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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Many fixes to get PETSc and --download-fblaslapack working with nagfor compiler

Works with --download-fblaslapack, --download-scalapack, --download-mpich (does not work with --download-mumps)

Uses

Many fixes to get PETSc and --download-fblaslapack working with nagfor compiler

Works with --download-fblaslapack, --download-scalapack, --download-mpich (does not work with --download-mumps)

Uses lib/petsc/bin/petscnagfor as wrapper compiler since nagfor cannot work natively with the PETSc/standard Unix build environment

Required fixes/modernizations for BLAS/LAPACK source code (updated in the branch used by this branch, need to make it a tag when done)

Found a couple of portability issues with PETSc mpif.h

When package build fails they will no longer dump all the (huge amount) build output to the screeen

Commit-type: portability-fix

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

Various improvements for GPUs (mostly for performance and CUDA)

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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Various improvements for GPUs (mostly for performance and CUDA)

1) Add VecPinToCPU() for CUDA vector and matrices
2) Move initialization of cuBLAS to PetscInitialize() since it takes 1/2 second and

Various improvements for GPUs (mostly for performance and CUDA)

1) Add VecPinToCPU() for CUDA vector and matrices
2) Move initialization of cuBLAS to PetscInitialize() since it takes 1/2 second and distorts timing with -log_view
3) Add logging for DMCreateMatrix (for large meshes this is very large)
4) Add VecGet/RestoreArrayWrite() to prevent unneeded copies from GPU (only implemented so far for CUDA);
added a small number of usages in the source so that snes tutorials ex19 does not do unneeded communication from the GPU
5) Automatically convert MAIJ matrices to AIJ for CUDA since they are not yet supported natively in PETSc's CUDA matrix implementation
6) Pinned objects should still use the CUDA/ViennaCL versions of Destroy to clean up the GPU stuff

Commit-type: feature

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Merge remote-tracking branch 'origin/maint'

Merged in balay/fix-more-mpi_2int/maint (pull request #1793)

remove code that assumes MPI_2INT is a macro.

Approved-by: BarryFSmith <bsmith@mcs.anl.gov>
Approved-by: Karl Rupp <me@karlrupp.net>

remove code that assumes MPI_2INT is a macro.

This is a continuation of the fix in bcb1dc63284765edb2c98905bc313bc2d01136a1

/p/work1/bctacct/sw/app/math/PETSc/3.11.2/include/petscmath.h:708:19: err

remove code that assumes MPI_2INT is a macro.

This is a continuation of the fix in bcb1dc63284765edb2c98905bc313bc2d01136a1

/p/work1/bctacct/sw/app/math/PETSc/3.11.2/include/petscmath.h:708:19: error: ‘MPI_2INT’ redeclared as different kind of symbol
#define MPIU_2INT MPI_2INT
^
/p/work1/bctacct/sw/app/math/PETSc/3.11.2/src/sys/objects/init.c:76:14: note: in expansion of macro ‘MPIU_2INT’
MPI_Datatype MPIU_2INT = 0;
^
In file included from /p/work1/bctacct/sw/app/math/PETSc/3.11.2/include/petscsys.h:134:0,
from /p/work1/bctacct/sw/app/math/PETSc/3.11.2/src/sys/objects/init.c:9:
/p/app/sgi/mpt/mpt-2.15/include/mpi.h:143:2: note: previous definition of ‘MPI_2INT’ was here
MPI_2INT = 34,
^

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Merge remote-tracking branch 'origin/psanan/docs-remove-manconcepts' [PR #1733]

Man pages: remove Concepts: fields

These fields were previously stripped from the man pages by logic removed in
21a59cba2737d49dc2f0bd12c08db0d2a3f3f209

Remove these fields from all man pages (but

Man pages: remove Concepts: fields

These fields were previously stripped from the man pages by logic removed in
21a59cba2737d49dc2f0bd12c08db0d2a3f3f209

Remove these fields from all man pages (but not from examples).

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 -not -path "*/examples/*" -not -name "*.html" -not -name "*.bib" -exec gsed -i '/Concepts:/ {N; /\n\s*$/d}' {} +
find src -type f -not -path "*/examples/*" -not -name "*.html" -not -name "*.bib" -exec gsed -i '/Concepts:/d' {} +
find include -type f -not -path "*/examples/*" -not -name "*.html" -not -name "*.bib" -exec gsed -i '/Concepts:/ {N; /\n\s*$/d}' {} +
find include -type f -not -path "*/examples/*" -not -name "*.html" -not -name "*.bib" -exec gsed -i '/Concepts:/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

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Merged in rmills/feature-cuda-show-device-assignment (pull request #1708)

Device assignments by rank are now printed by -cuda_show_devices.

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

compile fix for --with-64-bit-indicies

CUDA command line options now have proper documentation via -help.

Added -cuda_view; deprecated -cuda_show_devices. Added help for -cuda_view.

Merged in jed/sizeof (pull request #1706)

Migrate sizeof-related definitions to run-time/non-batch as appropriate

Approved-by: Lisandro Dalcin <dalcinl@gmail.com>
Approved-by: BarryFSmith <bsmith@m

Merged in jed/sizeof (pull request #1706)

Migrate sizeof-related definitions to run-time/non-batch as appropriate

Approved-by: Lisandro Dalcin <dalcinl@gmail.com>
Approved-by: BarryFSmith <bsmith@mcs.anl.gov>
Approved-by: Jed Brown <jed@59a2.org>

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MPIU_SIZE_T: define at run-time

MPIU_FORTRANADDR: define at run-time

Device assignments by rank are now printed by -cuda_show_devices.

Merged in barry/log-memory (pull request #1677)

Introduce logging of memory usage to the PETSc event logging infrastructure.

Introduce logging of memory usage to the PETSc event logging infrastructure.

The logging can be turned on and viewed with the options -log_view -log_view_memory

The logging requires the use of the

Introduce logging of memory usage to the PETSc event logging infrastructure.

The logging can be turned on and viewed with the options -log_view -log_view_memory

The logging requires the use of the PETSc malloc so may slow the runs slightly but since it is not
doing error checking of the memory it should not slow down the computations significently.

Four pieces of information about memory are logged and display in four additional columns in the table.
They are documented in the output above the table. Each column provides a particular "view" of the
memory usage in the event and they complement each other.

This should make it much easier for developers focusing on memory usage in their implementations
to understand the usage in the code, where the memory is being utilized, how it scales with problem size and number of processes etc.

Commit-type: feature

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Merge branch 'master' into jpusztay/feature-swarm-symplectic-example

Merged petsc/petsc into master

Merge branch 'master' into knepley/feature-snes-patch

Merged petsc/petsc into master

Merged petsc/petsc into master