that it doesn't support.
* Fix scikit-learn build with Apple clang
* Update compiler unit tests
* Fix unit tests
* Fix OpenMP dep
* recursive=True no longer necessary
* Add myself as a maintainer
* Specify which versions require OpenMP
* Typo fixes
* LLVM-OpenMP is the correct dependency, no OMPT
* Flake8 fix
* Undo Apple Clang OpenMP flag change, split into a separate PR
Later versions of libjpeg-turbo build with CMake; to build with
user-specified cflags, the user must supply these to CMake as
-DCMAKE_C_FLAGS (Spack's typical approach of injecting these flags
into the compiler wrapper invocation is insufficient in this case).
Currently libjpeg-turbo cannot be implemented as a CMakePackage
(and thereby take advantage of the flag_handler implementation it
provides) because not all versions of libjpeg-turbo use CMake, so
this adds a custom implementation of flag_handler and
flags_to_build_system_args to libjpeg-turbo.
* cmake: change c++ spec when building with Fujitsu compiler.
* cmake: define cxxflags using a Fujitsu compiler's method.
* cmake: Add condition of whether to add cxx11 option.
It seems that GitHub's output changed slightly for this patch (one more
letter for both short hashes on the index line), probably due to the
number of objects in the repository.
This PR adds the ability to specify the auto-dispatch targets that can
be used by the Intel compilers. The `-ax` flag will be written to the
respective compiler configuration files. This ability is very handy when
wanting to build optimized builds for various architectures. This PR
does not set any optimization flags, however.
The default library search for a package checks the lib/ and lib64/
directories for libraries before the root prefix, in order to save
time when searching for libraries provided by externals (which e.g.
may have '/usr/' as their root).
This moves that logic into the "find_libraries" utility method so
packages implementing their own custom library search logic can
benefit from it.
This also updates packages which appear to be replicating this logic
exactly, replacing it with a single call to "find_libraries".
This PR has several modifications for the r package.
- The tk package is always depended on but this pulls in X11, making the
'X' variant non-functional. This PR sets a dependency of tk on '+X'.
- There is a missing dependency on libxmu when '+X' is set.
- The libraries for R wind up in a non-standard location and are thus
left out of the RPATH settings. This PR adds that directory to RPATH.
- The MKL integer interface for gfortran is not in the BLAS libs. This
PR replaces the intel interface with the gfortran interface if needed.
- Use the `LibraryList` `ld_flags` method for blas as that is more in
line with th R Installation and Administration manual.
Note that this PR depends on PR #11956. This PR closes#8642.
TK can be built with support for libXft and X Screensaver. Both of these
are turned on in the Tk configure script. That means the system
libraries will get picked up if they are on the system and nothing is
specified in the package. Since the default for both of them is 'True' I
set the default value for the variants to 'True'.
* bowtie2: Add version 2.5.3.1 and fix to build on ARM
1. Add version 2.5.3.1.
2. Add simde for ARM.
3. Disable -fopenmp-simd when gcc 4.8.X or before for ARM.
4. Add Makefile option POPCNT_CAPABILITY=0 for ARM.
* flake8.
Fixes#11781
* Rename build log to spack-build-log.txt
* Rename environment variables file to spack-build-env.txt
* The name of the log and env files is now the same during the build
and after the build completes
* Update packages which referred to the build log/env files
* For packages installed before this commit using older names for the
build and env files, search for the older names
* ferret: use libx11 from spack
* ferret: use mpi library with or without fortran support
* ferret: add version 7.2
* ferret: no need to specify ~mpi
* ferret: creating symlinks may fail for external packages; set include/lib paths instead
* use autoreconf to regenerate configure script and config.guess for
newer architectures
* Add perl build dependency for older versions. The required perl
version is constrained because the perl script uses syntax that
is deprecated in older versions
Declare a conflict for TAU versions older than 2.28.1, that they
can't depend on libelf or libdwarf. The user can still install it
by specifying tau@2.24~libelf~libdwarf.
* py-antlr4-python3-runtime: new package
* py-antlr4-python3-runtime: fix for flake8
* py-antlr4-python3-runtime: indent docstring
* py-antlr4-python3-runtime: clarify role of this package vs ANTLR in docstring
* py-antlr4-python3-runtime: remove whitespace at end of line
The py-reportlab package includes binaries for easy_install and pip.
That blocks activation if py-setuptools and/or py-pip are installed.
This PR block the binaries from py-reportlab as easy_install and pip
should be installed with their respective packages.
* py-cf-units: new package
* py-cf-units: download from pypi.io
* py-cf-units: include py-pytest-runner as build dep
* py-cf-units: remove empty build_args function
* py-cf-units: fix for flake8
* py-cf-units: indent docstring
* py-cf-units: remove excess spaces
* py-cf-units: list master branch ahead of numeric versions
* py-cf-units: remove extension keyword from version
If R is provided by the system with a module (i.e. registered in
packages.yaml with a "module" entry) and has no discernible prefix,
this allows turbine to still make use of R.
This PR corrects a problem with the opa-psm2 package. It was
installing headers into <prefix>/usr/include and libraries into
<prefix>/usr/lib instead of <prefix>/include and <prefix>/lib.
The extra level of usr/ subdirectories causes dependent packages
like libfabric to fail to build.
The original packaging, with openfoam as a virtual and with
openfoam-com, openfoam-org and openfoam-extend as
providers, adds an obfuscation layer without any benefit.
- Rename `openfoam-com` to `openfoam`, and remove the
`openfoam` virtual package.
- `parse_anonymous_spec()` is a vestige of the days when Spack didn't
support nameless specs. We don't need it anymore because now we can
write Spec() for a spec that will match anything, and satisfies()
semantics work properly for anonymous specs.
- Delete `parse_anonymous_spec()` and replace its uses with simple calls
to the Spec() constructor.
- make then handling of when='...' specs in directives more consistent.
- clean up Spec.__contains__()
- refactor directives and tests slightly to accommodate the change.
Added a wrapperrpath variant to mpich that defaults to `True`.
Users can set this to `False` (e.g., spack install mpich~wrapperrpath) to
disable the wrapper RPATHs. This makes it easier to replacing an MPICH
installation in a container with an MPICH for the host system,
e.g., Cray MPICH with Shifter on Cori, Intel MPI, MVAPICH2, etc.
Co-authored-by: Todd Gamblin <tgamblin@llnl.gov>
The version of LLVM used by flang is new enough that CppBackend doesn't exist. Unfortunately, `flang-xxxxxxxx` is seen as < `3.9.0` by the version check.
* add a special case for `flang` versions.
* OpenFOAM: rationalize architecture options
- older versions of OpenFOAM had WM_ARCH_OPTION to choose a 32-bit
build on 64-bit architectures. This is not exactly relevant anymore
and has now been largely removed from OpenFOAM.
- simultaneously the newest version of OpenFOAM has rationalized the
handling of special settings for KNL by rolling these into the
compiler options. We now do the same thing here in spack.
1. Reuse the internal variable arch_option to convey processor-specific
optimizations and add these into the C++OPT=... statement.
2. Drop spack support for configuring a 32-bit build on 64-bit
hardware.
These changes can also be applied to older OpenFOAM versions, and to
various OpenFOAM forks without issue.
* update openfoam versions. New release 1906, patched 1812 version.
ncl does not build with newer versions of gdal (or rather proj). This
also needs a small change to gdal, otherwise we end up with both proj@5
and proj@6 in the spec.
* Remove individual font-* packages and add them as resources of the
font-util package
* Update font-util package to Autotools-based package, and call
autoreconf to regenerate the old configure script
* Add font-adobe-utopia-type1
* fmt: Add cxxstd variant, plus cmake/c++ patches
Spack supported versions of fmt default to C++11 for versions
less than 5, C++14 greater than 5, with fmt implementing
fallbacks to whatever compiler supports.
To give better ABI compatibility and use of newer standards, provide
a `cxxstd` variant defaulting to 11 with 98-17 options. Use cmake_args
to set CMAKE_CXX_STANDARD as appropriate, plus use of `FMT_USE_CPP11`
option for C++98 builds. Use `conflicts` to disable use of certain
standards in versions that don't support, or fail the build, with
those standards.
Add patches to unify use of `CMAKE_CXX_STANDARD` in 3.0 versions,
remove hard-coding of compiler flags in `fmt-config.cmake`, and
prevent use of C++11 features in 4.1.0 when in supported C++98
mode.
Default to not building documents as no dependency on Doxygen is
yet present, and they are not part of the "all" build.
* Use CMake to enforce C++ standard support
Fail configure step if fmt tries to build with a cxxstd variant
not supported by the compiler (or known to CMake).
* fmt: New version 5.3.0
* The py-pytables package depends on hdf5-blosc
* Further modifications to py-pytables package
The 3.2.2 version of py-pytables should still build with internal blosc.
The issue with locking in a multithreaded environment has been
fixed/worked around in version 3.3.
Also, add bzip2 and lzo variants.
* new package/py-blessed
* make flake8 happy
* fix docstring
* tab to spaces
* Update var/spack/repos/builtin/packages/py-blessed/package.py
specify dependency version.
Co-Authored-By: Adam J. Stewart <ajstewart426@gmail.com>
* Update var/spack/repos/builtin/packages/py-blessed/package.py
specify dependency version
Co-Authored-By: Adam J. Stewart <ajstewart426@gmail.com>
* add setuptools as depedency
Starting with 1.69.0, boost added a bjam option for the default symbol
visibility. Up to 1.68.0, the value was always 'global'. 1.69.0
changed the default to 'hidden' but added an option.
Most packages will work with hidden and won't notice. But some
packages may discover that an interface that they rely on is now
hidden and inaccessible.
https://boostorg.github.io/build/manual/develop/index.html#bbv2.builtin.features.visibility
For resources, it is desirable to use the expanded archive name of
the resource as the name of the directory when adding it to the root
staging area.
#11528 established 'spack-src' as the universal directory where
source files are placed, which also affected the behavior of
resources managed with Stages.
This adds a new property ('srcdir') to Stage to remember the name of
the expanded source directory, and uses this as the default name when
placing a resource directory in the root staging area.
This also:
* Ensures that downloaded sources are archived using the expanded
archive name (otherwise Spack will not be able to determine the
original directory name when using a cached archive).
* Updates working_dir context manager to guarantee restoration of
original working directory when an exception occurs
* Adds a "temp_cwd" context manager which creates a temporary
directory and sets it as the working directory
Starting with 2.1.0, backports.functools_lru_cache replaces functools32
when using python 2.7.x until python2 support is dropped in 3.0.0.
Change-Id: I8db61eac975da0042f6f5babe0f5f0c92807200e
Fixes#11526
The xfd configure script tests for libintl but incorrectly concludes
that no additional library is needed because gettext is provided in
libc. So we add '-lintl' to ldlibs to point to the Spack-installed
gettext. Note that the xfd configure script does not have a
--with-gettext option to do this for us.
Also add version 1.1.3
* xtensor-python: add version 0.23.1
* xtensor-python: update xtensor/xtl dependency version constraints
for 0.23.1
* xtensor-python: remove xtensor/xtl dependency version constraints
for the develop version to favor the latest (develop) version of
these dependencies
* xsimd: add version 7.2.3
* xtensor: add tbb variant to enable TBB parallelization
* xtensor: add version 0.20.7
* xtensor: update CMake args enable xsimd/tbb support based on
variant settings
* xtl: add version 0.6.4
* Added Cinch Spackage and updated Flecsi to Use It
Added spackage for Cinch build system and updated flecsi spackage to use
the external version of cinch
* Flake8 compliance for Cinch and Flecsi
* Fixed Cinch Issue and Requested PR Changes
Swapped cinch back to master branch rather than test branch and style
issues for PR
repeatmasker depended on HMMER but was never actually configured to
use it. The package also had many shebangs pointing to random perl
locations, now patched to use Spack's perl installation.
* Also add version 0.10.0
* Add leading '0' to 0.9.x versions (e.g. 0.09.1) and 0.8.x versions
* Don't mention acts-framework, that package isn't in Spack yet
* Updates to libMesh: added v1.3.1 checksum, added vtk variant, bugfix for enabling petsc when slepc variant is specified
* fixed indentation issues identified by Travis CI
* - updates version number
- added master as a version
- added new variant options for perflog, metaphysicl and blocked storage
-- bug-fix for metis
* fixes for spack indentation errors
* renaming develop to master following review comment of PR.
- A program that generates ASCII pictures of a cow with a message.
- This is used by the ISC19 Singularity tutorial, so we should probably
have it in Spack.
* new package: mutationpp
* Update package.py
* flake8: correct package.py for flake8-python-style
* Update package.py
* modifications as requested by reviewer for #11705
Change 'destination' to 'placement' in the use of resource() for
intel-xed and hpcviewer. Recent commits (1842873f and eb584d89)
changed the directory path for a resource and thus broke the build
for these packages.
#11528 updated Stage to always store a Package's source in a fixed
directory accessible via `Stage.source_path` This left behind a
number of packages which were expecting to access the source code
via `Stage.path`. This Updates those packages to use
`Stage.source_path` instead.
This also updates the name of the fixed directory: The original name
of the fixed directory was "src", so if an expanded archive created a
"src" directory, then users inspecting the directory structure could
see paths like "src/src" (which wasn't wrong but could be confusing).
Therefore this also updates the name of the fixed directory to
"spack-src".
* warpx: only allow master branch, and fix build on darwin
* warpx: Added CXXFLAGS=-std=c++11 for clang
* warpx: further clean up of openmp and c++11 flags
* warpx: Get around the problem with resources
The update uses placement instead of destination
Fixed logic behind flecsi backends to not require legion for an mpi
build and to better support required combinations.
Also made graphviz support and tutorial building optional
* Paraview/VTK: Fix failure on intel builds
Paraview@5.6.0 fails to build with intel compilers on certain platforms.
Error messages have been traced to the optional MotionFX lib.
(see https://discourse.paraview.org/t/error-build-5-6-0-rc1/572)
Turning off motionfx allows for succesful builds on these platforms.
ADIOS2 is the latest implementation of the ADaptable Input Output System,
ADIOS. This brand new architecture was designed to continue supporting the
performance legacy of ADIOS, and extend its current capabilities to address
current and future input/output (IO) challenges in the scientific data
lifecycle through effective research and development (R&D) activities.
ADIOS2 was recently added as a Third Party Library of Trilinos when it
was integrated to IOSS, a library inside the SEACAS package.
Due to the large number of issues this migration has caused, this rolls back
to the older autotools build. However, it still keeps the updates wrt
variants and virtual packages.
* Apply patch to git to make it search for config files from its current location instead of the locations hard coded at install.
* Add provenance info for patch
* Pass needed flags to make
* Environment variables need because of relocation
* Updating the TAU package with 2.28 and public repo
* Cleaning up TAU package and fixing binutils to install extras
The extras variant will install the extra ELF headers needed
by the TAU package. The TAU package has been cleaned up and
extended.
* Adding some comments to the changes in binutils
* Adding correct python support, finding include and lib paths.
* Added PDT 3.25.1.
* Added TAU v2.28.1 with libdwarf and libelf.
* When +libdwarf is activated, +libelf is not automatically activated. It checks separately for libelf.
* Xrootd: set PYTHON_EXECUTABLE with +python variant
When building with python3 PYTHON_EXECUTABLE needs to be set for deprecated FindPythonInterp to work as expected.
* Add comment
* Flake8
* More flake8
* Update package.py
* typo
* Also add versions 0.9.9.104, 0.9.9.52, 0.9.9.0, and 'develop'
* Replace version 0.9.7 with 0.9.7.0
* Update Rose to be an Autotools package
* Update boost dependency to 1.60.0 or later (previously 1.47.0)
* Add EDG binary identifiers for ROSE versions installing from
archives (rather than git)
* Add variants for mvapich2 backend, c++11, debug symbols,
optimization, and ROSE-based projects (codethorn, autopar, and
polyopt)
* Remove patch add_spack_compiler_recognition
* Improve C++ standard computation in ACTS package
* Use a more clever strategy for aligning ACTS cxxstd with ROOT cxxstd
* Add new ACTS releases
* ACTS is not compatible with the new Boost CMake build system yet
* Explain why Boost 1.70 does not work currently
* Add LSF package, which cannot be installed by Spack and must be
system-installed. The package install will fail if no external
LSF is registered in packages.yaml (LSF may not be installed in a
well-known location and the external entry helps Spack locate it
for dependents).
* Add LSF dependency to OpenMPI when schedulers=lsf is chosen
Previously, the vtkm package was adding a "../" option to the
cmake command line. I suppose this was supposed to be pointing
to the source code, but did not. Rather, Spack correctly adds
the source directory as the first argument to cmake. However,
because ../ was added, it used that as the source directory
instead.
Simply remove this argument to make CMake work correctly.
* bump eospac version
* Revert "bump eospac version"
This reverts commit 835b1f822d8c083f6ab9eb17222c00409e8eb3da.
* Add support for new package: unittest-cpp
Add variant 'pic' for including in shared libraries.
Add build dependency on perl. Compiling mbedtls runs several perl
scripts.
Add versions 2.7.10 and 2.16.1, the heads of the two main stable
branches.
This PR implements several refactors requested in #11373, specifically:
- Config scopes are used to handle builtin defaults, command line overrides
and package overrides (`parallel=False`)
- `Package.make_jobs` attribute has been removed; `make_jobs` remains
as a module-scope variable in the build environment.
- The use of the argument `-j` has been rationalized across commands
- move '-j'/'--jobs' argument into `spack.cmd.common.arguments`
- Add unit tests to check that setting parallel jobs works as expected
- add new test to ensure that build job setting is isolated to each build
- Fix packages that used `Package.make_jobs` (i.e. `bazel`)
* When fabrics=auto or schedulers=auto, the intent is to defer to the
OpenMPI configure and let it determine and use what it finds
available on the system. The current behavior for 'with_or_without'
in the case of 'auto' explicitly disables all possible values.
This updates the logic to call 'with_or_without' only when the
value of fabrics/schedulers is not 'auto'.
* To allow explicitly disabling all fabrics/schedulers, each of these
variants has added support for 'none' (which is also the default
value).
* Add a conflict for the loadleveler scheduler for openmpi-3 and
above as it is no longer a valid configure option.
* Update optional-lite and span-lite to use CMakePackage
These packages only have CMake installs on their most recent versions.
Therefore, we overload all of the CMake stages to fallback to the old
versions (no-op for most, copytree for install), and use CMakePackage on
the new versions.
* Add new string-view-lite version with CMake install support
* Only override phases for old versions of *-lite packages
* trilinos: add variant to disable chaco from seacas
keep it OFF by default due to the presence of the global symbol "divide"
that can lead to symbol clash with other libraries, for example see
https://github.com/dealii/dealii/issues/8170#issuecomment-492700787
* dealii: add conflict statement for adol-c and Trilinos SEACAS Chaco
* dyninst: rework the cmake args for version 10.1 and later
Add a separate when() case for the cmake args for Dyninst 10.1.0 and
later. The prereq args have changed enough that this makes things
easier going forward. (My previous commit 26b9369c was inaccurate and
temporary.)
Dyninst 10.1.0 accepts boost 1.70, but earlier dyninst are restricted
to <= 1.69 (not worth back porting every boost change).
Change all the dyninst versions to 3 digits for clarity and
consistency.
* Add version 10.1.0.
* added patch for intel-tbb@2019.1: with old compilers
* sparately specify when @:2018 and @2019
the reason we can't say @:2019 is that would include @2019.1 where the
patch doesn't work.
* should be possible to list when constraint as @:2019
According to my reading of ["Version ranges" in the Spack
docs](https://spack.readthedocs.io/en/latest/packaging_guide.html#version-ranges),
this should apply to up to `2019` but not `2019.1:`
* @:2019.0 appears to be necessary to specify 2019 but not 2019.1
* specifying 2019.1 2019.2 2019.3 2019.4 separately and explcitly
* flake8 fixes for long lines.
* add comments to explain why so many different patch directives
* remove blank like for flake8
* revert spec %gcc@4.8.0:4.99999 -> %gcc@4.8.0:
- CMake is built *very* frequently, and the number of dependencies it has
accumulated can take a very long time on some systems.
- Use +ownlibs by default to avoid the build overhead. This won't
interfere with other packages by introducing conflicting libraries, as
CMake is nearly always a build dependency.
This avoids using Boost 1.70.0, fixes library access in OpenSpeedShop
packages, adds new versions, and updates QT dependency constraints
in CBTF and OpenSpeedShop packages
- Constrain Boost dependency to 1.69.0 or earlier to avoid issues
with 1.70.0 for Open|SpeedShop and CBTF packages
- Update DYNINSTAPI_RT_LIB environment variable to use single library
from "find_libraries" (which returns a list) in OpenSpeedShop
packages
Fixes#11443
- Add version 1.9.3 for CBTF Argo Navis, CBTF Krell, CBTF LANL, and
CBTF packages
- Add version 2.4.1 for OpenSpeedShop Utils and OpenSpeedShop
packages
- Update QT dependency to 5.10.0 or greater for QtGraph and CBTF Argo
Navis packages
This makes several changes to make CDO work with gcc@9:
- Add version 1.9.7rc2
- Add a patch to make version 1.9.7rc2 build with gcc@9:
- Add a conflict with GCC 9 for earlier versions of CDO
It also adds a pkgconfig build dependency as configure checks for it.
* recon: new package at 1.08
* recon: add period
* recon: use proper decorators, better documentation
* recon: fix incorrect os import
* recon: add repeatmasker patch as variant
The source is managed as a set of files in an FTP URL. Since there
are no FetchStrategy's implemented for this setup, the files are
managed as a set of Resource's
Add dependencies to CMake and GnuTLS which would otherwise be
picked up from the system
* Add gnutls as explicit dependency of CMake
* Add new package libidn2 as explicit dependency for gnutls
* LBANN: add python dependency and required python library dependencies
* LBANN: add version 0.99 as alias for develop branch
* LBANN: build Conduit library by default
* LBANN: CUB is included with Hydrogen for later versions
* New package: py-graphviz (dependency for LBANN)
* New package: py-texttable (dependency for LBANN)
* New package: py-onnx (dependency for LBANN)
* New package: py-typing-extensions (dependency for py-onnx)
* Conduit: add version 0.4.0
* NCCL: Add versions 2.4.6-1 and 2.4.2-1
* Protobuf: Add versions 3.7.1 and 3.7.0
* py-protobuf: add version 3.7.1
* py-typing: add version 3.6.4
* cuDNN: add versions. The source differs depending on the
architecture, so the versions include a suffix to encode this.
For example this adds 7.5.1-10.1-x86_64 as well as
7.5.1-10.1-ppc64le
* cuDNN: Newer versions require newer versions of CUDA
* Hydrogen: add configure options for CUB and Aluminum
The --enable-relax-coord-bound option was added in 1.8.0. NetCDF
4.6.3 enabled relax coords by default and required it from PNetCDF.
PNetCDF 1.10.0 enabled it by default but for versions between 1.8.0
and 1.10.0 it should be enabled explicitly.
* megadock: new package at 4.0.3
* megadock: remove CudaPackage redundancies
* megadock: move env vars to build targets, use cuda_arch variant
* megadock: flake8 fixes, more flexible mathlib
* Fix py-yt for Python 2 by requesting older py-ipython version.
* Add conflicts statement to py-ipython because version 7: is not
compatible with python@2.7
f242f5f removed spec.architecture.platform_os, which was used to test
an option in the 'm4' package. The attribute is now accessed as
'spec.architecture.os'.
* Add versions 3.27.{0,1,2} and 3.28.0
* Add url_for_version: the URL format includes the year so this
function maps version ranges to years
* Restore patches for versions removed in 84c547c: this commit
removed versions before 3.26.0 due to a security issue with FTS
support. Add a +fts variant (default true) that enables FTS
support along with a conflict for +fts with earlier versions.
* Starting with the upcoming 10.1 release, Dyninst changed the names of
some cmake args to camel case: LIBELF_* to LibElf_* and LIBDWARF_* to
LibDwarf_*. This change is needed now for @develop and will be used
for 10.1 when it is released.
* New versions of Dyninst now requires cmake version 3.4.0 or later.
* Restrict boost dependency version to < 1.70.0 to avoid build error
+ The additional patch enables a non-optimized random123 code path that will
work on ARM architectures. This solution is provided only for version 1.09 to
allow the most current version of Random123 to function on ARM architectures.
+ A more complete, long term solution will be the addition of a native ARM
intrinsics-based implementation of random123. This solution is being worked
on but it is several weeks or months away. Once the full implementation is
available it will be provided to the author/maintainer of Random123.
The default install for llvm should just be the common typical case, i.e.
support for local host and cpu architectures. Enablingsupport for the wide
array of auxiliary architectures should be explicit rather than implicit.
* Mesa should depend_on('glproto')
The mesa package refers to `GL/glproto.h`. On systems that don't have
the OS packages installed, this leads to failures during the build
[e.g. this comment in
01482](https://github.com/spack/spack/pull/10482#issuecomment-488786745).
This fixes it. Tested on a minimally provisioned CentOS 7.
* Constrain glproto prereq to when +glx
* mesa: make glproto a build only dep
* The 'mkl' variant implementation was not complete and was
preventing the package from building, so remove it.
* The slate.hh file has moved in the 'develop' version (which is
currently the only version of SLATE listed)
* FAODEL: Add FAODEL package to spack
FAODEL (Flexible, Asynchronous, Object Data-Exchange Libraries) is a collection
of software libraries that are used to implement different data management
services on high-performance computing (HPC) platforms. This project is part of
the Advanced Technology Development and Mitigation (ATDM) effort for NNSA's ASC
program at Sandia National Laboratories.
(cherry picked from commit 6afe045d25b5c000b612116a5695aebbec56b61a)
* FAODEL: Update FAODEL package
Dependencies: set minimum versions for boost, cmake and libfabric
Dependencies: add conflict for boost v1.59.0
Patch: add a patch for v1.1803.1
Patch: add a when= for the v1.1811.1 specific patches
Compiler: check for C++11 support in gcc
(cherry picked from commit fb6ed2b3cf20d7e4fff647cba5a70887a78f627f)
* FAODEL: Update FAODEL package
* replace previous maintainers with @tkordenbrock and @craigulmer
* default to shared libs to meet Spack policy
* increase min boost version to 1.60.0 and remove boost 1.59.0 conflict
* replace complex version check with conflict for gcc <= 4.8.0 (C++11 support required)
* set type=build for cmake
* enable googletest for all versions with type=build
* enable tests for for all versions except when MPI is disabled
* FAODEL: Update FAODEL package
* add version v1.1811.2
* limit comment line length
* arm-forge: add all available versions
* Add TODO for the version hell
* Fix linting
Looks like 'black' formatter isn't Spack friendly
* Fix versions ordering
* Remove obsolete package (allinea-forge → arm-forge)
* Set mpi compiler wrappers using CC/etc. variables as recommended
at https://spack.readthedocs.io/en/latest/packaging_guide.html#compiler-wrappers
rather than setting CMake variables like -DCMAKE_C_COMPILER
* Use convenience functionality provided by inherited CMakePackage to
export all compiler flags as CMake options
* Remove old Singularity versions, add version 3.1.1
* Recent versions of Singularity build with go rather than autotools:
update dependencies and build logic
* Move old Singularity versions to new singularity-legacy package
which uses the autotools build system
* Some binaries built by Singularity need to be run as root: include
a script that the user can run after the Spack Singularity install
to change these permissions.
* The Singularity go build expects to work with a custom stage
directory relative to GOPATH: override the stage phase to create
this expected path.
* Update Singularity install config to point to Spack-installed
makesquashfs dependency
Based on the LLVM documentation [1], Python is used to run the automated
test suite. Therefore is it always a dependency for LLVM. However, if
build without Python (~python), we limit it to a build time dependency.
Note that py-lit is not added as a spack dependency even though it is
available as a spack package. This is because it is already included
in llvm and llvm is difficult to configure using an external py-lit
(several CMake variables to set correctly). Additionally, having
py-lit as a spack dependency adds Python as a runtime dependency
for llvm even though it is not required at runtime.
[1] https://llvm.org/docs/GettingStarted.html#requirements
* extend Version class so that 2.0 > 1.develop > 1.1
* add concretization tests, with preferences and preferred version.
* add master, head, trunk as develop-like versions, develop > master > head > trunk
* update documentation on version comparison
* Version 1.0.0 was released and the master branch tracks the
latest release.
* Multiple issues with MacOS have been fixed. The static patch is
now unneeded.
* Add support for building Ginkgo with the full Block Jacobi
performance (compilation takes a long time).
* Do not build anything which is not useful for the installation.
Namely, documentation, benchmarks, examples and tests.
* mesa: re-writen to new meson build system
* xorg-server: Remove unneeded mesa dependency
* glx: provide the virtual GLX package
* Convert most "mesa" dependencies to use virtual gl and glx dependencies
* mesa: Switch to always building from the git repo instead of a tarball
* Use gl and glx version ranges instead of exact versions
* glx: provide a default package
* add auto to swr variant
* Revert "add auto to swr variant"
This reverts commit 2e7cd8a8aca07767c00657d0d09985ddd6306883.
* update mesa package to version 19.0
* set +glx by default only when running on linux
* fix style issues in geant4 package
* remove virtual package "egl"
margo package is a required dependency for unifycr but the package
was not available in spack. margo requires a recent version of argobots
that has the ABT_SCHED_BASIC_WAIT scheduler (rc1 does while previously
available versions of this package in spack did not have it).
Kahip does not build with clang (conflicts('%clang') in kahip package.
Because of this, openfoam-com %clang fails concretization. Therefore,
this changes the default openfoam-com variant for kahip to False.
* 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
* Add versions 3.4.4 through 4.1.0 and 4.1.0-openvino
* Add conflict for gcc version >= 7 when building with +cuda
* Later version of protobuf is required for later versions of OpenCV
* Explicitly remove protobuf dependency with CMake option when not
building with +dnn
* root: new versions, variants and patches to bring in to line with FNAL's use.
* Support MySQL.
* Patches:
* Bigger stringbuf.
* Find MySQL even when it's called mariadb-c-client.
* Honor external provision of unuran.
* Properly handle the ROOT7 web GUI for 6.16/00.
* `memstat` variant is now default-OFF due to version-related constraints.
* Add missing dependencies.
* Propagate `python` to `libxml2`.
* Handle external FTGL dependency with X / OpenGL: depends on PR ####
* Force `SPACK_INCLUDE_DIRS` to avoid warning.
* New `gminimal` variant default ON per discussion with Javier Cervantes.
* Style fixes per flake8.
* Remove redundant `PATH_SUFFIX` per https://github.com/root-project/root/pull/1993#discussion_r276840329
* Comment patches per https://github.com/spack/spack/pull/11215#discussion_r276887199.
* Reflect the fact that MariaDB support patch is now upstream.
* Restore ncurses dependency for libtinfo.
Add zlib dependency to squashfs
On my CentOS system it was getting linked in (from Spack, no less)
fortuitously.
On a minimal Ubuntu system it failed until it was added as an explicit
dependency.
* ftgl: update to 2.1.3-rc5.
This updates to the last release (from 2008) with patches required to work with Spack and Root.
* Working 2.1.2 with/without docs, 2.1.3-rc5 without.
Allow specifying whether AVX2 or AVX512 should be enabled or disabled
on x86 targets.
As AVX2 hardware and toolchain support is quite ubiquitous by now,
AVX2 is enabled by default. Also AVX2 support is not disabled when
building the +virtual_machine variant.
AVX512 is not supported in older but still supported toolchains,
hardware is still expensive, and OpenBLAS AVX512 kernels still have
bugs. Thus AVX512 is disabled by default.
* Add Mercury version 1.0.1
* Remove cci and bmi dependency requirements: these are not currently
defined in Spack. If +bmi is enabled, the effect is that it may
use a system install of bmi
* Add a note that fabtests is deprecated and has been folded into the
libfabric package. Add the fabtests resource to the libfabric
package
* Add CMake option settings to Mercury based on variant settings
* Mercury: Set OFI testing protocol depending on how libfabric was
built
* Mercury: add version constraints to dependencies
Fixes#11226
MySQL 5.7.X and Boost 1.59.0 have a closer relationship than
MySQL >= 8.0 and their corresponding Boost versions: 5.7.X needs to
link against boost libraries which is indicated by marking boost as
a link dependency (removing the 'type' reverts to the default, which
includes link and build).
Starting with version 7.64.0, curl skips cookies specified with "-H"
(generic custom header specification) when following redirects, which
causes the "accept-license"-cookie for jdk to disappear. The result
is that jdk fails to download. This uses the "-b" option (which is
used specifically for configuring cookies) instead, which is more
permissive.
spec['dep'].libs.ld_flags can return system paths in some cases.
This is a targeted fix for the petsc package when retrieving
suite-sparse dependency libraries.
* added latest versions + malloc variant
* added a variant to activate different instrumentations
* added a variant to activate or not networking
* added a variant to activate or not cuda and tools
* enforce c++ standard and make it consistent with boost
* cflags and cxxflags from packages.yaml need to be passed into QMCPACK's CMake explictly for now.
* You need the ifcore library from the Intel compler to be manually linked in when you linked against a LAPACK provider that is not MKL.
* Update spec format to simpler syntax, maintain backwards compatibility
* Switch to new spec.format method throughout internals
* update package files for new format strings
* documentation and minor code cleanup. removed nonsensical variant sigils
* Initial commit for v2.0 of the CEED software suite.
* Update Nek packages and gslib
* Help spack concretize the hypre version for ceed-2.0.
* Fix nekcem install error
* Add support for gfortran v8 in nek5000 and nekcem.
* Split Nek5000 into Nek5000 and Nektools
* Get Nektools to build fine in Theta
* Fix travis failure: remove unused 'import numbers' from nek5000.
* Check for gfortran if it is wrapped
* Tweak the detection of gfortran in nek5000.
* Fix Nek packages to add -std=legacy when FC=gcc
* spack install ceed~petsc works fine on Theta
* Fix flake8 errors
* Fix more flake8 tests
* Fix an import issue
* Tweak the suite-sparse package to avoid interaction with existing system
installations of suite-sparse.
* petsc: update superlu-dist dependency
* Updates in the packages: occa, libceed, and ceed.
* In the libceed package, explicitly tell nvcc which host compiler to use.
* Fix python formatting.
* Simplify the test for gfortran in nek* packages.
* ceed: 2.0 uses petsc@3.11.0
* hpgmg-0.4; use from ceed@2.0.0
* Update the hypre dependency for ceed 2.0.
* Disable the superlu-dist dependency (through hypre) when using a
+quickbuild of ceed 2.0.
* petsc-3.11.0: add xlf fix
* nekcem: has a build dependency on Python 2.7+
* hpgmg: better setting of compiler options and use python for configure
* libceed: use v0.4 tag
* libceed: fix 0.4 release oops (pkgconfig version)
* Add a patch for magma-2.5.0 that brings it up the current 'master'.
* In the mfem package, install the examples, miniapps, and data under
$prefix/share/mfem.
* In the magma package, apply a patch to v2.5.0 that disables
magma_sparse - for testing purposes.
* In the magma package, link the 'magma' library with the
'nvToolsExt' library.
* In the magma package, update the 'magma-2.5.0.patch' with the latest
commits from the magma source repository. Also, remove the library
'nvToolsExt' from the 'magma-2.5.0-cmake.patch' - now it is not
needed.
* In the magma package, disable OpenMP when using v2.5.0 with the
IBM XL compiler.
Please enter the commit message for your changes. Lines starting
* In the mfem package, add version for the 'laghos-v2.0' tag; also,
prefix the versions `laghos-v*` with their respective development
version numbers -- this way they are properly ordered within spack
relative to the official numbered versions.
* petsc: add version 3.11.1 (#11179)
(cherry picked from commit 1eab6e3c86)
* ceed-2.0: use petsc-3.11.1
* this-is-so-dumb.f -> empty.f
* Add versions 1.4.0, 1.3.0, and 1.2.0
* Add dependencies and update constraints (e.g. version 1.4.0 of
precice requires a later version of boost)
* Add maintainers
A Spack hack for MKL usage was needed in QMCPACK prior to version 3.5
when non-Intel compilers were used. This Spack hack could have
undesirable side-effects and led to ugly code that was extra work to
maintain. For older versions of QMCPACK, we throw a conflict if you
want to use Intel MKL with the other compilers commonly found on x86.
Note that there is no impact to version of QMCPACK since 3.5.
* Fix bug when system perl is used.
If system perl is being used through packages.yaml there cannot be dependent modules.
The setup_dependent_packages function should not do anything in that case.
* Add versions 5.2.0 and 5.1.0
* Avoid adding version 6.0.0: this version has a new API that is
not compatible with older versions (and dependents may break with
it)
* Added comment block explaining the problems with version 6.x
* Replace old datumgrid resource (1.7) with new (1.8)
* Add speculative sqlite dependency for when a 6.x version is added
* add version 7.0.1
* replace md5 with sha256 for various versions.
* v7.0.1 fixes some environment hacking to properly find MPI and
system architecture
This adds a stub script for mpirun and other standard executables
when installing OpenMPI with slurm. The purpose is to make the
removal less of a surprise to administrators/users: it explains why
they were removed and how to restore them.
* adding package to install squashfs for singularity
* dont need os import
Signed-off-by: Vanessa Sochat <vsochat@stanford.edu>
* updating md5 to sha1 for squashfs package
Signed-off-by: Vanessa Sochat <vsochat@stanford.edu>
* two blank lines
Signed-off-by: Vanessa Sochat <vsochat@stanford.edu>
* Newer versions of IBM XL no longer define `__xlC__`, but define `__ibmxl__`
instead. This one-line patch fixes this problem in Random123.
* This patch was also provided to the Random123 maintiners
(Random123@DEShawResearch.com). I don't expect a new release from them for a
while, so I believe that this patch is the correct path forward (for now).
* initial work to make use of an 'upstream' spack installation: this uses the DB of the upstream installation to check if a package is installed
* need to query upstream dbs when adding new record to local db
* prevent reindexing upstream DBs
* set prefix on specs read from DB based on path stored in install record
* check that Spack does not install packages that are recorded as installed in an upstream db
* externals do not add their path to install records - need to use 'external_path' to get path of upstream externals
* views need to check for upstream installations when linking metadata
* package and spec now calculate upstream installation properties on-demand themselves rather than depending on concretization to set these properties up-front. The added tests for upstream installations don't work with this new strategy so they need to be updated
* only refresh modules for local specs (not those in upstream packages); optionally generate local module files for packages installed upstream
* when a user tries to locate a module file for a package installed upstream, tell them to use the upstream spack instance to locate it
* support recursive upstream databases (allow upstream databases to use their own upstream databases)
* separate upstream config into separate file with its own schema; each entry now also includes a name
* metadata_dir is no longer customizable on a per-instance basis for YamlDirectoryLayout
* treat metadata_dir as an instance variable but dont set it from kwargs; this follows several other hardcoded variables which must be consistent between upstream and downstream DBs. Also update DirectoryLayout.metadata_path to work entirely with Spec.prefix, since Spec.prefix is set from the DB when available (so metadata_path was duplicating that logic)
* Add latest libyogrt versions
* Add url_for_version to handle differing url formats for different
versions
* Add 'scheduler' variant to configure scheduler. Currently only
slurm can be installed with Spack. A value of 'system' indicates
to use the scheduler installed on the system
* py-prompt-toolkit: Add newer version for required for newer
py-ipython versions
* py-ipykernel:
* Add newer py-ipykernel version
* Depend on py-setuptools so a python egg isn't attempted to be
built
* Update dependency for newer py-ipykernel versions
* py-jupyter-console: Remove py-prompt-toolkit dependency since it is
picked up in py-ipython
* py-ipython:
* Add missing py-backcall dependency
* Adjust py-prompt-toolkit dependencies for newer versions of
ipython
* py-jupyter-notebook: Require newer version of py-ipykernel since
jupyter is broken with previous versions
* add cxxstd variant
* add CMake constraints based on platform/version
* add older versions
* update boost dependency version constraints (which are closely
tied to mysql version) and update boost cxxstd choice to be
the same as the cxxstd chosen for mysql
* add client-only support (including a patch for 5.5.x)
* record the mysql package as a provider of the mysql-client virtual
Improve management of the Fiber library and C++ standard support:
* Remove Fiber from list of libraries to build
* Improve variant management for Fiber; add variants for Context and
Coroutine libraries.
* Add known conflict with C++17 for boost < 1.63.0
* Remove C++ standard "default" option, which left the choice of
C++ standard to the compiler used to build boost
* record conflicts with compiler versions which don't provide
required c++ standard support
* add doxygen (build) dependency
* add note that range-v3 is header-only as of 0.3.6 and update
package description
We add new variants to handle readline vs libedit, a client-only
build and install, and bindings to TCL, Python and Perl. We also add
new versions and the ability to detect remote versions not otherwise
dealt with.
This avoids using a system-installed CUDA package. In the future a
variant can be added to allow using Spack-installed CUDA, but for
now CUDA support is always disabled.
