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Commit 1d64aa96 authored by Matthieu Schaller's avatar Matthieu Schaller
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Implement more general conversion functions for i/o. Can now add one that does... 

Implement more general conversion functions for i/o. Can now add one that does box-wrapping  of particles.
parent bee23d1c
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1 merge request!460Improvements to i/o and parallel-i/o
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src/gravity/Default/gravity_io.h
+ 18
− 4
View file @ 1d64aa96
...@@ -21,6 +21,20 @@ ...@@ -21,6 +21,20 @@
#include "io_properties.h" #include "io_properties.h"
void convert_gpart_pos(const struct engine* e, const struct gpart* gp,
double* ret) {
if (e->s->periodic) {
ret[0] = box_wrap(gp->x[0], 0.0, e->s->dim[0]);
ret[1] = box_wrap(gp->x[1], 0.0, e->s->dim[1]);
ret[2] = box_wrap(gp->x[2], 0.0, e->s->dim[2]);
} else {
ret[0] = gp->x[0];
ret[1] = gp->x[1];
ret[2] = gp->x[2];
}
}
/** /**
* @brief Specifies which g-particle fields to read from a dataset * @brief Specifies which g-particle fields to read from a dataset
* *
...@@ -52,15 +66,15 @@ void darkmatter_read_particles(struct gpart* gparts, struct io_props* list, ...@@ -52,15 +66,15 @@ void darkmatter_read_particles(struct gpart* gparts, struct io_props* list,
* @param list The list of i/o properties to write. * @param list The list of i/o properties to write.
* @param num_fields The number of i/o fields to write. * @param num_fields The number of i/o fields to write.
*/ */
void darkmatter_write_particles(struct gpart* gparts, struct io_props* list, void darkmatter_write_particles(const struct gpart* gparts,
int* num_fields) { struct io_props* list, int* num_fields) {
/* Say how much we want to read */ /* Say how much we want to read */
*num_fields = 5; *num_fields = 5;
/* List what we want to read */ /* List what we want to read */
list[0] = io_make_output_field("Coordinates", DOUBLE, 3, UNIT_CONV_LENGTH, list[0] = io_make_output_field_convert_gpart(
gparts, x); "Coordinates", DOUBLE, 3, UNIT_CONV_LENGTH, gparts, convert_gpart_pos);
list[1] = io_make_output_field("Velocities", FLOAT, 3, UNIT_CONV_SPEED, list[1] = io_make_output_field("Velocities", FLOAT, 3, UNIT_CONV_SPEED,
gparts, v_full); gparts, v_full);
list[2] = list[2] =
......
src/hydro/Gadget2/hydro_io.h
+ 23
− 9
View file @ 1d64aa96
...@@ -55,14 +55,28 @@ void hydro_read_particles(struct part* parts, struct io_props* list, ...@@ -55,14 +55,28 @@ void hydro_read_particles(struct part* parts, struct io_props* list,
UNIT_CONV_DENSITY, parts, rho); UNIT_CONV_DENSITY, parts, rho);
} }
float convert_u(struct engine* e, struct part* p) { void convert_u(const struct engine* e, const struct part* p, float* ret) {
return hydro_get_internal_energy(p); ret[0] = hydro_get_internal_energy(p);
} }
float convert_P(struct engine* e, struct part* p) { void convert_P(const struct engine* e, const struct part* p, float* ret) {
return hydro_get_pressure(p); ret[0] = hydro_get_pressure(p);
}
void convert_part_pos(const struct engine* e, const struct part* p,
double* ret) {
if (e->s->periodic) {
ret[0] = box_wrap(p->x[0], 0.0, e->s->dim[0]);
ret[1] = box_wrap(p->x[1], 0.0, e->s->dim[1]);
ret[2] = box_wrap(p->x[2], 0.0, e->s->dim[2]);
} else {
ret[0] = p->x[0];
ret[1] = p->x[1];
ret[2] = p->x[2];
}
} }
/** /**
...@@ -72,14 +86,14 @@ float convert_P(struct engine* e, struct part* p) { ...@@ -72,14 +86,14 @@ float convert_P(struct engine* e, struct part* p) {
* @param list The list of i/o properties to write. * @param list The list of i/o properties to write.
* @param num_fields The number of i/o fields to write. * @param num_fields The number of i/o fields to write.
*/ */
void hydro_write_particles(struct part* parts, struct io_props* list, void hydro_write_particles(const struct part* parts, struct io_props* list,
int* num_fields) { int* num_fields) {
*num_fields = 10; *num_fields = 10;
/* List what we want to write */ /* List what we want to write */
list[0] = io_make_output_field("Coordinates", DOUBLE, 3, UNIT_CONV_LENGTH, list[0] = io_make_output_field_convert_part(
parts, x); "Coordinates", DOUBLE, 3, UNIT_CONV_LENGTH, parts, convert_part_pos);
list[1] = list[1] =
io_make_output_field("Velocities", FLOAT, 3, UNIT_CONV_SPEED, parts, v); io_make_output_field("Velocities", FLOAT, 3, UNIT_CONV_SPEED, parts, v);
list[2] = list[2] =
...@@ -96,9 +110,9 @@ void hydro_write_particles(struct part* parts, struct io_props* list, ...@@ -96,9 +110,9 @@ void hydro_write_particles(struct part* parts, struct io_props* list,
io_make_output_field("Density", FLOAT, 1, UNIT_CONV_DENSITY, parts, rho); io_make_output_field("Density", FLOAT, 1, UNIT_CONV_DENSITY, parts, rho);
list[8] = io_make_output_field_convert_part("InternalEnergy", FLOAT, 1, list[8] = io_make_output_field_convert_part("InternalEnergy", FLOAT, 1,
UNIT_CONV_ENERGY_PER_UNIT_MASS, UNIT_CONV_ENERGY_PER_UNIT_MASS,
parts, rho, convert_u); parts, convert_u);
list[9] = io_make_output_field_convert_part( list[9] = io_make_output_field_convert_part(
"Pressure", FLOAT, 1, UNIT_CONV_PRESSURE, parts, rho, convert_P); "Pressure", FLOAT, 1, UNIT_CONV_PRESSURE, parts, convert_P);
} }
/** /**
......
src/io_properties.h
+ 131
− 35
View file @ 1d64aa96
...@@ -16,7 +16,6 @@ ...@@ -16,7 +16,6 @@
* along with this program. If not, see <http://www.gnu.org/licenses/>. * along with this program. If not, see <http://www.gnu.org/licenses/>.
* *
******************************************************************************/ ******************************************************************************/
#ifndef SWIFT_IO_PROPERTIES_H #ifndef SWIFT_IO_PROPERTIES_H
#define SWIFT_IO_PROPERTIES_H #define SWIFT_IO_PROPERTIES_H
...@@ -29,6 +28,16 @@ ...@@ -29,6 +28,16 @@
*/ */
enum DATA_IMPORTANCE { COMPULSORY = 1, OPTIONAL = 0, UNUSED = -1 }; enum DATA_IMPORTANCE { COMPULSORY = 1, OPTIONAL = 0, UNUSED = -1 };
/* Helper typedefs */
typedef void (*conversion_func_part_float)(const struct engine*,
const struct part*, float*);
typedef void (*conversion_func_part_double)(const struct engine*,
const struct part*, double*);
typedef void (*conversion_func_gpart_float)(const struct engine*,
const struct gpart*, float*);
typedef void (*conversion_func_gpart_double)(const struct engine*,
const struct gpart*, double*);
/** /**
* @brief The properties of a given dataset for i/o * @brief The properties of a given dataset for i/o
*/ */
...@@ -56,14 +65,19 @@ struct io_props { ...@@ -56,14 +65,19 @@ struct io_props {
size_t partSize; size_t partSize;
/* The particle arrays */ /* The particle arrays */
struct part* parts; const struct part* parts;
struct gpart* gparts; const struct gpart* gparts;
/* Are we converting? */
int conversion;
/* Conversion function for part */ /* Conversion function for part */
float (*convert_part)(struct engine*, struct part*); conversion_func_part_float convert_part_f;
conversion_func_part_double convert_part_d;
/* Conversion function for gpart */ /* Conversion function for gpart */
float (*convert_gpart)(struct engine*, struct gpart*); conversion_func_gpart_float convert_gpart_f;
conversion_func_gpart_double convert_gpart_d;
}; };
/** /**
...@@ -101,8 +115,11 @@ struct io_props io_make_input_field_(char name[FIELD_BUFFER_SIZE], ...@@ -101,8 +115,11 @@ struct io_props io_make_input_field_(char name[FIELD_BUFFER_SIZE],
r.partSize = partSize; r.partSize = partSize;
r.parts = NULL; r.parts = NULL;
r.gparts = NULL; r.gparts = NULL;
r.convert_part = NULL; r.conversion = 0;
r.convert_gpart = NULL; r.convert_part_f = NULL;
r.convert_part_d = NULL;
r.convert_gpart_f = NULL;
r.convert_gpart_d = NULL;
return r; return r;
} }
...@@ -140,8 +157,11 @@ struct io_props io_make_output_field_(char name[FIELD_BUFFER_SIZE], ...@@ -140,8 +157,11 @@ struct io_props io_make_output_field_(char name[FIELD_BUFFER_SIZE],
r.partSize = partSize; r.partSize = partSize;
r.parts = NULL; r.parts = NULL;
r.gparts = NULL; r.gparts = NULL;
r.convert_part = NULL; r.conversion = 0;
r.convert_gpart = NULL; r.convert_part_f = NULL;
r.convert_part_d = NULL;
r.convert_gpart_f = NULL;
r.convert_gpart_d = NULL;
return r; return r;
} }
...@@ -149,11 +169,10 @@ struct io_props io_make_output_field_(char name[FIELD_BUFFER_SIZE], ...@@ -149,11 +169,10 @@ struct io_props io_make_output_field_(char name[FIELD_BUFFER_SIZE],
/** /**
* @brief Constructs an #io_props (with conversion) from its parameters * @brief Constructs an #io_props (with conversion) from its parameters
*/ */
#define io_make_output_field_convert_part(name, type, dim, units, part, field, \ #define io_make_output_field_convert_part(name, type, dim, units, part, \
convert) \ convert) \
io_make_output_field_convert_part_(name, type, dim, units, \ io_make_output_field_convert_part_##type(name, type, dim, units, \
(char*)(&(part[0]).field), \ sizeof(part[0]), part, convert)
sizeof(part[0]), part, convert)
/** /**
* @brief Construct an #io_props from its parameters * @brief Construct an #io_props from its parameters
...@@ -162,17 +181,16 @@ struct io_props io_make_output_field_(char name[FIELD_BUFFER_SIZE], ...@@ -162,17 +181,16 @@ struct io_props io_make_output_field_(char name[FIELD_BUFFER_SIZE],
* @param type The type of the data * @param type The type of the data
* @param dimension Dataset dimension (1D, 3D, ...) * @param dimension Dataset dimension (1D, 3D, ...)
* @param units The units of the dataset * @param units The units of the dataset
* @param field Pointer to the field of the first particle
* @param partSize The size in byte of the particle * @param partSize The size in byte of the particle
* @param parts The particle array * @param parts The particle array
* @param functionPtr The function used to convert a particle to a float * @param functionPtr The function used to convert a particle to a float
* *
* Do not call this function directly. Use the macro defined above. * Do not call this function directly. Use the macro defined above.
*/ */
struct io_props io_make_output_field_convert_part_( struct io_props io_make_output_field_convert_part_FLOAT(
char name[FIELD_BUFFER_SIZE], enum IO_DATA_TYPE type, int dimension, char name[FIELD_BUFFER_SIZE], enum IO_DATA_TYPE type, int dimension,
enum unit_conversion_factor units, char* field, size_t partSize, enum unit_conversion_factor units, size_t partSize,
struct part* parts, float (*functionPtr)(struct engine*, struct part*)) { const struct part* parts, conversion_func_part_float functionPtr) {
struct io_props r; struct io_props r;
strcpy(r.name, name); strcpy(r.name, name);
...@@ -180,12 +198,52 @@ struct io_props io_make_output_field_convert_part_( ...@@ -180,12 +198,52 @@ struct io_props io_make_output_field_convert_part_(
r.dimension = dimension; r.dimension = dimension;
r.importance = UNUSED; r.importance = UNUSED;
r.units = units; r.units = units;
r.field = field; r.field = NULL;
r.partSize = partSize; r.partSize = partSize;
r.parts = parts; r.parts = parts;
r.gparts = NULL; r.gparts = NULL;
r.convert_part = functionPtr; r.conversion = 1;
r.convert_gpart = NULL; r.convert_part_f = functionPtr;
r.convert_part_d = NULL;
r.convert_gpart_f = NULL;
r.convert_gpart_d = NULL;
return r;
}
/**
* @brief Construct an #io_props from its parameters
*
* @param name Name of the field to read
* @param type The type of the data
* @param dimension Dataset dimension (1D, 3D, ...)
* @param units The units of the dataset
* @param partSize The size in byte of the particle
* @param parts The particle array
* @param functionPtr The function used to convert a particle to a float
*
* Do not call this function directly. Use the macro defined above.
*/
struct io_props io_make_output_field_convert_part_DOUBLE(
char name[FIELD_BUFFER_SIZE], enum IO_DATA_TYPE type, int dimension,
enum unit_conversion_factor units, size_t partSize,
const struct part* parts, conversion_func_part_double functionPtr) {
struct io_props r;
strcpy(r.name, name);
r.type = type;
r.dimension = dimension;
r.importance = UNUSED;
r.units = units;
r.field = NULL;
r.partSize = partSize;
r.parts = parts;
r.gparts = NULL;
r.conversion = 1;
r.convert_part_f = NULL;
r.convert_part_d = functionPtr;
r.convert_gpart_f = NULL;
r.convert_gpart_d = NULL;
return r; return r;
} }
...@@ -193,11 +251,10 @@ struct io_props io_make_output_field_convert_part_( ...@@ -193,11 +251,10 @@ struct io_props io_make_output_field_convert_part_(
/** /**
* @brief Constructs an #io_props (with conversion) from its parameters * @brief Constructs an #io_props (with conversion) from its parameters
*/ */
#define io_make_output_field_convert_gpart(name, type, dim, units, part, \ #define io_make_output_field_convert_gpart(name, type, dim, units, gpart, \
field, convert) \ convert) \
io_make_output_field_convert_gpart_(name, type, dim, units, \ io_make_output_field_convert_gpart_##type(name, type, dim, units, \
(char*)(&(part[0]).field), \ sizeof(gpart[0]), gpart, convert)
sizeof(part[0]), gpart, convert)
/** /**
* @brief Construct an #io_props from its parameters * @brief Construct an #io_props from its parameters
...@@ -206,17 +263,16 @@ struct io_props io_make_output_field_convert_part_( ...@@ -206,17 +263,16 @@ struct io_props io_make_output_field_convert_part_(
* @param type The type of the data * @param type The type of the data
* @param dimension Dataset dimension (1D, 3D, ...) * @param dimension Dataset dimension (1D, 3D, ...)
* @param units The units of the dataset * @param units The units of the dataset
* @param field Pointer to the field of the first particle * @param gpartSize The size in byte of the particle
* @param partSize The size in byte of the particle
* @param gparts The particle array * @param gparts The particle array
* @param functionPtr The function used to convert a g-particle to a float * @param functionPtr The function used to convert a g-particle to a float
* *
* Do not call this function directly. Use the macro defined above. * Do not call this function directly. Use the macro defined above.
*/ */
struct io_props io_make_output_field_convert_gpart_( struct io_props io_make_output_field_convert_gpart_FLOAT(
char name[FIELD_BUFFER_SIZE], enum IO_DATA_TYPE type, int dimension, char name[FIELD_BUFFER_SIZE], enum IO_DATA_TYPE type, int dimension,
enum unit_conversion_factor units, char* field, size_t partSize, enum unit_conversion_factor units, size_t gpartSize,
struct gpart* gparts, float (*functionPtr)(struct engine*, struct gpart*)) { const struct gpart* gparts, conversion_func_gpart_float functionPtr) {
struct io_props r; struct io_props r;
strcpy(r.name, name); strcpy(r.name, name);
...@@ -224,12 +280,52 @@ struct io_props io_make_output_field_convert_gpart_( ...@@ -224,12 +280,52 @@ struct io_props io_make_output_field_convert_gpart_(
r.dimension = dimension; r.dimension = dimension;
r.importance = UNUSED; r.importance = UNUSED;
r.units = units; r.units = units;
r.field = field; r.field = NULL;
r.partSize = partSize; r.partSize = gpartSize;
r.parts = NULL;
r.gparts = gparts;
r.conversion = 1;
r.convert_part_f = NULL;
r.convert_part_d = NULL;
r.convert_gpart_f = functionPtr;
r.convert_gpart_d = NULL;
return r;
}
/**
* @brief Construct an #io_props from its parameters
*
* @param name Name of the field to read
* @param type The type of the data
* @param dimension Dataset dimension (1D, 3D, ...)
* @param units The units of the dataset
* @param gpartSize The size in byte of the particle
* @param gparts The particle array
* @param functionPtr The function used to convert a g-particle to a float
*
* Do not call this function directly. Use the macro defined above.
*/
struct io_props io_make_output_field_convert_gpart_DOUBLE(
char name[FIELD_BUFFER_SIZE], enum IO_DATA_TYPE type, int dimension,
enum unit_conversion_factor units, size_t gpartSize,
const struct gpart* gparts, conversion_func_gpart_double functionPtr) {
struct io_props r;
strcpy(r.name, name);
r.type = type;
r.dimension = dimension;
r.importance = UNUSED;
r.units = units;
r.field = NULL;
r.partSize = gpartSize;
r.parts = NULL; r.parts = NULL;
r.gparts = gparts; r.gparts = gparts;
r.convert_part = NULL; r.conversion = 1;
r.convert_gpart = functionPtr; r.convert_part_f = NULL;
r.convert_part_d = NULL;
r.convert_gpart_f = NULL;
r.convert_gpart_d = functionPtr;
return r; return r;
} }
......
src/serial_io.c
+ 57
− 20
View file @ 1d64aa96
...@@ -176,9 +176,9 @@ void readArray(hid_t grp, const struct io_props props, size_t N, ...@@ -176,9 +176,9 @@ void readArray(hid_t grp, const struct io_props props, size_t N,
* Routines writing an output file * Routines writing an output file
*-----------------------------------------------------------------------------*/ *-----------------------------------------------------------------------------*/
void prepareArray(struct engine* e, hid_t grp, char* fileName, FILE* xmfFile, void prepareArray(const struct engine* e, hid_t grp, char* fileName,
char* partTypeGroupName, const struct io_props props, FILE* xmfFile, char* partTypeGroupName,
unsigned long long N_total, const struct io_props props, unsigned long long N_total,
const struct unit_system* internal_units, const struct unit_system* internal_units,
const struct unit_system* snapshot_units) { const struct unit_system* snapshot_units) {
...@@ -282,15 +282,17 @@ void prepareArray(struct engine* e, hid_t grp, char* fileName, FILE* xmfFile, ...@@ -282,15 +282,17 @@ void prepareArray(struct engine* e, hid_t grp, char* fileName, FILE* xmfFile,
* @todo A better version using HDF5 hyper-slabs to write the file directly from * @todo A better version using HDF5 hyper-slabs to write the file directly from
* the part array will be written once the structures have been stabilized. * the part array will be written once the structures have been stabilized.
*/ */
void writeArray(struct engine* e, hid_t grp, char* fileName, FILE* xmfFile, void writeArray(const struct engine* e, hid_t grp, char* fileName,
char* partTypeGroupName, const struct io_props props, size_t N, FILE* xmfFile, char* partTypeGroupName,
long long N_total, int mpi_rank, long long offset, const struct io_props props, size_t N, long long N_total,
int mpi_rank, long long offset,
const struct unit_system* internal_units, const struct unit_system* internal_units,
const struct unit_system* snapshot_units) { const struct unit_system* snapshot_units) {
const size_t typeSize = io_sizeof_type(props.type); const size_t typeSize = io_sizeof_type(props.type);
const size_t copySize = typeSize * props.dimension; const size_t copySize = typeSize * props.dimension;
const size_t num_elements = N * props.dimension; const size_t num_elements = N * props.dimension;
const size_t dim = props.dimension;
/* message("Writing '%s' array...", props.name); */ /* message("Writing '%s' array...", props.name); */
...@@ -300,28 +302,63 @@ void writeArray(struct engine* e, hid_t grp, char* fileName, FILE* xmfFile, ...@@ -300,28 +302,63 @@ void writeArray(struct engine* e, hid_t grp, char* fileName, FILE* xmfFile,
internal_units, snapshot_units); internal_units, snapshot_units);
/* Allocate temporary buffer */ /* Allocate temporary buffer */
void* temp = malloc(num_elements * io_sizeof_type(props.type)); void* temp = NULL;
if (temp == NULL) error("Unable to allocate memory for temporary buffer"); if (posix_memalign((void**)&temp, SWIFT_CACHE_ALIGNMENT,
num_elements * io_sizeof_type(props.type)) != 0)
error("Unable to allocate temporary i/o buffer");
/* Copy particle data to temporary buffer */ /* Copy particle data to temporary buffer */
if (props.convert_part == NULL && if (props.conversion == 0) { /* No conversion */
props.convert_gpart == NULL) { /* No conversion */
char* temp_c = temp; char* temp_c = temp;
for (size_t i = 0; i < N; ++i) for (size_t i = 0; i < N; ++i)
memcpy(&temp_c[i * copySize], props.field + i * props.partSize, copySize); memcpy(&temp_c[i * copySize], props.field + i * props.partSize, copySize);
} else if (props.convert_part != NULL) { /* conversion (for parts)*/ } else { /* Converting particle to data */
float* temp_f = temp; if (props.convert_part_f != NULL) {
for (size_t i = 0; i < N; ++i)
temp_f[i] = props.convert_part(e, &props.parts[i]);
} else if (props.convert_gpart != NULL) { /* conversion (for gparts)*/ swift_declare_aligned_ptr(float, temp_f, temp, SWIFT_CACHE_ALIGNMENT);
swift_declare_aligned_ptr(const struct part, parts, props.parts,
SWIFT_STRUCT_ALIGNMENT);
float* temp_f = temp; /* float conversion for parts */
for (size_t i = 0; i < N; ++i) for (size_t i = 0; i < N; i++)
temp_f[i] = props.convert_gpart(e, &props.gparts[i]); props.convert_part_f(e, &parts[i], &temp_f[i * dim]);
} else if (props.convert_part_d != NULL) {
swift_declare_aligned_ptr(double, temp_d, temp, SWIFT_CACHE_ALIGNMENT);
swift_declare_aligned_ptr(const struct part, parts, props.parts,
SWIFT_STRUCT_ALIGNMENT);
/* double conversion for parts */
for (size_t i = 0; i < N; i++)
props.convert_part_d(e, &parts[i], &temp_d[i * dim]);
} else if (props.convert_gpart_f != NULL) {
swift_declare_aligned_ptr(float, temp_f, temp, SWIFT_CACHE_ALIGNMENT);
swift_declare_aligned_ptr(const struct gpart, gparts, props.gparts,
SWIFT_STRUCT_ALIGNMENT);
/* float conversion for gparts */
for (size_t i = 0; i < N; i++)
props.convert_gpart_f(e, &gparts[i], &temp_f[i * dim]);
} else if (props.convert_gpart_d != NULL) {
swift_declare_aligned_ptr(double, temp_d, temp, SWIFT_CACHE_ALIGNMENT);
swift_declare_aligned_ptr(const struct gpart, gparts, props.gparts,
SWIFT_STRUCT_ALIGNMENT);
/* double conversion for gparts */
for (size_t i = 0; i < N; i++)
props.convert_gpart_d(e, &gparts[i], &temp_d[i * dim]);
} else {
error("Missing conversion function");
}
} }
/* Unit conversion if necessary */ /* Unit conversion if necessary */
...@@ -332,10 +369,10 @@ void writeArray(struct engine* e, hid_t grp, char* fileName, FILE* xmfFile, ...@@ -332,10 +369,10 @@ void writeArray(struct engine* e, hid_t grp, char* fileName, FILE* xmfFile,
/* message("Converting ! factor=%e", factor); */ /* message("Converting ! factor=%e", factor); */
if (io_is_double_precision(props.type)) { if (io_is_double_precision(props.type)) {
double* temp_d = temp; swift_declare_aligned_ptr(double, temp_d, temp, SWIFT_CACHE_ALIGNMENT);
for (size_t i = 0; i < num_elements; ++i) temp_d[i] *= factor; for (size_t i = 0; i < num_elements; ++i) temp_d[i] *= factor;
} else { } else {
float* temp_f = temp; swift_declare_aligned_ptr(float, temp_f, temp, SWIFT_CACHE_ALIGNMENT);
for (size_t i = 0; i < num_elements; ++i) temp_f[i] *= factor; for (size_t i = 0; i < num_elements; ++i) temp_f[i] *= factor;
} }
} }
......
src/single_io.c
+ 53
− 16
View file @ 1d64aa96
...@@ -169,40 +169,77 @@ void readArray(hid_t h_grp, const struct io_props prop, size_t N, ...@@ -169,40 +169,77 @@ void readArray(hid_t h_grp, const struct io_props prop, size_t N,
* @todo A better version using HDF5 hyper-slabs to write the file directly from * @todo A better version using HDF5 hyper-slabs to write the file directly from
* the part array will be written once the structures have been stabilized. * the part array will be written once the structures have been stabilized.
*/ */
void writeArray(struct engine* e, hid_t grp, char* fileName, FILE* xmfFile, void writeArray(const struct engine* e, hid_t grp, char* fileName,
char* partTypeGroupName, const struct io_props props, size_t N, FILE* xmfFile, char* partTypeGroupName,
const struct io_props props, size_t N,
const struct unit_system* internal_units, const struct unit_system* internal_units,
const struct unit_system* snapshot_units) { const struct unit_system* snapshot_units) {
const size_t typeSize = io_sizeof_type(props.type); const size_t typeSize = io_sizeof_type(props.type);
const size_t copySize = typeSize * props.dimension; const size_t copySize = typeSize * props.dimension;
const size_t num_elements = N * props.dimension; const size_t num_elements = N * props.dimension;
const size_t dim = props.dimension;
/* message("Writing '%s' array...", props.name); */ /* message("Writing '%s' array...", props.name); */
/* Allocate temporary buffer */ /* Allocate temporary buffer */
void* temp = malloc(num_elements * io_sizeof_type(props.type)); void* temp = NULL;
if (temp == NULL) error("Unable to allocate memory for temporary buffer"); if (posix_memalign((void**)&temp, SWIFT_CACHE_ALIGNMENT,
num_elements * io_sizeof_type(props.type)) != 0)
error("Unable to allocate temporary i/o buffer");
/* Copy particle data to temporary buffer */ /* Copy particle data to temporary buffer */
if (props.convert_part == NULL && if (props.conversion == 0) { /* No conversion */
props.convert_gpart == NULL) { /* No conversion */
char* temp_c = temp; char* temp_c = temp;
for (size_t i = 0; i < N; ++i) for (size_t i = 0; i < N; ++i)
memcpy(&temp_c[i * copySize], props.field + i * props.partSize, copySize); memcpy(&temp_c[i * copySize], props.field + i * props.partSize, copySize);
} else if (props.convert_part != NULL) { /* conversion (for parts)*/ } else { /* Converting particle to data */
float* temp_f = temp; if (props.convert_part_f != NULL) {
for (size_t i = 0; i < N; ++i)
temp_f[i] = props.convert_part(e, &props.parts[i]);
} else if (props.convert_gpart != NULL) { /* conversion (for gparts)*/ swift_declare_aligned_ptr(float, temp_f, temp, SWIFT_CACHE_ALIGNMENT);
swift_declare_aligned_ptr(const struct part, parts, props.parts,
SWIFT_STRUCT_ALIGNMENT);
float* temp_f = temp; /* float conversion for parts */
for (size_t i = 0; i < N; ++i) for (size_t i = 0; i < N; i++)
temp_f[i] = props.convert_gpart(e, &props.gparts[i]); props.convert_part_f(e, &parts[i], &temp_f[i * dim]);
} else if (props.convert_part_d != NULL) {
swift_declare_aligned_ptr(double, temp_d, temp, SWIFT_CACHE_ALIGNMENT);
swift_declare_aligned_ptr(const struct part, parts, props.parts,
SWIFT_STRUCT_ALIGNMENT);
/* double conversion for parts */
for (size_t i = 0; i < N; i++)
props.convert_part_d(e, &parts[i], &temp_d[i * dim]);
} else if (props.convert_gpart_f != NULL) {
swift_declare_aligned_ptr(float, temp_f, temp, SWIFT_CACHE_ALIGNMENT);
swift_declare_aligned_ptr(const struct gpart, gparts, props.gparts,
SWIFT_STRUCT_ALIGNMENT);
/* float conversion for gparts */
for (size_t i = 0; i < N; i++)
props.convert_gpart_f(e, &gparts[i], &temp_f[i * dim]);
} else if (props.convert_gpart_d != NULL) {
swift_declare_aligned_ptr(double, temp_d, temp, SWIFT_CACHE_ALIGNMENT);
swift_declare_aligned_ptr(const struct gpart, gparts, props.gparts,
SWIFT_STRUCT_ALIGNMENT);
/* double conversion for gparts */
for (size_t i = 0; i < N; i++)
props.convert_gpart_d(e, &gparts[i], &temp_d[i * dim]);
} else {
error("Missing conversion function");
}
} }
/* Unit conversion if necessary */ /* Unit conversion if necessary */
...@@ -213,10 +250,10 @@ void writeArray(struct engine* e, hid_t grp, char* fileName, FILE* xmfFile, ...@@ -213,10 +250,10 @@ void writeArray(struct engine* e, hid_t grp, char* fileName, FILE* xmfFile,
/* message("Converting ! factor=%e", factor); */ /* message("Converting ! factor=%e", factor); */
if (io_is_double_precision(props.type)) { if (io_is_double_precision(props.type)) {
double* temp_d = temp; swift_declare_aligned_ptr(double, temp_d, temp, SWIFT_CACHE_ALIGNMENT);
for (size_t i = 0; i < num_elements; ++i) temp_d[i] *= factor; for (size_t i = 0; i < num_elements; ++i) temp_d[i] *= factor;
} else { } else {
float* temp_f = temp; swift_declare_aligned_ptr(float, temp_f, temp, SWIFT_CACHE_ALIGNMENT);
for (size_t i = 0; i < num_elements; ++i) temp_f[i] *= factor; for (size_t i = 0; i < num_elements; ++i) temp_f[i] *= factor;
} }
} }
......
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