/*@C
PetscMemoryShowUsage - Shows the amount of memory currently being used
in a communicator.
Collective on PetscViewer
Input Parameter:
+ viewer - the viewer that defines the communicator
- message - string printed before values
Level: intermediate
Concepts: memory usage
.seealso: PetscMallocDump(), PetscMemoryGetCurrentUsage()
@*/
PetscErrorCode PetscMemoryShowUsage(PetscViewer viewer,const char message[])
{
PetscLogDouble allocated,maximum,resident,residentmax;
PetscErrorCode ierr;
PetscMPIInt rank;
MPI_Comm comm;
PetscFunctionBegin;
if (!viewer) viewer = PETSC_VIEWER_STDOUT_WORLD;
ierr = PetscMallocGetCurrentUsage(&allocated);CHKERRQ(ierr);
ierr = PetscMallocGetMaximumUsage(&maximum);CHKERRQ(ierr);
ierr = PetscMemoryGetCurrentUsage(&resident);CHKERRQ(ierr);
ierr = PetscMemoryGetMaximumUsage(&residentmax);CHKERRQ(ierr);
if (residentmax > 0) residentmax = PetscMax(resident,residentmax);
ierr = PetscObjectGetComm((PetscObject)viewer,&comm);CHKERRQ(ierr);
ierr = MPI_Comm_rank(comm,&rank);CHKERRQ(ierr);
ierr = PetscViewerASCIIPrintf(viewer,message);CHKERRQ(ierr);
ierr = PetscViewerASCIISynchronizedAllow(viewer,PETSC_TRUE);CHKERRQ(ierr);
if (resident && residentmax && allocated) {
ierr = PetscViewerASCIISynchronizedPrintf(viewer,"[%d]Current space PetscMalloc()ed %g, max space PetscMalloced() %g\n[%d]Current process memory %g max process memory %g\n",rank,allocated,maximum,rank,resident,residentmax);CHKERRQ(ierr);
} else if (resident && residentmax) {
ierr = PetscViewerASCIISynchronizedPrintf(viewer,"[%d]Run with -malloc to get statistics on PetscMalloc() calls\n[%d]Current process memory %g max process memory %g\n",rank,rank,resident,residentmax);CHKERRQ(ierr);
} else if (resident && allocated) {
ierr = PetscViewerASCIISynchronizedPrintf(viewer,"[%d]Current space PetscMalloc()ed %g, max space PetscMalloced() %g\n[%d]Current process memory %g, run with -memory_info to get max memory usage\n",rank,allocated,maximum,rank,resident);CHKERRQ(ierr);
} else if (allocated) {
ierr = PetscViewerASCIISynchronizedPrintf(viewer,"[%d]Current space PetscMalloc()ed %g, max space PetscMalloced() %g\n[%d]OS cannot compute process memory\n",rank,allocated,maximum,rank);CHKERRQ(ierr);
} else {
ierr = PetscViewerASCIIPrintf(viewer,"Run with -malloc to get statistics on PetscMalloc() calls\nOS cannot compute process memory\n");CHKERRQ(ierr);
}
ierr = PetscViewerFlush(viewer);CHKERRQ(ierr);
ierr = PetscViewerASCIISynchronizedAllow(viewer,PETSC_FALSE);CHKERRQ(ierr);
PetscFunctionReturn(0);
}
/*@C
PetscTraceBackErrorHandler - Default error handler routine that generates
a traceback on error detection.
Not Collective
Input Parameters:
+ comm - communicator over which error occurred
. line - the line number of the error (indicated by __LINE__)
. func - the function where error is detected (indicated by __FUNCT__)
. file - the file in which the error was detected (indicated by __FILE__)
. mess - an error text string, usually just printed to the screen
. n - the generic error number
. p - PETSC_ERROR_INITIAL if this is the first call the error handler, otherwise PETSC_ERROR_REPEAT
- ctx - error handler context
Level: developer
Notes:
Most users need not directly employ this routine and the other error
handlers, but can instead use the simplified interface SETERRQ, which has
the calling sequence
$ SETERRQ(comm,number,n,mess)
Notes for experienced users:
Use PetscPushErrorHandler() to set the desired error handler. The
currently available PETSc error handlers include PetscTraceBackErrorHandler(),
PetscAttachDebuggerErrorHandler(), PetscAbortErrorHandler(), and PetscMPIAbortErrorHandler()
Concepts: error handler^traceback
Concepts: traceback^generating
.seealso: PetscPushErrorHandler(), PetscAttachDebuggerErrorHandler(),
PetscAbortErrorHandler()
@*/
PetscErrorCode PetscTraceBackErrorHandler(MPI_Comm comm,int line,const char *fun,const char *file,PetscErrorCode n,PetscErrorType p,const char *mess,void *ctx)
{
PetscLogDouble mem,rss;
PetscBool flg1 = PETSC_FALSE,flg2 = PETSC_FALSE,flg3 = PETSC_FALSE;
PetscMPIInt rank = 0;
PetscFunctionBegin;
if (comm != PETSC_COMM_SELF) MPI_Comm_rank(comm,&rank);
if (!rank) {
PetscBool ismain,isunknown;
static int cnt = 1;
if (p == PETSC_ERROR_INITIAL) {
PetscErrorPrintfHilight();
(*PetscErrorPrintf)("--------------------- Error Message --------------------------------------------------------------\n");
PetscErrorPrintfNormal();
if (n == PETSC_ERR_MEM) {
(*PetscErrorPrintf)("Out of memory. This could be due to allocating\n");
(*PetscErrorPrintf)("too large an object or bleeding by not properly\n");
(*PetscErrorPrintf)("destroying unneeded objects.\n");
PetscMallocGetCurrentUsage(&mem);
PetscMemoryGetCurrentUsage(&rss);
PetscOptionsGetBool(NULL,"-malloc_dump",&flg1,NULL);
PetscOptionsGetBool(NULL,"-malloc_log",&flg2,NULL);
PetscOptionsHasName(NULL,"-malloc_log_threshold",&flg3);
if (flg2 || flg3) PetscMallocDumpLog(stdout);
else {
(*PetscErrorPrintf)("Memory allocated %.0f Memory used by process %.0f\n",mem,rss);
if (flg1) PetscMallocDump(stdout);
else (*PetscErrorPrintf)("Try running with -malloc_dump or -malloc_log for info.\n");
}
} else {
const char *text;
PetscErrorMessage(n,&text,NULL);
if (text) (*PetscErrorPrintf)("%s\n",text);
}
if (mess) (*PetscErrorPrintf)("%s\n",mess);
(*PetscErrorPrintf)("See http://www.mcs.anl.gov/petsc/documentation/faq.html for trouble shooting.\n");
(*PetscErrorPrintf)("%s\n",version);
if (PetscErrorPrintfInitializeCalled) (*PetscErrorPrintf)("%s on a %s named %s by %s %s\n",pname,arch,hostname,username,date);
(*PetscErrorPrintf)("Configure options %s\n",petscconfigureoptions);
}
/* print line of stack trace */
(*PetscErrorPrintf)("#%d %s() line %d in %s\n",cnt++,fun,line,file);
PetscStrncmp(fun,"main",4,&ismain);
PetscStrncmp(fun,"unknown",7,&isunknown);
if (ismain || isunknown) {
PetscOptionsViewError();
PetscErrorPrintfHilight();
(*PetscErrorPrintf)("----------------End of Error Message -------send entire error message to [email protected]\n");
PetscErrorPrintfNormal();
}
} else {
/* do not print error messages since process 0 will print them, sleep before aborting so will not accidently kill process 0*/
PetscSleep(10.0);
abort();
}
PetscFunctionReturn(n);
}
PetscErrorCode PetscLogEventEndComplete(PetscLogEvent event, int t, PetscObject o1, PetscObject o2, PetscObject o3, PetscObject o4)
{
PetscStageLog stageLog;
PetscEventRegLog eventRegLog;
PetscEventPerfLog eventPerfLog = NULL;
Action *tmpAction;
PetscLogDouble start, end;
PetscLogDouble curTime;
int stage;
PetscErrorCode ierr;
PetscFunctionBegin;
/* Dynamically enlarge logging structures */
if (petsc_numActions >= petsc_maxActions) {
PetscTime(&start);
ierr = PetscMalloc(petsc_maxActions*2 * sizeof(Action), &tmpAction);CHKERRQ(ierr);
ierr = PetscMemcpy(tmpAction, petsc_actions, petsc_maxActions * sizeof(Action));CHKERRQ(ierr);
ierr = PetscFree(petsc_actions);CHKERRQ(ierr);
petsc_actions = tmpAction;
petsc_maxActions *= 2;
PetscTime(&end);
petsc_BaseTime += (end - start);
}
/* Record the event */
ierr = PetscLogGetStageLog(&stageLog);CHKERRQ(ierr);
ierr = PetscStageLogGetCurrent(stageLog, &stage);CHKERRQ(ierr);
ierr = PetscStageLogGetEventRegLog(stageLog, &eventRegLog);CHKERRQ(ierr);
ierr = PetscStageLogGetEventPerfLog(stageLog, stage, &eventPerfLog);CHKERRQ(ierr);
PetscTime(&curTime);
if (petsc_logActions) {
petsc_actions[petsc_numActions].time = curTime - petsc_BaseTime;
petsc_actions[petsc_numActions].action = ACTIONEND;
petsc_actions[petsc_numActions].event = event;
petsc_actions[petsc_numActions].classid = eventRegLog->eventInfo[event].classid;
if (o1) petsc_actions[petsc_numActions].id1 = o1->id;
else petsc_actions[petsc_numActions].id1 = -1;
if (o2) petsc_actions[petsc_numActions].id2 = o2->id;
else petsc_actions[petsc_numActions].id2 = -1;
if (o3) petsc_actions[petsc_numActions].id3 = o3->id;
else petsc_actions[petsc_numActions].id3 = -1;
petsc_actions[petsc_numActions].flops = petsc_TotalFlops;
ierr = PetscMallocGetCurrentUsage(&petsc_actions[petsc_numActions].mem);CHKERRQ(ierr);
ierr = PetscMallocGetMaximumUsage(&petsc_actions[petsc_numActions].maxmem);CHKERRQ(ierr);
petsc_numActions++;
}
/* Check for double counting */
eventPerfLog->eventInfo[event].depth--;
if (eventPerfLog->eventInfo[event].depth > 0) PetscFunctionReturn(0);
else if (eventPerfLog->eventInfo[event].depth < 0) SETERRQ(PETSC_COMM_SELF,PETSC_ERR_ARG_WRONGSTATE, "Logging event had unbalanced begin/end pairs");
/* Log the performance info */
eventPerfLog->eventInfo[event].count++;
eventPerfLog->eventInfo[event].time += curTime;
eventPerfLog->eventInfo[event].flops += petsc_TotalFlops;
eventPerfLog->eventInfo[event].numMessages += petsc_irecv_ct + petsc_isend_ct + petsc_recv_ct + petsc_send_ct;
eventPerfLog->eventInfo[event].messageLength += petsc_irecv_len + petsc_isend_len + petsc_recv_len + petsc_send_len;
eventPerfLog->eventInfo[event].numReductions += petsc_allreduce_ct + petsc_gather_ct + petsc_scatter_ct;
PetscFunctionReturn(0);
}
PetscErrorCode PetscLogEventEndComplete(PetscLogEvent event, int t, PetscObject o1, PetscObject o2, PetscObject o3, PetscObject o4)
{
StageLog stageLog;
EventRegLog eventRegLog;
EventPerfLog eventPerfLog;
Action *tmpAction;
PetscLogDouble start, end;
PetscLogDouble curTime;
int stage;
PetscErrorCode ierr;
PetscFunctionBegin;
/* Dynamically enlarge logging structures */
if (numActions >= maxActions) {
PetscTime(start);
ierr = PetscMalloc(maxActions*2 * sizeof(Action), &tmpAction);CHKERRQ(ierr);
ierr = PetscMemcpy(tmpAction, actions, maxActions * sizeof(Action));CHKERRQ(ierr);
ierr = PetscFree(actions);CHKERRQ(ierr);
actions = tmpAction;
maxActions *= 2;
PetscTime(end);
BaseTime += (end - start);
}
/* Record the event */
ierr = PetscLogGetStageLog(&stageLog);CHKERRQ(ierr);
ierr = StageLogGetCurrent(stageLog, &stage);CHKERRQ(ierr);
ierr = StageLogGetEventRegLog(stageLog, &eventRegLog);CHKERRQ(ierr);
ierr = StageLogGetEventPerfLog(stageLog, stage, &eventPerfLog);CHKERRQ(ierr);
PetscTime(curTime);
if (logActions) {
actions[numActions].time = curTime - BaseTime;
actions[numActions].action = ACTIONEND;
actions[numActions].event = event;
actions[numActions].cookie = eventRegLog->eventInfo[event].cookie;
if (o1) actions[numActions].id1 = o1->id; else actions[numActions].id1 = -1;
if (o2) actions[numActions].id2 = o2->id; else actions[numActions].id2 = -1;
if (o3) actions[numActions].id3 = o3->id; else actions[numActions].id3 = -1;
actions[numActions].flops = _TotalFlops;
ierr = PetscMallocGetCurrentUsage(&actions[numActions].mem);CHKERRQ(ierr);
ierr = PetscMallocGetMaximumUsage(&actions[numActions].maxmem);CHKERRQ(ierr);
numActions++;
}
/* Check for double counting */
eventPerfLog->eventInfo[event].depth--;
if (eventPerfLog->eventInfo[event].depth > 0) {
PetscFunctionReturn(0);
} else if (eventPerfLog->eventInfo[event].depth < 0) {
SETERRQ(PETSC_ERR_ARG_WRONGSTATE, "Logging event had unbalanced begin/end pairs");
}
/* Log the performance info */
eventPerfLog->eventInfo[event].count++;
eventPerfLog->eventInfo[event].time += curTime;
eventPerfLog->eventInfo[event].flops += _TotalFlops;
eventPerfLog->eventInfo[event].numMessages += irecv_ct + isend_ct + recv_ct + send_ct;
eventPerfLog->eventInfo[event].messageLength += irecv_len + isend_len + recv_len + send_len;
eventPerfLog->eventInfo[event].numReductions += allreduce_ct;
PetscFunctionReturn(0);
}
PetscErrorCode PetscMemoryTrace(const char label[])
{
PetscErrorCode ierr;
PetscLogDouble mem,mal;
static PetscLogDouble oldmem = 0,oldmal = 0;
PetscFunctionBegin;
ierr = PetscMemoryGetCurrentUsage(&mem);CHKERRQ(ierr);
ierr = PetscMallocGetCurrentUsage(&mal);CHKERRQ(ierr);
ierr = PetscPrintf(PETSC_COMM_WORLD,"%s High water %8.3f MB increase %8.3f MB Current %8.3f MB increase %8.3f MB\n",label,mem*1e-6,(mem - oldmem)*1e-6,mal*1e-6,(mal - oldmal)*1e-6);CHKERRQ(ierr);
oldmem = mem;
oldmal = mal;
PetscFunctionReturn(0);
}
/*@C
TSMonitorFunctionError - Monitors progress of the TS solvers by the solution norm
Input Parameters:
+ ts - the TS context
. step - current time-step
. ptime - current time
@*/
PetscErrorCode TSMonitorFunctionError(TS ts,PetscInt step,PetscReal ptime,Vec u,void *user)
{
PetscErrorCode ierr;
PetscReal norm, funcnorm;
PetscLogDouble space =0;
PetscInt size;
Vec func;
PetscFunctionBegin;
if (step%10==0) {
ierr = TSGetRHSFunction(ts, &func,NULL, NULL);CHKERRQ(ierr);
ierr = VecNorm(func,NORM_2,&funcnorm);CHKERRQ(ierr);
//ierr = VecView(func, PETSC_VIEWER_STDOUT_WORLD);CHKERRQ(ierr);
ierr = VecNorm(u,NORM_2,&norm);CHKERRQ(ierr);
ierr = VecGetSize(u, &size);CHKERRQ(ierr);
norm = norm/size;
ierr = PetscPrintf(PETSC_COMM_WORLD,"Step %D at time %g with solution norm = %g right hand side function norm = %f\n",step, ptime,norm, funcnorm);CHKERRQ(ierr);
ierr = PetscMallocGetCurrentUsage(&space);CHKERRQ(ierr);
ierr = PetscPrintf(PETSC_COMM_WORLD,"Current space PetscMalloc()ed %g M\n", space/(1024*1024));CHKERRQ(ierr);
}
PetscFunctionReturn(0);
}
int main(int argc, char **argv)
{
MPI_Comm comm;
PetscMPIInt rank;
PetscErrorCode ierr;
User user;
PetscLogDouble v1, v2;
PetscInt nplot = 0;
char filename1[2048], fileName[2048];
PetscBool set = PETSC_FALSE;
PetscInt steps_output;
ierr = PetscInitialize(&argc, &argv, (char*) 0, help);CHKERRQ(ierr);
comm = PETSC_COMM_WORLD;
ierr = MPI_Comm_rank(comm, &rank);CHKERRQ(ierr);
ierr = PetscNew(&user);CHKERRQ(ierr);
ierr = PetscNew(&user->algebra);CHKERRQ(ierr);
ierr = PetscNew(&user->model);CHKERRQ(ierr);
ierr = PetscNew(&user->model->physics);CHKERRQ(ierr);
Algebra algebra = user->algebra;
ierr = LoadOptions(comm, user);CHKERRQ(ierr);
ierr = PetscTime(&v1);CHKERRQ(ierr);
ierr = CreateMesh(comm, user);CHKERRQ(ierr);
ierr = PetscTime(&v2);CHKERRQ(ierr);
ierr = PetscPrintf(PETSC_COMM_WORLD,
"Read and Distribute mesh takes %f sec \n", v2 - v1);CHKERRQ(ierr);
ierr = SetUpLocalSpace(user);CHKERRQ(ierr); //Set up the dofs of each element
ierr = ConstructGeometryFVM(&user->facegeom, &user->cellgeom, user);CHKERRQ(ierr);
ierr = LimiterSetup(user);CHKERRQ(ierr);
if(user->output_solution){
// the output file options
ierr = PetscOptionsBegin(PETSC_COMM_WORLD,0,"Options for output solution",0);CHKERRQ(ierr);
ierr = PetscOptionsString("-solutionfile", "solution file", "AeroSim.c", filename1,filename1, 2048, &set);CHKERRQ(ierr);
if(!set){SETERRQ(PETSC_COMM_SELF, PETSC_ERR_ARG_NULL,"please use option -solutionfile to specify solution file name \n");}
ierr = PetscOptionsInt("-steps_output", "the number of time steps between two outputs", "", steps_output, &steps_output, &set);CHKERRQ(ierr);
if(!set){ steps_output = 1;}
ierr = PetscOptionsEnd();CHKERRQ(ierr);
}
if (user->TimeIntegralMethod == EXPLICITMETHOD) {
if(user->myownexplicitmethod){
ierr = PetscPrintf(PETSC_COMM_WORLD,"Using the fully explicit method based on my own routing\n");CHKERRQ(ierr);
user->current_time = user->initial_time;
user->current_step = 1;
ierr = DMCreateGlobalVector(user->dm, &algebra->solution);CHKERRQ(ierr);
ierr = PetscObjectSetName((PetscObject) algebra->solution, "solution");CHKERRQ(ierr);
ierr = SetInitialCondition(user->dm, algebra->solution, user);CHKERRQ(ierr);
ierr = VecDuplicate(algebra->solution, &algebra->fn);CHKERRQ(ierr);
ierr = VecDuplicate(algebra->solution, &algebra->oldsolution);CHKERRQ(ierr);
if(user->Explicit_RK2){
ierr = PetscPrintf(PETSC_COMM_WORLD,"Use the second order Runge Kutta method \n");CHKERRQ(ierr);
}else{
ierr = PetscPrintf(PETSC_COMM_WORLD,"Use the first order forward Euler method \n");CHKERRQ(ierr);
}
nplot = 0; //the plot step
while(user->current_time < (user->final_time - 0.05 * user->dt)){
user->current_time = user->current_time + user->dt;
ierr = FormTimeStepFunction(user, algebra, algebra->solution, algebra->fn);CHKERRQ(ierr);
PetscReal fnnorm;
ierr = VecNorm(algebra->fn,NORM_INFINITY,&fnnorm);CHKERRQ(ierr);
if(0){
PetscViewer viewer;
ierr = OutputVTK(user->dm, "function.vtk", &viewer);CHKERRQ(ierr);
ierr = VecView(algebra->fn, viewer);CHKERRQ(ierr);
ierr = PetscViewerDestroy(&viewer);CHKERRQ(ierr);
ierr = PetscPrintf(PETSC_COMM_WORLD,"Step %D at time %g with founction norm = %g \n",
user->current_step, user->current_time, fnnorm);CHKERRQ(ierr);
//break;
}
if(user->Explicit_RK2){
ierr = VecCopy(algebra->solution, algebra->oldsolution);CHKERRQ(ierr);//U^n
ierr = VecAXPY(algebra->solution, user->dt, algebra->fn);CHKERRQ(ierr);//U^{(1)}
ierr = FormTimeStepFunction(user, algebra, algebra->solution, algebra->fn);CHKERRQ(ierr);//f(U^{(1)})
ierr = VecAXPY(algebra->solution, 1.0, algebra->oldsolution);CHKERRQ(ierr);//U^n + U^{(1)}
ierr = VecAXPY(algebra->solution, user->dt, algebra->fn);CHKERRQ(ierr);// + dt*f(U^{(1)})
ierr = VecScale(algebra->solution, 0.5);CHKERRQ(ierr);
}else{
ierr = VecCopy(algebra->solution, algebra->oldsolution);CHKERRQ(ierr);
ierr = VecAXPY(algebra->solution, user->dt, algebra->fn);CHKERRQ(ierr);
}
{// Monitor the solution and function norms
PetscReal norm;
PetscLogDouble space =0;
PetscInt size;
ierr = VecNorm(algebra->solution,NORM_INFINITY,&norm);CHKERRQ(ierr);
ierr = VecGetSize(algebra->solution, &size);CHKERRQ(ierr);
norm = norm/size;
if (norm>1.e5) {
SETERRQ2(PETSC_COMM_WORLD, PETSC_ERR_LIB,
"The norm of the solution is: %f (current time: %f). The explicit method is going to DIVERGE!!!", norm, user->current_time);
}
if (user->current_step%10==0) {
ierr = PetscPrintf(PETSC_COMM_WORLD,"Step %D at time %g with solution norm = %g and founction norm = %g \n",
user->current_step, user->current_time, norm, fnnorm);CHKERRQ(ierr);
}
ierr = PetscMallocGetCurrentUsage(&space);CHKERRQ(ierr);
// if (user->current_step%10==0) {
// ierr = PetscPrintf(PETSC_COMM_WORLD,"Current space PetscMalloc()ed %g M\n",
// space/(1024*1024));CHKERRQ(ierr);
// }
}
{ // Monitor the difference of two steps' solution
PetscReal norm;
ierr = VecAXPY(algebra->oldsolution, -1, algebra->solution);CHKERRQ(ierr);
ierr = VecNorm(algebra->oldsolution,NORM_INFINITY,&norm);CHKERRQ(ierr);
if (user->current_step%10==0) {
ierr = PetscPrintf(PETSC_COMM_WORLD,"Step %D at time %g with ||u_k-u_{k-1}|| = %g \n",
user->current_step, user->current_time, norm);CHKERRQ(ierr);
}
if((norm<1.e-6)||(user->current_step > user->max_time_its)) break;
}
// output the solution
if (user->output_solution && (user->current_step%steps_output==0)){
PetscViewer viewer;
// update file name for the current time step
ierr = PetscSNPrintf(fileName, sizeof(fileName),"%s_%d.vtk",filename1, nplot);CHKERRQ(ierr);
ierr = PetscPrintf(PETSC_COMM_WORLD,"Outputing solution %s (current time %f)\n", fileName, user->current_time);CHKERRQ(ierr);
ierr = OutputVTK(user->dm, fileName, &viewer);CHKERRQ(ierr);
ierr = VecView(algebra->solution, viewer);CHKERRQ(ierr);
ierr = PetscViewerDestroy(&viewer);CHKERRQ(ierr);
nplot++;
}
user->current_step++;
}
ierr = VecDestroy(&algebra->fn);CHKERRQ(ierr);
}else{
PetscReal ftime;
TS ts;
TSConvergedReason reason;
PetscInt nsteps;
ierr = PetscPrintf(PETSC_COMM_WORLD,"Using the fully explicit method based on the PETSC TS routing\n");CHKERRQ(ierr);
ierr = DMCreateGlobalVector(user->dm, &algebra->solution);CHKERRQ(ierr);
ierr = PetscObjectSetName((PetscObject) algebra->solution, "solution");CHKERRQ(ierr);
ierr = SetInitialCondition(user->dm, algebra->solution, user);CHKERRQ(ierr);
ierr = TSCreate(comm, &ts);CHKERRQ(ierr);
ierr = TSSetType(ts, TSEULER);CHKERRQ(ierr);
ierr = TSSetDM(ts, user->dm);CHKERRQ(ierr);
ierr = TSMonitorSet(ts,TSMonitorFunctionError,&user,NULL);CHKERRQ(ierr);
ierr = TSSetRHSFunction(ts, NULL, MyRHSFunction, user);CHKERRQ(ierr);
ierr = TSSetDuration(ts, 1000, user->final_time);CHKERRQ(ierr);
ierr = TSSetInitialTimeStep(ts, user->initial_time, user->dt);CHKERRQ(ierr);
ierr = TSSetFromOptions(ts);CHKERRQ(ierr);
ierr = TSSolve(ts, algebra->solution);CHKERRQ(ierr);
ierr = TSGetSolveTime(ts, &ftime);CHKERRQ(ierr);
ierr = TSGetTimeStepNumber(ts, &nsteps);CHKERRQ(ierr);
ierr = TSGetConvergedReason(ts, &reason);CHKERRQ(ierr);
ierr = PetscPrintf(PETSC_COMM_WORLD,"%s at time %g after %D steps\n",TSConvergedReasons[reason],ftime,nsteps);CHKERRQ(ierr);
ierr = TSDestroy(&ts);CHKERRQ(ierr);
}
if(user->benchmark_couette) {
ierr = DMCreateGlobalVector(user->dm, &algebra->exactsolution);CHKERRQ(ierr);
ierr = ComputeExactSolution(user->dm, user->final_time, algebra->exactsolution, user);CHKERRQ(ierr);
}
if (user->output_solution){
PetscViewer viewer;
ierr = OutputVTK(user->dm, "solution.vtk", &viewer);CHKERRQ(ierr);
ierr = VecView(algebra->solution, viewer);CHKERRQ(ierr);
ierr = PetscViewerDestroy(&viewer);CHKERRQ(ierr);
}
if(user->benchmark_couette) {
PetscViewer viewer;
PetscReal norm;
ierr = OutputVTK(user->dm, "exact_solution.vtk", &viewer);CHKERRQ(ierr);
ierr = VecView(algebra->exactsolution, viewer);CHKERRQ(ierr);
ierr = PetscViewerDestroy(&viewer);CHKERRQ(ierr);
ierr = VecAXPY(algebra->exactsolution, -1, algebra->solution);CHKERRQ(ierr);
ierr = VecNorm(algebra->exactsolution,NORM_INFINITY,&norm);CHKERRQ(ierr);
ierr = PetscPrintf(PETSC_COMM_WORLD,"Final time at %f, Error: ||u_k-u|| = %g \n", user->final_time, norm);CHKERRQ(ierr);
ierr = OutputVTK(user->dm, "Error.vtk", &viewer);CHKERRQ(ierr);
ierr = VecView(algebra->exactsolution, viewer);CHKERRQ(ierr);
ierr = PetscViewerDestroy(&viewer);CHKERRQ(ierr);
}
ierr = VecDestroy(&algebra->solution);CHKERRQ(ierr);
ierr = VecDestroy(&algebra->oldsolution);CHKERRQ(ierr);
ierr = DMDestroy(&user->dm);CHKERRQ(ierr);
} else if (user->TimeIntegralMethod == IMPLICITMETHOD) {
ierr = PetscPrintf(PETSC_COMM_WORLD,"Using the fully implicit method\n");CHKERRQ(ierr);
ierr = SNESCreate(comm,&user->snes);CHKERRQ(ierr);
ierr = SNESSetDM(user->snes,user->dm);CHKERRQ(ierr);
ierr = DMCreateGlobalVector(user->dm, &algebra->solution);CHKERRQ(ierr);
ierr = VecDuplicate(algebra->solution, &algebra->oldsolution);CHKERRQ(ierr);
ierr = VecDuplicate(algebra->solution, &algebra->f);CHKERRQ(ierr);
ierr = VecDuplicate(algebra->solution, &algebra->fn);CHKERRQ(ierr);
ierr = VecDuplicate(algebra->solution, &algebra->oldfn);CHKERRQ(ierr);
ierr = PetscObjectSetName((PetscObject) algebra->solution, "solution");CHKERRQ(ierr);
ierr = SetInitialCondition(user->dm, algebra->solution, user);CHKERRQ(ierr);
ierr = DMSetMatType(user->dm, MATAIJ);CHKERRQ(ierr);
// ierr = DMCreateMatrix(user->dm, &algebra->A);CHKERRQ(ierr);
ierr = DMCreateMatrix(user->dm, &algebra->J);CHKERRQ(ierr);
if (user->JdiffP) {
/*Set up the preconditioner matrix*/
ierr = DMCreateMatrix(user->dm, &algebra->P);CHKERRQ(ierr);
}else{
algebra->P = algebra->J;
}
ierr = MatSetOption(algebra->J, MAT_NEW_NONZERO_ALLOCATION_ERR, PETSC_FALSE);CHKERRQ(ierr);
/*set nonlinear function */
ierr = SNESSetFunction(user->snes, algebra->f, FormFunction, (void*)user);CHKERRQ(ierr);
/* compute Jacobian */
ierr = SNESSetJacobian(user->snes, algebra->J, algebra->P, FormJacobian, (void*)user);CHKERRQ(ierr);
ierr = SNESSetFromOptions(user->snes);CHKERRQ(ierr);
/* do the solve */
if (user->timestep == TIMESTEP_STEADY_STATE) {
ierr = SolveSteadyState(user);CHKERRQ(ierr);
} else {
ierr = SolveTimeDependent(user);CHKERRQ(ierr);
}
if (user->output_solution){
PetscViewer viewer;
ierr = OutputVTK(user->dm, "solution.vtk", &viewer);CHKERRQ(ierr);
ierr = VecView(algebra->solution, viewer);CHKERRQ(ierr);
ierr = PetscViewerDestroy(&viewer);CHKERRQ(ierr);
}
if(user->benchmark_couette) {
PetscViewer viewer;
PetscReal norm;
ierr = OutputVTK(user->dm, "exact_solution.vtk", &viewer);CHKERRQ(ierr);
ierr = VecView(algebra->exactsolution, viewer);CHKERRQ(ierr);
ierr = PetscViewerDestroy(&viewer);CHKERRQ(ierr);
ierr = VecAXPY(algebra->exactsolution, -1, algebra->solution);CHKERRQ(ierr);
ierr = VecNorm(algebra->exactsolution,NORM_INFINITY,&norm);CHKERRQ(ierr);
ierr = PetscPrintf(PETSC_COMM_WORLD,"Error: ||u_k-u|| = %g \n", norm);CHKERRQ(ierr);
ierr = OutputVTK(user->dm, "Error.vtk", &viewer);CHKERRQ(ierr);
ierr = VecView(algebra->exactsolution, viewer);CHKERRQ(ierr);
ierr = PetscViewerDestroy(&viewer);CHKERRQ(ierr);
}
ierr = VecDestroy(&algebra->solution);CHKERRQ(ierr);
ierr = VecDestroy(&algebra->f);CHKERRQ(ierr);
ierr = VecDestroy(&algebra->oldsolution);CHKERRQ(ierr);
ierr = VecDestroy(&algebra->fn);CHKERRQ(ierr);
ierr = VecDestroy(&algebra->oldfn);CHKERRQ(ierr);
ierr = SNESDestroy(&user->snes);CHKERRQ(ierr);
ierr = DMDestroy(&user->dm);CHKERRQ(ierr);
} else {
SETERRQ(PETSC_COMM_SELF,PETSC_ERR_USER,"WRONG option for the time integral method. Using the option '-time_integral_method 0 or 1'");
}
ierr = VecDestroy(&user->cellgeom);CHKERRQ(ierr);
ierr = VecDestroy(&user->facegeom);CHKERRQ(ierr);
ierr = DMDestroy(&user->dmGrad);CHKERRQ(ierr);
ierr = PetscFunctionListDestroy(&LimitList);CHKERRQ(ierr);
ierr = PetscFree(user->model->physics);CHKERRQ(ierr);
ierr = PetscFree(user->algebra);CHKERRQ(ierr);
ierr = PetscFree(user->model);CHKERRQ(ierr);
ierr = PetscFree(user);CHKERRQ(ierr);
{
PetscLogDouble space =0;
ierr = PetscMallocGetCurrentUsage(&space);CHKERRQ(ierr);
ierr = PetscPrintf(PETSC_COMM_WORLD,"Unfreed space at the End %g M\n", space/(1024*1024));CHKERRQ(ierr);
}
ierr = PetscFinalize();
return(0);
}
/*@C
PetscTraceBackErrorHandler - Default error handler routine that generates
a traceback on error detection.
Not Collective
Input Parameters:
+ comm - communicator over which error occurred
. line - the line number of the error (indicated by __LINE__)
. func - the function where error is detected (indicated by __FUNCT__)
. file - the file in which the error was detected (indicated by __FILE__)
. dir - the directory of the file (indicated by __SDIR__)
. mess - an error text string, usually just printed to the screen
. n - the generic error number
. p - PETSC_ERROR_INITIAL if this is the first call the the error handler, otherwise PETSC_ERROR_REPEAT
- ctx - error handler context
Level: developer
Notes:
Most users need not directly employ this routine and the other error
handlers, but can instead use the simplified interface SETERRQ, which has
the calling sequence
$ SETERRQ(comm,number,n,mess)
Notes for experienced users:
Use PetscPushErrorHandler() to set the desired error handler. The
currently available PETSc error handlers include PetscTraceBackErrorHandler(),
PetscAttachDebuggerErrorHandler(), PetscAbortErrorHandler(), and PetscMPIAbortErrorHandler()
Concepts: error handler^traceback
Concepts: traceback^generating
.seealso: PetscPushErrorHandler(), PetscAttachDebuggerErrorHandler(),
PetscAbortErrorHandler()
@*/
PetscErrorCode PetscTraceBackErrorHandler(MPI_Comm comm,int line,const char *fun,const char* file,const char *dir,PetscErrorCode n,PetscErrorType p,const char *mess,void *ctx)
{
PetscLogDouble mem,rss;
PetscBool flg1 = PETSC_FALSE,flg2 = PETSC_FALSE,flg3 = PETSC_FALSE;
PetscMPIInt rank = 0;
PetscFunctionBegin;
if (comm != PETSC_COMM_SELF) {
MPI_Comm_rank(comm,&rank);
}
if (!rank) {
if (p == PETSC_ERROR_INITIAL) {
(*PetscErrorPrintf)("--------------------- Error Message ------------------------------------\n");
if (n == PETSC_ERR_MEM) {
(*PetscErrorPrintf)("Out of memory. This could be due to allocating\n");
(*PetscErrorPrintf)("too large an object or bleeding by not properly\n");
(*PetscErrorPrintf)("destroying unneeded objects.\n");
PetscMallocGetCurrentUsage(&mem);
PetscMemoryGetCurrentUsage(&rss);
PetscOptionsGetBool(PETSC_NULL,"-malloc_dump",&flg1,PETSC_NULL);
PetscOptionsGetBool(PETSC_NULL,"-malloc_log",&flg2,PETSC_NULL);
PetscOptionsHasName(PETSC_NULL,"-malloc_log_threshold",&flg3);
if (flg2 || flg3) {
PetscMallocDumpLog(stdout);
} else {
(*PetscErrorPrintf)("Memory allocated %.0f Memory used by process %.0f\n",mem,rss);
if (flg1) {
PetscMallocDump(stdout);
} else {
(*PetscErrorPrintf)("Try running with -malloc_dump or -malloc_log for info.\n");
}
}
} else {
const char *text;
PetscErrorMessage(n,&text,PETSC_NULL);
if (text) (*PetscErrorPrintf)("%s!\n",text);
}
if (mess) {
(*PetscErrorPrintf)("%s!\n",mess);
}
(*PetscErrorPrintf)("------------------------------------------------------------------------\n");
(*PetscErrorPrintf)("%s\n",version);
(*PetscErrorPrintf)("See docs/changes/index.html for recent updates.\n");
(*PetscErrorPrintf)("See docs/faq.html for hints about trouble shooting.\n");
(*PetscErrorPrintf)("See docs/index.html for manual pages.\n");
(*PetscErrorPrintf)("------------------------------------------------------------------------\n");
if (PetscErrorPrintfInitializeCalled) {
(*PetscErrorPrintf)("%s on a %s named %s by %s %s\n",pname,arch,hostname,username,date);
}
(*PetscErrorPrintf)("Libraries linked from %s\n",PETSC_LIB_DIR);
(*PetscErrorPrintf)("Configure run at %s\n",petscconfigureruntime);
(*PetscErrorPrintf)("Configure options %s\n",petscconfigureoptions);
(*PetscErrorPrintf)("------------------------------------------------------------------------\n");
}
/* print line of stack trace */
(*PetscErrorPrintf)("%s() line %d in %s%s\n",fun,line,dir,file);
} else {
/* do not print error messages since process 0 will print them, sleep before aborting so will not accidently kill process 0*/
PetscSleep(10.0);
abort();
}
PetscFunctionReturn(n);
}
int main(int argc, char **argv)
{
MPI_Comm comm;
PetscMPIInt rank;
PetscErrorCode ierr;
User user;
PetscLogDouble v1, v2;
PetscInt nplot = 0;
char fileName[2048];
ierr = PetscInitialize(&argc, &argv, (char*) 0, help);CHKERRQ(ierr);
comm = PETSC_COMM_WORLD;
ierr = MPI_Comm_rank(comm, &rank);CHKERRQ(ierr);
ierr = PetscNew(&user);CHKERRQ(ierr);
ierr = PetscNew(&user->algebra);CHKERRQ(ierr);
ierr = PetscNew(&user->model);CHKERRQ(ierr);
ierr = PetscNew(&user->model->physics);CHKERRQ(ierr);
Algebra algebra = user->algebra;
ierr = LoadOptions(comm, user);CHKERRQ(ierr);
ierr = PetscTime(&v1);CHKERRQ(ierr);
ierr = CreateMesh(comm, user);CHKERRQ(ierr);
ierr = PetscTime(&v2);CHKERRQ(ierr);
ierr = PetscPrintf(PETSC_COMM_WORLD,
"Read and Distribute mesh takes %f sec \n", v2 - v1);CHKERRQ(ierr);
ierr = SetUpLocalSpace(user);CHKERRQ(ierr); //Set up the dofs of each element
ierr = ConstructGeometryFVM(&user->facegeom, &user->cellgeom, user);CHKERRQ(ierr);
ierr = LimiterSetup(user);CHKERRQ(ierr);
if (user->TimeIntegralMethod == EXPLICITMETHOD) { // explicit method
if(user->myownexplicitmethod){// Using the fully explicit method based on my own routing
ierr = PetscPrintf(PETSC_COMM_WORLD,"Using the fully explicit method based on my own routing\n");CHKERRQ(ierr);
user->current_time = user->initial_time;
user->current_step = 1;
ierr = DMCreateGlobalVector(user->dm, &algebra->solution);CHKERRQ(ierr);
ierr = PetscObjectSetName((PetscObject) algebra->solution, "solution");CHKERRQ(ierr);
ierr = VecSet(algebra->solution, 0);CHKERRQ(ierr);
ierr = SetInitialCondition(user->dm, algebra->solution, user);CHKERRQ(ierr);
if(1){
PetscViewer viewer;
ierr = OutputVTK(user->dm, "intialcondition.vtk", &viewer);CHKERRQ(ierr);
ierr = VecView(algebra->solution, viewer);CHKERRQ(ierr);
ierr = PetscViewerDestroy(&viewer);CHKERRQ(ierr);
ierr = PetscPrintf(PETSC_COMM_WORLD,"Outputing the initial condition intialcondition.vtk!!! \n");CHKERRQ(ierr);
}
ierr = VecDuplicate(algebra->solution, &algebra->fn);CHKERRQ(ierr);
ierr = VecDuplicate(algebra->solution, &algebra->oldsolution);CHKERRQ(ierr);
if(user->Explicit_RK2||user->Explicit_RK4){
ierr = PetscPrintf(PETSC_COMM_WORLD,"Use the second order Runge Kutta method \n");CHKERRQ(ierr);
}else{
ierr = PetscPrintf(PETSC_COMM_WORLD,"Use the first order forward Euler method \n");CHKERRQ(ierr);
}
nplot = 0; //the plot step
while(user->current_time < (user->final_time - 0.05 * user->dt)){
user->current_time = user->current_time + user->dt;
ierr = FormTimeStepFunction(user, algebra, algebra->solution, algebra->fn);CHKERRQ(ierr);
if(0){
PetscViewer viewer;
ierr = OutputVTK(user->dm, "function.vtk", &viewer);CHKERRQ(ierr);
ierr = VecView(algebra->fn, viewer);CHKERRQ(ierr);
ierr = PetscViewerDestroy(&viewer);CHKERRQ(ierr);
}
if(user->Explicit_RK2){
/*
U^n_1 = U^n + 0.5*dt*f(U^n)
U^{n+1} = U^n + dt*f(U^n_1)
*/
ierr = VecCopy(algebra->solution, algebra->oldsolution);CHKERRQ(ierr);
//note that algebra->oldsolution and algebra->solution are both U^n
ierr = VecAXPY(algebra->solution, 0.5*user->dt, algebra->fn);CHKERRQ(ierr);
//U^n_1 = U^n + 0.5*dt*f(U^n), now algebra->solution is U^n_1, and algebra->fn is f(U^n)
ierr = FormTimeStepFunction(user, algebra, algebra->solution, algebra->fn);CHKERRQ(ierr);
//algebra->fn is f(U^n_1)
// reset the algebra->solution to U^n
ierr = VecCopy(algebra->oldsolution, algebra->solution);CHKERRQ(ierr);
ierr = VecAXPY(algebra->solution, user->dt, algebra->fn);CHKERRQ(ierr);
// now algebra->solution is U^{n+1} = U^n + dt*f(U^n_1)
}else if(user->Explicit_RK4){
/* refer to https://en.wikipedia.org/wiki/Runge%E2%80%93Kutta_methods
k_1 = f(U^n)
U^n_1 = U^n + 0.5*dt*k_1
k_2 = f(U^n_1)
U^n_2 = U^n + 0.5*dt*k_2
k_3 = f(U^n_2)
U^n_3 = U^n + 0.5*dt*k_3
k_4 = f(U^n_3)
U^{n+1} = U^n + dt/6*(k_1 + 2*k_2 + 2*k_3 + k_4)
*/
Vec VecTemp; // store the U^n_1
Vec k1, k2, k3, k4;
ierr = VecDuplicate(algebra->solution, &k1);CHKERRQ(ierr);
ierr = VecDuplicate(algebra->solution, &k2);CHKERRQ(ierr);
ierr = VecDuplicate(algebra->solution, &k3);CHKERRQ(ierr);
ierr = VecDuplicate(algebra->solution, &k4);CHKERRQ(ierr);
ierr = VecCopy(algebra->solution, algebra->oldsolution);CHKERRQ(ierr);
ierr = VecCopy(algebra->fn, k1);CHKERRQ(ierr);
//note that algebra->oldsolution and algebra->solution are both U^n
ierr = VecAXPY(algebra->solution, 0.5*user->dt, k1);CHKERRQ(ierr);
//U^n_1 = U^n + 0.5*dt*k1, now algebra->solution is U^n_1, and algebra->fn is f(U^n)
ierr = FormTimeStepFunction(user, algebra, algebra->solution, algebra->fn);CHKERRQ(ierr);
//algebra->fn is f(U^n_1)
ierr = VecCopy(algebra->fn, k2);CHKERRQ(ierr);
// reset the algebra->solution to U^n
ierr = VecCopy(algebra->oldsolution, algebra->solution);CHKERRQ(ierr);
ierr = VecAXPY(algebra->solution, 0.5*user->dt, k2);CHKERRQ(ierr);
//U^n_2 = U^n + 0.5*dt*k2, now algebra->solution is U^n_2, and algebra->fn is f(U^n_1)
ierr = FormTimeStepFunction(user, algebra, algebra->solution, algebra->fn);CHKERRQ(ierr);
//algebra->fn is f(U^n_2)
ierr = VecCopy(algebra->fn, k3);CHKERRQ(ierr);
// reset the algebra->solution to U^n
ierr = VecCopy(algebra->oldsolution, algebra->solution);CHKERRQ(ierr);
ierr = VecAXPY(algebra->solution, 0.5*user->dt, k3);CHKERRQ(ierr);
//U^n_3 = U^n + 0.5*dt*k3, now algebra->solution is U^n_3, and algebra->fn is f(U^n_2)
ierr = FormTimeStepFunction(user, algebra, algebra->solution, algebra->fn);CHKERRQ(ierr);
//algebra->fn is f(U^n_3)
ierr = VecCopy(algebra->fn, k4);CHKERRQ(ierr);
//U^{n+1} = U^n + dt/6*(k_1 + 2*k_2 + 2*k_3 + k_4)
PetscReal temp;
temp = user->dt/6;
// reset the algebra->solution to U^n
ierr = VecCopy(algebra->oldsolution, algebra->solution);CHKERRQ(ierr);
ierr = VecAXPY(algebra->solution, temp, k1);CHKERRQ(ierr);
// now algebra->solution is U^n + dt/6*k_1
ierr = VecAXPY(algebra->solution, 2*temp, k2);CHKERRQ(ierr);
// now algebra->solution is U^n + dt/6*k_1 + 2*dt/6*k_2
ierr = VecAXPY(algebra->solution, 2*temp, k3);CHKERRQ(ierr);
// now algebra->solution is U^n + dt/6*k_1 + 2*dt/6*k_2 + 2*dt/6*k_3
ierr = VecAXPY(algebra->solution, temp, k4);CHKERRQ(ierr);
// now algebra->solution is U^n + dt/6*k_1 + 2*dt/6*k_2 + 2*dt/6*k_3 + dt/6*k_4
ierr = VecDestroy(&k1);CHKERRQ(ierr);
ierr = VecDestroy(&k2);CHKERRQ(ierr);
ierr = VecDestroy(&k3);CHKERRQ(ierr);
ierr = VecDestroy(&k4);CHKERRQ(ierr);
}else{
ierr = VecCopy(algebra->solution, algebra->oldsolution);CHKERRQ(ierr);
ierr = VecAXPY(algebra->solution, user->dt, algebra->fn);CHKERRQ(ierr);
}
{// Monitor the solution and function norms
PetscReal norm;
PetscLogDouble space =0;
PetscInt size;
PetscReal fnnorm;
ierr = VecNorm(algebra->fn,NORM_2,&fnnorm);CHKERRQ(ierr);
//ierr = VecView(algebra->fn, PETSC_VIEWER_STDOUT_WORLD);CHKERRQ(ierr);
ierr = VecNorm(algebra->solution,NORM_2,&norm);CHKERRQ(ierr);
ierr = VecGetSize(algebra->solution, &size);CHKERRQ(ierr);
norm = norm/size;
fnnorm = fnnorm/size;
if (norm>1.e5) {
SETERRQ2(PETSC_COMM_WORLD, PETSC_ERR_LIB,
"The norm of the solution is: %f (current time: %f). The explicit method is going to DIVERGE!!!", norm, user->current_time);
}
if (user->current_step%10==0) {
ierr = PetscPrintf(PETSC_COMM_WORLD,"Step %D at time %g with solution norm = %g and founction norm = %g \n",
user->current_step, user->current_time, norm, fnnorm);CHKERRQ(ierr);
}
// ierr = PetscMallocGetCurrentUsage(&space);CHKERRQ(ierr);
// if (user->current_step%10==0) {
// ierr = PetscPrintf(PETSC_COMM_WORLD,"Current space PetscMalloc()ed %g M\n",
// space/(1024*1024));CHKERRQ(ierr);
// }
}
{ // Monitor the difference of two steps' solution
PetscReal norm;
ierr = VecAXPY(algebra->oldsolution, -1, algebra->solution);CHKERRQ(ierr);
ierr = VecNorm(algebra->oldsolution,NORM_2,&norm);CHKERRQ(ierr);
if (user->current_step%10==0) {
ierr = PetscPrintf(PETSC_COMM_WORLD,"Step %D at time %g with ||u_k-u_{k-1}|| = %g \n",
user->current_step, user->current_time, norm);CHKERRQ(ierr);
}
if((norm<1.e-6)||(user->current_step > user->max_time_its)){
if(norm<1.e-6) ierr = PetscPrintf(PETSC_COMM_WORLD,"\n Convergence with ||u_k-u_{k-1}|| = %g < 1.e-6\n\n", norm);CHKERRQ(ierr);
if(user->current_step > user->max_time_its) ierr = PetscPrintf(PETSC_COMM_WORLD,"\n Convergence with reaching the max time its\n\n");CHKERRQ(ierr);
break;
}
}
// output the solution
if (user->output_solution && (user->current_step%user->steps_output==0)){
PetscViewer viewer;
Vec solution_unscaled; // Note the the algebra->solution is scaled by the density, so this is for the unscaled solution
nplot = user->current_step/user->steps_output;
// update file name for the current time step
ierr = VecDuplicate(algebra->solution, &solution_unscaled);CHKERRQ(ierr);
ierr = ReformatSolution(algebra->solution, solution_unscaled, user);CHKERRQ(ierr);
ierr = PetscSNPrintf(fileName, sizeof(fileName),"%s_%d.vtk",user->solutionfile, nplot);CHKERRQ(ierr);
ierr = PetscPrintf(PETSC_COMM_WORLD,"Outputing solution %s (current time %f)\n", fileName, user->current_time);CHKERRQ(ierr);
ierr = OutputVTK(user->dm, fileName, &viewer);CHKERRQ(ierr);
ierr = VecView(solution_unscaled, viewer);CHKERRQ(ierr);
ierr = VecDestroy(&solution_unscaled);CHKERRQ(ierr);
ierr = PetscViewerDestroy(&viewer);CHKERRQ(ierr);
}
user->current_step++;
}
ierr = VecDestroy(&algebra->fn);CHKERRQ(ierr);
}else{ // Using the fully explicit method based on the PETSC TS routing
PetscReal ftime;
TS ts;
TSConvergedReason reason;
PetscInt nsteps;
//PetscReal minRadius;
//ierr = DMPlexTSGetGeometry(user->dm, NULL, NULL, &minRadius);CHKERRQ(ierr);
//user->dt = 0.9*4 * minRadius / 1.0;
ierr = PetscPrintf(PETSC_COMM_WORLD,"Using the fully explicit method based on the PETSC TS routing\n");CHKERRQ(ierr);
ierr = DMCreateGlobalVector(user->dm, &algebra->solution);CHKERRQ(ierr);
ierr = PetscObjectSetName((PetscObject) algebra->solution, "solution");CHKERRQ(ierr);
ierr = VecSet(algebra->solution, 0.0);CHKERRQ(ierr);
ierr = SetInitialCondition(user->dm, algebra->solution, user);CHKERRQ(ierr);
ierr = TSCreate(comm, &ts);CHKERRQ(ierr);
ierr = TSSetType(ts, TSEULER);CHKERRQ(ierr);
ierr = TSSetDM(ts, user->dm);CHKERRQ(ierr);
ierr = TSMonitorSet(ts,TSMonitorFunctionError,(void*)user,NULL);CHKERRQ(ierr);
ierr = TSSetRHSFunction(ts, NULL, MyRHSFunction, user);CHKERRQ(ierr);
ierr = TSSetDuration(ts, 1000, user->final_time);CHKERRQ(ierr);
ierr = TSSetInitialTimeStep(ts, user->initial_time, user->dt);CHKERRQ(ierr);
ierr = TSSetFromOptions(ts);CHKERRQ(ierr);
ierr = TSSolve(ts, algebra->solution);CHKERRQ(ierr);
ierr = TSGetSolveTime(ts, &ftime);CHKERRQ(ierr);
ierr = TSGetTimeStepNumber(ts, &nsteps);CHKERRQ(ierr);
ierr = TSGetConvergedReason(ts, &reason);CHKERRQ(ierr);
ierr = PetscPrintf(PETSC_COMM_WORLD,"%s at time %g after %D steps\n",TSConvergedReasons[reason],ftime,nsteps);CHKERRQ(ierr);
ierr = TSDestroy(&ts);CHKERRQ(ierr);
}
if(user->benchmark_couette) {
ierr = DMCreateGlobalVector(user->dm, &algebra->exactsolution);CHKERRQ(ierr);
ierr = ComputeExactSolution(user->dm, user->current_time, algebra->exactsolution, user);CHKERRQ(ierr);
}
if(user->benchmark_couette) {
PetscViewer viewer;
PetscReal norm;
ierr = OutputVTK(user->dm, "exact_solution.vtk", &viewer);CHKERRQ(ierr);
ierr = VecView(algebra->exactsolution, viewer);CHKERRQ(ierr);
ierr = PetscViewerDestroy(&viewer);CHKERRQ(ierr);
ierr = VecAXPY(algebra->exactsolution, -1, algebra->solution);CHKERRQ(ierr);
ierr = VecNorm(algebra->exactsolution,NORM_INFINITY,&norm);CHKERRQ(ierr);
ierr = PetscPrintf(PETSC_COMM_WORLD,"Final time at %f, Error: ||u_k-u|| = %g \n", user->current_time, norm);CHKERRQ(ierr);
ierr = OutputVTK(user->dm, "Error.vtk", &viewer);CHKERRQ(ierr);
ierr = VecView(algebra->exactsolution, viewer);CHKERRQ(ierr);
ierr = PetscViewerDestroy(&viewer);CHKERRQ(ierr);
}
ierr = VecDestroy(&algebra->solution);CHKERRQ(ierr);
if(user->myownexplicitmethod){ierr = VecDestroy(&algebra->oldsolution);CHKERRQ(ierr);}
ierr = VecDestroy(&algebra->exactsolution);CHKERRQ(ierr);
ierr = DMDestroy(&user->dm);CHKERRQ(ierr);
} else if (user->TimeIntegralMethod == IMPLICITMETHOD) { // Using the fully implicit method
ierr = PetscPrintf(PETSC_COMM_WORLD,"Using the fully implicit method\n");CHKERRQ(ierr);
ierr = SNESCreate(comm,&user->snes);CHKERRQ(ierr);
ierr = SNESSetDM(user->snes,user->dm);CHKERRQ(ierr);
ierr = DMCreateGlobalVector(user->dm, &algebra->solution);CHKERRQ(ierr);
ierr = VecDuplicate(algebra->solution, &algebra->oldsolution);CHKERRQ(ierr);
ierr = VecDuplicate(algebra->solution, &algebra->f);CHKERRQ(ierr);
ierr = VecDuplicate(algebra->solution, &algebra->fn);CHKERRQ(ierr);
ierr = VecDuplicate(algebra->solution, &algebra->oldfn);CHKERRQ(ierr);
ierr = PetscObjectSetName((PetscObject) algebra->solution, "solution");CHKERRQ(ierr);
ierr = SetInitialCondition(user->dm, algebra->solution, user);CHKERRQ(ierr);
ierr = DMSetMatType(user->dm, MATAIJ);CHKERRQ(ierr);
// ierr = DMCreateMatrix(user->dm, &algebra->A);CHKERRQ(ierr);
ierr = DMCreateMatrix(user->dm, &algebra->J);CHKERRQ(ierr);
if (user->JdiffP) {
/*Set up the preconditioner matrix*/
ierr = DMCreateMatrix(user->dm, &algebra->P);CHKERRQ(ierr);
}else{
algebra->P = algebra->J;
}
ierr = MatSetOption(algebra->J, MAT_NEW_NONZERO_ALLOCATION_ERR, PETSC_FALSE);CHKERRQ(ierr);
/*set nonlinear function */
ierr = SNESSetFunction(user->snes, algebra->f, FormFunction, (void*)user);CHKERRQ(ierr);
/* compute Jacobian */
ierr = SNESSetJacobian(user->snes, algebra->J, algebra->P, FormJacobian, (void*)user);CHKERRQ(ierr);
ierr = SNESSetFromOptions(user->snes);CHKERRQ(ierr);
/* do the solve */
if (user->timestep == TIMESTEP_STEADY_STATE) {
ierr = SolveSteadyState(user);CHKERRQ(ierr);
} else {
ierr = SolveTimeDependent(user);CHKERRQ(ierr);
}
if (user->output_solution){
PetscViewer viewer;
Vec solution_unscaled; // Note the the algebra->solution is scaled by the density, so this is for the unscaled solution
ierr = VecDuplicate(algebra->solution, &solution_unscaled);CHKERRQ(ierr);
ierr = ReformatSolution(algebra->solution, solution_unscaled, user);CHKERRQ(ierr);
ierr = OutputVTK(user->dm, "solution.vtk", &viewer);CHKERRQ(ierr);
ierr = VecView(solution_unscaled, viewer);CHKERRQ(ierr);
ierr = VecDestroy(&solution_unscaled);CHKERRQ(ierr);
ierr = PetscViewerDestroy(&viewer);CHKERRQ(ierr);
}
if(user->benchmark_couette) {
PetscViewer viewer;
PetscReal norm;
ierr = OutputVTK(user->dm, "exact_solution.vtk", &viewer);CHKERRQ(ierr);
ierr = VecView(algebra->exactsolution, viewer);CHKERRQ(ierr);
ierr = PetscViewerDestroy(&viewer);CHKERRQ(ierr);
ierr = VecAXPY(algebra->exactsolution, -1, algebra->solution);CHKERRQ(ierr);
ierr = VecNorm(algebra->exactsolution,NORM_INFINITY,&norm);CHKERRQ(ierr);
ierr = PetscPrintf(PETSC_COMM_WORLD,"Error: ||u_k-u|| = %g \n", norm);CHKERRQ(ierr);
ierr = OutputVTK(user->dm, "Error.vtk", &viewer);CHKERRQ(ierr);
ierr = VecView(algebra->exactsolution, viewer);CHKERRQ(ierr);
ierr = PetscViewerDestroy(&viewer);CHKERRQ(ierr);
}
ierr = VecDestroy(&algebra->solution);CHKERRQ(ierr);
ierr = VecDestroy(&algebra->f);CHKERRQ(ierr);
ierr = VecDestroy(&algebra->oldsolution);CHKERRQ(ierr);
ierr = VecDestroy(&algebra->fn);CHKERRQ(ierr);
ierr = VecDestroy(&algebra->oldfn);CHKERRQ(ierr);
ierr = SNESDestroy(&user->snes);CHKERRQ(ierr);
ierr = DMDestroy(&user->dm);CHKERRQ(ierr);
} else {
SETERRQ(PETSC_COMM_SELF,PETSC_ERR_USER,"WRONG option for the time integral method. Using the option '-time_integral_method 0 or 1'");
}
ierr = VecDestroy(&user->cellgeom);CHKERRQ(ierr);
ierr = VecDestroy(&user->facegeom);CHKERRQ(ierr);
ierr = DMDestroy(&user->dmGrad);CHKERRQ(ierr);
ierr = PetscFunctionListDestroy(&LimitList);CHKERRQ(ierr);
ierr = PetscFree(user->model->physics);CHKERRQ(ierr);
ierr = PetscFree(user->algebra);CHKERRQ(ierr);
ierr = PetscFree(user->model);CHKERRQ(ierr);
ierr = PetscFree(user);CHKERRQ(ierr);
{
PetscLogDouble space =0;
ierr = PetscMallocGetCurrentUsage(&space);CHKERRQ(ierr);
ierr = PetscPrintf(PETSC_COMM_WORLD,"Unfreed space at the End %g M\n", space/(1024*1024));CHKERRQ(ierr);
}
ierr = PetscFinalize();
return(0);
}
/*@C
PetscMemoryView - Shows the amount of memory currently being used
in a communicator.
Collective on PetscViewer
Input Parameter:
+ viewer - the viewer that defines the communicator
- message - string printed before values
Options Database:
+ -malloc - have PETSc track how much memory it has allocated
- -memory_view - during PetscFinalize() have this routine called
Level: intermediate
Concepts: memory usage
.seealso: PetscMallocDump(), PetscMemoryGetCurrentUsage(), PetscMemorySetGetMaximumUsage()
@*/
PetscErrorCode PetscMemoryView(PetscViewer viewer,const char message[])
{
PetscLogDouble allocated,allocatedmax,resident,residentmax,gallocated,gallocatedmax,gresident,gresidentmax,maxgallocated,maxgallocatedmax,maxgresident,maxgresidentmax;
PetscLogDouble mingallocated,mingallocatedmax,mingresident,mingresidentmax;
PetscErrorCode ierr;
MPI_Comm comm;
PetscFunctionBegin;
if (!viewer) viewer = PETSC_VIEWER_STDOUT_WORLD;
ierr = PetscMallocGetCurrentUsage(&allocated);CHKERRQ(ierr);
ierr = PetscMallocGetMaximumUsage(&allocatedmax);CHKERRQ(ierr);
ierr = PetscMemoryGetCurrentUsage(&resident);CHKERRQ(ierr);
ierr = PetscMemoryGetMaximumUsage(&residentmax);CHKERRQ(ierr);
if (residentmax > 0) residentmax = PetscMax(resident,residentmax);
ierr = PetscObjectGetComm((PetscObject)viewer,&comm);CHKERRQ(ierr);
ierr = PetscViewerASCIIPrintf(viewer,message);CHKERRQ(ierr);
if (resident && residentmax && allocated) {
ierr = MPI_Reduce(&residentmax,&gresidentmax,1,MPIU_PETSCLOGDOUBLE,MPI_SUM,0,comm);CHKERRQ(ierr);
ierr = MPI_Reduce(&residentmax,&maxgresidentmax,1,MPIU_PETSCLOGDOUBLE,MPI_MAX,0,comm);CHKERRQ(ierr);
ierr = MPI_Reduce(&residentmax,&mingresidentmax,1,MPIU_PETSCLOGDOUBLE,MPI_MIN,0,comm);CHKERRQ(ierr);
ierr = PetscViewerASCIIPrintf(viewer,"Maximum (over computational time) process memory: total %5.4e max %5.4e min %5.4e\n",gresidentmax,maxgresidentmax,mingresidentmax);CHKERRQ(ierr);
ierr = MPI_Reduce(&resident,&gresident,1,MPIU_PETSCLOGDOUBLE,MPI_SUM,0,comm);CHKERRQ(ierr);
ierr = MPI_Reduce(&resident,&maxgresident,1,MPIU_PETSCLOGDOUBLE,MPI_MAX,0,comm);CHKERRQ(ierr);
ierr = MPI_Reduce(&resident,&mingresident,1,MPIU_PETSCLOGDOUBLE,MPI_MIN,0,comm);CHKERRQ(ierr);
ierr = PetscViewerASCIIPrintf(viewer,"Current process memory: total %5.4e max %5.4e min %5.4e\n",gresident,maxgresident,mingresident);CHKERRQ(ierr);
ierr = MPI_Reduce(&allocatedmax,&gallocatedmax,1,MPIU_PETSCLOGDOUBLE,MPI_SUM,0,comm);CHKERRQ(ierr);
ierr = MPI_Reduce(&allocatedmax,&maxgallocatedmax,1,MPIU_PETSCLOGDOUBLE,MPI_MAX,0,comm);CHKERRQ(ierr);
ierr = MPI_Reduce(&allocatedmax,&mingallocatedmax,1,MPIU_PETSCLOGDOUBLE,MPI_MIN,0,comm);CHKERRQ(ierr);
ierr = PetscViewerASCIIPrintf(viewer,"Maximum (over computational time) space PetscMalloc()ed: total %5.4e max %5.4e min %5.4e\n",gallocatedmax,maxgallocatedmax,mingallocatedmax);CHKERRQ(ierr);
ierr = MPI_Reduce(&allocated,&gallocated,1,MPIU_PETSCLOGDOUBLE,MPI_SUM,0,comm);CHKERRQ(ierr);
ierr = MPI_Reduce(&allocated,&maxgallocated,1,MPIU_PETSCLOGDOUBLE,MPI_MAX,0,comm);CHKERRQ(ierr);
ierr = MPI_Reduce(&allocated,&mingallocated,1,MPIU_PETSCLOGDOUBLE,MPI_MIN,0,comm);CHKERRQ(ierr);
ierr = PetscViewerASCIIPrintf(viewer,"Current space PetscMalloc()ed: total %5.4e max %5.4e min %5.4e\n",gallocated,maxgallocated,mingallocated);CHKERRQ(ierr);
} else if (resident && residentmax) {
ierr = MPI_Reduce(&residentmax,&gresidentmax,1,MPIU_PETSCLOGDOUBLE,MPI_SUM,0,comm);CHKERRQ(ierr);
ierr = MPI_Reduce(&residentmax,&maxgresidentmax,1,MPIU_PETSCLOGDOUBLE,MPI_MAX,0,comm);CHKERRQ(ierr);
ierr = MPI_Reduce(&residentmax,&mingresidentmax,1,MPIU_PETSCLOGDOUBLE,MPI_MIN,0,comm);CHKERRQ(ierr);
ierr = PetscViewerASCIIPrintf(viewer,"Maximum (over computational time) process memory: total %5.4e max %5.4e min %5.4e\n",gresidentmax,maxgresidentmax,mingresidentmax);CHKERRQ(ierr);
ierr = MPI_Reduce(&resident,&gresident,1,MPIU_PETSCLOGDOUBLE,MPI_SUM,0,comm);CHKERRQ(ierr);
ierr = MPI_Reduce(&resident,&maxgresident,1,MPIU_PETSCLOGDOUBLE,MPI_MAX,0,comm);CHKERRQ(ierr);
ierr = MPI_Reduce(&resident,&mingresident,1,MPIU_PETSCLOGDOUBLE,MPI_MIN,0,comm);CHKERRQ(ierr);
ierr = PetscViewerASCIIPrintf(viewer,"Current process memory: total %5.4e max %5.4e min %5.4e\n",gresident,maxgresident,mingresident);CHKERRQ(ierr);
} else if (resident && allocated) {
ierr = MPI_Reduce(&resident,&gresident,1,MPIU_PETSCLOGDOUBLE,MPI_SUM,0,comm);CHKERRQ(ierr);
ierr = MPI_Reduce(&resident,&maxgresident,1,MPIU_PETSCLOGDOUBLE,MPI_MAX,0,comm);CHKERRQ(ierr);
ierr = MPI_Reduce(&resident,&mingresident,1,MPIU_PETSCLOGDOUBLE,MPI_MIN,0,comm);CHKERRQ(ierr);
ierr = PetscViewerASCIIPrintf(viewer,"Current process memory: total %5.4e max %5.4e min %5.4e\n",gresident,maxgresident,mingresident);CHKERRQ(ierr);
ierr = MPI_Reduce(&allocated,&gallocated,1,MPIU_PETSCLOGDOUBLE,MPI_SUM,0,comm);CHKERRQ(ierr);
ierr = MPI_Reduce(&allocated,&maxgallocated,1,MPIU_PETSCLOGDOUBLE,MPI_MAX,0,comm);CHKERRQ(ierr);
ierr = MPI_Reduce(&allocated,&mingallocated,1,MPIU_PETSCLOGDOUBLE,MPI_MIN,0,comm);CHKERRQ(ierr);
ierr = PetscViewerASCIIPrintf(viewer,"Current space PetscMalloc()ed: total %5.4e max %5.4e min %5.4e\n",gallocated,maxgallocated,mingallocated);CHKERRQ(ierr);
ierr = PetscViewerASCIIPrintf(viewer,"Run with -memory_view to get maximum memory usage\n");CHKERRQ(ierr);
} else if (allocated) {
ierr = MPI_Reduce(&allocated,&gallocated,1,MPIU_PETSCLOGDOUBLE,MPI_SUM,0,comm);CHKERRQ(ierr);
ierr = MPI_Reduce(&allocated,&maxgallocated,1,MPIU_PETSCLOGDOUBLE,MPI_MAX,0,comm);CHKERRQ(ierr);
ierr = MPI_Reduce(&allocated,&mingallocated,1,MPIU_PETSCLOGDOUBLE,MPI_MIN,0,comm);CHKERRQ(ierr);
ierr = PetscViewerASCIIPrintf(viewer,"Current space PetscMalloc()ed: total %5.4e max %5.4e min %5.4e\n",gallocated,maxgallocated,mingallocated);CHKERRQ(ierr);
ierr = PetscViewerASCIIPrintf(viewer,"Run with -memory_view to get maximum memory usage\n");CHKERRQ(ierr);
ierr = PetscViewerASCIIPrintf(viewer,"OS cannot compute process memory\n");CHKERRQ(ierr);
} else {
ierr = PetscViewerASCIIPrintf(viewer,"Run with -malloc to get statistics on PetscMalloc() calls\nOS cannot compute process memory\n");CHKERRQ(ierr);
}
ierr = PetscViewerFlush(viewer);CHKERRQ(ierr);
PetscFunctionReturn(0);
}
