[svn-r20146] Description:

	Bring r19714:20145 from trunk to revise_chunks branch.

Tested on:
        FreeBSD/32 6.3 (duty) in debug mode
        FreeBSD/64 6.3 (liberty) w/C++ & FORTRAN, in debug mode
        Linux/32 2.6 (jam) w/PGI compilers, w/default API=1.8.x,
                w/C++ & FORTRAN, w/threadsafe, in debug mode
        Linux/64-amd64 2.6 (amani) w/Intel compilers, w/default API=1.6.x,
                w/C++ & FORTRAN, in production mode
        Solaris/32 2.10 (linew) w/deprecated symbols disabled, w/C++ & FORTRAN,
                w/szip filter, w/threadsafe, in production mode
        Linux/PPC 2.6 (heiwa) w/C++ & FORTRAN, w/threadsafe, in debug mode
        Linux/64-amd64 2.6 (abe) w/parallel, w/FORTRAN, in debug mode
        Mac OS X/32 10.6.6 (amazon) in debug mode
        Mac OS X/32 10.6.6 (amazon) w/C++ & FORTRAN, w/threadsafe,
                in production mode

11 files changed, 174 insertions, 167 deletions

diff --git a/tools/h5repack/CMakeLists.txt b/tools/h5repack/CMakeLists.txt
index 56029fd..92933d4 100644
--- a/tools/h5repack/CMakeLists.txt
+++ b/tools/h5repack/CMakeLists.txt
@@ -21,8 +21,7 @@ SET (REPACK_COMMON_SRCS
 )
 
 ADD_EXECUTABLE (h5repack ${REPACK_COMMON_SRCS} ${HDF5_TOOLS_H5REPACK_SOURCE_DIR}/h5repack_main.c)
-H5_NAMING (h5repack)
-TARGET_WIN_PROPERTIES (h5repack)
+H5_NAMING (h5repack ${LIB_TYPE})
 TARGET_LINK_LIBRARIES (h5repack  ${HDF5_TOOLS_LIB_TARGET} ${HDF5_LIB_TARGET})
 
 SET (H5_DEP_EXECUTABLES h5repack)
@@ -38,8 +37,7 @@ IF (BUILD_TESTING)
   # Add h5Repack test executables
   # --------------------------------------------------------------------
   ADD_EXECUTABLE (testh5repack_detect_szip ${HDF5_TOOLS_H5REPACK_SOURCE_DIR}/testh5repack_detect_szip.c)
-  H5_NAMING (testh5repack_detect_szip)
-  TARGET_WIN_PROPERTIES (testh5repack_detect_szip)
+  H5_NAMING (testh5repack_detect_szip ${LIB_TYPE})
   TARGET_LINK_LIBRARIES (testh5repack_detect_szip ${HDF5_LIB_TARGET} ${HDF5_TOOLS_LIB_TARGET} ${HDF5_TEST_LIB_TARGET})
 
   ADD_TEST (NAME testh5repack_detect_szip COMMAND $<TARGET_FILE:testh5repack_detect_szip>)
@@ -57,11 +55,11 @@ IF (BUILD_TESTING)
   ENDIF (HDF5_ENABLE_SZIP_SUPPORT)
 
   ADD_EXECUTABLE (h5repacktest ${REPACK_COMMON_SRCS} ${HDF5_TOOLS_H5REPACK_SOURCE_DIR}/h5repacktst.c)
-  H5_NAMING (h5repacktest)
-  TARGET_WIN_PROPERTIES (h5repacktest)
+  H5_NAMING (h5repacktest ${LIB_TYPE})
   TARGET_LINK_LIBRARIES (h5repacktest  ${HDF5_TOOLS_LIB_TARGET} ${HDF5_TEST_LIB_TARGET})
 
   ADD_TEST (NAME h5repacktest COMMAND $<TARGET_FILE:h5repacktest>)
+  SET_TESTS_PROPERTIES (h5repacktest PROPERTIES DEPENDS testh5repack_detect_szip)
 
   IF (HDF5_TEST_VFD)
 
@@ -180,10 +178,15 @@ IF (BUILD_TESTING)
           NAME H5REPACK-${testname}
           COMMAND $<TARGET_FILE:h5repack> ${ARGN} ${PROJECT_BINARY_DIR}/testfiles/${testfile} ${PROJECT_BINARY_DIR}/testfiles/out.${testfile}
       )
+      IF (NOT "${last_test}" STREQUAL "")
+        SET_TESTS_PROPERTIES (H5REPACK-${testname} PROPERTIES DEPENDS ${last_test})
+      ENDIF (NOT "${last_test}" STREQUAL "")
       ADD_TEST (
           NAME H5REPACK-DIFF_${testname}
           COMMAND $<TARGET_FILE:h5diff> ${PROJECT_BINARY_DIR}/testfiles/${testfile} ${PROJECT_BINARY_DIR}/testfiles/out.${testfile}
       )
+      SET_TESTS_PROPERTIES (H5REPACK-DIFF_${testname} PROPERTIES DEPENDS H5REPACK-${testname})
+      SET (last_test "H5REPACK-DIFF_${testname}")
     ENDIF (${testtype} STREQUAL "SKIP")
   ENDMACRO (ADD_H5_TEST)
 
@@ -206,6 +209,10 @@ IF (BUILD_TESTING)
               -D "TEST_REFERENCE=testfiles/${resultfile}.ddl"
               -P "${HDF5_RESOURCES_DIR}/runTest.cmake"
       )
+      IF (NOT "${last_test}" STREQUAL "")
+        SET_TESTS_PROPERTIES (H5REPACK-${testname} PROPERTIES DEPENDS ${last_test})
+      ENDIF (NOT "${last_test}" STREQUAL "")
+      SET (last_test "H5REPACK-${testname}")
     ENDIF (${testtype} STREQUAL "SKIP")
   ENDMACRO (ADD_H5_CMP_TEST)
 
@@ -229,6 +236,8 @@ IF (BUILD_TESTING)
                 -D "TEST_REFERENCE=${testfilter}"
                 -P "${HDF5_RESOURCES_DIR}/grepTest.cmake"
         )
+        SET_TESTS_PROPERTIES (H5REPACK_VERIFY_LAYOUT-${testname} PROPERTIES DEPENDS H5REPACK-${testname})
+        SET (last_test "H5REPACK_VERIFY_LAYOUT-${testname}")
       ELSE (${resultcode} STREQUAL "0")
         IF (${testfilter} STREQUAL "CHUNKED")
           SET (nottestfilter "(CONTIGUOUS|COMPACT)")
@@ -251,6 +260,8 @@ IF (BUILD_TESTING)
                 -D "TEST_REFERENCE=${testfilter}"
                 -P "${HDF5_RESOURCES_DIR}/grepTest.cmake"
         )
+        SET_TESTS_PROPERTIES (H5REPACK_VERIFY_LAYOUT_ALL-${testname} PROPERTIES DEPENDS H5REPACK-${testname})
+        SET (last_test "H5REPACK_VERIFY_LAYOUT-${testname}")
       ENDIF (${resultcode} STREQUAL "0")
     ENDIF (${testtype} STREQUAL "SKIP")
   ENDMACRO (ADD_H5_VERIFY_TEST)
@@ -326,6 +337,10 @@ IF (BUILD_TESTING)
           h5repack_ub_out.h5
           h5repack_attr_refs_out.h5
   )
+  IF (NOT "${last_test}" STREQUAL "")
+    SET_TESTS_PROPERTIES (H5REPACK-clearall-objects PROPERTIES DEPENDS ${last_test})
+  ENDIF (NOT "${last_test}" STREQUAL "")
+  SET (last_test "H5REPACK-clearall-objects")
 
   # --------------------------------------------------------------------
   # test file names 
diff --git a/tools/h5repack/Makefile.in b/tools/h5repack/Makefile.in
index b4e6b48..77b6734 100644
--- a/tools/h5repack/Makefile.in
+++ b/tools/h5repack/Makefile.in
@@ -160,6 +160,7 @@ DEFS = @DEFS@
 DEPDIR = @DEPDIR@
 DEPRECATED_SYMBOLS = @DEPRECATED_SYMBOLS@
 DIRECT_VFD = @DIRECT_VFD@
+DLLTOOL = @DLLTOOL@
 DSYMUTIL = @DSYMUTIL@
 DUMPBIN = @DUMPBIN@
 DYNAMIC_DIRS = @DYNAMIC_DIRS@
@@ -221,6 +222,7 @@ LTLIBOBJS = @LTLIBOBJS@
 LT_STATIC_EXEC = @LT_STATIC_EXEC@
 MAINT = @MAINT@
 MAKEINFO = @MAKEINFO@
+MANIFEST_TOOL = @MANIFEST_TOOL@
 MKDIR_P = @MKDIR_P@
 MPE = @MPE@
 MPI_GET_SIZE = @MPI_GET_SIZE@
@@ -277,6 +279,7 @@ abs_builddir = @abs_builddir@
 abs_srcdir = @abs_srcdir@
 abs_top_builddir = @abs_top_builddir@
 abs_top_srcdir = @abs_top_srcdir@
+ac_ct_AR = @ac_ct_AR@
 ac_ct_CC = @ac_ct_CC@
 ac_ct_CXX = @ac_ct_CXX@
 ac_ct_DUMPBIN = @ac_ct_DUMPBIN@
diff --git a/tools/h5repack/h5repack.c b/tools/h5repack/h5repack.c
index eaca09e..1e7e0ed 100644
--- a/tools/h5repack/h5repack.c
+++ b/tools/h5repack/h5repack.c
@@ -409,7 +409,7 @@ int copy_attr(hid_t loc_in,
     hid_t      ftype_id=-1;       /* file type ID */
     hid_t      wtype_id=-1;       /* read/write type ID */
     size_t     msize;             /* size of type */
-    void       *buf=NULL;         /* data buffer */
+    void       *buf = NULL;       /* data buffer */
     hsize_t    nelmts;            /* number of elements in dataset */
     int        rank;              /* rank of dataset */
     htri_t     is_named;          /* Whether the datatype is named */
@@ -426,28 +426,23 @@ int copy_attr(hid_t loc_in,
     * copy all attributes
     *-------------------------------------------------------------------------
     */
-
-    for ( u = 0; u < (unsigned)oinfo.num_attrs; u++)
-    {
-        buf=NULL;
-
+    for(u = 0; u < (unsigned)oinfo.num_attrs; u++) {
         /* open attribute */
         if((attr_id = H5Aopen_by_idx(loc_in, ".", H5_INDEX_CRT_ORDER, H5_ITER_INC, (hsize_t)u, H5P_DEFAULT, H5P_DEFAULT)) < 0)
             goto error;
 
         /* get name */
-        if (H5Aget_name( attr_id, (size_t)255, name ) < 0)
+        if(H5Aget_name(attr_id, (size_t)255, name) < 0)
             goto error;
 
         /* get the file datatype  */
-        if ((ftype_id = H5Aget_type( attr_id )) < 0 )
+        if((ftype_id = H5Aget_type(attr_id)) < 0 )
             goto error;
 
         /* Check if the datatype is committed */
         if((is_named = H5Tcommitted(ftype_id)) < 0)
             goto error;
-        if(is_named) 
-        {
+        if(is_named && travt) {
             hid_t fidout;
 
             /* Create out file id */
@@ -465,29 +460,27 @@ int copy_attr(hid_t loc_in,
             if(H5Fclose(fidout) < 0)
                 goto error;
         } /* end if */
+        else {
+            if(options->use_native == 1)
+                wtype_id = h5tools_get_native_type(ftype_id);
+            else
+                wtype_id = H5Tcopy(ftype_id);
+        } /* end else */
+
 
         /* get the dataspace handle  */
-        if ((space_id = H5Aget_space( attr_id )) < 0 )
+        if((space_id = H5Aget_space(attr_id)) < 0)
             goto error;
 
         /* get dimensions  */
-        if ( (rank = H5Sget_simple_extent_dims(space_id, dims, NULL)) < 0 )
+        if((rank = H5Sget_simple_extent_dims(space_id, dims, NULL)) < 0)
             goto error;
 
-        nelmts=1;
-        for (j=0; j<rank; j++)
-            nelmts*=dims[j];
-
-        /* wtype_id will have already been set if using a named dtype */
-        if(!is_named) 
-        {
-            if (options->use_native==1)
-                wtype_id = h5tools_get_native_type(ftype_id);
-            else
-                wtype_id = H5Tcopy(ftype_id);
-        } /* end if */
+        nelmts = 1;
+        for(j = 0; j < rank; j++)
+            nelmts *= dims[j];
 
-        if ((msize=H5Tget_size(wtype_id))==0)
+        if((msize = H5Tget_size(wtype_id)) == 0)
             goto error;
 
         /*-------------------------------------------------------------------------
@@ -498,23 +491,20 @@ int copy_attr(hid_t loc_in,
         *-------------------------------------------------------------------------
         */
 
-        if (H5T_REFERENCE==H5Tget_class(wtype_id))
-        {
+        if(H5T_REFERENCE == H5Tget_class(wtype_id)) {
             ;
         }
-        else
-        {
+        else {
             /*-------------------------------------------------------------------------
             * read to memory
             *-------------------------------------------------------------------------
             */
 
             buf = (void *)HDmalloc((size_t)(nelmts * msize));
-            if(buf == NULL) 
-            {
+            if(buf == NULL) {
                 error_msg("h5repack", "cannot read into memory\n" );
                 goto error;
-            }
+            } /* end if */
             if(H5Aread(attr_id, wtype_id, buf) < 0)
                 goto error;
 
@@ -532,10 +522,12 @@ int copy_attr(hid_t loc_in,
             if(H5Aclose(attr_out) < 0)
                 goto error;
 
-
-            if(buf)
-                free(buf);
-
+            /* Check if we have VL data in the attribute's  datatype that must
+             * be reclaimed */
+            if(TRUE == H5Tdetect_class(wtype_id, H5T_VLEN))
+                H5Dvlen_reclaim(wtype_id, space_id, H5P_DEFAULT, buf);
+            HDfree(buf);
+            buf = NULL;
         } /*H5T_REFERENCE*/
 
 
@@ -547,28 +539,39 @@ int copy_attr(hid_t loc_in,
         *-------------------------------------------------------------------------
         */
 
-        if (H5Tclose(ftype_id) < 0) goto error;
-        if (H5Tclose(wtype_id) < 0) goto error;
-        if (H5Sclose(space_id) < 0) goto error;
-        if (H5Aclose(attr_id) < 0) goto error;
-
+        if(H5Tclose(ftype_id) < 0)
+            goto error;
+        if(H5Tclose(wtype_id) < 0)
+            goto error;
+        if(H5Sclose(space_id) < 0)
+            goto error;
+        if(H5Aclose(attr_id) < 0)
+            goto error;
     } /* u */
 
-
     return 0;
 
 error:
     H5E_BEGIN_TRY {
+        if(buf) {
+            /* Check if we have VL data in the attribute's  datatype that must
+             * be reclaimed */
+            if(TRUE == H5Tdetect_class(wtype_id, H5T_VLEN))
+                H5Dvlen_reclaim(wtype_id, space_id, H5P_DEFAULT, buf);
+
+            /* Free buf */
+            free(buf);
+        } /* end if */
+
         H5Tclose(ftype_id);
         H5Tclose(wtype_id);
         H5Sclose(space_id);
         H5Aclose(attr_id);
         H5Aclose(attr_out);
-        if (buf)
-            free(buf);
     } H5E_END_TRY;
+
     return -1;
-}
+} /* end copy_attr() */
 
 /*-------------------------------------------------------------------------
 * Function: check_options
diff --git a/tools/h5repack/h5repack.h b/tools/h5repack/h5repack.h
index 0e959a2..8d009a4 100644
--- a/tools/h5repack/h5repack.h
+++ b/tools/h5repack/h5repack.h
@@ -17,8 +17,7 @@
 #ifndef H5REPACK_H__
 #define H5REPACK_H__
 
-#include <assert.h>
-#include <string.h>
+#include "H5private.h"
 #include "hdf5.h"
 #include "h5trav.h"
 
diff --git a/tools/h5repack/h5repack_copy.c b/tools/h5repack/h5repack_copy.c
index 6c47cfb..5153cc4 100644
--- a/tools/h5repack/h5repack_copy.c
+++ b/tools/h5repack/h5repack_copy.c
@@ -13,11 +13,7 @@
 * access to either file, you may request a copy from help@hdfgroup.org.     *
 * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * */
 
-#include <stdlib.h>
-#include <string.h>
-#include <stdio.h>
 #include "h5repack.h"
-#include "H5private.h"
 #include "h5tools.h"
 #include "h5tools_utils.h"
 
@@ -543,22 +539,23 @@ int do_copy_objects(hid_t fidin,
                     trav_table_t *travt,
                     pack_opt_t *options) /* repack options */
 {
-    hid_t    grp_in=-1;         /* group ID */
-    hid_t    grp_out=-1;        /* group ID */
-    hid_t    dset_in=-1;        /* read dataset ID */
-    hid_t    dset_out=-1;       /* write dataset ID */
-    hid_t    gcpl_in=-1;        /* group creation property list */
-    hid_t    gcpl_out=-1;       /* group creation property list */
-    hid_t    type_in=-1;        /* named type ID */
-    hid_t    type_out=-1;       /* named type ID */
-    hid_t    dcpl_id=-1;        /* dataset creation property list ID */
-    hid_t    dcpl_out=-1;       /* dataset creation property list ID */
-    hid_t    f_space_id=-1;     /* file space ID */
-    hid_t    ftype_id=-1;       /* file type ID */
-    hid_t    wtype_id=-1;       /* read/write type ID */
-    named_dt_t *named_dt_head=NULL; /* Pointer to the stack of named datatypes copied */
+    hid_t    grp_in = -1;       /* group ID */
+    hid_t    grp_out = -1;      /* group ID */
+    hid_t    dset_in = -1;      /* read dataset ID */
+    hid_t    dset_out = -1;     /* write dataset ID */
+    hid_t    gcpl_in = -1;      /* group creation property list */
+    hid_t    gcpl_out = -1;     /* group creation property list */
+    hid_t    type_in = -1;      /* named type ID */
+    hid_t    type_out = -1;     /* named type ID */
+    hid_t    dcpl_id = -1;      /* dataset creation property list ID */
+    hid_t    dcpl_out = -1;     /* dataset creation property list ID */
+    hid_t    f_space_id = -1;   /* file space ID */
+    hid_t    ftype_id = -1;     /* file type ID */
+    hid_t    wtype_id = -1;     /* read/write type ID */
+    named_dt_t *named_dt_head = NULL; /* Pointer to the stack of named datatypes copied */
     size_t   msize;             /* size of type */
     hsize_t  nelmts;            /* number of elements in dataset */
+    H5D_space_status_t space_status; /* determines whether space has been allocated for the dataset  */
     int      rank;              /* rank of dataset */
     hsize_t  dims[H5S_MAX_RANK];/* dimensions of dataset */
     hsize_t  dsize_in;          /* input dataset size before filter */
@@ -688,7 +685,7 @@ int do_copy_objects(hid_t fidin,
             /* check if filters were requested for individual objects */
             for (u = 0; u < options->op_tbl->nelems; u++) {
 
-                if (strcmp(travt->objs[i].name, options->op_tbl->objs[u].path) == 0) {
+                if (HDstrcmp(travt->objs[i].name, options->op_tbl->objs[u].path) == 0) {
                         if (options->op_tbl->objs[u].filter->filtn > 0) {
                             req_filter = 1;
                         }
@@ -746,11 +743,13 @@ int do_copy_objects(hid_t fidin,
                 HDmemset(dims, 0, sizeof dims);
                 if(H5Sget_simple_extent_dims(f_space_id, dims, NULL) < 0)
                     goto error;
+
+                if(H5Dget_space_status(dset_in, &space_status) < 0)
+                    goto error;
+
                 nelmts = 1;
-                for ( j = 0; j < rank; j++)
-                {
+                for(j = 0; j < rank; j++)
                     nelmts *= dims[j];
-                }
 
                 /* wtype_id will have already been set if using a named dtype */
                 if(!is_named) {
@@ -834,20 +833,26 @@ int do_copy_objects(hid_t fidin,
                         * read/write
                         *-------------------------------------------------------------------------
                         */
-                        if (nelmts)
+                        if(nelmts > 0 && space_status != H5D_SPACE_STATUS_NOT_ALLOCATED)
                         {
-                            size_t need = (size_t)(nelmts*msize);  /* bytes needed */
-                            if ( need < H5TOOLS_MALLOCSIZE )
+                            size_t need = (size_t)(nelmts * msize);  /* bytes needed */
+
+                            /* have to read the whole dataset if there is only one element in the dataset */
+                            if(need < H5TOOLS_MALLOCSIZE)
                                 buf = HDmalloc(need);
 
-                            if (buf != NULL )
-                            {
-                                if (H5Dread(dset_in,wtype_id,H5S_ALL,H5S_ALL,H5P_DEFAULT,buf) < 0)
+                            if(buf != NULL) {
+                                if(H5Dread(dset_in, wtype_id, H5S_ALL, H5S_ALL, H5P_DEFAULT, buf) < 0)
                                     goto error;
-                                if (H5Dwrite(dset_out,wtype_id,H5S_ALL,H5S_ALL,H5P_DEFAULT,buf) < 0)
+                                if(H5Dwrite(dset_out, wtype_id, H5S_ALL, H5S_ALL, H5P_DEFAULT, buf) < 0)
                                     goto error;
-                            }
 
+                                /* Check if we have VL data in the dataset's
+                                 * datatype that must be reclaimed */
+                                if(TRUE == H5Tdetect_class(wtype_id, H5T_VLEN))
+                                    if(H5Dvlen_reclaim(wtype_id, f_space_id, H5P_DEFAULT, buf) < 0)
+                                        goto error;
+                            }
                             else /* possibly not enough memory, read/write by hyperslabs */
                             {
                                 size_t        p_type_nbytes = msize; /*size of memory type */
@@ -949,7 +954,7 @@ int do_copy_objects(hid_t fidin,
                                     sm_buf=NULL;
                                 }
                             } /* hyperslab read */
-                        }/*nelmts*/
+                        } /* if (nelmts>0 && space_status==H5D_SPACE_STATUS_NOT_ALLOCATED) */
 
                         /*-------------------------------------------------------------------------
                         * amount of compression used
@@ -1212,7 +1217,7 @@ static void print_dataset_info(hid_t dcpl_id,
     int          i;
 
 
-    strcpy(strfilter,"\0");
+    HDstrcpy(strfilter,"\0");
 
     /* get information about input filters */
     if((nfilters = H5Pget_nfilters(dcpl_id)) < 0)
@@ -1229,51 +1234,51 @@ static void print_dataset_info(hid_t dcpl_id,
             break;
 
         case H5Z_FILTER_DEFLATE:
-            strcat(strfilter,"GZIP ");
+            HDstrcat(strfilter,"GZIP ");
 
 #if defined (PRINT_DEBUG)
             {
                 unsigned level=cd_values[0];
                 sprintf(temp,"(%d)",level);
-                strcat(strfilter,temp);
+                HDstrcat(strfilter,temp);
             }
 #endif
             break;
 
         case H5Z_FILTER_SZIP:
-            strcat(strfilter,"SZIP ");
+            HDstrcat(strfilter,"SZIP ");
 
 #if defined (PRINT_DEBUG)
             {
                 unsigned options_mask=cd_values[0]; /* from dcpl, not filt*/
                 unsigned ppb=cd_values[1];
                 sprintf(temp,"(%d,",ppb);
-                strcat(strfilter,temp);
+                HDstrcat(strfilter,temp);
                 if (options_mask & H5_SZIP_EC_OPTION_MASK)
-                    strcpy(temp,"EC) ");
+                    HDstrcpy(temp,"EC) ");
                 else if (options_mask & H5_SZIP_NN_OPTION_MASK)
-                    strcpy(temp,"NN) ");
+                    HDstrcpy(temp,"NN) ");
             }
-            strcat(strfilter,temp);
+            HDstrcat(strfilter,temp);
 
 #endif
 
             break;
 
         case H5Z_FILTER_SHUFFLE:
-            strcat(strfilter,"SHUF ");
+            HDstrcat(strfilter,"SHUF ");
             break;
 
         case H5Z_FILTER_FLETCHER32:
-            strcat(strfilter,"FLET ");
+            HDstrcat(strfilter,"FLET ");
             break;
 
         case H5Z_FILTER_NBIT:
-            strcat(strfilter,"NBIT ");
+            HDstrcat(strfilter,"NBIT ");
             break;
 
         case H5Z_FILTER_SCALEOFFSET:
-            strcat(strfilter,"SCALEOFFSET ");
+            HDstrcat(strfilter,"SCALEOFFSET ");
             break;
         } /* switch */
     }/*i*/
@@ -1283,10 +1288,10 @@ static void print_dataset_info(hid_t dcpl_id,
     else
     {
         char str[255], temp[20];
-        strcpy(str,"dset     ");
-        strcat(str,strfilter);
+        HDstrcpy(str,"dset     ");
+        HDstrcat(str,strfilter);
         sprintf(temp,"  (%.3f:1)",ratio);
-        strcat(str,temp);
+        HDstrcat(str,temp);
         printf(FORMAT_OBJ,str,objname);
     }
 }
@@ -1364,7 +1369,7 @@ copy_user_block(const char *infile, const char *outfile, hsize_t size)
         } /* end while */
 
         /* Update size of userblock left to transfer */
-        size -= nread;
+        size = size - (hsize_t)nread;
     } /* end while */
 
 done:
diff --git a/tools/h5repack/h5repack_filters.c b/tools/h5repack/h5repack_filters.c
index d4a3479..213ff65 100644
--- a/tools/h5repack/h5repack_filters.c
+++ b/tools/h5repack/h5repack_filters.c
@@ -14,7 +14,6 @@
  * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * */
 
 #include "h5repack.h"
-#include "h5test.h"
 #include "h5tools.h"
 
 /* number of members in an array */
@@ -45,13 +44,13 @@ int aux_find_obj(const char* name,          /* object name from traverse list */
 
  for ( i=0; i<options->op_tbl->nelems; i++)
  {
-     if (strcmp(options->op_tbl->objs[i].path,name)==0)
+     if (HDstrcmp(options->op_tbl->objs[i].path,name)==0)
      {
          *obj =  options->op_tbl->objs[i];
          return i;
      }
 
-     pdest  = strstr(name,options->op_tbl->objs[i].path);
+     pdest  = HDstrstr(name,options->op_tbl->objs[i].path);
      result = (int)(pdest - name);
 
      /* found at position 1, meaning without '/' */
diff --git a/tools/h5repack/h5repack_main.c b/tools/h5repack/h5repack_main.c
index 9f8a701..6ec1647 100644
--- a/tools/h5repack/h5repack_main.c
+++ b/tools/h5repack/h5repack_main.c
@@ -13,10 +13,6 @@
  * access to either file, you may request a copy from help@hdfgroup.org.     *
  * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * */
 
-#include <stdlib.h>
-#include <string.h>
-#include <ctype.h>
-
 #include "h5tools_utils.h"
 #include "h5repack.h"
 
@@ -124,7 +120,7 @@ int main(int argc, const char **argv)
             infile = argv[ opt_ind ];
             outfile = argv[ opt_ind + 1 ];
 
-            if ( strcmp( infile, outfile ) == 0 )
+            if ( HDstrcmp( infile, outfile ) == 0 )
             {
                 error_msg("file names cannot be the same\n");
                 usage(h5tools_getprogname());
@@ -390,7 +386,7 @@ void parse_command_line(int argc, const char **argv, pack_opt_t* options)
 
                 int idx = 0;
                 int ssize = 0;
-                char *msgPtr = strchr( opt_arg, ':');
+                char *msgPtr = HDstrchr( opt_arg, ':');
                 options->latest = 1; /* must use latest format */
                 if (msgPtr == NULL)
                 {
@@ -401,22 +397,22 @@ void parse_command_line(int argc, const char **argv, pack_opt_t* options)
                 else
                 {
                     char msgType[10];
-                    strcpy(msgType, msgPtr+1);
+                    HDstrcpy(msgType, msgPtr+1);
                     msgPtr[0] = '\0';
                     ssize = atoi( opt_arg );
-                    if (strncmp(msgType, "dspace",6) == 0) {
+                    if (HDstrncmp(msgType, "dspace",6) == 0) {
                         options->msg_size[0] = ssize;
                     }
-                    else if (strncmp(msgType, "dtype", 5) == 0) {
+                    else if (HDstrncmp(msgType, "dtype", 5) == 0) {
                         options->msg_size[1] = ssize;
                     }
-                    else if (strncmp(msgType, "fill", 4) == 0) {
+                    else if (HDstrncmp(msgType, "fill", 4) == 0) {
                         options->msg_size[2] = ssize;
                     }
-                    else if (strncmp(msgType, "pline", 5) == 0) {
+                    else if (HDstrncmp(msgType, "pline", 5) == 0) {
                         options->msg_size[3] = ssize;
                     }
-                    else if (strncmp(msgType, "attr", 4) == 0) {
+                    else if (HDstrncmp(msgType, "attr", 4) == 0) {
                         options->msg_size[4] = ssize;
                     }
                 }
@@ -454,14 +450,14 @@ void parse_command_line(int argc, const char **argv, pack_opt_t* options)
 	{
             char strategy[MAX_NC_NAME];
 
-            strcpy(strategy, opt_arg);
-            if(!strcmp(strategy, "ALL_PERSIST"))
+            HDstrcpy(strategy, opt_arg);
+            if(!HDstrcmp(strategy, "ALL_PERSIST"))
                 options->fs_strategy = H5F_FILE_SPACE_ALL_PERSIST;
-            else if(!strcmp(strategy, "ALL"))
+            else if(!HDstrcmp(strategy, "ALL"))
                 options->fs_strategy = H5F_FILE_SPACE_ALL;
-            else if(!strcmp(strategy, "AGGR_VFD"))
+            else if(!HDstrcmp(strategy, "AGGR_VFD"))
                 options->fs_strategy = H5F_FILE_SPACE_AGGR_VFD;
-            else if(!strcmp(strategy, "VFD"))
+            else if(!HDstrcmp(strategy, "VFD"))
                 options->fs_strategy = H5F_FILE_SPACE_VFD;
             else {
                 error_msg("invalid file space management strategy\n", opt_arg );
@@ -533,7 +529,7 @@ void read_info(const char *filename,
         * filter
         *-------------------------------------------------------------------------
         */
-        if (strcmp(stype,"-f") == 0) {
+        if (HDstrcmp(stype,"-f") == 0) {
 
             /* find begining of info */
             i=0; c='0';
@@ -563,7 +559,7 @@ void read_info(const char *filename,
         * layout
         *-------------------------------------------------------------------------
         */
-        else if (strcmp(stype,"-l") == 0) {
+        else if (HDstrcmp(stype,"-l") == 0) {
 
             /* find begining of info */
             i=0; c='0';
diff --git a/tools/h5repack/h5repack_opttable.c b/tools/h5repack/h5repack_opttable.c
index 50f97bd..57b5fa7 100644
--- a/tools/h5repack/h5repack_opttable.c
+++ b/tools/h5repack/h5repack_opttable.c
@@ -13,8 +13,6 @@
  * access to either file, you may request a copy from help@hdfgroup.org.     *
  * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * */
 
-#include <stdlib.h>
-#include <string.h>
 #include "h5repack.h"
 #include "h5tools_utils.h"
 
@@ -32,7 +30,7 @@ void init_packobject(pack_info_t *obj)
 {
     int j, k;
 
-    strcpy(obj->path,"\0");
+    HDstrcpy(obj->path,"\0");
     for ( j=0; j<H5_REPACK_MAX_NFILTERS; j++)
     {
         obj->filter[j].filtn        = -1;
@@ -225,7 +223,7 @@ int options_add_layout( obj_list_t *obj_list,
             for (i = 0; i < table->nelems; i++)
             {
                 /*already on the table */
-                if (strcmp(obj_list[j].obj,table->objs[i].path)==0)
+                if (HDstrcmp(obj_list[j].obj,table->objs[i].path)==0)
                 {
                     /* already chunk info inserted for this one; exit */
                     if (table->objs[i].chunk.rank>0)
@@ -248,7 +246,7 @@ int options_add_layout( obj_list_t *obj_list,
                 /* keep the grow in a temp var */
                 I = table->nelems + added;
                 added++;
-                strcpy(table->objs[I].path,obj_list[j].obj);
+                HDstrcpy(table->objs[I].path,obj_list[j].obj);
                 aux_tblinsert_layout(table,I,pack);
             }
             /* cases where we have an already inserted name but there is a new name also
@@ -256,12 +254,12 @@ int options_add_layout( obj_list_t *obj_list,
             -f dset1:GZIP=1 -l dset1,dset2:CHUNK=20x20
             dset1 is already inserted, but dset2 must also be
             */
-            else if (found==1 && strcmp(obj_list[j].obj,table->objs[i].path)!=0)
+            else if (found==1 && HDstrcmp(obj_list[j].obj,table->objs[i].path)!=0)
             {
                 /* keep the grow in a temp var */
                 I = table->nelems + added;
                 added++;
-                strcpy(table->objs[I].path,obj_list[j].obj);
+                HDstrcpy(table->objs[I].path,obj_list[j].obj);
                 aux_tblinsert_layout(table,I,pack);
             }
         } /* j */
@@ -275,7 +273,7 @@ int options_add_layout( obj_list_t *obj_list,
         {
             I = table->nelems + added;
             added++;
-            strcpy(table->objs[I].path,obj_list[j].obj);
+            HDstrcpy(table->objs[I].path,obj_list[j].obj);
             aux_tblinsert_layout(table,I,pack);
 
         }
@@ -324,7 +322,7 @@ int options_add_filter(obj_list_t *obj_list,
             for (i = 0; i < table->nelems; i++)
             {
                 /*already on the table */
-                if (strcmp(obj_list[j].obj,table->objs[i].path)==0)
+                if (HDstrcmp(obj_list[j].obj,table->objs[i].path)==0)
                 {
                     /* insert */
                     aux_tblinsert_filter(table,i,filt);
@@ -338,7 +336,7 @@ int options_add_filter(obj_list_t *obj_list,
                 /* keep the grow in a temp var */
                 I = table->nelems + added;
                 added++;
-                strcpy(table->objs[I].path,obj_list[j].obj);
+                HDstrcpy(table->objs[I].path,obj_list[j].obj);
                 aux_tblinsert_filter(table,I,filt);
             }
             /* cases where we have an already inserted name but there is a new name also
@@ -346,12 +344,12 @@ int options_add_filter(obj_list_t *obj_list,
             -l dset1:CHUNK=20x20 -f dset1,dset2:GZIP=1
             dset1 is already inserted, but dset2 must also be
             */
-            else if (found==1 && strcmp(obj_list[j].obj,table->objs[i].path)!=0)
+            else if (found==1 && HDstrcmp(obj_list[j].obj,table->objs[i].path)!=0)
             {
                 /* keep the grow in a temp var */
                 I = table->nelems + added;
                 added++;
-                strcpy(table->objs[I].path,obj_list[j].obj);
+                HDstrcpy(table->objs[I].path,obj_list[j].obj);
                 aux_tblinsert_filter(table,I,filt);
             }
         } /* j */
@@ -365,7 +363,7 @@ int options_add_filter(obj_list_t *obj_list,
         {
             I = table->nelems + added;
             added++;
-            strcpy(table->objs[I].path,obj_list[j].obj);
+            HDstrcpy(table->objs[I].path,obj_list[j].obj);
             aux_tblinsert_filter(table,I,filt);
         }
     }
@@ -393,7 +391,7 @@ pack_info_t* options_get_object( const char *path,
     for ( i = 0; i < table->nelems; i++)
     {
         /* found it */
-        if (strcmp(table->objs[i].path,path)==0)
+        if (HDstrcmp(table->objs[i].path,path)==0)
         {
             return (&table->objs[i]);
         }
diff --git a/tools/h5repack/h5repack_parse.c b/tools/h5repack/h5repack_parse.c
index d3a7419..d3c6014 100644
--- a/tools/h5repack/h5repack_parse.c
+++ b/tools/h5repack/h5repack_parse.c
@@ -13,11 +13,6 @@
  * access to either file, you may request a copy from help@hdfgroup.org.     *
  * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * */
 
-#include <stdlib.h>
-#include <string.h>
-#include <stdio.h>
-#include <ctype.h>
-
 #include "h5repack.h"
 #include "h5tools_utils.h"
 
@@ -109,7 +104,7 @@ obj_list_t* parse_filter(const char *str,
         if ( c==',' || j==end_obj-1)
         {
             if ( c==',') sobj[k]='\0'; else sobj[k+1]='\0';
-            strcpy(obj_list[n].obj,sobj);
+            HDstrcpy(obj_list[n].obj,sobj);
             memset(sobj,0,sizeof(sobj));
             n++;
             k=-1;
@@ -143,7 +138,7 @@ obj_list_t* parse_filter(const char *str,
                 * example SZIP=8,NN
                 *-------------------------------------------------------------------------
                 */
-                if (strcmp(scomp,"SZIP")==0)
+                if (HDstrcmp(scomp,"SZIP")==0)
                 {
                     l=-1; /* mask index check */
                     for ( m=0,u=i+1; u<len; u++,m++)
@@ -171,9 +166,9 @@ obj_list_t* parse_filter(const char *str,
                                 smask[l]='\0';
                                 i=len-1; /* end */
                                 (*n_objs)--; /* we counted an extra ',' */
-                                if (strcmp(smask,"NN")==0)
+                                if (HDstrcmp(smask,"NN")==0)
                                     filt->cd_values[j++]=H5_SZIP_NN_OPTION_MASK;
-                                else if (strcmp(smask,"EC")==0)
+                                else if (HDstrcmp(smask,"EC")==0)
                                     filt->cd_values[j++]=H5_SZIP_EC_OPTION_MASK;
                                 else
                                 {
@@ -203,7 +198,7 @@ obj_list_t* parse_filter(const char *str,
                   *-------------------------------------------------------------------------
                 */
 
-                else if (strcmp(scomp,"SOFF")==0)
+                else if (HDstrcmp(scomp,"SOFF")==0)
                 {
                     l=-1; /* mask index check */
                     for ( m=0,u=i+1; u<len; u++,m++)
@@ -231,9 +226,9 @@ obj_list_t* parse_filter(const char *str,
                                 smask[l]='\0';
                                 i=len-1; /* end */
                                 (*n_objs)--; /* we counted an extra ',' */
-                                if (strcmp(smask,"IN")==0)
+                                if (HDstrcmp(smask,"IN")==0)
                                     filt->cd_values[j++]=H5Z_SO_INT;
-                                else if (strcmp(smask,"DS")==H5Z_SO_FLOAT_DSCALE)
+                                else if (HDstrcmp(smask,"DS")==H5Z_SO_FLOAT_DSCALE)
                                     filt->cd_values[j++]=H5Z_SO_FLOAT_DSCALE;
                                 else
                                 {
@@ -290,7 +285,7 @@ obj_list_t* parse_filter(const char *str,
    * H5Z_FILTER_NONE
    *-------------------------------------------------------------------------
    */
-   if (strcmp(scomp,"NONE")==0)
+   if (HDstrcmp(scomp,"NONE")==0)
    {
        filt->filtn=H5Z_FILTER_NONE;
        filt->cd_nelmts = 0;
@@ -300,7 +295,7 @@ obj_list_t* parse_filter(const char *str,
    * H5Z_FILTER_DEFLATE
    *-------------------------------------------------------------------------
    */
-   else if (strcmp(scomp,"GZIP")==0)
+   else if (HDstrcmp(scomp,"GZIP")==0)
    {
        filt->filtn=H5Z_FILTER_DEFLATE;
        filt->cd_nelmts = 1;
@@ -316,7 +311,7 @@ obj_list_t* parse_filter(const char *str,
    * H5Z_FILTER_SZIP
    *-------------------------------------------------------------------------
    */
-   else if (strcmp(scomp,"SZIP")==0)
+   else if (HDstrcmp(scomp,"SZIP")==0)
    {
        filt->filtn=H5Z_FILTER_SZIP;
        filt->cd_nelmts = 2;
@@ -332,7 +327,7 @@ obj_list_t* parse_filter(const char *str,
    * H5Z_FILTER_SHUFFLE
    *-------------------------------------------------------------------------
    */
-   else if (strcmp(scomp,"SHUF")==0)
+   else if (HDstrcmp(scomp,"SHUF")==0)
    {
        filt->filtn=H5Z_FILTER_SHUFFLE;
        filt->cd_nelmts = 0;
@@ -347,7 +342,7 @@ obj_list_t* parse_filter(const char *str,
    * H5Z_FILTER_FLETCHER32
    *-------------------------------------------------------------------------
    */
-   else if (strcmp(scomp,"FLET")==0)
+   else if (HDstrcmp(scomp,"FLET")==0)
    {
        filt->filtn=H5Z_FILTER_FLETCHER32;
        filt->cd_nelmts = 0;
@@ -362,7 +357,7 @@ obj_list_t* parse_filter(const char *str,
    * H5Z_FILTER_NBIT
    *-------------------------------------------------------------------------
    */
-   else if (strcmp(scomp,"NBIT")==0)
+   else if (HDstrcmp(scomp,"NBIT")==0)
    {
        filt->filtn=H5Z_FILTER_NBIT;
        filt->cd_nelmts = 0;
@@ -377,7 +372,7 @@ obj_list_t* parse_filter(const char *str,
    * H5Z_FILTER_SCALEOFFSET
    *-------------------------------------------------------------------------
    */
-   else if (strcmp(scomp,"SOFF")==0)
+   else if (HDstrcmp(scomp,"SOFF")==0)
    {
        filt->filtn=H5Z_FILTER_SCALEOFFSET;
        filt->cd_nelmts = 2;
@@ -437,7 +432,7 @@ obj_list_t* parse_filter(const char *str,
            error_msg("pixels_per_block is too large in <%s>\n",str);
            exit(EXIT_FAILURE);
        }
-       if ( (strcmp(smask,"NN")!=0) && (strcmp(smask,"EC")!=0) )
+       if ( (HDstrcmp(smask,"NN")!=0) && (HDstrcmp(smask,"EC")!=0) )
        {
            if (obj_list) free(obj_list);
            error_msg("szip mask must be 'NN' or 'EC' \n");
@@ -530,7 +525,7 @@ obj_list_t* parse_layout(const char *str,
         if ( c==',' || j==end_obj-1)
         {
             if ( c==',') sobj[k]='\0'; else sobj[k+1]='\0';
-            strcpy(obj_list[n].obj,sobj);
+            HDstrcpy(obj_list[n].obj,sobj);
             memset(sobj,0,sizeof(sobj));
             n++;
             k=-1;
@@ -551,11 +546,11 @@ obj_list_t* parse_layout(const char *str,
         if (n==5)
         {
             slayout[n]='\0';  /*cut string */
-            if (strcmp(slayout,"COMPA")==0)
+            if (HDstrcmp(slayout,"COMPA")==0)
                 pack->layout=H5D_COMPACT;
-            else if (strcmp(slayout,"CONTI")==0)
+            else if (HDstrcmp(slayout,"CONTI")==0)
                 pack->layout=H5D_CONTIGUOUS;
-            else if (strcmp(slayout,"CHUNK")==0)
+            else if (HDstrcmp(slayout,"CHUNK")==0)
                 pack->layout=H5D_CHUNKED;
             else {
                 error_msg("in parse layout, not a valid layout in <%s>\n",str);
@@ -618,7 +613,7 @@ obj_list_t* parse_layout(const char *str,
                 else if (i==len-1) { /*no more parameters */
                     sdim[k]='\0';
                     k=0;
-                    if (strcmp(sdim,"NONE")==0)
+                    if (HDstrcmp(sdim,"NONE")==0)
                     {
                         pack->chunk.rank=-2;
                     }
diff --git a/tools/h5repack/h5repack_refs.c b/tools/h5repack/h5repack_refs.c
index aa2e823..091133e 100644
--- a/tools/h5repack/h5repack_refs.c
+++ b/tools/h5repack/h5repack_refs.c
@@ -14,12 +14,7 @@
  * access to either file, you may request a copy from help@hdfgroup.org.     *
  * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * */
 
-
-#include <stdlib.h>
-#include <string.h>
-#include <stdio.h>
 #include "h5repack.h"
-#include "H5private.h"
 #include "h5diff.h"
 #include "h5tools.h"
 
diff --git a/tools/h5repack/h5repack_verify.c b/tools/h5repack/h5repack_verify.c
index 34c5dd6..b0ab1d1 100644
--- a/tools/h5repack/h5repack_verify.c
+++ b/tools/h5repack/h5repack_verify.c
@@ -14,7 +14,6 @@
  * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * */
 
 #include "h5repack.h"
-#include "h5test.h"
 #include "h5tools_utils.h"
 
 static int verify_layout(hid_t pid, pack_info_t *obj);