On Cori(Cray-XC40), I need to pass the entire path for the compilers, this is what is saved in c_compiler, cpp_compiler, f_compiler. Therefore, when for the MPI wrappers only the binary name is provided I run into the same issue. There is no drawback of passing the entire path, this is set by the user through the compiler path anyways.
* added -lpthread flag in kv/tests/CMakeLists.txt
* Update var/spack/repos/builtin/packages/papyrus/package.py
Co-authored-by: Adam J. Stewart <ajstewart426@gmail.com>
Co-authored-by: Adam J. Stewart <ajstewart426@gmail.com>
PHP supports an initial shebang, but its comment syntax can't handle our 2-line
shebangs. So, we need to embed the 2nd-line shebang comment to look like a
PHP comment:
<?php #!/path/to/php ?>
This adds patching support to the sbang hook and support for
instrumenting php shebangs.
This also patches `phar`, which is a tool used to create php packages.
`phar` itself has to add sbangs to those packages (as phar archives
apparently contain UTF-8, as well as binary blobs), and `phar` sets a
checksum based on the contents of the package.
Co-authored-by: Todd Gamblin <tgamblin@llnl.gov>
* New package: py-minrpc
* Delete package.py.save
* Update var/spack/repos/builtin/packages/py-minrpc/package.py
Co-authored-by: Adam J. Stewart <ajstewart426@gmail.com>
Co-authored-by: Adam J. Stewart <ajstewart426@gmail.com>
* package/gunrock add v1.2
* Update var/spack/repos/builtin/packages/gunrock/package.py
Co-authored-by: Adam J. Stewart <ajstewart426@gmail.com>
Co-authored-by: sbulut <sbulut@3vgeomatics.com>
Co-authored-by: Adam J. Stewart <ajstewart426@gmail.com>
`sbang` is not always accessible to users of packages, e.g., if Spack
is installed in someone's home directory and they deploy software
for others. Avoid this by:
1. Always installing the `sbang` script in the `install_tree`
2. Relocating binaries to point to the copy in the `install_tree`
and not the one in the Spack installation.
This PR also:
- ensures that `sbang` is reinstalled if it is modified in Spack
- adds tests
- updates the way `gobject-introspection` patches Makefiles
to support `sbang`
Co-authored-by: Todd Gamblin <tgamblin@llnl.gov>
* Add BLT package
* Switch install function
Co-authored-by: Adam J. Stewart <ajstewart426@gmail.com>
* Add type='run' to cmake dependency
Co-authored-by: Adam J. Stewart <ajstewart426@gmail.com>
* Add git attribute to BLT
Co-authored-by: Adam J. Stewart <ajstewart426@gmail.com>
* cp2k: locate correct include dir when using intel-parallel-studio+mkl for fftw-api
* libxc: drop arch-specific intel opt. flags
fixes#17794
* libint: drop arch-specific intel opt. flags, always build Fortran example with FC
fixes#17509
* package/pmdk add variants, version 1.9
* add dependency
* Update var/spack/repos/builtin/packages/pmdk/package.py
Co-authored-by: Adam J. Stewart <ajstewart426@gmail.com>
Co-authored-by: sbulut <sbulut@3vgeomatics.com>
Co-authored-by: Adam J. Stewart <ajstewart426@gmail.com>
The logic in `config.py` merges lists correctly so that list elements
from higher-precedence config files come first, but the way we merge
`dict` elements reverses the precedence.
Since `mirrors.yaml` relies on `OrderedDict` for precedence, this bug
causes mirrors in lower-precedence config scopes to be checked before
higher-precedence scopes.
We should probably convert `mirrors.yaml` to use a list at some point,
but in the meantie here's a fix for `OrderedDict`.
- [x] ensuring that keys are ordered correctly in `OrderedDict` by
re-inserting keys from the destination `dict` after adding the keys from
the source `dict`.
- [x] also simplify the logic in `merge_yaml` by always reinserting
common keys -- this preserves mark information without all the special
cases, and makes it simpler to preserve insertion order.
Assuming a default spack configuration, if we run this:
```console
$ spack mirror add foo https://bar.com
```
Results before this change:
```console
$ spack config blame mirrors
--- mirrors:
/Users/gamblin2/src/spack/etc/spack/defaults/mirrors.yaml:2 spack-public: https://spack-llnl-mirror.s3-us-west-2.amazonaws.com/
/Users/gamblin2/.spack/mirrors.yaml:2 foo: https://bar.com
```
Results after:
```console
$ spack config blame mirrors
--- mirrors:
/Users/gamblin2/.spack/mirrors.yaml:2 foo: https://bar.com
/Users/gamblin2/src/spack/etc/spack/defaults/mirrors.yaml:2 spack-public: https://spack-llnl-mirror.s3-us-west-2.amazonaws.com/
```
Shell integration no longer requires setting `SPACK_ROOT`, so we can
simplify the documentation on it. The docs on shell support and using
packages are getting a bit old, and information on `spack load` (which
seems to be everyone's most common way of using packages) is hard to
find.
This PR simplifies the shell documentation to remove SPACK_ROOT, and also
moves some sections around for clearer organization.
- [x] make docs on sourcing setup scripts clearer and simpler
- [x] introduce `spack load` early in the basic usage guide instead of
burying it in the module docs
- [x] clean up module docs so that spack module tcl loads comes later
- [x] be clear about the different ways to use packages so that the users
can find the docs better.
Co-authored-by: Massimiliano Culpo <massimiliano.culpo@gmail.com>
GROMACS still requires a version of FFTW when compiling it to utilize
NVIDIA GPUs. In fact, the type of calculation that depends on FFTW --
Particle-Mesh Ewald (PME) -- is generally run on the host system's CPUs,
even when GPUs are available.
* New package: py-rise
* Fix URL and add description
* Update var/spack/repos/builtin/packages/py-rise/package.py
Co-authored-by: Adam J. Stewart <ajstewart426@gmail.com>
Co-authored-by: Adam J. Stewart <ajstewart426@gmail.com>
* gaussian-src: initial commit to build from source
* do not install the source to ensure to not accidentally distribute
it to users
* set required runtime env vars based on the login.profile
* gaussian-view: update to 6.1.1
PR #19482 updated gcc to only apply the zstd patch until @10.2 but the
releases/gcc-10 branch actually does not contain the patch yet, that is,
gcc@10.3 will most likely have the same problem. Apply the patch for all
10.x releases instead.
* gemini dep -py-bcolz +
* Update var/spack/repos/builtin/packages/py-bcolz/package.py
Co-authored-by: Adam J. Stewart <ajstewart426@gmail.com>
* Update var/spack/repos/builtin/packages/py-bcolz/package.py
Co-authored-by: Adam J. Stewart <ajstewart426@gmail.com>
* py-bcolz URL fix
* Update var/spack/repos/builtin/packages/py-bcolz/package.py
Co-authored-by: Adam J. Stewart <ajstewart426@gmail.com>
Co-authored-by: Adam J. Stewart <ajstewart426@gmail.com>
fixes#19476
Module file content is written to file in a
temporary location and read back to be analyzed
by unit tests.
The approach to patch "open" and write to a
StringIO in memory has been abandoned, since
over time other operations insisting on the
filesystem have been added to the module file
generator.
