* qt: move licence acceptance from qt3krell.patch to qt3accept.patch
* qt: ensure that ptrdiff_t is defined for qt@3.3.8b
* qt: disable webglplugin for qt@5.10~opengl
* qt: depend on libxext (for qt@3 and @4)
* qt: avoid X dependencies on darwin platforms
* Revert "qt: avoid X dependencies on darwin platforms"
This reverts commit 05ce08de94be1e02d7e2f2dae0c1ae59baa3f65a.
* qt: limit range of versions depending on libxext
See #6794
This fixes cases where test-only dependencies were omitted from
consideration when modifying the environment at build time. This
includes an update to the python package definition to add
testing-related python extensions to its specialized environment
setup.
* coinhsl: add version 2014.01.10 (stable)
* coinhsl: make 2014.01.10 preferred version
Make Harwell Subroutines Library for IPOPT version 2014.01.10 the
preferred version because it is the latest stable version released.
* coinhsl: add option to link w/ BLAS libraries
Building emacs on darwin throws an error when trying to build an Emacs
app in the nextstep/Emacs.app path of the build tree. For now, disable
building this app.
It's possible to enable building the app also; Homebrew offers options
to this effect, and also adds Mac-specific options for starting the
emacs daemon. However, for the sake of simplicity and getting a
workable up-to-date emacs installation on my machine as quickly as
possible, this commit focuses on a minimal viable modification.
* Add a new package: unblur.
* Add a new package: unblur.
* Add a new package: unblur.
* Add a new package: unblur.
Conflicts:
var/spack/repos/builtin/packages/unblur/package.py
* Add a new package: unblur.
* Fix git on ubuntu, first cut
Spack needs to pass information about where the linker
can find `libintl`. We're currently using `LDFLAGS` to do so.
The `LDFLAGS` info is pasted into the command line upstream
of the a file (`libgit.a`) that includes unresolved symbols that
need that library. This fails on Ubuntu, although it seems to
work on CentOS (see #6841).
This change allows git to build on a Ubuntu 16.04.3 droplet.
TODO: test on other platforms...
* Add a bit of useful commentary
* Upgrade recipe for parmetis to be a CMakePackage
+ Eliminate `install` method (use the one from CMakePackage).
+ Move configure options to new method `cmake_args`
+ Move special install instructions for DarwinOS to a `run_after` method.
* Fix run_after section; Remove variant +debug.
Control the find_package of the PNG variant explicitly.
This avoids picking up an "external" PNGwriter install in
case `~png` is picked by changing the default "AUTO" search
to explicit "ON" (required) of "OFF" (ignore if exists).
* py-psyclone: Code generation for the PSyKAl framework from the GungHo project
* py-psyclone: add installation tests based on py.test
* py-psyclone: define 'develop' version as latest master branch
* py-psyclone: extract tagged version 1.5.1 from git repo
* py-psyclone: whitespace adjustments for flake8
* py-psyclone: use compatible versions of py-fparser
* py-psyclone: use type='test' for selected dependencies
* Updating OpenFAST to use explicit lapack and blas libraries from Spack.
* Simplifying openfast blas lib logic and fixes flake8 errors.
* Changing order of blas and lapack libs in openfast package.
* py-pybedtools: Create new package
* py-pybedtools: add py-six requirement
* py-pybedtools: remove py-cython dependency for release version
* py-pybedtools: include minimum version of py-pysam
* Provide build_type variant for Metis.
+ Ideally, we would make Metis a CMakePackage, but `metis@:5` doesn't use CMake.
+ For now, provide a `build_type=` variant similar what is found in
CMakePackage.
+ There is a potential for duplicate specification of `CMAKE_BUILD_TYPE` if both
variants `+debug` and `build_type=` are specified. I am looking for advice on
how this can be resolved.
* Update metis recipe in response to flake8 and user comments.
+ Wrap comment lines that used more than 80 columns.
+ Change `+debug` variant to avoid potential for multiple `-DCMAKE_BUID_TYPE=`
arguments provided to cmake. Specifying this variant no longer appends this
configure option. However, if `+debug` is specified, require
`build_type=Debug` to maintain expected behavior.
* For metis, remove +debug variant; use build_type= instead.
+ Update recipe for metis@4 to extract `build_type=` values and set `OPTFLAGS`
accordingly.
+ For metis@5:, the behavior from the previously supported variant `+debug` can
be obtained with the options `+gdb build_type=Debug`
* Conflicts added for metis@4 when build_type != Release|Debug.
* Use spack function conflicts instead of 'raise InstallError'.
* Create a symbolic link for MotionCor2.
* Create a symbolic link for MotionCor2.
* Create a symbolic link for MotionCor2.
* Create a symbolic link for MotionCor2.
* Adding NEURON package widely used in computational neuroscience community
* flake8 fixes
* Add rx3d variant
* Addressed review comments from Adam
* Addressed 2nd review comments
* Added check for +mpi on bg-q
* Filter spack compiler wrappers in NEURON scripts
Add gcc march=native flag to make front-end build robust
* Make develop as preferred version due to bug in long filename handlings in <= v7.4
* Avoid use of gcc in cross compiling environment
Use arch specific options on cray and bg-q arch
* Simplify cross compiling build:
- v7.5 added and no longer need develop as preferred version
- legacy cray related options removed
- cross compiling args reduced
- python arguments reduced as neuron finds proper libraries
* Simplify bg-q configurations
* Cleanup and unify arch options
* Make sure to add commonly available packages as dependency
* Arch path added to dependent_environment as nrniv needed at runtime
* Support for Power 8 architecture
* Fix python3 on OS X
* flake8 fix
* remove unnecessary conflcist directives
* Added a package for the MDAnalysis toolkit.
* Added a patch file to get rid of compiler warnings with intel compiler
and inlining. Added checksum values for other versions of protobuf.
* Added dependency on Intel compiler for intel patch
* added variant examples to paraview package.py
* qt: added libxt dependency
* add variant to use external hdf5, this is needed when compiling with gcc@4.8.5
* paraview: added python dependecies to PYTHONPATH
* Start adding Nek5000 package
* Add tools to install: genmap, prenek, postnek
* Address comments by @davydden
* Use install_tree (thanks @junghans) and polish
* Update url
* Fix flake formatting errors
* Change F77 and CC compilers
Apparently spack compilers can't be called outside spack and we
have an underscore test in our Nek5000/core/makenek.inc file which
calls F77 compiler.
* Add support for visit and profiling options
* Fix a typo
* Fix a typo
* Remove the C check
* Add visit variant
* Update the install of int_tp tool
* Let MAXNEL to be set during installation
* Added magma package
* Incorporated Serban's change
* Remove deleted files
* argparse.py
* Sync forked Spack repo in github
* Add spectrum-mpi lib path to LD_LIBRAY_PATH in spack_env.
As a result of supporting alternate installation directories, spectrum-mpi does
not use rpath anymore, so we need to set LD_LIBRARY_PATH in spack_env to allow
MPI programs to run during dependent package configuration.
* Fix flake8 error (blank line at EOF)
* xios: XML-IO-SERVER library for IO management of climate models
* xios: install to prefix directory
* xios: add a test case
* xios: define versions to use cache and mirror directories
* xios: use proper svn URL for version 910
* xios: package url must be defined, otherwise uninstall fails
* xios: add trunk version to allow building latest revision
* xios: enable parallel build
* xios: allow installation with mpif90 compiler wrappers
* xios: use mpi variants of dependencies
* xios: allow user to specify MPI launcher via MPIRUN environment variable
* xios: prefer spack versions of blitz and boost (needed for gcc@7)
* xios: enable builds with clang+gfortran on OSX
* xios: use numeric versions for releases, @develop for trunk
* xios: different patches required for @1.0 and @develop
* xios: patch function for clang works across revisions
* xios: link blitz library
* xios: workaround bug 17782 in llvm
* xios: whitespace adjustments for flake8
* xios: avoid bare except clause
* xios: netcdf-fortran inherits ^netcdf+mpi from xios dependencies
* combine all patches for 1612 into a single file, with additional
comments to explain the rational.
* Add kahip decomposition variant.
* Add support for ARM64 architecture.
* filter instead of patching etc/config.*/settings. This eliminates
patch files for 1706, perhaps for the future as well.
* URLs at or before version 1612 have a different structure, so
provide a url_for_version implementation to handle this
* singularity - added master branch as this has latest fixes - 2.4 does not compile on centos 6 without use of this branch
* renamed to develop
* added master branch properly
* add OctavePackage
1. remove import CudaPackage which is not needed anymore
2. mention CudaPackage and OctavePackage in packaging guide
3. adjust OctavePackageTemplate
4. add clue file for Octave build
5. sanity check on self.prefix
* use setup_environment
* esmf: put .mod files in the spack compiler search path
* esmf: allow building with Cray mpi
* esmf: create run-path dependent libraries on osx
* esmf: link fortran interface libraries when building with mpich
* Fix detection of blas and lapack: provide libraries/includes as
arguments to CMake rather than using CMake's auto-detection.
This includes a patch to QMCPACK's CMake files to refer to
Spack-built blas/lapack implementations. This also includes
special-case logic for the intel-mkl implementation of blas/lapack
* Break up unit tests and short tests. Only hard failure if the unit
tests fail, if short tests fail issue a warning only.
* Add QMCPACK 3.3.0, get rid of 3.0.0
- define MPICH_SKIP_MPICXX, link libmpich instead of libmpi
(as per disussion in PR #4990)
ENH: more flexible editing/patching of openfoam env files
CONFIG: comment out requirement for openmpi+thread_multiple
- was originally slated for the 1712 release and beyond, but there are
reportedly unstable version/network combinations.
Leave as comment for future reference, since it may be arise again.
STYLE: renamed openfoam-site.patch as 1706-site.patch (and reformatted)
- to preserve against impending changes in the layout of
config.{csh,sh}/settings
* fix post install method for py3 in mercurial
* Update package.py
* Update package.py
* use print_str instead of manual print detection
* Update package.py
* use only depends_on
* Update package.py
* Update package.py
State py3 compatibility for @4.3: according to setup.py from the 4.3.tar.gz from pypi
Add preferred version 2.0.3. Added beta version. Added conflict with
gcc versions >= 5 when building with cuda@8 (which is currently the
only supported cuda version). Added cuda architecture variant. Added
comment about current lack of cuda@9 support.
Fixes#6522
Patch psxevars.sh and psxevars.csh only when year > 2016.
pxevars.csh does not exist for versions before 2017. psxevars.sh
does not appear to require this patch for versions before 2017.
Fixes#6521.
Bazel's build system filters environment variables, including those
set by Spack for use by its compiler wrapper. This updates the patch
to include the SPACK_DEBUG_LOG_ID variable added in #5837.
* optional path to use spacks py-site-pkgs, install host-cfg for provenance
* add more comments and address review requests
* only use st-pkgs-dir when +python
* ascent does not need doxygen
* capture mpiexec if it exists
* added missing import
* flake8 fix
* default adios variant to False
* ascent develop now reqs conduit master
* optional path to use spacks py-site-pkgs, install host-cfg for provenance
* add more comments and address review requests
* only use st-pkgs-dir when +python
* ascent does not need doxygen
* capture mpiexec if it exists
* added missing import
* flake8 fix
* default adios variant to False
* ascent develop now reqs conduit master
* conduit: use hdf5 1.8 for wider output compat
* Add: Py-Plotly
The requirements of py-plotlit are rather strict fixed to specific
versions, so I did not add an "upper versions" `:` to the constrains.
See
https://github.com/plotly/plotly.py/blob/master/requirements.txt
* Py-Requests, Py-Six, Py-Pytz: Older Versions
Add two older versions of requests, pytz and six for plotly.
- depends on GTK+ with X enabled
(btw, non-X backends are deprecated/removed in GTK+)
- patch for 3.0.1-3.0.2: missing include caused multiple
`error: call of overloaded ‘abs(XYPOSITION)’ is ambiguous`
(seen in GCC 6.3.0); fixed in 3.0.3+
* Update CGNS to be able to be used in Trilinos.
* Updating Trilinos to be able to use CGNS.
* Fixing wrong cmake defines in trilinos for enabling cgns and cleaning up cgns package.
* Changing cgns parallel variant to mpi. Removing explicit dependence on parallel-netcdf in trilinos.
Add additional transform libraries to ADIOS.
Also modifies existing transforms to the versions they were
introduced (otherwise this was resulting in unknown configure flags).
* xsdk: Added MFEM rc package.
* xsdk: add version entry for xsdk-0.3.0-rc1 - and set it as preferred version
* xsdk: remove 'xsdk' from version - recommended by Todd.
Now the usage is:
'spack install xsdk@0.3.0-rc1'
instead of the previous usage:
'spack install xsdk@xsdk-0.2.0'
* xsdk: add petsc@3.8.0 as a dependency for xsdk-0.3.0-rc1
* mfem: fix dependency to use the corrected xsdk version
* Updated the mfem version tags.
* mfem: fix merge
* fix flake8 warning
* Modified xSDK scripts
* fixing the default package.yaml
* fix bad revert
* revert changes to superlu-dist so that the 5.2.1 update can be merged
* update xsdk to use superlu-dist-5.2.1
* update alquimia for xsdk
* fix whitespace
* update hypre for xsdk
* update sundials for xsdk
* update sundials for xsdk
* Fix checking for MKL and extend range of GCC versions
* pflotran: update to release branch
* plasma: fix spec -> self.spec
* Changes to enable mfem hooks into hypre, superlu-dist, and petsc. Sundials hooks may come in the future.
* adding plasma with comment
* Bumped the version of mfem up to handle integration with sundials3.0.0. Also enabled hypre in sundials.
* Turn on the plasma package definition for testing
* Fix conflict declaration to obey ordering rules
* xsdk: udate superlu-dist dependency to v5.2.2
* plasma: change gcc dependency to workarround potential spack bug #5778
* trilinos: update hdf5 dependency to use 'hdf5+hl'
Without this change - I get the following error [triggered by 161dca6d5c9810f808 changes]
$ ./bin/spack install trilinos+hdf5
==> Error: An unsatisfiable variant constraint has been detected for spec:
hdf5@1.10.1%gcc@7~cxx~debug~fortran~hl+mpi+pic+shared~szip~threadsafe arch=linux-fedora27-x86_64
while trying to concretize the partial spec:
netcdf+mpi
^m4
^mpich@3.3a2%gcc@7 device=ch3 +hydra netmod=tcp +pmi+romio~verbs arch=linux-fedora27-x86_64
^zlib@1.2.11%gcc@7+optimize+pic+shared arch=linux-fedora27-x86_64
netcdf requires hdf5 variant +hl, but spec asked for ~hl
* plasma: add in -lm dependency per #6046
* update sundials version to 3.0.0
* Add fixes to support Netlib LAPACK
* mfem does not use cmake for builds [anymore] - so remove code corresponding to this dependency.
This enables mfem build on OSX [with xcode/clang compilers]
* mfem: update to v3.3.2-rc4
* add patch for building sundials on mac
* xsdk: enable plasma for gcc-4.9+ - same as what plasma/package.py does.
* magma: Fix for cuda-9.0 as it does not support sm20
nvcc fatal : Unsupported gpu architecture 'compute_20'
* add in code for 'spack install xsdk+cuda' - which installs magma
* fix flake8 warning
* fix flake8 warnings
* Updated to the latest MFEM RC.
* alquimia: fix to use petsc-3.8.0+ versions
* petsc: update to version 3.8.1
* petsc: add in conflict between petsc-3.8.0 & mkl
* xsdk: update petsc to 3.8.1 to get MKL build fix
* petsc: fix superlu_dist dependency
* petsc: when hdf5 depends on zlib - petsc+hdf5 should also be configured with zlib
* petsc: fix dependency [of zlib to be on hdf5 - and not on petsc]
* petsc: fix pkgconfig error - with incorrect library link order that can break mfem examples with static build
* petsc: use the fact that hdf5/package.py has a hard dependency on zlib [so no need to check for this dependency in code]
recommended-by: @davydden
* petsc: change hdf5 dependency to 'hdf5+hl' as petsc configure is looing for -lhdf5_hl
https://github.com/spack/spack/issues/5846
* plasma: also detect -lgfortran
* update sundials version to 3.1.0
* alquimia: xsdk-0.3.0-rc -> xsdk-0.3.0
* petsc: update to version 3.8.2
Includes pkgconfig fix [for mfem static build failure]
* Revert "petsc: fix pkgconfig error - with incorrect library link order that can break mfem examples with static build"
This reverts commit d1afa8c20d4313fdc42a27e5380573b035b32998.
* xsdk: update to use petsc-3.8.2
* Fixed a problem with MFEM trying to use mpicxx instead of the spack defined compiler.
* Minor changes to the mfem build and pointing at mfem's release branch that is currently undergoing internal testing.
* Enabling shared build for Plasma
* plasma: do not look for libgfortran on cray - spack finds the wrong one from the frontend
'-L/usr/lib64/gcc/x86_64-suse-linux/4.3 -L/usr/lib64 -lgfortran'
* Some changes to the mfem package that are in the process of being pulled into spack/develop.
* xsdk: switch from 0.3.0-rc1 to 0.3.0
* fix flake8 warnings
* plasma: extract plasma changes from xsdk-0.3.0
* plasma: cleanup per review
- netlib-lapack: add support for spec['lapack:c'].libs, spec['blas:c'].libs
- add getblaslapacklibs() to eliminate duplicate code in edit() and build_targets()
- eliminate string manipulation of ld_flags
- remove gfortran check (will check later)
- remove build() (will check later)
* netlib-lapack: fix tuple per review
* netlib-lapack: use spec[lapack:c,fortran]
* Adding version 2.4.3 to ViennaRNA
* Replaced tab indent with spaces
Flake8 error correction
* no swig for viennarna v2.4.3 only
* correcting version/argument conditional syntax error
libtool is also needed for linking, otherwise downstream
dependencies such as clfft will fail linking against pocl's
libOpenCL.so with errors such as:
```
>> 182 /usr/bin/ld: warning: libltdl.so.7, needed by /usr/local/opt/spack/linux-ubuntu16.04-x86_64/gcc-5.4.0/pocl-0.14-rwo73qzkcxfupndxoz3pcl2s34o5pt6i/lib/libOpenCL.so, not found (try using -rpath or -rpath-link)
>> 183 /usr/local/opt/spack/linux-ubuntu16.04-x86_64/gcc-5.4.0/pocl-0.14-rwo73qzkcxfupndxoz3pcl2s34o5pt6i/lib/libOpenCL.so: undefined reference to `lt_dlinit'
>> 184 /usr/local/opt/spack/linux-ubuntu16.04-x86_64/gcc-5.4.0/pocl-0.14-rwo73qzkcxfupndxoz3pcl2s34o5pt6i/lib/libOpenCL.so: undefined reference to `lt_dlerror'
>> 185 /usr/local/opt/spack/linux-ubuntu16.04-x86_64/gcc-5.4.0/pocl-0.14-rwo73qzkcxfupndxoz3pcl2s34o5pt6i/lib/libOpenCL.so: undefined reference to `lt_dlopen'
>> 186 /usr/local/opt/spack/linux-ubuntu16.04-x86_64/gcc-5.4.0/pocl-0.14-rwo73qzkcxfupndxoz3pcl2s34o5pt6i/lib/libOpenCL.so: undefined reference to `lt_dlsym'
>> 187 collect2: error: ld returned 1 exit status
```
* py-petsc4py: Update version to 3.8.0 and add dependencies
- Added explicit dependency on python and numpy
* Kept old version - and corrected minimal python version
* Update to 3.8.1
* add ascent package and and deps
* proper use of site_packages_dir prop
* flake8
* add maitain, small updates
* flake8
* flake8
* fixs for docstrings for sphinx
* petsc: when hdf5 depends on zlib - petsc+hdf5 should also be configured with zlib
* petsc: fix dependency [of zlib to be on hdf5 - and not on petsc]
* petsc: use the fact that hdf5/package.py has a hard dependency on zlib [so no need to check for this dependency in code]
recommended-by: @davydden
* petsc: change hdf5 dependency to 'hdf5+hl' as petsc configure is looing for -lhdf5_hl
https://github.com/spack/spack/issues/5846
* Added missing deps to libffs
* SOSflow spack package pointing to sos_flow feature/spack branch
* Using tag for spack build
* Change url to spack/spack
nghttp2 depends on python, and requires the install directory to exist,
and contain the python module directory which it will eventually
install the python modules into.
* trilinos: update hdf5 dependency to use 'hdf5+hl'
Without this change - I get the following error [triggered by 161dca6d5c9810f808 changes]
$ ./bin/spack install trilinos+hdf5
==> Error: An unsatisfiable variant constraint has been detected for spec:
hdf5@1.10.1%gcc@7~cxx~debug~fortran~hl+mpi+pic+shared~szip~threadsafe arch=linux-fedora27-x86_64
while trying to concretize the partial spec:
netcdf+mpi
^m4
^mpich@3.3a2%gcc@7 device=ch3 +hydra netmod=tcp +pmi+romio~verbs arch=linux-fedora27-x86_64
^zlib@1.2.11%gcc@7+optimize+pic+shared arch=linux-fedora27-x86_64
netcdf requires hdf5 variant +hl, but spec asked for ~hl
* fix flake8 warning
* added relion v 2.1
* relion 2.1 - misssed comma
* relion now pulling from master branch - removed 2.03 - added cuda 8 as dependency given 9 does not yet work with relion per https://github.com/3dem/relion/issues/296
* r-igraph: find old packages in the archive
Fixes#6104.
* r-irlba: find old packages in the archive
Fixes#6101.
* r-lazyeval: find old packages in the archive
Fixes#6102.
* packages: set list_url for all packages hosted on CRAN
* packages: consistently use the CRAN archive URLs
Aspell compiles in the paths it looks for rather than looking relative
to its binary location. There are also no environment variables to
redirect it other than changing the path to the configuration file it
looks at.
- hdf5's +hl variant is required because the build uses libhdf5_hl.
- sz is only compatible up to version 1.4.10 because the library has
been renamed to libSZ in 1.4.11.
* Fixed the datatype flag in the LBANN package.
Fixed where the datatype flag should be set.
* Added variant to OpenCV to disable building DNN support
* Fixed a bug in how the elemental package tries to find its Fortran
library. The current method does not work with Intel compilers.
* Added necessary paths for cuDNN and CUB.
* Addressed flake8 issues in Elemental package.
* Fixed several flake8 errors. Added variant to build with or without
support for arbitrary-precision floating point arithmetic.
* Added the proper CMake flag when MPFR support is disabled.
* Fixed a bug in how the cudnn path was being set when there was no
cudnn requested. Also requested that OpenCV is built without eigen
support.
* Fixed another bug where a dependency may not be there and thus should
not be always checked.
* Added a package for the MDAnalysis toolkit.
* Changed dependency for the eigen library to not include support for
multiple-precision (arbitrary-precision) floating point arithmetic,
since OpenCV does not support these data types.
* Fixed incorrect implementation
* dockbook: remove update to dependent environment
Remove override of setup_dependent_environment in both docbook-xml
and docbook-xsl, which seems to generate a warning from spack about
"Suspicious requests to set or unset 'XML_CATLOG_FILES' found."
* flux: update version/dependencies to 0.8.0
Update flux-core to v0.8.0. Clean up dependencies and remove unneeded
extra invocation of ./autogen.sh when building from @master.
* flux: modify environment for Lua tests
Modify Spack environment to add `./?.lua` to LUA_PATH so that
fluxometer.lua can be found by tests during `make check` run
from `spack install --tests all flux`
* flux: fix broken flux version when on master
When building @master with spack, the flux version test from
`make check` fails because spack is using a shallow clone. Add
a setup section for @master that calls git pull --depth=50 --tags
to pull down tags and (hopefully) enough information for git-describe
to work properly.
A recent update (#5907) to htslib added a different URL for an old
version of htslib.
Now the package is using that URL as the pattern for the newer
versions too.
I have a vague memory of running into this before, that it's a known
issue.
This fixes it by adding an explicit `url_for_version` routine.
* Add bowtie2@2.3.0, fix dependencies and sbangs
Add support for bowtie2@2.3.0
- digest
- a patch for 2.3.0 that parallels the existing package. Truth be
told it builds (for me) without this, but I'm assuming that they're
there for a reason...).
- tune up dependencies
- need tbb
- don't need readline or zlib
Several things were installed with sbang's that use `/usr/bin/env` to
fine perl or python. Fix the dependency and clean up the sbang lines.
* Fix python exe name, avoid path banging
I'd cut and pasted the python bit from the perl bit and missed one
reference to perl.
While I'm there, use the cleaner `spec['perl'].command` instead of
banging together the path from its bits.
* Fix up the "when" constraints on the dependencies
Get the edge cases right.
- 2.2.5 doesn't need tbb, 2.3.[01] do.
- 2.3.1 needs readline and zlib.
