* Use separate build directory for gzip
At least on mac systems (perhaps because of a case sensitivity issue?)
gzip fails to build inside the source tree:
```
config.status: linking /var/folders/fy/x2xtwh1n7fn0_0q2kk29xkv9vvmbqb/T/spack-stage/s3j/spack-stage-gzip-1.10-iatwtuk2l5xgwmuh4pwu5bf27yezpydj/spack-src/GNUmakefile to GNUmakefile
config.status: executing depfiles commands
==> Executing phase: 'build'
==> [2020-02-14-09:32:45.502913] 'make' '-j12'
make: GNUmakefile: Too many levels of symbolic links
make: stat: GNUmakefile: Too many levels of symbolic links
make: *** No rule to make target `GNUmakefile'. Stop.
```
* Simplify build directory and add gmake dependency
Libmng only needs gzip to compress man files for distribution, so it
builds fine without it. The spack
gzip currently fails to compile.
```
config.status: linking /var/folders/fy/x2xtwh1n7fn0_0q2kk29xkv9vvmbqb/T/spack-stage/s3j/spack-stage-gzip-1.10-iatwtuk2l5xgwmuh4pwu5bf27yezpydj/spack-src/GNUmakefile to GNUmakefile
config.status: executing depfiles commands
==> Executing phase: 'build'
==> [2020-02-14-09:32:45.502913] 'make' '-j12'
make: GNUmakefile: Too many levels of symbolic links
make: stat: GNUmakefile: Too many levels of symbolic links
make: *** No rule to make target `GNUmakefile'. Stop.
```
* Modify Flang NVidia GPU variant to make use of built-in CudaPackage
* Add OpenMP Offload patch if March 2019 compiler is selected.
* Flang parallel build has a race condition.
* llvm-flang now uses built-in CudaPackage.
* Add variant for different build releases.
* Fix OpenMP target offload for NVidia GPUs.
* Additional commong flags that are needed with comments.
* NVidia BC required for libomp target requires special treatment. Use clang built in previous step to re-compile libomptarget.
* Add a new package: Metall
* Fix errors in metall/package.py
* Update var/spack/repos/builtin/packages/metall/package.py
Change to https style URL
Co-Authored-By: Adam J. Stewart <ajstewart426@gmail.com>
* Update in metall/package.py. Change Metall to depend on Boost always
* Update in metall/package.py. Change to install Boost with the default variants
* Update metall/package.py. Removed a comment
Co-authored-by: Adam J. Stewart <ajstewart426@gmail.com>
Add the OpenBLAS variant `+consistentFPCSR`, by default `False`, which adds the compile definition `CONSISTENT_FPCSR=1` as documented in OpenBLAS `Makefile.rule`.
This PR adds an updated version to the r-rhtslib package as well as fix
the build.
- add patches to use compiler flags from R
- add variables for bzip2 and xz dependencies
- use the spack Makeconf file when building the in-tree htslib
- make patchelf available to allow R to remove reference to temporary
installation directory in htslib shared object
- Add new version of r-rsamtools as the r-rsamtools and r-rhtlib
packages are closely paired.
* Fix run environment
Trying to install Avizo, i get "Error: NameError: name 'run_env' is not defined". Correcting it to be just "env"
* fix identation
Starting with 2020, the tar files are named v2020.0.tar.gz,
v2020.1.tar.gz, etc, not 2020_U1.tar.gz.
https://github.com/intel/tbb/releases
The previous commit (7a10478708) fixed the checksum mismatch, but
didn't update url_for_version (my bad).
UnifyFS no longer has an option to depend on numa. This removes the
numa variant, dependency, and associated conflict.
This commit also
- renames the `pmpi` variant to the more appropriate `auto-mount`
- changes the preferred version to the most recent release
WarpX removed the `dev` branch in favor of a simpler,
`master`-centric development model.
`master` is the new development branch and there is no
stable branch anymore (we use tags and release branches
instead).
* Hydrogen now depends on `aluminum +nccl` vs. `aluminum +mpi_cuda`
* Hydrogen: Simplify Mac OS OpenMP-detection logic
* Aluminum: Add Mac OS OpenMP-detection logic
* LBANN: depend on conduit@0.4.0: instead of conduit@master
Fixes#10019
If multiple instances of a package were installed in a single
instance of Spack, and they differed in terms of dependencies, then
"spack find" would not distinguish specs based on their dependencies.
For example if two instances of X were installed, one with Y and one
with Z, then "spack find X ^Y" would display both instances of X.
