Fix manual pages for MatXXXYBAIJSetPreallocationCSR() routines

Commit-type: documentation

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>

show more ...

Merge from doc-fixes branch

Fixes for doctext update

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

show more ...

Added MatUpdateMPIAIJWithArrays()

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

Add PetscArraycmp(), PetscArraycpy(), PetscArrayzero(), PetscArraymove(), update code to use new forms

Replace a couple multi-mallocs with a single malloc
Replace backwards loops in MatSetValues_*()

Add PetscArraycmp(), PetscArraycpy(), PetscArrayzero(), PetscArraymove(), update code to use new forms

Replace a couple multi-mallocs with a single malloc
Replace backwards loops in MatSetValues_*() with PetscArraymove()

Commit-type: style-fix, feature

show more ...

Merge remote-tracking branch 'origin/maint'

Fixed misspelling of "paradigm" throughout manual pages.

Update the use of Collective on in the manual pages to reflect the new style

Commit-type: style-fix, documentation
Thanks-to: Patrick Sanan <patrick.sanan@gmail.com>

Man pages: remove .keywords: fields

This field is recognized by doctext from Sowing (http://wgropp.cs.illinois.edu/projects/software/sowing/doctext/node20.htm#Node20),
but it doesn't seem to be unif

Man pages: remove .keywords: fields

This field is recognized by doctext from Sowing (http://wgropp.cs.illinois.edu/projects/software/sowing/doctext/node20.htm#Node20),
but it doesn't seem to be uniformly used or maintained.

Thus, remove all .keywords: fields, and a following blank line, if present.

This is accomplished with GNU sed (gsed on OS X), with the following commands.
*Warning* that this type of command can corrupt a .git directory,
so be cautious in reusing or modifying these commands. They first look
for and delete matching lines with a following line consisting of only whitespace,
and then delete any remaining matching lines.

find src/ -type f -exec gsed -i '/keywords:/ {N; /\n\s*$/d}' {} +
find src/ -type f -exec gsed -i '/keywords:/d' {} +
find include/ -type f -exec gsed -i '/keywords:/ {N; /\n\s*$/d}' {} +
find include/ -type f -exec gsed -i '/keywords:/d' {} +

Hints on the sed command obtained from: https://unix.stackexchange.com/questions/100754/how-to-delete-a-specific-line-and-the-following-blank-line-using-gnu-sed

show more ...

Binary I/O: Various fixes and enhancements

* Change PetscBinary[Synchronized]Read() to allow for reading
items up to EOF without erroring
* Fix PetscViewerBinaryRead() to properly return the numbe

Binary I/O: Various fixes and enhancements

* Change PetscBinary[Synchronized]Read() to allow for reading
items up to EOF without erroring
* Fix PetscViewerBinaryRead() to properly return the number of items read
* Fix PetscViewerRead() to prevent infinite loops at EOF
* Various fixes for PetscDataType PETSC_COMPLEX

show more ...

Merged in stefano_zampini/fix-matcomputeexplicitop (pull request #1570)

Allow specifying an operator type when computing operators explicitly

Approved-by: BarryFSmith <bsmith@mcs.anl.gov>
Approved-

Merged in stefano_zampini/fix-matcomputeexplicitop (pull request #1570)

Allow specifying an operator type when computing operators explicitly

Approved-by: BarryFSmith <bsmith@mcs.anl.gov>
Approved-by: Patrick Sanan <patrick.sanan@gmail.com>

show more ...

Mat{MPI|MPISB|MPIB|Seq|SeqB|SeqSB}AIJSetPreallocation: optimize nonzeros

set number of columns of offdiag blocks to zero for sequential cases
no need to allocate more than the the number of columns

Mat{MPI|MPISB|MPIB|Seq|SeqB|SeqSB}AIJSetPreallocation: optimize nonzeros

set number of columns of offdiag blocks to zero for sequential cases
no need to allocate more than the the number of columns for sequential matrices

Update outputs for testsuite

show more ...

MatConvert_{MPI|Seq}SBAIJ_*: add MAT_REUSE_MATRIX support

MatCopy_{MPI,Seq}SBAIJ: error if not using the symmetric storage

MatCopy_SeqSBAIJ: fix improper array size

MatSetValues_SeqSBAIJ: fix values insertion for diagonal block entries

It is unbelievable that this bug was never been caught
add proper initialization of "high" (now it matches the other MatSetValu

MatSetValues_SeqSBAIJ: fix values insertion for diagonal block entries

It is unbelievable that this bug was never been caught
add proper initialization of "high" (now it matches the other MatSetValues_*AIJ implementations)

show more ...

housekeeping

remove trailing blanks
remove functions that are no longer part of PETSc