PetscInitialize#

Initializes the PETSc database and MPI. PetscInitialize() calls MPI_Init() if that has yet to be called, so this routine should always be called near the beginning of your program – usually the very first line!

Synopsis#

#include "petscsys.h"   
PetscErrorCode PetscInitialize(int *argc, char ***args, const char file[], const char help[])

Collective on MPI_COMM_WORLD or PETSC_COMM_WORLD if it has been set

Input Parameters#

  • argc - count of number of command line arguments

  • args - the command line arguments

  • file - [optional] PETSc database file, append “:yaml” to filename to specify YAML options format. Use NULL or empty string to not check for code specific file. Also checks ~/.petscrc, .petscrc and petscrc. Use -skip_petscrc in the code specific file (or command line) to skip ~/.petscrc, .petscrc and petscrc files.

  • help - [optional] Help message to print, use NULL for no message

If you wish PETSc code to run ONLY on a subcommunicator of MPI_COMM_WORLD, create that communicator first and assign it to PETSC_COMM_WORLD BEFORE calling PetscInitialize(). Thus if you are running a four process job and two processes will run PETSc and have PetscInitialize() and PetscFinalize() and two process will not, then do this. If ALL processes in the job are using PetscInitialize() and PetscFinalize() then you don’t need to do this, even if different subcommunicators of the job are doing different things with PETSc.

Options Database Keys#

  • -help [intro] - prints help method for each option; if intro is given the program stops after printing the introductory help message

  • -start_in_debugger [noxterm,dbx,xdb,gdb,…] - Starts program in debugger

  • -on_error_attach_debugger [noxterm,dbx,xdb,gdb,…] - Starts debugger when error detected

  • -on_error_emacs - causes emacsclient to jump to error file

  • -on_error_abort - calls abort() when error detected (no traceback)

  • -on_error_mpiabort - calls MPI_abort() when error detected

  • -error_output_stdout - prints PETSc error messages to stdout instead of the default stderr

  • -error_output_none - does not print the error messages (but handles errors in the same way as if this was not called)

  • -debugger_ranks [rank1,rank2,…] - Indicates ranks to start in debugger

  • -debugger_pause [sleeptime] (in seconds) - Pauses debugger

  • -stop_for_debugger - Print message on how to attach debugger manually to process and wait (-debugger_pause) seconds for attachment

  • -malloc - Indicates use of PETSc error-checking malloc (on by default for debug version of libraries) (deprecated, use -malloc_debug)

  • -malloc no - Indicates not to use error-checking malloc (deprecated, use -malloc_debug no)

  • -malloc_debug - check for memory corruption at EVERY malloc or free, see PetscMallocSetDebug()

  • -malloc_dump - prints a list of all unfreed memory at the end of the run

  • -malloc_test - like -malloc_dump -malloc_debug, but only active for debugging builds, ignored in optimized build. May want to set in PETSC_OPTIONS environmental variable

  • -malloc_view - show a list of all allocated memory during PetscFinalize()

  • -malloc_view_threshold - only list memory allocations of size greater than t with -malloc_view

  • -malloc_requested_size - malloc logging will record the requested size rather than size after alignment

  • -fp_trap - Stops on floating point exceptions

  • -no_signal_handler - Indicates not to trap error signals

  • -shared_tmp - indicates /tmp directory is shared by all processors

  • -not_shared_tmp - each processor has own /tmp

  • -tmp - alternative name of /tmp directory

  • -get_total_flops - returns total flops done by all processors

  • -memory_view - Print memory usage at end of run

Options Database Keys for Option Database#

  • -skip_petscrc - skip the default option files ~/.petscrc, .petscrc, petscrc

  • -options_monitor - monitor all set options to standard output for the whole program run

  • -options_monitor_cancel - cancel options monitoring hard-wired using PetscOptionsMonitorSet()

Options -options_monitor_{all,cancel} are position-independent and apply to all options set since the PETSc start. They can be used also in option files.

See PetscOptionsMonitorSet() to do monitoring programmatically.

Options Database Keys for Profiling#

See Users-Manual: ch_profiling for details.

  • -info [filename][:[~]<list,of,classnames>[:[~]self]] - Prints verbose information. See PetscInfo().

  • -log_sync - Enable barrier synchronization for all events. This option is useful to debug imbalance within each event, however it slows things down and gives a distorted view of the overall runtime.

  • -log_trace [filename] - Print traces of all PETSc calls to the screen (useful to determine where a program hangs without running in the debugger). See PetscLogTraceBegin().

  • -log_view [:filename:format] - Prints summary of flop and timing information to screen or file, see PetscLogView().

  • -log_view_memory - Includes in the summary from -log_view the memory used in each event, see PetscLogView().

  • -log_view_gpu_time - Includes in the summary from -log_view the time used in each GPU kernel, see `PetscLogView().

  • -log_summary [filename] - (Deprecated, use -log_view) Prints summary of flop and timing information to screen. If the filename is specified the summary is written to the file. See PetscLogView().

  • -log_exclude: <vec,mat,pc,ksp,snes> - excludes subset of object classes from logging

  • -log_all [filename] - Logs extensive profiling information See PetscLogDump().

  • -log [filename] - Logs basic profiline information See PetscLogDump().

  • -log_mpe [filename] - Creates a logfile viewable by the utility Jumpshot (in MPICH distribution)

  • -viewfromoptions on,off - Enable or disable XXXSetFromOptions() calls, for applications with many small solves turn this off

  • -check_pointer_intensity 0,1,2 - if pointers are checked for validity (debug version only), using 0 will result in faster code

Only one of -log_trace, -log_view, -log_all, -log, or -log_mpe may be used at a time

Options Database Keys for SAWs#

  • -saws_port - port number to publish SAWs data, default is 8080

  • -saws_port_auto_select - have SAWs select a new unique port number where it publishes the data, the URL is printed to the screen this is useful when you are running many jobs that utilize SAWs at the same time

  • -saws_log - save a log of all SAWs communication

  • -saws_https - have SAWs use HTTPS instead of HTTP

  • -saws_root - allow SAWs to have access to the given directory to search for requested resources and files

Environmental Variables#

  • PETSC_TMP - alternative tmp directory

  • PETSC_SHARED_TMP - tmp is shared by all processes

  • PETSC_NOT_SHARED_TMP - each process has its own private tmp

  • PETSC_OPTIONS - a string containing additional options for petsc in the form of command line “-key value” pairs

  • PETSC_OPTIONS_YAML - (requires configuring PETSc to use libyaml) a string containing additional options for petsc in the form of a YAML document

  • PETSC_VIEWER_SOCKET_PORT - socket number to use for socket viewer

  • PETSC_VIEWER_SOCKET_MACHINE - machine to use for socket viewer to connect to

Note#

If for some reason you must call MPI_Init() separately, call it before PetscInitialize().

Fortran Notes#

In Fortran this routine can be called with

       call PetscInitialize(ierr)
       call PetscInitialize(file,ierr) or
       call PetscInitialize(file,help,ierr)

If your main program is C but you call Fortran code that also uses PETSc you need to call PetscInitializeFortran() soon after calling PetscInitialize().

Options Database Key for Developers#

  • -checkfunctionlist - automatically checks that function lists associated with objects are correctly cleaned up. Produces messages of the form: “function name: MatInodeGetInodeSizes_C” if they are not cleaned up. This flag is always set for the test harness (in framework.py)

See Also#

PetscFinalize(), PetscInitializeFortran(), PetscGetArgs(), PetscInitializeNoArguments(), PetscLogGpuTime()

Level#

beginner

Location#

src/sys/objects/pinit.c

Examples#

src/dm/dt/dualspace/impls/lagrange/tutorials/ex1.c
src/dm/dt/dualspace/impls/lagrange/tutorials/ex2.c
src/dm/field/tutorials/ex1.c
src/dm/impls/forest/tutorials/ex1.c
src/dm/impls/plex/tutorials/ex1.c
src/dm/impls/plex/tutorials/ex10.c
src/dm/impls/plex/tutorials/ex11.c
src/dm/impls/plex/tutorials/ex13.c
src/dm/impls/plex/tutorials/ex14.c
src/dm/impls/plex/tutorials/ex1f90.F90
src/dm/impls/plex/tutorials/ex3f90.F90

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