147c6ae99SBarry Smith 247c6ae99SBarry Smith /* 3aa219208SBarry Smith Plots vectors obtained with DMDACreate2d() 447c6ae99SBarry Smith */ 547c6ae99SBarry Smith 6af0996ceSBarry Smith #include <petsc/private/dmdaimpl.h> /*I "petscdmda.h" I*/ 78135c375SStefano Zampini #include <petsc/private/glvisvecimpl.h> 82d95be3dSVaclav Hapla #include <petsc/private/viewerhdf5impl.h> 99804daf3SBarry Smith #include <petscdraw.h> 1047c6ae99SBarry Smith 1147c6ae99SBarry Smith /* 1247c6ae99SBarry Smith The data that is passed into the graphics callback 1347c6ae99SBarry Smith */ 1447c6ae99SBarry Smith typedef struct { 15e5ab1681SLisandro Dalcin PetscMPIInt rank; 16e5ab1681SLisandro Dalcin PetscInt m, n, dof, k; 17e5ab1681SLisandro Dalcin PetscReal xmin, xmax, ymin, ymax, min, max; 185edff71fSBarry Smith const PetscScalar *xy, *v; 197fe7c8feSLisandro Dalcin PetscBool showaxis, showgrid; 20109c9344SBarry Smith const char *name0, *name1; 2147c6ae99SBarry Smith } ZoomCtx; 2247c6ae99SBarry Smith 2347c6ae99SBarry Smith /* 2447c6ae99SBarry Smith This does the drawing for one particular field 2547c6ae99SBarry Smith in one particular set of coordinates. It is a callback 2647c6ae99SBarry Smith called from PetscDrawZoom() 2747c6ae99SBarry Smith */ 289371c9d4SSatish Balay PetscErrorCode VecView_MPI_Draw_DA2d_Zoom(PetscDraw draw, void *ctx) { 2947c6ae99SBarry Smith ZoomCtx *zctx = (ZoomCtx *)ctx; 30e5ab1681SLisandro Dalcin PetscInt m, n, i, j, k, dof, id, c1, c2, c3, c4; 31e5ab1681SLisandro Dalcin PetscReal min, max, x1, x2, x3, x4, y_1, y2, y3, y4; 32e5ab1681SLisandro Dalcin const PetscScalar *xy, *v; 3347c6ae99SBarry Smith 3447c6ae99SBarry Smith PetscFunctionBegin; 3547c6ae99SBarry Smith m = zctx->m; 3647c6ae99SBarry Smith n = zctx->n; 37e5ab1681SLisandro Dalcin dof = zctx->dof; 3847c6ae99SBarry Smith k = zctx->k; 3947c6ae99SBarry Smith xy = zctx->xy; 40e5ab1681SLisandro Dalcin v = zctx->v; 4147c6ae99SBarry Smith min = zctx->min; 42f3f0eb19SBarry Smith max = zctx->max; 4347c6ae99SBarry Smith 4447c6ae99SBarry Smith /* PetscDraw the contour plot patch */ 45d0609cedSBarry Smith PetscDrawCollectiveBegin(draw); 4647c6ae99SBarry Smith for (j = 0; j < n - 1; j++) { 4747c6ae99SBarry Smith for (i = 0; i < m - 1; i++) { 480e4fe250SBarry Smith id = i + j * m; 490e4fe250SBarry Smith x1 = PetscRealPart(xy[2 * id]); 500e4fe250SBarry Smith y_1 = PetscRealPart(xy[2 * id + 1]); 51e5ab1681SLisandro Dalcin c1 = PetscDrawRealToColor(PetscRealPart(v[k + dof * id]), min, max); 520e4fe250SBarry Smith 530e4fe250SBarry Smith id = i + j * m + 1; 540e4fe250SBarry Smith x2 = PetscRealPart(xy[2 * id]); 55a39a4c7dSLisandro Dalcin y2 = PetscRealPart(xy[2 * id + 1]); 56e5ab1681SLisandro Dalcin c2 = PetscDrawRealToColor(PetscRealPart(v[k + dof * id]), min, max); 570e4fe250SBarry Smith 580e4fe250SBarry Smith id = i + j * m + 1 + m; 59a39a4c7dSLisandro Dalcin x3 = PetscRealPart(xy[2 * id]); 600e4fe250SBarry Smith y3 = PetscRealPart(xy[2 * id + 1]); 61e5ab1681SLisandro Dalcin c3 = PetscDrawRealToColor(PetscRealPart(v[k + dof * id]), min, max); 620e4fe250SBarry Smith 630e4fe250SBarry Smith id = i + j * m + m; 64a39a4c7dSLisandro Dalcin x4 = PetscRealPart(xy[2 * id]); 65a39a4c7dSLisandro Dalcin y4 = PetscRealPart(xy[2 * id + 1]); 66e5ab1681SLisandro Dalcin c4 = PetscDrawRealToColor(PetscRealPart(v[k + dof * id]), min, max); 67f3f0eb19SBarry Smith 689566063dSJacob Faibussowitsch PetscCall(PetscDrawTriangle(draw, x1, y_1, x2, y2, x3, y3, c1, c2, c3)); 699566063dSJacob Faibussowitsch PetscCall(PetscDrawTriangle(draw, x1, y_1, x3, y3, x4, y4, c1, c3, c4)); 7047c6ae99SBarry Smith if (zctx->showgrid) { 719566063dSJacob Faibussowitsch PetscCall(PetscDrawLine(draw, x1, y_1, x2, y2, PETSC_DRAW_BLACK)); 729566063dSJacob Faibussowitsch PetscCall(PetscDrawLine(draw, x2, y2, x3, y3, PETSC_DRAW_BLACK)); 739566063dSJacob Faibussowitsch PetscCall(PetscDrawLine(draw, x3, y3, x4, y4, PETSC_DRAW_BLACK)); 749566063dSJacob Faibussowitsch PetscCall(PetscDrawLine(draw, x4, y4, x1, y_1, PETSC_DRAW_BLACK)); 7547c6ae99SBarry Smith } 7647c6ae99SBarry Smith } 7747c6ae99SBarry Smith } 787fe7c8feSLisandro Dalcin if (zctx->showaxis && !zctx->rank) { 79e5ab1681SLisandro Dalcin if (zctx->name0 || zctx->name1) { 80109c9344SBarry Smith PetscReal xl, yl, xr, yr, x, y; 819566063dSJacob Faibussowitsch PetscCall(PetscDrawGetCoordinates(draw, &xl, &yl, &xr, &yr)); 82e5ab1681SLisandro Dalcin x = xl + .30 * (xr - xl); 83109c9344SBarry Smith xl = xl + .01 * (xr - xl); 84e5ab1681SLisandro Dalcin y = yr - .30 * (yr - yl); 85109c9344SBarry Smith yl = yl + .01 * (yr - yl); 869566063dSJacob Faibussowitsch if (zctx->name0) PetscCall(PetscDrawString(draw, x, yl, PETSC_DRAW_BLACK, zctx->name0)); 879566063dSJacob Faibussowitsch if (zctx->name1) PetscCall(PetscDrawStringVertical(draw, xl, y, PETSC_DRAW_BLACK, zctx->name1)); 88109c9344SBarry Smith } 890e4fe250SBarry Smith /* 900e4fe250SBarry Smith Ideally we would use the PetscDrawAxis object to manage displaying the coordinate limits 910e4fe250SBarry Smith but that may require some refactoring. 920e4fe250SBarry Smith */ 93e5ab1681SLisandro Dalcin { 947fe7c8feSLisandro Dalcin double xmin = (double)zctx->xmin, ymin = (double)zctx->ymin; 957fe7c8feSLisandro Dalcin double xmax = (double)zctx->xmax, ymax = (double)zctx->ymax; 969371c9d4SSatish Balay char value[16]; 979371c9d4SSatish Balay size_t len; 989371c9d4SSatish Balay PetscReal w; 999566063dSJacob Faibussowitsch PetscCall(PetscSNPrintf(value, 16, "%0.2e", xmin)); 1009566063dSJacob Faibussowitsch PetscCall(PetscDrawString(draw, xmin, ymin - .05 * (ymax - ymin), PETSC_DRAW_BLACK, value)); 1019566063dSJacob Faibussowitsch PetscCall(PetscSNPrintf(value, 16, "%0.2e", xmax)); 1029566063dSJacob Faibussowitsch PetscCall(PetscStrlen(value, &len)); 1039566063dSJacob Faibussowitsch PetscCall(PetscDrawStringGetSize(draw, &w, NULL)); 1049566063dSJacob Faibussowitsch PetscCall(PetscDrawString(draw, xmax - len * w, ymin - .05 * (ymax - ymin), PETSC_DRAW_BLACK, value)); 1059566063dSJacob Faibussowitsch PetscCall(PetscSNPrintf(value, 16, "%0.2e", ymin)); 1069566063dSJacob Faibussowitsch PetscCall(PetscDrawString(draw, xmin - .05 * (xmax - xmin), ymin, PETSC_DRAW_BLACK, value)); 1079566063dSJacob Faibussowitsch PetscCall(PetscSNPrintf(value, 16, "%0.2e", ymax)); 1089566063dSJacob Faibussowitsch PetscCall(PetscDrawString(draw, xmin - .05 * (xmax - xmin), ymax, PETSC_DRAW_BLACK, value)); 109e5ab1681SLisandro Dalcin } 110e5ab1681SLisandro Dalcin } 111d0609cedSBarry Smith PetscDrawCollectiveEnd(draw); 11247c6ae99SBarry Smith PetscFunctionReturn(0); 11347c6ae99SBarry Smith } 11447c6ae99SBarry Smith 1159371c9d4SSatish Balay PetscErrorCode VecView_MPI_Draw_DA2d(Vec xin, PetscViewer viewer) { 1169a42bb27SBarry Smith DM da, dac, dag; 117a74ba6f7SBarry Smith PetscInt N, s, M, w, ncoors = 4; 11847c6ae99SBarry Smith const PetscInt *lx, *ly; 119e5ab1681SLisandro Dalcin PetscReal coors[4]; 12047c6ae99SBarry Smith PetscDraw draw, popup; 12147c6ae99SBarry Smith PetscBool isnull, useports = PETSC_FALSE; 12247c6ae99SBarry Smith MPI_Comm comm; 12347c6ae99SBarry Smith Vec xlocal, xcoor, xcoorl; 124bff4a2f0SMatthew G. Knepley DMBoundaryType bx, by; 125aa219208SBarry Smith DMDAStencilType st; 12647c6ae99SBarry Smith ZoomCtx zctx; 1270298fd71SBarry Smith PetscDrawViewPorts *ports = NULL; 12847c6ae99SBarry Smith PetscViewerFormat format; 12920d0051dSBarry Smith PetscInt *displayfields; 13067dd0837SBarry Smith PetscInt ndisplayfields, i, nbounds; 13167dd0837SBarry Smith const PetscReal *bounds; 13247c6ae99SBarry Smith 13347c6ae99SBarry Smith PetscFunctionBegin; 13447c6ae99SBarry Smith zctx.showgrid = PETSC_FALSE; 1357fe7c8feSLisandro Dalcin zctx.showaxis = PETSC_TRUE; 1368865f1eaSKarl Rupp 1379566063dSJacob Faibussowitsch PetscCall(PetscViewerDrawGetDraw(viewer, 0, &draw)); 1389566063dSJacob Faibussowitsch PetscCall(PetscDrawIsNull(draw, &isnull)); 1395b399a63SLisandro Dalcin if (isnull) PetscFunctionReturn(0); 1405b399a63SLisandro Dalcin 1419566063dSJacob Faibussowitsch PetscCall(PetscViewerDrawGetBounds(viewer, &nbounds, &bounds)); 14247c6ae99SBarry Smith 1439566063dSJacob Faibussowitsch PetscCall(VecGetDM(xin, &da)); 1447a8be351SBarry Smith PetscCheck(da, PetscObjectComm((PetscObject)xin), PETSC_ERR_ARG_WRONG, "Vector not generated from a DMDA"); 14547c6ae99SBarry Smith 1469566063dSJacob Faibussowitsch PetscCall(PetscObjectGetComm((PetscObject)xin, &comm)); 1479566063dSJacob Faibussowitsch PetscCallMPI(MPI_Comm_rank(comm, &zctx.rank)); 14847c6ae99SBarry Smith 1499566063dSJacob Faibussowitsch PetscCall(DMDAGetInfo(da, NULL, &M, &N, NULL, &zctx.m, &zctx.n, NULL, &w, &s, &bx, &by, NULL, &st)); 1509566063dSJacob Faibussowitsch PetscCall(DMDAGetOwnershipRanges(da, &lx, &ly, NULL)); 15147c6ae99SBarry Smith 15247c6ae99SBarry Smith /* 15347c6ae99SBarry Smith Obtain a sequential vector that is going to contain the local values plus ONE layer of 154aa219208SBarry Smith ghosted values to draw the graphics from. We also need its corresponding DMDA (dac) that will 15547c6ae99SBarry Smith update the local values pluse ONE layer of ghost values. 15647c6ae99SBarry Smith */ 1579566063dSJacob Faibussowitsch PetscCall(PetscObjectQuery((PetscObject)da, "GraphicsGhosted", (PetscObject *)&xlocal)); 15847c6ae99SBarry Smith if (!xlocal) { 159bff4a2f0SMatthew G. Knepley if (bx != DM_BOUNDARY_NONE || by != DM_BOUNDARY_NONE || s != 1 || st != DMDA_STENCIL_BOX) { 16047c6ae99SBarry Smith /* 16147c6ae99SBarry Smith if original da is not of stencil width one, or periodic or not a box stencil then 162aa219208SBarry Smith create a special DMDA to handle one level of ghost points for graphics 16347c6ae99SBarry Smith */ 1649566063dSJacob Faibussowitsch PetscCall(DMDACreate2d(comm, DM_BOUNDARY_NONE, DM_BOUNDARY_NONE, DMDA_STENCIL_BOX, M, N, zctx.m, zctx.n, w, 1, lx, ly, &dac)); 1659566063dSJacob Faibussowitsch PetscCall(DMSetUp(dac)); 1666aad120cSJose E. Roman PetscCall(PetscInfo(da, "Creating auxiliary DMDA for managing graphics ghost points\n")); 16747c6ae99SBarry Smith } else { 16847c6ae99SBarry Smith /* otherwise we can use the da we already have */ 16947c6ae99SBarry Smith dac = da; 17047c6ae99SBarry Smith } 17147c6ae99SBarry Smith /* create local vector for holding ghosted values used in graphics */ 1729566063dSJacob Faibussowitsch PetscCall(DMCreateLocalVector(dac, &xlocal)); 17347c6ae99SBarry Smith if (dac != da) { 174aa219208SBarry Smith /* don't keep any public reference of this DMDA, is is only available through xlocal */ 1759566063dSJacob Faibussowitsch PetscCall(PetscObjectDereference((PetscObject)dac)); 17647c6ae99SBarry Smith } else { 17747c6ae99SBarry Smith /* remove association between xlocal and da, because below we compose in the opposite 17847c6ae99SBarry Smith direction and if we left this connect we'd get a loop, so the objects could 17947c6ae99SBarry Smith never be destroyed */ 1809566063dSJacob Faibussowitsch PetscCall(PetscObjectRemoveReference((PetscObject)xlocal, "__PETSc_dm")); 18147c6ae99SBarry Smith } 1829566063dSJacob Faibussowitsch PetscCall(PetscObjectCompose((PetscObject)da, "GraphicsGhosted", (PetscObject)xlocal)); 1839566063dSJacob Faibussowitsch PetscCall(PetscObjectDereference((PetscObject)xlocal)); 18447c6ae99SBarry Smith } else { 185bff4a2f0SMatthew G. Knepley if (bx != DM_BOUNDARY_NONE || by != DM_BOUNDARY_NONE || s != 1 || st != DMDA_STENCIL_BOX) { 1869566063dSJacob Faibussowitsch PetscCall(VecGetDM(xlocal, &dac)); 187f7923d8aSBarry Smith } else { 188f7923d8aSBarry Smith dac = da; 18947c6ae99SBarry Smith } 19047c6ae99SBarry Smith } 19147c6ae99SBarry Smith 19247c6ae99SBarry Smith /* 19347c6ae99SBarry Smith Get local (ghosted) values of vector 19447c6ae99SBarry Smith */ 1959566063dSJacob Faibussowitsch PetscCall(DMGlobalToLocalBegin(dac, xin, INSERT_VALUES, xlocal)); 1969566063dSJacob Faibussowitsch PetscCall(DMGlobalToLocalEnd(dac, xin, INSERT_VALUES, xlocal)); 1979566063dSJacob Faibussowitsch PetscCall(VecGetArrayRead(xlocal, &zctx.v)); 19847c6ae99SBarry Smith 199832b7cebSLisandro Dalcin /* 200832b7cebSLisandro Dalcin Get coordinates of nodes 201832b7cebSLisandro Dalcin */ 2029566063dSJacob Faibussowitsch PetscCall(DMGetCoordinates(da, &xcoor)); 20347c6ae99SBarry Smith if (!xcoor) { 2049566063dSJacob Faibussowitsch PetscCall(DMDASetUniformCoordinates(da, 0.0, 1.0, 0.0, 1.0, 0.0, 0.0)); 2059566063dSJacob Faibussowitsch PetscCall(DMGetCoordinates(da, &xcoor)); 20647c6ae99SBarry Smith } 20747c6ae99SBarry Smith 20847c6ae99SBarry Smith /* 20947c6ae99SBarry Smith Determine the min and max coordinates in plot 21047c6ae99SBarry Smith */ 2119566063dSJacob Faibussowitsch PetscCall(VecStrideMin(xcoor, 0, NULL, &zctx.xmin)); 2129566063dSJacob Faibussowitsch PetscCall(VecStrideMax(xcoor, 0, NULL, &zctx.xmax)); 2139566063dSJacob Faibussowitsch PetscCall(VecStrideMin(xcoor, 1, NULL, &zctx.ymin)); 2149566063dSJacob Faibussowitsch PetscCall(VecStrideMax(xcoor, 1, NULL, &zctx.ymax)); 2159566063dSJacob Faibussowitsch PetscCall(PetscOptionsGetBool(NULL, NULL, "-draw_contour_axis", &zctx.showaxis, NULL)); 2167fe7c8feSLisandro Dalcin if (zctx.showaxis) { 2179371c9d4SSatish Balay coors[0] = zctx.xmin - .05 * (zctx.xmax - zctx.xmin); 2189371c9d4SSatish Balay coors[1] = zctx.ymin - .05 * (zctx.ymax - zctx.ymin); 2199371c9d4SSatish Balay coors[2] = zctx.xmax + .05 * (zctx.xmax - zctx.xmin); 2209371c9d4SSatish Balay coors[3] = zctx.ymax + .05 * (zctx.ymax - zctx.ymin); 2217fe7c8feSLisandro Dalcin } else { 2229371c9d4SSatish Balay coors[0] = zctx.xmin; 2239371c9d4SSatish Balay coors[1] = zctx.ymin; 2249371c9d4SSatish Balay coors[2] = zctx.xmax; 2259371c9d4SSatish Balay coors[3] = zctx.ymax; 2267fe7c8feSLisandro Dalcin } 2279566063dSJacob Faibussowitsch PetscCall(PetscOptionsGetRealArray(NULL, NULL, "-draw_coordinates", coors, &ncoors, NULL)); 2289566063dSJacob Faibussowitsch PetscCall(PetscInfo(da, "Preparing DMDA 2d contour plot coordinates %g %g %g %g\n", (double)coors[0], (double)coors[1], (double)coors[2], (double)coors[3])); 229a74ba6f7SBarry Smith 23047c6ae99SBarry Smith /* 231832b7cebSLisandro Dalcin Get local ghosted version of coordinates 23247c6ae99SBarry Smith */ 2339566063dSJacob Faibussowitsch PetscCall(PetscObjectQuery((PetscObject)da, "GraphicsCoordinateGhosted", (PetscObject *)&xcoorl)); 23447c6ae99SBarry Smith if (!xcoorl) { 235aa219208SBarry Smith /* create DMDA to get local version of graphics */ 2369566063dSJacob Faibussowitsch PetscCall(DMDACreate2d(comm, DM_BOUNDARY_NONE, DM_BOUNDARY_NONE, DMDA_STENCIL_BOX, M, N, zctx.m, zctx.n, 2, 1, lx, ly, &dag)); 2379566063dSJacob Faibussowitsch PetscCall(DMSetUp(dag)); 2386aad120cSJose E. Roman PetscCall(PetscInfo(dag, "Creating auxiliary DMDA for managing graphics coordinates ghost points\n")); 2399566063dSJacob Faibussowitsch PetscCall(DMCreateLocalVector(dag, &xcoorl)); 2409566063dSJacob Faibussowitsch PetscCall(PetscObjectCompose((PetscObject)da, "GraphicsCoordinateGhosted", (PetscObject)xcoorl)); 2419566063dSJacob Faibussowitsch PetscCall(PetscObjectDereference((PetscObject)dag)); 2429566063dSJacob Faibussowitsch PetscCall(PetscObjectDereference((PetscObject)xcoorl)); 2431baa6e33SBarry Smith } else PetscCall(VecGetDM(xcoorl, &dag)); 2449566063dSJacob Faibussowitsch PetscCall(DMGlobalToLocalBegin(dag, xcoor, INSERT_VALUES, xcoorl)); 2459566063dSJacob Faibussowitsch PetscCall(DMGlobalToLocalEnd(dag, xcoor, INSERT_VALUES, xcoorl)); 2469566063dSJacob Faibussowitsch PetscCall(VecGetArrayRead(xcoorl, &zctx.xy)); 2479566063dSJacob Faibussowitsch PetscCall(DMDAGetCoordinateName(da, 0, &zctx.name0)); 2489566063dSJacob Faibussowitsch PetscCall(DMDAGetCoordinateName(da, 1, &zctx.name1)); 24947c6ae99SBarry Smith 25047c6ae99SBarry Smith /* 25147c6ae99SBarry Smith Get information about size of area each processor must do graphics for 25247c6ae99SBarry Smith */ 2539566063dSJacob Faibussowitsch PetscCall(DMDAGetInfo(dac, NULL, &M, &N, NULL, NULL, NULL, NULL, &zctx.dof, NULL, &bx, &by, NULL, NULL)); 2549566063dSJacob Faibussowitsch PetscCall(DMDAGetGhostCorners(dac, NULL, NULL, NULL, &zctx.m, &zctx.n, NULL)); 2559566063dSJacob Faibussowitsch PetscCall(PetscOptionsGetBool(NULL, NULL, "-draw_contour_grid", &zctx.showgrid, NULL)); 2564e6118eeSBarry Smith 2579566063dSJacob Faibussowitsch PetscCall(DMDASelectFields(da, &ndisplayfields, &displayfields)); 2589566063dSJacob Faibussowitsch PetscCall(PetscViewerGetFormat(viewer, &format)); 2599566063dSJacob Faibussowitsch PetscCall(PetscOptionsGetBool(NULL, NULL, "-draw_ports", &useports, NULL)); 260832b7cebSLisandro Dalcin if (format == PETSC_VIEWER_DRAW_PORTS) useports = PETSC_TRUE; 261832b7cebSLisandro Dalcin if (useports) { 2629566063dSJacob Faibussowitsch PetscCall(PetscViewerDrawGetDraw(viewer, 0, &draw)); 2639566063dSJacob Faibussowitsch PetscCall(PetscDrawCheckResizedWindow(draw)); 2649566063dSJacob Faibussowitsch PetscCall(PetscDrawClear(draw)); 2659566063dSJacob Faibussowitsch PetscCall(PetscDrawViewPortsCreate(draw, ndisplayfields, &ports)); 266e5ab1681SLisandro Dalcin } 26720d0051dSBarry Smith 268832b7cebSLisandro Dalcin /* 269832b7cebSLisandro Dalcin Loop over each field; drawing each in a different window 270832b7cebSLisandro Dalcin */ 27120d0051dSBarry Smith for (i = 0; i < ndisplayfields; i++) { 27220d0051dSBarry Smith zctx.k = displayfields[i]; 2735b399a63SLisandro Dalcin 274e5ab1681SLisandro Dalcin /* determine the min and max value in plot */ 2759566063dSJacob Faibussowitsch PetscCall(VecStrideMin(xin, zctx.k, NULL, &zctx.min)); 2769566063dSJacob Faibussowitsch PetscCall(VecStrideMax(xin, zctx.k, NULL, &zctx.max)); 27767dd0837SBarry Smith if (zctx.k < nbounds) { 278f3f0eb19SBarry Smith zctx.min = bounds[2 * zctx.k]; 279f3f0eb19SBarry Smith zctx.max = bounds[2 * zctx.k + 1]; 28067dd0837SBarry Smith } 28147c6ae99SBarry Smith if (zctx.min == zctx.max) { 28247c6ae99SBarry Smith zctx.min -= 1.e-12; 28347c6ae99SBarry Smith zctx.max += 1.e-12; 28447c6ae99SBarry Smith } 2859566063dSJacob Faibussowitsch PetscCall(PetscInfo(da, "DMDA 2d contour plot min %g max %g\n", (double)zctx.min, (double)zctx.max)); 28647c6ae99SBarry Smith 287832b7cebSLisandro Dalcin if (useports) { 2889566063dSJacob Faibussowitsch PetscCall(PetscDrawViewPortsSet(ports, i)); 289832b7cebSLisandro Dalcin } else { 290832b7cebSLisandro Dalcin const char *title; 2919566063dSJacob Faibussowitsch PetscCall(PetscViewerDrawGetDraw(viewer, i, &draw)); 2929566063dSJacob Faibussowitsch PetscCall(DMDAGetFieldName(da, zctx.k, &title)); 2939566063dSJacob Faibussowitsch if (title) PetscCall(PetscDrawSetTitle(draw, title)); 294832b7cebSLisandro Dalcin } 295832b7cebSLisandro Dalcin 2969566063dSJacob Faibussowitsch PetscCall(PetscDrawGetPopup(draw, &popup)); 2979566063dSJacob Faibussowitsch PetscCall(PetscDrawScalePopup(popup, zctx.min, zctx.max)); 2989566063dSJacob Faibussowitsch PetscCall(PetscDrawSetCoordinates(draw, coors[0], coors[1], coors[2], coors[3])); 2999566063dSJacob Faibussowitsch PetscCall(PetscDrawZoom(draw, VecView_MPI_Draw_DA2d_Zoom, &zctx)); 3009566063dSJacob Faibussowitsch if (!useports) PetscCall(PetscDrawSave(draw)); 30147c6ae99SBarry Smith } 302832b7cebSLisandro Dalcin if (useports) { 3039566063dSJacob Faibussowitsch PetscCall(PetscViewerDrawGetDraw(viewer, 0, &draw)); 3049566063dSJacob Faibussowitsch PetscCall(PetscDrawSave(draw)); 305832b7cebSLisandro Dalcin } 306832b7cebSLisandro Dalcin 3079566063dSJacob Faibussowitsch PetscCall(PetscDrawViewPortsDestroy(ports)); 3089566063dSJacob Faibussowitsch PetscCall(PetscFree(displayfields)); 3099566063dSJacob Faibussowitsch PetscCall(VecRestoreArrayRead(xcoorl, &zctx.xy)); 3109566063dSJacob Faibussowitsch PetscCall(VecRestoreArrayRead(xlocal, &zctx.v)); 31147c6ae99SBarry Smith PetscFunctionReturn(0); 31247c6ae99SBarry Smith } 31347c6ae99SBarry Smith 3140da24e51SJuha Jäykkä #if defined(PETSC_HAVE_HDF5) 3159371c9d4SSatish Balay static PetscErrorCode VecGetHDF5ChunkSize(DM_DA *da, Vec xin, PetscInt dimension, PetscInt timestep, hsize_t *chunkDims) { 316d4190030SJed Brown PetscMPIInt comm_size; 317561a82e7SJed Brown hsize_t chunk_size, target_size, dim; 318561a82e7SJed Brown hsize_t vec_size = sizeof(PetscScalar) * da->M * da->N * da->P * da->w; 319561a82e7SJed Brown hsize_t avg_local_vec_size, KiB = 1024, MiB = KiB * KiB, GiB = MiB * KiB, min_size = MiB; 320561a82e7SJed Brown hsize_t max_chunks = 64 * KiB; /* HDF5 internal limitation */ 321561a82e7SJed Brown hsize_t max_chunk_size = 4 * GiB; /* HDF5 internal limitation */ 32284179ffaSJed Brown PetscInt zslices = da->p, yslices = da->n, xslices = da->m; 3230da24e51SJuha Jäykkä 324cb5c4f94SJuha Jäykkä PetscFunctionBegin; 3259566063dSJacob Faibussowitsch PetscCallMPI(MPI_Comm_size(PetscObjectComm((PetscObject)xin), &comm_size)); 326faa75363SBarry Smith avg_local_vec_size = (hsize_t)PetscCeilInt(vec_size, comm_size); /* we will attempt to use this as the chunk size */ 3270da24e51SJuha Jäykkä 328faa75363SBarry Smith target_size = (hsize_t)PetscMin((PetscInt64)vec_size, PetscMin((PetscInt64)max_chunk_size, PetscMax((PetscInt64)avg_local_vec_size, PetscMax(PetscCeilInt64(vec_size, max_chunks), (PetscInt64)min_size)))); 3297d310018SBarry Smith /* following line uses sizeof(PetscReal) instead of sizeof(PetscScalar) because the last dimension of chunkDims[] captures the 2* when complex numbers are being used */ 3307d310018SBarry Smith chunk_size = (hsize_t)PetscMax(1, chunkDims[0]) * PetscMax(1, chunkDims[1]) * PetscMax(1, chunkDims[2]) * PetscMax(1, chunkDims[3]) * PetscMax(1, chunkDims[4]) * PetscMax(1, chunkDims[5]) * sizeof(PetscReal); 3310da24e51SJuha Jäykkä 332cb5c4f94SJuha Jäykkä /* 333cb5c4f94SJuha Jäykkä if size/rank > max_chunk_size, we need radical measures: even going down to 334cb5c4f94SJuha Jäykkä avg_local_vec_size is not enough, so we simply use chunk size of 4 GiB no matter 335cb5c4f94SJuha Jäykkä what, composed in the most efficient way possible. 336cb5c4f94SJuha Jäykkä N.B. this minimises the number of chunks, which may or may not be the optimal 337cb5c4f94SJuha Jäykkä solution. In a BG, for example, the optimal solution is probably to make # chunks = # 338cb5c4f94SJuha Jäykkä IO nodes involved, but this author has no access to a BG to figure out how to 339cb5c4f94SJuha Jäykkä reliably find the right number. And even then it may or may not be enough. 340cb5c4f94SJuha Jäykkä */ 3410da24e51SJuha Jäykkä if (avg_local_vec_size > max_chunk_size) { 342cb5c4f94SJuha Jäykkä /* check if we can just split local z-axis: is that enough? */ 343faa75363SBarry Smith zslices = PetscCeilInt(vec_size, da->p * max_chunk_size) * zslices; 3440da24e51SJuha Jäykkä if (zslices > da->P) { 345cb5c4f94SJuha Jäykkä /* lattice is too large in xy-directions, splitting z only is not enough */ 3460da24e51SJuha Jäykkä zslices = da->P; 347faa75363SBarry Smith yslices = PetscCeilInt(vec_size, zslices * da->n * max_chunk_size) * yslices; 3480da24e51SJuha Jäykkä if (yslices > da->N) { 349cb5c4f94SJuha Jäykkä /* lattice is too large in x-direction, splitting along z, y is not enough */ 3500da24e51SJuha Jäykkä yslices = da->N; 351faa75363SBarry Smith xslices = PetscCeilInt(vec_size, zslices * yslices * da->m * max_chunk_size) * xslices; 3520da24e51SJuha Jäykkä } 3530da24e51SJuha Jäykkä } 3540da24e51SJuha Jäykkä dim = 0; 3559371c9d4SSatish Balay if (timestep >= 0) { ++dim; } 356cb5c4f94SJuha Jäykkä /* prefer to split z-axis, even down to planar slices */ 357c73cfb54SMatthew G. Knepley if (dimension == 3) { 358cb5c4f94SJuha Jäykkä chunkDims[dim++] = (hsize_t)da->P / zslices; 359cb5c4f94SJuha Jäykkä chunkDims[dim++] = (hsize_t)da->N / yslices; 360cb5c4f94SJuha Jäykkä chunkDims[dim++] = (hsize_t)da->M / xslices; 3610da24e51SJuha Jäykkä } else { 362cb5c4f94SJuha Jäykkä /* This is a 2D world exceeding 4GiB in size; yes, I've seen them, even used myself */ 363cb5c4f94SJuha Jäykkä chunkDims[dim++] = (hsize_t)da->N / yslices; 364cb5c4f94SJuha Jäykkä chunkDims[dim++] = (hsize_t)da->M / xslices; 3650da24e51SJuha Jäykkä } 3660da24e51SJuha Jäykkä chunk_size = (hsize_t)PetscMax(1, chunkDims[0]) * PetscMax(1, chunkDims[1]) * PetscMax(1, chunkDims[2]) * PetscMax(1, chunkDims[3]) * PetscMax(1, chunkDims[4]) * PetscMax(1, chunkDims[5]) * sizeof(double); 3670da24e51SJuha Jäykkä } else { 3680da24e51SJuha Jäykkä if (target_size < chunk_size) { 369cb5c4f94SJuha Jäykkä /* only change the defaults if target_size < chunk_size */ 3700da24e51SJuha Jäykkä dim = 0; 3719371c9d4SSatish Balay if (timestep >= 0) { ++dim; } 372cb5c4f94SJuha Jäykkä /* prefer to split z-axis, even down to planar slices */ 373c73cfb54SMatthew G. Knepley if (dimension == 3) { 374cb5c4f94SJuha Jäykkä /* try splitting the z-axis to core-size bits, i.e. divide chunk size by # comm_size in z-direction */ 3750da24e51SJuha Jäykkä if (target_size >= chunk_size / da->p) { 376cb5c4f94SJuha Jäykkä /* just make chunks the size of <local_z>x<whole_world_y>x<whole_world_x>x<dof> */ 377faa75363SBarry Smith chunkDims[dim] = (hsize_t)PetscCeilInt(da->P, da->p); 3780da24e51SJuha Jäykkä } else { 379cb5c4f94SJuha Jäykkä /* oops, just splitting the z-axis is NOT ENOUGH, need to split more; let's be 380cb5c4f94SJuha Jäykkä radical and let everyone write all they've got */ 381faa75363SBarry Smith chunkDims[dim++] = (hsize_t)PetscCeilInt(da->P, da->p); 382faa75363SBarry Smith chunkDims[dim++] = (hsize_t)PetscCeilInt(da->N, da->n); 383faa75363SBarry Smith chunkDims[dim++] = (hsize_t)PetscCeilInt(da->M, da->m); 3840da24e51SJuha Jäykkä } 3850da24e51SJuha Jäykkä } else { 386cb5c4f94SJuha Jäykkä /* This is a 2D world exceeding 4GiB in size; yes, I've seen them, even used myself */ 3870da24e51SJuha Jäykkä if (target_size >= chunk_size / da->n) { 388cb5c4f94SJuha Jäykkä /* just make chunks the size of <local_z>x<whole_world_y>x<whole_world_x>x<dof> */ 389faa75363SBarry Smith chunkDims[dim] = (hsize_t)PetscCeilInt(da->N, da->n); 3900da24e51SJuha Jäykkä } else { 391cb5c4f94SJuha Jäykkä /* oops, just splitting the z-axis is NOT ENOUGH, need to split more; let's be 392cb5c4f94SJuha Jäykkä radical and let everyone write all they've got */ 393faa75363SBarry Smith chunkDims[dim++] = (hsize_t)PetscCeilInt(da->N, da->n); 394faa75363SBarry Smith chunkDims[dim++] = (hsize_t)PetscCeilInt(da->M, da->m); 3950da24e51SJuha Jäykkä } 3960da24e51SJuha Jäykkä } 3970da24e51SJuha Jäykkä chunk_size = (hsize_t)PetscMax(1, chunkDims[0]) * PetscMax(1, chunkDims[1]) * PetscMax(1, chunkDims[2]) * PetscMax(1, chunkDims[3]) * PetscMax(1, chunkDims[4]) * PetscMax(1, chunkDims[5]) * sizeof(double); 3980da24e51SJuha Jäykkä } else { 399cb5c4f94SJuha Jäykkä /* precomputed chunks are fine, we don't need to do anything */ 4000da24e51SJuha Jäykkä } 4010da24e51SJuha Jäykkä } 4020da24e51SJuha Jäykkä PetscFunctionReturn(0); 4030da24e51SJuha Jäykkä } 4040da24e51SJuha Jäykkä #endif 40547c6ae99SBarry Smith 40647c6ae99SBarry Smith #if defined(PETSC_HAVE_HDF5) 4079371c9d4SSatish Balay PetscErrorCode VecView_MPI_HDF5_DA(Vec xin, PetscViewer viewer) { 4082d95be3dSVaclav Hapla PetscViewer_HDF5 *hdf5 = (PetscViewer_HDF5 *)viewer->data; 4099b2a5a86SJed Brown DM dm; 4109b2a5a86SJed Brown DM_DA *da; 41147c6ae99SBarry Smith hid_t filespace; /* file dataspace identifier */ 4128e2ae6d7SMichael Kraus hid_t chunkspace; /* chunk dataset property identifier */ 41347c6ae99SBarry Smith hid_t dset_id; /* dataset identifier */ 41447c6ae99SBarry Smith hid_t memspace; /* memory dataspace identifier */ 41547c6ae99SBarry Smith hid_t file_id; 41615214e8eSMatthew G Knepley hid_t group; 4179a0502c6SHåkon Strandenes hid_t memscalartype; /* scalar type for mem (H5T_NATIVE_FLOAT or H5T_NATIVE_DOUBLE) */ 4189a0502c6SHåkon Strandenes hid_t filescalartype; /* scalar type for file (H5T_NATIVE_FLOAT or H5T_NATIVE_DOUBLE) */ 419d9a4edebSJed Brown hsize_t dim; 4200da24e51SJuha Jäykkä hsize_t maxDims[6] = {0}, dims[6] = {0}, chunkDims[6] = {0}, count[6] = {0}, offset[6] = {0}; /* we depend on these being sane later on */ 421d7dd068bSVaclav Hapla PetscBool timestepping = PETSC_FALSE, dim2, spoutput; 422d7dd068bSVaclav Hapla PetscInt timestep = PETSC_MIN_INT, dimension; 4235edff71fSBarry Smith const PetscScalar *x; 4248e2ae6d7SMichael Kraus const char *vecname; 42547c6ae99SBarry Smith 42647c6ae99SBarry Smith PetscFunctionBegin; 4279566063dSJacob Faibussowitsch PetscCall(PetscViewerHDF5OpenGroup(viewer, &file_id, &group)); 4289566063dSJacob Faibussowitsch PetscCall(PetscViewerHDF5IsTimestepping(viewer, ×tepping)); 429*48a46eb9SPierre Jolivet if (timestepping) PetscCall(PetscViewerHDF5GetTimestep(viewer, ×tep)); 4309566063dSJacob Faibussowitsch PetscCall(PetscViewerHDF5GetBaseDimension2(viewer, &dim2)); 4319566063dSJacob Faibussowitsch PetscCall(PetscViewerHDF5GetSPOutput(viewer, &spoutput)); 43215214e8eSMatthew G Knepley 4339566063dSJacob Faibussowitsch PetscCall(VecGetDM(xin, &dm)); 4347a8be351SBarry Smith PetscCheck(dm, PetscObjectComm((PetscObject)xin), PETSC_ERR_ARG_WRONG, "Vector not generated from a DMDA"); 4359b2a5a86SJed Brown da = (DM_DA *)dm->data; 4369566063dSJacob Faibussowitsch PetscCall(DMGetDimension(dm, &dimension)); 43747c6ae99SBarry Smith 4388e2ae6d7SMichael Kraus /* Create the dataspace for the dataset. 4398e2ae6d7SMichael Kraus * 4408e2ae6d7SMichael Kraus * dims - holds the current dimensions of the dataset 4418e2ae6d7SMichael Kraus * 4428e2ae6d7SMichael Kraus * maxDims - holds the maximum dimensions of the dataset (unlimited 4438e2ae6d7SMichael Kraus * for the number of time steps with the current dimensions for the 4448e2ae6d7SMichael Kraus * other dimensions; so only additional time steps can be added). 4458e2ae6d7SMichael Kraus * 4468e2ae6d7SMichael Kraus * chunkDims - holds the size of a single time step (required to 4478e2ae6d7SMichael Kraus * permit extending dataset). 4488e2ae6d7SMichael Kraus */ 4498e2ae6d7SMichael Kraus dim = 0; 4508e2ae6d7SMichael Kraus if (timestep >= 0) { 4518e2ae6d7SMichael Kraus dims[dim] = timestep + 1; 4528e2ae6d7SMichael Kraus maxDims[dim] = H5S_UNLIMITED; 4538e2ae6d7SMichael Kraus chunkDims[dim] = 1; 4548e2ae6d7SMichael Kraus ++dim; 4558e2ae6d7SMichael Kraus } 456c73cfb54SMatthew G. Knepley if (dimension == 3) { 4579566063dSJacob Faibussowitsch PetscCall(PetscHDF5IntCast(da->P, dims + dim)); 4588e2ae6d7SMichael Kraus maxDims[dim] = dims[dim]; 4598e2ae6d7SMichael Kraus chunkDims[dim] = dims[dim]; 4608e2ae6d7SMichael Kraus ++dim; 4618e2ae6d7SMichael Kraus } 462c73cfb54SMatthew G. Knepley if (dimension > 1) { 4639566063dSJacob Faibussowitsch PetscCall(PetscHDF5IntCast(da->N, dims + dim)); 4648e2ae6d7SMichael Kraus maxDims[dim] = dims[dim]; 4658e2ae6d7SMichael Kraus chunkDims[dim] = dims[dim]; 4668e2ae6d7SMichael Kraus ++dim; 4678e2ae6d7SMichael Kraus } 4689566063dSJacob Faibussowitsch PetscCall(PetscHDF5IntCast(da->M, dims + dim)); 4698e2ae6d7SMichael Kraus maxDims[dim] = dims[dim]; 4708e2ae6d7SMichael Kraus chunkDims[dim] = dims[dim]; 4718e2ae6d7SMichael Kraus ++dim; 47282ea9b62SBarry Smith if (da->w > 1 || dim2) { 4739566063dSJacob Faibussowitsch PetscCall(PetscHDF5IntCast(da->w, dims + dim)); 4748e2ae6d7SMichael Kraus maxDims[dim] = dims[dim]; 4758e2ae6d7SMichael Kraus chunkDims[dim] = dims[dim]; 4768e2ae6d7SMichael Kraus ++dim; 4778e2ae6d7SMichael Kraus } 47847c6ae99SBarry Smith #if defined(PETSC_USE_COMPLEX) 4798e2ae6d7SMichael Kraus dims[dim] = 2; 4808e2ae6d7SMichael Kraus maxDims[dim] = dims[dim]; 4818e2ae6d7SMichael Kraus chunkDims[dim] = dims[dim]; 4828e2ae6d7SMichael Kraus ++dim; 48347c6ae99SBarry Smith #endif 4840da24e51SJuha Jäykkä 4859566063dSJacob Faibussowitsch PetscCall(VecGetHDF5ChunkSize(da, xin, dimension, timestep, chunkDims)); 4860da24e51SJuha Jäykkä 487792fecdfSBarry Smith PetscCallHDF5Return(filespace, H5Screate_simple, (dim, dims, maxDims)); 48847c6ae99SBarry Smith 48915214e8eSMatthew G Knepley #if defined(PETSC_USE_REAL_SINGLE) 4909a0502c6SHåkon Strandenes memscalartype = H5T_NATIVE_FLOAT; 4919a0502c6SHåkon Strandenes filescalartype = H5T_NATIVE_FLOAT; 49215214e8eSMatthew G Knepley #elif defined(PETSC_USE_REAL___FLOAT128) 49315214e8eSMatthew G Knepley #error "HDF5 output with 128 bit floats not supported." 494570b7f6dSBarry Smith #elif defined(PETSC_USE_REAL___FP16) 495570b7f6dSBarry Smith #error "HDF5 output with 16 bit floats not supported." 49615214e8eSMatthew G Knepley #else 4979a0502c6SHåkon Strandenes memscalartype = H5T_NATIVE_DOUBLE; 4989a0502c6SHåkon Strandenes if (spoutput == PETSC_TRUE) filescalartype = H5T_NATIVE_FLOAT; 4999a0502c6SHåkon Strandenes else filescalartype = H5T_NATIVE_DOUBLE; 50015214e8eSMatthew G Knepley #endif 50115214e8eSMatthew G Knepley 50247c6ae99SBarry Smith /* Create the dataset with default properties and close filespace */ 5039566063dSJacob Faibussowitsch PetscCall(PetscObjectGetName((PetscObject)xin, &vecname)); 50415214e8eSMatthew G Knepley if (!H5Lexists(group, vecname, H5P_DEFAULT)) { 5058e2ae6d7SMichael Kraus /* Create chunk */ 506792fecdfSBarry Smith PetscCallHDF5Return(chunkspace, H5Pcreate, (H5P_DATASET_CREATE)); 507792fecdfSBarry Smith PetscCallHDF5(H5Pset_chunk, (chunkspace, dim, chunkDims)); 5088e2ae6d7SMichael Kraus 509792fecdfSBarry Smith PetscCallHDF5Return(dset_id, H5Dcreate2, (group, vecname, filescalartype, filespace, H5P_DEFAULT, chunkspace, H5P_DEFAULT)); 51015214e8eSMatthew G Knepley } else { 511792fecdfSBarry Smith PetscCallHDF5Return(dset_id, H5Dopen2, (group, vecname, H5P_DEFAULT)); 512792fecdfSBarry Smith PetscCallHDF5(H5Dset_extent, (dset_id, dims)); 51315214e8eSMatthew G Knepley } 514792fecdfSBarry Smith PetscCallHDF5(H5Sclose, (filespace)); 51547c6ae99SBarry Smith 51647c6ae99SBarry Smith /* Each process defines a dataset and writes it to the hyperslab in the file */ 5178e2ae6d7SMichael Kraus dim = 0; 5188e2ae6d7SMichael Kraus if (timestep >= 0) { 5198e2ae6d7SMichael Kraus offset[dim] = timestep; 5208e2ae6d7SMichael Kraus ++dim; 5218e2ae6d7SMichael Kraus } 5229566063dSJacob Faibussowitsch if (dimension == 3) PetscCall(PetscHDF5IntCast(da->zs, offset + dim++)); 5239566063dSJacob Faibussowitsch if (dimension > 1) PetscCall(PetscHDF5IntCast(da->ys, offset + dim++)); 5249566063dSJacob Faibussowitsch PetscCall(PetscHDF5IntCast(da->xs / da->w, offset + dim++)); 52582ea9b62SBarry Smith if (da->w > 1 || dim2) offset[dim++] = 0; 52647c6ae99SBarry Smith #if defined(PETSC_USE_COMPLEX) 5278e2ae6d7SMichael Kraus offset[dim++] = 0; 52847c6ae99SBarry Smith #endif 5298e2ae6d7SMichael Kraus dim = 0; 5308e2ae6d7SMichael Kraus if (timestep >= 0) { 5318e2ae6d7SMichael Kraus count[dim] = 1; 5328e2ae6d7SMichael Kraus ++dim; 5338e2ae6d7SMichael Kraus } 5349566063dSJacob Faibussowitsch if (dimension == 3) PetscCall(PetscHDF5IntCast(da->ze - da->zs, count + dim++)); 5359566063dSJacob Faibussowitsch if (dimension > 1) PetscCall(PetscHDF5IntCast(da->ye - da->ys, count + dim++)); 5369566063dSJacob Faibussowitsch PetscCall(PetscHDF5IntCast((da->xe - da->xs) / da->w, count + dim++)); 5379566063dSJacob Faibussowitsch if (da->w > 1 || dim2) PetscCall(PetscHDF5IntCast(da->w, count + dim++)); 53847c6ae99SBarry Smith #if defined(PETSC_USE_COMPLEX) 5398e2ae6d7SMichael Kraus count[dim++] = 2; 54047c6ae99SBarry Smith #endif 541792fecdfSBarry Smith PetscCallHDF5Return(memspace, H5Screate_simple, (dim, count, NULL)); 542792fecdfSBarry Smith PetscCallHDF5Return(filespace, H5Dget_space, (dset_id)); 543792fecdfSBarry Smith PetscCallHDF5(H5Sselect_hyperslab, (filespace, H5S_SELECT_SET, offset, NULL, count, NULL)); 54447c6ae99SBarry Smith 5459566063dSJacob Faibussowitsch PetscCall(VecGetArrayRead(xin, &x)); 546792fecdfSBarry Smith PetscCallHDF5(H5Dwrite, (dset_id, memscalartype, memspace, filespace, hdf5->dxpl_id, x)); 547792fecdfSBarry Smith PetscCallHDF5(H5Fflush, (file_id, H5F_SCOPE_GLOBAL)); 5489566063dSJacob Faibussowitsch PetscCall(VecRestoreArrayRead(xin, &x)); 54947c6ae99SBarry Smith 550e0552f36Ssajid__ali #if defined(PETSC_USE_COMPLEX) 551e0552f36Ssajid__ali { 552e0552f36Ssajid__ali PetscBool tru = PETSC_TRUE; 5539566063dSJacob Faibussowitsch PetscCall(PetscViewerHDF5WriteObjectAttribute(viewer, (PetscObject)xin, "complex", PETSC_BOOL, &tru)); 554e0552f36Ssajid__ali } 555e0552f36Ssajid__ali #endif 556*48a46eb9SPierre Jolivet if (timestepping) PetscCall(PetscViewerHDF5WriteObjectAttribute(viewer, (PetscObject)xin, "timestepping", PETSC_BOOL, ×tepping)); 557e0552f36Ssajid__ali 55847c6ae99SBarry Smith /* Close/release resources */ 5599371c9d4SSatish Balay if (group != file_id) { PetscCallHDF5(H5Gclose, (group)); } 560792fecdfSBarry Smith PetscCallHDF5(H5Sclose, (filespace)); 561792fecdfSBarry Smith PetscCallHDF5(H5Sclose, (memspace)); 562792fecdfSBarry Smith PetscCallHDF5(H5Dclose, (dset_id)); 5639566063dSJacob Faibussowitsch PetscCall(PetscInfo(xin, "Wrote Vec object with name %s\n", vecname)); 56447c6ae99SBarry Smith PetscFunctionReturn(0); 56547c6ae99SBarry Smith } 56647c6ae99SBarry Smith #endif 56747c6ae99SBarry Smith 56809573ac7SBarry Smith extern PetscErrorCode VecView_MPI_Draw_DA1d(Vec, PetscViewer); 56947c6ae99SBarry Smith 57047c6ae99SBarry Smith #if defined(PETSC_HAVE_MPIIO) 5719371c9d4SSatish Balay static PetscErrorCode DMDAArrayMPIIO(DM da, PetscViewer viewer, Vec xin, PetscBool write) { 57247c6ae99SBarry Smith MPI_File mfdes; 57347c6ae99SBarry Smith PetscMPIInt gsizes[4], lsizes[4], lstarts[4], asiz, dof; 57447c6ae99SBarry Smith MPI_Datatype view; 57547c6ae99SBarry Smith const PetscScalar *array; 57647c6ae99SBarry Smith MPI_Offset off; 57747c6ae99SBarry Smith MPI_Aint ub, ul; 57847c6ae99SBarry Smith PetscInt type, rows, vecrows, tr[2]; 57947c6ae99SBarry Smith DM_DA *dd = (DM_DA *)da->data; 5800c169764Sdmay PetscBool skipheader; 58147c6ae99SBarry Smith 58247c6ae99SBarry Smith PetscFunctionBegin; 5839566063dSJacob Faibussowitsch PetscCall(VecGetSize(xin, &vecrows)); 5849566063dSJacob Faibussowitsch PetscCall(PetscViewerBinaryGetSkipHeader(viewer, &skipheader)); 58547c6ae99SBarry Smith if (!write) { 58647c6ae99SBarry Smith /* Read vector header. */ 5870c169764Sdmay if (!skipheader) { 5889566063dSJacob Faibussowitsch PetscCall(PetscViewerBinaryRead(viewer, tr, 2, NULL, PETSC_INT)); 58947c6ae99SBarry Smith type = tr[0]; 59047c6ae99SBarry Smith rows = tr[1]; 59108401ef6SPierre Jolivet PetscCheck(type == VEC_FILE_CLASSID, PetscObjectComm((PetscObject)da), PETSC_ERR_ARG_WRONG, "Not vector next in file"); 59208401ef6SPierre Jolivet PetscCheck(rows == vecrows, PetscObjectComm((PetscObject)da), PETSC_ERR_ARG_SIZ, "Vector in file not same size as DMDA vector"); 5930c169764Sdmay } 59447c6ae99SBarry Smith } else { 59547c6ae99SBarry Smith tr[0] = VEC_FILE_CLASSID; 59647c6ae99SBarry Smith tr[1] = vecrows; 597*48a46eb9SPierre Jolivet if (!skipheader) PetscCall(PetscViewerBinaryWrite(viewer, tr, 2, PETSC_INT)); 5980c169764Sdmay } 59947c6ae99SBarry Smith 6009566063dSJacob Faibussowitsch PetscCall(PetscMPIIntCast(dd->w, &dof)); 6014dc2109aSBarry Smith gsizes[0] = dof; 6029566063dSJacob Faibussowitsch PetscCall(PetscMPIIntCast(dd->M, gsizes + 1)); 6039566063dSJacob Faibussowitsch PetscCall(PetscMPIIntCast(dd->N, gsizes + 2)); 6049566063dSJacob Faibussowitsch PetscCall(PetscMPIIntCast(dd->P, gsizes + 3)); 6054dc2109aSBarry Smith lsizes[0] = dof; 6069566063dSJacob Faibussowitsch PetscCall(PetscMPIIntCast((dd->xe - dd->xs) / dof, lsizes + 1)); 6079566063dSJacob Faibussowitsch PetscCall(PetscMPIIntCast(dd->ye - dd->ys, lsizes + 2)); 6089566063dSJacob Faibussowitsch PetscCall(PetscMPIIntCast(dd->ze - dd->zs, lsizes + 3)); 6094dc2109aSBarry Smith lstarts[0] = 0; 6109566063dSJacob Faibussowitsch PetscCall(PetscMPIIntCast(dd->xs / dof, lstarts + 1)); 6119566063dSJacob Faibussowitsch PetscCall(PetscMPIIntCast(dd->ys, lstarts + 2)); 6129566063dSJacob Faibussowitsch PetscCall(PetscMPIIntCast(dd->zs, lstarts + 3)); 6139566063dSJacob Faibussowitsch PetscCallMPI(MPI_Type_create_subarray(da->dim + 1, gsizes, lsizes, lstarts, MPI_ORDER_FORTRAN, MPIU_SCALAR, &view)); 6149566063dSJacob Faibussowitsch PetscCallMPI(MPI_Type_commit(&view)); 61547c6ae99SBarry Smith 6169566063dSJacob Faibussowitsch PetscCall(PetscViewerBinaryGetMPIIODescriptor(viewer, &mfdes)); 6179566063dSJacob Faibussowitsch PetscCall(PetscViewerBinaryGetMPIIOOffset(viewer, &off)); 6189566063dSJacob Faibussowitsch PetscCallMPI(MPI_File_set_view(mfdes, off, MPIU_SCALAR, view, (char *)"native", MPI_INFO_NULL)); 6199566063dSJacob Faibussowitsch PetscCall(VecGetArrayRead(xin, &array)); 62047c6ae99SBarry Smith asiz = lsizes[1] * (lsizes[2] > 0 ? lsizes[2] : 1) * (lsizes[3] > 0 ? lsizes[3] : 1) * dof; 6211baa6e33SBarry Smith if (write) PetscCall(MPIU_File_write_all(mfdes, (PetscScalar *)array, asiz, MPIU_SCALAR, MPI_STATUS_IGNORE)); 6221baa6e33SBarry Smith else PetscCall(MPIU_File_read_all(mfdes, (PetscScalar *)array, asiz, MPIU_SCALAR, MPI_STATUS_IGNORE)); 6239566063dSJacob Faibussowitsch PetscCallMPI(MPI_Type_get_extent(view, &ul, &ub)); 6249566063dSJacob Faibussowitsch PetscCall(PetscViewerBinaryAddMPIIOOffset(viewer, ub)); 6259566063dSJacob Faibussowitsch PetscCall(VecRestoreArrayRead(xin, &array)); 6269566063dSJacob Faibussowitsch PetscCallMPI(MPI_Type_free(&view)); 62747c6ae99SBarry Smith PetscFunctionReturn(0); 62847c6ae99SBarry Smith } 62947c6ae99SBarry Smith #endif 63047c6ae99SBarry Smith 6319371c9d4SSatish Balay PetscErrorCode VecView_MPI_DA(Vec xin, PetscViewer viewer) { 6329a42bb27SBarry Smith DM da; 63347c6ae99SBarry Smith PetscInt dim; 63447c6ae99SBarry Smith Vec natural; 6358135c375SStefano Zampini PetscBool isdraw, isvtk, isglvis; 63647c6ae99SBarry Smith #if defined(PETSC_HAVE_HDF5) 63747c6ae99SBarry Smith PetscBool ishdf5; 63847c6ae99SBarry Smith #endif 6393f3fd955SJed Brown const char *prefix, *name; 640a261c58fSBarry Smith PetscViewerFormat format; 64147c6ae99SBarry Smith 64247c6ae99SBarry Smith PetscFunctionBegin; 6439566063dSJacob Faibussowitsch PetscCall(VecGetDM(xin, &da)); 6447a8be351SBarry Smith PetscCheck(da, PetscObjectComm((PetscObject)xin), PETSC_ERR_ARG_WRONG, "Vector not generated from a DMDA"); 6459566063dSJacob Faibussowitsch PetscCall(PetscObjectTypeCompare((PetscObject)viewer, PETSCVIEWERDRAW, &isdraw)); 6469566063dSJacob Faibussowitsch PetscCall(PetscObjectTypeCompare((PetscObject)viewer, PETSCVIEWERVTK, &isvtk)); 64747c6ae99SBarry Smith #if defined(PETSC_HAVE_HDF5) 6489566063dSJacob Faibussowitsch PetscCall(PetscObjectTypeCompare((PetscObject)viewer, PETSCVIEWERHDF5, &ishdf5)); 64947c6ae99SBarry Smith #endif 6509566063dSJacob Faibussowitsch PetscCall(PetscObjectTypeCompare((PetscObject)viewer, PETSCVIEWERGLVIS, &isglvis)); 65147c6ae99SBarry Smith if (isdraw) { 6529566063dSJacob Faibussowitsch PetscCall(DMDAGetInfo(da, &dim, NULL, NULL, NULL, NULL, NULL, NULL, NULL, NULL, NULL, NULL, NULL, NULL)); 65347c6ae99SBarry Smith if (dim == 1) { 6549566063dSJacob Faibussowitsch PetscCall(VecView_MPI_Draw_DA1d(xin, viewer)); 65547c6ae99SBarry Smith } else if (dim == 2) { 6569566063dSJacob Faibussowitsch PetscCall(VecView_MPI_Draw_DA2d(xin, viewer)); 65763a3b9bcSJacob Faibussowitsch } else SETERRQ(PetscObjectComm((PetscObject)da), PETSC_ERR_SUP, "Cannot graphically view vector associated with this dimensional DMDA %" PetscInt_FMT, dim); 65801d7c5c3SPatrick Sanan } else if (isvtk) { /* Duplicate the Vec */ 6594061b8bfSJed Brown Vec Y; 6609566063dSJacob Faibussowitsch PetscCall(VecDuplicate(xin, &Y)); 661b51b94faSJed Brown if (((PetscObject)xin)->name) { 662b51b94faSJed Brown /* If xin was named, copy the name over to Y. The duplicate names are safe because nobody else will ever see Y. */ 6639566063dSJacob Faibussowitsch PetscCall(PetscObjectSetName((PetscObject)Y, ((PetscObject)xin)->name)); 664b51b94faSJed Brown } 6659566063dSJacob Faibussowitsch PetscCall(VecCopy(xin, Y)); 666a8f87f1dSPatrick Sanan { 667a8f87f1dSPatrick Sanan PetscObject dmvtk; 668a8f87f1dSPatrick Sanan PetscBool compatible, compatibleSet; 6699566063dSJacob Faibussowitsch PetscCall(PetscViewerVTKGetDM(viewer, &dmvtk)); 670a8f87f1dSPatrick Sanan if (dmvtk) { 671064a246eSJacob Faibussowitsch PetscValidHeaderSpecific((DM)dmvtk, DM_CLASSID, 2); 6729566063dSJacob Faibussowitsch PetscCall(DMGetCompatibility(da, (DM)dmvtk, &compatible, &compatibleSet)); 6737a8be351SBarry Smith PetscCheck(compatibleSet && compatible, PetscObjectComm((PetscObject)da), PETSC_ERR_ARG_INCOMP, "Cannot confirm compatibility of DMs associated with Vecs viewed in the same VTK file. Check that grids are the same."); 674a8f87f1dSPatrick Sanan } 6759566063dSJacob Faibussowitsch PetscCall(PetscViewerVTKAddField(viewer, (PetscObject)da, DMDAVTKWriteAll, PETSC_DEFAULT, PETSC_VTK_POINT_FIELD, PETSC_FALSE, (PetscObject)Y)); 676a8f87f1dSPatrick Sanan } 67747c6ae99SBarry Smith #if defined(PETSC_HAVE_HDF5) 67847c6ae99SBarry Smith } else if (ishdf5) { 6799566063dSJacob Faibussowitsch PetscCall(VecView_MPI_HDF5_DA(xin, viewer)); 68047c6ae99SBarry Smith #endif 6818135c375SStefano Zampini } else if (isglvis) { 6829566063dSJacob Faibussowitsch PetscCall(VecView_GLVis(xin, viewer)); 68347c6ae99SBarry Smith } else { 68447c6ae99SBarry Smith #if defined(PETSC_HAVE_MPIIO) 68547c6ae99SBarry Smith PetscBool isbinary, isMPIIO; 68647c6ae99SBarry Smith 6879566063dSJacob Faibussowitsch PetscCall(PetscObjectTypeCompare((PetscObject)viewer, PETSCVIEWERBINARY, &isbinary)); 68847c6ae99SBarry Smith if (isbinary) { 6899566063dSJacob Faibussowitsch PetscCall(PetscViewerBinaryGetUseMPIIO(viewer, &isMPIIO)); 69047c6ae99SBarry Smith if (isMPIIO) { 6919566063dSJacob Faibussowitsch PetscCall(DMDAArrayMPIIO(da, viewer, xin, PETSC_TRUE)); 69247c6ae99SBarry Smith PetscFunctionReturn(0); 69347c6ae99SBarry Smith } 69447c6ae99SBarry Smith } 69547c6ae99SBarry Smith #endif 69647c6ae99SBarry Smith 69747c6ae99SBarry Smith /* call viewer on natural ordering */ 6989566063dSJacob Faibussowitsch PetscCall(PetscObjectGetOptionsPrefix((PetscObject)xin, &prefix)); 6999566063dSJacob Faibussowitsch PetscCall(DMDACreateNaturalVector(da, &natural)); 7009566063dSJacob Faibussowitsch PetscCall(PetscObjectSetOptionsPrefix((PetscObject)natural, prefix)); 7019566063dSJacob Faibussowitsch PetscCall(DMDAGlobalToNaturalBegin(da, xin, INSERT_VALUES, natural)); 7029566063dSJacob Faibussowitsch PetscCall(DMDAGlobalToNaturalEnd(da, xin, INSERT_VALUES, natural)); 7039566063dSJacob Faibussowitsch PetscCall(PetscObjectGetName((PetscObject)xin, &name)); 7049566063dSJacob Faibussowitsch PetscCall(PetscObjectSetName((PetscObject)natural, name)); 705a261c58fSBarry Smith 7069566063dSJacob Faibussowitsch PetscCall(PetscViewerGetFormat(viewer, &format)); 707a261c58fSBarry Smith if (format == PETSC_VIEWER_BINARY_MATLAB) { 708a261c58fSBarry Smith /* temporarily remove viewer format so it won't trigger in the VecView() */ 7099566063dSJacob Faibussowitsch PetscCall(PetscViewerPushFormat(viewer, PETSC_VIEWER_DEFAULT)); 710a261c58fSBarry Smith } 711a261c58fSBarry Smith 71223f88b65SBarry Smith ((PetscObject)natural)->donotPetscObjectPrintClassNamePrefixType = PETSC_TRUE; 7139566063dSJacob Faibussowitsch PetscCall(VecView(natural, viewer)); 71423f88b65SBarry Smith ((PetscObject)natural)->donotPetscObjectPrintClassNamePrefixType = PETSC_FALSE; 715a261c58fSBarry Smith 716a261c58fSBarry Smith if (format == PETSC_VIEWER_BINARY_MATLAB) { 717a261c58fSBarry Smith MPI_Comm comm; 718a261c58fSBarry Smith FILE *info; 719a261c58fSBarry Smith const char *fieldname; 720da88d4d4SJed Brown char fieldbuf[256]; 721a261c58fSBarry Smith PetscInt dim, ni, nj, nk, pi, pj, pk, dof, n; 722a261c58fSBarry Smith 723a261c58fSBarry Smith /* set the viewer format back into the viewer */ 7249566063dSJacob Faibussowitsch PetscCall(PetscViewerPopFormat(viewer)); 7259566063dSJacob Faibussowitsch PetscCall(PetscObjectGetComm((PetscObject)viewer, &comm)); 7269566063dSJacob Faibussowitsch PetscCall(PetscViewerBinaryGetInfoPointer(viewer, &info)); 7279566063dSJacob Faibussowitsch PetscCall(DMDAGetInfo(da, &dim, &ni, &nj, &nk, &pi, &pj, &pk, &dof, NULL, NULL, NULL, NULL, NULL)); 7289566063dSJacob Faibussowitsch PetscCall(PetscFPrintf(comm, info, "#--- begin code written by PetscViewerBinary for MATLAB format ---#\n")); 7299566063dSJacob Faibussowitsch PetscCall(PetscFPrintf(comm, info, "#$$ tmp = PetscBinaryRead(fd); \n")); 730*48a46eb9SPierre Jolivet if (dim == 1) PetscCall(PetscFPrintf(comm, info, "#$$ tmp = reshape(tmp,%" PetscInt_FMT ",%" PetscInt_FMT ");\n", dof, ni)); 731*48a46eb9SPierre Jolivet if (dim == 2) PetscCall(PetscFPrintf(comm, info, "#$$ tmp = reshape(tmp,%" PetscInt_FMT ",%" PetscInt_FMT ",%" PetscInt_FMT ");\n", dof, ni, nj)); 732*48a46eb9SPierre Jolivet if (dim == 3) PetscCall(PetscFPrintf(comm, info, "#$$ tmp = reshape(tmp,%" PetscInt_FMT ",%" PetscInt_FMT ",%" PetscInt_FMT ",%" PetscInt_FMT ");\n", dof, ni, nj, nk)); 733a261c58fSBarry Smith 734a261c58fSBarry Smith for (n = 0; n < dof; n++) { 7359566063dSJacob Faibussowitsch PetscCall(DMDAGetFieldName(da, n, &fieldname)); 736da88d4d4SJed Brown if (!fieldname || !fieldname[0]) { 73763a3b9bcSJacob Faibussowitsch PetscCall(PetscSNPrintf(fieldbuf, sizeof fieldbuf, "field%" PetscInt_FMT, n)); 738da88d4d4SJed Brown fieldname = fieldbuf; 739a261c58fSBarry Smith } 740*48a46eb9SPierre Jolivet if (dim == 1) PetscCall(PetscFPrintf(comm, info, "#$$ Set.%s.%s = squeeze(tmp(%" PetscInt_FMT ",:))';\n", name, fieldname, n + 1)); 741*48a46eb9SPierre Jolivet if (dim == 2) PetscCall(PetscFPrintf(comm, info, "#$$ Set.%s.%s = squeeze(tmp(%" PetscInt_FMT ",:,:))';\n", name, fieldname, n + 1)); 742*48a46eb9SPierre Jolivet if (dim == 3) PetscCall(PetscFPrintf(comm, info, "#$$ Set.%s.%s = permute(squeeze(tmp(%" PetscInt_FMT ",:,:,:)),[2 1 3]);\n", name, fieldname, n + 1)); 743a261c58fSBarry Smith } 7449566063dSJacob Faibussowitsch PetscCall(PetscFPrintf(comm, info, "#$$ clear tmp; \n")); 7459566063dSJacob Faibussowitsch PetscCall(PetscFPrintf(comm, info, "#--- end code written by PetscViewerBinary for MATLAB format ---#\n\n")); 746a261c58fSBarry Smith } 747a261c58fSBarry Smith 7489566063dSJacob Faibussowitsch PetscCall(VecDestroy(&natural)); 74947c6ae99SBarry Smith } 75047c6ae99SBarry Smith PetscFunctionReturn(0); 75147c6ae99SBarry Smith } 75247c6ae99SBarry Smith 75347c6ae99SBarry Smith #if defined(PETSC_HAVE_HDF5) 7549371c9d4SSatish Balay PetscErrorCode VecLoad_HDF5_DA(Vec xin, PetscViewer viewer) { 7552d95be3dSVaclav Hapla PetscViewer_HDF5 *hdf5 = (PetscViewer_HDF5 *)viewer->data; 7569a42bb27SBarry Smith DM da; 75715b861d2SVaclav Hapla int dim, rdim; 758ec7ae49cSHåkon Strandenes hsize_t dims[6] = {0}, count[6] = {0}, offset[6] = {0}; 759d7dd068bSVaclav Hapla PetscBool dim2 = PETSC_FALSE, timestepping = PETSC_FALSE; 760d7dd068bSVaclav Hapla PetscInt dimension, timestep = PETSC_MIN_INT, dofInd; 76147c6ae99SBarry Smith PetscScalar *x; 76247c6ae99SBarry Smith const char *vecname; 76347c6ae99SBarry Smith hid_t filespace; /* file dataspace identifier */ 76447c6ae99SBarry Smith hid_t dset_id; /* dataset identifier */ 76547c6ae99SBarry Smith hid_t memspace; /* memory dataspace identifier */ 766bfd264e7SBarry Smith hid_t file_id, group; 7677bcbaff4SBarry Smith hid_t scalartype; /* scalar type (H5T_NATIVE_FLOAT or H5T_NATIVE_DOUBLE) */ 7689c7c4993SBarry Smith DM_DA *dd; 76947c6ae99SBarry Smith 77047c6ae99SBarry Smith PetscFunctionBegin; 7717bcbaff4SBarry Smith #if defined(PETSC_USE_REAL_SINGLE) 7727bcbaff4SBarry Smith scalartype = H5T_NATIVE_FLOAT; 7737bcbaff4SBarry Smith #elif defined(PETSC_USE_REAL___FLOAT128) 7747bcbaff4SBarry Smith #error "HDF5 output with 128 bit floats not supported." 775570b7f6dSBarry Smith #elif defined(PETSC_USE_REAL___FP16) 776570b7f6dSBarry Smith #error "HDF5 output with 16 bit floats not supported." 7777bcbaff4SBarry Smith #else 7787bcbaff4SBarry Smith scalartype = H5T_NATIVE_DOUBLE; 7797bcbaff4SBarry Smith #endif 7807bcbaff4SBarry Smith 7819566063dSJacob Faibussowitsch PetscCall(PetscViewerHDF5OpenGroup(viewer, &file_id, &group)); 7829566063dSJacob Faibussowitsch PetscCall(PetscObjectGetName((PetscObject)xin, &vecname)); 7839566063dSJacob Faibussowitsch PetscCall(PetscViewerHDF5CheckTimestepping_Internal(viewer, vecname)); 7849566063dSJacob Faibussowitsch PetscCall(PetscViewerHDF5IsTimestepping(viewer, ×tepping)); 785*48a46eb9SPierre Jolivet if (timestepping) PetscCall(PetscViewerHDF5GetTimestep(viewer, ×tep)); 7869566063dSJacob Faibussowitsch PetscCall(VecGetDM(xin, &da)); 7879c7c4993SBarry Smith dd = (DM_DA *)da->data; 7889566063dSJacob Faibussowitsch PetscCall(DMGetDimension(da, &dimension)); 78947c6ae99SBarry Smith 790ec7ae49cSHåkon Strandenes /* Open dataset */ 791792fecdfSBarry Smith PetscCallHDF5Return(dset_id, H5Dopen2, (group, vecname, H5P_DEFAULT)); 79247c6ae99SBarry Smith 793ec7ae49cSHåkon Strandenes /* Retrieve the dataspace for the dataset */ 794792fecdfSBarry Smith PetscCallHDF5Return(filespace, H5Dget_space, (dset_id)); 795792fecdfSBarry Smith PetscCallHDF5Return(rdim, H5Sget_simple_extent_dims, (filespace, dims, NULL)); 796ec7ae49cSHåkon Strandenes 797ec7ae49cSHåkon Strandenes /* Expected dimension for holding the dof's */ 79847c6ae99SBarry Smith #if defined(PETSC_USE_COMPLEX) 799ec7ae49cSHåkon Strandenes dofInd = rdim - 2; 800ec7ae49cSHåkon Strandenes #else 801ec7ae49cSHåkon Strandenes dofInd = rdim - 1; 80247c6ae99SBarry Smith #endif 803ec7ae49cSHåkon Strandenes 804ec7ae49cSHåkon Strandenes /* The expected number of dimensions, assuming basedimension2 = false */ 805ec7ae49cSHåkon Strandenes dim = dimension; 806ec7ae49cSHåkon Strandenes if (dd->w > 1) ++dim; 807ec7ae49cSHåkon Strandenes if (timestep >= 0) ++dim; 80847c6ae99SBarry Smith #if defined(PETSC_USE_COMPLEX) 809ec7ae49cSHåkon Strandenes ++dim; 81047c6ae99SBarry Smith #endif 811ec7ae49cSHåkon Strandenes 812ec7ae49cSHåkon Strandenes /* In this case the input dataset have one extra, unexpected dimension. */ 813ec7ae49cSHåkon Strandenes if (rdim == dim + 1) { 814ec7ae49cSHåkon Strandenes /* In this case the block size unity */ 815ec7ae49cSHåkon Strandenes if (dd->w == 1 && dims[dofInd] == 1) dim2 = PETSC_TRUE; 816ec7ae49cSHåkon Strandenes 817ec7ae49cSHåkon Strandenes /* Special error message for the case where dof does not match the input file */ 81863a3b9bcSJacob Faibussowitsch else PetscCheck(dd->w == (PetscInt)dims[dofInd], PETSC_COMM_SELF, PETSC_ERR_FILE_UNEXPECTED, "Number of dofs in file is %" PetscInt_FMT ", not %" PetscInt_FMT " as expected", (PetscInt)dims[dofInd], dd->w); 819ec7ae49cSHåkon Strandenes 820ec7ae49cSHåkon Strandenes /* Other cases where rdim != dim cannot be handled currently */ 82163a3b9bcSJacob Faibussowitsch } else PetscCheck(rdim == dim, PETSC_COMM_SELF, PETSC_ERR_FILE_UNEXPECTED, "Dimension of array in file is %d, not %d as expected with dof = %" PetscInt_FMT, rdim, dim, dd->w); 822ec7ae49cSHåkon Strandenes 823ec7ae49cSHåkon Strandenes /* Set up the hyperslab size */ 824ec7ae49cSHåkon Strandenes dim = 0; 825ec7ae49cSHåkon Strandenes if (timestep >= 0) { 826ec7ae49cSHåkon Strandenes offset[dim] = timestep; 827ec7ae49cSHåkon Strandenes count[dim] = 1; 828ec7ae49cSHåkon Strandenes ++dim; 829ec7ae49cSHåkon Strandenes } 830ec7ae49cSHåkon Strandenes if (dimension == 3) { 8319566063dSJacob Faibussowitsch PetscCall(PetscHDF5IntCast(dd->zs, offset + dim)); 8329566063dSJacob Faibussowitsch PetscCall(PetscHDF5IntCast(dd->ze - dd->zs, count + dim)); 833ec7ae49cSHåkon Strandenes ++dim; 834ec7ae49cSHåkon Strandenes } 835ec7ae49cSHåkon Strandenes if (dimension > 1) { 8369566063dSJacob Faibussowitsch PetscCall(PetscHDF5IntCast(dd->ys, offset + dim)); 8379566063dSJacob Faibussowitsch PetscCall(PetscHDF5IntCast(dd->ye - dd->ys, count + dim)); 838ec7ae49cSHåkon Strandenes ++dim; 839ec7ae49cSHåkon Strandenes } 8409566063dSJacob Faibussowitsch PetscCall(PetscHDF5IntCast(dd->xs / dd->w, offset + dim)); 8419566063dSJacob Faibussowitsch PetscCall(PetscHDF5IntCast((dd->xe - dd->xs) / dd->w, count + dim)); 842ec7ae49cSHåkon Strandenes ++dim; 843ec7ae49cSHåkon Strandenes if (dd->w > 1 || dim2) { 844ec7ae49cSHåkon Strandenes offset[dim] = 0; 8459566063dSJacob Faibussowitsch PetscCall(PetscHDF5IntCast(dd->w, count + dim)); 846ec7ae49cSHåkon Strandenes ++dim; 847ec7ae49cSHåkon Strandenes } 848ec7ae49cSHåkon Strandenes #if defined(PETSC_USE_COMPLEX) 849ec7ae49cSHåkon Strandenes offset[dim] = 0; 850ec7ae49cSHåkon Strandenes count[dim] = 2; 851ec7ae49cSHåkon Strandenes ++dim; 852ec7ae49cSHåkon Strandenes #endif 853ec7ae49cSHåkon Strandenes 854ec7ae49cSHåkon Strandenes /* Create the memory and filespace */ 855792fecdfSBarry Smith PetscCallHDF5Return(memspace, H5Screate_simple, (dim, count, NULL)); 856792fecdfSBarry Smith PetscCallHDF5(H5Sselect_hyperslab, (filespace, H5S_SELECT_SET, offset, NULL, count, NULL)); 85747c6ae99SBarry Smith 8589566063dSJacob Faibussowitsch PetscCall(VecGetArray(xin, &x)); 859792fecdfSBarry Smith PetscCallHDF5(H5Dread, (dset_id, scalartype, memspace, filespace, hdf5->dxpl_id, x)); 8609566063dSJacob Faibussowitsch PetscCall(VecRestoreArray(xin, &x)); 86147c6ae99SBarry Smith 86247c6ae99SBarry Smith /* Close/release resources */ 8639371c9d4SSatish Balay if (group != file_id) { PetscCallHDF5(H5Gclose, (group)); } 864792fecdfSBarry Smith PetscCallHDF5(H5Sclose, (filespace)); 865792fecdfSBarry Smith PetscCallHDF5(H5Sclose, (memspace)); 866792fecdfSBarry Smith PetscCallHDF5(H5Dclose, (dset_id)); 86747c6ae99SBarry Smith PetscFunctionReturn(0); 86847c6ae99SBarry Smith } 86947c6ae99SBarry Smith #endif 87047c6ae99SBarry Smith 8719371c9d4SSatish Balay PetscErrorCode VecLoad_Binary_DA(Vec xin, PetscViewer viewer) { 8729a42bb27SBarry Smith DM da; 87347c6ae99SBarry Smith Vec natural; 87447c6ae99SBarry Smith const char *prefix; 87547c6ae99SBarry Smith PetscInt bs; 87647c6ae99SBarry Smith PetscBool flag; 87747c6ae99SBarry Smith DM_DA *dd; 87847c6ae99SBarry Smith #if defined(PETSC_HAVE_MPIIO) 87947c6ae99SBarry Smith PetscBool isMPIIO; 88047c6ae99SBarry Smith #endif 88147c6ae99SBarry Smith 88247c6ae99SBarry Smith PetscFunctionBegin; 8839566063dSJacob Faibussowitsch PetscCall(VecGetDM(xin, &da)); 88447c6ae99SBarry Smith dd = (DM_DA *)da->data; 88547c6ae99SBarry Smith #if defined(PETSC_HAVE_MPIIO) 8869566063dSJacob Faibussowitsch PetscCall(PetscViewerBinaryGetUseMPIIO(viewer, &isMPIIO)); 88747c6ae99SBarry Smith if (isMPIIO) { 8889566063dSJacob Faibussowitsch PetscCall(DMDAArrayMPIIO(da, viewer, xin, PETSC_FALSE)); 88947c6ae99SBarry Smith PetscFunctionReturn(0); 89047c6ae99SBarry Smith } 89147c6ae99SBarry Smith #endif 89247c6ae99SBarry Smith 8939566063dSJacob Faibussowitsch PetscCall(PetscObjectGetOptionsPrefix((PetscObject)xin, &prefix)); 8949566063dSJacob Faibussowitsch PetscCall(DMDACreateNaturalVector(da, &natural)); 8959566063dSJacob Faibussowitsch PetscCall(PetscObjectSetName((PetscObject)natural, ((PetscObject)xin)->name)); 8969566063dSJacob Faibussowitsch PetscCall(PetscObjectSetOptionsPrefix((PetscObject)natural, prefix)); 8979566063dSJacob Faibussowitsch PetscCall(VecLoad(natural, viewer)); 8989566063dSJacob Faibussowitsch PetscCall(DMDANaturalToGlobalBegin(da, natural, INSERT_VALUES, xin)); 8999566063dSJacob Faibussowitsch PetscCall(DMDANaturalToGlobalEnd(da, natural, INSERT_VALUES, xin)); 9009566063dSJacob Faibussowitsch PetscCall(VecDestroy(&natural)); 9019566063dSJacob Faibussowitsch PetscCall(PetscInfo(xin, "Loading vector from natural ordering into DMDA\n")); 9029566063dSJacob Faibussowitsch PetscCall(PetscOptionsGetInt(NULL, ((PetscObject)xin)->prefix, "-vecload_block_size", &bs, &flag)); 903*48a46eb9SPierre Jolivet if (flag && bs != dd->w) PetscCall(PetscInfo(xin, "Block size in file %" PetscInt_FMT " not equal to DMDA's dof %" PetscInt_FMT "\n", bs, dd->w)); 90447c6ae99SBarry Smith PetscFunctionReturn(0); 90547c6ae99SBarry Smith } 90647c6ae99SBarry Smith 9079371c9d4SSatish Balay PetscErrorCode VecLoad_Default_DA(Vec xin, PetscViewer viewer) { 9089a42bb27SBarry Smith DM da; 90947c6ae99SBarry Smith PetscBool isbinary; 91047c6ae99SBarry Smith #if defined(PETSC_HAVE_HDF5) 91147c6ae99SBarry Smith PetscBool ishdf5; 91247c6ae99SBarry Smith #endif 91347c6ae99SBarry Smith 91447c6ae99SBarry Smith PetscFunctionBegin; 9159566063dSJacob Faibussowitsch PetscCall(VecGetDM(xin, &da)); 9167a8be351SBarry Smith PetscCheck(da, PetscObjectComm((PetscObject)xin), PETSC_ERR_ARG_WRONG, "Vector not generated from a DMDA"); 91747c6ae99SBarry Smith 91847c6ae99SBarry Smith #if defined(PETSC_HAVE_HDF5) 9199566063dSJacob Faibussowitsch PetscCall(PetscObjectTypeCompare((PetscObject)viewer, PETSCVIEWERHDF5, &ishdf5)); 92047c6ae99SBarry Smith #endif 9219566063dSJacob Faibussowitsch PetscCall(PetscObjectTypeCompare((PetscObject)viewer, PETSCVIEWERBINARY, &isbinary)); 92247c6ae99SBarry Smith 92347c6ae99SBarry Smith if (isbinary) { 9249566063dSJacob Faibussowitsch PetscCall(VecLoad_Binary_DA(xin, viewer)); 92547c6ae99SBarry Smith #if defined(PETSC_HAVE_HDF5) 92647c6ae99SBarry Smith } else if (ishdf5) { 9279566063dSJacob Faibussowitsch PetscCall(VecLoad_HDF5_DA(xin, viewer)); 92847c6ae99SBarry Smith #endif 92998921bdaSJacob Faibussowitsch } else SETERRQ(PETSC_COMM_SELF, PETSC_ERR_SUP, "Viewer type %s not supported for vector loading", ((PetscObject)viewer)->type_name); 93047c6ae99SBarry Smith PetscFunctionReturn(0); 93147c6ae99SBarry Smith } 932