Changes in graph.py

80794ad0d33546c630dd24cf675e30370edae276 - Merge branch 'barry/2019-07-27/error-check-mpiexec' into 'master'

Tue, 24 Sep 2019 03:06:19 +0000

Merge branch 'barry/2019-07-27/error-check-mpiexec' into 'master'Large number of fixes, optimizations for configure, speeds up the configureSee merge request petsc/petsc!2046 List of files: /petsc/config/BuildSystem/graph.py

0542e31a63bf85c93992c9e34728883db83474ac - Large number of fixes, optimizations for configure, speeds up the configure

Sat, 27 Jul 2019 17:36:52 +0000

Large number of fixes, optimizations for configure, speeds up the configure1) turn off checking if MPI library is shared since that code has been broken for 3+ years2) move pure Fortran configure tests to compilersFortran.py3) turned threads back on but only use them for performing timeout for *runtest() commands (since they slow everything down if used everywhere)4) changed parallel configure (which doesn't work anyways) to use --useParallel and not overload --useThreads5) added runtime check of mpiexec that uses timeout (replaces previous test in MPI shared libraries)6) removed unused tests in configure in the interest of speed7) minor refactorization of configure for better support of parallel configure (which doesn't work)8) added timing results in configure.log. These may be accessed with grep child configure.log | sort -k3 -g9) add check that mpiexec given in configure test matches the MPI compilers and libraries usedCommit-type: optimization, bug-fix, portability-fix, featureReported-by: Carl Steefel List of files: /petsc/config/BuildSystem/graph.py

83c10b7ed13e5cf0bac5061cf1169b930c013b5f - Merged petsc/petsc into master

Tue, 04 Dec 2018 05:09:32 +0000

Merged petsc/petsc into master List of files: /petsc/config/BuildSystem/graph.py

a5a49157e8f0cda1ee246d4b38ccd40aa8bd8906 - Merge branch 'master' into jpusztay/feature-swarm-symplectic-example

Thu, 25 Oct 2018 15:44:39 +0000

Merge branch 'master' into jpusztay/feature-swarm-symplectic-example List of files: /petsc/config/BuildSystem/graph.py

e901d7f783378c340f80a71ad0d479b16cb27ec8 - Merge branch 'master' into jpustay/feature-swarm-example

Thu, 25 Oct 2018 15:37:37 +0000

Merge branch 'master' into jpustay/feature-swarm-example List of files: /petsc/config/BuildSystem/graph.py

baeaa64efad046693dfe8565b2a340832b8902ce - Merged petsc/petsc into master

Thu, 25 Oct 2018 15:34:14 +0000

Merged petsc/petsc into master List of files: /petsc/config/BuildSystem/graph.py

df90af5656ec20a6e3cb673af4e9b5c5d856317c - Merge branch 'master' into arcowie-rem/feature-error-logging

Wed, 24 Oct 2018 18:29:36 +0000

Merge branch 'master' into arcowie-rem/feature-error-logging* master: (393 commits) Bib: Update reference Mat: Doc fix Bib: Updated ref PetscDS: Doc fixes PC+LU: Do not try to refactor an already factored matrix Mat: Small fix for checking and docs Mat: Added MatSetFactorType() - Needed it when making a shell matrix look factored PetscDS: Added PetscDSUpdateBoundary() - Lets the user change the boundary condition single precision produces different convergence history p4est: has a dependency on zlib - so handle it correctly Add -mat_mffd_complex to use the Lyness complex number trick to compute J_u * v instead of differencing. Replace VecWAXPY by VecAXPY if needed Revert "Replace VecWAXPY by VecAXPY if needed" Replace VecWAXPY by VecAXPY if needed MatHermitianTransposeGetMat and MatCreateVecs ex19: Updated test filter to avoid false positives. DM: Improved Global-To-Natural docs Suggested-by: Josh L Do not build shared openblas when doing static build Upgrade OpenBLAS to 0.3.3 test: add alt output file for changes in OSX-10.14 and Xcode-10.0 [perhaps related to ML] ...Conflicts: src/vec/is/utils/vsectionis.c List of files: /petsc/config/BuildSystem/graph.py

27821aea53b95b424fe865570a4f61259f97b2ea - Merge branch 'jed/python3-futurize' [PR #1122]

Mon, 22 Oct 2018 15:49:06 +0000

Merge branch 'jed/python3-futurize' [PR #1122]Merge announces support for Python 3.4+ in changes/dev.html.* jed/python3-futurize: (44 commits) gmakegentest: avoid prefix matching in regex dm tests ex23.c: fix test args: -one -two -three gmakegentest: more fixes gmakegentest: fix processing of arguments containing number followed by "-" gmakegentest: always loop over nsize; Python-3 fixes python3: add in a python-3.4 test python: fix build on osx/opensolaris - where 'RANLIB=ranlib -c' i.e with a space.. python3: fix --download-ptscotch error configure: glob() gets executed early - whereas we need to get file list later [after 'make all' or equivalent] so revert back to using shell to get file-list python3: map() requires a list modifier for this usage. python: replace ModuleNotFoundError a python3.6+ feature with ImportError config: call setup to ensure that debugLevel is set nightlies: switch linux-pkg-dbg-ftn-interfaces to python3 config: enable Python-3 config: urllib/urlparse updates for Python-3 compatibility config fblaslapack: use isIBM instead of manual test python: replace commands with subprocess Fix LOCDIR paths generateetags.py: switch from commands to subprocess; unicode fix python: don't import commands when it isn't used ... List of files: /petsc/config/BuildSystem/graph.py

bb3dd2f65ef2449c5a5d945281d1be9b0cb6d0de - config: futurize filter()

Wed, 19 Sep 2018 04:24:05 +0000

config: futurize filter()Returns a list in Python-2, but a filter object in Python-3. Thereare many places that test isinstance(f, list) to distinguish stringsfrom lists, but a filter object behaves like a list for most purposes. List of files: /petsc/config/BuildSystem/graph.py

13a035b13f0d57cc952439d2c8f7ce514226f11a - Merge branch 'master' into knepley/feature-plex-elasticity-test

Mon, 13 Aug 2018 15:19:56 +0000

Merge branch 'master' into knepley/feature-plex-elasticity-test* master: (1553 commits) -options_table was changed to options_view in 2014 but documentation was not updated to reflect it configure: fix F2003 test 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 Tao: Added alternative output for chwirut2 test. TS ex45,ex46: Removed overly refined tests for faster nightly tests. KSP ex72: Fixed needlessly long-running PCTFS tests. SNES ex56: Reduced test size to speed up nightly test suite. KSPSolve_LSQR: don't compute unused norm of rhs SNES ex13: Reduced problem sizes for nightly tests. PetscOptionsDeprecated(): fix for NULL prefix PetscOptionsDeprecated(): add option to print additional info SNES ex12: Reduced sizes for BDDC tests. PetscFileRetrieve(): Suppress output to STDERR when downloading a file. MatMatMult: Fixed unused variable pN. DMDestroy: Guard call to dm->ops->destroy * Similar guards are in place in many other methods (IS,Vec,Mat) and permit the DM to be destroyed even if DMSetType() was never called. ... List of files: /petsc/config/BuildSystem/graph.py

59e7829ccff665372c1d09026a11beea9cbf8624 - Merge branch 'master' into knepley/feature-plex-parallel-submesh

Tue, 07 Aug 2018 17:51:05 +0000

Merge branch 'master' into knepley/feature-plex-parallel-submesh* master: (2931 commits) remove N in docs for SNESQN replaced test tolerance with PETSC_SQRT_MACHINE_EPSILON fortran: PetscComplex type is missing from fortran initialize variables so that static analyzer doesn't mistakenly think they are used uninitialized. Move access of prefix until it is actually used Remove DMDASplitComm2d(), used in one example that was not tested Functions that do not return PetscErrorCode should not use PetscFunctionBegin/End paradgm remove unneeded reassignment of same value Missing CHKERRQ(); Mostly in Tao code Remove clang static analyser warning about passing NULL variable to strncat() missing newline in -ts_monitor_extreme minor fixes for integer counters Configure: Deal with '__func__' in C89 builds with newer Clang and GCC. Jenkinsfile: Increased timeout for tests to 5 minutes. 3.9 changes: further clarify removal of -pc_factor_mat_solver_package Options deprecations: add "PETSc" to inline warning removing unused variable MatShift support added to MATSUBMAT. Mimics MATSHELL functionality. Needed for matrix-free Hessians in TAO Newton-Line-Search methods. Add -ts_monitor_extreme Dev manual: add note on deprecating options database keys ...Conflicts: src/dm/impls/plex/examples/tests/ex4.c List of files: /petsc/config/BuildSystem/graph.py

2f07c833297f1c1acc6a9f8c100af3fa2b180e36 - Merge branch 'master' into knepley/feature-snes-ex13-spectral

Sat, 14 Apr 2018 13:36:45 +0000

Merge branch 'master' into knepley/feature-snes-ex13-spectral* master: (2350 commits) migrate warning fix from next-tmp Revert "Remove dead code." clarifying comment in the code Remove dead code. Add JuMP citation Copyedits and updates to developers manual Add more protection to intrinsics MPI: protect arguments in MPI macros Add the missing conditionals for 64-bit build Plex+VTK: Fix field type determination Fix bug in name cleanup Bib: Added ref Plex+VTK: Fix field type determination Plex: Updated test output - I am now hating this shit forgot to save file after moving prototypes to petscsys.h update Apple example project settings per Xcode Two functions should actually be public, used, for example from Apple MacOS and iOS programs includes should always be included relative to include directory Apple removed old locations of docsets SNES ex12: Updated test output ...Conflicts: src/snes/examples/tutorials/ex13.c List of files: /petsc/config/BuildSystem/graph.py

9044fa666813e72067b2d44bab405329fb3f183c - Merge branch 'master' into knepley/fix-plex-residual-loop

Sat, 14 Apr 2018 11:17:56 +0000

Merge branch 'master' into knepley/fix-plex-residual-loopWarning: This merge includes real changes* master: (188 commits) Add JuMP citation Copyedits and updates to developers manual Add more protection to intrinsics MPI: protect arguments in MPI macros Add the missing conditionals for 64-bit build Plex+VTK: Fix field type determination Fix bug in name cleanup Bib: Added ref Plex+VTK: Fix field type determination Plex: Updated test output - I am now hating this shit forgot to save file after moving prototypes to petscsys.h update Apple example project settings per Xcode Two functions should actually be public, used, for example from Apple MacOS and iOS programs includes should always be included relative to include directory Apple removed old locations of docsets SNES ex12: Updated test output SNES ex62: Set name of solution vector - Update test output revert sources to dev - reset PETSC_VERSION_RELEASE - reset changes/dev.html release: set v3.9 strings move output file to the correct location. i.e fix 305862f9cd0dc399542ae11dd744508e4b6ad2e3 ...Conflicts: src/snes/utils/dmplexsnes.c src/ts/utils/dmplexts.c List of files: /petsc/config/BuildSystem/graph.py

e4bc0d72a7a62106b6c16a682dc8072909a4b1f1 - Merge branch 'master' into knepley/feature-pc-patch

Sun, 08 Apr 2018 18:11:26 +0000

Merge branch 'master' into knepley/feature-pc-patch* master: (440 commits) revert sources to dev - reset PETSC_VERSION_RELEASE - reset changes/dev.html release: set v3.9 strings fix grep usage on solaris [use egrep] opensolaris: fix errors Update timer reporting and minor reporting fix Remove redundant if statement. Found by @jedbrown Fixed problem with order of developer photos on website. superlu_dist: use correct flag in example [PETSC_HAVE_SUPERLU -> PETSC_HAVE_SUPERLU_DIST] Bib: PERMON ref fix for osx doc: more author fixes doc: more author fixes Italicized "orderings" in MPI process placement discussion. Added Richard to the user manual author list. Added Richard to the list of active developers on the website. add string check for MS-MPI and IMPI timeout errors opensolaris does not have multiple grep utils - but default one does not support -F. So use fgrep instead Standardizing timeout checks Report wall clock time of total tests Use time instead of date %s ...Conflicts: include/petscpc.h src/ksp/ksp/interface/itfunc.c List of files: /petsc/config/BuildSystem/graph.py

bccf594b29529893b47f8e18e56a9576025917fe - Merge remote-tracking branch 'origin/jed/futurize-stage-1'

Wed, 04 Apr 2018 20:39:42 +0000

Merge remote-tracking branch 'origin/jed/futurize-stage-1' List of files: /petsc/config/BuildSystem/graph.py

5b6bfdb9644f185dbf5e5a09b808ec241507e1e7 - python: futurize stage 1 (modernize python-2 code)

Mon, 02 Apr 2018 20:46:25 +0000

python: futurize stage 1 (modernize python-2 code)This should have no behavioral change. It was generated by running futurize -1 -nw config lib setup.py src systemsfollowed by reverting some "from . import" relative imports (PEP 328without 366) and fixing up RDict.py __contains__ to not cause recursion. List of files: /petsc/config/BuildSystem/graph.py

e366c154b69cf29c88be23f768f0f07dd2b3250c - Merge commit 'd47bf9aaf1e5266cc3f0ff499f934c85788965a9' into jed/fix-matcreatempibaij/maint

Wed, 15 Nov 2017 03:23:31 +0000

Merge commit 'd47bf9aaf1e5266cc3f0ff499f934c85788965a9' into jed/fix-matcreatempibaij/maintObtain changed (v3.5) handling of MatMPIBAIJSetPreallocationCSR to matchdocumentation. List of files: /petsc/config/BuildSystem/graph.py

e1b06f76ad35ce2a89fc667d1feb3b2de35f6e0a - Merge branch 'master' into knepley/solkx

Wed, 20 May 2015 13:47:27 +0000

Merge branch 'master' into knepley/solkx* master: (6933 commits) Bib: Added reference Includegraph: Updated for compatibility with new folder layout. Add SNESLineSearchReason to fortran includes Also truncate names to fit 32 char fortran limit fix compile warnings /usr/home/balay/petsc.clone-2/src/vec/vec/interface/vector.c:1944: warning: division by zero in '1.0e+0 / 0.' /usr/home/balay/petsc.clone-2/src/ksp/ksp/interface/itfunc.c:508: warning: 'vec_rhs' may be used uninitialized in this function updated output for new trust region initial size initial size of the trust region is set as a percent of the norm of the initial guess, it should not be related to the initial norm of the function (which is kind of nuts). The default bounds for SNESVISetVariableBounds() in the manual page were reversed from correct values Bib: Added refs Bib: Update MPICH webpage Plex: Forgot to close file removed nonexistent ex46f from makefile test rule Revert "fixed bad merge into master" fixed bad merge into master fix memory leak in mkl_pardiso fix some formatting in mkl_pardiso code mv runex111 from TESTEXAMPLES_C to TESTEXAMPLES_DATAFILESPATH Mat+Doc: More Fortran docs Plex ex3: Run tests with the correct number of field components Bib: Added TetGen cite parmetis: make sure 'ldd libparmetis.so' points to the correct libmetis.so that its linked with. small fix as reported by the nightly test ...Conflicts: config/builder.py List of files: /petsc/config/BuildSystem/graph.py

898446f941de989eb59a155860a54be7cc14d054 - Merge branch 'master' into shri/ts-is-for-differential-variables

Wed, 11 Mar 2015 04:17:30 +0000

Merge branch 'master' into shri/ts-is-for-differential-variablesConflicts: include/petsc-private/tsimpl.h src/ts/impls/eimex/eimex.c src/ts/interface/ts.c List of files: /petsc/config/BuildSystem/graph.py

9c925a2c1965a879ab6e2178d4282b2f82226662 - Merge branch 'master' into shri/ts-events

Tue, 18 Mar 2014 19:03:28 +0000

Merge branch 'master' into shri/ts-eventsConflicts: src/ts/interface/ts.c List of files: /petsc/config/BuildSystem/graph.py