ErikFabrizzi/NuSiF-Solver
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First draft. Compiles. Untested.

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This commit is contained in:
Jan Eitzinger
2023-02-06 20:09:11 +01:00
parent 394e4643ec
commit f7e04a19ac
4 changed files with 147 additions and 323 deletions
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202
BasicSolver/3D-mpi-io/src/comm.c
View File

@@ -113,60 +113,6 @@ static void setupCommunication(Comm* c, Direction direction, int layer)
}
}
static void assembleResult(Comm* c,
double* src,
double* dst,
int imaxLocal[],
int jmaxLocal[],
int kmaxLocal[],
int offset[],
int kmax,
int jmax,
int imax)
{
int numRequests = 1;
if (c->rank == 0) {
numRequests = c->size + 1;
}
MPI_Request requests[numRequests];
/* all ranks send their interpolated bulk array */
MPI_Isend(src,
c->imaxLocal * c->jmaxLocal * c->kmaxLocal,
MPI_DOUBLE,
0,
0,
c->comm,
&requests[0]);
/* rank 0 assembles the subdomains */
if (c->rank == 0) {
for (int i = 0; i < c->size; i++) {
MPI_Datatype domainType;
int oldSizes[NDIMS] = { kmax, jmax, imax };
int newSizes[NDIMS] = { kmaxLocal[i], jmaxLocal[i], imaxLocal[i] };
int starts[NDIMS] = { offset[i * NDIMS + KDIM],
offset[i * NDIMS + JDIM],
offset[i * NDIMS + IDIM] };
MPI_Type_create_subarray(NDIMS,
oldSizes,
newSizes,
starts,
MPI_ORDER_C,
MPI_DOUBLE,
&domainType);
MPI_Type_commit(&domainType);
MPI_Irecv(dst, 1, domainType, i, 0, c->comm, &requests[i + 1]);
MPI_Type_free(&domainType);
}
}
MPI_Waitall(numRequests, requests, MPI_STATUSES_IGNORE);
}
static int sum(int* sizes, int position)
{
int sum = 0;
@@ -284,148 +230,26 @@ void commShift(Comm* c, double* f, double* g, double* h)
MPI_Waitall(6, requests, MPI_STATUSES_IGNORE);
}
#define G(v, i, j, k) \
v[(k) * (imaxLocal + 2) * (jmaxLocal + 2) + (j) * (imaxLocal + 2) + (i)]
void commCollectResult(Comm* c,
double* ug,
double* vg,
double* wg,
double* pg,
double* u,
double* v,
double* w,
double* p,
int kmax,
int jmax,
int imax)
void commGetOffsets(Comm* c, int offsets[], int kmax, int jmax, int imax)
{
int imaxLocal = c->imaxLocal;
int jmaxLocal = c->jmaxLocal;
int kmaxLocal = c->kmaxLocal;
int sum = 0;
int offset[c->size * NDIMS];
int imaxLocalAll[c->size];
int jmaxLocalAll[c->size];
int kmaxLocalAll[c->size];
MPI_Gather(&imaxLocal, 1, MPI_INT, imaxLocalAll, 1, MPI_INT, 0, MPI_COMM_WORLD);
MPI_Gather(&jmaxLocal, 1, MPI_INT, jmaxLocalAll, 1, MPI_INT, 0, MPI_COMM_WORLD);
MPI_Gather(&kmaxLocal, 1, MPI_INT, kmaxLocalAll, 1, MPI_INT, 0, MPI_COMM_WORLD);
if (c->rank == 0) {
for (int i = 0; i < c->size; i++) {
int coords[NCORDS];
MPI_Cart_coords(c->comm, i, NDIMS, coords);
offset[i * NDIMS + IDIM] = sum(imaxLocalAll, coords[ICORD]);
offset[i * NDIMS + JDIM] = sum(jmaxLocalAll, coords[JCORD]);
offset[i * NDIMS + KDIM] = sum(kmaxLocalAll, coords[KCORD]);
printf("Rank: %d, Coords(k,j,i): %d %d %d, Size(k,j,i): %d %d %d, "
"Offset(k,j,i): %d %d %d\n",
i,
coords[KCORD],
coords[JCORD],
coords[ICORD],
kmaxLocalAll[i],
jmaxLocalAll[i],
imaxLocalAll[i],
offset[i * NDIMS + KDIM],
offset[i * NDIMS + JDIM],
offset[i * NDIMS + IDIM]);
}
for (int i = 0; i < c->coords[ICORD]; i++) {
sum += sizeOfRank(i, c->dims[ICORD], imax);
}
offsets[IDIM] = sum;
sum = 0;
size_t bytesize = imaxLocal * jmaxLocal * kmaxLocal * sizeof(double);
double* tmp = allocate(64, bytesize);
int idx = 0;
/* collect P */
for (int k = 1; k < kmaxLocal + 1; k++) {
for (int j = 1; j < jmaxLocal + 1; j++) {
for (int i = 1; i < imaxLocal + 1; i++) {
tmp[idx++] = G(p, i, j, k);
}
}
for (int i = 0; i < c->coords[JCORD]; i++) {
sum += sizeOfRank(i, c->dims[JCORD], jmax);
}
offsets[JDIM] = sum;
sum = 0;
assembleResult(c,
tmp,
pg,
imaxLocalAll,
jmaxLocalAll,
kmaxLocalAll,
offset,
kmax,
jmax,
imax);
/* collect U */
idx = 0;
for (int k = 1; k < kmaxLocal + 1; k++) {
for (int j = 1; j < jmaxLocal + 1; j++) {
for (int i = 1; i < imaxLocal + 1; i++) {
tmp[idx++] = (G(u, i, j, k) + G(u, i - 1, j, k)) / 2.0;
}
}
for (int i = 0; i < c->coords[KCORD]; i++) {
sum += sizeOfRank(i, c->dims[KCORD], kmax);
}
assembleResult(c,
tmp,
ug,
imaxLocalAll,
jmaxLocalAll,
kmaxLocalAll,
offset,
kmax,
jmax,
imax);
/* collect V */
idx = 0;
for (int k = 1; k < kmaxLocal + 1; k++) {
for (int j = 1; j < jmaxLocal + 1; j++) {
for (int i = 1; i < imaxLocal + 1; i++) {
tmp[idx++] = (G(v, i, j, k) + G(v, i, j - 1, k)) / 2.0;
}
}
}
assembleResult(c,
tmp,
vg,
imaxLocalAll,
jmaxLocalAll,
kmaxLocalAll,
offset,
kmax,
jmax,
imax);
/* collect W */
idx = 0;
for (int k = 1; k < kmaxLocal + 1; k++) {
for (int j = 1; j < jmaxLocal + 1; j++) {
for (int i = 1; i < imaxLocal + 1; i++) {
tmp[idx++] = (G(w, i, j, k) + G(w, i, j, k - 1)) / 2.0;
}
}
}
assembleResult(c,
tmp,
wg,
imaxLocalAll,
jmaxLocalAll,
kmaxLocalAll,
offset,
kmax,
jmax,
imax);
free(tmp);
offsets[KDIM] = sum;
}
void commPrintConfig(Comm* c)

13
BasicSolver/3D-mpi-io/src/comm.h
View File

@@ -40,18 +40,7 @@ extern void commExchange(Comm*, double*);
extern void commShift(Comm* c, double* f, double* g, double* h);
extern void commReduction(double* v, int op);
extern int commIsBoundary(Comm* c, Direction direction);
extern void commCollectResult(Comm* c,
double* ug,
double* vg,
double* wg,
double* pg,
double* u,
double* v,
double* w,
double* p,
int kmax,
int jmax,
int imax);
extern void commGetOffsets(Comm* c, int offsets[], int kmax, int jmax, int imax);
static inline int commIsMaster(Comm* c) { return c->rank == 0; }
#endif // __COMM_H_

33
BasicSolver/3D-mpi-io/src/main.c
View File

@@ -76,39 +76,10 @@ int main(int argc, char** argv)
printf("Solution took %.2fs\n", timeStop - timeStart);
}
// testInit(&solver);
// commExchange(&solver.comm, solver.p);
// testPrintHalo(&solver, solver.p);
double *pg, *ug, *vg, *wg;
if (commIsMaster(&solver.comm)) {
size_t bytesize = solver.grid.imax * solver.grid.jmax * solver.grid.kmax *
sizeof(double);
pg = allocate(64, bytesize);
ug = allocate(64, bytesize);
vg = allocate(64, bytesize);
wg = allocate(64, bytesize);
}
commCollectResult(&solver.comm,
ug,
vg,
wg,
pg,
solver.u,
solver.v,
solver.w,
solver.p,
solver.grid.kmax,
solver.grid.jmax,
solver.grid.imax);
VtkOptions opts = { .grid = solver.grid, .comm = solver.comm };
vtkOpen(&opts, solver.problem);
vtkScalar(&opts, "pressure", pg);
vtkVector(&opts, "velocity", (VtkVector) { ug, vg, wg });
vtkScalar(&opts, "pressure", solver.p);
vtkVector(&opts, "velocity", (VtkVector) { solver.u, solver.v, solver.w });
vtkClose(&opts);
commFree(&solver.comm);

222
BasicSolver/3D-mpi-io/src/vtkWriter.c
View File

@@ -4,29 +4,15 @@
* Use of this source code is governed by a MIT style
* license that can be found in the LICENSE file.
*/
#include <mpi.h>
#include <stdbool.h>
#include <stdio.h>
#include <stdlib.h>
#include <string.h>
#include "mpi.h"
#include "allocate.h"
#include "comm.h"
#include "vtkWriter.h"
#define G(v, i, j, k) v[(k)*imax * jmax + (j)*imax + (i)]
static float floatSwap(float f)
{
union {
float f;
char b[4];
} dat1, dat2;
dat1.f = f;
dat2.b[0] = dat1.b[3];
dat2.b[1] = dat1.b[2];
dat2.b[2] = dat1.b[1];
dat2.b[3] = dat1.b[0];
return dat2.f;
}
static void writeHeader(VtkOptions* o)
{
@@ -54,8 +40,16 @@ static void writeHeader(VtkOptions* o)
cursor += sprintf(cursor,
"POINT_DATA %d\n",
o->grid.imax * o->grid.jmax * o->grid.kmax);
if (commIsMaster(&o->comm)) {
MPI_File_write_at(o->fh, 0, header, strlen(header), MPI_CHAR, MPI_STATUS_IGNORE);
}
o->disp = strlen(header);
free(header);
}
// TODO Check inputs for length
void vtkOpen(VtkOptions* o, char* problem)
{
char filename[50];
@@ -67,98 +61,144 @@ void vtkOpen(VtkOptions* o, char* problem)
MPI_INFO_NULL,
&o->fh);
if (commIsMaster(&o->comm)) printf("Writing VTK output for %s\n", problem);
if (commIsMaster(&o->comm)) {
printf("Writing VTK output for %s\n", problem);
}
writeHeader(o);
}
static void writeScalar(VtkOptions* o, double* s)
static void resetFileview(VtkOptions* o)
{
int imax = o->grid.imax;
int jmax = o->grid.jmax;
int kmax = o->grid.kmax;
for (int k = 0; k < kmax; k++) {
for (int j = 0; j < jmax; j++) {
for (int i = 0; i < imax; i++) {
if (o->fmt == ASCII) {
fprintf(o->fh, "%f\n", G(s, i, j, k));
} else if (o->fmt == BINARY) {
fwrite((float[1]) { floatSwap(G(s, i, j, k)) },
sizeof(float),
1,
o->fh);
}
}
}
}
if (o->fmt == BINARY) fprintf(o->fh, "\n");
}
static bool isInitialized(FILE* ptr)
{
if (ptr == NULL) {
printf("vtkWriter not initialize! Call vtkOpen first!\n");
return false;
}
return true;
// reset fileview for output of string header
MPI_Offset disp;
MPI_File_get_size(o->fh, &disp);
MPI_File_set_view(o->fh, disp, MPI_CHAR, MPI_CHAR, "native", MPI_INFO_NULL);
}
void vtkScalar(VtkOptions* o, char* name, double* s)
{
resetFileview(o);
if (commIsMaster(&o->comm)) printf("Register scalar %s\n", name);
const size_t MAX_HEADER = 100;
if (o->mode == UNIX) {
if (commIsMaster(&o->comm)) {
if (!isInitialized(o->fh)) return;
fprintf(o->fh, "SCALARS %s float 1\n", name);
fprintf(o->fh, "LOOKUP_TABLE default\n");
writeScalar(o, s);
}
} else if (o->mode == MPI) {
char* header = (char*)malloc(MAX_HEADER);
char* cursor = header;
cursor += sprintf(cursor, "SCALARS %s float 1\n", name);
cursor += sprintf(cursor, "LOOKUP_TABLE default\n");
if (commIsMaster(&o->comm)) {
MPI_File_write(o->fh, header, strlen(header), MPI_CHAR, MPI_STATUS_IGNORE);
}
free(header);
int offsets[NDIMS];
commGetOffsets(&o->comm, offsets, o->grid.imax, o->grid.jmax, o->grid.kmax);
// set global view in file
MPI_Offset disp;
MPI_Datatype fileViewType;
MPI_File_get_size(o->fh, &disp);
MPI_Type_create_subarray(NDIMS,
(int[NDIMS]) { o->grid.kmax, o->grid.jmax, o->grid.imax },
(int[NDIMS]) { o->comm.kmaxLocal, o->comm.jmaxLocal, o->comm.imaxLocal },
offsets,
MPI_ORDER_C,
MPI_DOUBLE,
&fileViewType);
MPI_Type_commit(&fileViewType);
MPI_File_set_view(o->fh, disp, MPI_DOUBLE, fileViewType, "external32", MPI_INFO_NULL);
// create local bulk type
MPI_Datatype bulkType;
MPI_Type_create_subarray(NDIMS,
(int[NDIMS]) { o->comm.kmaxLocal + 2,
o->comm.jmaxLocal + 2,
o->comm.imaxLocal + 2 }, // oldsizes
(int[NDIMS]) { o->comm.kmaxLocal,
o->comm.jmaxLocal,
o->comm.imaxLocal }, // newsizes
(int[NDIMS]) { 1, 1, 1 }, // offsets
MPI_ORDER_C,
MPI_DOUBLE,
&bulkType);
MPI_Type_commit(&bulkType);
MPI_File_write(o->fh, s, 1, bulkType, MPI_STATUS_IGNORE);
MPI_Type_free(&bulkType);
MPI_Type_free(&fileViewType);
// Binary segment must be terminated with newline character
resetFileview(o);
if (commIsMaster(&o->comm)) {
MPI_File_write(o->fh, "\n", 1, MPI_CHAR, MPI_STATUS_IGNORE);
}
}
static void writeVector(VtkOptions* o, VtkVector vec)
{
int imax = o->grid.imax;
int jmax = o->grid.jmax;
int kmax = o->grid.kmax;
for (int k = 0; k < kmax; k++) {
for (int j = 0; j < jmax; j++) {
for (int i = 0; i < imax; i++) {
if (o->fmt == ASCII) {
fprintf(o->fh,
"%f %f %f\n",
G(vec.u, i, j, k),
G(vec.v, i, j, k),
G(vec.w, i, j, k));
} else if (o->fmt == BINARY) {
fwrite((float[3]) { floatSwap(G(vec.u, i, j, k)),
floatSwap(G(vec.v, i, j, k)),
floatSwap(G(vec.w, i, j, k)) },
sizeof(float),
3,
o->fh);
}
}
}
}
if (o->fmt == BINARY) fprintf(o->fh, "\n");
}
#define G(v, i, j, k) \
v[(k) * (imaxLocal + 2) * (jmaxLocal + 2) + (j) * (imaxLocal + 2) + (i)]
void vtkVector(VtkOptions* o, char* name, VtkVector vec)
{
if (commIsMaster(&o->comm)) printf("Register vector %s\n", name);
int imaxLocal = o->comm.imaxLocal;
int jmaxLocal = o->comm.jmaxLocal;
int kmaxLocal = o->comm.kmaxLocal;
if (o->mode == UNIX) {
if (commIsMaster(&o->comm)) {
if (!isInitialized(o->fh)) return;
fprintf(o->fh, "VECTORS %s float\n", name);
writeVector(o, vec);
if (commIsMaster(&o->comm)) printf("Register vector %s\n", name);
const size_t MAX_HEADER = 100;
char* header = (char*)malloc(MAX_HEADER);
sprintf(header, "VECTORS %s float\n", name);
resetFileview(o);
if (commIsMaster(&o->comm)) {
MPI_File_write(o->fh, header, strlen(header), MPI_CHAR, MPI_STATUS_IGNORE);
}
int offsets[NDIMS];
commGetOffsets(&o->comm, offsets, o->grid.imax, o->grid.jmax, o->grid.kmax);
// set global view in file
MPI_Offset disp;
MPI_Datatype fileViewType;
MPI_File_get_size(o->fh, &disp);
MPI_Type_create_subarray(NDIMS + 1,
(int[NDIMS + 1]) { o->grid.kmax, o->grid.jmax, o->grid.imax, NDIMS },
(int[NDIMS + 1]) { kmaxLocal, jmaxLocal, imaxLocal, NDIMS },
offsets,
MPI_ORDER_C,
MPI_DOUBLE,
&fileViewType);
MPI_Type_commit(&fileViewType);
MPI_File_set_view(o->fh, disp, MPI_DOUBLE, fileViewType, "external32", MPI_INFO_NULL);
size_t cnt = imaxLocal * jmaxLocal * kmaxLocal * NDIMS;
double* tmp = allocate(64, cnt * sizeof(double));
int idx = 0;
for (int k = 1; k < kmaxLocal + 1; k++) {
for (int j = 1; j < jmaxLocal + 1; j++) {
for (int i = 1; i < imaxLocal + 1; i++) {
tmp[idx++] = (G(vec.u, i, j, k) + G(vec.u, i - 1, j, k)) / 2.0;
tmp[idx++] = (G(vec.v, i, j, k) + G(vec.v, i, j - 1, k)) / 2.0;
tmp[idx++] = (G(vec.w, i, j, k) + G(vec.w, i, j, k - 1)) / 2.0;
}
}
} else if (o->mode == MPI) {
}
MPI_File_write(o->fh, tmp, cnt, MPI_DOUBLE, MPI_STATUS_IGNORE);
MPI_Type_free(&fileViewType);
// Binary segment must be terminated with newline character
resetFileview(o);
if (commIsMaster(&o->comm)) {
MPI_File_write(o->fh, "\n", 1, MPI_CHAR, MPI_STATUS_IGNORE);
}
}
void vtkClose(VtkOptions* o) { MPI_File_close(o->fh); }
void vtkClose(VtkOptions* o) { MPI_File_close(&o->fh); }