rewriting for H5hut

tools/H5PartMerge/configure

@@ -605,9 +605,9 @@ ac_includes_default="\
 ac_subst_vars='am__EXEEXT_FALSE
 am__EXEEXT_TRUE
 LTLIBOBJS
+LIBOBJS
 AM_LDFLAGS
 AM_CPPFLAGS
-LIBOBJS
 CXXCPP
 EGREP
 GREP
@@ -1947,48 +1947,6 @@ $as_echo "$ac_res" >&6; }
   eval $as_lineno_stack; ${as_lineno_stack:+:} unset as_lineno
 
 } # ac_fn_cxx_check_type
-
-# ac_fn_cxx_try_run LINENO
-# ------------------------
-# Try to link conftest.$ac_ext, and return whether this succeeded. Assumes
-# that executables *can* be run.
-ac_fn_cxx_try_run ()
-{
-  as_lineno=${as_lineno-"$1"} as_lineno_stack=as_lineno_stack=$as_lineno_stack
-  if { { ac_try="$ac_link"
-case "(($ac_try" in
-  *\"* | *\`* | *\\*) ac_try_echo=\$ac_try;;
-  *) ac_try_echo=$ac_try;;
-esac
-eval ac_try_echo="\"\$as_me:${as_lineno-$LINENO}: $ac_try_echo\""
-$as_echo "$ac_try_echo"; } >&5
-  (eval "$ac_link") 2>&5
-  ac_status=$?
-  $as_echo "$as_me:${as_lineno-$LINENO}: \$? = $ac_status" >&5
-  test $ac_status = 0; } && { ac_try='./conftest$ac_exeext'
-  { { case "(($ac_try" in
-  *\"* | *\`* | *\\*) ac_try_echo=\$ac_try;;
-  *) ac_try_echo=$ac_try;;
-esac
-eval ac_try_echo="\"\$as_me:${as_lineno-$LINENO}: $ac_try_echo\""
-$as_echo "$ac_try_echo"; } >&5
-  (eval "$ac_try") 2>&5
-  ac_status=$?
-  $as_echo "$as_me:${as_lineno-$LINENO}: \$? = $ac_status" >&5
-  test $ac_status = 0; }; }; then :
-  ac_retval=0
-else
-  $as_echo "$as_me: program exited with status $ac_status" >&5
-       $as_echo "$as_me: failed program was:" >&5
-sed 's/^/| /' conftest.$ac_ext >&5
-
-       ac_retval=$ac_status
-fi
-  rm -rf conftest.dSYM conftest_ipa8_conftest.oo
-  eval $as_lineno_stack; ${as_lineno_stack:+:} unset as_lineno
-  as_fn_set_status $ac_retval
-
-} # ac_fn_cxx_try_run
 cat >config.log <<_ACEOF
 This file contains any messages produced by compilers while
 running configure, to aid debugging if configure makes a mistake.
@@ -4828,6 +4786,50 @@ else
 
 fi
 
+  { $as_echo "$as_me:${as_lineno-$LINENO}: checking for main in -lH5hutC" >&5
+$as_echo_n "checking for main in -lH5hutC... " >&6; }
+if ${ac_cv_lib_H5hutC_main+:} false; then :
+  $as_echo_n "(cached) " >&6
+else
+  ac_check_lib_save_LIBS=$LIBS
+LIBS="-lH5hutC  $LIBS"
+cat confdefs.h - <<_ACEOF >conftest.$ac_ext
+/* end confdefs.h.  */
+
+
+int
+main ()
+{
+return main ();
+  ;
+  return 0;
+}
+_ACEOF
+if ac_fn_c_try_link "$LINENO"; then :
+  ac_cv_lib_H5hutC_main=yes
+else
+  ac_cv_lib_H5hutC_main=no
+fi
+rm -f core conftest.err conftest.$ac_objext \
+    conftest$ac_exeext conftest.$ac_ext
+LIBS=$ac_check_lib_save_LIBS
+fi
+{ $as_echo "$as_me:${as_lineno-$LINENO}: result: $ac_cv_lib_H5hutC_main" >&5
+$as_echo "$ac_cv_lib_H5hutC_main" >&6; }
+if test "x$ac_cv_lib_H5hutC_main" = xyes; then :
+  cat >>confdefs.h <<_ACEOF
+#define HAVE_LIBH5HUTC 1
+_ACEOF
+
+  LIBS="-lH5hutC $LIBS"
+
+else
+  as_fn_error $? "H5hut library not found!" "$LINENO" 5
+
+fi
+
+
+
 ac_ext=c
 ac_cpp='$CPP $CPPFLAGS'
 ac_compile='$CC -c $CFLAGS $CPPFLAGS conftest.$ac_ext >&5'
@@ -5211,73 +5213,7 @@ fi
 
 
 # Checks for library functions.
-for ac_header in stdlib.h
-do :
-  ac_fn_cxx_check_header_mongrel "$LINENO" "stdlib.h" "ac_cv_header_stdlib_h" "$ac_includes_default"
-if test "x$ac_cv_header_stdlib_h" = xyes; then :
-  cat >>confdefs.h <<_ACEOF
-#define HAVE_STDLIB_H 1
-_ACEOF
-
-fi
-
-done
-
-{ $as_echo "$as_me:${as_lineno-$LINENO}: checking for GNU libc compatible malloc" >&5
-$as_echo_n "checking for GNU libc compatible malloc... " >&6; }
-if ${ac_cv_func_malloc_0_nonnull+:} false; then :
-  $as_echo_n "(cached) " >&6
-else
-  if test "$cross_compiling" = yes; then :
-  ac_cv_func_malloc_0_nonnull=no
-else
-  cat confdefs.h - <<_ACEOF >conftest.$ac_ext
-/* end confdefs.h.  */
-#if defined STDC_HEADERS || defined HAVE_STDLIB_H
-# include <stdlib.h>
-#else
-char *malloc ();
-#endif
-
-int
-main ()
-{
-return ! malloc (0);
-  ;
-  return 0;
-}
-_ACEOF
-if ac_fn_cxx_try_run "$LINENO"; then :
-  ac_cv_func_malloc_0_nonnull=yes
-else
-  ac_cv_func_malloc_0_nonnull=no
-fi
-rm -f core *.core core.conftest.* gmon.out bb.out conftest$ac_exeext \
-  conftest.$ac_objext conftest.beam conftest.$ac_ext
-fi
-
-fi
-{ $as_echo "$as_me:${as_lineno-$LINENO}: result: $ac_cv_func_malloc_0_nonnull" >&5
-$as_echo "$ac_cv_func_malloc_0_nonnull" >&6; }
-if test $ac_cv_func_malloc_0_nonnull = yes; then :
-
-$as_echo "#define HAVE_MALLOC 1" >>confdefs.h
-
-else
-  $as_echo "#define HAVE_MALLOC 0" >>confdefs.h
-
-   case " $LIBOBJS " in
-  *" malloc.$ac_objext "* ) ;;
-  *) LIBOBJS="$LIBOBJS malloc.$ac_objext"
- ;;
-esac
-
-
-$as_echo "#define malloc rpl_malloc" >>confdefs.h
-
-fi
-
-
+#AC_FUNC_MALLOC
 
 CPPFLAGS=$CPPFLAGS" -m64 -mtune=k8"
 LDFLAGS=$LDFLAGS" -lm"

tools/H5PartMerge/configure.ac

@@ -95,6 +95,14 @@ AC_LANG_PUSH(C)
     [],
     [AC_MSG_ERROR(H5hut library not found!)]
   )
+  AC_CHECK_LIB(
+    [H5hutC],
+    [main],
+    [],
+    [AC_MSG_ERROR(H5hut library not found!)]
+  )
+
+
 AC_LANG_POP
 AC_LANG(C++)
 
@@ -139,7 +147,7 @@ AC_C_CONST
 AC_TYPE_SIZE_T
 
 # Checks for library functions.
-AC_FUNC_MALLOC
+#AC_FUNC_MALLOC
 
 CPPFLAGS=$CPPFLAGS" -m64 -mtune=k8"
 LDFLAGS=$LDFLAGS" -lm"

tools/H5PartMerge/src/H5merge.cpp

@@ -20,6 +20,7 @@
  * 
  *  \todo H5hut port
  */
+
 #include <hdf5.h>
 #include "H5hut.h"
 
@@ -32,6 +33,8 @@
 
 #include "optparse.hh"
 
+#include <stdlib.h>
+
 #ifdef USE_BOOST
 #include <boost/any.hpp>
 #endif
@@ -61,17 +64,17 @@ typedef map<string, boost::any, StringCmp> StringAnyValueMap;
 typedef map<string, int, StringCmp> StringIntMap;
 typedef map<string, h5_int64_t, StringCmp> StringInt64Map;
 
-h5_int64_t copyFileAttribute(h5_file_t* In, h5_file_t* Out, string AttrName,  h5_int64_t Type, h5_int64_t Num);
-h5_int64_t copyFileToStepAttribute(h5_file_t* In, h5_file_t* Out, string AttrName,  h5_int64_t Type, h5_int64_t Num);
+h5_int64_t copyFileAttribute(h5_file_t* In, h5_file_t* Out, string AttrName,  h5_int64_t Type, h5_size_t Num);
+h5_int64_t copyFileToStepAttribute(h5_file_t* In, h5_file_t* Out, string AttrName,  h5_int64_t Type, h5_size_t Num);
 
 #ifdef USE_BOOST
 h5_int64_t copyFileAttribute(h5_file_t* In, h5_file_t* Out, StringAnyValueMap &FileAttributes, string AttrName,  
-			     h5_int64_t Type, h5_int64_t Num);
+			     h5_int64_t Type, h5_size_t Num);
 h5_int64_t copyFileToStepAttribute(h5_file_t* In, h5_file_t* Out, StringAnyValueMap &FileAttributes, string AttrName,  
-				   h5_int64_t Type, h5_int64_t Num);
+				   h5_int64_t Type, h5_size_t Num);
 #endif
 
-h5_int64_t copyStepAttribute(h5_file_t* In, h5_file_t* Out, string AttrName,  h5_int64_t Type, h5_int64_t Num);
+h5_int64_t copyStepAttribute(h5_file_t* In, h5_file_t* Out, string AttrName,  h5_int64_t Type, h5_size_t Num);
 h5_int64_t copyDataset(h5_file_t* In, h5_file_t* Out, string SetName, 
 		       h5_int64_t Type,  h5_float64_t* FloatArray, h5_int64_t* IntArray);
 
@@ -127,6 +130,7 @@ int main(int argc, char **argv){
   StringIntMap::iterator itName;
   StringInt64Map::iterator itType;
   StringInt64Map::iterator itNumType;
+
   
   h5_int64_t NumParticles = 0;
   h5_int64_t maxNumParticles = 0;
@@ -140,8 +144,9 @@ int main(int argc, char **argv){
 
   h5_int64_t Type;
   h5_int64_t SetType;
-  h5_int64_t NumType;
-  h5_int64_t SetNum;
+  h5_size_t NumType;
+  
+  h5_size_t SetNum;
 
   int verbosity = 0;
   h5_int64_t rc;
@@ -308,7 +313,7 @@ int main(int argc, char **argv){
 
   for (int i = 0; i < effNumInput; ++i)
     {
-      H5InFile = H5OpenFile(InputFilenames[i].c_str(), H5_O_RDONLY, NULL);
+      H5InFile = H5OpenFile(InputFilenames[i].c_str(), H5_O_RDONLY, 0);
 
       /**************************************************************\
        * fix range if values are negative
@@ -409,7 +414,7 @@ int main(int argc, char **argv){
             
           for (int k = from[i]; k <= to[i]; ++k)
             { 
-              H5PartSetStep(H5InFile,k);         
+              H5SetStep(H5InFile,k);         
          
               if (parser.get<bool>("intersect-datasets"))
                 {
@@ -647,7 +652,7 @@ int main(int argc, char **argv){
     }
    
     
-  H5OutFile = H5OpenFile(OutputFilename.c_str(), H5_O_WRONLY, NULL);
+  H5OutFile = H5OpenFile(OutputFilename.c_str(), H5_O_WRONLY, 0);
   if (H5OutFile == NULL)
     {
       cerr << "ABORT: could not open '" << OutputFilename << "' for writing!" << endl;
@@ -659,7 +664,7 @@ int main(int argc, char **argv){
 
   for (int i = 0; i < effNumInput; ++i)
     {
-      H5InFile = H5OpenFile(InputFilenames[i].c_str(), H5_O_RDONLY, NULL );
+      H5InFile = H5OpenFile(InputFilenames[i].c_str(), H5_O_RDONLY, 0);
 
       H5SetStep(H5InFile,from[i]);
       H5SetStep(H5OutFile,effStep);
@@ -695,7 +700,7 @@ int main(int argc, char **argv){
           h5_int64_t NumFileAttr = H5GetNumFileAttribs(H5InFile);
           for (h5_int64_t l = 0; l < NumFileAttr; ++l)
             {
-	      H5PartGetFileAttribInfo(H5InFile, l, AttrName, MAX_LEN, &Type, &NumType);
+	      H5GetFileAttribInfo(H5InFile, l, AttrName, MAX_LEN, &Type, &NumType);
               if (i == 0)
                 {
 #ifdef USE_BOOST
@@ -770,7 +775,7 @@ int main(int argc, char **argv){
               h5_int64_t NumStepAttr = H5GetNumStepAttribs(H5InFile);
               for (h5_int64_t m = 0; m < NumStepAttr; ++m)
                 {
-                  H5PartGetStepAttribInfo(H5InFile, m, StepAttrName, MAX_LEN, &Type, &NumType);
+                  H5GetStepAttribInfo(H5InFile, m, StepAttrName, MAX_LEN, &Type, &NumType);
                   rc = copyStepAttribute(H5InFile, H5OutFile, string(StepAttrName), Type, NumType);
                   if (rc != H5_SUCCESS)
                     cerr << "WARNING: could not write step attribute '" << StepAttrName << "'" << endl;
@@ -816,33 +821,33 @@ int main(int argc, char **argv){
   delete[] to;
 }
 
-h5_int64_t copyFileAttribute(h5_file_t* In, h5_file_t* Out, string AttrName,  h5_int64_t Type, h5_int64_t Num)
+h5_int64_t copyFileAttribute(h5_file_t* In, h5_file_t* Out, string AttrName,  h5_int64_t Type, h5_size_t Num)
 {
   h5_int64_t rc;
   if (Type == H5T_NATIVE_DOUBLE)
     {
       void *Attrib = (double*)malloc(sizeof(double)*Num);
-      rc = H5PartReadFileAttrib(In, AttrName.c_str(), (double*)Attrib);
+      rc = H5ReadFileAttribFloat64(In, AttrName.c_str(), (double*)Attrib);
       if (rc == H5_SUCCESS)
-        rc = H5PartWriteFileAttrib(Out, AttrName.c_str(), Type, (double*)Attrib, Num);
+        rc = H5WriteFileAttribFloat64(Out, AttrName.c_str(), (double*)Attrib, Num);
       free(Attrib);
       return rc;
     }
   else if (Type == H5T_NATIVE_CHAR)
     {
       void *Attrib = (char*)malloc(sizeof(char)*Num);
-      rc = H5ReadFileAttrib(In, AttrName.c_str(), (char*)Attrib);
+      rc = H5ReadFileAttribString(In, AttrName.c_str(), (char*)Attrib);
       if (rc == H5_SUCCESS)
-        rc = H5WriteFileAttrib(Out, AttrName.c_str(), Type, (char*)Attrib, Num);
+        rc = H5WriteFileAttribString(Out, AttrName.c_str(), (char*)Attrib);
       free(Attrib);
       return rc;
     }
   else if (Type == H5T_NATIVE_INT64)
     {
       void *Attrib = (h5_int64_t*)malloc(sizeof(h5_int64_t)*Num);
-      rc = H5PartReadFileAttrib(In, AttrName.c_str(), (h5_int64_t*)Attrib);
+      rc = H5ReadFileAttribInt64(In, AttrName.c_str(), (h5_int64_t*)Attrib);
       if (rc == H5_SUCCESS)
-        rc = H5PartWriteFileAttrib(Out, AttrName.c_str(), Type, (h5_int64_t*)Attrib, Num);
+        rc = H5WriteFileAttribInt64(Out, AttrName.c_str(), (h5_int64_t*)Attrib, Num);
       free(Attrib);
       return rc;
     }
@@ -854,33 +859,33 @@ h5_int64_t copyFileAttribute(h5_file_t* In, h5_file_t* Out, string AttrName,  h5
 }
 
 
-h5_int64_t copyFileToStepAttribute(h5_file_t* In, h5_file_t* Out, string AttrName,  h5_int64_t Type, h5_int64_t Num)
+h5_int64_t copyFileToStepAttribute(h5_file_t* In, h5_file_t* Out, string AttrName,  h5_int64_t Type, h5_size_t Num)
 {
   h5_int64_t rc;
   if (Type == H5T_NATIVE_DOUBLE)
     {
       void *Attrib = (double*)malloc(sizeof(double)*Num);
-      rc = H5PartReadFileAttrib(In, AttrName.c_str(), (double*)Attrib);
+      rc = H5ReadFileAttribFloat64(In, AttrName.c_str(), (double*)Attrib);
       if (rc == H5_SUCCESS)
-        rc = H5PartWriteStepAttrib(Out, AttrName.c_str(), Type, (double*)Attrib, Num);
+        rc = H5WriteStepAttribFloat64(Out, AttrName.c_str(), (double*)Attrib, Num);
       free(Attrib);
       return rc;
     }
   else if (Type == H5T_NATIVE_CHAR)
     {
       void *Attrib = (char*)malloc(sizeof(char)*Num);
-      rc = H5PartReadFileAttrib(In, AttrName.c_str(), (char*)Attrib);
+      rc = H5ReadFileAttribString(In, AttrName.c_str(), (char*)Attrib);
       if (rc == H5_SUCCESS)
-        rc = H5PartWriteStepAttrib(Out, AttrName.c_str(), Type, (char*)Attrib, Num);
+        rc = H5WriteStepAttribString(Out, AttrName.c_str(), (char*)Attrib);
       free(Attrib);
       return rc;
     }
   else if (Type == H5T_NATIVE_INT64)
     {
       void *Attrib = (h5_int64_t*)malloc(sizeof(h5_int64_t)*Num);
-      rc = H5PartReadFileAttrib(In, AttrName.c_str(), (h5_int64_t*)Attrib);
+      rc = H5ReadFileAttribInt64(In, AttrName.c_str(), (h5_int64_t*)Attrib);
       if (rc == H5_SUCCESS)
-        rc = H5PartWriteStepAttrib(Out, AttrName.c_str(), Type, (h5_int64_t*)Attrib, Num);
+        rc = H5WriteStepAttribInt64(Out, AttrName.c_str(), (h5_int64_t*)Attrib, Num);
       free(Attrib);
       return rc;
     }
@@ -891,33 +896,33 @@ h5_int64_t copyFileToStepAttribute(h5_file_t* In, h5_file_t* Out, string AttrNam
     }
 }
 
-h5_int64_t copyStepAttribute(h5_file_t* In, h5_file_t* Out, string AttrName,  h5_int64_t Type, h5_int64_t Num)
+h5_int64_t copyStepAttribute(h5_file_t* In, h5_file_t* Out, string AttrName,  h5_int64_t Type, h5_size_t Num)
 {
   h5_int64_t rc;
   if (Type == H5T_NATIVE_DOUBLE)
     {
       void* Attrib = (double*)malloc(sizeof(double)*Num);;
-      rc = H5PartReadStepAttrib(In, AttrName.c_str(), (double*)Attrib);
+      rc = H5ReadStepAttribFloat64(In, AttrName.c_str(), (double*)Attrib);
       if (rc == H5_SUCCESS)
-        rc = H5PartWriteStepAttrib(Out, AttrName.c_str(), Type, (double*)Attrib, Num);
+        rc = H5WriteStepAttribFloat64(Out, AttrName.c_str(), (double*)Attrib, Num);
       free(Attrib);
       return rc;
     }
   else if (Type == H5T_NATIVE_CHAR)
     {
       void* Attrib = (char*)malloc(sizeof(char)*Num);;
-      rc = H5PartReadStepAttrib(In, AttrName.c_str(), (char*)Attrib);
+      rc = H5ReadStepAttribString(In, AttrName.c_str(), (char*)Attrib);
       if (rc == H5_SUCCESS)
-        rc = H5PartWriteStepAttrib(Out, AttrName.c_str(), Type, (char*)Attrib, Num);
+        rc = H5WriteStepAttribString(Out, AttrName.c_str(), (char*)Attrib);
       free(Attrib);
       return rc;
     }
   else if (Type == H5T_NATIVE_INT64)
     {
       void* Attrib = (h5_int64_t*)malloc(sizeof(h5_int64_t)*Num);
-      rc = H5PartReadStepAttrib(In, AttrName.c_str(), (h5_int64_t*)Attrib);
+      rc = H5ReadStepAttribInt64(In, AttrName.c_str(), (h5_int64_t*)Attrib);
       if (rc == H5_SUCCESS)
-        rc = H5PartWriteStepAttrib(Out, AttrName.c_str(), Type, (h5_int64_t*)Attrib, Num);
+        rc = H5WriteStepAttribInt64(Out, AttrName.c_str(), (h5_int64_t*)Attrib, Num);
       free(Attrib);
       return rc;
     }