int read_mesh(const std::string &exo_file,
Problem_Description* problem,
Mesh_Description<INT>* mesh,
Weight_Description<INT>* weight
)
{
float version, *xptr, *yptr, *zptr;
char elem_type[MAX_STR_LENGTH+1];
E_Type blk_elem_type;
/*---------------------------Execution Begins--------------------------------*/
/* Open the ExodusII file */
int exoid, cpu_ws=0, io_ws=0;
int mode = EX_READ | problem->int64api;
if((exoid=ex_open(exo_file.c_str(), mode, &cpu_ws, &io_ws, &version)) < 0)
{
Gen_Error(0, "fatal: unable to open ExodusII mesh file");
return 0;
}
/* Read the coordinates, if desired */
xptr = yptr = zptr = NULL;
if(problem->read_coords == ELB_TRUE)
{
switch(mesh->num_dims)
{
case 3:
zptr = (mesh->coords)+2*(mesh->num_nodes);
/* FALLTHRU */
case 2:
yptr = (mesh->coords)+(mesh->num_nodes);
/* FALLTHRU */
case 1:
xptr = mesh->coords;
}
if(ex_get_coord(exoid, xptr, yptr, zptr) < 0)
{
Gen_Error(0, "fatal: unable to read coordinate values for mesh");
return 0;
}
} /* End "if(problem->read_coords == ELB_TRUE)" */
/* Read the element block IDs */
std::vector<INT> el_blk_ids(mesh->num_el_blks);
std::vector<INT> el_blk_cnts(mesh->num_el_blks);
if(ex_get_elem_blk_ids(exoid, &el_blk_ids[0]) < 0)
{
Gen_Error(0, "fatal: unable to read element block IDs");
return 0;
}
/* Read the element connectivity */
size_t gelem_cnt=0;
for(size_t cnt=0; cnt < mesh->num_el_blks; cnt++) {
INT nodes_per_elem, num_attr;
if(ex_get_elem_block(exoid, el_blk_ids[cnt], elem_type,
&(el_blk_cnts[cnt]), &nodes_per_elem,
&num_attr) < 0)
{
Gen_Error(0, "fatal: unable to read element block");
return 0;
}
blk_elem_type = get_elem_type(elem_type, nodes_per_elem, mesh->num_dims);
INT *blk_connect = (INT*)malloc(sizeof(INT)*el_blk_cnts[cnt]*nodes_per_elem);
if(!blk_connect)
{
Gen_Error(0, "fatal: insufficient memory");
return 0;
}
/* Get the connectivity for this element block */
if(ex_get_elem_conn(exoid, el_blk_ids[cnt], blk_connect) < 0)
{
Gen_Error(0, "fatal: failed to get element connectivity");
return 0;
}
/* find out if this element block is weighted */
int wgt = -1;
if (weight->type & EL_BLK)
wgt = in_list(el_blk_ids[cnt], weight->elemblk);
/* Fill the 2D global connectivity array */
if (((problem->type == ELEMENTAL) && (weight->type & EL_BLK)) ||
((problem->type == NODAL) && (weight->type & EL_BLK))) {
for(int64_t cnt2=0; cnt2 < el_blk_cnts[cnt]; cnt2++) {
mesh->elem_type[gelem_cnt] = blk_elem_type;
/* while going through the blocks, take care of the weighting */
if ((problem->type == ELEMENTAL) && (weight->type & EL_BLK)) {
/* is this block weighted */
if (wgt >= 0) {
/* check if there is a read value */
if (weight->vertices[gelem_cnt] >= 1) {
/* and if it should be overwritten */
if (weight->ow_read)
weight->vertices[gelem_cnt] = weight->elemblk_wgt[wgt];
}
else
weight->vertices[gelem_cnt] = weight->elemblk_wgt[wgt];
}
else {
/* now check if this weight has been initialized */
if (weight->vertices[gelem_cnt] < 1)
weight->vertices[gelem_cnt] = 1;
}
}
for(int64_t cnt3=0; cnt3 < nodes_per_elem; cnt3++) {
INT node = blk_connect[cnt3 + cnt2*nodes_per_elem] - 1;
assert(node >= 0);
mesh->connect[gelem_cnt][cnt3] = node;
/* deal with the weighting if necessary */
if ((problem->type == NODAL) && (weight->type & EL_BLK)) {
/* is this block weighted */
if (wgt >= 0) {
/* check if I read an exodus file */
if (weight->type & READ_EXO) {
/* check if it can be overwritten */
if (weight->ow_read) {
/* check if it has been overwritten already */
if (weight->ow[node]) {
weight->vertices[node] =
MAX(weight->vertices[node], weight->elemblk_wgt[wgt]);
}
else {
weight->vertices[node] = weight->elemblk_wgt[wgt];
weight->ow[node] = 1; /* read value has been overwritten */
}
}
}
else {
weight->vertices[node] =
MAX(weight->vertices[node], weight->elemblk_wgt[wgt]);
}
}
else {
/* now check if this weight has been initialized */
if (weight->vertices[node] < 1)
weight->vertices[node] = 1;
}
}
}
gelem_cnt++;
}
} else {
// No weights...
for (int64_t cnt2=0; cnt2 < el_blk_cnts[cnt]; cnt2++) {
mesh->elem_type[gelem_cnt] = blk_elem_type;
for (int64_t cnt3=0; cnt3 < nodes_per_elem; cnt3++) {
INT node = blk_connect[cnt2*nodes_per_elem + cnt3] - 1;
assert(node >= 0);
mesh->connect[gelem_cnt][cnt3] = node;
}
gelem_cnt++;
}
}
/* Free up memory */
free(blk_connect);
} /* End "for(cnt=0; cnt < mesh->num_el_blks; cnt++)" */
/* if there is a group designator, then parse it here */
if (problem->groups != NULL) {
if (!parse_groups(&el_blk_ids[0], &el_blk_cnts[0], mesh, problem)) {
Gen_Error(0, "fatal: unable to parse group designator");
ex_close(exoid);
return 0;
}
}
else problem->num_groups = 1; /* there is always one group */
/* Close the ExodusII file */
if(ex_close(exoid) < 0)
Gen_Error(0, "warning: failed to close ExodusII mesh file");
return 1;
} /*---------------------------End read_mesh()-------------------------------*/
int write_vis(std::string &nemI_out_file,
std::string &exoII_inp_file,
Machine_Description* machine,
Problem_Description* prob,
Mesh_Description<INT>* mesh,
LB_Description<INT>* lb)
{
int exid_vis, exid_inp;
char title[MAX_LINE_LENGTH+1];
const char *coord_names[] = {"X", "Y", "Z"};
/*-----------------------------Execution Begins------------------------------*/
/* Generate the file name for the visualization file */
std::string vis_file_name = remove_extension(nemI_out_file);
vis_file_name += "-vis.exoII";
/* Generate the title for the file */
strcpy(title, UTIL_NAME);
strcat(title, " ");
strcat(title, ELB_VERSION);
strcat(title, " load balance visualization file");
/*
* If the vis technique is to be by element block then calculate the
* number of element blocks.
*/
int vis_nelem_blks;
if(prob->type == ELEMENTAL)
vis_nelem_blks = machine->num_procs;
else
vis_nelem_blks = machine->num_procs + 1;
/* Create the ExodusII file */
std::cout << "Outputting load balance visualization file " << vis_file_name.c_str() << "\n";
int cpu_ws = 0;
int io_ws = 0;
int mode = EX_CLOBBER;
if (prob->int64db|prob->int64api) {
mode |= EX_NETCDF4|EX_NOCLASSIC|prob->int64db|prob->int64api;
}
if((exid_vis=ex_create(vis_file_name.c_str(), mode, &cpu_ws, &io_ws)) < 0) {
Gen_Error(0, "fatal: unable to create visualization output file");
return 0;
}
ON_BLOCK_EXIT(ex_close, exid_vis);
/*
* Open the original input ExodusII file, read the values for the
* element blocks and output them to the visualization file.
*/
int icpu_ws=0;
int iio_ws=0;
float vers=0.0;
mode = EX_READ | prob->int64api;
if((exid_inp=ex_open(exoII_inp_file.c_str(), mode, &icpu_ws, &iio_ws, &vers)) < 0) {
Gen_Error(0, "fatal: unable to open input ExodusII file");
return 0;
}
ON_BLOCK_EXIT(ex_close, exid_inp);
char **elem_type = (char**)array_alloc(2, mesh->num_el_blks, MAX_STR_LENGTH+1,
sizeof(char));
if(!elem_type) {
Gen_Error(0, "fatal: insufficient memory");
return 0;
}
ON_BLOCK_EXIT(free, elem_type);
std::vector<INT> el_blk_ids(mesh->num_el_blks);
std::vector<INT> el_cnt_blk(mesh->num_el_blks);
std::vector<INT> node_pel_blk(mesh->num_el_blks);
std::vector<INT> nattr_el_blk(mesh->num_el_blks);
if(ex_get_elem_blk_ids(exid_inp, TOPTR(el_blk_ids)) < 0) {
Gen_Error(0, "fatal: unable to get element block IDs");
return 0;
}
int acc_vis = ELB_TRUE; // Output a different element block per processor
if (prob->vis_out == 2)
acc_vis = ELB_FALSE; // Output a nodal/element variable showing processor
size_t nsize = 0;
/*
* Find out if the mesh consists of mixed elements. If not then
* element blocks will be used to visualize the partitioning. Otherwise
* nodal/element results will be used.
*/
for(size_t ecnt=0; ecnt < mesh->num_el_blks; ecnt++) {
if(ex_get_elem_block(exid_inp, el_blk_ids[ecnt], elem_type[ecnt],
&el_cnt_blk[ecnt], &node_pel_blk[ecnt],
&nattr_el_blk[ecnt]) < 0) {
Gen_Error(0, "fatal: unable to get element block parameters");
return 0;
}
nsize += el_cnt_blk[ecnt]*node_pel_blk[ecnt];
if(strcmp(elem_type[0], elem_type[ecnt]) == 0) {
if(node_pel_blk[0] != node_pel_blk[ecnt])
acc_vis = ELB_FALSE;
}
else
acc_vis = ELB_FALSE;
}
if(acc_vis == ELB_TRUE) {
/* Output the initial information */
if(ex_put_init(exid_vis, title, mesh->num_dims, mesh->num_nodes,
mesh->num_elems, vis_nelem_blks, 0, 0) < 0) {
Gen_Error(0, "fatal: unable to output initial params to vis file");
return 0;
}
/* Output the nodal coordinates */
float *xptr = nullptr;
float *yptr = nullptr;
float *zptr = nullptr;
switch(mesh->num_dims) {
case 3:
zptr = (mesh->coords) + 2*mesh->num_nodes;
/* FALLTHRU */
case 2:
yptr = (mesh->coords) + mesh->num_nodes;
/* FALLTHRU */
case 1:
xptr = mesh->coords;
}
if(ex_put_coord(exid_vis, xptr, yptr, zptr) < 0) {
Gen_Error(0, "fatal: unable to output coords to vis file");
return 0;
}
if(ex_put_coord_names(exid_vis, (char**)coord_names) < 0) {
Gen_Error(0, "fatal: unable to output coordinate names");
return 0;
}
std::vector<INT> elem_block(mesh->num_elems);
std::vector<INT> elem_map(mesh->num_elems);
std::vector<INT> tmp_connect(nsize);
for(size_t ecnt=0; ecnt < mesh->num_elems; ecnt++) {
elem_map[ecnt] = ecnt+1;
if(prob->type == ELEMENTAL)
elem_block[ecnt] = lb->vertex2proc[ecnt];
else {
int proc = lb->vertex2proc[mesh->connect[ecnt][0]];
int nnodes = get_elem_info(NNODES, mesh->elem_type[ecnt]);
elem_block[ecnt] = proc;
for(int ncnt=1; ncnt < nnodes; ncnt++) {
if(lb->vertex2proc[mesh->connect[ecnt][ncnt]] != proc) {
elem_block[ecnt] = machine->num_procs;
break;
}
}
}
}
int ccnt = 0;
std::vector<INT> vis_el_blk_ptr(vis_nelem_blks+1);
for(INT bcnt=0; bcnt < vis_nelem_blks; bcnt++) {
vis_el_blk_ptr[bcnt] = ccnt;
int pos = 0;
int old_pos = 0;
INT* el_ptr = TOPTR(elem_block);
size_t ecnt = mesh->num_elems;
while(pos != -1) {
pos = in_list(bcnt, ecnt, el_ptr);
if(pos != -1) {
old_pos += pos + 1;
ecnt = mesh->num_elems - old_pos;
el_ptr = TOPTR(elem_block) + old_pos;
int nnodes = get_elem_info(NNODES, mesh->elem_type[old_pos-1]);
for(int ncnt=0; ncnt < nnodes; ncnt++)
tmp_connect[ccnt++] = mesh->connect[old_pos-1][ncnt] + 1;
}
}
}
vis_el_blk_ptr[vis_nelem_blks] = ccnt;
/* Output the element map */
if(ex_put_map(exid_vis, TOPTR(elem_map)) < 0) {
Gen_Error(0, "fatal: unable to output element number map");
return 0;
}
/* Output the visualization element blocks */
for(int bcnt=0; bcnt < vis_nelem_blks; bcnt++) {
/*
* Note this assumes all the blocks contain the same type
* element.
*/
int ecnt = (vis_el_blk_ptr[bcnt+1]-vis_el_blk_ptr[bcnt])/node_pel_blk[0];
if(ex_put_elem_block(exid_vis, bcnt+1, elem_type[0],
ecnt, node_pel_blk[0], 0) < 0) {
Gen_Error(0, "fatal: unable to output element block params");
return 0;
}
/* Output the connectivity */
if(ex_put_elem_conn(exid_vis, bcnt+1,
&tmp_connect[vis_el_blk_ptr[bcnt]]) < 0) {
Gen_Error(0, "fatal: unable to output element connectivity");
return 0;
}
}
}
else { /* For nodal/element results visualization of the partioning. */
// Copy the mesh portion to the vis file.
ex_copy(exid_inp, exid_vis);
/* Set up the file for nodal/element results */
float time_val = 0.0;
if(ex_put_time(exid_vis, 1, &time_val) < 0) {
Gen_Error(0, "fatal: unable to output time to vis file");
return 0;
}
const char *var_names[] = {"proc"};
if(prob->type == NODAL) {
/* Allocate memory for the nodal values */
std::vector<float> proc_vals(mesh->num_nodes);
if(ex_put_variable_param(exid_vis, EX_NODAL, 1) < 0) {
Gen_Error(0, "fatal: unable to output var params to vis file");
return 0;
}
if(ex_put_variable_names(exid_vis, EX_NODAL, 1, (char**)var_names) < 0) {
Gen_Error(0, "fatal: unable to output variable name");
return 0;
}
/* Do some problem specific assignment */
for(size_t ncnt=0; ncnt < mesh->num_nodes; ncnt++)
proc_vals[ncnt] = lb->vertex2proc[ncnt];
for(int pcnt=0; pcnt < machine->num_procs; pcnt++) {
for(auto & elem : lb->bor_nodes[pcnt])
proc_vals[elem] = machine->num_procs + 1;
}
/* Output the nodal variables */
if(ex_put_nodal_var(exid_vis, 1, 1, mesh->num_nodes, TOPTR(proc_vals)) < 0) {
Gen_Error(0, "fatal: unable to output nodal variables");
return 0;
}
}
else if(prob->type == ELEMENTAL) {
/* Allocate memory for the element values */
std::vector<float> proc_vals(mesh->num_elems);
if(ex_put_variable_param(exid_vis, EX_ELEM_BLOCK, 1) < 0) {
Gen_Error(0, "fatal: unable to output var params to vis file");
return 0;
}
if(ex_put_variable_names(exid_vis, EX_ELEM_BLOCK, 1, (char**)var_names) < 0) {
Gen_Error(0, "fatal: unable to output variable name");
return 0;
}
/* Do some problem specific assignment */
for(int proc=0; proc < machine->num_procs; proc++) {
for (size_t e = 0; e < lb->int_elems[proc].size(); e++) {
size_t ecnt = lb->int_elems[proc][e];
proc_vals[ecnt] = proc;
}
for (size_t e = 0; e < lb->bor_elems[proc].size(); e++) {
size_t ecnt = lb->bor_elems[proc][e];
proc_vals[ecnt] = proc;
}
}
/* Output the element variables */
size_t offset = 0;
for (size_t i=0; i < mesh->num_el_blks; i++) {
if(ex_put_var(exid_vis, 1, EX_ELEM_BLOCK, 1, el_blk_ids[i],
el_cnt_blk[i], &proc_vals[offset]) < 0) {
Gen_Error(0, "fatal: unable to output nodal variables");
return 0;
}
offset += el_cnt_blk[i];
}
}
}
return 1;
} /*---------------------------End write_vis()-------------------------------*/
int read_mesh_params(const std::string &exo_file,
Problem_Description* problem,
Mesh_Description<INT>* mesh,
Sphere_Info* sphere
)
{
int exoid, cpu_ws=0, io_ws=0;
float version;
char elem_type[MAX_STR_LENGTH+1];
/*---------------------------Execution Begins--------------------------------*/
/* Open the ExodusII geometry file */
int mode = EX_READ | problem->int64api;
if((exoid=ex_open(exo_file.c_str(), mode, &cpu_ws, &io_ws, &version)) < 0)
{
Gen_Error(0, "fatal: unable to open ExodusII file for mesh params");
return 0;
}
/* Get the init info */
ex_init_params exo;
if(ex_get_init_ext(exoid, &exo))
{
Gen_Error(0, "fatal: unable to get init info from ExodusII file");
ex_close(exoid);
return 0;
}
strcpy(mesh->title, exo.title);
mesh->num_dims = exo.num_dim;
mesh->num_nodes = exo.num_nodes;
mesh->num_elems = exo.num_elem;
mesh->num_el_blks = exo.num_elem_blk;
mesh->num_node_sets = exo.num_node_sets;
mesh->num_side_sets = exo.num_side_sets;
/* Get the length of the concatenated node set node list */
if(mesh->num_node_sets > 0)
{
mesh->ns_list_len = ex_inquire_int(exoid, EX_INQ_NS_NODE_LEN);
}
else
mesh->ns_list_len = 0;
/* Allocate and initialize memory for the sphere adjustment */
sphere->adjust = (int*)malloc(sizeof(int)*3*(mesh->num_el_blks));
if(!(sphere->adjust)) {
Gen_Error(0, "fatal: insufficient memory");
ex_close(exoid);
return 0;
}
else {
sphere->begin = sphere->adjust + mesh->num_el_blks;
sphere->end = sphere->begin + mesh->num_el_blks;
for(size_t cnt=0; cnt < mesh->num_el_blks; cnt++) {
sphere->adjust[cnt] = 0;
sphere->begin[cnt] = 0;
sphere->end[cnt] = 0;
}
}
std::vector<INT> el_blk_ids(mesh->num_el_blks);
/* Read the element block IDs */
if(ex_get_elem_blk_ids(exoid, &el_blk_ids[0]) < 0) {
Gen_Error(0, "fatal: unable to get element block IDs");
ex_close(exoid);
return 0;
}
/* Determine the maximum number of nodes per element */
mesh->max_np_elem = 0;
for(size_t cnt=0; cnt < mesh->num_el_blks; cnt++) {
INT num_elems, idum;
INT nodes_in_elem;
if(ex_get_elem_block(exoid, el_blk_ids[cnt], elem_type,
&num_elems, &nodes_in_elem, &idum) < 0)
{
Gen_Error(0, "fatal: unable to get element block");
ex_close(exoid);
return 0;
}
if(cnt == 0)
sphere->end[0] = num_elems;
if(get_elem_type(elem_type, nodes_in_elem, mesh->num_dims) == SPHERE && problem->no_sph != 1) {
sphere->num += num_elems;
sphere->adjust[cnt] = 0;
}
else
sphere->adjust[cnt] = sphere->num;
if(cnt != 0) {
sphere->begin[cnt] = sphere->end[cnt-1];
sphere->end[cnt] = sphere->begin[cnt] + num_elems;
}
mesh->max_np_elem = MAX(mesh->max_np_elem, (size_t)nodes_in_elem);
}
/* Close the ExodusII file */
if(ex_close(exoid) < 0)
Gen_Error(1, "warning: unable to close ExodusII file");
printf("ExodusII mesh information\n");
if(strlen(mesh->title) > 0)
printf("\ttitle: %s\n", mesh->title);
printf("\tgeometry dimension: "ST_ZU"\n", mesh->num_dims);
printf("\tnumber of nodes: "ST_ZU"\tnumber of elements: "ST_ZU"\n", mesh->num_nodes,
mesh->num_elems);
printf("\tnumber of element blocks: "ST_ZU"\n", mesh->num_el_blks);
printf("\tnumber of node sets: "ST_ZU"\tnumber of side sets: "ST_ZU"\n",
mesh->num_node_sets, mesh->num_side_sets);
return 1;
} /*--------------------------End read_mesh_params()-------------------------*/
