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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.
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Ensure that netcdf-cxx uses the Spack-installed hdf5 and netcdf4
rather than system-installed versions.
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Also constrain the py-arrow version to depend on the same version
of arrow (e.g. 0.12.1 of py-arrow depends on 0.12.1 of arrow)
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* 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>
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BLAS and LAPACK providers, no longer forced to use MKL. (#11019)
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* add libs property to IntelMkl and IntelParallelStudio
* fix scalapack_libs when MPI is provided by intel-parallel-studio
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* 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).
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* preserve the order in which patches are applied by packages (in spite of grouping them by 'when')
* add tests confirming patch order
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* 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)
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* 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
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Also add conflicts for PPC
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* 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
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