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Merge 3D mpi versions

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This commit is contained in:
Jan Eitzinger 2024-01-31 17:40:36 +01:00
parent d53da89b95
commit 91cbb29f6e
52 changed files with 149 additions and 2344 deletions
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71
BasicSolver/3D-mpi-io/Makefile
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#=======================================================================================
# Copyright (C) 2022 NHR@FAU, University Erlangen-Nuremberg.
# All rights reserved.
# Use of this source code is governed by a MIT-style
# license that can be found in the LICENSE file.
#=======================================================================================
#CONFIGURE BUILD SYSTEM
TARGET = exe-$(TAG)
BUILD_DIR = ./$(TAG)
SRC_DIR = ./src
MAKE_DIR = ./
Q ?= @
#DO NOT EDIT BELOW
include $(MAKE_DIR)/config.mk
include $(MAKE_DIR)/include_$(TAG).mk
INCLUDES += -I$(SRC_DIR) -I$(BUILD_DIR)
VPATH = $(SRC_DIR)
SRC = $(wildcard $(SRC_DIR)/*.c)
ASM = $(patsubst $(SRC_DIR)/%.c, $(BUILD_DIR)/%.s, $(SRC))
OBJ = $(patsubst $(SRC_DIR)/%.c, $(BUILD_DIR)/%.o, $(SRC))
SOURCES = $(SRC) $(wildcard $(SRC_DIR)/*.h)
CPPFLAGS := $(CPPFLAGS) $(DEFINES) $(OPTIONS) $(INCLUDES)
${TARGET}: $(BUILD_DIR) $(OBJ)
$(info ===> LINKING $(TARGET))
$(Q)${LINKER} ${LFLAGS} -o $(TARGET) $(OBJ) $(LIBS)
$(BUILD_DIR)/%.o: %.c $(MAKE_DIR)/include_$(TAG).mk $(MAKE_DIR)/config.mk
$(info ===> COMPILE $@)
$(CC) -c $(CPPFLAGS) $(CFLAGS) $< -o $@
$(Q)$(GCC) $(CPPFLAGS) -MT $(@:.d=.o) -MM $< > $(BUILD_DIR)/$*.d
$(BUILD_DIR)/%.s: %.c
$(info ===> GENERATE ASM $@)
$(CC) -S $(CPPFLAGS) $(CFLAGS) $< -o $@
.PHONY: clean distclean tags info asm format
clean:
$(info ===> CLEAN)
@rm -rf $(BUILD_DIR)
@rm -f tags
distclean: clean
$(info ===> DIST CLEAN)
@rm -f $(TARGET)
info:
$(info $(CFLAGS))
$(Q)$(CC) $(VERSION)
asm: $(BUILD_DIR) $(ASM)
tags:
$(info ===> GENERATE TAGS)
$(Q)ctags -R
format:
@for src in $(SOURCES) ; do \
echo "Formatting $$src" ; \
clang-format -i $$src ; \
done
@echo "Done"
$(BUILD_DIR):
@mkdir $(BUILD_DIR)
-include $(OBJ:.o=.d)

78
BasicSolver/3D-mpi-io/README.md
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# C source skeleton
## Build
1. Configure the toolchain and additional options in `config.mk`:
```
# Supported: GCC, CLANG, ICC
TAG ?= GCC
ENABLE_OPENMP ?= false
OPTIONS += -DARRAY_ALIGNMENT=64
#OPTIONS += -DVERBOSE
#OPTIONS += -DVERBOSE_AFFINITY
#OPTIONS += -DVERBOSE_DATASIZE
#OPTIONS += -DVERBOSE_TIMER
```
The verbosity options enable detailed output about solver, affinity settings, allocation sizes and timer resolution.
For debugging you may want to set the VERBOSE option:
```
# Supported: GCC, CLANG, ICC
TAG ?= GCC
ENABLE_OPENMP ?= false
OPTIONS += -DARRAY_ALIGNMENT=64
OPTIONS += -DVERBOSE
#OPTIONS += -DVERBOSE_AFFINITY
#OPTIONS += -DVERBOSE_DATASIZE
#OPTIONS += -DVERBOSE_TIMER
`
2. Build with:
```
make
```
You can build multiple toolchains in the same directory, but notice that the Makefile is only acting on the one currently set.
Intermediate build results are located in the `<TOOLCHAIN>` directory.
To output the executed commands use:
```
make Q=
```
3. Clean up with:
```
make clean
```
to clean intermediate build results.
```
make distclean
```
to clean intermediate build results and binary.
4. (Optional) Generate assembler:
```
make asm
```
The assembler files will also be located in the `<TOOLCHAIN>` directory.
## Usage
You have to provide a parameter file describing the problem you want to solve:
```
./exe-CLANG dcavity.par
```
Examples are given in in dcavity (a lid driven cavity test case) and canal (simulating a empty canal).
You can plot the resulting velocity and pressure fields using gnuplot:
```
gnuplot vector.plot
```
and for the pressure:
```
gnuplot surface.plot
```

52
BasicSolver/3D-mpi-io/canal.par
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#==============================================================================
# Laminar Canal Flow
#==============================================================================
# Problem specific Data:
# ---------------------
name canal # name of flow setup
bcLeft 3 # flags for boundary conditions
bcRight 3 # 1 = no-slip 3 = outflow
bcBottom 1 # 2 = free-slip 4 = periodic
bcTop 1 #
bcFront 1 #
bcBack 1 #
gx 0.0 # Body forces (e.g. gravity)
gy 0.0 #
gz 0.0 #
re 100.0 # Reynolds number
u_init 1.0 # initial value for velocity in x-direction
v_init 0.0 # initial value for velocity in y-direction
w_init 0.0 # initial value for velocity in z-direction
p_init 0.0 # initial value for pressure
# Geometry Data:
# -------------
xlength 30.0 # domain size in x-direction
ylength 4.0 # domain size in y-direction
zlength 4.0 # domain size in z-direction
imax 200 # number of interior cells in x-direction
jmax 50 # number of interior cells in y-direction
kmax 50 # number of interior cells in z-direction
# Time Data:
# ---------
te 100.0 # final time
dt 0.02 # time stepsize
tau 0.5 # safety factor for time stepsize control (<0 constant delt)
# Pressure Iteration Data:
# -----------------------
itermax 500 # maximal number of pressure iteration in one time step
eps 0.0001 # stopping tolerance for pressure iteration
omg 1.3 # relaxation parameter for SOR iteration
gamma 0.9 # upwind differencing factor gamma
#===============================================================================

13
BasicSolver/3D-mpi-io/config.mk
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# Supported: GCC, CLANG, ICC
TAG ?= CLANG
ENABLE_MPI ?= true
ENABLE_OPENMP ?= false
#Feature options
OPTIONS += -DARRAY_ALIGNMENT=64
OPTIONS += -DVERBOSE
#OPTIONS += -DDEBUG
#OPTIONS += -DBOUNDCHECK
#OPTIONS += -DVERBOSE_AFFINITY
#OPTIONS += -DVERBOSE_DATASIZE
#OPTIONS += -DVERBOSE_TIMER

52
BasicSolver/3D-mpi-io/dcavity.par
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#==============================================================================
# Driven Cavity
#==============================================================================
# Problem specific Data:
# ---------------------
name dcavity # name of flow setup
bcLeft 1 # flags for boundary conditions
bcRight 1 # 1 = no-slip 3 = outflow
bcBottom 1 # 2 = free-slip 4 = periodic
bcTop 1 #
bcFront 1 #
bcBack 1 #
gx 0.0 # Body forces (e.g. gravity)
gy 0.0 #
gz 0.0 #
re 1000.0 # Reynolds number
u_init 0.0 # initial value for velocity in x-direction
v_init 0.0 # initial value for velocity in y-direction
w_init 0.0 # initial value for velocity in z-direction
p_init 0.0 # initial value for pressure
# Geometry Data:
# -------------
xlength 1.0 # domain size in x-direction
ylength 1.0 # domain size in y-direction
zlength 1.0 # domain size in z-direction
imax 128 # number of interior cells in x-direction
jmax 128 # number of interior cells in y-direction
kmax 128 # number of interior cells in z-direction
# Time Data:
# ---------
te 10.0 # final time
dt 0.02 # time stepsize
tau 0.5 # safety factor for time stepsize control (<0 constant delt)
# Pressure Iteration Data:
# -----------------------
itermax 1000 # maximal number of pressure iteration in one time step
eps 0.001 # stopping tolerance for pressure iteration
omg 1.8 # relaxation parameter for SOR iteration
gamma 0.9 # upwind differencing factor gamma
#===============================================================================

21
BasicSolver/3D-mpi-io/include_CLANG.mk
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ifeq ($(ENABLE_MPI),true)
CC = mpicc
DEFINES = -D_MPI
else
CC = cc
endif
GCC = cc
LINKER = $(CC)
ifeq ($(ENABLE_OPENMP),true)
OPENMP = -fopenmp
#OPENMP = -Xpreprocessor -fopenmp #required on Macos with homebrew libomp
LIBS = # -lomp
endif
VERSION = --version
CFLAGS = -Ofast -std=c17
LFLAGS = $(OPENMP) -lm
DEFINES += -D_GNU_SOURCE# -DDEBUG
INCLUDES =

14
BasicSolver/3D-mpi-io/include_GCC.mk
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CC = gcc
GCC = gcc
LINKER = $(CC)
ifeq ($(ENABLE_OPENMP),true)
OPENMP = -fopenmp
endif
VERSION = --version
CFLAGS = -Ofast -ffreestanding -std=c99 $(OPENMP)
LFLAGS = $(OPENMP)
DEFINES = -D_GNU_SOURCE
INCLUDES =
LIBS =

14
BasicSolver/3D-mpi-io/include_ICC.mk
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CC = icc
GCC = gcc
LINKER = $(CC)
ifeq ($(ENABLE_OPENMP),true)
OPENMP = -qopenmp
endif
VERSION = --version
CFLAGS = -O3 -xHost -qopt-zmm-usage=high -std=c99 $(OPENMP)
LFLAGS = $(OPENMP)
DEFINES = -D_GNU_SOURCE
INCLUDES =
LIBS =

38
BasicSolver/3D-mpi-io/src/allocate.c
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/*
* Copyright (C) 2022 NHR@FAU, University Erlangen-Nuremberg.
* All rights reserved.
* Use of this source code is governed by a MIT-style
* license that can be found in the LICENSE file.
*/
#include <errno.h>
#include <stddef.h>
#include <stdio.h>
#include <stdlib.h>
#include "allocate.h"
void* allocate(size_t alignment, size_t bytesize)
{
int errorCode;
void* ptr;
errorCode = posix_memalign(&ptr, alignment, bytesize);
if (errorCode) {
if (errorCode == EINVAL) {
fprintf(stderr, "Error: Alignment parameter is not a power of two\n");
exit(EXIT_FAILURE);
}
if (errorCode == ENOMEM) {
fprintf(stderr, "Error: Insufficient memory to fulfill the request\n");
exit(EXIT_FAILURE);
}
}
if (ptr == NULL) {
fprintf(stderr, "Error: posix_memalign failed!\n");
exit(EXIT_FAILURE);
}
return ptr;
}

13
BasicSolver/3D-mpi-io/src/allocate.h
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/*
* Copyright (C) 2022 NHR@FAU, University Erlangen-Nuremberg.
* All rights reserved.
* Use of this source code is governed by a MIT-style
* license that can be found in the LICENSE file.
*/
#ifndef __ALLOCATE_H_
#define __ALLOCATE_H_
#include <stdlib.h>
extern void* allocate(size_t alignment, size_t bytesize);
#endif

359
BasicSolver/3D-mpi-io/src/comm.c
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/*
* Copyright (C) 2022 NHR@FAU, University Erlangen-Nuremberg.
* All rights reserved. This file is part of nusif-solver.
* Use of this source code is governed by a MIT style
* license that can be found in the LICENSE file.
*/
#if defined(_MPI)
#include <mpi.h>
#endif
#include <stddef.h>
#include <stdio.h>
#include <stdlib.h>
#include "allocate.h"
#include "comm.h"
#if defined(_MPI)
// subroutines local to this module
static int sizeOfRank(int rank, int size, int N)
{
return N / size + ((N % size > rank) ? 1 : 0);
}
static void setupCommunication(Comm* c, Direction direction, int layer)
{
int imaxLocal = c->imaxLocal;
int jmaxLocal = c->jmaxLocal;
int kmaxLocal = c->kmaxLocal;
size_t dblsize = sizeof(double);
int sizes[NDIMS];
int subSizes[NDIMS];
int starts[NDIMS];
int offset = 0;
sizes[IDIM] = imaxLocal + 2;
sizes[JDIM] = jmaxLocal + 2;
sizes[KDIM] = kmaxLocal + 2;
if (layer == HALO) {
offset = 1;
}
switch (direction) {
case LEFT:
subSizes[IDIM] = 1;
subSizes[JDIM] = jmaxLocal;
subSizes[KDIM] = kmaxLocal;
starts[IDIM] = 1 - offset;
starts[JDIM] = 1;
starts[KDIM] = 1;
break;
case RIGHT:
subSizes[IDIM] = 1;
subSizes[JDIM] = jmaxLocal;
subSizes[KDIM] = kmaxLocal;
starts[IDIM] = imaxLocal + offset;
starts[JDIM] = 1;
starts[KDIM] = 1;
break;
case BOTTOM:
subSizes[IDIM] = imaxLocal;
subSizes[JDIM] = 1;
subSizes[KDIM] = kmaxLocal;
starts[IDIM] = 1;
starts[JDIM] = 1 - offset;
starts[KDIM] = 1;
break;
case TOP:
subSizes[IDIM] = imaxLocal;
subSizes[JDIM] = 1;
subSizes[KDIM] = kmaxLocal;
starts[IDIM] = 1;
starts[JDIM] = jmaxLocal + offset;
starts[KDIM] = 1;
break;
case FRONT:
subSizes[IDIM] = imaxLocal;
subSizes[JDIM] = jmaxLocal;
subSizes[KDIM] = 1;
starts[IDIM] = 1;
starts[JDIM] = 1;
starts[KDIM] = 1 - offset;
break;
case BACK:
subSizes[IDIM] = imaxLocal;
subSizes[JDIM] = jmaxLocal;
subSizes[KDIM] = 1;
starts[IDIM] = 1;
starts[JDIM] = 1;
starts[KDIM] = kmaxLocal + offset;
break;
case NDIRS:
printf("ERROR!\n");
break;
}
if (layer == HALO) {
MPI_Type_create_subarray(NDIMS,
sizes,
subSizes,
starts,
MPI_ORDER_C,
MPI_DOUBLE,
&c->rbufferTypes[direction]);
MPI_Type_commit(&c->rbufferTypes[direction]);
} else if (layer == BULK) {
MPI_Type_create_subarray(NDIMS,
sizes,
subSizes,
starts,
MPI_ORDER_C,
MPI_DOUBLE,
&c->sbufferTypes[direction]);
MPI_Type_commit(&c->sbufferTypes[direction]);
}
}
static int sum(int* sizes, int position)
{
int sum = 0;
for (int i = 0; i < position; i++) {
sum += sizes[i];
}
return sum;
}
#endif
// exported subroutines
void commReduction(double* v, int op)
{
#if defined(_MPI)
if (op == MAX) {
MPI_Allreduce(MPI_IN_PLACE, v, 1, MPI_DOUBLE, MPI_MAX, MPI_COMM_WORLD);
} else if (op == SUM) {
MPI_Allreduce(MPI_IN_PLACE, v, 1, MPI_DOUBLE, MPI_SUM, MPI_COMM_WORLD);
}
#endif
}
int commIsBoundary(Comm* c, Direction direction)
{
#if defined(_MPI)
switch (direction) {
case LEFT:
return c->coords[ICORD] == 0;
break;
case RIGHT:
return c->coords[ICORD] == (c->dims[ICORD] - 1);
break;
case BOTTOM:
return c->coords[JCORD] == 0;
break;
case TOP:
return c->coords[JCORD] == (c->dims[JCORD] - 1);
break;
case FRONT:
return c->coords[KCORD] == 0;
break;
case BACK:
return c->coords[KCORD] == (c->dims[KCORD] - 1);
break;
case NDIRS:
printf("ERROR!\n");
break;
}
#endif
return 1;
}
void commExchange(Comm* c, double* grid)
{
#if defined(_MPI)
int counts[6] = { 1, 1, 1, 1, 1, 1 };
MPI_Aint displs[6] = { 0, 0, 0, 0, 0, 0 };
MPI_Neighbor_alltoallw(grid,
counts,
displs,
c->sbufferTypes,
grid,
counts,
displs,
c->rbufferTypes,
c->comm);
#endif
}
void commShift(Comm* c, double* f, double* g, double* h)
{
#if defined(_MPI)
MPI_Request requests[6] = { MPI_REQUEST_NULL,
MPI_REQUEST_NULL,
MPI_REQUEST_NULL,
MPI_REQUEST_NULL,
MPI_REQUEST_NULL,
MPI_REQUEST_NULL };
/* shift G */
/* receive ghost cells from bottom neighbor */
MPI_Irecv(g,
1,
c->rbufferTypes[BOTTOM],
c->neighbours[BOTTOM],
0,
c->comm,
&requests[0]);
/* send ghost cells to top neighbor */
MPI_Isend(g, 1, c->sbufferTypes[TOP], c->neighbours[TOP], 0, c->comm, &requests[1]);
/* shift F */
/* receive ghost cells from left neighbor */
MPI_Irecv(f, 1, c->rbufferTypes[LEFT], c->neighbours[LEFT], 1, c->comm, &requests[2]);
/* send ghost cells to right neighbor */
MPI_Isend(f,
1,
c->sbufferTypes[RIGHT],
c->neighbours[RIGHT],
1,
c->comm,
&requests[3]);
/* shift H */
/* receive ghost cells from front neighbor */
MPI_Irecv(h,
1,
c->rbufferTypes[FRONT],
c->neighbours[FRONT],
2,
c->comm,
&requests[4]);
/* send ghost cells to back neighbor */
MPI_Isend(h, 1, c->sbufferTypes[BACK], c->neighbours[BACK], 2, c->comm, &requests[5]);
MPI_Waitall(6, requests, MPI_STATUSES_IGNORE);
#endif
}
void commGetOffsets(Comm* c, int offsets[], int kmax, int jmax, int imax)
{
#if defined(_MPI)
int sum = 0;
for (int i = 0; i < c->coords[ICORD]; i++) {
sum += sizeOfRank(i, c->dims[ICORD], imax);
}
offsets[IDIM] = sum;
sum = 0;
for (int i = 0; i < c->coords[JCORD]; i++) {
sum += sizeOfRank(i, c->dims[JCORD], jmax);
}
offsets[JDIM] = sum;
sum = 0;
for (int i = 0; i < c->coords[KCORD]; i++) {
sum += sizeOfRank(i, c->dims[KCORD], kmax);
}
offsets[KDIM] = sum;
#endif
}
void commPrintConfig(Comm* c)
{
#if defined(_MPI)
fflush(stdout);
MPI_Barrier(MPI_COMM_WORLD);
if (commIsMaster(c)) {
printf("Communication setup:\n");
}
for (int i = 0; i < c->size; i++) {
if (i == c->rank) {
printf("\tRank %d of %d\n", c->rank, c->size);
printf("\tNeighbours (front, back, bottom, top, left, right): %d, %d, %d, "
"%d, %d, %d\n",
c->neighbours[FRONT],
c->neighbours[BACK],
c->neighbours[BOTTOM],
c->neighbours[TOP],
c->neighbours[LEFT],
c->neighbours[RIGHT]);
printf("\tCoordinates (k,j,i) %d %d %d\n",
c->coords[KCORD],
c->coords[JCORD],
c->coords[ICORD]);
printf("\tLocal domain size (k,j,i) %dx%dx%d\n",
c->kmaxLocal,
c->jmaxLocal,
c->imaxLocal);
fflush(stdout);
}
}
MPI_Barrier(MPI_COMM_WORLD);
#endif
}
void commInit(Comm* c, int argc, char** argv)
{
#if defined(_MPI)
MPI_Init(&argc, &argv);
MPI_Comm_rank(MPI_COMM_WORLD, &(c->rank));
MPI_Comm_size(MPI_COMM_WORLD, &(c->size));
#endif
}
void commPartition(Comm* c, int kmax, int jmax, int imax)
{
#if defined(_MPI)
int dims[NDIMS] = { 0, 0, 0 };
int periods[NDIMS] = { 0, 0, 0 };
MPI_Dims_create(c->size, NDIMS, dims);
MPI_Cart_create(MPI_COMM_WORLD, NCORDS, dims, periods, 0, &c->comm);
MPI_Cart_shift(c->comm, ICORD, 1, &c->neighbours[LEFT], &c->neighbours[RIGHT]);
MPI_Cart_shift(c->comm, JCORD, 1, &c->neighbours[BOTTOM], &c->neighbours[TOP]);
MPI_Cart_shift(c->comm, KCORD, 1, &c->neighbours[FRONT], &c->neighbours[BACK]);
MPI_Cart_get(c->comm, NCORDS, c->dims, periods, c->coords);
c->imaxLocal = sizeOfRank(c->rank, dims[ICORD], imax);
c->jmaxLocal = sizeOfRank(c->rank, dims[JCORD], jmax);
c->kmaxLocal = sizeOfRank(c->rank, dims[KCORD], kmax);
// setup buffer types for communication
setupCommunication(c, LEFT, BULK);
setupCommunication(c, LEFT, HALO);
setupCommunication(c, RIGHT, BULK);
setupCommunication(c, RIGHT, HALO);
setupCommunication(c, BOTTOM, BULK);
setupCommunication(c, BOTTOM, HALO);
setupCommunication(c, TOP, BULK);
setupCommunication(c, TOP, HALO);
setupCommunication(c, FRONT, BULK);
setupCommunication(c, FRONT, HALO);
setupCommunication(c, BACK, BULK);
setupCommunication(c, BACK, HALO);
#else
c->imaxLocal = imax;
c->jmaxLocal = jmax;
c->kmaxLocal = kmax;
#endif
}
void commFinalize(Comm* c)
{
#if defined(_MPI)
for (int i = 0; i < NDIRS; i++) {
MPI_Type_free(&c->sbufferTypes[i]);
MPI_Type_free(&c->rbufferTypes[i]);
}
MPI_Finalize();
#endif
}

51
BasicSolver/3D-mpi-io/src/comm.h
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/*
* Copyright (C) 2024 NHR@FAU, University Erlangen-Nuremberg.
* All rights reserved. This file is part of nusif-solver.
* Use of this source code is governed by a MIT style
* license that can be found in the LICENSE file.
*/
#ifndef __COMM_H_
#define __COMM_H_
#if defined(_MPI)
#include <mpi.h>
#endif
/*
* Spatial directions:
* ICORD (0) from 0 (LEFT) to imax (RIGHT)
* JCORD (1) from 0 (BOTTOM) to jmax (TOP)
* KCORD (2) from 0 (FRONT) to kmax (BACK)
* All derived Subarray types are in C ordering
* with indices KDIM (0), JDIM(1) and IDIM(2)
* */
typedef enum direction { LEFT = 0, RIGHT, BOTTOM, TOP, FRONT, BACK, NDIRS } Direction;
typedef enum coordinates { ICORD = 0, JCORD, KCORD, NCORDS } Coordinates;
typedef enum dimension { KDIM = 0, JDIM, IDIM, NDIMS } Dimension;
enum layer { HALO = 0, BULK };
enum op { MAX = 0, SUM };
typedef struct {
int rank;
int size;
#if defined(_MPI)
MPI_Comm comm;
MPI_Datatype sbufferTypes[NDIRS];
MPI_Datatype rbufferTypes[NDIRS];
#endif
int neighbours[NDIRS];
int coords[NDIMS], dims[NDIMS];
int imaxLocal, jmaxLocal, kmaxLocal;
MPI_File fh;
} Comm;
extern void commInit(Comm* c, int argc, char** argv);
extern void commPartition(Comm* c, int kmax, int jmax, int imax);
extern void commFinalize(Comm* comm);
extern void commPrintConfig(Comm*);
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 commGetOffsets(Comm* c, int offsets[], int kmax, int jmax, int imax);
static inline int commIsMaster(Comm* c) { return c->rank == 0; }
#endif // __COMM_H_

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BasicSolver/3D-mpi-io/src/grid.h
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/*
* Copyright (C) 2022 NHR@FAU, University Erlangen-Nuremberg.
* All rights reserved. This file is part of nusif-solver.
* Use of this source code is governed by a MIT style
* license that can be found in the LICENSE file.
*/
#ifndef __GRID_H_
#define __GRID_H_
typedef struct {
double dx, dy, dz;
int imax, jmax, kmax;
double xlength, ylength, zlength;
} Grid;
#endif // __GRID_H_

54
BasicSolver/3D-mpi-io/src/likwid-marker.h
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/*
* =======================================================================================
*
* Author: Jan Eitzinger (je), jan.eitzinger@fau.de
* Copyright (c) 2020 RRZE, University Erlangen-Nuremberg
*
* Permission is hereby granted, free of charge, to any person obtaining a copy
* of this software and associated documentation files (the "Software"), to deal
* in the Software without restriction, including without limitation the rights
* to use, copy, modify, merge, publish, distribute, sublicense, and/or sell
* copies of the Software, and to permit persons to whom the Software is
* furnished to do so, subject to the following conditions:
*
* The above copyright notice and this permission notice shall be included in all
* copies or substantial portions of the Software.
*
* THE SOFTWARE IS PROVIDED "AS IS", WITHOUT WARRANTY OF ANY KIND, EXPRESS OR
* IMPLIED, INCLUDING BUT NOT LIMITED TO THE WARRANTIES OF MERCHANTABILITY,
* FITNESS FOR A PARTICULAR PURPOSE AND NONINFRINGEMENT. IN NO EVENT SHALL THE
* AUTHORS OR COPYRIGHT HOLDERS BE LIABLE FOR ANY CLAIM, DAMAGES OR OTHER
* LIABILITY, WHETHER IN AN ACTION OF CONTRACT, TORT OR OTHERWISE, ARISING FROM,
* OUT OF OR IN CONNECTION WITH THE SOFTWARE OR THE USE OR OTHER DEALINGS IN THE
* SOFTWARE.
*
* =======================================================================================
*/
#ifndef LIKWID_MARKERS_H
#define LIKWID_MARKERS_H
#ifdef LIKWID_PERFMON
#include <likwid.h>
#define LIKWID_MARKER_INIT likwid_markerInit()
#define LIKWID_MARKER_THREADINIT likwid_markerThreadInit()
#define LIKWID_MARKER_SWITCH likwid_markerNextGroup()
#define LIKWID_MARKER_REGISTER(regionTag) likwid_markerRegisterRegion(regionTag)
#define LIKWID_MARKER_START(regionTag) likwid_markerStartRegion(regionTag)
#define LIKWID_MARKER_STOP(regionTag) likwid_markerStopRegion(regionTag)
#define LIKWID_MARKER_CLOSE likwid_markerClose()
#define LIKWID_MARKER_RESET(regionTag) likwid_markerResetRegion(regionTag)
#define LIKWID_MARKER_GET(regionTag, nevents, events, time, count) \
likwid_markerGetRegion(regionTag, nevents, events, time, count)
#else /* LIKWID_PERFMON */
#define LIKWID_MARKER_INIT
#define LIKWID_MARKER_THREADINIT
#define LIKWID_MARKER_SWITCH
#define LIKWID_MARKER_REGISTER(regionTag)
#define LIKWID_MARKER_START(regionTag)
#define LIKWID_MARKER_STOP(regionTag)
#define LIKWID_MARKER_CLOSE
#define LIKWID_MARKER_GET(regionTag, nevents, events, time, count)
#define LIKWID_MARKER_RESET(regionTag)
#endif /* LIKWID_PERFMON */
#endif /*LIKWID_MARKERS_H*/

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BasicSolver/3D-mpi-io/src/main.c
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/*
* Copyright (C) 2024 NHR@FAU, University Erlangen-Nuremberg.
* All rights reserved.
* Use of this source code is governed by a MIT-style
* license that can be found in the LICENSE file.
*/
#include <float.h>
#include <limits.h>
#include <stdio.h>
#include <stdlib.h>
#include <unistd.h>
#include "allocate.h"
#include "comm.h"
#include "parameter.h"
#include "progress.h"
#include "solver.h"
#include "timing.h"
#include "vtkWriter.h"
int main(int argc, char** argv)
{
double timeStart, timeStop;
Parameter p;
Solver s;
commInit(&s.comm, argc, argv);
initParameter(&p);
if (argc != 2) {
printf("Usage: %s <configFile>\n", argv[0]);
exit(EXIT_SUCCESS);
}
readParameter(&p, argv[1]);
commPartition(&s.comm, p.kmax, p.jmax, p.imax);
if (commIsMaster(&s.comm)) {
printParameter(&p);
}
initSolver(&s, &p);
#ifndef VERBOSE
initProgress(s.te);
#endif
double tau = s.tau;
double te = s.te;
double t = 0.0;
timeStart = getTimeStamp();
while (t <= te) {
if (tau > 0.0) computeTimestep(&s);
setBoundaryConditions(&s);
setSpecialBoundaryCondition(&s);
computeFG(&s);
computeRHS(&s);
solve(&s);
adaptUV(&s);
t += s.dt;
#ifdef VERBOSE
if (commIsMaster(&s.comm)) {
printf("TIME %f , TIMESTEP %f\n", t, s.dt);
}
#else
printProgress(t);
#endif
}
timeStop = getTimeStamp();
#ifndef VERBOSE
stopProgress();
#endif
if (commIsMaster(&s.comm)) {
printf("Solution took %.2fs\n", timeStop - timeStart);
}
VtkOptions opts = { .grid = s.grid, .comm = s.comm };
vtkOpen(&opts, s.problem);
vtkScalar(&opts, "pressure", s.p);
vtkVector(&opts, "velocity", (VtkVector) { s.u, s.v, s.w });
vtkClose(&opts);
commFinalize(&s.comm);
return EXIT_SUCCESS;
}

126
BasicSolver/3D-mpi-io/src/parameter.c
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/*
* Copyright (C) 2022 NHR@FAU, University Erlangen-Nuremberg.
* All rights reserved. This file is part of nusif-solver.
* Use of this source code is governed by a MIT style
* license that can be found in the LICENSE file.
*/
#include <stdio.h>
#include <stdlib.h>
#include <string.h>
#include "parameter.h"
#include "util.h"
#define MAXLINE 4096
void initParameter(Parameter* param)
{
param->xlength = 1.0;
param->ylength = 1.0;
param->zlength = 1.0;
param->imax = 100;
param->jmax = 100;
param->kmax = 100;
param->itermax = 1000;
param->eps = 0.0001;
param->omg = 1.7;
param->re = 100.0;
param->gamma = 0.9;
param->tau = 0.5;
}
void readParameter(Parameter* param, const char* filename)
{
FILE* fp = fopen(filename, "r");
char line[MAXLINE];
int i;
if (!fp) {
fprintf(stderr, "Could not open parameter file: %s\n", filename);
exit(EXIT_FAILURE);
}
while (!feof(fp)) {
line[0] = '\0';
fgets(line, MAXLINE, fp);
for (i = 0; line[i] != '\0' && line[i] != '#'; i++)
;
line[i] = '\0';
char* tok = strtok(line, " ");
char* val = strtok(NULL, " ");
#define PARSE_PARAM(p, f) \
if (strncmp(tok, #p, sizeof(#p) / sizeof(#p[0]) - 1) == 0) { \
param->p = f(val); \
}
#define PARSE_STRING(p) PARSE_PARAM(p, strdup)
#define PARSE_INT(p) PARSE_PARAM(p, atoi)
#define PARSE_REAL(p) PARSE_PARAM(p, atof)
if (tok != NULL && val != NULL) {
PARSE_REAL(xlength);
PARSE_REAL(ylength);
PARSE_REAL(zlength);
PARSE_INT(imax);
PARSE_INT(jmax);
PARSE_INT(kmax);
PARSE_INT(itermax);
PARSE_REAL(eps);
PARSE_REAL(omg);
PARSE_REAL(re);
PARSE_REAL(tau);
PARSE_REAL(gamma);
PARSE_REAL(dt);
PARSE_REAL(te);
PARSE_REAL(gx);
PARSE_REAL(gy);
PARSE_REAL(gz);
PARSE_STRING(name);
PARSE_INT(bcLeft);
PARSE_INT(bcRight);
PARSE_INT(bcBottom);
PARSE_INT(bcTop);
PARSE_INT(bcFront);
PARSE_INT(bcBack);
PARSE_REAL(u_init);
PARSE_REAL(v_init);
PARSE_REAL(w_init);
PARSE_REAL(p_init);
}
}
fclose(fp);
}
void printParameter(Parameter* param)
{
printf("Parameters for %s\n", param->name);
printf("Boundary conditions Left:%d Right:%d Bottom:%d Top:%d Front:%d "
"Back:%d\n",
param->bcLeft,
param->bcRight,
param->bcBottom,
param->bcTop,
param->bcFront,
param->bcBack);
printf("\tReynolds number: %.2f\n", param->re);
printf("\tInit arrays: U:%.2f V:%.2f W:%.2f P:%.2f\n",
param->u_init,
param->v_init,
param->w_init,
param->p_init);
printf("Geometry data:\n");
printf("\tDomain box size (x, y, z): %.2f, %.2f, %.2f\n",
param->xlength,
param->ylength,
param->zlength);
printf("\tCells (x, y, z): %d, %d, %d\n", param->imax, param->jmax, param->kmax);
printf("Timestep parameters:\n");
printf("\tDefault stepsize: %.2f, Final time %.2f\n", param->dt, param->te);
printf("\tTau factor: %.2f\n", param->tau);
printf("Iterative solver parameters:\n");
printf("\tMax iterations: %d\n", param->itermax);
printf("\tepsilon (stopping tolerance) : %f\n", param->eps);
printf("\tgamma (stopping tolerance) : %f\n", param->gamma);
printf("\tomega (SOR relaxation): %f\n", param->omg);
}

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BasicSolver/3D-mpi-io/src/parameter.h
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/*
* Copyright (C) 2022 NHR@FAU, University Erlangen-Nuremberg.
* All rights reserved. This file is part of nusif-solver.
* Use of this source code is governed by a MIT style
* license that can be found in the LICENSE file.
*/
#ifndef __PARAMETER_H_
#define __PARAMETER_H_
typedef struct {
int imax, jmax, kmax;
double xlength, ylength, zlength;
int itermax;
double eps, omg;
double re, tau, gamma;
double te, dt;
double gx, gy, gz;
char* name;
int bcLeft, bcRight, bcBottom, bcTop, bcFront, bcBack;
double u_init, v_init, w_init, p_init;
} Parameter;
void initParameter(Parameter*);
void readParameter(Parameter*, const char*);
void printParameter(Parameter*);
#endif

51
BasicSolver/3D-mpi-io/src/progress.c
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@ -1,51 +0,0 @@
/*
* Copyright (C) 2022 NHR@FAU, University Erlangen-Nuremberg.
* All rights reserved. This file is part of nusif-solver.
* Use of this source code is governed by a MIT style
* license that can be found in the LICENSE file.
*/
#include <math.h>
#include <stdio.h>
#include <stdlib.h>
#include <string.h>
#include "progress.h"
static double _end;
static int _current;
void initProgress(double end)
{
_end = end;
_current = 0;
printf("[ ]");
fflush(stdout);
}
void printProgress(double current)
{
int new = (int)rint((current / _end) * 10.0);
if (new > _current) {
char progress[11];
_current = new;
progress[0] = 0;
for (int i = 0; i < 10; i++) {
if (i < _current) {
sprintf(progress + strlen(progress), "#");
} else {
sprintf(progress + strlen(progress), " ");
}
}
printf("\r[%s]", progress);
}
fflush(stdout);
}
void stopProgress()
{
printf("\n");
fflush(stdout);
}

14
BasicSolver/3D-mpi-io/src/progress.h
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/*
* Copyright (C) 2022 NHR@FAU, University Erlangen-Nuremberg.
* All rights reserved.
* Use of this source code is governed by a MIT-style
* license that can be found in the LICENSE file.
*/
#ifndef __PROGRESS_H_
#define __PROGRESS_H_
extern void initProgress(double);
extern void printProgress(double);
extern void stopProgress(void);
#endif

853
BasicSolver/3D-mpi-io/src/solver.c
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/*
* Copyright (C) 2022 NHR@FAU, University Erlangen-Nuremberg.
* All rights reserved. This file is part of nusif-solver.
* Use of this source code is governed by a MIT style
* license that can be found in the LICENSE file.
*/
#include <float.h>
#include <math.h>
#include <stdio.h>
#include <stdlib.h>
#include <string.h>
#include "allocate.h"
#include "comm.h"
#include "parameter.h"
#include "solver.h"
#include "util.h"
#define P(i, j, k) \
p[(k) * (imaxLocal + 2) * (jmaxLocal + 2) + (j) * (imaxLocal + 2) + (i)]
#define F(i, j, k) \
f[(k) * (imaxLocal + 2) * (jmaxLocal + 2) + (j) * (imaxLocal + 2) + (i)]
#define G(i, j, k) \
g[(k) * (imaxLocal + 2) * (jmaxLocal + 2) + (j) * (imaxLocal + 2) + (i)]
#define H(i, j, k) \
h[(k) * (imaxLocal + 2) * (jmaxLocal + 2) + (j) * (imaxLocal + 2) + (i)]
#define U(i, j, k) \
u[(k) * (imaxLocal + 2) * (jmaxLocal + 2) + (j) * (imaxLocal + 2) + (i)]
#define V(i, j, k) \
v[(k) * (imaxLocal + 2) * (jmaxLocal + 2) + (j) * (imaxLocal + 2) + (i)]
#define W(i, j, k) \
w[(k) * (imaxLocal + 2) * (jmaxLocal + 2) + (j) * (imaxLocal + 2) + (i)]
#define RHS(i, j, k) \
rhs[(k) * (imaxLocal + 2) * (jmaxLocal + 2) + (j) * (imaxLocal + 2) + (i)]
static void printConfig(Solver* s)
{
if (commIsMaster(&s->comm)) {
printf("Parameters for #%s#\n", s->problem);
printf("BC Left:%d Right:%d Bottom:%d Top:%d Front:%d Back:%d\n",
s->bcLeft,
s->bcRight,
s->bcBottom,
s->bcTop,
s->bcFront,
s->bcBack);
printf("\tReynolds number: %.2f\n", s->re);
printf("\tGx Gy: %.2f %.2f %.2f\n", s->gx, s->gy, s->gz);
printf("Geometry data:\n");
printf("\tDomain box size (x, y, z): %.2f, %.2f, %.2f\n",
s->grid.xlength,
s->grid.ylength,
s->grid.zlength);
printf("\tCells (x, y, z): %d, %d, %d\n",
s->grid.imax,
s->grid.jmax,
s->grid.kmax);
printf("\tCell size (dx, dy, dz): %f, %f, %f\n",
s->grid.dx,
s->grid.dy,
s->grid.dz);
printf("Timestep parameters:\n");
printf("\tDefault stepsize: %.2f, Final time %.2f\n", s->dt, s->te);
printf("\tdt bound: %.6f\n", s->dtBound);
printf("\tTau factor: %.2f\n", s->tau);
printf("Iterative parameters:\n");
printf("\tMax iterations: %d\n", s->itermax);
printf("\tepsilon (stopping tolerance) : %f\n", s->eps);
printf("\tgamma factor: %f\n", s->gamma);
printf("\tomega (SOR relaxation): %f\n", s->omega);
}
commPrintConfig(&s->comm);
}
void initSolver(Solver* s, Parameter* params)
{
s->problem = params->name;
s->bcLeft = params->bcLeft;
s->bcRight = params->bcRight;
s->bcBottom = params->bcBottom;
s->bcTop = params->bcTop;
s->bcFront = params->bcFront;
s->bcBack = params->bcBack;
s->grid.imax = params->imax;
s->grid.jmax = params->jmax;
s->grid.kmax = params->kmax;
s->grid.xlength = params->xlength;
s->grid.ylength = params->ylength;
s->grid.zlength = params->zlength;
s->grid.dx = params->xlength / params->imax;
s->grid.dy = params->ylength / params->jmax;
s->grid.dz = params->zlength / params->kmax;
s->eps = params->eps;
s->omega = params->omg;
s->itermax = params->itermax;
s->re = params->re;
s->gx = params->gx;
s->gy = params->gy;
s->gz = params->gz;
s->dt = params->dt;
s->te = params->te;
s->tau = params->tau;
s->gamma = params->gamma;
/* allocate arrays */
int imaxLocal = s->comm.imaxLocal;
int jmaxLocal = s->comm.jmaxLocal;
int kmaxLocal = s->comm.kmaxLocal;
size_t size = (imaxLocal + 2) * (jmaxLocal + 2) * (kmaxLocal + 2);
s->u = allocate(64, size * sizeof(double));
s->v = allocate(64, size * sizeof(double));
s->w = allocate(64, size * sizeof(double));
s->p = allocate(64, size * sizeof(double));
s->rhs = allocate(64, size * sizeof(double));
s->f = allocate(64, size * sizeof(double));
s->g = allocate(64, size * sizeof(double));
s->h = allocate(64, size * sizeof(double));
for (int i = 0; i < size; i++) {
s->u[i] = params->u_init;
s->v[i] = params->v_init;
s->w[i] = params->w_init;
s->p[i] = params->p_init;
s->rhs[i] = 0.0;
s->f[i] = 0.0;
s->g[i] = 0.0;
s->h[i] = 0.0;
}
double dx = s->grid.dx;
double dy = s->grid.dy;
double dz = s->grid.dz;
double invSqrSum = 1.0 / (dx * dx) + 1.0 / (dy * dy) + 1.0 / (dz * dz);
s->dtBound = 0.5 * s->re * 1.0 / invSqrSum;
#ifdef VERBOSE
printConfig(s);
#endif /* VERBOSE */
}
void computeRHS(Solver* s)
{
int imaxLocal = s->comm.imaxLocal;
int jmaxLocal = s->comm.jmaxLocal;
int kmaxLocal = s->comm.kmaxLocal;
double idx = 1.0 / s->grid.dx;
double idy = 1.0 / s->grid.dy;
double idz = 1.0 / s->grid.dz;
double idt = 1.0 / s->dt;
double* rhs = s->rhs;
double* f = s->f;
double* g = s->g;
double* h = s->h;
commShift(&s->comm, f, g, h);
for (int k = 1; k < kmaxLocal + 1; k++) {
for (int j = 1; j < jmaxLocal + 1; j++) {
for (int i = 1; i < imaxLocal + 1; i++) {
RHS(i, j, k) = ((F(i, j, k) - F(i - 1, j, k)) * idx +
(G(i, j, k) - G(i, j - 1, k)) * idy +
(H(i, j, k) - H(i, j, k - 1)) * idz) *
idt;
}
}
}
}
void solve(Solver* s)
{
int imaxLocal = s->comm.imaxLocal;
int jmaxLocal = s->comm.jmaxLocal;
int kmaxLocal = s->comm.kmaxLocal;
int imax = s->grid.imax;
int jmax = s->grid.jmax;
int kmax = s->grid.kmax;
double eps = s->eps;
int itermax = s->itermax;
double dx2 = s->grid.dx * s->grid.dx;
double dy2 = s->grid.dy * s->grid.dy;
double dz2 = s->grid.dz * s->grid.dz;
double idx2 = 1.0 / dx2;
double idy2 = 1.0 / dy2;
double idz2 = 1.0 / dz2;
double factor = s->omega * 0.5 * (dx2 * dy2 * dz2) /
(dy2 * dz2 + dx2 * dz2 + dx2 * dy2);
double* p = s->p;
double* rhs = s->rhs;
double epssq = eps * eps;
int it = 0;
double res = 1.0;
int pass, ksw, jsw, isw;
while ((res >= epssq) && (it < itermax)) {
ksw = 1;
for (pass = 0; pass < 2; pass++) {
jsw = ksw;
commExchange(&s->comm, p);
for (int k = 1; k < kmaxLocal + 1; k++) {
isw = jsw;
for (int j = 1; j < jmaxLocal + 1; j++) {
for (int i = isw; i < imaxLocal + 1; i += 2) {
double r =
RHS(i, j, k) -
((P(i + 1, j, k) - 2.0 * P(i, j, k) + P(i - 1, j, k)) * idx2 +
(P(i, j + 1, k) - 2.0 * P(i, j, k) + P(i, j - 1, k)) *
idy2 +
(P(i, j, k + 1) - 2.0 * P(i, j, k) + P(i, j, k - 1)) *
idz2);
P(i, j, k) -= (factor * r);
res += (r * r);
}
isw = 3 - isw;
}
jsw = 3 - jsw;
}
ksw = 3 - ksw;
}
if (commIsBoundary(&s->comm, FRONT)) {
for (int j = 1; j < jmaxLocal + 1; j++) {
for (int i = 1; i < imaxLocal + 1; i++) {
P(i, j, 0) = P(i, j, 1);
}
}
}
if (commIsBoundary(&s->comm, BACK)) {
for (int j = 1; j < jmaxLocal + 1; j++) {
for (int i = 1; i < imaxLocal + 1; i++) {
P(i, j, kmaxLocal + 1) = P(i, j, kmaxLocal);
}
}
}
if (commIsBoundary(&s->comm, BOTTOM)) {
for (int k = 1; k < kmaxLocal + 1; k++) {
for (int i = 1; i < imaxLocal + 1; i++) {
P(i, 0, k) = P(i, 1, k);
}
}
}
if (commIsBoundary(&s->comm, TOP)) {
for (int k = 1; k < kmaxLocal + 1; k++) {
for (int i = 1; i < imaxLocal + 1; i++) {
P(i, jmaxLocal + 1, k) = P(i, jmaxLocal, k);
}
}
}
if (commIsBoundary(&s->comm, LEFT)) {
for (int k = 1; k < kmaxLocal + 1; k++) {
for (int j = 1; j < jmaxLocal + 1; j++) {
P(0, j, k) = P(1, j, k);
}
}
}
if (commIsBoundary(&s->comm, RIGHT)) {
for (int k = 1; k < kmaxLocal + 1; k++) {
for (int j = 1; j < jmaxLocal + 1; j++) {
P(imaxLocal + 1, j, k) = P(imaxLocal, j, k);
}
}
}
commReduction(&res, SUM);
res = res / (double)(imax * jmax * kmax);
#ifdef DEBUG
if (commIsMaster(&s->comm)) {
printf("%d Residuum: %e\n", it, res);
}
#endif
commExchange(&s->comm, p);
it++;
}
#ifdef VERBOSE
if (commIsMaster(&s->comm)) {
printf("Solver took %d iterations to reach %f\n", it, sqrt(res));
}
#endif
}
static double maxElement(Solver* s, double* m)
{
int size = (s->comm.imaxLocal + 2) * (s->comm.jmaxLocal + 2) *
(s->comm.kmaxLocal + 2);
double maxval = DBL_MIN;
for (int i = 0; i < size; i++) {
maxval = MAX(maxval, fabs(m[i]));
}
commReduction(&maxval, MAX);
return maxval;
}
void normalizePressure(Solver* s)
{
int imaxLocal = s->comm.imaxLocal;
int jmaxLocal = s->comm.jmaxLocal;
int kmaxLocal = s->comm.kmaxLocal;
double* p = s->p;
double avgP = 0.0;
for (int k = 1; k < kmaxLocal + 1; k++) {
for (int j = 1; j < jmaxLocal + 1; j++) {
for (int i = 1; i < imaxLocal + 1; i++) {
avgP += P(i, j, k);
}
}
}
commReduction(&avgP, SUM);
avgP /= (s->grid.imax * s->grid.jmax * s->grid.kmax);
for (int k = 1; k < kmaxLocal + 1; k++) {
for (int j = 1; j < jmaxLocal + 1; j++) {
for (int i = 1; i < imaxLocal + 1; i++) {
P(i, j, k) = P(i, j, k) - avgP;
}
}
}
}
void computeTimestep(Solver* s)
{
double dt = s->dtBound;
double dx = s->grid.dx;
double dy = s->grid.dy;
double dz = s->grid.dz;
double umax = maxElement(s, s->u);
double vmax = maxElement(s, s->v);
double wmax = maxElement(s, s->w);
if (umax > 0) {
dt = (dt > dx / umax) ? dx / umax : dt;
}
if (vmax > 0) {
dt = (dt > dy / vmax) ? dy / vmax : dt;
}
if (wmax > 0) {
dt = (dt > dz / wmax) ? dz / wmax : dt;
}
s->dt = dt * s->tau;
}
void setBoundaryConditions(Solver* s)
{
int imaxLocal = s->comm.imaxLocal;
int jmaxLocal = s->comm.jmaxLocal;
int kmaxLocal = s->comm.kmaxLocal;
double* u = s->u;
double* v = s->v;
double* w = s->w;
if (commIsBoundary(&s->comm, TOP)) {
switch (s->bcTop) {
case NOSLIP:
for (int k = 1; k < kmaxLocal + 1; k++) {
for (int i = 1; i < imaxLocal + 1; i++) {
U(i, jmaxLocal + 1, k) = -U(i, jmaxLocal, k);
V(i, jmaxLocal, k) = 0.0;
W(i, jmaxLocal + 1, k) = -W(i, jmaxLocal, k);
}
}
break;
case SLIP:
for (int k = 1; k < kmaxLocal + 1; k++) {
for (int i = 1; i < imaxLocal + 1; i++) {
U(i, jmaxLocal + 1, k) = U(i, jmaxLocal, k);
V(i, jmaxLocal, k) = 0.0;
W(i, jmaxLocal + 1, k) = W(i, jmaxLocal, k);
}
}
break;
case OUTFLOW:
for (int k = 1; k < kmaxLocal + 1; k++) {
for (int i = 1; i < imaxLocal + 1; i++) {
U(i, jmaxLocal + 1, k) = U(i, jmaxLocal, k);
V(i, jmaxLocal, k) = V(i, jmaxLocal - 1, k);
W(i, jmaxLocal + 1, k) = W(i, jmaxLocal, k);
}
}
break;
case PERIODIC:
break;
}
}
if (commIsBoundary(&s->comm, BOTTOM)) {
switch (s->bcBottom) {
case NOSLIP:
for (int k = 1; k < kmaxLocal + 1; k++) {
for (int i = 1; i < imaxLocal + 1; i++) {
U(i, 0, k) = -U(i, 1, k);
V(i, 0, k) = 0.0;
W(i, 0, k) = -W(i, 1, k);
}
}
break;
case SLIP:
for (int k = 1; k < kmaxLocal + 1; k++) {
for (int i = 1; i < imaxLocal + 1; i++) {
U(i, 0, k) = U(i, 1, k);
V(i, 0, k) = 0.0;
W(i, 0, k) = W(i, 1, k);
}
}
break;
case OUTFLOW:
for (int k = 1; k < kmaxLocal + 1; k++) {
for (int i = 1; i < imaxLocal + 1; i++) {
U(i, 0, k) = U(i, 1, k);
V(i, 0, k) = V(i, 1, k);
W(i, 0, k) = W(i, 1, k);
}
}
break;
case PERIODIC:
break;
}
}
if (commIsBoundary(&s->comm, LEFT)) {
switch (s->bcLeft) {
case NOSLIP:
for (int k = 1; k < kmaxLocal + 1; k++) {
for (int j = 1; j < jmaxLocal + 1; j++) {
U(0, j, k) = 0.0;
V(0, j, k) = -V(1, j, k);
W(0, j, k) = -W(1, j, k);
}
}
break;
case SLIP:
for (int k = 1; k < kmaxLocal + 1; k++) {
for (int j = 1; j < jmaxLocal + 1; j++) {
U(0, j, k) = 0.0;
V(0, j, k) = V(1, j, k);
W(0, j, k) = W(1, j, k);
}
}
break;
case OUTFLOW:
for (int k = 1; k < kmaxLocal + 1; k++) {
for (int j = 1; j < jmaxLocal + 1; j++) {
U(0, j, k) = U(1, j, k);
V(0, j, k) = V(1, j, k);
W(0, j, k) = W(1, j, k);
}
}
break;
case PERIODIC:
break;
}
}
if (commIsBoundary(&s->comm, RIGHT)) {
switch (s->bcRight) {
case NOSLIP:
for (int k = 1; k < kmaxLocal + 1; k++) {
for (int j = 1; j < jmaxLocal + 1; j++) {
U(imaxLocal, j, k) = 0.0;
V(imaxLocal + 1, j, k) = -V(imaxLocal, j, k);
W(imaxLocal + 1, j, k) = -W(imaxLocal, j, k);
}
}
break;
case SLIP:
for (int k = 1; k < kmaxLocal + 1; k++) {
for (int j = 1; j < jmaxLocal + 1; j++) {
U(imaxLocal, j, k) = 0.0;
V(imaxLocal + 1, j, k) = V(imaxLocal, j, k);
W(imaxLocal + 1, j, k) = W(imaxLocal, j, k);
}
}
break;
case OUTFLOW:
for (int k = 1; k < kmaxLocal + 1; k++) {
for (int j = 1; j < jmaxLocal + 1; j++) {
U(imaxLocal, j, k) = U(imaxLocal - 1, j, k);
V(imaxLocal + 1, j, k) = V(imaxLocal, j, k);
W(imaxLocal + 1, j, k) = W(imaxLocal, j, k);
}
}
break;
case PERIODIC:
break;
}
}
if (commIsBoundary(&s->comm, FRONT)) {
switch (s->bcFront) {
case NOSLIP:
for (int j = 1; j < jmaxLocal + 1; j++) {
for (int i = 1; i < imaxLocal + 1; i++) {
U(i, j, 0) = -U(i, j, 1);
V(i, j, 0) = -V(i, j, 1);
W(i, j, 0) = 0.0;
}
}
break;
case SLIP:
for (int j = 1; j < jmaxLocal + 1; j++) {
for (int i = 1; i < imaxLocal + 1; i++) {
U(i, j, 0) = U(i, j, 1);
V(i, j, 0) = V(i, j, 1);
W(i, j, 0) = 0.0;
}
}
break;
case OUTFLOW:
for (int j = 1; j < jmaxLocal + 1; j++) {
for (int i = 1; i < imaxLocal + 1; i++) {
U(i, j, 0) = U(i, j, 1);
V(i, j, 0) = V(i, j, 1);
W(i, j, 0) = W(i, j, 1);
}
}
break;
case PERIODIC:
break;
}
}
if (commIsBoundary(&s->comm, BACK)) {
switch (s->bcBack) {
case NOSLIP:
for (int j = 1; j < jmaxLocal + 1; j++) {
for (int i = 1; i < imaxLocal + 1; i++) {
U(i, j, kmaxLocal + 1) = -U(i, j, kmaxLocal);
V(i, j, kmaxLocal + 1) = -V(i, j, kmaxLocal);
W(i, j, kmaxLocal) = 0.0;
}
}
break;
case SLIP:
for (int j = 1; j < jmaxLocal + 1; j++) {
for (int i = 1; i < imaxLocal + 1; i++) {
U(i, j, kmaxLocal + 1) = U(i, j, kmaxLocal);
V(i, j, kmaxLocal + 1) = V(i, j, kmaxLocal);
W(i, j, kmaxLocal) = 0.0;
}
}
break;
case OUTFLOW:
for (int j = 1; j < jmaxLocal + 1; j++) {
for (int i = 1; i < imaxLocal + 1; i++) {
U(i, j, kmaxLocal + 1) = U(i, j, kmaxLocal);
V(i, j, kmaxLocal + 1) = V(i, j, kmaxLocal);
W(i, j, kmaxLocal) = W(i, j, kmaxLocal - 1);
}
}
break;
case PERIODIC:
break;
}
}
}
void setSpecialBoundaryCondition(Solver* s)
{
int imaxLocal = s->comm.imaxLocal;
int jmaxLocal = s->comm.jmaxLocal;
int kmaxLocal = s->comm.kmaxLocal;
double* u = s->u;
if (strcmp(s->problem, "dcavity") == 0) {
if (commIsBoundary(&s->comm, TOP)) {
for (int k = 1; k < kmaxLocal; k++) {
for (int i = 1; i < imaxLocal; i++) {
U(i, jmaxLocal + 1, k) = 2.0 - U(i, jmaxLocal, k);
}
}
}
} else if (strcmp(s->problem, "canal") == 0) {
if (commIsBoundary(&s->comm, LEFT)) {
for (int k = 1; k < kmaxLocal + 1; k++) {
for (int j = 1; j < jmaxLocal + 1; j++) {
U(0, j, k) = 2.0;
}
}
}
}
}
void computeFG(Solver* s)
{
int imaxLocal = s->comm.imaxLocal;
int jmaxLocal = s->comm.jmaxLocal;
int kmaxLocal = s->comm.kmaxLocal;
double* u = s->u;
double* v = s->v;
double* w = s->w;
double* f = s->f;
double* g = s->g;
double* h = s->h;
double gx = s->gx;
double gy = s->gy;
double gz = s->gz;
double dt = s->dt;
double gamma = s->gamma;
double inverseRe = 1.0 / s->re;
double inverseDx = 1.0 / s->grid.dx;
double inverseDy = 1.0 / s->grid.dy;
double inverseDz = 1.0 / s->grid.dz;
double du2dx, dv2dy, dw2dz;
double duvdx, duwdx, duvdy, dvwdy, duwdz, dvwdz;
double du2dx2, du2dy2, du2dz2;
double dv2dx2, dv2dy2, dv2dz2;
double dw2dx2, dw2dy2, dw2dz2;
commExchange(&s->comm, u);
commExchange(&s->comm, v);
commExchange(&s->comm, w);
for (int k = 1; k < kmaxLocal + 1; k++) {
for (int j = 1; j < jmaxLocal + 1; j++) {
for (int i = 1; i < imaxLocal + 1; i++) {
du2dx = inverseDx * 0.25 *
((U(i, j, k) + U(i + 1, j, k)) *
(U(i, j, k) + U(i + 1, j, k)) -
(U(i, j, k) + U(i - 1, j, k)) *
(U(i, j, k) + U(i - 1, j, k))) +
gamma * inverseDx * 0.25 *
(fabs(U(i, j, k) + U(i + 1, j, k)) *
(U(i, j, k) - U(i + 1, j, k)) +
fabs(U(i, j, k) + U(i - 1, j, k)) *
(U(i, j, k) - U(i - 1, j, k)));
duvdy = inverseDy * 0.25 *
((V(i, j, k) + V(i + 1, j, k)) *
(U(i, j, k) + U(i, j + 1, k)) -
(V(i, j - 1, k) + V(i + 1, j - 1, k)) *
(U(i, j, k) + U(i, j - 1, k))) +
gamma * inverseDy * 0.25 *
(fabs(V(i, j, k) + V(i + 1, j, k)) *
(U(i, j, k) - U(i, j + 1, k)) +
fabs(V(i, j - 1, k) + V(i + 1, j - 1, k)) *
(U(i, j, k) - U(i, j - 1, k)));
duwdz = inverseDz * 0.25 *
((W(i, j, k) + W(i + 1, j, k)) *
(U(i, j, k) + U(i, j, k + 1)) -
(W(i, j, k - 1) + W(i + 1, j, k - 1)) *
(U(i, j, k) + U(i, j, k - 1))) +
gamma * inverseDz * 0.25 *
(fabs(W(i, j, k) + W(i + 1, j, k)) *
(U(i, j, k) - U(i, j, k + 1)) +
fabs(W(i, j, k - 1) + W(i + 1, j, k - 1)) *
(U(i, j, k) - U(i, j, k - 1)));
du2dx2 = inverseDx * inverseDx *
(U(i + 1, j, k) - 2.0 * U(i, j, k) + U(i - 1, j, k));
du2dy2 = inverseDy * inverseDy *
(U(i, j + 1, k) - 2.0 * U(i, j, k) + U(i, j - 1, k));
du2dz2 = inverseDz * inverseDz *
(U(i, j, k + 1) - 2.0 * U(i, j, k) + U(i, j, k - 1));
F(i, j, k) = U(i, j, k) + dt * (inverseRe * (du2dx2 + du2dy2 + du2dz2) -
du2dx - duvdy - duwdz + gx);
duvdx = inverseDx * 0.25 *
((U(i, j, k) + U(i, j + 1, k)) *
(V(i, j, k) + V(i + 1, j, k)) -
(U(i - 1, j, k) + U(i - 1, j + 1, k)) *
(V(i, j, k) + V(i - 1, j, k))) +
gamma * inverseDx * 0.25 *
(fabs(U(i, j, k) + U(i, j + 1, k)) *
(V(i, j, k) - V(i + 1, j, k)) +
fabs(U(i - 1, j, k) + U(i - 1, j + 1, k)) *
(V(i, j, k) - V(i - 1, j, k)));
dv2dy = inverseDy * 0.25 *
((V(i, j, k) + V(i, j + 1, k)) *
(V(i, j, k) + V(i, j + 1, k)) -
(V(i, j, k) + V(i, j - 1, k)) *
(V(i, j, k) + V(i, j - 1, k))) +
gamma * inverseDy * 0.25 *
(fabs(V(i, j, k) + V(i, j + 1, k)) *
(V(i, j, k) - V(i, j + 1, k)) +
fabs(V(i, j, k) + V(i, j - 1, k)) *
(V(i, j, k) - V(i, j - 1, k)));
dvwdz = inverseDz * 0.25 *
((W(i, j, k) + W(i, j + 1, k)) *
(V(i, j, k) + V(i, j, k + 1)) -
(W(i, j, k - 1) + W(i, j + 1, k - 1)) *
(V(i, j, k) + V(i, j, k + 1))) +
gamma * inverseDz * 0.25 *
(fabs(W(i, j, k) + W(i, j + 1, k)) *
(V(i, j, k) - V(i, j, k + 1)) +
fabs(W(i, j, k - 1) + W(i, j + 1, k - 1)) *
(V(i, j, k) - V(i, j, k + 1)));
dv2dx2 = inverseDx * inverseDx *
(V(i + 1, j, k) - 2.0 * V(i, j, k) + V(i - 1, j, k));
dv2dy2 = inverseDy * inverseDy *
(V(i, j + 1, k) - 2.0 * V(i, j, k) + V(i, j - 1, k));
dv2dz2 = inverseDz * inverseDz *
(V(i, j, k + 1) - 2.0 * V(i, j, k) + V(i, j, k - 1));
G(i, j, k) = V(i, j, k) + dt * (inverseRe * (dv2dx2 + dv2dy2 + dv2dz2) -
duvdx - dv2dy - dvwdz + gy);
duwdx = inverseDx * 0.25 *
((U(i, j, k) + U(i, j, k + 1)) *
(W(i, j, k) + W(i + 1, j, k)) -
(U(i - 1, j, k) + U(i - 1, j, k + 1)) *
(W(i, j, k) + W(i - 1, j, k))) +
gamma * inverseDx * 0.25 *
(fabs(U(i, j, k) + U(i, j, k + 1)) *
(W(i, j, k) - W(i + 1, j, k)) +
fabs(U(i - 1, j, k) + U(i - 1, j, k + 1)) *
(W(i, j, k) - W(i - 1, j, k)));
dvwdy = inverseDy * 0.25 *
((V(i, j, k) + V(i, j, k + 1)) *
(W(i, j, k) + W(i, j + 1, k)) -
(V(i, j - 1, k + 1) + V(i, j - 1, k)) *
(W(i, j, k) + W(i, j - 1, k))) +
gamma * inverseDy * 0.25 *
(fabs(V(i, j, k) + V(i, j, k + 1)) *
(W(i, j, k) - W(i, j + 1, k)) +
fabs(V(i, j - 1, k + 1) + V(i, j - 1, k)) *
(W(i, j, k) - W(i, j - 1, k)));
dw2dz = inverseDz * 0.25 *
((W(i, j, k) + W(i, j, k + 1)) *
(W(i, j, k) + W(i, j, k + 1)) -
(W(i, j, k) + W(i, j, k - 1)) *
(W(i, j, k) + W(i, j, k - 1))) +
gamma * inverseDz * 0.25 *
(fabs(W(i, j, k) + W(i, j, k + 1)) *
(W(i, j, k) - W(i, j, k + 1)) +
fabs(W(i, j, k) + W(i, j, k - 1)) *
(W(i, j, k) - W(i, j, k - 1)));
dw2dx2 = inverseDx * inverseDx *
(W(i + 1, j, k) - 2.0 * W(i, j, k) + W(i - 1, j, k));
dw2dy2 = inverseDy * inverseDy *
(W(i, j + 1, k) - 2.0 * W(i, j, k) + W(i, j - 1, k));
dw2dz2 = inverseDz * inverseDz *
(W(i, j, k + 1) - 2.0 * W(i, j, k) + W(i, j, k - 1));
H(i, j, k) = W(i, j, k) + dt * (inverseRe * (dw2dx2 + dw2dy2 + dw2dz2) -
duwdx - dvwdy - dw2dz + gz);
}
}
}
/* ----------------------------- boundary of F ---------------------------
*/
if (commIsBoundary(&s->comm, LEFT)) {
for (int k = 1; k < kmaxLocal + 1; k++) {
for (int j = 1; j < jmaxLocal + 1; j++) {
F(0, j, k) = U(0, j, k);
}
}
}
if (commIsBoundary(&s->comm, RIGHT)) {
for (int k = 1; k < kmaxLocal + 1; k++) {
for (int j = 1; j < jmaxLocal + 1; j++) {
F(imaxLocal, j, k) = U(imaxLocal, j, k);
}
}
}
/* ----------------------------- boundary of G ---------------------------
*/
if (commIsBoundary(&s->comm, BOTTOM)) {
for (int k = 1; k < kmaxLocal + 1; k++) {
for (int i = 1; i < imaxLocal + 1; i++) {
G(i, 0, k) = V(i, 0, k);
}
}
}
if (commIsBoundary(&s->comm, TOP)) {
for (int k = 1; k < kmaxLocal + 1; k++) {
for (int i = 1; i < imaxLocal + 1; i++) {
G(i, jmaxLocal, k) = V(i, jmaxLocal, k);
}
}
}
/* ----------------------------- boundary of H ---------------------------
*/
if (commIsBoundary(&s->comm, FRONT)) {
for (int j = 1; j < jmaxLocal + 1; j++) {
for (int i = 1; i < imaxLocal + 1; i++) {
H(i, j, 0) = W(i, j, 0);
}
}
}
if (commIsBoundary(&s->comm, BACK)) {
for (int j = 1; j < jmaxLocal + 1; j++) {
for (int i = 1; i < imaxLocal + 1; i++) {
H(i, j, kmaxLocal) = W(i, j, kmaxLocal);
}
}
}
}
void adaptUV(Solver* s)
{
int imaxLocal = s->comm.imaxLocal;
int jmaxLocal = s->comm.jmaxLocal;
int kmaxLocal = s->comm.kmaxLocal;
double* p = s->p;
double* u = s->u;
double* v = s->v;
double* w = s->w;
double* f = s->f;
double* g = s->g;
double* h = s->h;
double factorX = s->dt / s->grid.dx;
double factorY = s->dt / s->grid.dy;
double factorZ = s->dt / s->grid.dz;
for (int k = 1; k < kmaxLocal + 1; k++) {
for (int j = 1; j < jmaxLocal + 1; j++) {
for (int i = 1; i < imaxLocal + 1; i++) {
U(i, j, k) = F(i, j, k) - (P(i + 1, j, k) - P(i, j, k)) * factorX;
V(i, j, k) = G(i, j, k) - (P(i, j + 1, k) - P(i, j, k)) * factorY;
W(i, j, k) = H(i, j, k) - (P(i, j, k + 1) - P(i, j, k)) * factorZ;
}
}
}
}

45
BasicSolver/3D-mpi-io/src/solver.h
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@ -1,45 +0,0 @@
/*
* Copyright (C) 2022 NHR@FAU, University Erlangen-Nuremberg.
* All rights reserved. This file is part of nusif-solver.
* Use of this source code is governed by a MIT style
* license that can be found in the LICENSE file.
*/
#ifndef __SOLVER_H_
#define __SOLVER_H_
#include "comm.h"
#include "grid.h"
#include "parameter.h"
enum BC { NOSLIP = 1, SLIP, OUTFLOW, PERIODIC };
typedef struct {
/* geometry and grid information */
Grid grid;
/* arrays */
double *p, *rhs;
double *f, *g, *h;
double *u, *v, *w;
/* parameters */
double eps, omega;
double re, tau, gamma;
double gx, gy, gz;
/* time stepping */
int itermax;
double dt, te;
double dtBound;
char* problem;
int bcLeft, bcRight, bcBottom, bcTop, bcFront, bcBack;
/* communication */
Comm comm;
} Solver;
extern void initSolver(Solver*, Parameter*);
extern void computeRHS(Solver*);
extern void solve(Solver*);
extern void normalizePressure(Solver*);
extern void computeTimestep(Solver*);
extern void setBoundaryConditions(Solver*);
extern void setSpecialBoundaryCondition(Solver*);
extern void computeFG(Solver*);
extern void adaptUV(Solver*);
#endif

129
BasicSolver/3D-mpi-io/src/test.c
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@ -1,129 +0,0 @@
/*
* Copyright (C) 2022 NHR@FAU, University Erlangen-Nuremberg.
* All rights reserved.
* Use of this source code is governed by a MIT-style
* license that can be found in the LICENSE file.
*/
#include <stdio.h>
#include <string.h>
#include "test.h"
#define G(v, i, j, k) \
v[(k) * (imaxLocal + 2) * (jmaxLocal + 2) + (j) * (imaxLocal + 2) + (i)]
void testInit(Solver* s)
{
int imaxLocal = s->comm.imaxLocal;
int jmaxLocal = s->comm.jmaxLocal;
int kmaxLocal = s->comm.kmaxLocal;
int myrank = s->comm.rank;
double* p = s->p;
double* f = s->f;
double* g = s->g;
double* h = s->h;
for (int k = 0; k < kmaxLocal + 2; k++) {
for (int j = 0; j < jmaxLocal + 2; j++) {
for (int i = 0; i < imaxLocal + 2; i++) {
G(p, i, j, k) = 10.0;
G(f, i, j, k) = myrank + 1.0;
G(g, i, j, k) = myrank + 1.0;
G(h, i, j, k) = myrank + 1.0;
}
}
}
for (int k = 1; k < kmaxLocal + 1; k++) {
for (int j = 1; j < jmaxLocal + 1; j++) {
for (int i = 1; i < imaxLocal + 1; i++) {
G(p, i, j, k) = myrank + 1.0;
G(f, i, j, k) = myrank + 1.0;
G(g, i, j, k) = myrank + 1.0;
G(h, i, j, k) = myrank + 1.0;
}
}
}
}
static char* direction2String(Direction dir)
{
switch (dir) {
case LEFT:
return "left";
break;
case RIGHT:
return "right";
break;
case BOTTOM:
return "bottom";
break;
case TOP:
return "top";
break;
case FRONT:
return "front";
break;
case BACK:
return "back";
break;
case NDIRS:
return "ERROR";
default:
return "ERROR";
}
}
static void printPlane(Solver* s, double* a, int ymax, int xmax, Direction dir)
{
int imaxLocal = s->comm.imaxLocal;
int jmaxLocal = s->comm.jmaxLocal;
int kmaxLocal = s->comm.kmaxLocal;
char filename[50];
snprintf(filename, 50, "halo-%s-r%d.txt", direction2String(dir), s->comm.rank);
FILE* fh = fopen(filename, "w");
for (int y = 0; y < ymax; y++) {
for (int x = 0; x < xmax; x++) {
switch (dir) {
case LEFT:
fprintf(fh, "%12.8f ", G(a, 0, x, y));
break;
case RIGHT:
fprintf(fh, "%12.8f ", G(a, imaxLocal + 1, x, y));
break;
case BOTTOM:
fprintf(fh, "%12.8f ", G(a, x, 0, y));
break;
case TOP:
fprintf(fh, "%12.8f ", G(a, x, jmaxLocal + 1, y));
break;
case FRONT:
fprintf(fh, "%12.8f ", G(a, x, y, 0));
break;
case BACK:
fprintf(fh, "%12.8f ", G(a, x, y, kmaxLocal + 1));
break;
case NDIRS:
printf("ERROR\n");
break;
}
}
fprintf(fh, "\n");
}
fclose(fh);
}
void testPrintHalo(Solver* s, double* a)
{
int imaxLocal = s->comm.imaxLocal;
int jmaxLocal = s->comm.jmaxLocal;
int kmaxLocal = s->comm.kmaxLocal;
printPlane(s, a, kmaxLocal + 2, imaxLocal + 2, BOTTOM);
printPlane(s, a, kmaxLocal + 2, imaxLocal + 2, TOP);
printPlane(s, a, kmaxLocal + 2, jmaxLocal + 2, LEFT);
printPlane(s, a, kmaxLocal + 2, jmaxLocal + 2, RIGHT);
printPlane(s, a, jmaxLocal + 2, imaxLocal + 2, FRONT);
printPlane(s, a, jmaxLocal + 2, imaxLocal + 2, BACK);
}

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

@ -1,13 +0,0 @@
/*
* Copyright (C) 2022 NHR@FAU, University Erlangen-Nuremberg.
* All rights reserved. This file is part of nusif-solver.
* Use of this source code is governed by a MIT style
* license that can be found in the LICENSE file.
*/
#ifndef __TEST_H_
#define __TEST_H_
#include "solver.h"
extern void testInit(Solver* s);
extern void testPrintHalo(Solver* s, double* a);
#endif // __TEST_H_

22
BasicSolver/3D-mpi-io/src/timing.c
View File

@ -1,22 +0,0 @@
/*
* Copyright (C) 2022 NHR@FAU, University Erlangen-Nuremberg.
* All rights reserved.
* Use of this source code is governed by a MIT-style
* license that can be found in the LICENSE file.
*/
#include <stdlib.h>
#include <time.h>
double getTimeStamp(void)
{
struct timespec ts;
clock_gettime(CLOCK_MONOTONIC, &ts);
return (double)ts.tv_sec + (double)ts.tv_nsec * 1.e-9;
}
double getTimeResolution(void)
{
struct timespec ts;
clock_getres(CLOCK_MONOTONIC, &ts);
return (double)ts.tv_sec + (double)ts.tv_nsec * 1.e-9;
}

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

@ -1,13 +0,0 @@
/*
* Copyright (C) 2022 NHR@FAU, University Erlangen-Nuremberg.
* All rights reserved.
* Use of this source code is governed by a MIT-style
* license that can be found in the LICENSE file.
*/
#ifndef __TIMING_H_
#define __TIMING_H_
extern double getTimeStamp(void);
extern double getTimeResolution(void);
#endif // __TIMING_H_

22
BasicSolver/3D-mpi-io/src/util.h
View File

@ -1,22 +0,0 @@
/*
* Copyright (C) 2022 NHR@FAU, University Erlangen-Nuremberg.
* All rights reserved.
* Use of this source code is governed by a MIT-style
* license that can be found in the LICENSE file.
*/
#ifndef __UTIL_H_
#define __UTIL_H_
#define HLINE \
"----------------------------------------------------------------------------\n"
#ifndef MIN
#define MIN(x, y) ((x) < (y) ? (x) : (y))
#endif
#ifndef MAX
#define MAX(x, y) ((x) > (y) ? (x) : (y))
#endif
#ifndef ABS
#define ABS(a) ((a) >= 0 ? (a) : -(a))
#endif
#endif // __UTIL_H_

29
BasicSolver/3D-mpi-io/src/vtkWriter.h
View File

@ -1,29 +0,0 @@
/*
* Copyright (C) 2022 NHR@FAU, University Erlangen-Nuremberg.
* All rights reserved. This file is part of nusif-solver.
* Use of this source code is governed by a MIT style
* license that can be found in the LICENSE file.
*/
#ifndef __VTKWRITER_H_
#define __VTKWRITER_H_
#include <mpi.h>
#include <stdio.h>
#include "comm.h"
#include "grid.h"
typedef struct VtkOptions {
Grid grid;
MPI_File fh;
Comm comm;
} VtkOptions;
typedef struct VtkVector {
double *u, *v, *w;
} VtkVector;
extern void vtkOpen(VtkOptions* opts, char* filename);
extern void vtkVector(VtkOptions* opts, char* name, VtkVector vec);
extern void vtkScalar(VtkOptions* opts, char* name, double* p);
extern void vtkClose(VtkOptions* opts);
#endif // __VTKWRITER_H_

19
BasicSolver/3D-mpi/Makefile
View File

@ -1,5 +1,5 @@
#=======================================================================================
# Copyright (C) 2022 NHR@FAU, University Erlangen-Nuremberg.
# Copyright (C) NHR@FAU, University Erlangen-Nuremberg.
# All rights reserved.
# Use of this source code is governed by a MIT-style
# license that can be found in the LICENSE file.
@ -18,13 +18,18 @@ include $(MAKE_DIR)/include_$(TAG).mk
INCLUDES += -I$(SRC_DIR) -I$(BUILD_DIR)
VPATH = $(SRC_DIR)
SRC = $(wildcard $(SRC_DIR)/*.c)
SRC = $(filter-out $(wildcard $(SRC_DIR)/*-*.c),$(wildcard $(SRC_DIR)/*.c))
ASM = $(patsubst $(SRC_DIR)/%.c, $(BUILD_DIR)/%.s, $(SRC))
OBJ = $(patsubst $(SRC_DIR)/%.c, $(BUILD_DIR)/%.o, $(SRC))
OBJ += $(BUILD_DIR)/vtkWriter-$(VTK_OUTPUT_FMT).o
SOURCES = $(SRC) $(wildcard $(SRC_DIR)/*.h)
ifeq ($(VTK_OUTPUT_FMT),mpi)
DEFINES += -D_VTK_WRITER_MPI
endif
CPPFLAGS := $(CPPFLAGS) $(DEFINES) $(OPTIONS) $(INCLUDES)
${TARGET}: $(BUILD_DIR) $(OBJ)
${TARGET}: sanity-checks $(BUILD_DIR) $(OBJ)
$(info ===> LINKING $(TARGET))
$(Q)${LINKER} ${LFLAGS} -o $(TARGET) $(OBJ) $(LIBS)
@ -65,6 +70,14 @@ format:
done
@echo "Done"
sanity-checks:
ifeq ($(VTK_OUTPUT_FMT),mpi)
ifeq ($(ENABLE_MPI),false)
$(error VTK_OUTPUT_FMT mpi only supported for ENABLE_MPI true!)
endif
endif
$(BUILD_DIR):
@mkdir $(BUILD_DIR)

2
BasicSolver/3D-mpi/config.mk
View File

@ -2,6 +2,8 @@
TAG ?= CLANG
ENABLE_MPI ?= true
ENABLE_OPENMP ?= false
# Supported: seq, mpi
VTK_OUTPUT_FMT ?= seq
#Feature options
OPTIONS += -DARRAY_ALIGNMENT=64

2
BasicSolver/3D-mpi/include_CLANG.mk
View File

@ -18,4 +18,4 @@ VERSION = --version
CFLAGS = -Ofast -std=c17
LFLAGS = $(OPENMP) -lm
DEFINES += -D_GNU_SOURCE# -DDEBUG
INCLUDES =
INCLUDES = -I/opt/homebrew/include

8
BasicSolver/3D-mpi/include_GCC.mk
View File

@ -1,4 +1,10 @@
ifeq ($(ENABLE_MPI),true)
CC = mpicc
DEFINES = -D_MPI
else
CC = gcc
endif
GCC = gcc
LINKER = $(CC)
@ -9,6 +15,6 @@ endif
VERSION = --version
CFLAGS = -Ofast -ffreestanding -std=c99 $(OPENMP)
LFLAGS = $(OPENMP)
DEFINES = -D_GNU_SOURCE
DEFINES += -D_GNU_SOURCE
INCLUDES =
LIBS =

8
BasicSolver/3D-mpi/include_ICC.mk
View File

@ -1,4 +1,10 @@
ifeq ($(ENABLE_MPI),true)
CC = mpiicc
DEFINES = -D_MPI
else
CC = icc
endif
GCC = gcc
LINKER = $(CC)
@ -9,6 +15,6 @@ endif
VERSION = --version
CFLAGS = -O3 -xHost -qopt-zmm-usage=high -std=c99 $(OPENMP)
LFLAGS = $(OPENMP)
DEFINES = -D_GNU_SOURCE
DEFINES += -D_GNU_SOURCE
INCLUDES =
LIBS =

2
BasicSolver/3D-mpi/src/allocate.c
View File

@ -1,5 +1,5 @@
/*
* Copyright (C) 2022 NHR@FAU, University Erlangen-Nuremberg.
* Copyright (C) NHR@FAU, University Erlangen-Nuremberg.
* All rights reserved.
* Use of this source code is governed by a MIT-style
* license that can be found in the LICENSE file.

2
BasicSolver/3D-mpi/src/allocate.h
View File

@ -1,5 +1,5 @@
/*
* Copyright (C) 2022 NHR@FAU, University Erlangen-Nuremberg.
* Copyright (C) NHR@FAU, University Erlangen-Nuremberg.
* All rights reserved.
* Use of this source code is governed by a MIT-style
* license that can be found in the LICENSE file.

34
BasicSolver/3D-mpi/src/comm.c
View File

@ -1,5 +1,5 @@
/*
* Copyright (C) 2022 NHR@FAU, University Erlangen-Nuremberg.
* Copyright (C) NHR@FAU, University Erlangen-Nuremberg.
* All rights reserved. This file is part of nusif-solver.
* Use of this source code is governed by a MIT style
* license that can be found in the LICENSE file.
@ -296,6 +296,30 @@ void commShift(Comm* c, double* f, double* g, double* h)
#endif
}
void commGetOffsets(Comm* c, int offsets[], int kmax, int jmax, int imax)
{
#if defined(_MPI)
int sum = 0;
for (int i = 0; i < c->coords[ICORD]; i++) {
sum += sizeOfRank(i, c->dims[ICORD], imax);
}
offsets[IDIM] = sum;
sum = 0;
for (int i = 0; i < c->coords[JCORD]; i++) {
sum += sizeOfRank(i, c->dims[JCORD], jmax);
}
offsets[JDIM] = sum;
sum = 0;
for (int i = 0; i < c->coords[KCORD]; i++) {
sum += sizeOfRank(i, c->dims[KCORD], kmax);
}
offsets[KDIM] = sum;
#endif
}
#define G(v, i, j, k) \
v[(k) * (imaxLocal + 2) * (jmaxLocal + 2) + (j) * (imaxLocal + 2) + (i)]
@ -445,7 +469,7 @@ void commCollectResult(Comm* c,
for (int k = 1; k < kmaxLocal + 1; k++) {
for (int j = 1; j < jmaxLocal + 1; j++) {
for (int i = 1; i < imaxLocal + 1; i++) {
pg[idx++] = G(s->p, i, j, k);
pg[idx++] = G(p, i, j, k);
}
}
}
@ -455,7 +479,7 @@ void commCollectResult(Comm* c,
for (int k = 1; k < kmaxLocal + 1; k++) {
for (int j = 1; j < jmaxLocal + 1; j++) {
for (int i = 1; i < imaxLocal + 1; i++) {
ug[idx++] = (G(s->u, i, j, k) + G(s->u, i - 1, j, k)) / 2.0;
ug[idx++] = (G(u, i, j, k) + G(u, i - 1, j, k)) / 2.0;
}
}
}
@ -465,7 +489,7 @@ void commCollectResult(Comm* c,
for (int k = 1; k < kmaxLocal + 1; k++) {
for (int j = 1; j < jmaxLocal + 1; j++) {
for (int i = 1; i < imaxLocal + 1; i++) {
vg[idx++] = (G(s->v, i, j, k) + G(s->v, i, j - 1, k)) / 2.0;
vg[idx++] = (G(v, i, j, k) + G(v, i, j - 1, k)) / 2.0;
}
}
}
@ -475,7 +499,7 @@ void commCollectResult(Comm* c,
for (int k = 1; k < kmaxLocal + 1; k++) {
for (int j = 1; j < jmaxLocal + 1; j++) {
for (int i = 1; i < imaxLocal + 1; i++) {
wg[idx++] = (G(s->w, i, j, k) + G(s->w, i, j, k - 1)) / 2.0;
wg[idx++] = (G(w, i, j, k) + G(w, i, j, k - 1)) / 2.0;
}
}
}

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

@ -1,5 +1,5 @@
/*
* Copyright (C) 2024 NHR@FAU, University Erlangen-Nuremberg.
* Copyright (C) NHR@FAU, University Erlangen-Nuremberg.
* All rights reserved. This file is part of nusif-solver.
* Use of this source code is governed by a MIT style
* license that can be found in the LICENSE file.
@ -44,6 +44,7 @@ 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 commGetOffsets(Comm* c, int offsets[], int kmax, int jmax, int imax);
extern void commCollectResult(Comm* c,
double* ug,
double* vg,

2
BasicSolver/3D-mpi/src/grid.h
View File

@ -1,5 +1,5 @@
/*
* Copyright (C) 2022 NHR@FAU, University Erlangen-Nuremberg.
* Copyright (C) NHR@FAU, University Erlangen-Nuremberg.
* All rights reserved. This file is part of nusif-solver.
* Use of this source code is governed by a MIT style
* license that can be found in the LICENSE file.

12
BasicSolver/3D-mpi/src/main.c
View File

@ -1,11 +1,9 @@
/*
* Copyright (C) 2024 NHR@FAU, University Erlangen-Nuremberg.
* Copyright (C) NHR@FAU, University Erlangen-Nuremberg.
* All rights reserved.
* Use of this source code is governed by a MIT-style
* license that can be found in the LICENSE file.
*/
#include <float.h>
#include <limits.h>
#include <stdio.h>
#include <stdlib.h>
#include <unistd.h>
@ -73,6 +71,13 @@ int main(int argc, char** argv)
printf("Solution took %.2fs\n", timeStop - timeStart);
}
#ifdef _VTK_WRITER_MPI
VtkOptions opts = { .grid = s.grid, .comm = s.comm };
vtkOpen(&opts, s.problem);
vtkScalar(&opts, "pressure", s.p);
vtkVector(&opts, "velocity", (VtkVector) { s.u, s.v, s.w });
vtkClose(&opts);
#else
double *pg, *ug, *vg, *wg;
if (commIsMaster(&s.comm)) {
@ -104,6 +109,7 @@ int main(int argc, char** argv)
vtkVector(&opts, "velocity", (VtkVector) { ug, vg, wg });
vtkClose(&opts);
}
#endif
commFinalize(&s.comm);
return EXIT_SUCCESS;

2
BasicSolver/3D-mpi/src/parameter.c
View File

@ -1,5 +1,5 @@
/*
* Copyright (C) 2022 NHR@FAU, University Erlangen-Nuremberg.
* Copyright (C) NHR@FAU, University Erlangen-Nuremberg.
* All rights reserved. This file is part of nusif-solver.
* Use of this source code is governed by a MIT style
* license that can be found in the LICENSE file.

2
BasicSolver/3D-mpi/src/parameter.h
View File

@ -1,5 +1,5 @@
/*
* Copyright (C) 2022 NHR@FAU, University Erlangen-Nuremberg.
* Copyright (C) NHR@FAU, University Erlangen-Nuremberg.
* All rights reserved. This file is part of nusif-solver.
* Use of this source code is governed by a MIT style
* license that can be found in the LICENSE file.

2
BasicSolver/3D-mpi/src/progress.c
View File

@ -1,5 +1,5 @@
/*
* Copyright (C) 2022 NHR@FAU, University Erlangen-Nuremberg.
* Copyright (C) NHR@FAU, University Erlangen-Nuremberg.
* All rights reserved. This file is part of nusif-solver.
* Use of this source code is governed by a MIT style
* license that can be found in the LICENSE file.

2
BasicSolver/3D-mpi/src/progress.h
View File

@ -1,5 +1,5 @@
/*
* Copyright (C) 2022 NHR@FAU, University Erlangen-Nuremberg.
* Copyright (C) NHR@FAU, University Erlangen-Nuremberg.
* All rights reserved.
* Use of this source code is governed by a MIT-style
* license that can be found in the LICENSE file.

2
BasicSolver/3D-mpi/src/solver.c
View File

@ -1,5 +1,5 @@
/*
* Copyright (C) 2022 NHR@FAU, University Erlangen-Nuremberg.
* Copyright (C) NHR@FAU, University Erlangen-Nuremberg.
* All rights reserved. This file is part of nusif-solver.
* Use of this source code is governed by a MIT style
* license that can be found in the LICENSE file.

2
BasicSolver/3D-mpi/src/solver.h
View File

@ -1,5 +1,5 @@
/*
* Copyright (C) 2022 NHR@FAU, University Erlangen-Nuremberg.
* Copyright (C) NHR@FAU, University Erlangen-Nuremberg.
* All rights reserved. This file is part of nusif-solver.
* Use of this source code is governed by a MIT style
* license that can be found in the LICENSE file.

21
BasicSolver/3D-mpi/src/test.c
View File

@ -1,5 +1,5 @@
/*
* Copyright (C) 2022 NHR@FAU, University Erlangen-Nuremberg.
* Copyright (C) NHR@FAU, University Erlangen-Nuremberg.
* All rights reserved.
* Use of this source code is governed by a MIT-style
* license that can be found in the LICENSE file.
@ -26,10 +26,21 @@ void testInit(Solver* s)
for (int k = 0; k < kmaxLocal + 2; k++) {
for (int j = 0; j < jmaxLocal + 2; j++) {
for (int i = 0; i < imaxLocal + 2; i++) {
G(p, i, j, k) = myrank;
G(f, i, j, k) = myrank;
G(g, i, j, k) = myrank;
G(h, i, j, k) = myrank;
G(p, i, j, k) = 10.0;
G(f, i, j, k) = myrank + 1.0;
G(g, i, j, k) = myrank + 1.0;
G(h, i, j, k) = myrank + 1.0;
}
}
}
for (int k = 1; k < kmaxLocal + 1; k++) {
for (int j = 1; j < jmaxLocal + 1; j++) {
for (int i = 1; i < imaxLocal + 1; i++) {
G(p, i, j, k) = myrank + 1.0;
G(f, i, j, k) = myrank + 1.0;
G(g, i, j, k) = myrank + 1.0;
G(h, i, j, k) = myrank + 1.0;
}
}
}

2
BasicSolver/3D-mpi/src/test.h
View File

@ -1,5 +1,5 @@
/*
* Copyright (C) 2022 NHR@FAU, University Erlangen-Nuremberg.
* Copyright (C) NHR@FAU, University Erlangen-Nuremberg.
* All rights reserved. This file is part of nusif-solver.
* Use of this source code is governed by a MIT style
* license that can be found in the LICENSE file.

2
BasicSolver/3D-mpi/src/timing.c
View File

@ -1,5 +1,5 @@
/*
* Copyright (C) 2022 NHR@FAU, University Erlangen-Nuremberg.
* Copyright (C) NHR@FAU, University Erlangen-Nuremberg.
* All rights reserved.
* Use of this source code is governed by a MIT-style
* license that can be found in the LICENSE file.

2
BasicSolver/3D-mpi/src/timing.h
View File

@ -1,5 +1,5 @@
/*
* Copyright (C) 2022 NHR@FAU, University Erlangen-Nuremberg.
* Copyright (C) NHR@FAU, University Erlangen-Nuremberg.
* All rights reserved.
* Use of this source code is governed by a MIT-style
* license that can be found in the LICENSE file.

2
BasicSolver/3D-mpi/src/util.h
View File

@ -1,5 +1,5 @@
/*
* Copyright (C) 2022 NHR@FAU, University Erlangen-Nuremberg.
* Copyright (C) NHR@FAU, University Erlangen-Nuremberg.
* All rights reserved.
* Use of this source code is governed by a MIT-style
* license that can be found in the LICENSE file.

47
BasicSolver/3D-mpi-io/src/vtkWriter.c → BasicSolver/3D-mpi/src/vtkWriter-mpi.c
View File

@ -1,5 +1,5 @@
/*
* Copyright (C) 2022 NHR@FAU, University Erlangen-Nuremberg.
* Copyright (C) NHR@FAU, University Erlangen-Nuremberg.
* All rights reserved. This file is part of nusif-solver.
* Use of this source code is governed by a MIT style
* license that can be found in the LICENSE file.
@ -14,24 +14,32 @@
#include "comm.h"
#include "vtkWriter.h"
// reset fileview for output of string headers
static void resetFileview(VtkOptions* o)
{
// reset fileview for output of string header
MPI_Offset disp;
MPI_File_sync(o->fh);
MPI_Barrier(o->comm.comm);
MPI_File_get_size(o->fh, &disp);
MPI_File_set_view(o->fh, disp, MPI_CHAR, MPI_CHAR, "native", MPI_INFO_NULL);
// printf("Rank %d disp %lld\n", o->comm.rank, disp);
}
static void writeVersion(VtkOptions* o)
{
char header[50] = "# vtk DataFile Version 3.0\n";
// always overwrite exiting files
MPI_File_set_view(o->fh, 0, MPI_CHAR, MPI_CHAR, "native", MPI_INFO_NULL);
if (commIsMaster(&o->comm)) {
MPI_File_write(o->fh, header, (int)strlen(header), MPI_CHAR, MPI_STATUS_IGNORE);
}
}
static void writeHeader(VtkOptions* o)
{
const size_t MAX_HEADER = 200;
char* header = (char*)malloc(MAX_HEADER);
char header[400];
char* cursor = header;
cursor += sprintf(cursor, "# vtk DataFile Version 3.0\n");
cursor += sprintf(cursor, "PAMPI cfd solver output\n");
cursor += sprintf(cursor, "BINARY\n");
@ -52,13 +60,10 @@ static void writeHeader(VtkOptions* o)
o->grid.imax * o->grid.jmax * o->grid.kmax);
if (commIsMaster(&o->comm)) {
MPI_File_write(o->fh, header, strlen(header), MPI_CHAR, MPI_STATUS_IGNORE);
MPI_File_write(o->fh, header, (int)strlen(header), MPI_CHAR, MPI_STATUS_IGNORE);
}
free(header);
}
// TODO Check inputs for length
void vtkOpen(VtkOptions* o, char* problem)
{
char filename[50];
@ -66,7 +71,7 @@ void vtkOpen(VtkOptions* o, char* problem)
snprintf(filename, 50, "%s-p%d.vtk", problem, o->comm.size);
MPI_File_open(o->comm.comm,
filename,
MPI_MODE_WRONLY | MPI_MODE_CREATE | MPI_MODE_EXCL,
MPI_MODE_WRONLY | MPI_MODE_CREATE,
MPI_INFO_NULL,
&o->fh);
@ -74,35 +79,32 @@ void vtkOpen(VtkOptions* o, char* problem)
printf("Writing VTK output for %s\n", problem);
}
resetFileview(o);
writeVersion(o);
writeHeader(o);
}
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;
char* header = (char*)malloc(MAX_HEADER);
char header[100];
char* cursor = header;
cursor += sprintf(cursor, "SCALARS %s double 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);
MPI_File_write(o->fh, header, (int)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);
commGetOffsets(&o->comm, offsets, o->grid.kmax, o->grid.jmax, o->grid.imax);
// set global view in file
MPI_Offset disp;
MPI_Datatype fileViewType;
MPI_File_sync(o->fh);
MPI_Barrier(o->comm.comm);
MPI_File_get_size(o->fh, &disp);
@ -172,15 +174,16 @@ void vtkVector(VtkOptions* o, char* name, VtkVector vec)
resetFileview(o);
if (commIsMaster(&o->comm)) {
MPI_File_write(o->fh, header, strlen(header), MPI_CHAR, MPI_STATUS_IGNORE);
MPI_File_write(o->fh, header, (int)strlen(header), MPI_CHAR, MPI_STATUS_IGNORE);
}
int offsets[NDIMS];
commGetOffsets(&o->comm, offsets, o->grid.imax, o->grid.jmax, o->grid.kmax);
commGetOffsets(&o->comm, offsets, o->grid.kmax, o->grid.jmax, o->grid.imax);
// set global view in file
MPI_Offset disp;
MPI_Datatype fileViewType, vectorType;
MPI_File_sync(o->fh);
MPI_Barrier(o->comm.comm);
MPI_File_get_size(o->fh, &disp);

2
BasicSolver/3D-mpi/src/vtkWriter.c → BasicSolver/3D-mpi/src/vtkWriter-seq.c
View File

@ -1,5 +1,5 @@
/*
* Copyright (C) 2022 NHR@FAU, University Erlangen-Nuremberg.
* Copyright (C) NHR@FAU, University Erlangen-Nuremberg.
* All rights reserved. This file is part of nusif-solver.
* Use of this source code is governed by a MIT style
* license that can be found in the LICENSE file.

10
BasicSolver/3D-mpi/src/vtkWriter.h
View File

@ -1,5 +1,5 @@
/*
* Copyright (C) 2022 NHR@FAU, University Erlangen-Nuremberg.
* Copyright (C) NHR@FAU, University Erlangen-Nuremberg.
* All rights reserved. This file is part of nusif-solver.
* Use of this source code is governed by a MIT style
* license that can be found in the LICENSE file.
@ -8,14 +8,20 @@
#define __VTKWRITER_H_
#include <stdio.h>
#include "comm.h"
#include "grid.h"
typedef enum VtkFormat { ASCII = 0, BINARY } VtkFormat;
typedef struct VtkOptions {
VtkFormat fmt;
Grid grid;
#ifdef _VTK_WRITER_MPI
MPI_File fh;
#else
FILE* fh;
VtkFormat fmt;
#endif // _VTK_WRITER_MPI
Comm comm;
} VtkOptions;
typedef struct VtkVector {