Other PETSc Features

PETSc on a process subset

Users who wish to employ PETSc routines on only a subset of processes within a larger parallel job, or who wish to use a “manager” process to coordinate the work of “worker” PETSc processes, should specify an alternative communicator for PETSC_COMM_WORLD by directly setting its value, for example to an existing MPI_COMM_WORLD,

PETSC_COMM_WORLD=MPI_COMM_WORLD; /* To use an existing MPI_COMM_WORLD */

before calling PetscInitialize(), but, obviously, after calling MPI_Init().

Runtime Options

Allowing the user to modify parameters and options easily at runtime is very desirable for many applications. PETSc provides a simple mechanism to enable such customization. To print a list of available options for a given program, simply specify the option -help at runtime, e.g.,

mpiexec -n 1 ./ex1 -help

Note that all runtime options correspond to particular PETSc routines that can be explicitly called from within a program to set compile-time defaults. For many applications it is natural to use a combination of compile-time and runtime choices. For example, when solving a linear system, one could explicitly specify use of the Krylov subspace technique BiCGStab by calling

One could then override this choice at runtime with the option

-ksp_type tfqmr

to select the Transpose-Free QMR algorithm. (See KSP: Linear System Solvers for details.)

The remainder of this section discusses details of runtime options.

The Options Database

Each PETSc process maintains a database of option names and values (stored as text strings). This database is generated with the command PetscInitialize(), which is listed below in its C/C++ and Fortran variants, respectively:

PetscInitialize(int *argc,char ***args,const char *file,const char *help); /* C */
call PetscInitialize(character file,integer ierr) ! Fortran

The arguments argc and args (in the C/C++ version only) are the addresses of usual command line arguments, while the file is a name of a file that can contain additional options. By default this file is called .petscrc in the user’s home directory. The user can also specify options via the environmental variable PETSC_OPTIONS. The options are processed in the following order:

  1. file

  2. environmental variable

  3. command line

Thus, the command line options supersede the environmental variable options, which in turn supersede the options file.

The file format for specifying options is

-optionname possible_value
-anotheroptionname possible_value
...

All of the option names must begin with a dash (-) and have no intervening spaces. Note that the option values cannot have intervening spaces either, and tab characters cannot be used between the option names and values. The user can employ any naming convention. For uniformity throughout PETSc, we employ the format -[prefix_]package_option (for instance, -ksp_type, -mat_view ::info, or -mg_levels_ksp_type).

Users can specify an alias for any option name (to avoid typing the sometimes lengthy default name) by adding an alias to the .petscrc file in the format

alias -newname -oldname

For example,

alias -kspt -ksp_type
alias -sd -start_in_debugger

Comments can be placed in the .petscrc file by using # in the first column of a line.

Options Prefixes

Options prefixes allow specific objects to be controlled from the options database. For instance, PCMG gives prefixes to its nested KSP objects; one may control the coarse grid solver by adding the mg_coarse prefix, for example -mg_coarse_ksp_type preonly. One may also use KSPSetOptionsPrefix(),DMSetOptionsPrefix() , SNESSetOptionsPrefix(), TSSetOptionsPrefix(), and similar functions to assign custom prefixes, useful for applications with multiple or nested solvers.

Adding options from a file

PETSc can load additional options from a file using PetscOptionsInsertFile(), which can also be used from the command line, e.g. -options_file my_options.opts.

One can also use YAML files this way (relying on PetscOptionsInsertFileYAML()). For example, the following file:

$$: ignored
$$tail: ignored

$$ans: &ans 42
$$eu:  &eu  2.72
$$pi:  &pi  3.14

opt:
  bool: true
  int: *ans
  real: *pi
  imag: 2.72i
  cmplx: -3.14+2.72i
  str: petsc

$$1: &seq-bool [true, false]
$$2: &seq-int  [123, 456, 789]
$$3: &seq-real [*pi, *eu]
$$4: &seq-str  [abc, ijk, fgh]

seq1: {
  bool: *seq-bool,
  int:  *seq-int,
  real: *seq-real,
  str:  *seq-str,
}

seq2:
  bool:
    - true
    - false
  int:
    - 123
    - 456
    - 789
  real:
    - *pi
    - *eu
  str:
    - rst
    - uvw
    - xyz

map:
  - key0: 0
  - key1: 1
  - key2: 2
  - $$: ignored
  - $$tail: ignored

corresponds to the following PETSc options:

-map key0,key1,key2
-map_key0 0
-map_key1 1
-map_key2 2
-opt_bool true
-opt_cmplx -3.14+2.72i
-opt_imag 2.72i
-opt_int 42
-opt_real 3.14
-opt_str petsc
-seq1_bool true,false
-seq1_int 123,456,789
-seq1_real 3.14,2.72
-seq1_str abc,ijk,fgh
-seq2_bool true,false
-seq2_int 123,456,789
-seq2_real 3.14,2.72
-seq2_str rst,uvw,xyz

With -options_file, PETSc will parse the file as YAML if it ends in a standard YAML or JSON 4 extension or if one uses a :yaml postfix, e.g. -options_file my_options.yaml or -options_file my_options.txt:yaml

PETSc will also check the first line of the options file itself and parse the file as YAML if it matches certain criteria, for example.

%YAML 1.2
---
name: value

and

---
name: value

both correspond to options

-name value

User-Defined PetscOptions

Any subroutine in a PETSc program can add entries to the database with the command

PetscOptionsSetValue(PetscOptions options,char *name,char *value);

though this is rarely done. To locate options in the database, one should use the commands

PetscOptionsHasName(PetscOptions options,char *pre,char *name,PetscBool *flg);
PetscOptionsGetInt(PetscOptions options,char *pre,char *name,PetscInt *value,PetscBool *flg);
PetscOptionsGetReal(PetscOptions options,char *pre,char *name,PetscReal *value,PetscBool *flg);
PetscOptionsGetString(PetscOptions options,char *pre,char *name,char *value,int maxlen,PetscBool  *flg);
PetscOptionsGetStringArray(PetscOptions options,char *pre,char *name,char **values,PetscInt *nmax,PetscBool *flg);
PetscOptionsGetIntArray(PetscOptions options,char *pre,char *name,int *value,PetscInt *nmax,PetscBool *flg);
PetscOptionsGetRealArray(PetscOptions options,char *pre,char *name,PetscReal *value, PetscInt *nmax,PetscBool *flg);

All of these routines set flg=PETSC_TRUE if the corresponding option was found, flg=PETSC_FALSE if it was not found. The optional argument pre indicates that the true name of the option is the given name (with the dash “-” removed) prepended by the prefix pre. Usually pre should be set to NULL (or PETSC_NULL_CHARACTER for Fortran); its purpose is to allow someone to rename all the options in a package without knowing the names of the individual options. For example, when using block Jacobi preconditioning, the KSP and PC methods used on the individual blocks can be controlled via the options -sub_ksp_type and -sub_pc_type.

Keeping Track of Options

One useful means of keeping track of user-specified runtime options is use of -options_view, which prints to stdout during PetscFinalize() a table of all runtime options that the user has specified. A related option is -options_left, which prints the options table and indicates any options that have not been requested upon a call to PetscFinalize(). This feature is useful to check whether an option has been activated for a particular PETSc object (such as a solver or matrix format), or whether an option name may have been accidentally misspelled.

Viewers: Looking at PETSc Objects

PETSc employs a consistent scheme for examining, printing, and saving objects through commands of the form

XXXView(XXX obj,PetscViewer viewer);

Here obj is any PETSc object of type XXX, where XXX is Mat, Vec, SNES, etc. There are several predefined viewers.

The user can control the format of ASCII printed objects with viewers created by PetscViewerASCIIOpen() by calling

Formats include PETSC_VIEWER_DEFAULT, PETSC_VIEWER_ASCII_MATLAB, and PETSC_VIEWER_ASCII_IMPL. The implementation-specific format, PETSC_VIEWER_ASCII_IMPL, displays the object in the most natural way for a particular implementation.

The routines

allow one to temporarily change the format of a viewer.

As discussed above, one can output PETSc objects in binary format by first opening a binary viewer with PetscViewerBinaryOpen() and then using MatView(), VecView(), etc. The corresponding routines for input of a binary object have the form XXXLoad(). In particular, matrix and vector binary input is handled by the following routines:

MatLoad(PetscViewer viewer,MatType outtype,Mat *newmat);
VecLoad(PetscViewer viewer,VecType outtype,Vec *newvec);

These routines generate parallel matrices and vectors if the viewer’s communicator has more than one process. The particular matrix and vector formats are determined from the options database; see the manual pages for details.

One can provide additional information about matrix data for matrices stored on disk by providing an optional file matrixfilename.info, where matrixfilename is the name of the file containing the matrix. The format of the optional file is the same as the .petscrc file and can (currently) contain the following:

-matload_block_size <bs>

The block size indicates the size of blocks to use if the matrix is read into a block oriented data structure (for example, MATMPIBAIJ). The diagonal information s1,s2,s3,... indicates which (block) diagonals in the matrix have nonzero values.

Viewing From Options

Command-line options provide a particularly convenient way to view PETSc objects. All options of the form -xxx_view accept colon(:)-separated compound arguments which specify a viewer type, format, and/or destination (e.g. file name or socket) if appropriate. For example, to quickly export a binary file containing a matrix, one may use -mat_view binary:matrix.out, or to output to a MATLAB-compatible ASCII file, one may use -mat_view ascii:matrix.m:ascii_matlab. See the PetscOptionsGetViewer() man page for full details, as well as the XXXViewFromOptions() man pages (for instance, PetscDrawSetFromOptions()) for many other convenient command-line options.

Using Viewers to Check Load Imbalance

The PetscViewer format PETSC_VIEWER_LOAD_BALANCE will cause certain objects to display simple measures of their imbalance. For example

-n 4 ./ex32 -ksp_view_mat ::load_balance

will display

Nonzeros: Min 162  avg 168  max 174

indicating that one process has 162 nonzero entries in the matrix, the average number of nonzeros per process is 168 and the maximum number of nonzeros is 174. Similar for vectors one can see the load balancing with, for example,

-n 4 ./ex32 -ksp_view_rhs ::load_balance

The measurements of load balancing can also be done within the program with calls to the appropriate object viewer with the viewer format PETSC_VIEWER_LOAD_BALANCE.

Using SAWs with PETSc

The Scientific Application Web server, SAWs 1, allows one to monitor running PETSc applications from a browser. configure PETSc with the additional option --download-saws. Options to use SAWs include

  • -saws_options - allows setting values in the PETSc options database via the browser (works only on one process).

  • -stack_view saws - allows monitoring the current stack frame that PETSc is in; refresh to see the new location.

  • -snes_monitor_saws, -ksp_monitor_saws - monitor the solvers’ iterations from the web browser.

For each of these you need to point your browser to http://hostname:8080, for example http://localhost:8080. Options that control behavior of SAWs include

  • -saws_log filename - log all SAWs actions in a file.

  • -saws_https certfile - use HTTPS instead of HTTP with a certificate.

  • -saws_port_auto_select - have SAWs pick a port number instead of using 8080.

  • -saws_port port - use port instead of 8080.

  • -saws_root rootdirectory - local directory to which the SAWs browser will have read access.

  • -saws_local - use the local file system to obtain the SAWS javascript files (they much be in rootdirectory/js).

Also see the manual pages for PetscSAWsBlock, PetscObjectSAWsTakeAccess, PetscObjectSAWsGrantAccess, PetscObjectSAWsSetBlock, PetscStackSAWsGrantAccess PetscStackSAWsTakeAccess, KSPMonitorSAWs, and SNESMonitorSAWs.

Debugging

PETSc programs may be debugged using one of the two options below.

  • -start_in_debugger [noxterm,dbx,xxgdb,xdb,xldb,lldb] [-display name] - start all processes in debugger

  • -on_error_attach_debugger [noxterm,dbx,xxgdb,xdb,xldb,lldb] [-display name] - start debugger only on encountering an error

Note that, in general, debugging MPI programs cannot be done in the usual manner of starting the programming in the debugger (because then it cannot set up the MPI communication and remote processes).

By default the GNU debugger gdb is used when -start_in_debugger or -on_error_attach_debugger is specified. To employ either xxgdb or the common UNIX debugger dbx, one uses command line options as indicated above. On HP-UX machines the debugger xdb should be used instead of dbx; on RS/6000 machines the xldb debugger is supported as well. On OS X systems with XCode tools, lldb is available. By default, the debugger will be started in a new xterm (to enable running separate debuggers on each process), unless the option noxterm is used. In order to handle the MPI startup phase, the debugger command cont should be used to continue execution of the program within the debugger. Rerunning the program through the debugger requires terminating the first job and restarting the processor(s); the usual run option in the debugger will not correctly handle the MPI startup and should not be used. Not all debuggers work on all machines, the user may have to experiment to find one that works correctly.

You can select a subset of the processes to be debugged (the rest just run without the debugger) with the option

-debugger_ranks rank1,rank2,...

where you simply list the ranks you want the debugger to run with.

Error Handling

Errors are handled through the routine PetscError(). This routine checks a stack of error handlers and calls the one on the top. If the stack is empty, it selects PetscTraceBackErrorHandler(), which tries to print a traceback. A new error handler can be put on the stack with

PetscPushErrorHandler(PetscErrorCode (*HandlerFunction)(int line,char *dir,char *file,char *message,int number,void*),void *HandlerContext)

The arguments to HandlerFunction() are the line number where the error occurred, the file in which the error was detected, the corresponding directory, the error message, the error integer, and the HandlerContext. The routine

removes the last error handler and discards it.

PETSc provides two additional error handlers besides PetscTraceBackErrorHandler():

PetscAbortErrorHandler()
PetscAttachErrorHandler()

The function PetscAbortErrorHandler() calls abort on encountering an error, while PetscAttachErrorHandler() attaches a debugger to the running process if an error is detected. At runtime, these error handlers can be set with the options -on_error_abort or -on_error_attach_debugger [noxterm, dbx, xxgdb, xldb] [-display DISPLAY].

All PETSc calls can be traced (useful for determining where a program is hanging without running in the debugger) with the option

-log_trace [filename]

where filename is optional. By default the traces are printed to the screen. This can also be set with the command PetscLogTraceBegin(FILE*).

It is also possible to trap signals by using the command

PetscPushSignalHandler( PetscErrorCode (*Handler)(int,void *),void *ctx);

The default handler PetscSignalHandlerDefault() calls PetscError() and then terminates. In general, a signal in PETSc indicates a catastrophic failure. Any error handler that the user provides should try to clean up only before exiting. By default all PETSc programs use the default signal handler, although the user can turn this off at runtime with the option -no_signal_handler .

There is a separate signal handler for floating-point exceptions. The option -fp_trap turns on the floating-point trap at runtime, and the routine

PetscSetFPTrap(PetscFPTrap flag);

can be used in-line. A flag of PETSC_FP_TRAP_ON indicates that floating-point exceptions should be trapped, while a value of PETSC_FP_TRAP_OFF (the default) indicates that they should be ignored. Note that on certain machines, in particular the IBM RS/6000, trapping is very expensive.

A small set of macros is used to make the error handling lightweight. These macros are used throughout the PETSc libraries and can be employed by the application programmer as well. When an error is first detected, one should set it by calling

SETERRQ(MPI_Comm comm,PetscErrorCode flag,,char *message);

The user should check the return codes for all PETSc routines (and possibly user-defined routines as well) with

ierr = PetscRoutine(...);CHKERRQ(PetscErrorCode ierr);

Likewise, all memory allocations should be checked with

ierr = PetscMalloc1(n, &ptr);CHKERRQ(ierr);

If this procedure is followed throughout all of the user’s libraries and codes, any error will by default generate a clean traceback of the location of the error.

Note that the macro PETSC_FUNCTION_NAME is used to keep track of routine names during error tracebacks. Users need not worry about this macro in their application codes; however, users can take advantage of this feature if desired by setting this macro before each user-defined routine that may call SETERRQ(), CHKERRQ(). A simple example of usage is given below.

PetscErrorCode MyRoutine1()
{
    /* Declarations Here */
    PetscFunctionBeginUser;
    /* code here */
    PetscFunctionReturn(0);
}

Numbers

PETSc supports the use of complex numbers in application programs written in C, C++, and Fortran. To do so, we employ either the C99 complex type or the C++ versions of the PETSc libraries in which the basic “scalar” datatype, given in PETSc codes by PetscScalar, is defined as complex (or complex<double> for machines using templated complex class libraries). To work with complex numbers, the user should run configure with the additional option --with-scalar-type=complex. The installation instructions provide detailed instructions for installing PETSc. You can use --with-clanguage=c (the default) to use the C99 complex numbers or --with-clanguage=c++ to use the C++ complex type 2.

Recall that each variant of the PETSc libraries is stored in a different directory, given by $PETSC_DIR/lib/$PETSC_ARCH

according to the architecture. Thus, the libraries for complex numbers are maintained separately from those for real numbers. When using any of the complex numbers versions of PETSc, all vector and matrix elements are treated as complex, even if their imaginary components are zero. Of course, one can elect to use only the real parts of the complex numbers when using the complex versions of the PETSc libraries; however, when working only with real numbers in a code, one should use a version of PETSc for real numbers for best efficiency.

The program KSP Tutorial ex11 solves a linear system with a complex coefficient matrix. Its Fortran counterpart is KSP Tutorial ex11f.

Parallel Communication

When used in a message-passing environment, all communication within PETSc is done through MPI, the message-passing interface standard [For94]. Any file that includes petscsys.h (or any other PETSc include file) can freely use any MPI routine.

Graphics

The PETSc graphics library is not intended to compete with high-quality graphics packages. Instead, it is intended to be easy to use interactively with PETSc programs. We urge users to generate their publication-quality graphics using a professional graphics package. If a user wants to hook certain packages into PETSc, he or she should send a message to petsc-maint@mcs.anl.gov; we will see whether it is reasonable to try to provide direct interfaces.

Windows as PetscViewers

For drawing predefined PETSc objects such as matrices and vectors, one may first create a viewer using the command

PetscViewerDrawOpen(MPI_Comm comm,char *display,char *title,int x,int y,int w,int h,PetscViewer *viewer);

This viewer may be passed to any of the XXXView() routines. Alternately, one may use command-line options to quickly specify viewer formats, including PetscDraw-based ones; see Viewing From Options.

To draw directly into the viewer, one must obtain the PetscDraw object with the command

Then one can call any of the PetscDrawXXX commands on the draw object. If one obtains the draw object in this manner, one does not call the PetscDrawOpenX() command discussed below.

Predefined viewers, PETSC_VIEWER_DRAW_WORLD and PETSC_VIEWER_DRAW_SELF, may be used at any time. Their initial use will cause the appropriate window to be created.

Implementations using OpenGL, TikZ, and other formats may be selected with PetscDrawSetType(). PETSc can also produce movies; see PetscDrawSetSaveMovie(), and note that command-line options can also be convenient; see the PetscDrawSetFromOptions() man page.

By default, PETSc drawing tools employ a private colormap, which remedies the problem of poor color choices for contour plots due to an external program’s mangling of the colormap. Unfortunately, this may cause flashing of colors as the mouse is moved between the PETSc windows and other windows. Alternatively, a shared colormap can be used via the option -draw_x_shared_colormap.

Simple PetscDrawing

With the default format, one can open a window that is not associated with a viewer directly under the X11 Window System or OpenGL with the command

PetscDrawCreate(MPI_Comm comm,char *display,char *title,int x,int y,int w,int h,PetscDraw *win);
PetscDrawSetFromOptions(win);

All drawing routines are performed relative to the window’s coordinate system and viewport. By default, the drawing coordinates are from (0,0) to (1,1), where (0,0) indicates the lower left corner of the window. The application program can change the window coordinates with the command

By default, graphics will be drawn in the entire window. To restrict the drawing to a portion of the window, one may use the command

These arguments, which indicate the fraction of the window in which the drawing should be done, must satisfy \(0 \leq {\tt xl} \leq {\tt xr} \leq 1\) and \(0 \leq {\tt yl} \leq {\tt yr} \leq 1.\)

To draw a line, one uses the command

The argument cl indicates the color (which is an integer between 0 and 255) of the line. A list of predefined colors may be found in include/petscdraw.h and includes PETSC_DRAW_BLACK, PETSC_DRAW_RED, PETSC_DRAW_BLUE etc.

To ensure that all graphics actually have been displayed, one should use the command

When displaying by using double buffering, which is set with the command

all processes must call

in order to swap the buffers. From the options database one may use -draw_pause n, which causes the PETSc application to pause n seconds at each PetscDrawPause(). A time of -1 indicates that the application should pause until receiving mouse input from the user.

Text can be drawn with commands

PetscDrawString(PetscDraw win,PetscReal x,PetscReal y,int color,char *text);
PetscDrawStringVertical(PetscDraw win,PetscReal x,PetscReal y,int color,const char *text);
PetscDrawStringCentered(PetscDraw win,PetscReal x,PetscReal y,int color,const char *text);
PetscDrawStringBoxed(PetscDraw draw,PetscReal sxl,PetscReal syl,int sc,int bc,const char text[],PetscReal *w,PetscReal *h);

The user can set the text font size or determine it with the commands

Line Graphs

PETSc includes a set of routines for manipulating simple two-dimensional graphs. These routines, which begin with PetscDrawAxisDraw(), are usually not used directly by the application programmer. Instead, the programmer employs the line graph routines to draw simple line graphs. As shown in the listing below, line graphs are created with the command

The argument ncurves indicates how many curves are to be drawn. Points can be added to each of the curves with the command

The arguments x and y are arrays containing the next point value for each curve. Several points for each curve may be added with

The line graph is drawn (or redrawn) with the command

A line graph that is no longer needed can be destroyed with the command

To plot new curves, one can reset a linegraph with the command

The line graph automatically determines the range of values to display on the two axes. The user can change these defaults with the command

It is also possible to change the display of the axes and to label them. This procedure is done by first obtaining the axes context with the command

One can set the axes’ colors and labels, respectively, by using the commands

PetscDrawAxisSetColors(PetscDrawAxis axis,int axis_lines,int ticks,int text);
PetscDrawAxisSetLabels(PetscDrawAxis axis,char *top,char *x,char *y);

It is possible to turn off all graphics with the option -nox. This will prevent any windows from being opened or any drawing actions to be done. This is useful for running large jobs when the graphics overhead is too large, or for timing.

The full example, Draw Test ex3, follows.

Listing: src/classes/draw/tests/ex3.c


static char help[] = "Plots a simple line graph.\n";

#if defined(PETSC_APPLE_FRAMEWORK)
#import <PETSc/petscsys.h>
#import <PETSc/petscdraw.h>
#else

#include <petscsys.h>
#include <petscdraw.h>
#endif

int main(int argc,char **argv)
{
  PetscDraw          draw;
  PetscDrawLG        lg;
  PetscDrawAxis      axis;
  PetscInt           n = 15,i,x = 0,y = 0,width = 400,height = 300,nports = 1;
  PetscBool          useports,flg;
  const char         *xlabel,*ylabel,*toplabel,*legend;
  PetscReal          xd,yd;
  PetscDrawViewPorts *ports = NULL;
  PetscErrorCode     ierr;

  toplabel = "Top Label"; xlabel = "X-axis Label"; ylabel = "Y-axis Label"; legend = "Legend";

  ierr = PetscInitialize(&argc,&argv,NULL,help);if (ierr) return ierr;
  ierr = PetscOptionsGetInt(NULL,NULL,"-x",&x,NULL);CHKERRQ(ierr);
  ierr = PetscOptionsGetInt(NULL,NULL,"-y",&y,NULL);CHKERRQ(ierr);
  ierr = PetscOptionsGetInt(NULL,NULL,"-width",&width,NULL);CHKERRQ(ierr);
  ierr = PetscOptionsGetInt(NULL,NULL,"-height",&height,NULL);CHKERRQ(ierr);
  ierr = PetscOptionsGetInt(NULL,NULL,"-n",&n,NULL);CHKERRQ(ierr);
  ierr = PetscOptionsGetInt(NULL,NULL,"-nports",&nports,&useports);CHKERRQ(ierr);
  ierr = PetscOptionsHasName(NULL,NULL,"-nolegend",&flg);CHKERRQ(ierr);
  if (flg) legend = NULL;
  ierr = PetscOptionsHasName(NULL,NULL,"-notoplabel",&flg);CHKERRQ(ierr);
  if (flg) toplabel = NULL;
  ierr = PetscOptionsHasName(NULL,NULL,"-noxlabel",&flg);CHKERRQ(ierr);
  if (flg) xlabel = NULL;
  ierr = PetscOptionsHasName(NULL,NULL,"-noylabel",&flg);CHKERRQ(ierr);
  if (flg) ylabel = NULL;
  ierr = PetscOptionsHasName(NULL,NULL,"-nolabels",&flg);CHKERRQ(ierr);
  if (flg) {toplabel = NULL; xlabel = NULL; ylabel = NULL;}

  ierr = PetscDrawCreate(PETSC_COMM_WORLD,0,"Title",x,y,width,height,&draw);CHKERRQ(ierr);
  ierr = PetscDrawSetFromOptions(draw);CHKERRQ(ierr);
  if (useports) {
    ierr = PetscDrawViewPortsCreate(draw,nports,&ports);CHKERRQ(ierr);
    ierr = PetscDrawViewPortsSet(ports,0);CHKERRQ(ierr);
  }
  ierr = PetscDrawLGCreate(draw,1,&lg);CHKERRQ(ierr);
  ierr = PetscDrawLGSetUseMarkers(lg,PETSC_TRUE);CHKERRQ(ierr);
  ierr = PetscDrawLGGetAxis(lg,&axis);CHKERRQ(ierr);
  ierr = PetscDrawAxisSetColors(axis,PETSC_DRAW_BLACK,PETSC_DRAW_RED,PETSC_DRAW_BLUE);CHKERRQ(ierr);
  ierr = PetscDrawAxisSetLabels(axis,toplabel,xlabel,ylabel);CHKERRQ(ierr);
  ierr = PetscDrawLGSetLegend(lg,&legend);CHKERRQ(ierr);
  ierr = PetscDrawLGSetFromOptions(lg);CHKERRQ(ierr);

  for (i=0; i<=n; i++) {
    xd   = (PetscReal)(i - 5); yd = xd*xd;
    ierr = PetscDrawLGAddPoint(lg,&xd,&yd);CHKERRQ(ierr);
  }
  ierr = PetscDrawLGDraw(lg);CHKERRQ(ierr);
  ierr = PetscDrawLGSave(lg);CHKERRQ(ierr);

  ierr = PetscDrawViewPortsDestroy(ports);CHKERRQ(ierr);
  ierr = PetscDrawLGDestroy(&lg);CHKERRQ(ierr);
  ierr = PetscDrawDestroy(&draw);CHKERRQ(ierr);
  ierr = PetscFinalize();
  return ierr;
}

Graphical Convergence Monitor

For both the linear and nonlinear solvers default routines allow one to graphically monitor convergence of the iterative method. These are accessed via the command line with -ksp_monitor draw::draw_lg and -snes_monitor draw::draw_lg. See also Convergence Monitoring and Convergence Monitoring.

Disabling Graphics at Compile Time

To disable all X-window-based graphics, run configure with the additional option --with-x=0

Emacs Users

Many PETSc developers use Emacs, which can be used as a “simple” text editor or a comprehensive development environment. For a more integrated development environment, we recommend using lsp-mode (or eglot) with clangd. The most convenient way to teach clangd what compilation flags to use is to install Bear (“build ear”) and run:

bear make -B

which will do a complete rebuild (-B) of PETSc and capture the compilation commands in a file named compile_commands.json, which will be automatically picked up by clangd. You can use the same procedure when building examples or your own project. It can also be used with any other editor that supports clangd, including VS Code and Vim. When lsp-mode is accompanied by flycheck, Emacs will provide real-time feedback and syntax checking, along with refactoring tools provided by clangd.

The easiest way to install packages in recent Emacs is to use the “Options” menu to select “Manage Emacs Packages”.

Tags

It is sometimes useful to cross-reference tags across projects. Regardless of whether you use lsp-mode, it can be useful to use GNU Global (install gtags) to provide reverse lookups (e.g. find all call sites for a given function) across all projects you might work on/browse. Tags for PETSc can be generated by running make allgtags from $PETSC_DIR, or one can generate tags for all projects by running a command such as

find $PETSC_DIR/{include,src,tutorials,$PETSC_ARCH/include} any/other/paths \
   -regex '.*\.\(cc\|hh\|cpp\|cxx\|C\|hpp\|c\|h\|cu\)$' \
   | grep -v ftn-auto | gtags -f -

from your home directory or wherever you keep source code. If you are making large changes, it is useful to either set this up to run as a cron job or to make a convenient alias so that refreshing is easy. Then add the following to ~/.emacs to enable gtags and specify key bindings.

(when (require 'gtags)
  (global-set-key (kbd "C-c f") 'gtags-find-file)
  (global-set-key (kbd "C-c .") 'gtags-find-tag)
  (global-set-key (kbd "C-c r") 'gtags-find-rtag)
  (global-set-key (kbd "C-c ,") 'gtags-pop-stack))
(add-hook 'c-mode-common-hook
          '(lambda () (gtags-mode t))) ; Or add to existing hook

A more basic alternative to the GNU Global (gtags) approach that does not require adding packages is to use the builtin etags feature. First, run make alletags from the PETSc home directory to generate the file $PETSC_DIR/TAGS, and then from within Emacs, run

M-x visit-tags-table

where M denotes the Emacs Meta key, and enter the name of the TAGS file. Then the command M-. will cause Emacs to find the file and line number where a desired PETSc function is defined. Any string in any of the PETSc files can be found with the command M-x tags-search. To find repeated occurrences, one can simply use M-, to find the next occurrence.

VS Code Users

VS Code (unlike Visual Studio Users, described below) is an open source editor with a rich extension ecosystem. It has excellent integration with clangd and will automatically pick up compile_commands.json as produced by a command such as bear make -B (see Emacs Users). If you have no prior attachment to a specific code editor, we recommend trying VS Code.

Vi and Vim Users

This section lists helpful Vim commands for PETSc. Ones that configure Vim can be placed in a .vimrc file in the top of the PETSc directory and will be loaded automatically.

Vim has configurable keymaps: all of the “command mode” commands given that start with a colon (such as :help) can be assigned to short sequences in “normal mode,” which is how most Vim users use their most frequently used commands.

See the Emacs Users discussion above for configuration of clangd, which provides integrated development environment.

Tags

The tags feature can be used to search PETSc files quickly and efficiently. To use this feature, one should first check if the file, $PETSC_DIR/CTAGS exists. If this file is not present, it should be generated by running make alletags from the PETSc home directory. Once the file exists, from Vi/Vim the user should issue the command

:set tags=CTAGS

from the $PETSC_DIR directory and enter the name of the CTAGS file. The command :tag functionname will cause Vi/Vim to open the file and line number where a desired PETSc function is defined in the current window. <Ctrl-o> will return the screen to your previous location.

The command :stag functionname will split the current window and then open the file and line number for that function in one half. Some prefer this because it is easier to compare the file you are editing to the function definition this way.

Cscope and gtags

Vim can also use the cscope utility to navigate source code. One useful thing it can do that the basic tags feature can’t is search for references to a symbol, rather than its definition, which can be useful for refactoring. The command

:cs find s functionname

opens a list of all of the places the function is called in PETSc, and opens the file and line that you choose. The variant :scs find s functionname does the same but splits the window like stag.

The PETSc makefile does not have a command for building a cscope database, but GNU Global is cross-compatible with cscope: call make allgtags to make the gtags database, and run the commands

:set csprg=gtags-cscope
:cs add GTAGS

Quickfix

Rather than exiting editing a file to build the library and check for errors or warnings, calling :make runs the make command without leaving Vim and collects the errors and warnings in a “quickfix” window. Move the cursor to one of the errors or warnings in the quickfix window and press <Enter> and the main window will jump to the file and line with the error. The following commands filter lines of out PETSc’s make output that can clutter the quickfix window:

:set efm^=%-GStarting\ make\ run\ on\ %.%#
:set efm^=%-GMachine\ characteristics:\ %.%#
:set efm^=%-G#define\ PETSC%.%#

Autocompletion and snippets

Autocompletion of long function names can be helpful when working with PETSc. If you have a tags file, you can press <Ctrl-N> when you have partially typed a word to bring up a list of potential completions that you can choose from with <Tab>.

More powerful autocompletion, such as completing the fieldname of a struct, is available from external plugins that can be added to Vim, such as SuperTab, VimCompletesMe, or YouCompleteMe.

Along the same lines, plugins can be added that fill in the boilerplate associated with PETSc programming with code snippets. One such tool is UltiSnips.

LSP for Vim

Several plugins provide the equivalent of emacs’ lsp-mode: YouCompleteMe, mentioned above, is one; another popular one is ale. These can check for syntax errors, check for compilation errors in the background, and provide sophisticated tools for refactoring. Like lsp-mode, they also rely on a compilation database, so bear -- make -B should be used as well to generate the file compile_commands.json.

Etc.

See online tutorials for additional Vi/Vim options.

Eclipse Users

If you are interested in developing code that uses PETSc from Eclipse or developing PETSc in Eclipse and have knowledge of how to do indexing and build libraries in Eclipse, please contact us at petsc-dev@mcs.anl.gov.

One way to index and build PETSc in Eclipse is as follows.

  1. Open “File\(\rightarrow\)Import\(\rightarrow\)Git\(\rightarrow\)Projects from Git”. In the next two panels, you can either add your existing local repository or download PETSc from Bitbucket by providing the URL. Most Eclipse distributions come with Git support. If not, install the EGit plugin. When importing the project, select the wizard “Import as general project”.

  2. Right-click on the project (or the “File” menu on top) and select “New \(\rightarrow\) Convert to a C/C++ Project (Adds C/C++ Nature)”. In the setting window, choose “C Project” and specify the project type as “Shared Library”.

  3. Right-click on the C project and open the “Properties” panel. Under “C/C++ Build \(\rightarrow\) Builder Settings”, set the Build directory to $PETSC_DIR and make sure “Generate Makefiles automatically” is unselected. Under the section “C/C++ General\(\rightarrow\)Paths and Symbols”, add the PETSc paths to “Includes”.

     $PETSC_DIR/include
     $PETSC_DIR/$PETSC_ARCH/include

Under the section “C/C++ General\ :math:`\rightarrow`\ index”, choose
“Use active build configuration”.
  1. Configure PETSc normally outside Eclipse to generate a makefile and then build the project in Eclipse. The source code will be parsed by Eclipse.

If you launch Eclipse from the Dock on Mac OS X, .bashrc will not be loaded (a known OS X behavior, for security reasons). This will be a problem if you set the environment variables $PETSC_DIR and $PETSC_ARCH in .bashrc. A solution which involves replacing the executable can be found at `/questions/829749/launch-mac-eclipse-with-environment-variables-set </questions/829749/launch-mac-eclipse-with-environment-variables-set>`__. Alternatively, you can add $PETSC_DIR and $PETSC_ARCH manually under “Properties \(\rightarrow\) C/C++ Build \(\rightarrow\) Environment”.

To allow an Eclipse code to compile with the PETSc include files and link with the PETSc libraries, a PETSc user has suggested the following.

  1. Right-click on your C project and select “Properties \(\rightarrow\) C/C++ Build \(\rightarrow\) Settings”

  2. A new window on the righthand side appears with various settings options. Select “Includes” and add the required PETSc paths,

$PETSC_DIR/include
$PETSC_DIR/$PETSC_ARCH/include
  1. Select “Libraries” under the header Linker and set the library search path:

   $PETSC_DIR/$PETSC_ARCH/lib

and the libraries, for example
m, petsc, stdc++, mpichxx, mpich, lapack, blas, gfortran, dl, rt,gcc_s, pthread, X11

Another PETSc user has provided the following steps to build an Eclipse index for PETSc that can be used with their own code, without compiling PETSc source into their project.

  1. In the user project source directory, create a symlink to the PETSC src/ directory.

  2. Refresh the project explorer in Eclipse, so the new symlink is followed.

  3. Right-click on the project in the project explorer, and choose “Index \(\rightarrow\) Rebuild”. The index should now be built.

  4. Right-click on the PETSc symlink in the project explorer, and choose “Exclude from build…” to make sure Eclipse does not try to compile PETSc with the project.

For further examples of using Eclipse with a PETSc-based application, see the documentation for LaMEM 3.

Qt Creator Users

This information was provided by Mohammad Mirzadeh. The Qt Creator IDE is part of the Qt SDK, developed for cross-platform GUI programming using C++. It is available under GPL v3, LGPL v2 and a commercial license and may be obtained, either as part of the Qt SDK or as stand-alone software. It supports automatic makefile generation using cross-platform qmake and cmake build systems as well as allowing one to import projects based on existing, possibly hand-written, makefiles. Qt Creator has a visual debugger using GDB and LLDB (on Linux and OS X) or Microsoft’s CDB (on Windows) as backends. It also has an interface to Valgrind’s “memcheck” and “callgrind” tools to detect memory leaks and profile code. It has built-in support for a variety of version control systems including git, mercurial, and subversion. Finally, Qt Creator comes fully equipped with auto-completion, function look-up, and code refactoring tools. This enables one to easily browse source files, find relevant functions, and refactor them across an entire project.

Creating a Project

When using Qt Creator with qmake, one needs a .pro file. This configuration file tells Qt Creator about all build/compile options and locations of source files. One may start with a blank .pro file and fill in configuration options as needed. For example:

# The name of the application executable
TARGET = ex1

# There are two ways to add PETSc functionality
# 1-Manual: Set all include path and libs required by PETSc
PETSC_INCLUDE = path/to/petsc_includes # e.g. obtained via running `make getincludedirs'
PETSC_LIBS = path/to/petsc_libs # e.g. obtained via running `make getlinklibs'

INCLUDEPATH += $$PETSC_INCLUDES
LIBS += $$PETSC_LIBS

# 2-Automatic: Use the PKGCONFIG funtionality
# NOTE: petsc.pc must be in the pkgconfig path. You might need to adjust PKG_CONFIG_PATH
CONFIG += link_pkgconfig
PKGCONFIG += PETSc

# Set appropriate compiler and its flags
QMAKE_CC = path/to/mpicc
QMAKE_CXX = path/to/mpicxx # if this is a cpp project
QMAKE_LINK = path/to/mpicxx # if this is a cpp project

QMAKE_CFLAGS   += -O3 # add extra flags here
QMAKE_CXXFLAGS += -O3
QMAKE_LFLAGS   += -O3

# Add all files that must be compiled
SOURCES += ex1.c source1.c source2.cpp

HEADERS += source1.h source2.h

# OTHER_FILES are ignored during compilation but will be shown in file panel in Qt Creator
OTHER_FILES += \
    path/to/resource_file \
    path/to/another_file

In this example, keywords include:

  • TARGET: The name of the application executable.

  • INCLUDEPATH: Used at compile time to point to required include files. Essentially, it is used as an -I \$\$INCLUDEPATH flag for the compiler. This should include all application-specific header files and those related to PETSc (which may be found via make getincludedirs).

  • LIBS: Defines all required external libraries to link with the application. To get PETSc’s linking libraries, use make getlinklibs.

  • CONFIG: Configuration options to be used by qmake. Here, the option link_pkgconfig instructs qmake to internally use pkgconfig to resolve INCLUDEPATH and LIBS variables.

  • PKGCONFIG: Name of the configuration file (the .pc file – here petsc.pc) to be passed to pkgconfig. Note that for this functionality to work, petsc.pc must be in path which might require adjusting the PKG_CONFIG_PATH enviroment variable. For more information see the Qt Creator documentation.

  • QMAKE_CC and QMAKE_CXX: Define which C/C++ compilers use.

  • QMAKE_LINK: Defines the proper linker to be used. Relevant if compiling C++ projects.

  • QMAKE_CFLAGS, QMAKE_CXXFLAGS and QMAKE_LFLAGS: Set the corresponding compile and linking flags.

  • SOURCES: Source files to be compiled.

  • HEADERS: Header files required by the application.

  • OTHER_FILES: Other files to include (source, header, or any other extension). Note that none of the source files placed here are compiled.

More options can be included in a .pro file; see https://doc.qt.io/qt-5/qmake-project-files.html. Once the .pro file is generated, the user can simply open it via Qt Creator. Upon opening, one has the option to create two different build options, debug and release, and switch between the two. For more information on using the Qt Creator interface and other more advanced aspects of the IDE, refer to https://www.qt.io/qt-features-libraries-apis-tools-and-ide/

Visual Studio Users

To use PETSc from MS Visual Studio, one would have to compile a PETSc example with its corresponding makefile and then transcribe all compiler and linker options used in this build into a Visual Studio project file, in the appropriate format in Visual Studio project settings.

XCode Users (The Apple GUI Development System)

Mac OS X

Follow the instructions in $PETSC_DIR/systems/Apple/OSX/bin/makeall to build the PETSc framework and documentation suitable for use in XCode.

You can then use the PETSc framework in $PETSC_DIR/arch-osx/PETSc.framework in the usual manner for Apple frameworks. See the examples in $PETSC_DIR/systems/Apple/OSX/examples. When working in XCode, things like function name completion should work for all PETSc functions as well as MPI functions. You must also link against the Apple Accelerate.framework.

iPhone/iPad iOS

Follow the instructions in $PETSC_DIR/systems/Apple/iOS/bin/iosbuilder.py to build the PETSc library for use on the iPhone/iPad.

You can then use the PETSc static library in $PETSC_DIR/arch-osx/libPETSc.a in the usual manner for Apple libraries inside your iOS XCode projects; see the examples in $PETSC_DIR/systems/Apple/iOS/examples. You must also link against the Apple Accelerate.framework.

Footnotes

1

Saws wiki on Bitbucket

2

Note that this option is not required to use PETSc with C++

3

doc/ at https://bitbucket.org/bkaus/lamem

4

JSON is a subset of YAML