split out netcdf read&write functions

Parallel_Algorithm/OpenMP/Kmean_omp.c

@@ -1,5 +1,6 @@
 #include "../shared/timing.h" //for timer seconds()
 #include "../shared/make_2D_array.h"
+#include "../shared/ncdf_util.h"
 #include <stdio.h>
 #include <stdlib.h>
 #include <float.h> //for FLT_MAX
@@ -10,97 +11,6 @@
 #define TOL 0.0001 
 #define MAX_ITER 100 
 
-/* Handle errors by printing an error message and exiting with a
- * non-zero status. */
-#define ERRCODE 2
-#define ERR(e) {printf("Error: %s\n", nc_strerror(e)); exit(ERRCODE);}
-
-/* Read the input data from NetCDF file. 
- * Dynamically allocate the array based on the data size.
- * 
- * Why need 3-levels of pointers:
- * The first two levels are for 2D dynamic array, 
- * the last level is for modifying function arguments in place.
- * (need to pass the address)
- */
-int readX(float*** p_X,int*** p_GUESS,
- size_t* p_N_samples,size_t* p_N_features, 
- size_t* p_N_clusters,size_t* p_N_repeat ) {
- int ncid, varid,dimid;
- int retval;
-
- /* Open the file. NC_NOWRITE tells netCDF we want read-only access
- * to the file.*/
- if ((retval = nc_open(FILE_NAME, NC_NOWRITE, &ncid)))
- ERR(retval);
-
- /* Get the size of the data for dynamical allocation*/
- nc_inq_dimid(ncid,"N_samples",&dimid);
- nc_inq_dimlen(ncid,dimid,p_N_samples);
- printf("Number of samples: %d \n",*p_N_samples);
-
- nc_inq_dimid(ncid,"N_features",&dimid);
- nc_inq_dimlen(ncid,dimid,p_N_features);
- printf("Number of features: %d \n",*p_N_features);
-
- nc_inq_dimid(ncid,"N_clusters",&dimid);
- nc_inq_dimlen(ncid,dimid,p_N_clusters);
- printf("Number of clusters: %d \n",*p_N_clusters);
-
- nc_inq_dimid(ncid,"N_repeat",&dimid);
- nc_inq_dimlen(ncid,dimid,p_N_repeat);
- printf("Number of repeated runs: %d \n",*p_N_repeat);
-
- /* Get the varid of the data variable, based on its name. */
- if ((retval = nc_inq_varid(ncid, "X", &varid)))
- ERR(retval);
- /* Read the data. */
- *p_X = Make2DFloatArray(*p_N_samples,*p_N_features);
- if ((retval = nc_get_var_float(ncid, varid, (*p_X)[0])))
- ERR(retval);
-
- /* Initial Guess*/ 
- if ((retval = nc_inq_varid(ncid, "GUESS", &varid)))
- ERR(retval);
- *p_GUESS = Make2DIntArray(*p_N_repeat,*p_N_clusters);
- if ((retval = nc_get_var_int(ncid, varid, (*p_GUESS)[0])))
- ERR(retval);
-
- /*close the netcdf file*/
- if ((retval = nc_close(ncid) ))
- ERR(retval);
-
- printf("=====reading data finished======\n");
-
- return 0;
-}
-
-int writeY(int* labels, float inert) { 
- int ncid, varid;
- int retval;
-
- if ((retval = nc_open(FILE_NAME, NC_WRITE, &ncid)))
- ERR(retval);
-
- if ((retval = nc_inq_varid(ncid, "INERT_C", &varid)))
- ERR(retval)
- if ((retval = nc_put_var_float(ncid, varid, &inert )))
- ERR(retval);
-
- if ((retval = nc_inq_varid(ncid, "Y_C", &varid)))
- ERR(retval)
- if ((retval = nc_put_var_int(ncid, varid, labels )))
- ERR(retval);
-
- /*close the netcdf file*/
- if ((retval = nc_close(ncid) ))
- ERR(retval);
-
- printf("=====writting data finished======\n");
-
- return 0;
-}
-
 // square of the distance between x1[N_features] and x2[N_features]
 float distance(int N_features,float *x1,float *x2){
  float dist=0.0;
@@ -109,7 +19,6 @@ float distance(int N_features,float *x1,float *x2){
  return(dist);
 }
 
-
 int main() {
 
  size_t N_samples,N_features,N_clusters,N_repeat;
@@ -122,7 +31,7 @@ int main() {
 
  // get input data and its size
  double iStart1 = seconds();
- readX(&X,&GUESS,&N_samples,&N_features,&N_clusters,&N_repeat);
+ readX(FILE_NAME,&X,&GUESS,&N_samples,&N_features,&N_clusters,&N_repeat);
  double iElaps1 = seconds() - iStart1;
 
  // each data point belongs to which cluster
@@ -234,7 +143,7 @@ int main() {
 
 
  // write data back to NetCDF file
- writeY(labels_best, inert_best);
+ writeY(FILE_NAME,labels_best, inert_best);
 
  // print summary
  printf("Best inertia: %f \n",inert_best);

Parallel_Algorithm/OpenMP/compile.sh

@@ -1,4 +1,4 @@
-gcc -O2 -std=c99 -lnetcdf -fopenmp -lpthread ../shared/make_2D_array.c Kmean_omp.c -o Kmean_omp.out
+gcc -O2 -std=c99 -lnetcdf -fopenmp -lpthread ../shared/make_2D_array.c ../shared/ncdf_util.c Kmean_omp.c -o Kmean_omp.out
 
 #For debugging with gdb
 #gcc -g -O0 -std=c99 -lnetcdf Kmean_seq.c -o Kmean_seq.out

Parallel_Algorithm/shared/make_2D_array.c

@@ -1,5 +1,5 @@
-#include "./make_2D_array.h"
 #include <stdlib.h> //for malloc
+#include "make_2D_array.h"
 
 /* For dynamically allocating 2D array in pure-C environment.
 Unlke in HW2, the array here is contagious!

Parallel_Algorithm/shared/make_2D_array.h

@@ -1,2 +1,7 @@
+#ifndef MAKE_2D_ARRAY_H 
+#define MAKE_2D_ARRAY_H
+
 float** Make2DFloatArray(int rows, int cols);
 int** Make2DIntArray(int rows, int cols);
+
+#endif // MAKE_2D_ARRAY_H 

Parallel_Algorithm/shared/ncdf_util.c

@@ -0,0 +1,98 @@
+#include <stdio.h>
+#include <stdlib.h>
+#include <netcdf.h>
+#include "make_2D_array.h"
+#include "ncdf_util.h"
+// including <stdlib.h> at last leads to "error: unknown type name ‘size_t’"
+// no idea why?
+
+/* Handle errors by printing an error message and exiting with a
+ * non-zero status. */
+#define ERRCODE 2
+#define ERR(e) {printf("Error: %s\n", nc_strerror(e)); exit(ERRCODE);}
+
+/* Read the input data from NetCDF file. 
+ * Dynamically allocate the array based on the data size.
+ * 
+ * Why need 3-levels of pointers:
+ * The first two levels are for 2D dynamic array, 
+ * the last level is for modifying function arguments in place.
+ * (need to pass the address)
+ */
+int readX(char* FILE_NAME, float*** p_X,int*** p_GUESS,
+ size_t* p_N_samples,size_t* p_N_features,
+ size_t* p_N_clusters,size_t* p_N_repeat ) {
+ int ncid, varid,dimid;
+ int retval;
+
+ /* Open the file. NC_NOWRITE tells netCDF we want read-only access
+ * to the file.*/
+ if ((retval = nc_open(FILE_NAME, NC_NOWRITE, &ncid)))
+ ERR(retval);
+
+ /* Get the size of the data for dynamical allocation*/
+ nc_inq_dimid(ncid,"N_samples",&dimid);
+ nc_inq_dimlen(ncid,dimid,p_N_samples);
+ printf("Number of samples: %d \n",*p_N_samples);
+
+ nc_inq_dimid(ncid,"N_features",&dimid);
+ nc_inq_dimlen(ncid,dimid,p_N_features);
+ printf("Number of features: %d \n",*p_N_features);
+
+ nc_inq_dimid(ncid,"N_clusters",&dimid);
+ nc_inq_dimlen(ncid,dimid,p_N_clusters);
+ printf("Number of clusters: %d \n",*p_N_clusters);
+
+ nc_inq_dimid(ncid,"N_repeat",&dimid);
+ nc_inq_dimlen(ncid,dimid,p_N_repeat);
+ printf("Number of repeated runs: %d \n",*p_N_repeat);
+
+ /* Get the varid of the data variable, based on its name. */
+ if ((retval = nc_inq_varid(ncid, "X", &varid)))
+ ERR(retval);
+ /* Read the data. */
+ *p_X = Make2DFloatArray(*p_N_samples,*p_N_features);
+ if ((retval = nc_get_var_float(ncid, varid, (*p_X)[0])))
+ ERR(retval);
+
+ /* Initial Guess*/
+ if ((retval = nc_inq_varid(ncid, "GUESS", &varid)))
+ ERR(retval);
+ *p_GUESS = Make2DIntArray(*p_N_repeat,*p_N_clusters);
+ if ((retval = nc_get_var_int(ncid, varid, (*p_GUESS)[0])))
+ ERR(retval);
+
+ /*close the netcdf file*/
+ if ((retval = nc_close(ncid) ))
+ ERR(retval);
+
+ printf("=====reading data finished======\n");
+
+ return 0;
+}
+
+int writeY(char* FILE_NAME, int* labels, float inert) {
+ int ncid, varid;
+ int retval;
+
+ if ((retval = nc_open(FILE_NAME, NC_WRITE, &ncid)))
+ ERR(retval);
+
+ if ((retval = nc_inq_varid(ncid, "INERT_C", &varid)))
+ ERR(retval)
+ if ((retval = nc_put_var_float(ncid, varid, &inert )))
+ ERR(retval);
+
+ if ((retval = nc_inq_varid(ncid, "Y_C", &varid)))
+ ERR(retval)
+ if ((retval = nc_put_var_int(ncid, varid, labels )))
+ ERR(retval);
+
+ /*close the netcdf file*/
+ if ((retval = nc_close(ncid) ))
+ ERR(retval);
+
+ printf("=====writting data finished======\n");
+
+ return 0;
+}

Parallel_Algorithm/shared/ncdf_util.h

@@ -0,0 +1,10 @@
+#ifndef NCDF_UTIL_H 
+#define NCDF_UTIL_H
+
+int readX(char* FILE_NAME, float*** p_X,int*** p_GUESS,
+ size_t* p_N_samples,size_t* p_N_features,
+ size_t* p_N_clusters,size_t* p_N_repeat );
+
+int writeY(char* FILE_NAME, int* labels, float inert);
+
+#endif // NCDF_UTIL_H