Get szip working under cmake

CMakeLists.txt

@@ -689,10 +689,11 @@ IF(USE_HDF5 OR ENABLE_NETCDF_4)
   CHECK_LIBRARY_EXISTS(${HDF5_C_LIBRARY_hdf5} H5Pset_deflate "" HAVE_H5PSET_DEFLATE)
 
   #Check to see if H5Z_SZIP exists in HDF5_Libraries. If so, we must use szip.
-  CHECK_LIBRARY_EXISTS(${HDF5_C_LIBRARY_hdf5} H5P_SZIP "" USE_SZIP)
+  CHECK_LIBRARY_EXISTS(${HDF5_C_LIBRARY_hdf5} H5Z_SZIP "" USE_SZIP)
   IF(USE_SZIP)
     FIND_LIBRARY(SZIP NAMES szip sz)
     IF(SZIP)
+      SET(HAVE_H5Z_SZIP 1)
       SET(SZIP_LIBRARY ${SZIP})
       SET(CMAKE_REQUIRED_LIBRARIES ${CMAKE_REQUIRED_LIBRARIES} ${SZIP})
     ELSE()

cf

@@ -6,6 +6,7 @@ FAST=1
 
 HDF5=1
 DAP=1
+SZIP=1
 #HDF4=1
 #PNETCDF=1
 #PAR4=1
@@ -69,6 +70,10 @@ if test "x$HDF4" = "x1" ; then
 LDFLAGS="$LDFLAGS -ljpeg"
 fi
 
+if test "x$SZIP" = "x1" ; then
+LDFLAGS="$LDFLAGS -lsz -laec"
+fi
+
 export PKG_CONFIG_PATH=/usr/lib/pkgconfig
 if test "x$DAP" = "x1" ; then
 if curl-config --version >/dev/null ; then

cf.cmake

@@ -1,5 +1,5 @@
 # Visual Studio
-VS=1
+#VS=1
 #VSSETUP=1
 
 #export NCPATHDEBUG=1
@@ -16,8 +16,10 @@ DAP=1
 
 if test "x$VS" != x ; then
 FLAGS="-DCMAKE_PREFIX_PATH=c:/tools/nccmake"
-fi
 FLAGS="$FLAGS -DCMAKE_INSTALL_PREFIX=d:/ignore"
+else
+FLAGS="$FLAGS -DCMAKE_INSTALL_PREFIX=/tmp/ignore"
+fi
 
 if test "x$DAP" = x ; then
 FLAGS="$FLAGS -DENABLE_DAP=false"

nc_test4/Make0

@@ -29,7 +29,14 @@ all:: cmp
 
 cmp::
 	export LD_LIBRARY_PATH=${LLP}; export CFLAGS; export LDFLAGS; \
-	${CC} -o t ${CFLAGS} ${T}.c ${SRC} ${LDFLAGS}; \
+	${CC} -o t ${CFLAGS} ${T}.c ${SRC} ${LDFLAGS}
 
 cpp::
 	${CC} -E ${CFLAGS} ${T}.c > ${T}.txt
+
+H5=H5szip_example
+EXT=testszip.nc
+hdf5::
+	export LD_LIBRARY_PATH=${LLP}; export CFLAGS; export LDFLAGS; \
+	${CC} -o h5 ${CFLAGS} ${H5}.c ${SRC} ${LDFLAGS}; \
+	${CMD} ./h5 ${EXT}

nc_test4/Makefile.am

@@ -106,6 +106,13 @@ endif # USE_HDF4_FILE_TESTS
 #-lhdf5 -lz
 endif # USE_HDF4
 
+# Szip Tests
+if USE_SZIP
+check_PROGRAMS += tst_szip
+TESTS += tst_szip
+endif
+
+
 # This will run a bunch of the test programs with valgrind, the memory
 # checking tool. (Valgrind must be present for this to work.)
 if USE_VALGRIND_TESTS

nc_test4/h5testszip.c

@@ -0,0 +1,135 @@
+/*
+ * Example illustrates the use of SZIP compression in HDF5
+ */
+
+#include <stdio.h>
+#include "hdf5.h"
+#define NX 500
+#define NY 600
+#define CH_NX 100
+#define CH_NY 25
+
+static void initialize();
+
+static float buf[NX][NY];
+static float buf_r[NX][NY];
+
+int main(int argc, char** argv)
+{
+   hid_t file, data_space, dataset32;
+   hid_t properties, lcpl_id, dapl_id;
+   hsize_t dims[2], chunk_size[2];
+   int i, j;
+   unsigned szip_options_mask;
+   unsigned szip_pixels_per_block;
+   const char* existingfile = NULL;
+
+   if(argc > 1)
+	existingfile = argv[1];
+
+   initialize();
+
+   if(!existingfile) {
+
+   /* Describe the size of the array. */
+   dims[0] = NX;
+   dims[1] = NY;
+   data_space = H5Screate_simple (2, dims, NULL);
+
+  /*
+   * Create a new file using read/write access, default file 
+   * creation properties, and default file access properties.
+   */
+   file = H5Fcreate ("test.h5", H5F_ACC_TRUNC, H5P_DEFAULT, H5P_DEFAULT);
+
+  /*
+   * Set the dataset creation property list to specify that
+   * the raw data is to be partitioned into 100x100 element
+   * chunks and that each chunk is to be compressed.
+   */
+   chunk_size[0] = CH_NX;
+   chunk_size[1] = CH_NY;
+   properties = H5Pcreate (H5P_DATASET_CREATE);
+   H5Pset_chunk (properties, 2, chunk_size);
+
+  /* 
+   * Set parameters for SZIP compression; check the description of
+   * the H5Pset_szip function in the HDF5 Reference Manual for more 
+   * information.
+   */
+   szip_options_mask=H5_SZIP_NN_OPTION_MASK;
+   szip_pixels_per_block=32;
+
+   H5Pset_szip (properties, szip_options_mask, szip_pixels_per_block);
+
+  /*
+   * Create a new dataset within the file.  The datatype
+   * and data space describe the data on disk, which may
+   * be different from the format used in the application's
+   * memory.
+   */
+
+   lcpl_id = H5Pcreate (H5P_LINK_CREATE);
+   dapl_id = H5Pcreate (H5P_DATASET_ACCESS);
+
+   dataset32 = H5Dcreate (file, "datasetF32", H5T_NATIVE_FLOAT, data_space, lcpl_id, properties, dapl_id);
+
+  /*
+   * Write the array to the file.  The datatype and dataspace
+   * describe the format of the data in the `buf' buffer.
+   * The raw data is translated to the format required on disk, 
+   * as defined above.  We use default raw data transfer properties.
+   */
+
+   H5Dwrite (dataset32, H5T_NATIVE_FLOAT, H5S_ALL, H5S_ALL,
+            H5P_DEFAULT, buf);
+
+   } /*!existingfile */
+
+
+   if(existingfile) {
+     file = H5Fopen (existingfile, H5F_ACC_RDONLY, H5P_DEFAULT);
+     properties = H5Pcreate(H5P_DATASET_ACCESS);
+     dataset32 = H5Dopen(file, "datasetF32", properties);
+   } /*!existingfile */
+
+  /*
+   * Read the array.  This is similar to writing data,
+   * except the data flows in the opposite direction.
+   * Note: Decompression is automatic.
+   */
+
+   H5Dread (dataset32, H5T_NATIVE_FLOAT, H5S_ALL, H5S_ALL,
+           H5P_DEFAULT, buf_r);
+
+   /* Do comparison */
+   for (i=0; i < NX; i++) {
+      for (j=0; j < NY; j++) {
+        if(buf[i][j] != buf_r[i][j]) {
+	  printf("mismatch: [%d][%d]: write = %f read=%f\n",
+		 i,j,buf[i][j],buf_r[i][j]);
+	}
+     }
+   }
+
+
+   if(!existingfile) {
+     H5Sclose (data_space);
+     H5Pclose (properties);
+   }
+   H5Dclose (dataset32);
+   H5Fclose (file);
+   return 0;
+}
+
+static void
+initialize(void)
+{
+   int i, j;
+   /* Initialize data buffer with some bogus data. */
+   for(i=0; i < NX; i++) {
+     for(j=0; j < NY; j++) {
+       buf[i][j] = (float)(i + j);
+     }
+   }
+}

nc_test4/tst_szip.c

@@ -16,15 +16,19 @@
 #include "netcdf.h"
 #include "netcdf_filter.h"
 
-#define PLAIN
-#undef USECLOSE
+#undef PLAIN
+#define USECLOSE
 
 /* Szip Constants. */
 #define HDF5_FILTER_SZIP 4
-#define H5_SZIP_EC_OPTION_MASK 4
-#define H5_SZIP_NN_OPTION_MASK 32
 #define H5_SZIP_MAX_PIXELS_PER_BLOCK 32
 
+/* Option Mask Flags (Refere to HDF5 szip documentation)  */
+#define H5_SZIP_ALLOW_K13_OPTION_MASK 1 /*Allows k split = 13 compression mode. (Default)*/
+#define H5_SZIP_CHIP_OPTION_MASK      2 /*Compresses exactly as in hardware*/
+#define H5_SZIP_EC_OPTION_MASK        4 /*Selects entropy coding method. (Default)*/
+#define H5_SZIP_NN_OPTION_MASK       32 /*Selects nearest neighbor coding method*/
+
 #define NX 500
 #define NY 600
 #define CH_NX 100
@@ -50,7 +54,10 @@ main(void)
     if(nc_def_dim(ncid, "y", dims[1], &dimids[1])) ERR;
 
     /* Create a dimensioned variable */
-    if(nc_def_var(ncid, "var", NC_FLOAT, 2, dimids, &varid)) ERR;
+    if(nc_def_var(ncid, "datasetF32", NC_FLOAT, 2, dimids, &varid)) ERR;
+
+    /* no fill */
+    if(nc_def_var_fill(ncid, varid, 1, NULL)) ERR;
 
     /* Define chunking for the variable:
     * the raw data is to be partitioned into 100x100 element chunks.
@@ -67,7 +74,12 @@ main(void)
      */
     szip_params[0] = H5_SZIP_NN_OPTION_MASK;
     szip_params[1] = H5_SZIP_MAX_PIXELS_PER_BLOCK;
-    if(nc_def_var_filter(ncid, varid, HDF5_FILTER_SZIP, 2, szip_params)) ERR;
+    { int stat = nc_def_var_filter(ncid, varid, HDF5_FILTER_SZIP, 2, szip_params);
+       if(stat) {
+         fprintf(stderr,"XXX: %d %s\b",stat,nc_strerror(stat));
+         ERR;
+       }
+    }
 #endif
 
     if(nc_enddef(ncid)) ERR;
@@ -82,11 +94,11 @@ main(void)
     /* Write the array to the file */
     if(nc_put_var_float(ncid, varid, &buf[0][0])) ERR;
 
-#if USECLOSE
+#ifdef USECLOSE
     /* Close and re-open the file */
     if(nc_close(ncid)) ERR;
-    if(nc_open("testszip.nc", NC_NETCDF4. &ncid)) ERR;
-    if(nc_inq_varid(ncid, "var", &varid)) ERR;
+    if(nc_open("testszip.nc", NC_NETCDF4, &ncid)) ERR;
+    if(nc_inq_varid(ncid, "datasetF32", &varid)) ERR;
 #endif
 
     /*