| 31c15585 | 19-Apr-2017 |
Barry Smith <bsmith@mcs.anl.gov> |
Merge branch 'dalcinl/fix-bdf-adapt' into barry/update-petscfileretrieve |
| e1eafdbb | 19-Apr-2017 |
Barry Smith <bsmith@mcs.anl.gov> |
update tchem commit to get version that allows ./configure to control CFLAGS argument (for example passing -g)
Commit-type: bug-fix
Funded-by: IMEX
Project: chemistry
Thanks-to: Jed Brown <jed@jedbr
update tchem commit to get version that allows ./configure to control CFLAGS argument (for example passing -g)
Commit-type: bug-fix
Funded-by: IMEX
Project: chemistry
Thanks-to: Jed Brown <jed@jedbrown.org>
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| 5c62c43c | 18-Apr-2017 |
Matthew G. Knepley <knepley@gmail.com> |
Configure: Give precision a default (double) |
| 3afe00f5 | 18-Apr-2017 |
Matthew G. Knepley <knepley@gmail.com> |
Configure: There should be no PETSc dependencies in BuildSystem
- Also, these look unused |
| f6891b87 | 18-Apr-2017 |
Satish Balay <balay@mcs.anl.gov> |
pflotran: switch to using the new upstream git repo
Thanks-to: Hammond, Glenn E <gehammo@sandia.gov> |
| a12b9eaf | 18-Apr-2017 |
Toby Isaac <tisaac@uchicago.edu> |
Merge branch 'tisaac/feature-plex-deterministic-viewing' into tisaac/feature-plex-tests-new
* tisaac/feature-plex-deterministic-viewing:
DMLabel: sort strata after distributing
PetscError() did
Merge branch 'tisaac/feature-plex-deterministic-viewing' into tisaac/feature-plex-tests-new
* tisaac/feature-plex-deterministic-viewing:
DMLabel: sort strata after distributing
PetscError() did not properly copy over the specific error message when error type was PETSC_ERROR_INITIAL
Additional clarification for MatMeshToCellGraph() manual page
med: --with-hdf5, not --with-hdf5-dir
DMPlex_GMSH: revert to not inverting triangles
sys tests ex13f: fix type mismatch in composition test
PCBDDC: use a sparse rhs when the solver is MUMPS
Sys ex13: Added test for object composition in Fortran
Sys: Added Fortran binding for object composition
MatMUMPS: added support for sparse right-hand sides in sequential
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| 92a3a55e | 13-Apr-2017 |
Toby Isaac <tisaac@uchicago.edu> |
med: --with-hdf5, not --with-hdf5-dir
at least in the version of med that I got from --download-med |
| a57b75f0 | 12-Apr-2017 |
Toby Isaac <tisaac@uchicago.edu> |
Merge branch 'tisaac/fix-dm-tests' into tisaac/feature-plex-tests-new
* tisaac/fix-dm-tests:
dmplex tests ex1: update output for ISLocalToGlobalMapping changes
DMNetwork: Use the default section
Merge branch 'tisaac/fix-dm-tests' into tisaac/feature-plex-tests-new
* tisaac/fix-dm-tests:
dmplex tests ex1: update output for ISLocalToGlobalMapping changes
DMNetwork: Use the default sections with plex when getting offset.
Add another extchem test case
Fix for extchem.c when envelop monitor is on, but graphical monitoring is off
TSAdapt ascii view should show dt_min and dt_max
Forgot to include example file
Change extchem.c to accept mole values for initial conditions instead of mole fractions
Update extchem.c example to 1) use pressure, 2) use options file, 3) read initial conditions from file
DMNetwork: API to return the underlying DMPlex.
deprecate MatGetSubMatXXX Requested-by: Jed Brown <jed@jedbrown.org>
Work around for Apple Xcode bug with rpath
DMPlex_GMSH: triangles are inverted
bib: fix URL for StarForest note
rm MatLUFactorNumeric_SeqBAIJ_11_NaturalOrdering() because it does not improve performance add MatSolve_SeqBAIJ_bs_NaturalOrdering(), bs=12,...,14 add test runex50_2
experiment PetscKernel_A_gets_A_minus_B_times_C_11
add timer to MatLUFactorNumeric_SeqBAIJ_11_NaturalOrdering()
test new A = A*B
implement MatSolve_SeqBAIJ_11_NaturalOrdering
Merge two line TSAdapt monitor to a single line, shorten line, reorder presented values
implement PetscKernel_A_gets_A_times_B_11()
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| f239ade3 | 12-Apr-2017 |
Toby Isaac <tisaac@uchicago.edu> |
Merge branch 'tisaac/feature-fe-dual-apply' into tisaac/feature-plex-tests-new
There has unfortunately been a lot of interplay between our work to
change the petscspace/dualspace to accept vector co
Merge branch 'tisaac/feature-fe-dual-apply' into tisaac/feature-plex-tests-new
There has unfortunately been a lot of interplay between our work to
change the petscspace/dualspace to accept vector components, and the
work to transfer the tests in config/builder.py to the new test harness.
I'm merging them together to get them to play nice with each other, and
so that I only have one feature branch to handler when merging into
master/next.
* tisaac/feature-fe-dual-apply: (64 commits)
snes tutorials ex12: fix restart test arguments
nightly build fixes for arch-viennacl
fix run command to match the command in master/makefile. [the diff will be correct in master/next]
PetscFE: fix typo in for loop declaration
PetscPartitioner: use simple partitioning for regression tests
DT tests ex1: fix test arguments to match regression output
DT ex1: fix options
DMPlexCreateHexBoxMesh: no cells in z direction for 2D
PCBDDC: use %D for PetscInt printfs
Plex: helper function used in all cases now
Plex tests ex7: make partitions portable for testing
Plex: use MPIU_2INT instead of MPI_2INT
MatAIJ KLU: remove redefinition of SuiteSparse_long
DMPlexRefine_CTetgen() mimics DMPlexRefine_Tetgen()
DMPlexGenerate_Tetgen(): mimic ctetgen so it can be used equivalently
Plex: Cylinder fixes for complex
Plex ex1: Test for periodic cylinder
Plex: I think periodic cylinder is working
Plex ex1: Updated torus test
Plex: Torus can now be arbitrarily refined
...
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| 0c4f890a | 08-Apr-2017 |
Barry Smith <bsmith@mcs.anl.gov> |
Update PetscFileRetrieve() to use curl, clarify documentation, and no longer save to /tmp directory
Update tchem.py to install the periodictable.dat file
Update extchem.c example to utilize PetscFil
Update PetscFileRetrieve() to use curl, clarify documentation, and no longer save to /tmp directory
Update tchem.py to install the periodictable.dat file
Update extchem.c example to utilize PetscFileRetrieve() allowing users to directly provide the URL
of needed chemistry and thermo data files.
Update extchem.c to automatically copy over periodictable.dat from installed location if needed
Commit-type: feature, documentation, example
Funded-by: IMEX
Project: chemistry
Time: 2.5 hours
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| fbfa34dc | 03-Apr-2017 |
Barry Smith <bsmith@mcs.anl.gov> |
Merge branch 'maint' |
| 56847a4e | 03-Apr-2017 |
Barry Smith <bsmith@mcs.anl.gov> |
Work around for Apple Xcode bug with rpath
Commit-type: bug-fix
Reported-by: Lawrence Mitchell <lawrence.mitchell@imperial.ac.uk> |
| 8bee6947 | 30-Mar-2017 |
Matthew G. Knepley <knepley@gmail.com> |
Merge branch 'master' into knepley/feature-plex-tests-new
* master: (108 commits)
Bib: Added ref
Bib: Updated reference
Bib: Updated reference
Work around problems with Apple Xcode 8.3 and h
Merge branch 'master' into knepley/feature-plex-tests-new
* master: (108 commits)
Bib: Added ref
Bib: Updated reference
Bib: Updated reference
Work around problems with Apple Xcode 8.3 and handling of rpath argument with gfortran
help menu update for MatCreateSubMatrices() Reported-by: Brad Aagaard <baagaard@usgs.gov>
fix flops for PCApply_PBJacobi_1 and PCApply_PBJacobi_7 Reported-by: Pierre Jolivet <pierre.jolivet@enseeiht.fr>
TSRK: Fix FSAL optimization to not skip update and check or stages.
Travis-CI: Workaround too long TMPDIR in macOS with Open MPI
test: Fix type mismatch in KSP test.
test: Fix warnings from gfortran -Wconversion (OS X, Homebrew build)
MPIUNI: Silence GCC -Wconversion warnings
Fortran: Add error checking for incorrect PETSC_NULL_XXX argument when expecting function
fix test output per changes in 517c9301b2e9239931bfd644803fd6bb859387ea
MUMPS: update to version 5.1.1 with opensolaris compile fixes
TSRK: Mention 5BS in the changelog.
TSRK: Mention the new 5BS scheme in the manual.
fix 'unused variable' warning
Remove unused code
added hbw_realloc
fixed undefined ptr
...
Conflicts:
config/BuildSystem/config/packages/med.py
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| 4fe14646 | 29-Mar-2017 |
Barry Smith <bsmith@mcs.anl.gov> |
Merge branch 'maint' |
| 4f290403 | 29-Mar-2017 |
Barry Smith <bsmith@mcs.anl.gov> |
Work around problems with Apple Xcode 8.3 and handling of rpath argument with gfortran
Configure produced errors of the form:
Executing: gfortran -o /var/folders/c1/ldz_dt8n2r3dtwv_chp5pfr40000gn/T
Work around problems with Apple Xcode 8.3 and handling of rpath argument with gfortran
Configure produced errors of the form:
Executing: gfortran -o /var/folders/c1/ldz_dt8n2r3dtwv_chp5pfr40000gn/T/petsc-rEw79r/config.setCompilers/conftest -Wl,-multiply_defined,suppress -Wl,-multiply_defined -Wl,suppress -Wl,-commons,use_dylibs -Wl,-search_paths_first -Wl,-no_compact_unwind -Wall -ffree-line-length-0 -Wno-unused-dummy-argument -g /var/folders/c1/ldz_dt8n2r3dtwv_chp5pfr40000gn/T/petsc-rEw79r/config.setCompilers/conftest.o -lto_library -Wl,-rpath,/Applications/Xcode.app/Contents/Developer/Toolchains/XcodeDefault.xctoolchain/usr/lib -L/Applications/Xcode.app/Contents/Developer/Toolchains/XcodeDefault.xctoolchain/usr/lib -lLTO -ldl -lSystem -Wl,-rpath,/Applications/Xcode.app/Contents/Developer/Toolchains/XcodeDefault.xctoolchain/usr/bin/../lib/clang/8.1.0/lib/darwin -L/Applications/Xcode.app/Contents/Developer/Toolchains/XcodeDefault.xctoolchain/usr/bin/../lib/clang/8.1.0/lib/darwin -lclang_rt.osx -ldl
Possible ERROR while running linker: exit code 256
stderr:
ld: can't map file, errno=22 file '/Applications/Xcode.app/Contents/Developer/Toolchains/XcodeDefault.xctoolchain/usr/lib' for architecture x86_64
collect2: error: ld returned 1 exit status
By avoid these -Wl,rpath we avoid the errors. This patch does not directly deal with the error above but merely bypasses the problem.
Commit-type: bug-fix
Funded-by: ECP
Project: ECP
Time: 2 hours
Reported-by: Denis Davydov <davydden@gmail.com>
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| 989ce014 | 25-Mar-2017 |
Satish Balay <balay@mcs.anl.gov> |
Merge remote-tracking branch 'origin/hongzh/knl' |
| b8fd506b | 25-Mar-2017 |
Satish Balay <balay@mcs.anl.gov> |
Merge remote-tracking branch 'origin/balay/update-sowing-1.1.25-p1' |
| 246807d0 | 25-Mar-2017 |
Satish Balay <balay@mcs.anl.gov> |
Merge remote-tracking branch 'origin/balay/update-mumps-5.1.1' |
| 83b9db01 | 25-Mar-2017 |
Satish Balay <balay@mcs.anl.gov> |
Merge remote-tracking branch 'origin/balay/hdf5-switch-zlib-to-odep' |
| 5bea24c4 | 25-Mar-2017 |
Satish Balay <balay@mcs.anl.gov> |
Merge remote-tracking branch 'origin/balay/enable-download-zlib-static' |
| e1db6d8b | 23-Mar-2017 |
Satish Balay <balay@mcs.anl.gov> |
MUMPS: update to version 5.1.1
with opensolaris compile fixes
Reported-by: Tim Steinhoff <kandanovian@gmail.com> |
| 2f21b5c6 | 29-Sep-2016 |
Hong Zhang <hongzhang@anl.gov> |
add HBW allocator and a special use case for adjoint checkpointing on KNL
Funded-by:
Project: PETSc for Theta
Time: 8 hours
Reported-by:
Thanks-to: |
| d6bfaaaf | 24-Mar-2017 |
Satish Balay <balay@mcs.anl.gov> |
configure: flag usage of type '--with-hdf5-dir=PATH --download-zlib' as error
Reported-by: Mark Adams <mfadams@lbl.gov>
Thanks-to: Barry Smith <bsmith@mcs.anl.gov> |
| 00f95474 | 24-Mar-2017 |
Satish Balay <balay@mcs.anl.gov> |
zlib: enable static build with --with-shared-libraries=0 option
- add -download-zlib-static option for use with --with-shared-libraries=1 - useful when libz.so build fails - but libpetsc.so would wor
zlib: enable static build with --with-shared-libraries=0 option
- add -download-zlib-static option for use with --with-shared-libraries=1 - useful when libz.so build fails - but libpetsc.so would work
Reported-by: Mark Adams <mfadams@lbl.gov>
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| b1227980 | 22-Mar-2017 |
Satish Balay <balay@mcs.anl.gov> |
pflotran: hdf5 is an optional dependency
Reported-by: Sergi Molins Rafa <smolins@lbl.gov>
Thanks-to: "Hammond, Glenn E" <gehammo@sandia.gov> |