void tl_set_handler(tl_timer * timer, void (*handler) (void *), void *ud)
{
timer->handler = handler;
timer->userdata = ud;
if (timer->group == asyncgroup)
update_async();
}
void tl_set_interval(tl_timer * timer, int interval)
{
if (timer->interval <= 0) {
tl_reset_timer(timer);
}
timer->interval = interval;
if (timer->group == asyncgroup)
update_async();
}
void tl_remove_timer(tl_timer * timer)
{
tl_group *g = timer->group;
timer->previous->next = timer->next;
if (timer->next != NULL)
timer->next->previous = timer->previous;
timer->group = NULL;
if (g == asyncgroup)
update_async();
}
void tl_set_interval(tl_timer * timer, int interval)
{
if (timer->interval > 0 && timer->wait > 0)
timer->wait += interval - timer->interval;
else
timer->wait = interval;
timer->interval = interval;
if (timer->group == asyncgroup)
update_async();
}
void tl_add_timer(tl_group * group, tl_timer * timer)
{
if (timer->group)
tl_remove_timer(timer);
timer->previous = group;
timer->next = group->next;
timer->group = group;
group->next = timer;
if (timer->group == asyncgroup)
update_async();
}
static void alarmhandler(int a)
{
if(!intimer) {
#ifdef __DJGPP__
/* asm volatile ("sti");*/
/* outportb(0x20,0x20);*/
#endif
intimer=1;
update_async();
signal(SIGALRM, alarmhandler);
intimer=0;
}
}
int main (int args, char* argv[])
{
double length = LENGTH; //Axial length of vessel to simulate (in micrometers).
double diameter= DIAMETER;
double pi = 3.1415; //Steady state diameter of the simulated vessel (in micrometers).
double hx_smc = HX_SMC;
double hy_smc = HY_SMC;
double hx_ec = HX_EC;
double hy_ec = HY_EC;
double new_length = (rint (length/hx_ec) ) * hx_ec;
if (( (int)(new_length) % (int) (hx_smc) )!=0)
hx_smc = new_length / (rint (new_length/hx_smc)) ;
double new_circ= (rint (diameter * pi /hy_smc) ) * hy_smc;
if (( (int)(new_circ) % (int) (hy_ec) )!=0)
hy_ec = new_circ / (rint (new_circ/hy_ec)) ;
grid.neq_smc = 26;
grid.neq_ec = 4;
grid.nodes_smc = (int) (length/hx_smc);
grid.layers_smc = (int) (new_circ/hy_smc);
grid.nodes_ec = (int) (length/hx_ec);
grid.layers_ec = (int) (new_circ/hy_ec);
grid.m = grid.nodes_smc*grid.layers_smc;
grid.n = grid.nodes_ec *grid.layers_ec ;
MPI_Init(&args, &argv);
int tasks,
myRank;
MPI_Status status1,stat1,stat2,stat3,stat4;
MPI_Request req1,req2,req3,req4;
MPI_Comm_size(MPI_COMM_WORLD,&tasks);
MPI_Comm_rank(MPI_COMM_WORLD,&myRank);
FILE *errPT;
char filename[10];int n;
int kB=1024, MB= 1024*1024;
sprintf(filename,"err.%d.txt",myRank);
errPT = fopen(filename,"w+");
int n_smc,n_ec;
if (myRank ==0)
{
printf("LENGTH = %2.5f\t\tDIAMETER(requested)= %2.5f\t\tDIAMETER(corrected)= %2.5f\t\tCIRCUMFERENCE = %2.5f\n\n",length,diameter,(new_circ/pi),new_circ);
printf("SMC GRID INFO:\nNodes = %d\nLayers = %d\nHX = %f,HY = %f\nTotal cells = %d\n",grid.nodes_smc,grid.layers_smc,hx_smc,hy_smc,grid.m);
printf("EC GRID INFO:\nNodes = %d\nLayers = %d\nHX = %f,HY = %f\nTotal cells = %d\n",grid.nodes_ec,grid.layers_ec,hx_ec,hy_ec,grid.n);
//EC bit
int r = grid.nodes_ec%tasks;
if (r ==0)
{
n_ec = grid.nodes_ec/tasks;
grid.n_ec= n_ec;
for (int i=1;i<tasks;i++)
MPI_Send(&n_ec,1,MPI_INT,i,000,MPI_COMM_WORLD);
}
else{
n_ec = (grid.nodes_ec - r )/tasks;
grid.n_ec= n_ec;
for (int i=1;i<tasks-1;i++)
MPI_Send(&n_ec,1,MPI_INT,i,000,MPI_COMM_WORLD);
n_ec=n_ec+r;
MPI_Send(&n_ec,1,MPI_INT,(tasks-1),000,MPI_COMM_WORLD);
}
}
else
MPI_Recv(&grid.n_ec,1,MPI_INT,MASTER,000,MPI_COMM_WORLD,&status1);
grid.n_smc = 13*grid.n_ec;
//Each should perform this bit locally
celltype1* smc_base;
celltype2* ec_base;
smc_base = (celltype1*) malloc((grid.layers_smc *grid.n_smc) * sizeof(celltype1));
if(smc_base==NULL){
fprintf(errPT,"Allocation failed for smc_base\n");
MPI_Abort(MPI_COMM_WORLD,100);
}
ec_base = (celltype2*) malloc((grid.layers_ec *grid.n_ec) * sizeof(celltype2));
if(ec_base==NULL){
fprintf(errPT,"Allocation failed for ec_base\n");
MPI_Abort(MPI_COMM_WORLD,100);
}
smc = (celltype1**) malloc(grid.layers_smc * sizeof(celltype1*));
if(smc==NULL){
fprintf(errPT,"Allocation failed for smc row dimension\n");
MPI_Abort(MPI_COMM_WORLD,100);
}
for (int i=0; i<grid.layers_smc; i++){
smc[i]= (celltype1*) malloc(grid.n_smc * sizeof(celltype1));
if(smc[i]==NULL){
fprintf(errPT,"Allocation failed for smc row # %d dimension\n",i);
MPI_Abort(MPI_COMM_WORLD,100);
}
smc[i]= smc_base+(i*grid.n_smc);
}
ec = (celltype2**) malloc(grid.layers_ec * sizeof(celltype2*));
if(smc==NULL){
fprintf(errPT,"Allocation failed for smc row dimension\n");
MPI_Abort(MPI_COMM_WORLD,100);
}
for (int i=0; i<grid.layers_ec; i++){
ec[i]= (celltype2*) malloc(grid.n_ec * sizeof(celltype2));
if(ec[i]==NULL){
fprintf(errPT,"Allocation failed for ec row # %d dimension\n",i);
MPI_Abort(MPI_COMM_WORLD,100);
}
ec[i]= ec_base+(i*grid.n_ec);
}
nn.sbuf_left = (double*)malloc( 3*(grid.layers_smc+grid.layers_ec) * sizeof(double));
if(nn.sbuf_left==NULL){
fprintf(errPT,"Allocation failed for nn.sbuf_left dimension\n");
MPI_Abort(MPI_COMM_WORLD,100);
}
nn.sbuf_right = (double*)malloc( 3*(grid.layers_smc+grid.layers_ec) * sizeof(double));
if(nn.sbuf_right==NULL){
fprintf(errPT,"Allocation failed for nn.sbuf_right dimension\n");
MPI_Abort(MPI_COMM_WORLD,100);
}
nn.rbuf_left = (double*)malloc( 3*(grid.layers_smc+grid.layers_ec) * sizeof(double));
if(nn.rbuf_left==NULL){
fprintf(errPT,"Allocation failed for nn.rbuf_left dimension\n");
MPI_Abort(MPI_COMM_WORLD,100);
}
nn.rbuf_right = (double*)malloc( 3*(grid.layers_smc+grid.layers_ec) * sizeof(double));
if(nn.rbuf_right==NULL){
fprintf(errPT,"Allocation failed for nn.rbuf_right dimension\n");
MPI_Abort(MPI_COMM_WORLD,100);
}
nn.left_smc_c = (double*)malloc( grid.layers_smc * sizeof(double));
if(nn.left_smc_c==NULL){
fprintf(errPT,"Allocation failed for nn.left_smc_c dimension\n");
MPI_Abort(MPI_COMM_WORLD,100);
}
nn.right_smc_c = (double*)malloc( grid.layers_smc * sizeof(double));
if(nn.right_smc_c==NULL){
fprintf(errPT,"Allocation failed for nn.right_smc_c dimension\n");
MPI_Abort(MPI_COMM_WORLD,100);
}
nn.left_ec_c = (double*)malloc( grid.layers_ec * sizeof(double));
if(nn.left_ec_c==NULL){
fprintf(errPT,"Allocation failed for nn.left_ec_c dimension\n");
MPI_Abort(MPI_COMM_WORLD,100);
}
nn.right_ec_c = (double*)malloc( grid.layers_ec * sizeof(double));
if(nn.right_ec_c==NULL){
fprintf(errPT,"Allocation failed for nn.right_ec_c dimension\n");
MPI_Abort(MPI_COMM_WORLD,100);
}
nn.left_smc_v = (double*)malloc( grid.layers_smc * sizeof(double));
if(nn.left_smc_v==NULL){
fprintf(errPT,"Allocation failed for nn.left_smc_v dimension\n");
MPI_Abort(MPI_COMM_WORLD,100);
}
nn.right_smc_v = (double*)malloc( grid.layers_smc * sizeof(double));
if(nn.right_smc_v==NULL){
fprintf(errPT,"Allocation failed for nn.right_smc_v dimension\n");
MPI_Abort(MPI_COMM_WORLD,100);
}
nn.left_ec_v = (double*)malloc( grid.layers_ec * sizeof(double));
if(nn.left_ec_v==NULL){
fprintf(errPT,"Allocation failed for nn.left_ec_v dimension\n");
MPI_Abort(MPI_COMM_WORLD,100);
}
nn.right_ec_v = (double*)malloc( grid.layers_ec * sizeof(double));
if(nn.right_ec_v==NULL){
fprintf(errPT,"Allocation failed for nn.right_ec_v dimension\n");
MPI_Abort(MPI_COMM_WORLD,100);
}
nn.left_smc_I = (double*)malloc( grid.layers_smc * sizeof(double));
if(nn.left_smc_I==NULL){
fprintf(errPT,"Allocation failed for nn.left_smc_I dimension\n");
MPI_Abort(MPI_COMM_WORLD,100);
}
nn.right_smc_I = (double*)malloc( grid.layers_smc * sizeof(double));
if(nn.right_smc_I==NULL){
fprintf(errPT,"Allocation failed for nn.right_smc_I dimension\n");
MPI_Abort(MPI_COMM_WORLD,100);
}
nn.left_ec_I = (double*)malloc( grid.layers_ec * sizeof(double));
if(nn.left_ec_I==NULL){
fprintf(errPT,"Allocation failed for nn.left_ec_I dimension\n");
MPI_Abort(MPI_COMM_WORLD,100);
}
nn.right_ec_I = (double*)malloc( grid.layers_ec * sizeof(double));
if(nn.right_ec_I==NULL){
fprintf(errPT,"Allocation failed for nn.right_ec_I dimension\n");
MPI_Abort(MPI_COMM_WORLD,100);
}
//Lodaing the information of rows and cols of each cell and allocating memory for various flux equations
for(int i=0; i<grid.layers_smc; i++)
{
for (int j=0;j<grid.n_smc;j++)
{
smc[i][j].row = i;
smc[i][j].col = j;
/* smc[i][j].A = (double*) malloc(12*sizeof(double));
if(smc[i][j].A==NULL){
fprintf(errPT,"Allocation failed for smc[i][j].A dimension\n");
MPI_Abort(MPI_COMM_WORLD,100);
}
smc[i][j].B = (double*) malloc(3*sizeof(double));
if(smc[i][j].B==NULL){
fprintf(errPT,"Allocation failed for smc[i][j].B dimension\n");
MPI_Abort(MPI_COMM_WORLD,100);
}
smc[i][j].C = (double*) malloc(3*sizeof(double));
if(smc[i][j].C==NULL){
fprintf(errPT,"Allocation failed for smc[i][j].C dimension\n");
MPI_Abort(MPI_COMM_WORLD,100);
}*/
}
}
for(int i=0; i<grid.layers_ec; i++)
{
for (int j=0;j<grid.n_ec;j++)
{
ec[i][j].row = i;
ec[i][j].col = j;
/* ec[i][j].A = (double*) malloc(12*sizeof(double));
if(ec[i][j].A==NULL){
fprintf(errPT,"Allocation failed for ec[i][j].A dimension\n");
MPI_Abort(MPI_COMM_WORLD,100);
}
ec[i][j].B = (double*) malloc(3*sizeof(double));
if(ec[i][j].B==NULL){
fprintf(errPT,"Allocation failed for ec[i][j].B dimension\n");
MPI_Abort(MPI_COMM_WORLD,100);
}
ec[i][j].C = (double*) malloc(3*sizeof(double));
if(ec[i][j].C==NULL){
fprintf(errPT,"Allocation failed for ec[i][j].C dimension\n");
MPI_Abort(MPI_COMM_WORLD,100);
}*/
}
}
int total = (grid.neq_smc * grid.n_smc * grid.layers_smc) + (grid.neq_ec * grid.n_ec * grid.layers_ec);
//Initialize and use the solver here
RKSUITE rksuite;
//Time variables
double tfinal = TFINAL;
double tnow = 0.0;
double interval= INTERVAL;
//File written every 1 second
int file_write_per_unit_time=(int)(1/interval);
//Error control variables
double TOL = 1e-7;
double thres[total];
for (int i= 0; i<total; i++)
thres[i] = 1e-7;
//Variables holding new and old values
double* y = (double*) malloc (total * sizeof(double));
/***** INITIALIZATION SECTION ******/
int offset = 0;
Initialize_tsoukias_smc(offset,y);
offset = grid.n_smc*grid.layers_smc * grid.neq_smc;
Initialize_koeingsberger_ec(offset, y);
int i,j,k;
for(i=0;i< grid.layers_smc; i++)
{
for (j=0;j<grid.n_smc;j++)
{
if (i>0)
k=(i*grid.n_smc*grid.neq_smc);
else if (i==0)
k=0;
smc[i][j].p = &y[k+(j*grid.neq_smc)+0];
}
}
offset = grid.n_smc*grid.layers_smc * grid.neq_smc;
for(i=0;i< grid.layers_ec; i++)
{
for (j=0;j<grid.n_ec;j++)
{
if (i>0)
k= offset+i*grid.n_ec*grid.neq_ec ;
else if (i==0)
k=offset+0;
ec[i][j].q = &y[k+(j*grid.neq_ec)+0];
}
}
for(i=0;i< grid.layers_smc; i++)
{
for (j=0;j<grid.n_smc;j++)
{
smc[i][j].NE = 0.0;
smc[i][j].NO = 0.0;
smc[i][j].I_stim= 0.0;
}
}
/***************************************************************/
double* yp= (double*) malloc (total * sizeof(double));
//Solver method
int method = 2; //RK(4,5)
//Statistics
int totf,stpcst,acptstp;
double waste,hnext;
//Error Flag
int cflag = 0, uflag =0;
//Error extent monitor, to select best constant step of tolerances
double* ymax = (double*) malloc(total * sizeof(double));
int state = couplingParms(CASE);
if (myRank==0)
printf("\n Step Size=%2.10lf\nUnit time in file write=%lf\n",interval,(double)file_write_per_unit_time*interval );
//Output file management
FILE
*time,*Task_info,
*ci,*cj,
*si,*sj,
*vi,*vj,
*Ii,*Ij,
*cpv_i,*cpc_i,*cpi_i,
*cpv_j,*cpc_j,*cpi_j;
n=sprintf(filename,"t%d.txt",myRank);
time = fopen(filename,"w+");
n=sprintf(filename,"Task_info%d.txt",myRank);
Task_info= fopen(filename,"w+");
n=sprintf(filename,"smc_c%d.txt",myRank);
ci = fopen(filename,"w+");
n=sprintf(filename,"ec_c%d.txt",myRank);
cj = fopen(filename,"w+");
n=sprintf(filename,"ec_s%d.txt",myRank);
sj = fopen(filename,"w+");
n=sprintf(filename,"smc_v%d.txt",myRank);
vi = fopen(filename,"w+");
n=sprintf(filename,"ec_v%d.txt",myRank);
vj = fopen(filename,"w+");
n=sprintf(filename,"smc_I%d.txt",myRank);
Ii = fopen(filename,"w+");
n=sprintf(filename,"ec_I%d.txt",myRank);
Ij = fopen(filename,"w+");
n=sprintf(filename,"cpv_i%d.txt",myRank);
cpv_i = fopen(filename,"w+");
n=sprintf(filename,"cpc_i%d.txt",myRank);
cpc_i = fopen(filename,"w+");
n=sprintf(filename,"cpi_i%d.txt",myRank);
cpi_i = fopen(filename,"w+");
n=sprintf(filename,"cpc_j%d.txt",myRank);
cpc_j = fopen(filename,"w+");
n=sprintf(filename,"cpv_j%d.txt",myRank);
cpv_j = fopen(filename,"w+");
n=sprintf(filename,"cpi_j%d.txt",myRank);
cpi_j = fopen(filename,"w+");
int count = 3*(grid.layers_smc+grid.layers_ec),
buf_offset = 3*grid.layers_smc;
int iteration=0;
double Per_MPI_time_t1,Per_MPI_time_t2,
Per_step_compute_time_t1,Per_step_compute_time_t2;
double t1 = MPI_Wtime();
/********************************************************************/
for(int i=0; i<grid.layers_smc;i++)
update_send_buffers_smc(myRank,tasks,i);
for(int i=0; i<grid.layers_ec;i++)
update_send_buffers_ec(myRank,tasks,i);
my_boundary(myRank);
update_async(myRank,tasks);
retrive_recv_buffers_smc(myRank,tasks);
retrive_recv_buffers_ec(myRank,tasks);
/************************************************************************/
/*********************SOLVER SECTION*************************/
/************************************************************************/
tend = interval;
rksuite.setup(total, tnow, y, tend, TOL, thres, method, "CT", false, 1e-5, false );
while (tnow <=10.00) {
// the ct() function does not guarantee to advance all the
// way to the stop time. Keep stepping until it does.
do {
computeDerivatives( tnow, y, yp );
rksuite.ct(computeDerivatives, tnow, y, yp, cflag );
if (cflag >= 5) {
printf("RKSUITE error %d\n", cflag );
MPI_Abort(MPI_COMM_WORLD,1000);
return false;
break;
}
} while (tnow < tend);
iteration++;
/************************************************/
/* Communication Block */
/************************************************/
update_async(myRank,tasks);
MPI_Barrier(MPI_COMM_WORLD);
if (iteration==5){
fprintf(Task_info,"COUPLING COEFFICIENTS\n\n");
fprintf(Task_info,"g_hm_smc=\t%6.2lf\ng_hm_ec=\t%6.2lf\np_hm_smc=\t%6.2lf\np_hm_ec=\t%6.2lf\npIP_hm_smc=\t%6.2lf\npIP_hm_ec=\t%6.2lf\ng_ht_smc=\t%6.2lf\tg_ht_ec=\t%6.2lf\np_ht_smc=\t%6.2lf\tp_ht_ec=\t%6.2lf\npIP_ht_smc=\t%6.2lf\tpIP_ht_ec=\t%6.2lf\n",
cpl_cef.g_hm_smc,cpl_cef.g_hm_ec,cpl_cef.p_hm_smc,cpl_cef.p_hm_ec,cpl_cef.pIP_hm_smc,cpl_cef.pIP_hm_ec,cpl_cef.g_ht_smc,cpl_cef.g_ht_ec,cpl_cef.p_ht_smc,cpl_cef.p_ht_ec,
cpl_cef.pIP_ht_smc,cpl_cef.pIP_ht_ec);
fprintf(Task_info,"\nSpatial Gradient info:\nMinimum JPLC\t=\t=%lf\nMaximum JPLC\t=\t=%lf\nGradient\t=\t=%lf\n"
,grid.min_jplc,grid.max_jplc,grid.gradient);
fprintf(Task_info,"\nTotal Tasks=%d\tMyRank=%d\n\n",tasks,myRank);
fprintf(Task_info,"LENGTH = %2.5f\nREQUESTED DIAMETER = %2.5f\nCORRECTED CIRCUMFERENCE = %2.5f\nTotal layers=%d\nTotal nodes=%d\n\n",length,diameter,new_circ,grid.layers_smc,grid.nodes_smc);
fprintf(Task_info,"SMC GRID INFO:\nNodes = %d\nLayers = %d\nHX = %lf,HY = %lf\nTotal cells = %d\n\n",grid.n_smc,grid.layers_smc,hx_smc,hy_smc,grid.m);
fprintf(Task_info,"EC GRID INFO:\nNodes = %d\nLayers = %d\nHX = %lf,HY = %lf\nTotal cells = %d\n\n",grid.n_ec,grid.layers_ec,hx_ec,hy_ec,grid.n);
fprintf(Task_info,"JPLC (at t<100 seconds) in axial direction per EC\n");
for (int p=0; p<grid.n_ec; p++)
fprintf(Task_info,"[%d]\t%lf\n",p,ec[0][p].JPLC);
}
if ((iteration==1)||(iteration % file_write_per_unit_time==0))
{
fprintf(time,"%lf\n",tnow);
for (int row=0; row<grid.layers_smc;row++)
{
for (int col=0; col<grid.n_smc; col++)
{
fprintf(ci,"%2.10lf",smc[row][col].p[smc_Ca_i]);
fprintf(vi,"%2.10lf",smc[row][col].p[smc_V_m]);
fprintf(Ii,"%2.10lf",smc[row][col].p[smc_IP3]);
if (col<(grid.n_smc-1)){
fprintf(ci,"\t");
fprintf(vi,"\t");
fprintf(Ii,"\t");
}
}
if (row<(grid.layers_smc-1)){
fprintf(ci,"\t");
fprintf(vi,"\t");
fprintf(Ii,"\t");
}
else if (row==(grid.layers_smc-1)){
fprintf(ci,"\n");
fprintf(vi,"\n");
fprintf(Ii,"\n");
}
}
for (int row=0; row<grid.layers_ec;row++)
{
for (int col=0; col<grid.n_ec; col++)
{
fprintf(cj,"%2.10lf\t",ec[row][col].q[ec_Ca]);
fprintf(sj,"%2.10lf\t",ec[row][col].q[ec_SR]);
fprintf(vj,"%2.10lf\t",ec[row][col].q[ec_Vm]);
fprintf(Ij,"%2.10lf\t",ec[row][col].q[ec_IP3]);
}
if (row<(grid.layers_ec-1)){
fprintf(cj,"\t");
fprintf(sj,"\t");
fprintf(vj,"\t");
fprintf(Ij,"\t");
}
else if (row==(grid.layers_ec-1)){
fprintf(cj,"\n");
fprintf(sj,"\n");
fprintf(vj,"\n");
fprintf(Ij,"\n");
}
}
fflush(time);fflush(Task_info);fflush(errPT);
//fflush(MPI_stat);
fflush(ci);fflush(cj);
fflush(sj);
fflush(vi);fflush(vj);
fflush(Ii);fflush(Ij);
fflush(cpv_i);
fflush(cpc_i);fflush(cpi_i);
fflush(cpv_j);fflush(cpc_j);
fflush(cpi_j);
}
tend += interval;
rksuite.reset(tend);
} //end while()
/****////////*******////////****************
/************************************************************************/
/*********************AFTER 10.00 seconds*************************/
/************************************************************************/
tend = tnow + interval;
rksuite.setup(total, tnow, y, tend, TOL, thres, method, "CT", false, 1e-5, false );
while (tnow <=100.00) {
// the ct() function does not guarantee to advance all the
// way to the stop time. Keep stepping until it does.
do {
computeDerivatives( tnow, y, yp );
rksuite.ct(computeDerivatives, tnow, y, yp, cflag );
if (cflag >= 5) {
printf("RKSUITE error %d\n", cflag );
MPI_Abort(MPI_COMM_WORLD,1000);
return false;
break;
}
} while (tnow < tend);
iteration++;
/************************************************/
/* Communication Block */
/************************************************/
update_async(myRank,tasks);
MPI_Barrier(MPI_COMM_WORLD);
if (iteration==5e3){
fprintf(Task_info,"JPLC (at 10<t<100 seconds) in axial direction per EC\n");
for (int p=0; p<grid.n_ec; p++)
fprintf(Task_info,"[%d]\t%lf\n",p,ec[0][p].JPLC);
}
if (iteration % file_write_per_unit_time==0)
{
fprintf(time,"%lf\n",tnow);
for (int row=0; row<grid.layers_smc;row++)
{
for (int col=0; col<grid.n_smc; col++)
{
fprintf(ci,"%2.10lf",smc[row][col].p[smc_Ca_i]);
fprintf(vi,"%2.10lf",smc[row][col].p[smc_V_m]);
fprintf(Ii,"%2.10lf",smc[row][col].p[smc_IP3]);
if (col<(grid.n_smc-1)){
fprintf(ci,"\t");
fprintf(vi,"\t");
fprintf(Ii,"\t");
}
}
if (row<(grid.layers_smc-1)){
fprintf(ci,"\t");
fprintf(vi,"\t");
fprintf(Ii,"\t");
}
else if (row==(grid.layers_smc-1)){
fprintf(ci,"\n");
fprintf(vi,"\n");
fprintf(Ii,"\n");
}
}
for (int row=0; row<grid.layers_ec;row++)
{
for (int col=0; col<grid.n_ec; col++)
{
fprintf(cj,"%2.10lf\t",ec[row][col].q[ec_Ca]);
fprintf(sj,"%2.10lf\t",ec[row][col].q[ec_SR]);
fprintf(vj,"%2.10lf\t",ec[row][col].q[ec_Vm]);
fprintf(Ij,"%2.10lf\t",ec[row][col].q[ec_IP3]);
}
if (row<(grid.layers_ec-1)){
fprintf(cj,"\t");
fprintf(sj,"\t");
fprintf(vj,"\t");
fprintf(Ij,"\t");
}
else if (row==(grid.layers_ec-1)){
fprintf(cj,"\n");
fprintf(sj,"\n");
fprintf(vj,"\n");
fprintf(Ij,"\n");
}
}
fflush(time);fflush(Task_info);fflush(errPT);
//fflush(MPI_stat);
fflush(ci);fflush(cj);
fflush(sj);
fflush(vi);fflush(vj);
fflush(Ii);fflush(Ij);
fflush(cpv_i);
fflush(cpc_i);fflush(cpi_i);
fflush(cpv_j);fflush(cpc_j);
fflush(cpi_j);
}
tend += interval;
rksuite.reset(tend);
} //end while()
/****////////*******////////****************
/************************************************************************/
/*** After 100 seconds ****/
/************************************************************************/
tend = tnow+interval;
rksuite.setup(total, tnow, y, tend, TOL, thres, method, "CT", false, 1e-6, false );
while (tnow <=tfinal) {
// the ct() function does not guarantee to advance all the
// way to the stop time. Keep stepping until it does.
do {
computeDerivatives( tnow, y, yp );
rksuite.ct(computeDerivatives, tnow, y, yp, cflag );
if (cflag >= 5) {
printf("RKSUITE error %d\n", cflag );
MPI_Abort(MPI_COMM_WORLD,1000);
return false;
break;
}
} while (tnow < tend);
iteration++;
/************************************************/
/* Communication Block */
/************************************************/
update_async(myRank,tasks);
MPI_Barrier(MPI_COMM_WORLD);
if (iteration==1e5)
{
fprintf(Task_info,"JPLC (at t>100 seconds) in axial direction per EC\n");
for (int p=0; p<grid.n_ec; p++)
fprintf(Task_info,"[%d]\t%lf\n",p,ec[0][p].JPLC);
}
if (iteration % file_write_per_unit_time==0)
{
fprintf(time,"%lf\n",tnow);
for (int row=0; row<grid.layers_smc;row++)
{
for (int col=0; col<grid.n_smc; col++)
{
fprintf(ci,"%2.10lf",smc[row][col].p[smc_Ca_i]);
fprintf(vi,"%2.10lf",smc[row][col].p[smc_V_m]);
fprintf(Ii,"%2.10lf",smc[row][col].p[smc_IP3]);
if (col<(grid.n_smc-1)){
fprintf(ci,"\t");
fprintf(vi,"\t");
fprintf(Ii,"\t");
}
}
if (row<(grid.layers_smc-1)){
fprintf(ci,"\t");
fprintf(vi,"\t");
fprintf(Ii,"\t");
}
else if (row==(grid.layers_smc-1)){
fprintf(ci,"\n");
fprintf(vi,"\n");
fprintf(Ii,"\n");
}
}
for (int row=0; row<grid.layers_ec;row++)
{
for (int col=0; col<grid.n_ec; col++)
{
fprintf(cj,"%2.10lf\t",ec[row][col].q[ec_Ca]);
fprintf(sj,"%2.10lf\t",ec[row][col].q[ec_SR]);
fprintf(vj,"%2.10lf\t",ec[row][col].q[ec_Vm]);
fprintf(Ij,"%2.10lf\t",ec[row][col].q[ec_IP3]);
}
if (row<(grid.layers_ec-1)){
fprintf(cj,"\t");
fprintf(sj,"\t");
fprintf(vj,"\t");
fprintf(Ij,"\t");
}
else if (row==(grid.layers_ec-1)){
fprintf(cj,"\n");
fprintf(sj,"\n");
fprintf(vj,"\n");
fprintf(Ij,"\n");
}
}
fflush(time);fflush(Task_info);fflush(errPT);
//fflush(MPI_stat);
fflush(ci);fflush(cj);
fflush(sj);
fflush(vi);fflush(vj);
fflush(Ii);fflush(Ij);
fflush(cpv_i);
fflush(cpc_i);fflush(cpi_i);
fflush(cpv_j);fflush(cpc_j);
fflush(cpi_j);
}
tend += interval;
rksuite.reset(tend);
} //end while()
/****////////*******////////****************
/************************************************************************/
double t2 = MPI_Wtime();
//printf("[%d] : Elapsed time = %lf\nMPI size=%d\ttfinal=%lf\tStep size=%lf\tcount=%d\n",myRank,(t2-t1),tasks,tfinal,interval,cnt2);
fprintf(Task_info,"Elapsed time = %lf\ntfinal=%lf\nStep size=%lf\n",(t2-t1),tasks,tfinal,interval);
MPI_Barrier(MPI_COMM_WORLD);
if (myRank==0)
printf("\nEND OF PROGRAM\n");
free(smc);free(smc_base);
free(ec);free(ec_base);
free(nn.sbuf_left);
free(nn.sbuf_right);
free(nn.rbuf_left);
free(nn.rbuf_right);
free(nn.left_smc_c);
free(nn.right_smc_c);
free(nn.left_ec_c);
free(nn.right_ec_c);
free(nn.left_smc_v);
free(nn.right_smc_v);
free(nn.left_ec_v);
free(nn.right_ec_v);
free(nn.left_smc_I);
free(nn.right_smc_I);
free(nn.left_ec_I);
free(nn.right_ec_I);
free(y);
free(yp);
free(ymax);
fclose(time);fclose(Task_info);
fclose(errPT);
fclose(ci);fclose(cj);
fclose(sj);
fclose(vi);fclose(vj);
fclose(Ii);fclose(Ij);
fclose(cpv_i);
fclose(cpc_i);fclose(cpi_i);
fclose(cpv_j);fclose(cpc_j);
fclose(cpi_j);
MPI_Finalize();
}
static void alarmhandler(int a)
{
update_async();
signal(SIGALRM, alarmhandler);
}
void tl_set_multihandler(tl_timer * timer, void (*handler) (int))
{
timer->multihandler = handler;
if (timer->group == asyncgroup)
update_async();
}
void tl_set_handler(tl_timer * timer, void (*handler) (void))
{
timer->handler = handler;
if (timer->group == asyncgroup)
update_async();
}