updated hoomd-blue to latest tagged release in repo. This version also supports newer gcc6 compilers, so added constraint for older version to avoid breaking existing installs.
+ Newer versions of zoltan2 are doing test compiles that link to parmetis. If
these checks don't find `metis.h`, the check fails.
+ This small tweak ensures that the zoltan2 configure step can find `metis.h`
that is provided by spack.
For hdf5 `1.8.10` and some compilers, the hdf5 build system adds the
'-ansi' flag. hdf5 1.8.10 is not actually ansi compliant so this
adds a patch to modify the places where it violates ansi
compatibility (which ends up being a few comments).
Make neuron package more generic
* find the bin directory dynamically for use in run_env and spack_env
* replace filter_compilers after install with filter_compiler_wrappers
* update checksum for _current_ 7.5 version
* make +python conflict with ~shared
* prepend the architecture specific lib directory to the LD_LIBRARY_PATH
Signed-off-by: Ricardo Silva <ricardo.silva@epfl.ch>
Fix installs as "root" user for the last libSplash release.
Missing quoting of string compares resulted in a CMake error
when run as root (e.g. in a Docker build).
This updates Cray.setup_platform_environment to use cray-specific
pkgconfig paths so that all providers of 'pkgconfig' have access
to them (previously the 'pkg-config' provider had this but the
'pkgconf' provider did not).
* [OpenMPI] Add the 'headers' property. This removes some redundant
headers from sub-directories, returned by the default '.headers'
handler.
* [OpenMPI] In the .headers property, add a fallback to search all of
prefix for the mpi.h header. Recommended by @junghans to support some
external configurations, see #7268.
* add verilator package
* try to add environment variable and include folder
* manually install existing scripts and patch out spack's CXX wrapper
* added some comments
* make flake8 happy
Adds Google's new cpu_features library.
Install was added recently, so don't take the `0.1.0` release but
the current `master` until a new version is published.
* Combined llvm and llvm-lld: removed the separate llvm-lld package
and added llvm-lld as an optional add on to the llvm package (the
way several other llvm tools are maintained e.g. lldb)
* Added more lld hashes to llvm package
* The 'CppBackend' target doesn't exist for version 3.9.0 or later
so exclude it for later versions
* Was incorrectly specifying 'sparc' as a target for the 'sparc'
architecture - needed to specify 'Sparc'
* Fix issue #7248 building llvm: don't make the LLVMDemangle target
for llvm < 4.0.0
* No longer need to patch CMake. Using CMAKE_CXX_FLAGS to include BLAS/LAPACK/MKL header files properly.
* Backport two patches to QMCPACK versions prior to 3.3.0: https://github.com/QMCPACK/qmcpack/pull/621, https://github.com/QMCPACK/qmcpack/pull/623
* Insufficient to include lapack_dir in CMAKE_CXX_FLAGS, CMAKE_C_FLAGS is also needed.
* Make patched Espresso a default variant instead of a hard dependency. This is easier on computer architectures where Espresso is hard to build.
* Fix patching with QE variant. Now using correct form of patch command.
* Add QMCPACK v3.4.0
* Backport patch to QMCPACK versions prior to 3.3.0: https://github.com/QMCPACK/qmcpack/pull/643
Yaml-cpp hasn't tagged a release in over 2 years, yet they have fixed
many things and now have the ability to use find_package in CMake.
Since we use this feature in Nalu, we require the latest yaml-cpp
until they tag a new release. I have also deprecated the now
unnecessary ENABLE_INSTALL flag.
* Added a package for the MDAnalysis toolkit.
* Adding a package for the Python virtualenvwrapper pacakge. Included
dependent virtualenv-clone and stevedore packages. Updated py-pbr with
a new version to support this.
* Added extra necessary dependencies and fixed the file download paths.
* Added a package for the MDAnalysis toolkit.
* Added a new package for pygpu, which is the python front end of the
libgpuarray. Additionally changed the dependency for theano so that
it properly picks up the pygpu library.
* Added the libcheck package. Fixed flake8 errors in py-pygpu recipe
and removed spurious dependency on cudnn for libgpuarray.
The edit phase of cbench was used to set environment variables. Though
this works, the variables set this way are not dumped to build.env.
This commit fixes the issue by setting those variables in the
`setup_environment` function.
* [SUNDIALS] Add the 'headers' and 'libs' properties, plus a couple of
small tweaks.
* [SUNDIALS] Revert incorrectly changed conflicts() directive. Fix style.
Fixes#5189
When working with non-normalized paths containing ".." on some
file systems, Spack was found to encounter a permission error when
writing to the path. This normalizes a path written by the
intel-parallel-studio package and also normalizes all paths
written by the license install hook (for all packages) to avoid
this issue for intel-parallel-studio.
Adds the first stable API release of ADIOS2, v.2.1.0.
Also adds a missing `pybind11` CMake flag for proper Python
selection (needed in both the new and previous version).
To accommodate build systems on Darwin which look for glibtool/ize,
#7060 attempted to provide glibtool/ize symlinks for libtool/ize
but accidentally created the same symlink twice. #7073 reverted this
and replaced libtool/ize with glibtool/ize on Darwin. This led to
#7163 since AutotoolsPackages depend on the presence of the 'libtool'
binary, so this returns to the approach of #7160 but makes the
correct symlinks.
XBraid installs `libbraid.a`, but the default `libs` method
implementation will search for `libxbraid`, which does not exist. This
commit fixes the behavior of the `libs` method for the `xbraid`
package by overriding package's `libs` method.
Prior to this commit, running `spack module refresh` with `gdbm`
installed throws the warning:
```console
==> Warning: Could not write module file [/Users/oxberry1/spack/share/spack/lmod/darwin-sierra-x86_64/Core/gdbm/1.14.1.lua]
==> Warning: --> global name 'spack_cc' is not defined <--
```
This warning is repeated for every `gdbm` installation in Spack.
The cause of the issue seems to be the same as in spack/spack (#6089):
using `spack_cc`, `spack_cxx`, or similar inside `configure_args`
causes the warnings to throw when module files are generated.
Moving the use of `spack_cc` into `setup_environment` seems to fix the
problem, even though it's a bit of a kludge.
Running `spack module refresh -m lmod --delete-tree -y` throws the
following warning:
```console
==> Warning: Could not write module file [/Users/oxberry1/spack/share/spack/lmod/darwin-sierra-x86_64/openblas/0.2.20-ibhtl5q/clang/5.0.1/ipopt/3.12.9.lua]
==> Warning: --> global name 'prefix' is not defined <--
```
This warning arises because the variable expansions in
`spack.modules.BaseFileWriter` occur at module/package scope. Even
though `prefix` is an argument to `install` methods in e.g.,
`MakefilePackage`, so using this argument within package methods is
legal, doing so defeats the introspection logic in
`spack.modules.BaseFileWriter`. Replacing `prefix` with `self.prefix`
resolves the problem, because the introspection logic in
`spack.modules.BaseFileWriter` can use introspection to query IPOPT's
prefix.
Following the discussion with Todd and Adam, find has been modified to
accept glob expressions. This should not affect performance as every
glob implementation I inspected has 3 cases (no wildcard, wildcard but
no directories involved, wildcard and directories involved) and uses
fnmatch underneath.
Mixins have been changed to do by default a non-recursive search (but
a recursive search can still be triggered using the recursive keyword).
Following a comment from Todd, the search path for the files listed in
`filter_compiler_wrappers` can now be narrowed. Anyhow, the function
implementation still makes use of `find`, the rationale being that we
have already seen packages that install artifacts in e.g. architecture
dependent folders. The possibility to have a relative search path might
be a good compromise between the previous approach and the one suggested
in the review.
Also: 'ignore_absent' and 'backup' keyword arguments can be optionally
forwarded to `filter_file`.
Implemented a declarative syntax for the additional behavior that can
get attached to classes. Implemented a function to filter compiler
wrappers that uses the mechanism above.
* Remove variants disabling blas and lapack for py-numpy, issues
building these have been resolved
* For CMake greater than 3.10, FindMPI changed, so use
MPIEXE_EXECUTABLE instead of MPIEXE for 3.10 and newer
fixes#7128
Before this PR packages that were indirectly dependent on python might
have failed due to inconsistency between the python found in the
environment and the standard libraries set in PYTHONHOME
This adds a static version of hpgmg (up to now only the latest commit
from the master branch was available). This also adds a debug variant
and sets optimization flags for ~debug when the compiler is gcc,
intel, or clang
Adds the latest release of libSplash (1.7.0) and newly learned
CMake flags for explicit dependency control.
Modifies HDF5 dependency: non-MPI splash does (and did) never run
with a parallel HDF5, due to it's internal cross-dependencies on
MPI.
* libdwarf: fix linker flags
* libdwarf: fix header install names
* libdwarf: add zlib dependency
Prior to this commit, libdwarf was linked to the system zlib. This
commit links it to spack-installed zlib.
* libdwarf: fix dynamic library suffix for Darwin
* Adding support for the Accelerate library on OS X
* Fixed guard on variable and added another depends_on statement to make sure that openblas gets selected even when openmp_blas variant is not turned on.
* Added a package for the MDAnalysis toolkit.
* Added some flags to fix the build RPATHs and OpenMP for LBANN on OS X.
* Fixed Hydrogen branch of Elemental to find OpenMP on OS X.
