Add code to initialize PetscMalloc() memory with Nan. Simplify and clarify the options for controlling PetscMalloc() debugging.

This now trivially detects an error that lay undetected in ts/examples

Add code to initialize PetscMalloc() memory with Nan. Simplify and clarify the options for controlling PetscMalloc() debugging.

This now trivially detects an error that lay undetected in ts/examples/tutorials/multistage/ex5.c for months

Commit-type: style-fix, feature, documentation

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fix compile warnings on arch-linux-pkgs-64idx triggered by c73702f59ac80eb68c197b7eea6d8474b9e9853c

/sandbox/petsc/petsc.next-3/src/ksp/ksp/impls/gmres/dgmres/dgmres.c: In function ‘KSPDGMRESCompute

fix compile warnings on arch-linux-pkgs-64idx triggered by c73702f59ac80eb68c197b7eea6d8474b9e9853c

/sandbox/petsc/petsc.next-3/src/ksp/ksp/impls/gmres/dgmres/dgmres.c: In function ‘KSPDGMRESComputeSchurForm_DGMRES’:
/sandbox/petsc/petsc.next-3/src/ksp/ksp/impls/gmres/dgmres/dgmres.c:770:8: warning: ‘bN’ may be used uninitialized in this function [-Wmaybe-uninitialized]
ldA = bN;
^

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Merge branch 'barry/2019-07-30/add-use-petscintcast-corrected' [PR #1924]

* barry/2019-07-30/add-use-petscintcast-corrected:
Add PetscIntCast() to check for integer overflow

Add PetscIntCast() to check for integer overflow

Used in MatSeqXAIJSetPreallocation() to determine if the number of nonzeros in the matrix
(and hence the ai[] column indices and lengths of a

Add PetscIntCast() to check for integer overflow

Used in MatSeqXAIJSetPreallocation() to determine if the number of nonzeros in the matrix
(and hence the ai[] column indices and lengths of aj[] columns indices and a[] numerical values) fit
in PetscInt.

Commit-type: error-checking
Reported-by: Karl Lin <karl.linkui@gmail.com>

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Merge branch 'stefano_zampini/GPU-matdensecuda' [PR #1911]

* stefano_zampini/GPU-matdensecuda:
GPU: Initial implementation for SeqDense class on GPUs.

PetscArraycpy: clarify source and destination in man page

Merge branch 'barry/10-7-2019/petscint-size-t' [PR #1860]

* barry/10-7-2019/petscint-size-t:
Change PetscInt count to size_t in PetscSegBufferGetInts()

Merged in barry/cleanup-petscconf-h (pull request #1834)

Remove testing and inserting into petscconf.h items that are not actually used by PETSc

Merge branch 'dalcinl/fix-clang-warning' [PR #1852]

* dalcinl/fix-clang-warning:
Sys: Remove extra semicolon to silence clang warning -Wextra-semi-stmt

Remove testing and inserting into petscconf.h items that are not actually used by PETSc

1) PETSC_HAVE_LIBXXXX - which was rarely used
be careful with the package libpng and libjpeg since they hav

Remove testing and inserting into petscconf.h items that are not actually used by PETSc

1) PETSC_HAVE_LIBXXXX - which was rarely used
be careful with the package libpng and libjpeg since they have lib in the name of the package
2) various system include files that are never used or always exist: for example stdlib.h
3) various system functions that are never used or always exist
4) fixes for requires for MUMPS and SuperLU_DIST when dependent packages are installed or not installed (unrelated to the rest of this pull request)
5) packages that always exist such as PETSC_HAVE_BLASLAPACK, or are not used by PETSc such as PETSC_HAVE_NETCFD
6) remove a couple of uses of HAVE_LIB* in the code that were not needed by adjusting the configure code slightly
7) remove all the #if guards for each entry in petscconf.h since petscconf.h already has a guard and
the values are never defined else where the extra guards just make the file cluttered

For a build with about 10 external packages this reduced the size of petscconf.h from 1236 lines to 828/4 around 220 entries.

Commit-type: style-fix, cleanup

Reported-by: Jed Brown <jed@jedbrown.org

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Change PetscInt count to size_t in PetscSegBufferGetInts()

Commit-type: style-fix

Merge branch 'barry/no-batch-script'

Merge branch 'maint'

Sys: Remove extra semicolons to silence clang warning -Wextra-semi-stmt

No more batch submission script; this is all due to a very smart idea of Lisandro Dalcin

*) removed or fixed all remaining --know-xx options that required a batch submission script
*) removed all de

No more batch submission script; this is all due to a very smart idea of Lisandro Dalcin

*) removed or fixed all remaining --know-xx options that required a batch submission script
*) removed all details of --known-size-- that are no longer needed
*) cleaned up BAIJMKL source code, made it work with the rest of PETSc and removed is
dependence on a batch submission script, added test case for BAIJMKL
*) update the installation guide on batsch submissions and OpenMP
*) print MKL version, print OpenMP usage with mkl_sparse options

Commit-type: bug-fix, portability-fix, style-fix, feature, documentation, example
Thanks-to: Lisandro Dalcin <dalcinl@gmail.com>

$ ./configure --with-batch
===============================================================================
Configuring PETSc to compile on your system
===============================================================================
=============================================================================== ***** WARNING: Cannot determine if MPI_INT64_T works on your system in batch-mode! Assuming it does work. Run with --known-mpi-int64_t=0 if you know it does not work (very unlikely). Run with --known-mpi-int64_t=1 to remove this warning message. warning message ***** =============================================================================== =============================================================================== ***** WARNING: Cannot determine if MPI_C_DOUBLE_COMPLEX works on your system in batch-mode! Assuming it does work. Run with --known-mpi-c-double-complex=0 if you know it does not work (very unlikely). Run with --known-mpi-c-double-complex=1 to remove this warning message. warning message ***** =============================================================================== =============================================================================== ***** WARNING: Cannot verify that MPI is a shared library - in batch-mode! If MPI is a static library but linked into multiple shared libraries that the application uses, sometimes compiles work - but one might get run-time errors. If you know that the MPI library is shared - run with --known-mpi-shared-libraries=1 option to remove this warning message ***** =============================================================================== =============================================================================== ***** WARNING: Cannot determine if BLAS/LAPACK uses 32 bit or 64 bit integers in batch-mode! Assuming 32 bit integers. Run with --known-64-bit-blas-indices if you know they are 64 bit. Run with --known-64-bit-blas-indices=0 to remove this warning message. warning message ***** ===============================================================================

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Fixed incomplete set of changes, did not remove __ from most use of __MPIUNI in the source

Commit-type: bug-fix
Reported-by: nightly tests

Remove use of _ and __ in front of PETSc include guards. Reason: C99 Reserved Identifiers

Commit-type: portability-fix

Merged in barry/cuda-multigrid-test (pull request #1763)

Various improvements for GPUs (mostly for performance and CUDA)

Merged in barry/optimize-aij-da (pull request #1762)

Non-numeric optimizations focused on AIJ, MatFDColoring, and DMCreateMatrix_DA_*AIJ, looking to improve performance in GPU environments

Non-numeric optimizations focused on AIJ, MatFDColoring, and DMCreateMatrix_DA_*AIJ, looking to improve performance in GPU environments

1) PetscCalloc*() now uses system calloc()
2) Merged some Pets

Non-numeric optimizations focused on AIJ, MatFDColoring, and DMCreateMatrix_DA_*AIJ, looking to improve performance in GPU environments

1) PetscCalloc*() now uses system calloc()
2) Merged some PetscMalloc*()
3) Eliminated unneeded PetscCalloc*()
4) Removed some memory allocations and copies in MatFDColoringSetUp(), added local variables for better compiler optimization
5) Added MatSetValues_SeqAIJ_SortedFull(), added MatSetOption(MAT_SORTED_FULL)
6) Optimized DMCreateMatrix_DA_*AIJ for nonperiodic case to automatically have sorted columns (faster MatSetValues() times)
7) Eliminated call to PetscMemzero() in PetscFree()

Commit-type: style-fix, feature

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Added PetscCUDAInitialize() which the user may call in the body of the program, -cuda_initialize 0 prevents PetscInitialize() from initializing CUDA

Add -cuda_initialize 0 as options database for CU

Added PetscCUDAInitialize() which the user may call in the body of the program, -cuda_initialize 0 prevents PetscInitialize() from initializing CUDA

Add -cuda_initialize 0 as options database for CUDA tests so machines won't load cuBLAS unless actually
utilizing it on the machine, update examples to filter option-cuda_initialize

Reported-by: Karl Rupp <me@karlrupp.net>
Commit-type: feature

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Merge remote-tracking branch 'origin/barry/add-petscarrayxxx-ops' [PR #1771]

Merge branch 'barry/petscoptionsint-help-message-new-value' [PR #1786]

* barry/petscoptionsint-help-message-new-value:
The -help message for PetscOptionInt(), PetscOptionsReal() etc now includes the

Merge branch 'barry/petscoptionsint-help-message-new-value' [PR #1786]

* barry/petscoptionsint-help-message-new-value:
The -help message for PetscOptionInt(), PetscOptionsReal() etc now includes the newly set value as well as the previous value.

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Added MatUpdateMPIAIJWithArrays()

Commit-type: optimization, feature, example
Reported-by: Hong Zhang <hongzhang@anl.gov>

Resolved issues brought up in PR

Commit-type: bug-fix, style-fix
Reported-by: Patrick Sanan <patrick.sanan@gmail.com>