CUDA: Removed check for ancient CUDA version >= 5000

CUDA: Remove ancient checks for CUDA >= 4.2

Merge branch 'jczhang/sf-more-opts' [PR #1567]

* jczhang/sf-more-opts:
Add more optimizations in SF and use it as the default for VecScatter.

Merge branch 'barry/2019-07-21/scalapack-mumps-parallel-make' [PR #1896]

* barry/2019-07-21/scalapack-mumps-parallel-make:
Parallel make for --download-scalapack --download-mumps

Mumps no Cholesky with Hermitian, no PetscMallocValidate() unless -malloc_*, example used PetscAbsScalar() on real

Mumps has no support for Cholesky for Hermitian matrix so document and error check

Mumps no Cholesky with Hermitian, no PetscMallocValidate() unless -malloc_*, example used PetscAbsScalar() on real

Mumps has no support for Cholesky for Hermitian matrix so document and error check
Documentation says CHKMEMQ() and PetscMallocValidate() with -malloc_debug or -malloc_test but in fact
it still checked memory even without those being set (slowing code)
Example used PetscAbsScalar() on real values, also had incorrect indentation formating

Commit-type: testing-fix, style-fix, documentation, example

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Parallel make for --download-scalapack --download-mumps

Required added a new Makefile.parallel and Makefile.objs to the scalapack git repository to handle it tag v2.0.2-p

Fixed spelling of controll

Parallel make for --download-scalapack --download-mumps

Required added a new Makefile.parallel and Makefile.objs to the scalapack git repository to handle it tag v2.0.2-p

Fixed spelling of controller in mpishm.c

Refactoring of part of MATMUMPS manual page to clafiy and simplify the discussion of hybrid MPI/OpenMP, note that it
supports both modesl for MPI/OpenMP

Commit-type: configuration

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MUMPS: Add comments for a TODO optimization

MUMPS: Use VecScatterCreateToZero to simplify RHS scatter code

removing comments

adding GPU-GPU data movement to logging

-package-prefix-hash=directory will prefix the external packages based on a hash of the config directory
and configure arguments

Based on a suggestion by Satish Balay

All PETSc builds go as usual f

-package-prefix-hash=directory will prefix the external packages based on a hash of the config directory
and configure arguments

Based on a suggestion by Satish Balay

All PETSc builds go as usual for testing into PETSC_DIR/PETSC_ARCH.

Running with a different branch with the same config will generate the same hash and hence
reuse the previous external package builds.
Any change in the hash results in a COMPLETELY new external packages prefix

If one assumes that most merge requests do not involve changes to config this will result in a dramatic
savings in configure time plus no longer require someone to manually manage the pre-building of external
libraries and keeping them up to date. The same directory can be used for tests for maint and master since
maint will generate different hashes and thus have its own copies of the external libraries.

Also supports --arch-hash that sets PETSC_ARCH based on the same config hash.

Commit-type: testing-fix, feature
Thanks-to: Satish Balay <balay@mcs.anl.gov>

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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 'gropp/doc-fixes-1' [PR #1838]

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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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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Merge branch 'hannah/gpu-computation-logging' [PR #1843]

* hannah/gpu-computation-logging:
Adding GPU flop rate and GPU time.

Merge branch 'pr1835/al007/reset-prealloc-comm/master' [PR #1835]

* pr1835/al007/reset-prealloc-comm/master:
Change the communicator for MatResetPreallocation_SeqAIJ error, otherwise the user doesn'

Merge branch 'pr1835/al007/reset-prealloc-comm/master' [PR #1835]

* pr1835/al007/reset-prealloc-comm/master:
Change the communicator for MatResetPreallocation_SeqAIJ error, otherwise the user doesn't get any meaningful error message

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Merge branch 'maint'

PetscLogGpuTimeStart -> Begin

Adding Gpu flop rate and GPU time

fix MatMissingDiagonal() for seqaij and seqbaij when matrix is non-square

Merge from doc-fixes branch

If local size zero, do nothing

Change the communicator for MatResetPreallocation_SeqAIJ error

Otherwise the user doesn't get any meaningful error message

Merged in hannah/gpu-communication-logging (pull request #1814)

Hannah/gpu communication logging

Approved-by: BarryFSmith <bsmith@mcs.anl.gov>
Approved-by: Richard Mills <rtm@eecs.utk.edu>