revise the SZ package for the builtin integration with HDF5 filter

CMakeLists.txt

@@ -31,10 +31,29 @@ endif()
 #compile with C-99 and standard C++14
 set(CMAKE_C_STANDARD 99)
 set(CMAKE_CXX_STANDARD 14)
+set(CMAKE_CXX_STANDARD_REQUIRED ON)
 set(CMAKE_CXX_EXTENSIONS OFF)
 set(CMAKE_EXPORT_COMPILE_COMMANDS ON)
 set(CMAKE_RUNTIME_OUTPUT_DIRECTORY ${CMAKE_BINARY_DIR}/bin)
 
+#  Check for the existence of certain header files
+include (CheckIncludeFiles)
+include (CheckFunctionExists)
+CHECK_INCLUDE_FILES ("unistd.h"        HAVE_UNISTD_H)
+CHECK_INCLUDE_FILES ("sys/time.h"      HAVE_SYS_TIME_H)
+
+if (WINDOWS)
+  set (HAVE_GETTIMEOFDAY 1)
+endif ()
+
+if (MINGW OR NOT WINDOWS)
+  CHECK_FUNCTION_EXISTS (gettimeofday           HAVE_GETTIMEOFDAY)
+  CHECK_FUNCTION_EXISTS (clock_gettime          HAVE_CLOCK_GETTIME)
+endif ()
+
+# Generate the config.h file containing user settings needed by compilation
+configure_file (config.h.cmake ${CMAKE_BINARY_DIR}/config.h @ONLY)
+
 #generate tags for the project if tags exist
 option(BUILD_CTAGS "enable ctags generation target" OFF)
 if(BUILD_CTAGS)
@@ -51,34 +70,47 @@ endif()
 option(BUILD_SHARED_LIBS "build shared libraries over static libraries" ON)
 
 #find dependencies
+option(SZ_FIND_DEPS "find dependent libraries or build ext libraries" ON)
 include(GNUInstallDirs)
-find_package(PkgConfig)
-pkg_search_module(ZSTD  IMPORTED_TARGET libzstd)
-
-#by default pass no 3rd party exports
-set(thirdparty_export "")
-
-if(ZSTD_FOUND)
-  set(ZSTD_dep PkgConfig::ZSTD)
-else()
-  add_subdirectory(zstd)
-  set(ZSTD_dep zstd)
-  list(APPEND thirdparty_export "zstd")
-endif()
+if(SZ_FIND_DEPS)
+  find_package(PkgConfig)
+  pkg_search_module(ZSTD  IMPORTED_TARGET libzstd)
+
+  #by default pass no 3rd party exports
+  set(thirdparty_export "")
+
+  if(ZSTD_FOUND)
+    set(ZSTD_dep PkgConfig::ZSTD)
+  else()
+    add_subdirectory(zstd)
+    set(ZSTD_dep zstd)
+    list(APPEND thirdparty_export "zstd")
+  endif()
 
-find_package(ZLIB)
-if(ZLIB_FOUND)
-  set(ZLIB_dep ZLIB::ZLIB)
+  find_package(ZLIB)
+  if(ZLIB_FOUND)
+    set(ZLIB_dep ZLIB::ZLIB)
+  else()
+    add_subdirectory(zlib)
+    set(ZLIB_dep ZLIB)
+    list(APPEND thirdparty_export "ZLIB")
+  endif()
 else()
-  add_subdirectory(zlib)
-  set(ZLIB_dep ZLIB)
-  list(APPEND thirdparty_export "ZLIB")
+    add_subdirectory(zstd)
+    set(ZSTD_dep zstd)
+    list(APPEND thirdparty_export "zstd")
+    add_subdirectory(zlib)
+    set(ZLIB_dep ZLIB)
+    list(APPEND thirdparty_export "ZLIB")
 endif()
 
 find_package(OpenMP)
 
 add_subdirectory(sz)
-add_subdirectory(example)
+option(BUILD_SZ_EXAMPLES "build sz example" OFF)
+if(BUILD_SZ_EXAMPLES)
+  add_subdirectory(example)
+endif()
 
 option(BUILD_PYTHON_WRAPPER "build python wrapper" OFF)
 if(BUILD_PYTHON_WRAPPER)

example/sz.c

@@ -3,6 +3,7 @@
 #include <math.h>
 #include "sz.h"
 #include "rw.h"
+#include <sys/time.h>
 
 struct timeval startTime;
 struct timeval endTime;  /* Start and end times */

example/sz_gsl.c

@@ -4,6 +4,7 @@
 #include <gsl/gsl_wavelet.h>
 #include "sz.h"
 #include "rw.h"
+#include <sys/time.h>
 
 struct timeval startTime;
 struct timeval endTime;  /* Start and end times */

example/sz_openmp.c

@@ -4,6 +4,7 @@
 #include "sz.h"
 #include "rw.h"
 #include "sz_omp.h"
+#include <sys/time.h>
 
 struct timeval startTime;
 struct timeval endTime;  /* Start and end times */

example/sz_pastri.c

@@ -3,6 +3,7 @@
 #include <math.h>
 #include "sz.h"
 #include "rw.h"
+#include <sys/time.h>
 
 struct timeval startTime;
 struct timeval endTime;  /* Start and end times */

example/sz_randomaccess.c

@@ -3,6 +3,7 @@
 #include <math.h>
 #include "sz.h"
 #include "rw.h"
+#include <sys/time.h>
 
 struct timeval startTime;
 struct timeval endTime;  /* Start and end times */

example/testdouble_compress.c

@@ -7,7 +7,7 @@
  *      See COPYRIGHT in top-level directory.
  */
 
-
+#include <sys/time.h>
 #include <stdio.h>
 #include <stdlib.h>
 #include "sz.h"

example/testdouble_decompress.c

@@ -7,7 +7,7 @@
  *      See COPYRIGHT in top-level directory.
  */
 
-
+#include <sys/time.h>
 #include <stdio.h>
 #include <stdlib.h>
 #include <string.h>
@@ -104,7 +104,7 @@ int main(int argc, char * argv[])
 
 
     char oriFilePath[650];
-    strncpy(oriFilePath, zipFilePath, (unsigned)strlen(zipFilePath)-3);
+    strcpy(oriFilePath, zipFilePath);
     oriFilePath[strlen(zipFilePath)-3] = '\0';
     double *ori_data = readDoubleData(oriFilePath, &totalNbEle, &status);
     if(status!=SZ_SCES)

example/testfloat_compress.c

@@ -7,7 +7,7 @@
  *      See COPYRIGHT in top-level directory.
  */
 
-
+#include <sys/time.h>
 #include <stdio.h>
 #include <stdlib.h>
 #include "sz.h"

example/testfloat_decompress.c

@@ -7,7 +7,7 @@
  *      See COPYRIGHT in top-level directory.
  */
 
-
+#include <sys/time.h>
 #include <stdio.h>
 #include <stdlib.h>
 #include <string.h>
@@ -106,7 +106,7 @@ int main(int argc, char * argv[])
     //SZ_Finalize();
 
     char oriFilePath[640];
-    strncpy(oriFilePath, zipFilePath, (unsigned)strlen(zipFilePath)-3);
+    strcpy(oriFilePath, zipFilePath);
     oriFilePath[strlen(zipFilePath)-3] = '\0';
     float *ori_data = readFloatData(oriFilePath, &totalNbEle, &status);
     if(status!=SZ_SCES)

example/testint_compress.c

@@ -7,7 +7,7 @@
  *      See COPYRIGHT in top-level directory.
  */
 
-
+#include <sys/time.h>
 #include <stdio.h>
 #include <stdlib.h>
 #include <string.h>

example/testint_decompress.c

@@ -7,7 +7,7 @@
  *      See COPYRIGHT in top-level directory.
  */
 
-
+#include <sys/time.h>
 #include <stdio.h>
 #include <stdlib.h>
 #include <string.h>
@@ -274,7 +274,7 @@ void assessDeCompressionData(int dataType, char* zipFilePath, void* decompressed
 	size_t i, totalNbEle;
 	int status;
     char oriFilePath[640];
-    strncpy(oriFilePath, zipFilePath, (unsigned)strlen(zipFilePath)-3);
+    strcpy(oriFilePath, zipFilePath);
     oriFilePath[strlen(zipFilePath)-3] = '\0';
 	int64_t *data = (int64_t*)malloc(sizeof(int64_t)*nbEle);//decompressed data
 	int64_t *ori_data = (int64_t*)malloc(sizeof(int64_t)*nbEle); //original data

sz/CMakeLists.txt

@@ -1,4 +1,10 @@
-add_library (SZ
+if (BUILD_SHARED_LIBS)
+  set (BUILD_EXT_LIBS_TYPE "SHARED")
+else ()
+  set (BUILD_EXT_LIBS_TYPE "STATIC")
+endif ()
+
+add_library (SZ ${BUILD_EXT_LIBS_TYPE}
   src/ArithmeticCoding.c
   src/ByteToolkit.c
   src/CacheTable.c
@@ -60,10 +66,31 @@ add_library (SZ
 )
 
 target_include_directories(SZ 
+  PRIVATE 
+  ${CMAKE_BINARY_DIR}
   PUBLIC 
   $<BUILD_INTERFACE:${CMAKE_CURRENT_SOURCE_DIR}/include>
   $<INSTALL_INTERFACE:${CMAKE_INSTALL_INCLUDEDIR}/sz>
   )
+if (${BUILD_EXT_LIBS_TYPE} MATCHES "SHARED")
+  set (LIB_RELEASE_NAME "SZ")
+  set (LIB_DEBUG_NAME "SZ${CMAKE_DEBUG_POSTFIX}")
+else ()
+  if (WIN32 AND NOT MINGW)
+    set (LIB_RELEASE_NAME "libSZ")
+    set (LIB_DEBUG_NAME "libSZ${CMAKE_DEBUG_POSTFIX}")
+  else ()
+    set (LIB_RELEASE_NAME "SZ")
+    set (LIB_DEBUG_NAME "SZ${CMAKE_DEBUG_POSTFIX}")
+  endif ()
+endif ()
+set_target_properties (SZ PROPERTIES
+    OUTPUT_NAME                ${LIB_RELEASE_NAME}
+#    OUTPUT_NAME_DEBUG          ${LIB_DEBUG_NAME}
+    OUTPUT_NAME_RELEASE        ${LIB_RELEASE_NAME}
+    OUTPUT_NAME_MINSIZEREL     ${LIB_RELEASE_NAME}
+    OUTPUT_NAME_RELWITHDEBINFO ${LIB_RELEASE_NAME}
+  )
 
 target_link_libraries (SZ PUBLIC ${ZLIB_dep} ${ZSTD_dep} m)
 

sz/include/ByteToolkit.h

@@ -18,29 +18,29 @@ extern "C" {
 
 //ByteToolkit.c
 
-unsigned short bytesToUInt16_bigEndian(unsigned char* bytes);
-unsigned int bytesToUInt32_bigEndian(unsigned char* bytes);
-unsigned long bytesToUInt64_bigEndian(unsigned char* b);
+extern unsigned short bytesToUInt16_bigEndian(unsigned char* bytes);
+extern unsigned int bytesToUInt32_bigEndian(unsigned char* bytes);
+extern unsigned long bytesToUInt64_bigEndian(unsigned char* b);
 
-short bytesToInt16_bigEndian(unsigned char* bytes);
-int bytesToInt32_bigEndian(unsigned char* bytes);
-long bytesToInt64_bigEndian(unsigned char* b);
-int bytesToInt_bigEndian(unsigned char* bytes);
+extern short bytesToInt16_bigEndian(unsigned char* bytes);
+extern int bytesToInt32_bigEndian(unsigned char* bytes);
+extern long bytesToInt64_bigEndian(unsigned char* b);
+extern int bytesToInt_bigEndian(unsigned char* bytes);
 
-void intToBytes_bigEndian(unsigned char *b, unsigned int num);
+extern void intToBytes_bigEndian(unsigned char *b, unsigned int num);
 
-void int64ToBytes_bigEndian(unsigned char *b, uint64_t num);
-void int32ToBytes_bigEndian(unsigned char *b, uint32_t num);
-void int16ToBytes_bigEndian(unsigned char *b, uint16_t num);
+extern void int64ToBytes_bigEndian(unsigned char *b, uint64_t num);
+extern void int32ToBytes_bigEndian(unsigned char *b, uint32_t num);
+extern void int16ToBytes_bigEndian(unsigned char *b, uint16_t num);
 
-long bytesToLong_bigEndian(unsigned char* b);
-void longToBytes_bigEndian(unsigned char *b, unsigned long num);
+extern long bytesToLong_bigEndian(unsigned char* b);
+extern void longToBytes_bigEndian(unsigned char *b, unsigned long num);
 long doubleToOSEndianLong(double value);
 int floatToOSEndianInt(float value);
-short getExponent_float(float value);
-short getPrecisionReqLength_float(float precision);
-short getExponent_double(double value);
-short getPrecisionReqLength_double(double precision);
+extern short getExponent_float(float value);
+extern short getPrecisionReqLength_float(float precision);
+extern short getExponent_double(double value);
+extern short getPrecisionReqLength_double(double precision);
 unsigned char numberOfLeadingZeros_Int(int i);
 unsigned char numberOfLeadingZeros_Long(long i);
 unsigned char getLeadingNumbers_Int(int v1, int v2);
@@ -49,15 +49,15 @@ short bytesToShort(unsigned char* bytes);
 void shortToBytes(unsigned char* b, short value);
 int bytesToInt(unsigned char* bytes);
 long bytesToLong(unsigned char* bytes);
-float bytesToFloat(unsigned char* bytes);
-void floatToBytes(unsigned char *b, float num);
-double bytesToDouble(unsigned char* bytes);
-void doubleToBytes(unsigned char *b, double num);
+extern float bytesToFloat(unsigned char* bytes);
+extern void floatToBytes(unsigned char *b, float num);
+extern double bytesToDouble(unsigned char* bytes);
+extern void doubleToBytes(unsigned char *b, double num);
 int extractBytes(unsigned char* byteArray, size_t k, int validLength);
 int getMaskRightCode(int m);
-int getLeftMovingCode(int kMod8);
-int getRightMovingSteps(int kMod8, int resiBitLength);
-int getRightMovingCode(int kMod8, int resiBitLength);
+extern int getLeftMovingCode(int kMod8);
+extern int getRightMovingSteps(int kMod8, int resiBitLength);
+extern int getRightMovingCode(int kMod8, int resiBitLength);
 short* convertByteDataToShortArray(unsigned char* bytes, size_t byteLength);
 unsigned short* convertByteDataToUShortArray(unsigned char* bytes, size_t byteLength);
 
@@ -68,8 +68,8 @@ void convertUIntArrayToBytes(unsigned int* states, size_t stateLength, unsigned
 void convertLongArrayToBytes(int64_t* states, size_t stateLength, unsigned char* bytes);
 void convertULongArrayToBytes(uint64_t* states, size_t stateLength, unsigned char* bytes);
 
-size_t bytesToSize(unsigned char* bytes);
-void sizeToBytes(unsigned char* outBytes, size_t size);
+extern size_t bytesToSize(unsigned char* bytes);
+extern void sizeToBytes(unsigned char* outBytes, size_t size);
 
 void put_codes_to_output(unsigned int buf, int bitSize, unsigned char** p, int* lackBits, size_t *outSize);
 

sz/include/CompressElement.h

@@ -40,33 +40,33 @@ typedef struct LossyCompressionElement
 	unsigned char integerMidBytes[8];
 	int integerMidBytes_Length; //they are mid_bits actually
 	//char curBytes[8];
-	//int curBytes_Length; //4 for single_precision or 8 for double_precision	
+	//int curBytes_Length; //4 for single_precision or 8 for double_precision
 	int resMidBitsLength;
 	int residualMidBits;
 } LossyCompressionElement;
 
 char* decompressGroupIDArray(unsigned char* bytes, size_t dataLength);
 
-short computeGroupNum_float(float value);
-short computeGroupNum_double(double value);
+extern short computeGroupNum_float(float value);
+extern short computeGroupNum_double(double value);
 
-void listAdd_double(double last3CmprsData[3], double value);
-void listAdd_float(float last3CmprsData[3], float value);
-void listAdd_int(int64_t last3CmprsData[3], int64_t value);
+extern void listAdd_double(double last3CmprsData[3], double value);
+extern void listAdd_float(float last3CmprsData[3], float value);
+extern void listAdd_int(int64_t last3CmprsData[3], int64_t value);
 void listAdd_int32(int32_t last3CmprsData[3], int32_t value);
-void listAdd_float_group(float *groups, int *flags, char groupNum, float oriValue, float decValue, char* curGroupID);
-void listAdd_double_group(double *groups, int *flags, char groupNum, double oriValue, double decValue, char* curGroupID);
+extern void listAdd_float_group(float *groups, int *flags, char groupNum, float oriValue, float decValue, char* curGroupID);
+extern void listAdd_double_group(double *groups, int *flags, char groupNum, double oriValue, double decValue, char* curGroupID);
 
 int validPrediction_double(double minErr, double precision);
 int validPrediction_float(float minErr, float precision);
 double* generateGroupErrBounds(int errorBoundMode, double realPrecision, double pwrErrBound);
 int generateGroupMaxIntervalCount(double* groupErrBounds);
 
-void new_LossyCompressionElement(LossyCompressionElement *lce, int leadingNum, unsigned char* intMidBytes, 
+void new_LossyCompressionElement(LossyCompressionElement *lce, int leadingNum, unsigned char* intMidBytes,
 		int intMidBytes_Length, int resiMidBitsLength, int resiBits);
-void updateLossyCompElement_Double(unsigned char* curBytes, unsigned char* preBytes, 
+void updateLossyCompElement_Double(unsigned char* curBytes, unsigned char* preBytes,
 		int reqBytesLength, int resiBitsLength,  LossyCompressionElement *lce);
-void updateLossyCompElement_Float(unsigned char* curBytes, unsigned char* preBytes, 
+extern void updateLossyCompElement_Float(unsigned char* curBytes, unsigned char* preBytes,
 		int reqBytesLength, int resiBitsLength,  LossyCompressionElement *lce);
 
 #ifdef __cplusplus