petsc-3.14.5 2021-03-03
Report Typos and Errors

# Documentation: Changes: 3.7

## CHANGES in the PETSc 3.7 Version

#### General:

- -log_summary is deprecated, you should use -log_view
- PetscViewerSetFormat() is deprecated, you should use PetscViewerPushFormat() followed after the viewing with PetscViewerPopFormat()
- PetscMemoryShowUsage() and -memory_info changed to PetscMemoryView() and -memory_view
- PetscOptionsSetValue() may now be called BEFORE PetscInitialize() and any options set then will be used in the initialization process. These options are overwritten by command line options.
- The following routines now take an optional PetscOptions object as the first argument, use NULL to get the previous behavior.

      PetscOptionsHasName(PetscOptions,const char[],const char[],PetscBool *);
      PetscOptionsGetInt(PetscOptions,const char[],const char [],PetscInt *,PetscBool *);
      PetscOptionsGetBool(PetscOptions,const char[],const char [],PetscBool  *,PetscBool *);
      PetscOptionsGetReal(PetscOptions,const char[],const char[],PetscReal *,PetscBool *);
      PetscOptionsGetScalar(PetscOptions,const char[],const char[],PetscScalar *,PetscBool *);
      PetscOptionsGetIntArray(PetscOptions,const char[],const char[],PetscInt[],PetscInt *,PetscBool *);
      PetscOptionsGetRealArray(PetscOptions,const char[],const char[],PetscReal[],PetscInt *,PetscBool *);
      PetscOptionsGetScalarArray(PetscOptions,const char[],const char[],PetscScalar[],PetscInt *,PetscBool *);
      PetscOptionsGetBoolArray(PetscOptions,const char[],const char[],PetscBool [],PetscInt *,PetscBool *);
      PetscOptionsGetString(PetscOptions,const char[],const char[],char[],size_t,PetscBool *);
      PetscOptionsGetStringArray(PetscOptions,const char[],const char[],char*[],PetscInt*,PetscBool *);
      PetscOptionsGetEList(PetscOptions,const char[],const char[],const char*const*,PetscInt,PetscInt*,PetscBool *);
      PetscOptionsGetEnum(PetscOptions,const char[],const char[],const char*const*,PetscEnum*,PetscBool *);
      PetscOptionsGetEnumArray(PetscOptions,const char[],const char[],const char*const*,PetscEnum*,PetscInt *,PetscBool *);
      PetscOptionsSetAlias(PetscOptions,const char[],const char[]);
      PetscOptionsSetValue(PetscOptions,const char[],const char[]);
      PetscOptionsClearValue(PetscOptions,const char[]);
      PetscOptionsAllUsed(PetscOptions,PetscInt*);
      PetscOptionsUsed(PetscOptions,const char *,PetscBool*);
      PetscOptionsView(PetscOptions,PetscViewer);
      PetscOptionsInsert(PetscOptions,int*,char ***,const char[]);
      PetscOptionsInsertFile(MPI_Comm,PetscOptions,const char[],PetscBool );
      PetscOptionsInsertString(PetscOptions,const char[]);
      PetscOptionsPrefixPush(PetscOptions,const char[]);
      PetscOptionsReject(PetscOptions,const char[],const char[]);
      PetscOptionsGetAll(PetscOptions,char*[]);

- PetscLogBegin() is now PetscLogDefaultBegin().

#### Configure/Build:

- Added --download-packages-dir=directory to support easy use of --download-xxx behind firewalls
- --download-package for externalpackage with a gitrepo will never be stale. Each time configure is invoked - it will do a 'git fetch' and 'git checkout commit-id'. And if the commit-id changes from the previous build - the package will be rebuilt. To prevent this sync [and use previous snapshot] - one can use --download-package-commit=HEAD
- Added --with-libpng/--with-giflib/--with-libjpeg and cooresponding --download versions to support PNG/GIF/JPEG image generation
- Removed support for AfterImage in favor of libpng/GIFLIB/libjpeg

#### IS:

#### PetscDraw:

- Added option -draw_cmap to use a named colormap (e.g., hue (default), jet, coolwarm, parula, viridis) in the drawing of contour plots.
- Support for saving images and movies was improved. Support for generating binary PPM images is built-in, but the format is uncompressed and images are large (640x480 pixels ~ 900 KiB). PETSc can optionally generate PNG/GIF/JPEG images using the libpng/GIFLIB/libjpeg packages (configure --with-package/--download-package). These libraries are popular, well maintained, and available through most packages managers (dnf/yum, apt, brew). For most users, PNG images should be enough.
- Added routine PetscDrawSave(), users should explicitly call it to save images after configuring with PetscDrawSetSave().
- The PetscDrawSynchronizedXXX() routines were removed, the corresponding PetscDrawXXX() are now collective.

#### PF:

#### Vec:

- For complex numbers VecNorm(v,NORM_1,) will return the traditional 1 norm of the 2 norm of the complex numbers; that is the 1 norm of the absolute values of the complex entries. Previously it returned the 1 norm of the 1 norm of the complex entries (what is returned by the BLAS routine asum()). Both are valid norms but most people expect the former.

#### VecScatter:

#### PetscSection:

#### Mat:

#### PC:

- If the DM has a CreateRestriction() function the PCMG automatically uses that to create the restriction operator instead of defaulting to using the transpose of the interpolation
- Added -pc_hypre_boomeramg_nodal_coarsen - where n is from 1 to 6 (see HYPRE_BOOMERAMGSetNodal())
- Added -pc_hypre_boomeramg_vec_interp_variant where v is from 1 to 4 (see HYPRE_BoomerAMGSetInterpVecVariant())
- see PCHYPRE to allow taking advantage of MatSetNearNullSpace() for hypre BoomerAMG
- Added PCTelescope which supports running solvers on sub-communicators. This PC allows re-partitioning of coarse levels solves within PCMG when using Galerkin coarse level operators.

#### KSP:

- KSPSetMonitor(KSPMonitorXXX, calls now require passing a viewer as the final argument, you can no longer pass a NULL)
You should replace

    ierr = KSPMonitorSet(ksp,KSPMonitorDefault,NULL,NULL);CHKERRQ(ierr);

with

    PetscViewerAndFormat *vf;
    ierr = PetscViewerAndFormatCreate(PETSC_VIEWER_STDOUT_WORLD,PETSC_VIEWER_DEFAULT,&vf);CHKERRQ(ierr);
    ierr = KSPMonitorSet(ksp,(PetscErrorCode (*)(KSP,PetscInt,PetscReal,void*))KSPMonitorDefault,vf,(PetscErrorCode (*)(void**))PetscViewerAndFormatDestroy);CHKERRQ(ierr);

- -ksp_monitor_solution now takes arguments of the form [viewertype[:filename[:formatoption]]] allowing viewing the solution in many ways. To get back the previous behavior use -ksp_monitor_solution draw
- A Flexible Conjugate Gradient (FCG) implementation has been added as KSPFCG.
- New implementations for pipelined, flexible Krylov methods have been added as KSPPIPEFGMRES, KSPPIPEFCG, and KSPPIPEGCR.

#### SNES:

- SNESSetMonitor(SNESMonitorXXX, calls now require passing a viewer as the final argument, you can no longer pass a NULL)
You should replace

    ierr = SNESMonitorSet(ksp,SNESMonitorDefault,NULL,NULL);CHKERRQ(ierr);

with

    PetscViewerAndFormat *vf;
    ierr = PetscViewerAndFormatCreate(PETSC_VIEWER_STDOUT_WORLD,PETSC_VIEWER_DEFAULT,&vf);CHKERRQ(ierr);
    ierr = SNESMonitorSet(ksp,(PetscErrorCode (*)(SNES,PetscInt,PetscReal,void*))SNESMonitorDefault,vf,(PetscErrorCode (*)(void**))PetscViewerAndFormatDestroy);CHKERRQ(ierr);

- -snes_monitor_solution/residual/solution_update now takes arguments of the form [viewertype[:filename[:formatoption]]] allowing viewing the solution in many ways. To get back the previous behavior use -ksp_monitor_solution draw

#### SNESLineSearch:

- -snes_linesearch_monitor now takes an optional [:filename] arguement, changed SNESLineSearchSet/GetMonitor to SNESLineSearchSet/GetDefaultMonitor
- Added SNESLineSearchMonitorSet()
- Partial support for -snes_linesearch_monitor_solution_update

#### TS:

- You must call TSSetExactFinalTime() or use the option -ts_exact_final_time before calling TSSolve()
- TSSetMonitor(TSMonitorXXX, calls now require passing a viewer as the final argument, you can no longer pass a NULL)
You should replace

    ierr = TSMonitorSet(ksp,TSMonitorDefault,NULL,NULL);CHKERRQ(ierr);

with

    PetscViewerAndFormat *vf;
    ierr = PetscViewerAndFormatCreate(PETSC_VIEWER_STDOUT_WORLD,PETSC_VIEWER_DEFAULT,&vf);CHKERRQ(ierr);
    ierr = TSMonitorSet(ksp,(PetscErrorCode (*)(TS,PetscInt,PetscReal,Vec,void*))TSMonitorDefault,vf,(PetscErrorCode (*)(void**))PetscViewerAndFormatDestroy);CHKERRQ(ierr);

- -ts_monitor_solution now takes arguments of the form [viewertype[:filename[:formatoption]]] allowing viewing the solution in many ways. To get back the previous behavior use -ksp_monitor_solution draw
- -ts_monitor_binary_solution filename should now be written as -ts_monitor_solution binary:filename
- Renamed TSSetEventMonitor() to TSSetEventHandler(). Updated many TS implementations to support event detection.
- Updated TSTHETA, TSBEULER, and TSCN to support time adaptivity by estimating the local truncation error with a BDF-2 formula.
- Updated TSALPHA implementation. Removed TSAlphaSetAdapt() and TSAlphaAdaptDefault(), use TSAlphaUseAdapt() instead.
- Added TSBDF, an implementation of backward difference formulas using constant order (1 to 6) and supporting time adaptivity.
- Implemented new interface for second-order systems to avoid using a first-order system formulation. Added TSALPHA2 implementation (generalized-alpha, Chung & Hubert 1993) featuring user-controlled damping of high-frequency modes and time adaptivity through a BDF-2 formula.

#### DM/DA:

- Added DMShellSetCreateRestriction
- Added the generic option prefix interfaces: DMGetOptionsPrefix(), DMAppendOptionsPrefix()
- DMLabel labels are now available to all DM objects, not just DMPlex object
- DMClone() now handles copying the coordinates, so that DMCopyCoordinates() is no longer necessary

#### DMPlex:

#### PetscViewer:

- Replaced PetscViewerASCIISynchronizedAllow() with PetscViewerASCIIPushSynchronized() PetscViewerASCIIPopSynchronized()

#### SYS:

#### Tao:

- Removed convergence tolerances -tao_fatol and tao_frtol also remove these two parameters from TAOSetTolerance() and TaoGetTolerance()

#### AO:

#### Sieve:

#### Fortran: