Merge branch 'tisaac/feature-multiple-fields-complex-dmplex-vtk' into 'master'

Allow multiple fields and complex numbers in DMPlex VTK visualization

See merge request petsc/petsc!2247

Support viewing vecs with multifields in VTK from DMPlex

Change precedence when finding sections in DMPletscVTKWriteALL

Searching for "section" before resorting to DM makes it easier to view just a

Support viewing vecs with multifields in VTK from DMPlex

Change precedence when finding sections in DMPletscVTKWriteALL

Searching for "section" before resorting to DM makes it easier to view just a single
field of a vector: rather than computing a subdm, we just get the field section and
compose it with a thin duplicate of the vector

Use composed "section" in DMPlexVTKWriteAll_VTU

Handle multifield vecs in VecView_Plex_Local_VTK

Test VTK multifield output in ascii and vtu in snes tutorials ex24

Make plexvtu use the sections composed with the vectors, provide vector output, and have more sensible names

Tranfer vector fields expanded to 3 components in one transfer

Only put a number on a field if there is more than one field

Add fieldnum argument to PetscViewerVTKAddField()

Now a vector can be added only for a single field to be printed. We can add the same field
multiple times. This avoids copying fields of a vector into separate vectors for viewing

show more ...

Merged in haplav/feature-hdf5-collective-options (pull request #1737)

add ability to turn on/off HDF5 collective transfer mode

Approved-by: Matthew Knepley <knepley@gmail.com>
Approved-by: BarryFSm

Merged in haplav/feature-hdf5-collective-options (pull request #1737)

add ability to turn on/off HDF5 collective transfer mode

Approved-by: Matthew Knepley <knepley@gmail.com>
Approved-by: BarryFSmith <bsmith@mcs.anl.gov>

show more ...

HDF5: Transfer mode defaults to independent wherever applicable and for all HDF5 versions.

Use PetscViewer_HDF5.dxpl_id instead of making new property list everytime.

Merge remote-tracking branch 'origin/maint'

Merged in sajid__ali/petsc/bugfix_complex_dmda_hdf5 (pull request #1615)

Fix complex DMDA write attribute bug

Approved-by: BarryFSmith <bsmith@mcs.anl.gov>
Approved-by: Matthew Knepley <knepley@gma

Merged in sajid__ali/petsc/bugfix_complex_dmda_hdf5 (pull request #1615)

Fix complex DMDA write attribute bug

Approved-by: BarryFSmith <bsmith@mcs.anl.gov>
Approved-by: Matthew Knepley <knepley@gmail.com>

show more ...

Fix complex DMDA write attribute bug
modified: src/dm/impls/da/gr2.c

Merge branch 'master' into wence/feature-patch-all-at-once

Merge branch 'haplav/fix-cray-warnings' [PR #1357]

* haplav/fix-cray-warnings:
Fixes warnings obtained with craycc

Merge branch 'haplav/maint/fix-cray-warnings' into maint [PR #1358]

* haplav/maint/fix-cray-warnings:
Fix a few craycc warnings

Cray had some good points

Cray had some good points

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

Merge branch 'master' into knepley/fix-plex-partition-parallel

* master: (414 commits)
very small updates to users manual
syntax is define(XXX) in examples tests not defined(XXX)
Increase patc

Merge branch 'master' into knepley/fix-plex-partition-parallel

* master: (414 commits)
very small updates to users manual
syntax is define(XXX) in examples tests not defined(XXX)
Increase patchlevel to 3.10.3
petsc4py: updat to latest maint snapshot with SNESTEST updates
Fix link for CUDA example in PETSc from GPUs.html page Minor fixes to installation instructions
Mat: Fixed types in Pardiso interface
Converted example comment to latex
This example crashes (for unknown reasons, probably related to the handling of extended derived types passed as arguments) with the PGI Fortran compiler
Remove outdated requires: from top of several examples
remove outdated test requires: command from top of source file
Fix the documentation for -ksp_gmres_cgs_refinement_type
Commit f20c2d659b168217cb455989f28afe052d71a64c broke lex.py so the users manual was no longer being built. There reverted the changes to lex.py
Plex: Add PetscPartitioner to fort list Suggested-by: Jiaoyan Li <Jiaoyan.Li@inl.gov>
Doc: Fix spelling Suggested-by: Manuel Colera Rico <m.colera@upm.es>
Mat ex88: check in double or quad precision only
Fix error with PetscComplex when PETSc is compiled with C and used in C++
configure: fix typo endwith -> endswith
Sys ex23: Migrated to ts_max_time in yaml file as well.
AO ex5: Fixed missing CHKERRQ();
Mat test ex88: add tests for MatMultAdd and MatMultTranposeAdd
...

Conflicts:
src/dm/impls/plex/examples/tests/ex12.c

show more ...

Merge branch 'haplav/drop-support-hdf5-older-than-1.8.0' [PR #1268]

* haplav/drop-support-hdf5-older-than-1.8.0:
Drop support for HDF5 older than 1.8.0.
No attempts to take advantage of 1.8.0+ API t

Merge branch 'haplav/drop-support-hdf5-older-than-1.8.0' [PR #1268]

* haplav/drop-support-hdf5-older-than-1.8.0:
Drop support for HDF5 older than 1.8.0.
No attempts to take advantage of 1.8.0+ API to simplify codes, will be done progressively later
See also https://lists.mcs.anl.gov/pipermail/petsc-dev/2018-December/023812.html for discussion.

show more ...

strip preprocessor conditionals regarding HDF5 version

Merge from master

Merged petsc/petsc into master

Merge branch 'master' into knepley/fix-superdm-is

* master: (455 commits)
bib: spell out some names for format consistency with related refs
bib: two 2018 pubs now appeared
cleaning up analyze

Merge branch 'master' into knepley/fix-superdm-is

* master: (455 commits)
bib: spell out some names for format consistency with related refs
bib: two 2018 pubs now appeared
cleaning up analyzer warnings
compile fixes (workarround PGI bug?):
undoing the branch's changes to leastsquares outputs
more fixes for complex builds
compile error fix for complex builds
1) Look for 64 bit integer MKL BLAS if 64 bit indices are used with PETSc 2) Fix Pardiso code to only compile pardiso_init64 when needed, otherwise can generate warnings/errors
jenkins: run 'cleantest' before 'allgtest-tap' - an attempt to fix errors of type:
cuda: protect cuda includes
fix cuda warnings.
fix complex compile error
Revert "Improved polymorphism of interfaces for MatSetValuesBlocked()"
Bib: Updated ref
Doc: More function documentation
petscvec: move PetscSFCreateFromZero from vscat to vec sources
Fixed an uninitialized variable and got rid of an unused one.
memleak fixed and output files updated
fixing build errors on some archs
Mat: obey options prefix of Mat in MatNullSpaceTest
...

Conflicts:
include/petsc/private/dmpleximpl.h
src/dm/interface/dmi.c

show more ...

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

* master: (281 commits)
compile fixes (workarround PGI bug?):
1) Look for 64 bit integer MKL BLAS if 64 bit indices are used with PETSc 2) Fix

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

* master: (281 commits)
compile fixes (workarround PGI bug?):
1) Look for 64 bit integer MKL BLAS if 64 bit indices are used with PETSc 2) Fix Pardiso code to only compile pardiso_init64 when needed, otherwise can generate warnings/errors
jenkins: run 'cleantest' before 'allgtest-tap' - an attempt to fix errors of type:
cuda: protect cuda includes
fix cuda warnings.
fix complex compile error
Revert "Improved polymorphism of interfaces for MatSetValuesBlocked()"
Bib: Updated ref
Doc: More function documentation
petscvec: move PetscSFCreateFromZero from vscat to vec sources
Mat: obey options prefix of Mat in MatNullSpaceTest
Plex+SNES: Must pass user context through
vscat: move ftn-custom to correct location remove custom vecscatterdestroy_()
vscat: move interface routines to correct location
vscat: delete dead code
fix compile error
FE: Correct coordinates in IntegrateBd
Bib: Added refs
SNES ex17: 3D tests must require a 3D grid generator
Plex+TS: We cannot run the check with the same vector that is the TS solution
...

Conflicts:
include/petsc/private/dmpleximpl.h
src/docs/website/documentation/changes/dev.html
src/snes/examples/tutorials/ex13.c
src/snes/utils/dmplexsnes.c

show more ...

Merge branch 'master' into arcowie-rem/feature-error-logging

* master: (249 commits)
Bib: Added refs
Netcdf should always build netcdf-4 (needed for example by exodusii.
trivial fixes of incor

Merge branch 'master' into arcowie-rem/feature-error-logging

* master: (249 commits)
Bib: Added refs
Netcdf should always build netcdf-4 (needed for example by exodusii.
trivial fixes of incorrect formatting in SNES linesearch routines
ISSetBlockSize_General: removed blockwise contiguity check.
netcdf: set zlib as optional dependency corretly [wrt --enable-netcdf-4] - otherwise netcdf configure errors out
config prefix: avoid ad-hoc path substitutions
config/install: no need to rename paths for installBinDir
rules: fix path in (evidently unimportant) uncrustify target
config pkgconfig: use ${prefix} in PETSc.pc and do not modify in install
fix gcov obj path
Improved polymorphism of interfaces for MatSetValuesBlocked()
-options_table was changed to options_view in 2014 but documentation was not updated to reflect it
configure: fix F2003 test
Dev manual: remove duplicate entry
Plex test ex5: Removed "future" test, as it resulted in issues in the nightly tests.
Some minor typos in TS
Add ADIOS2.py which I forgot to git add in the past
Plex ex5: Disable test
Doc: Added note for interface change
KSPLSQRMonitorDefault fixed for quad precision
...

show more ...