Check that SuperLU_DIST integer size matches PETSc indices size

Commit-type: error-checking, configure
\spend 30m
Reported-by: Drew Parsons (@RizzerAtGitLab)

Merge remote-tracking branch 'origin/jczhang/fix-kokkos-test'

Fix some config issues wrt Kokkos

See merge request petsc/petsc!4056

configure: HYPRE 2.22.0

Config: also check -Wl to include rpath in MPICXX_LIBS

Merge remote-tracking branch 'origin/balay/add-valgrind.h'

valgrind.h: add to petsc repo

See merge request petsc/petsc!4094

fix pragma poison and introduce new extraCompilerFlags ctx manager

valgrind.h: add to petsc at include/private/valgrind

MatHtool: new option -mat_htool_clustering

mpi4py: add with-mpi=1, --with-mpi4py-dir options

mpi4py: set PETSC_MPI4PY_PYTHONPATH etc in configureLibrary() - not in Install()

configure: print in summary when mpich or openmpi is used

Add configure support for GSL and example that utilizes GSL

\spend 4h

Merge remote-tracking branch 'origin/release'

Config: error out if mumps is used with 64-bit BLAS indices

Add the ability to not remove the directory when printing with logPrintBox()

This is used by mpi4py to print the needed PYTHONPATH argument

Commit-type: configure
\spend 20m
Thanks-to: Satish Balay

Add the ability to not remove the directory when printing with logPrintBox()

This is used by mpi4py to print the needed PYTHONPATH argument

Commit-type: configure
\spend 20m
Thanks-to: Satish Balay <sbalay@mcs.anl.gov>

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Change --download-mpi4py to install immediately instead of waiting until PETSc is built

This is to allow other external packages that depend on mpi4py to be built immediately instead of also waiting

Change --download-mpi4py to install immediately instead of waiting until PETSc is built

This is to allow other external packages that depend on mpi4py to be built immediately instead of also waiting until PETSc is built

Fix the messages regarding PYTHONPATH and the mpi4py make check to work with prefix installs

Commit-type: configure, enhancement
Funded-by: Brain project
Project: Brain
\spend 1.5h

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MatSetValuesDevice: Cleanup and simplify code, including example

User reported crash of example code. Kernel was passed an ierr that lived in CPU memory

MatSetValuesDevice: do not include private h

MatSetValuesDevice: Cleanup and simplify code, including example

User reported crash of example code. Kernel was passed an ierr that lived in CPU memory

MatSetValuesDevice: do not include private headers from public headers

Feature: MatSetValuesDevice determines automatically from the context (where it is included from) if it is being used from C, CUDA, or Kokkos, PETSC_DEVICE_FUNC_DEC no longer needs to be set before including petscaijdevice.h

Feature: MatSetValuesDevice() now ignores all values outside the global column range.

PetscSplitCSRDataStructure is now a pointer, not a struct, like most PETSc objects, please leave it that way.

Fix all uses of CTABLE that were related to the original MatSetValuesDevice()

Have atomicAdd use Kokkos atomic-add with CPU build when building with Kokkos.

Cuda should now work with --download-openmpi, this is done by updating updateCompilers() to rerun portions of packages/cuda.py after the compilers are reset to use MPI wrappers. This is needed because the resetting of the compilers removes all the compiler flags and packages/cuda.py sets certain values into these flags that was previously lost.

Add MPICXX_INCLUDES, MPICXX_LIBS to fix compile targets for Kokkos examples

'make check' now runs properly for Kokkos test of src/snes/ex3k, fixed bug in the makefile wrt MPI_IS_MPIUNI check

Testing makefile rules: add ex*cu binaries to clean rule

Reported-by: Sam Fagbemi <samkorede24@gmail.com>
Thanks-to: Stefano Zampini <stefano.zampini@gmail.com>
Thanks-to: Mark Adams <mfadams@lbl.gov>

/spend 16h

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Add sowing doctext -Wargdesc argument to error on missing argument descriptions

Save sowing doctext output to file so it can be checked after all manualpages
are built

Update sowing URl to retreive

Add sowing doctext -Wargdesc argument to error on missing argument descriptions

Save sowing doctext output to file so it can be checked after all manualpages
are built

Update sowing URl to retreive Sowing with additional error checking

Still to do is compare the name of the manual page with the name of the function

Commit-type: error-checking, docs
/spend 35m

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Merge remote-tracking branch 'origin/release'

configure: missing filter rule

ld: skipping incompatible /soft/gcc-7.5.0/lib/libcilkrts.so when searching for -lcilkrts

Merge branch 'barry/2021-05-26/debug-o0' into 'main'

Pass -O0 in when -with-debugging is on for configure to make the code truly debugable.

See merge request petsc/petsc!4030

Magma seems to use both NVCCFLAGS and DEVCFLAGS which causes repeat of -g -O0 and complaints on a CI machine

\spend 20m

Update -with-debugging=1 defaults for COPTFLAGS, FOPTFLAGS, CXXOPTFLAGS to use -O0 (or -Od for windows compilers) along with -g to make the code truly debuggable.

Commit-type: debuggability
\spend 1

Update -with-debugging=1 defaults for COPTFLAGS, FOPTFLAGS, CXXOPTFLAGS to use -O0 (or -Od for windows compilers) along with -g to make the code truly debuggable.

Commit-type: debuggability
\spend 10m

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Merge branch 'barry/2021-05-26/handle-dylib-like-so' into 'main'

Handle .dylib files like .so when generating argument lists

See merge request petsc/petsc!4025

packages/hdf5.py: disable --download-hdf5-fortran-bindings by default

gitcommit: follow-up to 3c43290cbaa09cbcaf486ab9c4f7393eb19a428c for changes in main