HDF5 performance

c.mk

#
# c.mk - Generic Makefile for Linux toy applications
#
# Required variables:
#
#   - $(SRC): C source files
#   - $(BIN): filename of linked binary
#
# Optional variables:
#
# 	- $(PKG_DEPS): List of pkg-config compatible packages
# 	- $(CFLAGS), $(LDFLAGS), GNU compliant directories
#
# Example Makefile:
#
#   PKG_DEPS = glib-2.0
#   SRC = foo.c
#   BIN = bar
#
#   include c.mk
#

OBJS = $(patsubst %.c,%.o,$(SRC))

#  Determine C flags and ld flags
ifdef PKG_DEPS
	PKG_CFLAGS = $(shell pkg-config --cflags $(PKG_DEPS))
	PKG_LDFLAGS = $(shell pkg-config --libs $(PKG_DEPS))
else
	PKG_CFLAGS =
	PKG_LDFLAGS =
endif

CFLAGS ?= -Wall -Werror -std=c99 -O2
CFLAGS += $(PKG_CFLAGS)
LDFLAGS += $(PKG_LDFLAGS)

# GNU-compliant install directories
prefix ?= /usr/local
exec_prefix ?= $(prefix)
bindir ?= $(exec_prefix)/bin

# Targets
.PHONY: clean

all: $(BIN)

%.o: %.c
	@echo " CC $@"
	@$(CC) -c $(CFLAGS) -o $@ $<

$(BIN): $(OBJS)
	@echo " LD $@"
	@$(CC) $(OBJS) -o $@ $(LDFLAGS)

clean:
	rm -f $(BIN) $(OBJS)

install: $(BIN)
	install -D -m 755 $(BIN) $(DESTDIR)$(bindir)/$(BIN)

Makefile

SRC = perf.c
BIN = perf
PKG_DEPS = glib-2.0
LDFLAGS = -lhdf5

include c.mk

perf.c

#include <glib.h>
#include <hdf5.h>


static const int WIDTH = 2048;
static const int HEIGHT = 1024;
static const int N_DARKS = 10;
static const int N_FLATS = 10;
static const int N_PROJS = 100;


static void
write_dataset (hid_t file, const char *name, const float *data, int n_items)
{
    GTimer *timer;
    hid_t datatype;
    hid_t dataspace;
    hid_t dataset;
    hsize_t dims[3];

    timer = g_timer_new ();

    dims[0] = WIDTH;
    dims[1] = HEIGHT;
    dims[2] = n_items;

    datatype = H5Tcopy (H5T_NATIVE_FLOAT);

    g_timer_start (timer);
    dataspace = H5Screate_simple (3, dims, NULL);
    g_timer_stop (timer);
    g_print (" H5Screate_simple: %3.5fs\n", g_timer_elapsed(timer, NULL));

    g_timer_start (timer);
    dataset = H5Dcreate (file, name, datatype, dataspace, H5P_DEFAULT);
    g_timer_stop (timer);
    g_print (" H5Dcreate: %3.5fs\n", g_timer_elapsed(timer, NULL));

    g_timer_start (timer);
    H5Dwrite (dataset, H5T_NATIVE_FLOAT, H5S_ALL, H5S_ALL, H5P_DEFAULT, data);
    g_timer_stop (timer);
    g_print (" H5Dwrite: %3.5fs\n", g_timer_elapsed(timer, NULL));
    
    H5Sclose (dataspace);
    H5Dclose (dataset);
    H5Tclose (datatype);
    g_timer_destroy (timer);
}

static void
create_individual_data_sets (hid_t file, const float *data)
{
    write_dataset (file, "projs", data, N_PROJS);
    write_dataset (file, "darks", data, N_DARKS);
    write_dataset (file, "flats", data, N_FLATS);
}

static void
create_single_dataset (hid_t file, const float *data)
{
    write_dataset (file, "all", data, N_DARKS + N_FLATS + N_PROJS);
}

static void
run (void (*func)(hid_t, const float *), const char *fname, const float *data)
{
    hid_t file;
    GTimer *timer;

    timer = g_timer_new ();

    g_timer_start (timer);
    file = H5Fcreate (fname, H5F_ACC_TRUNC, H5P_DEFAULT, H5P_DEFAULT);

    func (file, data);

    H5Fflush (file, H5F_SCOPE_GLOBAL);
    H5Fclose (file);

    g_timer_stop (timer);
    g_print (" Total: %3.5fs\n", g_timer_elapsed (timer, NULL));
    g_timer_destroy (timer);
}

int
main (int argc, char const* argv[])
{
    float *data;

    data = g_malloc (sizeof(float) * WIDTH * HEIGHT * (N_DARKS + N_FLATS + N_PROJS));

    g_print ("Single data set\n");
    run (create_single_dataset, "bar.h5", data);

    g_print ("\nIndividual data sets\n");
    run (create_individual_data_sets, "foo.h5", data);

    g_free (data);
    return 0;
}