PetscErrorCode BSSCR_GeneratePetscHeader_for_file( FILE *fd, MPI_Comm comm )
{
PetscErrorCode ierr;
char version[256];
char arch[50], hostname[64], username[16], pname[PETSC_MAX_PATH_LEN], date[64];
int size, rank;
char *_dir;
ierr = PetscGetArchType(arch, 50);CHKERRQ(ierr);
ierr = PetscGetHostName(hostname, 64);CHKERRQ(ierr);
ierr = PetscGetUserName(username, 16);CHKERRQ(ierr);
ierr = PetscGetProgramName(pname, PETSC_MAX_PATH_LEN);CHKERRQ(ierr);
ierr = PetscGetDate(date, 64);CHKERRQ(ierr);
ierr = PetscGetVersion(&version,256);CHKERRQ(ierr);
ierr = PetscGetPetscDir( (const char**)&_dir ); CHKERRQ(ierr);
MPI_Comm_size( comm, &size );
MPI_Comm_rank( comm, &rank );
if( rank != 0 ) PetscFunctionReturn(0);
if( size == 1 ) {
fprintf( fd,"## %s on a %s named %s with %d processor, by %s %s\n", pname, arch, hostname, size, username, date);
} else {
fprintf( fd,"## %s on a %s named %s with %d processors, by %s %s\n", pname, arch, hostname, size, username, date);
}
fprintf( fd, "## Using %s, installed at %s \n", version, _dir );
PetscFunctionReturn(0);
}
PetscErrorCode PetscViewerSetFromOptions_Socket(PetscViewer v)
{
PetscErrorCode ierr;
PetscInt def = -1;
char sdef[256];
PetscTruth tflg;
PetscFunctionBegin;
/*
These options are not processed here, they are processed in PetscViewerSocketSetConnection(), they
are listed here for the GUI to display
*/
ierr = PetscOptionsHead("Socket PetscViewer Options");CHKERRQ(ierr);
ierr = PetscOptionsGetenv(((PetscObject)v)->comm,"PETSC_VIEWER_SOCKET_PORT",sdef,16,&tflg);CHKERRQ(ierr);
if (tflg) {
ierr = PetscOptionsAtoi(sdef,&def);CHKERRQ(ierr);
} else {
def = PETSCSOCKETDEFAULTPORT;
}
ierr = PetscOptionsInt("-viewer_socket_port","Port number to use for socket","PetscViewerSocketSetConnection",def,0,0);CHKERRQ(ierr);
ierr = PetscOptionsString("-viewer_socket_machine","Machine to use for socket","PetscViewerSocketSetConnection",sdef,0,0,0);CHKERRQ(ierr);
ierr = PetscOptionsGetenv(((PetscObject)v)->comm,"PETSC_VIEWER_SOCKET_MACHINE",sdef,256,&tflg);CHKERRQ(ierr);
if (!tflg) {
ierr = PetscGetHostName(sdef,256);CHKERRQ(ierr);
}
ierr = PetscOptionsTail();CHKERRQ(ierr);
PetscFunctionReturn(0);
}
PetscErrorCode BSSCR_GeneratePetscHeader_for_viewer( PetscViewer viewer )
{
PetscErrorCode ierr;
char version[256];
char arch[50], hostname[64], username[16], pname[PETSC_MAX_PATH_LEN], date[64];
int size;
char *_dir;
MPI_Comm comm;
ierr = PetscGetArchType(arch, 50);CHKERRQ(ierr);
ierr = PetscGetHostName(hostname, 64);CHKERRQ(ierr);
ierr = PetscGetUserName(username, 16);CHKERRQ(ierr);
ierr = PetscGetProgramName(pname, PETSC_MAX_PATH_LEN);CHKERRQ(ierr);
ierr = PetscGetDate(date, 64);CHKERRQ(ierr);
ierr = PetscGetVersion(&version,256);CHKERRQ(ierr);
ierr = PetscGetPetscDir( (const char**)&_dir ); CHKERRQ(ierr);
PetscObjectGetComm( (PetscObject)viewer, &comm );
MPI_Comm_size( comm, &size );
if( size == 1 ) {
PetscViewerASCIIPrintf( viewer,"## %s on a %s named %s with %d processor, by %s %s\n", pname, arch, hostname, size, username, date);
} else {
PetscViewerASCIIPrintf( viewer,"## %s on a %s named %s with %d processors, by %s %s\n", pname, arch, hostname, size, username, date);
}
PetscViewerASCIIPrintf( viewer, "## Using %s, installed at %s \n", version, _dir );
PetscFunctionReturn(0);
}
EXTERN_C_END
#undef __FUNCT__
#define __FUNCT__ "PetscViewerSocketSetConnection"
/*@C
PetscViewerSocketSetConnection - Sets the machine and port that a PETSc socket
viewer is to use
Collective on PetscViewer
Input Parameters:
+ v - viewer to connect
. machine - host to connect to, use PETSC_NULL for the local machine,use "server" to passively wait for
a connection from elsewhere
- port - the port on the machine one is connecting to, use PETSC_DEFAULT for default
Level: advanced
.seealso: PetscViewerSocketOpen()
@*/
PetscErrorCode PETSC_DLLEXPORT PetscViewerSocketSetConnection(PetscViewer v,const char machine[],PetscInt port)
{
PetscErrorCode ierr;
PetscMPIInt rank;
char mach[256];
PetscTruth tflg;
PetscViewer_Socket *vmatlab = (PetscViewer_Socket *)v->data;
PetscFunctionBegin;
if (port <= 0) {
char portn[16];
ierr = PetscOptionsGetenv(((PetscObject)v)->comm,"PETSC_VIEWER_SOCKET_PORT",portn,16,&tflg);CHKERRQ(ierr);
if (tflg) {
ierr = PetscOptionsAtoi(portn,&port);CHKERRQ(ierr);
} else {
port = PETSCSOCKETDEFAULTPORT;
}
}
if (!machine) {
ierr = PetscOptionsGetenv(((PetscObject)v)->comm,"PETSC_VIEWER_SOCKET_MACHINE",mach,256,&tflg);CHKERRQ(ierr);
if (!tflg) {
ierr = PetscGetHostName(mach,256);CHKERRQ(ierr);
}
} else {
ierr = PetscStrncpy(mach,machine,256);CHKERRQ(ierr);
}
ierr = MPI_Comm_rank(((PetscObject)v)->comm,&rank);CHKERRQ(ierr);
if (!rank) {
ierr = PetscStrcmp(mach,"server",&tflg);CHKERRQ(ierr);
if (tflg) {
ierr = PetscInfo1(v,"Waiting for connection from socket process on port %D\n",port);CHKERRQ(ierr);
ierr = SOCKAnswer_Private((int)port,&vmatlab->port);CHKERRQ(ierr);
} else {
ierr = PetscInfo2(v,"Connecting to socket process on port %D machine %s\n",port,mach);CHKERRQ(ierr);
ierr = PetscOpenSocket(mach,(int)port,&vmatlab->port);CHKERRQ(ierr);
}
}
PetscFunctionReturn(0);
}
PetscErrorCode PetscViewerMathematicaSetupConnection_Private(PetscViewer v)
{
PetscViewer_Mathematica *vmath = (PetscViewer_Mathematica*) v->data;
#if defined(MATHEMATICA_3_0)
int argc = 6;
char *argv[6];
#else
int argc = 5;
char *argv[5];
#endif
char hostname[256];
long lerr;
PetscErrorCode ierr;
PetscFunctionBegin;
/* Link name */
argv[0] = "-linkname";
if (!vmath->linkname) argv[1] = "math -mathlink";
else argv[1] = vmath->linkname;
/* Link host */
argv[2] = "-linkhost";
if (!vmath->linkhost) {
ierr = PetscGetHostName(hostname, 255);
CHKERRQ(ierr);
argv[3] = hostname;
} else argv[3] = vmath->linkhost;
/* Link mode */
#if defined(MATHEMATICA_3_0)
argv[4] = "-linkmode";
switch (vmath->linkmode) {
case MATHEMATICA_LINK_CREATE:
argv[5] = "Create";
break;
case MATHEMATICA_LINK_CONNECT:
argv[5] = "Connect";
break;
case MATHEMATICA_LINK_LAUNCH:
argv[5] = "Launch";
break;
}
#else
switch (vmath->linkmode) {
case MATHEMATICA_LINK_CREATE:
argv[4] = "-linkcreate";
break;
case MATHEMATICA_LINK_CONNECT:
argv[4] = "-linkconnect";
break;
case MATHEMATICA_LINK_LAUNCH:
argv[4] = "-linklaunch";
break;
}
#endif
vmath->link = MLOpenInEnv(mathematicaEnv, argc, argv, &lerr);
#endif
PetscFunctionReturn(0);
}
/*@C
PetscViewerSocketSetConnection - Sets the machine and port that a PETSc socket
viewer is to use
Logically Collective on PetscViewer
Input Parameters:
+ v - viewer to connect
. machine - host to connect to, use NULL for the local machine,use "server" to passively wait for
a connection from elsewhere
- port - the port on the machine one is connecting to, use PETSC_DEFAULT for default
Level: advanced
.seealso: PetscViewerSocketOpen()
@*/
PetscErrorCode PetscViewerSocketSetConnection(PetscViewer v,const char machine[],int port)
{
PetscErrorCode ierr;
PetscMPIInt rank;
char mach[256];
PetscBool tflg;
PetscViewer_Socket *vmatlab = (PetscViewer_Socket*)v->data;
PetscFunctionBegin;
/* PetscValidLogicalCollectiveInt(v,port,3); not a PetscInt */
if (port <= 0) {
char portn[16];
ierr = PetscOptionsGetenv(PetscObjectComm((PetscObject)v),"PETSC_VIEWER_SOCKET_PORT",portn,16,&tflg);CHKERRQ(ierr);
if (tflg) {
PetscInt pport;
ierr = PetscOptionsStringToInt(portn,&pport);CHKERRQ(ierr);
port = (int)pport;
} else port = PETSCSOCKETDEFAULTPORT;
}
if (!machine) {
ierr = PetscOptionsGetenv(PetscObjectComm((PetscObject)v),"PETSC_VIEWER_SOCKET_MACHINE",mach,256,&tflg);CHKERRQ(ierr);
if (!tflg) {
ierr = PetscGetHostName(mach,256);CHKERRQ(ierr);
}
} else {
ierr = PetscStrncpy(mach,machine,256);CHKERRQ(ierr);
}
ierr = MPI_Comm_rank(PetscObjectComm((PetscObject)v),&rank);CHKERRQ(ierr);
if (!rank) {
ierr = PetscStrcmp(mach,"server",&tflg);CHKERRQ(ierr);
if (tflg) {
int listenport;
ierr = PetscInfo1(v,"Waiting for connection from socket process on port %D\n",port);CHKERRQ(ierr);
ierr = PetscSocketEstablish(port,&listenport);CHKERRQ(ierr);
ierr = PetscSocketListen(listenport,&vmatlab->port);CHKERRQ(ierr);
close(listenport);
} else {
ierr = PetscInfo2(v,"Connecting to socket process on port %D machine %s\n",port,mach);CHKERRQ(ierr);
ierr = PetscOpenSocket(mach,port,&vmatlab->port);CHKERRQ(ierr);
}
}
PetscFunctionReturn(0);
}
int main(int argc, char **args)
{
PetscErrorCode ierr;
ierr = PetscInitialize(&argc, &args, (char *) 0, ""); CHKERRQ(ierr);
ierr = PetscPrintf(PETSC_COMM_WORLD, "Start %s\n", __FILE__); CHKERRQ(ierr);
GA_Initialize();
ierr = MA_init(MT_DBL, 1000, 1000 );
if( !ierr ) GA_Error("\n\n\nga allocaltion failed\n\n",ierr);
size_t len = 1024;
char name[1024];
PetscGetHostName(name,len);
PetscPrintf(PETSC_COMM_SELF, "Hello from %s\n", name);
ierr = testCreate3D(); CHKERRQ(ierr);
GA_Terminate();
ierr = PetscPrintf(PETSC_COMM_WORLD, "End %s\n", __FILE__); CHKERRQ(ierr);
ierr = PetscFinalize(); CHKERRQ(ierr);
}
/*
Initializes arch, hostname, username,date so that system calls do NOT need
to be made during the error handler.
*/
PetscErrorCode PetscErrorPrintfInitialize()
{
PetscErrorCode ierr;
PetscBool use_stdout = PETSC_FALSE,use_none = PETSC_FALSE;
PetscFunctionBegin;
ierr = PetscGetArchType(arch,sizeof(arch));CHKERRQ(ierr);
ierr = PetscGetHostName(hostname,sizeof(hostname));CHKERRQ(ierr);
ierr = PetscGetUserName(username,sizeof(username));CHKERRQ(ierr);
ierr = PetscGetProgramName(pname,PETSC_MAX_PATH_LEN);CHKERRQ(ierr);
ierr = PetscGetDate(date,sizeof(date));CHKERRQ(ierr);
ierr = PetscGetVersion(version,sizeof(version));CHKERRQ(ierr);
ierr = PetscOptionsGetBool(NULL,"-error_output_stdout",&use_stdout,NULL);CHKERRQ(ierr);
if (use_stdout) PETSC_STDERR = PETSC_STDOUT;
ierr = PetscOptionsGetBool(NULL,"-error_output_none",&use_none,NULL);CHKERRQ(ierr);
if (use_none) PetscErrorPrintf = PetscErrorPrintfNone;
PetscErrorPrintfInitializeCalled = PETSC_TRUE;
PetscFunctionReturn(0);
}
static int setupConnection(MLENV *env, MLINK *link, const char *linkhost, LinkMode linkmode)
{
int argc = 5;
char *argv[5];
char hostname[256];
long lerr;
int ierr;
PetscFunctionBegin;
/* Link name */
argv[0] = "-linkname";
argv[1] = "8001";
/* Link host */
argv[2] = "-linkhost";
if (!linkhost) {
ierr = PetscGetHostName(hostname, 255);CHKERRQ(ierr);
argv[3] = hostname;
} else argv[3] = (char*) linkhost;
/* Link mode */
switch (linkmode) {
case MATHEMATICA_LINK_CREATE:
argv[4] = "-linkcreate";
break;
case MATHEMATICA_LINK_CONNECT:
argv[4] = "-linkconnect";
break;
case MATHEMATICA_LINK_LAUNCH:
argv[4] = "-linklaunch";
break;
}
*env = MLInitialize(0);
for (lerr = 0; lerr < argc; lerr++) printf("argv[%ld] = %s\n", lerr, argv[lerr]);
*link = MLOpenInEnv(*env, argc, argv, &lerr);
printf("lerr = %ld\n", lerr);
PetscFunctionReturn(0);
}
#include <petsc-private/fortranimpl.h>
#if defined(PETSC_HAVE_FORTRAN_CAPS)
#define petscgethostname_ PETSCGETHOSTNAME
#elif !defined(PETSC_HAVE_FORTRAN_UNDERSCORE)
#define petscgethostname_ petscgethostname
#endif
EXTERN_C_BEGIN
void PETSC_STDCALL petscgethostname_(CHAR str PETSC_MIXED_LEN(len),PetscErrorCode *ierr PETSC_END_LEN(len))
{
char *tstr;
size_t tlen;
tstr = str;
tlen = len; /* int to size_t */
*ierr = PetscGetHostName(tstr,tlen);
FIXRETURNCHAR(PETSC_TRUE,str,len);
}
EXTERN_C_END
PetscErrorCode PetscLogView_VecScatter(PetscViewer viewer)
{
MPI_Comm comm = PetscObjectComm((PetscObject) viewer);
PetscEventPerfInfo *eventInfo = NULL;
PetscLogDouble locTotalTime,stats[6],maxstats[6],minstats[6],sumstats[6],avetime,ksptime;
PetscStageLog stageLog;
const int stage = 2;
int event,events[] = {VEC_ScatterBegin,VEC_ScatterEnd};
PetscMPIInt rank,size;
PetscErrorCode ierr;
PetscInt i;
char arch[128],hostname[128],username[128],pname[PETSC_MAX_PATH_LEN],date[128],version[256];
PetscFunctionBegin;
PetscTime(&locTotalTime); locTotalTime -= petsc_BaseTime;
ierr = MPI_Comm_size(comm, &size);CHKERRQ(ierr);
ierr = MPI_Comm_rank(comm, &rank);CHKERRQ(ierr);
ierr = PetscLogGetStageLog(&stageLog);CHKERRQ(ierr);
ierr = PetscViewerASCIIPrintf(viewer,"numProcs = %d\n",size);CHKERRQ(ierr);
ierr = PetscGetArchType(arch,sizeof(arch));CHKERRQ(ierr);
ierr = PetscGetHostName(hostname,sizeof(hostname));CHKERRQ(ierr);
ierr = PetscGetUserName(username,sizeof(username));CHKERRQ(ierr);
ierr = PetscGetProgramName(pname,sizeof(pname));CHKERRQ(ierr);
ierr = PetscGetDate(date,sizeof(date));CHKERRQ(ierr);
ierr = PetscGetVersion(version,sizeof(version));CHKERRQ(ierr);
ierr = PetscViewerASCIIPrintf(viewer,"%s on a %s named %s with %d processors, by %s %s\n", pname, arch, hostname, size, username, date);CHKERRQ(ierr);
ierr = PetscViewerASCIIPrintf(viewer, "Using %s\n", version);CHKERRQ(ierr);
ierr = PetscViewerASCIIPrintf(viewer, "Configure options: %s",petscconfigureoptions);CHKERRQ(ierr);
ierr = PetscViewerASCIIPrintf(viewer, "%s", petscmachineinfo);CHKERRQ(ierr);
ierr = PetscViewerASCIIPrintf(viewer, "%s", petsccompilerinfo);CHKERRQ(ierr);
ierr = PetscViewerASCIIPrintf(viewer, "%s", petsccompilerflagsinfo);CHKERRQ(ierr);
ierr = PetscViewerASCIIPrintf(viewer, "%s", petsclinkerinfo);CHKERRQ(ierr);
ierr = PetscViewerASCIIPrintf(viewer, "%s\n", PETSC_MPICC_SHOW);CHKERRQ(ierr);
ierr = PetscOptionsView(NULL,viewer);CHKERRQ(ierr);
#if defined(PETSC_HAVE_HWLOC)
ierr = PetscProcessPlacementView(viewer);CHKERRQ(ierr);
#endif
ierr = PetscViewerASCIIPrintf(viewer, "----------------------------------------------------\n");CHKERRQ(ierr);
ierr = PetscViewerASCIIPrintf(viewer," Time Min to Max Range Proportion of KSP\n");CHKERRQ(ierr);
eventInfo = stageLog->stageInfo[stage].eventLog->eventInfo;
ierr = MPI_Allreduce(&eventInfo[KSP_Solve].time,&ksptime,1,MPIU_PETSCLOGDOUBLE,MPI_SUM,PETSC_COMM_WORLD);CHKERRQ(ierr);
ksptime = ksptime/size;
for (i=0; i<(int)(sizeof(events)/sizeof(int)); i++) {
event = events[i];
stats[COUNT] = eventInfo[event].count;
stats[TIME] = eventInfo[event].time;
stats[NUMMESS] = eventInfo[event].numMessages;
stats[MESSLEN] = eventInfo[event].messageLength;
stats[REDUCT] = eventInfo[event].numReductions;
stats[FLOPS] = eventInfo[event].flops;
ierr = MPI_Allreduce(stats,maxstats,6,MPIU_PETSCLOGDOUBLE,MPI_MAX,PETSC_COMM_WORLD);CHKERRQ(ierr);
ierr = MPI_Allreduce(stats,minstats,6,MPIU_PETSCLOGDOUBLE,MPI_MIN,PETSC_COMM_WORLD);CHKERRQ(ierr);
ierr = MPI_Allreduce(stats,sumstats,6,MPIU_PETSCLOGDOUBLE,MPI_SUM,PETSC_COMM_WORLD);CHKERRQ(ierr);
avetime = sumstats[1]/size;
ierr = PetscViewerASCIIPrintf(viewer,"%s %4.2e -%5.1f %% %5.1f %% %4.2e %%\n",stageLog->eventLog->eventInfo[event].name,
avetime,100.*(avetime-minstats[1])/avetime,100.*(maxstats[1]-avetime)/avetime,100.*avetime/ksptime);CHKERRQ(ierr);
}
ierr = PetscViewerFlush(viewer);CHKERRQ(ierr);
PetscFunctionReturn(0);
}
/*@C
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!
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, also checks ~username/.petscrc and .petscrc use NULL to not check for
code specific file. Use -skip_petscrc in the code specific file to skip the .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:
+ -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 <machinename> 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_stderr prints error messages to stderr instead of the default stdout
. -error_output_none does not print the error messages (but handles errors in the same way as if this was not called)
. -debugger_nodes [node1,node2,...] - Indicates nodes 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)
. -malloc no - Indicates not to use error-checking malloc
. -malloc_debug - check for memory corruption at EVERY malloc or free
. -malloc_test - like -malloc_dump -malloc_debug, but only active for debugging builds
. -fp_trap - Stops on floating point exceptions (Note that on the
IBM RS6000 this slows code by at least a factor of 10.)
. -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_info - Print memory usage at end of run
- -server <port> - start PETSc webserver (default port is 8080)
Options Database Keys for Profiling:
See the <a href="../../docs/manual.pdf#nameddest=ch_profiling">profiling chapter of the users manual</a> for details.
+ -info <optional filename> - Prints verbose information to the screen
. -info_exclude <null,vec,mat,pc,ksp,snes,ts> - Excludes some of the verbose messages
. -log_sync - Log the synchronization in scatters, inner products and norms
. -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_summary [filename] - Prints summary of flop and timing information to screen. If the filename is specified the
summary is written to the file. See PetscLogView().
. -log_summary_python [filename] - Prints data on of flop and timing usage to a file or screen. See PetscLogPrintSViewPython().
. -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)
Only one of -log_trace, -log_summary, -log_all, -log, or -log_mpe may be used at a time
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_VIEWER_SOCKET_PORT - socket number to use for socket viewer
- PETSC_VIEWER_SOCKET_MACHINE - machine to use for socket viewer to connect to
Level: beginner
Notes:
If for some reason you must call MPI_Init() separately, call
it before PetscInitialize().
Fortran Version:
In Fortran this routine has the format
$ call PetscInitialize(file,ierr)
+ ierr - error return code
- file - [optional] PETSc database file, also checks ~username/.petscrc and .petscrc use NULL_CHARACTER to not check for
code specific file. Use -skip_petscrc in the code specific file to skip the .petscrc files
Important Fortran Note:
In Fortran, you MUST use NULL_CHARACTER to indicate a
null character string; you CANNOT just use NULL as
in the C version. See the <a href="../../docs/manual.pdf">users manual</a> for details.
If your main program is C but you call Fortran code that also uses PETSc you need to call PetscInitializeFortran() soon after
calling PetscInitialize().
Concepts: initializing PETSc
.seealso: PetscFinalize(), PetscInitializeFortran(), PetscGetArgs(), PetscInitializeNoArguments()
@*/
PetscErrorCode PetscInitialize(int *argc,char ***args,const char file[],const char help[])
{
PetscErrorCode ierr;
PetscMPIInt flag, size;
PetscInt nodesize;
PetscBool flg;
char hostname[256];
PetscFunctionBegin;
if (PetscInitializeCalled) PetscFunctionReturn(0);
/* these must be initialized in a routine, not as a constant declaration*/
PETSC_STDOUT = stdout;
PETSC_STDERR = stderr;
ierr = PetscOptionsCreate();CHKERRQ(ierr);
/*
We initialize the program name here (before MPI_Init()) because MPICH has a bug in
it that it sets args[0] on all processors to be args[0] on the first processor.
*/
if (argc && *argc) {
ierr = PetscSetProgramName(**args);CHKERRQ(ierr);
} else {
ierr = PetscSetProgramName("Unknown Name");CHKERRQ(ierr);
}
ierr = MPI_Initialized(&flag);CHKERRQ(ierr);
if (!flag) {
if (PETSC_COMM_WORLD != MPI_COMM_NULL) SETERRQ(PETSC_COMM_SELF,PETSC_ERR_SUP,"You cannot set PETSC_COMM_WORLD if you have not initialized MPI first");
#if defined(PETSC_HAVE_MPI_INIT_THREAD)
{
PetscMPIInt provided;
ierr = MPI_Init_thread(argc,args,MPI_THREAD_FUNNELED,&provided);CHKERRQ(ierr);
}
#else
ierr = MPI_Init(argc,args);CHKERRQ(ierr);
#endif
PetscBeganMPI = PETSC_TRUE;
}
if (argc && args) {
PetscGlobalArgc = *argc;
PetscGlobalArgs = *args;
}
PetscFinalizeCalled = PETSC_FALSE;
if (PETSC_COMM_WORLD == MPI_COMM_NULL) PETSC_COMM_WORLD = MPI_COMM_WORLD;
ierr = MPI_Comm_set_errhandler(PETSC_COMM_WORLD,MPI_ERRORS_RETURN);CHKERRQ(ierr);
/* Done after init due to a bug in MPICH-GM? */
ierr = PetscErrorPrintfInitialize();CHKERRQ(ierr);
ierr = MPI_Comm_rank(MPI_COMM_WORLD,&PetscGlobalRank);CHKERRQ(ierr);
ierr = MPI_Comm_size(MPI_COMM_WORLD,&PetscGlobalSize);CHKERRQ(ierr);
MPIU_BOOL = MPI_INT;
MPIU_ENUM = MPI_INT;
/*
Initialized the global complex variable; this is because with
shared libraries the constructors for global variables
are not called; at least on IRIX.
*/
#if defined(PETSC_HAVE_COMPLEX)
{
#if defined(PETSC_CLANGUAGE_CXX)
PetscComplex ic(0.0,1.0);
PETSC_i = ic;
#elif defined(PETSC_CLANGUAGE_C)
PETSC_i = _Complex_I;
#endif
}
#if !defined(PETSC_HAVE_MPI_C_DOUBLE_COMPLEX)
ierr = MPI_Type_contiguous(2,MPI_DOUBLE,&MPIU_C_DOUBLE_COMPLEX);CHKERRQ(ierr);
ierr = MPI_Type_commit(&MPIU_C_DOUBLE_COMPLEX);CHKERRQ(ierr);
ierr = MPI_Type_contiguous(2,MPI_FLOAT,&MPIU_C_COMPLEX);CHKERRQ(ierr);
ierr = MPI_Type_commit(&MPIU_C_COMPLEX);CHKERRQ(ierr);
#endif
#endif /* PETSC_HAVE_COMPLEX */
/*
Create the PETSc MPI reduction operator that sums of the first
half of the entries and maxes the second half.
*/
ierr = MPI_Op_create(PetscMaxSum_Local,1,&PetscMaxSum_Op);CHKERRQ(ierr);
#if defined(PETSC_USE_REAL___FLOAT128)
ierr = MPI_Type_contiguous(2,MPI_DOUBLE,&MPIU___FLOAT128);CHKERRQ(ierr);
ierr = MPI_Type_commit(&MPIU___FLOAT128);CHKERRQ(ierr);
#if defined(PETSC_HAVE_COMPLEX)
ierr = MPI_Type_contiguous(4,MPI_DOUBLE,&MPIU___COMPLEX128);CHKERRQ(ierr);
ierr = MPI_Type_commit(&MPIU___COMPLEX128);CHKERRQ(ierr);
#endif
ierr = MPI_Op_create(PetscMax_Local,1,&MPIU_MAX);CHKERRQ(ierr);
ierr = MPI_Op_create(PetscMin_Local,1,&MPIU_MIN);CHKERRQ(ierr);
#endif
#if (defined(PETSC_HAVE_COMPLEX) && !defined(PETSC_HAVE_MPI_C_DOUBLE_COMPLEX)) || defined(PETSC_USE_REAL___FLOAT128)
ierr = MPI_Op_create(PetscSum_Local,1,&MPIU_SUM);CHKERRQ(ierr);
#endif
ierr = MPI_Type_contiguous(2,MPIU_SCALAR,&MPIU_2SCALAR);CHKERRQ(ierr);
ierr = MPI_Type_commit(&MPIU_2SCALAR);CHKERRQ(ierr);
ierr = MPI_Op_create(PetscADMax_Local,1,&PetscADMax_Op);CHKERRQ(ierr);
ierr = MPI_Op_create(PetscADMin_Local,1,&PetscADMin_Op);CHKERRQ(ierr);
#if defined(PETSC_USE_64BIT_INDICES) || !defined(MPI_2INT)
ierr = MPI_Type_contiguous(2,MPIU_INT,&MPIU_2INT);CHKERRQ(ierr);
ierr = MPI_Type_commit(&MPIU_2INT);CHKERRQ(ierr);
#endif
/*
Attributes to be set on PETSc communicators
*/
ierr = MPI_Keyval_create(MPI_NULL_COPY_FN,Petsc_DelCounter,&Petsc_Counter_keyval,(void*)0);CHKERRQ(ierr);
ierr = MPI_Keyval_create(MPI_NULL_COPY_FN,Petsc_DelComm_Outer,&Petsc_InnerComm_keyval,(void*)0);CHKERRQ(ierr);
ierr = MPI_Keyval_create(MPI_NULL_COPY_FN,Petsc_DelComm_Inner,&Petsc_OuterComm_keyval,(void*)0);CHKERRQ(ierr);
/*
Build the options database
*/
ierr = PetscOptionsInsert(argc,args,file);CHKERRQ(ierr);
/*
Print main application help message
*/
ierr = PetscOptionsHasName(NULL,"-help",&flg);CHKERRQ(ierr);
if (help && flg) {
ierr = PetscPrintf(PETSC_COMM_WORLD,help);CHKERRQ(ierr);
}
ierr = PetscOptionsCheckInitial_Private();CHKERRQ(ierr);
/* SHOULD PUT IN GUARDS: Make sure logging is initialized, even if we do not print it out */
#if defined(PETSC_USE_LOG)
ierr = PetscLogBegin_Private();CHKERRQ(ierr);
#endif
/*
Load the dynamic libraries (on machines that support them), this registers all
the solvers etc. (On non-dynamic machines this initializes the PetscDraw and PetscViewer classes)
*/
ierr = PetscInitialize_DynamicLibraries();CHKERRQ(ierr);
ierr = MPI_Comm_size(PETSC_COMM_WORLD,&size);CHKERRQ(ierr);
ierr = PetscInfo1(0,"PETSc successfully started: number of processors = %d\n",size);CHKERRQ(ierr);
ierr = PetscGetHostName(hostname,256);CHKERRQ(ierr);
ierr = PetscInfo1(0,"Running on machine: %s\n",hostname);CHKERRQ(ierr);
ierr = PetscOptionsCheckInitial_Components();CHKERRQ(ierr);
/* Check the options database for options related to the options database itself */
ierr = PetscOptionsSetFromOptions();CHKERRQ(ierr);
#if defined(PETSC_USE_PETSC_MPI_EXTERNAL32)
/*
Tell MPI about our own data representation converter, this would/should be used if extern32 is not supported by the MPI
Currently not used because it is not supported by MPICH.
*/
#if !defined(PETSC_WORDS_BIGENDIAN)
ierr = MPI_Register_datarep((char*)"petsc",PetscDataRep_read_conv_fn,PetscDataRep_write_conv_fn,PetscDataRep_extent_fn,NULL);CHKERRQ(ierr);
#endif
#endif
ierr = PetscOptionsGetInt(NULL,"-hmpi_spawn_size",&nodesize,&flg);CHKERRQ(ierr);
if (flg) {
#if defined(PETSC_HAVE_MPI_COMM_SPAWN)
ierr = PetscHMPISpawn((PetscMPIInt) nodesize);CHKERRQ(ierr); /* worker nodes never return from here; they go directly to PetscEnd() */
#else
SETERRQ(PETSC_COMM_SELF,PETSC_ERR_SUP,"PETSc built without MPI 2 (MPI_Comm_spawn) support, use -hmpi_merge_size instead");
#endif
} else {
ierr = PetscOptionsGetInt(NULL,"-hmpi_merge_size",&nodesize,&flg);CHKERRQ(ierr);
if (flg) {
ierr = PetscHMPIMerge((PetscMPIInt) nodesize,NULL,NULL);CHKERRQ(ierr);
if (PetscHMPIWorker) { /* if worker then never enter user code */
PetscInitializeCalled = PETSC_TRUE;
PetscEnd();
}
}
}
#if defined(PETSC_HAVE_CUDA)
{
PetscMPIInt p;
for (p = 0; p < PetscGlobalSize; ++p) {
if (p == PetscGlobalRank) cublasInit();
ierr = MPI_Barrier(PETSC_COMM_WORLD);CHKERRQ(ierr);
}
}
#endif
ierr = PetscOptionsHasName(NULL,"-python",&flg);CHKERRQ(ierr);
if (flg) {
PetscInitializeCalled = PETSC_TRUE;
ierr = PetscPythonInitialize(NULL,NULL);CHKERRQ(ierr);
}
ierr = PetscThreadCommInitializePackage();CHKERRQ(ierr);
/*
Setup building of stack frames for all function calls
*/
#if defined(PETSC_USE_DEBUG)
PetscThreadLocalRegister((PetscThreadKey*)&petscstack); /* Creates petscstack_key if needed */
ierr = PetscStackCreate();CHKERRQ(ierr);
#endif
#if defined(PETSC_SERIALIZE_FUNCTIONS)
ierr = PetscFPTCreate(10000);CHKERRQ(ierr);
#endif
/*
Once we are completedly initialized then we can set this variables
*/
PetscInitializeCalled = PETSC_TRUE;
PetscFunctionReturn(0);
}
/*@C
PetscStopForDebugger - Prints a message to the screen indicating how to
attach to the process with the debugger and then waits for the
debugger to attach.
Not Collective
Level: developer
Notes: This is likely never needed since PetscAttachDebugger() is easier to use and seems to always work.
Developer Notes: Since this can be called by the error handler, should it be calling SETERRQ() and CHKERRQ()?
Concepts: debugger^waiting for attachment
.seealso: PetscSetDebugger(), PetscAttachDebugger()
@*/
PetscErrorCode PetscStopForDebugger(void)
{
PetscErrorCode ierr;
PetscInt sleeptime=0;
#if !defined(PETSC_CANNOT_START_DEBUGGER)
int ppid;
PetscMPIInt rank;
char program[PETSC_MAX_PATH_LEN],hostname[256];
PetscBool isdbx,isxldb,isxxgdb,isddd,iskdbg,isups,isxdb,islldb;
#endif
PetscFunctionBegin;
#if defined(PETSC_CANNOT_START_DEBUGGER)
(*PetscErrorPrintf)("System cannot start debugger; just continuing program\n");
#else
ierr = MPI_Comm_rank(PETSC_COMM_WORLD,&rank);
if (ierr) rank = 0; /* ignore error since this may be already in error handler */
ierr = PetscGetHostName(hostname,256);
if (ierr) {
(*PetscErrorPrintf)("Cannot determine hostname; just continuing program\n");
PetscFunctionReturn(0);
}
ierr = PetscGetProgramName(program,256);
if (ierr) {
(*PetscErrorPrintf)("Cannot determine program name; just continuing program\n");
PetscFunctionReturn(0);
}
if (!program[0]) {
(*PetscErrorPrintf)("Cannot determine program name; just continuing program\n");
PetscFunctionReturn(0);
}
ppid = getpid();
ierr = PetscStrcmp(Debugger,"xxgdb",&isxxgdb);CHKERRQ(ierr);
ierr = PetscStrcmp(Debugger,"ddd",&isddd);CHKERRQ(ierr);
ierr = PetscStrcmp(Debugger,"kdbg",&iskdbg);CHKERRQ(ierr);
ierr = PetscStrcmp(Debugger,"ups",&isups);CHKERRQ(ierr);
ierr = PetscStrcmp(Debugger,"xldb",&isxldb);CHKERRQ(ierr);
ierr = PetscStrcmp(Debugger,"xdb",&isxdb);CHKERRQ(ierr);
ierr = PetscStrcmp(Debugger,"dbx",&isdbx);CHKERRQ(ierr);
ierr = PetscStrcmp(Debugger,"lldb",&islldb);CHKERRQ(ierr);
if (isxxgdb || isups || isddd || iskdbg) (*PetscErrorPrintf)("[%d]%s>>%s %s %d\n",rank,hostname,Debugger,program,ppid);
else if (isxldb) (*PetscErrorPrintf)("[%d]%s>>%s -a %d %s\n",rank,hostname,Debugger,ppid,program);
else if (islldb) (*PetscErrorPrintf)("[%d]%s>>%s -p %d\n",rank,hostname,Debugger,ppid);
else if (isdbx) {
#if defined(PETSC_USE_P_FOR_DEBUGGER)
(*PetscErrorPrintf)("[%d]%s>>%s -p %d %s\n",rank,hostname,Debugger,ppid,program);
#elif defined(PETSC_USE_LARGEP_FOR_DEBUGGER)
(*PetscErrorPrintf)("[%d]%s>>%s -l ALL -P %d %s\n",rank,hostname,Debugger,ppid,program);
#elif defined(PETSC_USE_A_FOR_DEBUGGER)
(*PetscErrorPrintf)("[%d]%s>>%s -a %d\n",rank,hostname,Debugger,ppid);
#elif defined(PETSC_USE_PID_FOR_DEBUGGER)
(*PetscErrorPrintf)("[%d]%s>>%s -pid %d %s\n",rank,hostname,Debugger,ppid,program);
#else
(*PetscErrorPrintf)("[%d]%s>>%s %s %d\n",rank,hostname,Debugger,program,ppid);
#endif
}
#endif /* PETSC_CANNOT_START_DEBUGGER */
fflush(stdout); /* ignore error because may already be in error handler */
sleeptime = 25; /* default to sleep waiting for debugger */
PetscOptionsGetInt(NULL,"-debugger_pause",&sleeptime,NULL); /* ignore error because may already be in error handler */
if (sleeptime < 0) sleeptime = -sleeptime;
#if defined(PETSC_NEED_DEBUGGER_NO_SLEEP)
/*
HP cannot attach process to sleeping debugger, hence count instead
*/
{
PetscReal x = 1.0;
int i =10000000;
while (i--) x++; /* cannot attach to sleeper */
}
#elif defined(PETSC_HAVE_SLEEP_RETURNS_EARLY)
/*
IBM sleep may return at anytime, hence must see if there is more time to sleep
*/
{
int left = sleeptime;
while (left > 0) left = sleep(left) - 1;
}
#else
PetscSleep(sleeptime);
#endif
PetscFunctionReturn(0);
}
/*@
PetscAttachDebugger - Attaches the debugger to the running process.
Not Collective
Level: advanced
Concepts: debugger^starting from program
Developer Notes: Since this can be called by the error handler should it be calling SETERRQ() and CHKERRQ()?
.seealso: PetscSetDebugger()
@*/
PetscErrorCode PetscAttachDebugger(void)
{
#if !defined(PETSC_CANNOT_START_DEBUGGER)
int child =0;
PetscReal sleeptime=0;
PetscErrorCode ierr;
char program[PETSC_MAX_PATH_LEN],display[256],hostname[64];
#endif
PetscFunctionBegin;
#if defined(PETSC_CANNOT_START_DEBUGGER) || !defined(PETSC_HAVE_FORK)
(*PetscErrorPrintf)("System cannot start debugger\n");
(*PetscErrorPrintf)("On Cray run program in Totalview debugger\n");
(*PetscErrorPrintf)("On Windows use Developer Studio(MSDEV)\n");
MPI_Abort(PETSC_COMM_WORLD,1);
#else
ierr = PetscGetDisplay(display,128);CHKERRQ(ierr);
ierr = PetscGetProgramName(program,PETSC_MAX_PATH_LEN);CHKERRQ(ierr);
if (ierr) {
(*PetscErrorPrintf)("Cannot determine program name\n");
PetscFunctionReturn(1);
}
if (!program[0]) {
(*PetscErrorPrintf)("Cannot determine program name\n");
PetscFunctionReturn(1);
}
child = (int)fork();
if (child < 0) {
(*PetscErrorPrintf)("Error in fork() attaching debugger\n");
PetscFunctionReturn(1);
}
/*
Swap role the parent and child. This is (I think) so that control c typed
in the debugger goes to the correct process.
*/
if (child) child = 0;
else child = (int)getppid();
if (child) { /* I am the parent, will run the debugger */
const char *args[10];
char pid[10];
PetscInt j,jj;
PetscBool isdbx,isidb,isxldb,isxxgdb,isups,isxdb,isworkshop,isddd,iskdbg,islldb;
ierr = PetscGetHostName(hostname,64);CHKERRQ(ierr);
/*
We need to send a continue signal to the "child" process on the
alpha, otherwise it just stays off forever
*/
#if defined(PETSC_NEED_KILL_FOR_DEBUGGER)
kill(child,SIGCONT);
#endif
sprintf(pid,"%d",child);
ierr = PetscStrcmp(Debugger,"xxgdb",&isxxgdb);CHKERRQ(ierr);
ierr = PetscStrcmp(Debugger,"ddd",&isddd);CHKERRQ(ierr);
ierr = PetscStrcmp(Debugger,"kdbg",&iskdbg);CHKERRQ(ierr);
ierr = PetscStrcmp(Debugger,"ups",&isups);CHKERRQ(ierr);
ierr = PetscStrcmp(Debugger,"xldb",&isxldb);CHKERRQ(ierr);
ierr = PetscStrcmp(Debugger,"xdb",&isxdb);CHKERRQ(ierr);
ierr = PetscStrcmp(Debugger,"dbx",&isdbx);CHKERRQ(ierr);
ierr = PetscStrcmp(Debugger,"idb",&isidb);CHKERRQ(ierr);
ierr = PetscStrcmp(Debugger,"workshop",&isworkshop);CHKERRQ(ierr);
ierr = PetscStrcmp(Debugger,"lldb",&islldb);CHKERRQ(ierr);
if (isxxgdb || isups || isddd) {
args[1] = program; args[2] = pid; args[3] = "-display";
args[0] = Debugger; args[4] = display; args[5] = 0;
(*PetscErrorPrintf)("PETSC: Attaching %s to %s %s on %s\n",args[0],args[1],pid,hostname);
if (execvp(args[0],(char**)args) < 0) {
perror("Unable to start debugger");
exit(0);
}
} else if (iskdbg) {
args[1] = "-p"; args[2] = pid; args[3] = program; args[4] = "-display";
args[0] = Debugger; args[5] = display; args[6] = 0;
(*PetscErrorPrintf)("PETSC: Attaching %s to %s %s on %s\n",args[0],args[3],pid,hostname);
if (execvp(args[0],(char**)args) < 0) {
perror("Unable to start debugger");
exit(0);
}
} else if (isxldb) {
args[1] = "-a"; args[2] = pid; args[3] = program; args[4] = "-display";
args[0] = Debugger; args[5] = display; args[6] = 0;
(*PetscErrorPrintf)("PETSC: Attaching %s to %s %s on %s\n",args[0],args[1],pid,hostname);
if (execvp(args[0],(char**)args) < 0) {
perror("Unable to start debugger");
exit(0);
}
} else if (isworkshop) {
args[1] = "-s"; args[2] = pid; args[3] = "-D"; args[4] = "-";
args[0] = Debugger; args[5] = pid; args[6] = "-display"; args[7] = display; args[8] = 0;
(*PetscErrorPrintf)("PETSC: Attaching %s to %s on %s\n",args[0],pid,hostname);
if (execvp(args[0],(char**)args) < 0) {
perror("Unable to start debugger");
exit(0);
}
} else {
j = 0;
if (Xterm) {
PetscBool cmp;
char *tmp,*tmp1;
ierr = PetscStrncmp(DebugTerminal,"screen",6,&cmp);CHKERRQ(ierr);
if (cmp) display[0] = 0; /* when using screen, we never pass -display */
args[j++] = tmp = DebugTerminal;
if (display[0]) {
args[j++] = "-display"; args[j++] = display;
}
while (*tmp) {
ierr = PetscStrchr(tmp,' ',&tmp1);CHKERRQ(ierr);
if (!tmp1) break;
*tmp1 = 0;
tmp = tmp1+1;
args[j++] = tmp;
}
}
args[j++] = Debugger;
jj = j;
args[j++] = program; args[j++] = pid; args[j++] = 0;
if (isidb) {
j = jj;
args[j++] = "-pid";
args[j++] = pid;
args[j++] = "-gdb";
args[j++] = program;
args[j++] = 0;
}
if (islldb) {
j = jj;
args[j++] = "-p";
args[j++] = pid;
args[j++] = 0;
}
if (isdbx) {
j = jj;
#if defined(PETSC_USE_P_FOR_DEBUGGER)
args[j++] = "-p";
args[j++] = pid;
args[j++] = program;
#elif defined(PETSC_USE_LARGEP_FOR_DEBUGGER)
args[j++] = "-l";
args[j++] = "ALL";
args[j++] = "-P";
args[j++] = pid;
args[j++] = program;
#elif defined(PETSC_USE_A_FOR_DEBUGGER)
args[j++] = "-a";
args[j++] = pid;
#elif defined(PETSC_USE_PID_FOR_DEBUGGER)
args[j++] = "-pid";
args[j++] = pid;
args[j++] = program;
#endif
args[j++] = 0;
}
if (Xterm) {
if (display[0]) (*PetscErrorPrintf)("PETSC: Attaching %s to %s of pid %s on display %s on machine %s\n",Debugger,program,pid,display,hostname);
else (*PetscErrorPrintf)("PETSC: Attaching %s to %s on pid %s on %s\n",Debugger,program,pid,hostname);
if (execvp(args[0],(char**)args) < 0) {
perror("Unable to start debugger in xterm");
exit(0);
}
} else {
(*PetscErrorPrintf)("PETSC: Attaching %s to %s of pid %s on %s\n",Debugger,program,pid,hostname);
if (execvp(args[0],(char**)args) < 0) {
perror("Unable to start debugger");
exit(0);
}
}
}
} else { /* I am the child, continue with user code */
sleeptime = 10; /* default to sleep waiting for debugger */
ierr = PetscOptionsGetReal(NULL,"-debugger_pause",&sleeptime,NULL);CHKERRQ(ierr);
if (sleeptime < 0) sleeptime = -sleeptime;
#if defined(PETSC_NEED_DEBUGGER_NO_SLEEP)
/*
HP cannot attach process to sleeping debugger, hence count instead
*/
{
PetscReal x = 1.0;
int i =10000000;
while (i--) x++; /* cannot attach to sleeper */
}
#elif defined(PETSC_HAVE_SLEEP_RETURNS_EARLY)
/*
IBM sleep may return at anytime, hence must see if there is more time to sleep
*/
{
int left = sleeptime;
while (left > 0) left = PetscSleep(left) - 1;
}
#else
PetscSleep(sleeptime);
#endif
}
#endif
PetscFunctionReturn(0);
}
/*@C
PetscSocketEstablish - starts a listener on a socket
Input Parameters:
. portnumber - the port to wait at
Output Parameters:
. ss - the socket to be used with PetscSocketListen()
Level: advanced
.seealso: PetscSocketListen(), PetscOpenSocket()
@*/
PETSC_INTERN PetscErrorCode PetscSocketEstablish(int portnum,int *ss)
{
char myname[MAXHOSTNAME+1];
int s;
PetscErrorCode ierr;
struct sockaddr_in sa;
struct hostent *hp;
PetscFunctionBegin;
ierr = PetscGetHostName(myname,MAXHOSTNAME);CHKERRQ(ierr);
ierr = PetscMemzero(&sa,sizeof(struct sockaddr_in));CHKERRQ(ierr);
hp = gethostbyname(myname);
if (!hp) SETERRQ(PETSC_COMM_SELF,PETSC_ERR_SYS,"Unable to get hostent information from system");
sa.sin_family = hp->h_addrtype;
sa.sin_port = htons((u_short)portnum);
if ((s = socket(AF_INET,SOCK_STREAM,0)) < 0) SETERRQ(PETSC_COMM_SELF,PETSC_ERR_SYS,"Error running socket() command");
#if defined(PETSC_HAVE_SO_REUSEADDR)
{
int optval = 1; /* Turn on the option */
ierr = setsockopt(s,SOL_SOCKET,SO_REUSEADDR,(char*)&optval,sizeof(optval));CHKERRQ(ierr);
}
#endif
while (bind(s,(struct sockaddr*)&sa,sizeof(sa)) < 0) {
#if defined(PETSC_HAVE_WSAGETLASTERROR)
ierr = WSAGetLastError();
if (ierr != WSAEADDRINUSE) {
#else
if (errno != EADDRINUSE) {
#endif
close(s);
SETERRQ(PETSC_COMM_SELF,PETSC_ERR_SYS,"Error from bind()");
}
}
listen(s,0);
*ss = s;
return(0);
}
/*@C
PetscSocketListen - Listens at a socket created with PetscSocketEstablish()
Input Parameter:
. listenport - obtained with PetscSocketEstablish()
Output Parameter:
. t - pass this to read() to read what is passed to this connection
Level: advanced
.seealso: PetscSocketEstablish()
@*/
PETSC_INTERN PetscErrorCode PetscSocketListen(int listenport,int *t)
{
struct sockaddr_in isa;
#if defined(PETSC_HAVE_ACCEPT_SIZE_T)
size_t i;
#else
int i;
#endif
PetscFunctionBegin;
/* wait for someone to try to connect */
i = sizeof(struct sockaddr_in);
if ((*t = accept(listenport,(struct sockaddr*)&isa,(socklen_t*)&i)) < 0) SETERRQ(PETSC_COMM_SELF,PETSC_ERR_SYS,"error from accept()\n");
PetscFunctionReturn(0);
}
/*@C
PetscViewerSocketOpen - Opens a connection to a MATLAB or other socket based server.
Collective on MPI_Comm
Input Parameters:
+ comm - the MPI communicator
. machine - the machine the server is running on,, use NULL for the local machine, use "server" to passively wait for
a connection from elsewhere
- port - the port to connect to, use PETSC_DEFAULT for the default
Output Parameter:
. lab - a context to use when communicating with the server
Level: intermediate
Notes:
Most users should employ the following commands to access the
MATLAB PetscViewers
$
$ PetscViewerSocketOpen(MPI_Comm comm, char *machine,int port,PetscViewer &viewer)
$ MatView(Mat matrix,PetscViewer viewer)
$
$ or
$
$ PetscViewerSocketOpen(MPI_Comm comm,char *machine,int port,PetscViewer &viewer)
$ VecView(Vec vector,PetscViewer viewer)
Options Database Keys:
For use with PETSC_VIEWER_SOCKET_WORLD, PETSC_VIEWER_SOCKET_SELF,
PETSC_VIEWER_SOCKET_() or if
NULL is passed for machine or PETSC_DEFAULT is passed for port
$ -viewer_socket_machine <machine>
$ -viewer_socket_port <port>
Environmental variables:
+ PETSC_VIEWER_SOCKET_PORT portnumber
- PETSC_VIEWER_SOCKET_MACHINE machine name
Currently the only socket client available is MATLAB. See
src/dm/examples/tests/ex12.c and ex12.m for an example of usage.
Notes:
The socket viewer is in some sense a subclass of the binary viewer, to read and write to the socket
use PetscViewerBinaryRead(), PetscViewerBinaryWrite(), PetscViewerBinarWriteStringArray(), PetscViewerBinaryGetDescriptor().
Use this for communicating with an interactive MATLAB session, see PETSC_VIEWER_MATLAB_() for writing output to a
.mat file. Use PetscMatlabEngineCreate() or PETSC_MATLAB_ENGINE_(), PETSC_MATLAB_ENGINE_SELF, or PETSC_MATLAB_ENGINE_WORLD
for communicating with a MATLAB Engine
Concepts: MATLAB^sending data
Concepts: sockets^sending data
.seealso: MatView(), VecView(), PetscViewerDestroy(), PetscViewerCreate(), PetscViewerSetType(),
PetscViewerSocketSetConnection(), PETSC_VIEWER_SOCKET_, PETSC_VIEWER_SOCKET_WORLD,
PETSC_VIEWER_SOCKET_SELF, PetscViewerBinaryWrite(), PetscViewerBinaryRead(), PetscViewerBinaryWriteStringArray(),
PetscBinaryViewerGetDescriptor(), PetscMatlabEngineCreate()
@*/
PetscErrorCode PetscViewerSocketOpen(MPI_Comm comm,const char machine[],int port,PetscViewer *lab)
{
PetscErrorCode ierr;
PetscFunctionBegin;
ierr = PetscViewerCreate(comm,lab);CHKERRQ(ierr);
ierr = PetscViewerSetType(*lab,PETSCVIEWERSOCKET);CHKERRQ(ierr);
ierr = PetscViewerSocketSetConnection(*lab,machine,port);CHKERRQ(ierr);
PetscFunctionReturn(0);
}
static PetscErrorCode SOCKEstablish_Private(u_short portnum,int *ss)
{
char myname[MAXHOSTNAME+1];
int s;
PetscErrorCode ierr;
struct sockaddr_in sa;
struct hostent *hp;
int optval = 1; /* Turn on the option */
PetscFunctionBegin;
ierr = PetscGetHostName(myname,MAXHOSTNAME);CHKERRQ(ierr);
ierr = PetscMemzero(&sa,sizeof(struct sockaddr_in));CHKERRQ(ierr);
hp = gethostbyname(myname);
if (!hp) SETERRQ(PETSC_ERR_SYS,"Unable to get hostent information from system");
sa.sin_family = hp->h_addrtype;
sa.sin_port = htons(portnum);
if ((s = socket(AF_INET,SOCK_STREAM,0)) < 0) {
SETERRQ(PETSC_ERR_SYS,"Error running socket() command");
}
ierr = setsockopt(s,SOL_SOCKET,SO_REUSEADDR,(char *)&optval,sizeof(optval));CHKERRQ(ierr);
while (bind(s,(struct sockaddr*)&sa,sizeof(sa)) < 0) {
#if defined(PETSC_HAVE_WSAGETLASTERROR)
ierr = WSAGetLastError();
if (ierr != WSAEADDRINUSE) {
#else
if (errno != EADDRINUSE) {
#endif
close(s);
SETERRQ(PETSC_ERR_SYS,"Error from bind()");
}
close(listenport);
}
listen(s,0);
*ss = s;
return(0);
}
#undef __FUNCT__
#define __FUNCT__ "SOCKAnswer_Private"
static PetscErrorCode SOCKAnswer_Private(int portnumber,int *t)
{
PetscErrorCode ierr;
struct sockaddr_in isa;
#if defined(PETSC_HAVE_ACCEPT_SIZE_T)
size_t i;
#else
int i;
#endif
PetscFunctionBegin;
/* open port*/
ierr = SOCKEstablish_Private((u_short) portnumber,&listenport);CHKERRQ(ierr);
/* wait for someone to try to connect */
i = sizeof(struct sockaddr_in);
if ((*t = accept(listenport,(struct sockaddr *)&isa,(socklen_t *)&i)) < 0) {
SETERRQ(PETSC_ERR_SYS,"error from accept()\n");
}
close(listenport);
PetscFunctionReturn(0);
}
static PetscErrorCode MatPartitioningApply_Scotch(MatPartitioning part, IS * partitioning)
{
PetscErrorCode ierr;
int *parttab, *locals = PETSC_NULL, rank, i, size;
size_t j;
Mat mat = part->adj, matMPI, matSeq;
int nb_locals = mat->rmap->n;
Mat_MPIAdj *adj = (Mat_MPIAdj *) mat->data;
MatPartitioning_Scotch *scotch = (MatPartitioning_Scotch *) part->data;
PetscTruth flg;
#ifdef PETSC_HAVE_UNISTD_H
int fd_stdout, fd_pipe[2], count,err;
#endif
PetscFunctionBegin;
/* check if the matrix is sequential, use MatGetSubMatrices if necessary */
ierr = MPI_Comm_size(((PetscObject)mat)->comm, &size);CHKERRQ(ierr);
ierr = PetscTypeCompare((PetscObject) mat, MATMPIADJ, &flg);CHKERRQ(ierr);
if (size > 1) {
int M, N;
IS isrow, iscol;
Mat *A;
if (flg) {
SETERRQ(0, "Distributed matrix format MPIAdj is not supported for sequential partitioners");
}
PetscPrintf(((PetscObject)part)->comm, "Converting distributed matrix to sequential: this could be a performance loss\n");CHKERRQ(ierr);
ierr = MatGetSize(mat, &M, &N);CHKERRQ(ierr);
ierr = ISCreateStride(PETSC_COMM_SELF, M, 0, 1, &isrow);CHKERRQ(ierr);
ierr = ISCreateStride(PETSC_COMM_SELF, N, 0, 1, &iscol);CHKERRQ(ierr);
ierr = MatGetSubMatrices(mat, 1, &isrow, &iscol, MAT_INITIAL_MATRIX, &A);CHKERRQ(ierr);
matSeq = *A;
ierr = PetscFree(A);CHKERRQ(ierr);
ierr = ISDestroy(isrow);CHKERRQ(ierr);
ierr = ISDestroy(iscol);CHKERRQ(ierr);
} else
matSeq = mat;
/* convert the the matrix to MPIADJ type if necessary */
if (!flg) {
ierr = MatConvert(matSeq, MATMPIADJ, MAT_INITIAL_MATRIX, &matMPI);CHKERRQ(ierr);
} else {
matMPI = matSeq;
}
adj = (Mat_MPIAdj *) matMPI->data; /* finaly adj contains adjacency graph */
ierr = MPI_Comm_rank(((PetscObject)part)->comm, &rank);CHKERRQ(ierr);
{
/* definition of Scotch library arguments */
SCOTCH_Strat stratptr; /* scotch strategy */
SCOTCH_Graph grafptr; /* scotch graph */
#if defined(DOES_NOT_COMPILE_DUE_TO_BROKEN_INTERFACE)
int vertnbr = mat->rmap->N; /* number of vertices in full graph */
int *verttab = adj->i; /* start of edge list for each vertex */
int *edgetab = adj->j; /* edge list data */
int edgenbr = adj->nz; /* number of edges */
int *velotab = NULL; /* not used by petsc interface */
int *vlbltab = NULL;
int *edlotab = NULL;
int flagval = 3; /* (cf doc scotch no weight edge & vertices) */
#endif
int baseval = 0; /* 0 for C array indexing */
char strategy[256];
ierr = PetscMalloc((mat->rmap->N) * sizeof(int), &parttab);CHKERRQ(ierr);
/* redirect output to buffer scotch -> mesg_log */
#ifdef PETSC_HAVE_UNISTD_H
fd_stdout = dup(1);
pipe(fd_pipe);
close(1);
dup2(fd_pipe[1], 1);
ierr = PetscMalloc(SIZE_LOG * sizeof(char), &(scotch->mesg_log));CHKERRQ(ierr);
#endif
/* library call */
/* Construction of the scotch graph object */
ierr = SCOTCH_graphInit(&grafptr);
#if defined(DOES_NOT_COMPILE_DUE_TO_BROKEN_INTERFACE)
ierr = SCOTCH_graphBuild((SCOTCH_Graph *) &grafptr,
(const SCOTCH_Num) vertnbr,
(const SCOTCH_Num) verttab,
(const SCOTCH_Num *)velotab,
(const SCOTCH_Num *)vlbltab,
(const SCOTCH_Num *)edgenbr,
(const SCOTCH_Num *)edgetab,
(const SCOTCH_Num) edlotab,
(const SCOTCH_Num *)baseval,
(const SCOTCH_Num *)flagval);CHKERRQ(ierr);
#else
SETERRQ(PETSC_ERR_SUP,"Scotch interface currently broken");
#endif
ierr = SCOTCH_graphCheck(&grafptr);CHKERRQ(ierr);
/* Construction of the strategy */
if (scotch->strategy[0] != 0) {
ierr = PetscStrcpy(strategy, scotch->strategy);CHKERRQ(ierr);
} else {
PetscStrcpy(strategy, "b{strat=");
if (scotch->multilevel) {
/* PetscStrcat(strategy,"m{vert=");
sprintf(strategy+strlen(strategy),"%d",scotch->nbvtxcoarsed);
PetscStrcat(strategy,",asc="); */
sprintf(strategy, "b{strat=m{vert=%d,asc=",
scotch->nbvtxcoarsed);
} else
PetscStrcpy(strategy, "b{strat=");
switch (scotch->global_method) {
case MP_SCOTCH_GREEDY:
PetscStrcat(strategy, "h");
break;
case MP_SCOTCH_GPS:
PetscStrcat(strategy, "g");
break;
case MP_SCOTCH_GR_GPS:
PetscStrcat(strategy, "g|h");
}
switch (scotch->local_method) {
case MP_SCOTCH_KERNIGHAN_LIN:
if (scotch->multilevel)
PetscStrcat(strategy, ",low=f}");
else
PetscStrcat(strategy, " f");
break;
case MP_SCOTCH_NONE:
if (scotch->multilevel)
PetscStrcat(strategy, ",asc=x}");
default:
break;
}
PetscStrcat(strategy, " x}");
}
PetscPrintf(((PetscObject)part)->comm, "strategy=[%s]\n", strategy);
ierr = SCOTCH_stratInit(&stratptr);CHKERRQ(ierr);
/*
TODO: Correct this part
Commented because this doesn't exists anymore
ierr = SCOTCH_stratMap(&stratptr, strategy);CHKERRQ(ierr);
*/
/* check for option mapping */
if (!scotch->map) {
/* ********************************************
* *
* TODO: Correct this part *
* *
* Won't work with this tmp SCOTCH_Strat... *
* *
* I just modified it to make scotch compile, *
* to be able to use PaStiX... *
* *
**********************************************/
#if defined (DOES_NOT_COMPILE_DUE_TO_BROKEN_INTERFACE)
SCOTCH_Strat tmp;
ierr = SCOTCH_graphPart((const SCOTCH_Graph *)&grafptr,
(const SCOTCH_Num) &stratptr,
(const SCOTCH_Strat *)&tmp, /* The Argument changed from scotch 3.04 it was part->n, */
(SCOTCH_Num *) parttab);CHKERRQ(ierr);
#else
SETERRQ(PETSC_ERR_SUP,"Scotch interface currently broken");
#endif
ierr = PetscPrintf(PETSC_COMM_SELF, "Partition simple without mapping\n");
} else {
SCOTCH_Graph grafarch;
SCOTCH_Num *listtab;
SCOTCH_Num listnbr = 0;
SCOTCH_Arch archptr; /* file in scotch architecture format */
SCOTCH_Strat archstrat;
int arch_total_size, *parttab_tmp,err;
int cpt;
char buf[256];
FILE *file1, *file2;
char host_buf[256];
/* generate the graph that represents the arch */
file1 = fopen(scotch->arch, "r");
if (!file1) SETERRQ1(PETSC_ERR_FILE_OPEN, "Scotch: unable to open architecture file %s", scotch->arch);
ierr = SCOTCH_graphInit(&grafarch);CHKERRQ(ierr);
ierr = SCOTCH_graphLoad(&grafarch, file1, baseval, 3);CHKERRQ(ierr);
ierr = SCOTCH_graphCheck(&grafarch);CHKERRQ(ierr);
SCOTCH_graphSize(&grafarch, &arch_total_size, &cpt);
err = fclose(file1);
if (err) SETERRQ(PETSC_ERR_SYS,"fclose() failed on file");
printf("total size = %d\n", arch_total_size);
/* generate the list of nodes currently working */
ierr = PetscGetHostName(host_buf, 256);CHKERRQ(ierr);
ierr = PetscStrlen(host_buf, &j);CHKERRQ(ierr);
file2 = fopen(scotch->host_list, "r");
if (!file2) SETERRQ1(PETSC_ERR_FILE_OPEN, "Scotch: unable to open host list file %s", scotch->host_list);
i = -1;
flg = PETSC_FALSE;
while (!feof(file2) && !flg) {
i++;
fgets(buf, 256, file2);
PetscStrncmp(buf, host_buf, j, &flg);
}
err = fclose(file2);
if (err) SETERRQ(PETSC_ERR_SYS,"fclose() failed on file");
if (!flg) SETERRQ1(PETSC_ERR_LIB, "Scotch: unable to find '%s' in host list file", host_buf);
listnbr = size;
ierr = PetscMalloc(sizeof(SCOTCH_Num) * listnbr, &listtab);CHKERRQ(ierr);
ierr = MPI_Allgather(&i, 1, MPI_INT, listtab, 1, MPI_INT, ((PetscObject)part)->comm);CHKERRQ(ierr);
printf("listnbr = %d, listtab = ", listnbr);
for (i = 0; i < listnbr; i++)
printf("%d ", listtab[i]);
printf("\n");
err = fflush(stdout);
if (err) SETERRQ(PETSC_ERR_SYS,"fflush() failed on file");
ierr = SCOTCH_stratInit(&archstrat);CHKERRQ(ierr);
/**************************************************************
* *
* TODO: Correct this part *
* *
* Commented because this doesn't exists anymore *
* *
* ierr = SCOTCH_stratBipart(&archstrat, "fx");CHKERRQ(ierr); *
**************************************************************/
ierr = SCOTCH_archInit(&archptr);CHKERRQ(ierr);
ierr = SCOTCH_archBuild(&archptr, &grafarch, listnbr, listtab,
&archstrat);CHKERRQ(ierr);
ierr = PetscMalloc((mat->rmap->N) * sizeof(int), &parttab_tmp);CHKERRQ(ierr);
/************************************************************************************
* *
* TODO: Correct this part *
* *
* Commented because this doesn't exists anymore *
* *
* ierr = SCOTCH_mapInit(&mappptr, &grafptr, &archptr, parttab_tmp);CHKERRQ(ierr); *
* *
* ierr = SCOTCH_mapCompute(&mappptr, &stratptr);CHKERRQ(ierr); *
* *
* ierr = SCOTCH_mapView(&mappptr, stdout);CHKERRQ(ierr); *
************************************************************************************/
/* now we have to set in the real parttab at the good place */
/* because the ranks order are different than position in */
/* the arch graph */
for (i = 0; i < mat->rmap->N; i++) {
parttab[i] = parttab_tmp[i];
}
ierr = PetscFree(listtab);CHKERRQ(ierr);
SCOTCH_archExit(&archptr);
/*************************************************
* TODO: Correct this part *
* *
* Commented because this doesn't exists anymore *
* SCOTCH_mapExit(&mappptr); *
*************************************************/
SCOTCH_stratExit(&archstrat);
}
/* dump to mesg_log... */
#ifdef PETSC_HAVE_UNISTD_H
err = fflush(stdout);
if (err) SETERRQ(PETSC_ERR_SYS,"fflush() failed on stdout");
count = read(fd_pipe[0], scotch->mesg_log, (SIZE_LOG - 1) * sizeof(char));
if (count < 0)
count = 0;
scotch->mesg_log[count] = 0;
close(1);
dup2(fd_stdout, 1);
close(fd_stdout);
close(fd_pipe[0]);
close(fd_pipe[1]);
#endif
SCOTCH_graphExit(&grafptr);
SCOTCH_stratExit(&stratptr);
}
if (ierr)
SETERRQ(PETSC_ERR_LIB, scotch->mesg_log);
/* Creation of the index set */
ierr = MPI_Comm_rank(((PetscObject)part)->comm, &rank);CHKERRQ(ierr);
ierr = MPI_Comm_size(((PetscObject)part)->comm, &size);CHKERRQ(ierr);
nb_locals = mat->rmap->N / size;
locals = parttab + rank * nb_locals;
if (rank < mat->rmap->N % size) {
nb_locals++;
locals += rank;
} else
locals += mat->rmap->N % size;
ierr = ISCreateGeneral(((PetscObject)part)->comm, nb_locals, locals, partitioning);CHKERRQ(ierr);
/* destroying old objects */
ierr = PetscFree(parttab);CHKERRQ(ierr);
if (matSeq != mat) {
ierr = MatDestroy(matSeq);CHKERRQ(ierr);
}
if (matMPI != mat) {
ierr = MatDestroy(matMPI);CHKERRQ(ierr);
}
PetscFunctionReturn(0);
}
