[svn-r21105] Fixed two bugs:

     - h5repack: h5repack failed to copy dataset if the layout is changed from chunked with
            unlimited dims to contiguous. (PC -- 2011/07/15)
     - h5diff: "--delta" option considers two NaN of the same type are different, which is wrong
            based on http://www.hdfgroup.org/HDF5/doc/RM/Tools.html#Tools-Diff. (PC -- 2011/07/15)

8 files changed, 132 insertions, 94 deletions

diff --git a/tools/h5diff/h5diffgentest.c b/tools/h5diff/h5diffgentest.c
index 2f65fca..719707f 100644
--- a/tools/h5diff/h5diffgentest.c
+++ b/tools/h5diff/h5diffgentest.c
@@ -335,7 +335,7 @@ int test_basic(const char *fname1, const char *fname2, const char *fname3)
     *-------------------------------------------------------------------------
     */
     {
-        /* epsilon = 0.0000001 = 1e-7 
+        /* epsilon = 0.0000001 = 1e-7
          * system epsilon for float : FLT_EPSILON = 1.19209E-07
          */
         float  data11[3][2] ={{0.000000f,0.0000001f},{0.0000001f, 0.00000022f},{0.0000001f,0.0000001f}};
@@ -416,7 +416,7 @@ int test_basic(const char *fname1, const char *fname2, const char *fname3)
         data17[5] = 1;
 
         data18[0] = (float) sqrt( (double)-1 );
-        data18[1] = (float) sqrt( (double)-1 );
+        data18[1] = (float) sqrt( (double)-10000 );
         data18[2] = 1;
         data18[3] = 1;
         data18[4] = 1;
@@ -424,6 +424,7 @@ int test_basic(const char *fname1, const char *fname2, const char *fname3)
 
         write_dset(gid1,1,dims1,"fp17",H5T_NATIVE_DOUBLE,data17);
         write_dset(gid1,1,dims1,"fp18",H5T_NATIVE_DOUBLE,data18);
+        write_dset(gid1,1,dims1,"fp18_COPY",H5T_NATIVE_DOUBLE,data18);
     }
 
     /*------------------------------------------------------------------------
@@ -932,7 +933,7 @@ int test_attributes(const char *file,
 /*-------------------------------------------------------------------------
 * Function: test_attributes_verbose_level
 *
-* Purpose: Cresting test files for testing attributes along with 
+* Purpose: Cresting test files for testing attributes along with
 * levels of verbos option
 *
 *-------------------------------------------------------------------------
@@ -1040,7 +1041,7 @@ static int test_attributes_verbose_level(const char *fname1, const char *fname2)
         goto out;
     }
 
-    
+
 
 
     /*----------------------------------------------------------------------
@@ -1121,7 +1122,7 @@ static int test_attributes_verbose_level(const char *fname1, const char *fname2)
 
    /*----------------------------------
     * CASE1 - Same attr number, all Same attr name
-    * add attr to group 
+    * add attr to group
     */
     write_attr(f1_gid,1,attr_dims,"integer1",H5T_NATIVE_INT,f1_attr_idata);
     write_attr(f1_gid,1,attr_dims,"float1",H5T_NATIVE_FLOAT,f1_attr_fdata);
@@ -1130,8 +1131,8 @@ static int test_attributes_verbose_level(const char *fname1, const char *fname2)
     write_attr(f2_gid,1,attr_dims,"float1",H5T_NATIVE_FLOAT,f2_attr_fdata);
 
    /*----------------------------------
-    * CASE2 - Same attr number, some Same attr name 
-    * add attr to dset 
+    * CASE2 - Same attr number, some Same attr name
+    * add attr to dset
     */
     write_attr(f1_did,1,attr_dims,"integer1",H5T_NATIVE_INT,f1_attr_idata);
     write_attr(f1_did,1,attr_dims,"float2",H5T_NATIVE_FLOAT,f1_attr_fdata);
@@ -1140,8 +1141,8 @@ static int test_attributes_verbose_level(const char *fname1, const char *fname2)
     write_attr(f2_did,1,attr_dims,"float3",H5T_NATIVE_FLOAT,f2_attr_fdata);
 
    /*----------------------------------
-    * CASE3 - Same attr number, all different attr name 
-    * add attr to ntype 
+    * CASE3 - Same attr number, all different attr name
+    * add attr to ntype
     */
     write_attr(f1_tid,1,attr_dims,"integer1",H5T_NATIVE_INT,f1_attr_idata);
     write_attr(f1_tid,1,attr_dims,"float2",H5T_NATIVE_FLOAT,f1_attr_fdata);
@@ -1161,11 +1162,11 @@ static int test_attributes_verbose_level(const char *fname1, const char *fname2)
 
     write_attr(f2_gid2,1,attr_dims,"integer1",H5T_NATIVE_INT,f2_attr_idata);
     write_attr(f2_gid2,1,attr_dims,"float2",H5T_NATIVE_FLOAT,f2_attr_fdata);
-    
+
 
    /*----------------------------------
     * CASE5 - Different attr number, all different attr name
-    * add attr to g3  
+    * add attr to g3
     */
     write_attr(f1_gid3,1,attr_dims,"integer10",H5T_NATIVE_INT,f1_attr_idata);
     write_attr(f1_gid3,1,attr_dims,"float11",H5T_NATIVE_FLOAT,f1_attr_fdata);
@@ -1307,10 +1308,10 @@ int test_special_datasets(const char *file,
     status = H5Sclose(sid0);
     assert(status >= 0);
 
-    /* Create a dataset with zero dimension size in one file but the other one 
+    /* Create a dataset with zero dimension size in one file but the other one
      * has a dataset with a non-zero dimension size */
     if(make_diffs) {
-        dims[1] = SPACE1_DIM2 + 4;        
+        dims[1] = SPACE1_DIM2 + 4;
     }
 
     sid = H5Screate_simple(SPACE1_RANK, dims, NULL);
@@ -2650,9 +2651,9 @@ static int test_group_recurse(const char *fname1, const char *fname2)
     }
 
     /*------------------------------
-     * external circle route test 
+     * external circle route test
      * file1/grp11 <-> file2/grp10  via elink_grp_circle link
-     */     
+     */
     /* file1 */
     status = H5Lcreate_external(fname2, "/grp11", gid10_f1, "elink_grp_circle", H5P_DEFAULT, H5P_DEFAULT);
     if (status < 0)
@@ -2697,7 +2698,7 @@ out:
 
 /*-------------------------------------------------------------------------
 *
-* Purpose: 
+* Purpose:
 *   For testing comparing group member objects recursively via multiple
 *   linked external links
 *
@@ -2865,7 +2866,7 @@ static int test_group_recurse2(void)
     fileid4 = H5Fcreate(GRP_RECURSE2_EXT3, H5F_ACC_TRUNC, H5P_DEFAULT, H5P_DEFAULT);
 
    /*-----------------------------------------------
-    * Groups 
+    * Groups
     */
     grp4 = H5Gcreate2(fileid4, "/g4", H5P_DEFAULT, H5P_DEFAULT, H5P_DEFAULT);
     if (grp4 < 0)
@@ -2902,7 +2903,7 @@ static int test_group_recurse2(void)
     fileid3 = H5Fcreate(GRP_RECURSE2_EXT2, H5F_ACC_TRUNC, H5P_DEFAULT, H5P_DEFAULT);
 
    /*-----------------------------------------------
-    * Groups 
+    * Groups
     */
     grp2 = H5Gcreate2(fileid3, "g2", H5P_DEFAULT, H5P_DEFAULT, H5P_DEFAULT);
     if (grp2 < 0)
@@ -2958,7 +2959,7 @@ static int test_group_recurse2(void)
     fileid2 = H5Fcreate(GRP_RECURSE2_EXT1, H5F_ACC_TRUNC, H5P_DEFAULT, H5P_DEFAULT);
 
    /*-----------------------------------------------
-    * Groups 
+    * Groups
     */
     grp1 = H5Gcreate2(fileid2, "g1", H5P_DEFAULT, H5P_DEFAULT, H5P_DEFAULT);
     if (grp1 < 0)
@@ -3087,7 +3088,7 @@ static int test_exclude_obj1(const char *fname1, const char *fname2)
 
 
     /*-----------------------------------------------------------------------
-    * Datasets 
+    * Datasets
     *------------------------------------------------------------------------*/
     /* file1 */
     status = write_dset(fid1,2,dims2,"dset1",H5T_NATIVE_INT,data1);
@@ -3161,7 +3162,7 @@ out:
 *
 * Purpose: Create test files for excluding obj.
 *          different structure and name
-* Test : exclude different objs to verify the rest are same 
+* Test : exclude different objs to verify the rest are same
 *
 * Programmer: Jonathan Kim (July, 21, 2010)
 *
@@ -3232,7 +3233,7 @@ static int test_exclude_obj2(const char *fname1, const char *fname2)
 
 
     /*-----------------------------------------------------------------------
-    * Datasets 
+    * Datasets
     *------------------------------------------------------------------------*/
     /* file1 */
     status = write_dset(fid1,2,dims2,"dset10",H5T_NATIVE_INT,data1);
@@ -3307,7 +3308,7 @@ out:
 /*-------------------------------------------------------------------------
 *
 * Purpose: Create test files for multiple variable length string/string array
-*          along with fixed length string/string array types in 
+*          along with fixed length string/string array types in
 *          a compound type dataset.
 *
 * Programmer: Jonathan Kim (Oct, 26, 2010)
@@ -3493,8 +3494,8 @@ static int test_comp_vlen_strings(const char *fname1, const char *grp_name, int
     /* objref */
     hsize_t    objref_dims[1]={1};
 
-    /*------------------------------------------ 
-     * compound dataset 
+    /*------------------------------------------
+     * compound dataset
      *------------------------------------------*/
     hid_t    sid_comp=0;      /* dataspace ID */
     hid_t    tid1_comp=0;      /* datatype ID */
@@ -3640,7 +3641,7 @@ static int test_comp_vlen_strings(const char *fname1, const char *grp_name, int
     }
 
     /*-----------------------------------------------------------------------
-    * Create group 
+    * Create group
     *------------------------------------------------------------------------*/
     gid = H5Gcreate2(fid1, grp_name, H5P_DEFAULT, H5P_DEFAULT, H5P_DEFAULT);
     if (gid < 0)
@@ -3883,7 +3884,7 @@ static int test_comp_vlen_strings(const char *fname1, const char *grp_name, int
         fprintf(stderr, "Error: %s> H5Dwrite failed.\n", fname1);
         status = FAIL;
         goto out;
-    } 
+    }
     H5Dclose(did_comp);
 
     /* Write data to compound 3 dataset buffer */
@@ -3894,7 +3895,7 @@ static int test_comp_vlen_strings(const char *fname1, const char *grp_name, int
         fprintf(stderr, "Error: %s> H5Dwrite failed.\n", fname1);
         status = FAIL;
         goto out;
-    } 
+    }
     H5Dclose(did_comp);
 
     /* Write data to compound 4 dataset buffer */
@@ -3905,7 +3906,7 @@ static int test_comp_vlen_strings(const char *fname1, const char *grp_name, int
         fprintf(stderr, "Error: %s> H5Dwrite failed.\n", fname1);
         status = FAIL;
         goto out;
-    } 
+    }
     H5Dclose(did_comp);
 
     /* Write data to compound 5 dataset buffer */
@@ -3916,7 +3917,7 @@ static int test_comp_vlen_strings(const char *fname1, const char *grp_name, int
         fprintf(stderr, "Error: %s> H5Dwrite failed.\n", fname1);
         status = FAIL;
         goto out;
-    } 
+    }
     H5Dclose(did_comp);
 
     /* Write data to compound 6 dataset buffer */
@@ -3927,7 +3928,7 @@ static int test_comp_vlen_strings(const char *fname1, const char *grp_name, int
         fprintf(stderr, "Error: %s> H5Dwrite failed.\n", fname1);
         status = FAIL;
         goto out;
-    } 
+    }
     H5Dclose(did_comp);
 
     /* Write data to compound 7 dataset buffer */
@@ -3938,7 +3939,7 @@ static int test_comp_vlen_strings(const char *fname1, const char *grp_name, int
         fprintf(stderr, "Error: %s> H5Dwrite failed.\n", fname1);
         status = FAIL;
         goto out;
-    } 
+    }
     H5Dclose(did_comp);
 
     /* Write data to compound 8 dataset buffer */
@@ -3949,7 +3950,7 @@ static int test_comp_vlen_strings(const char *fname1, const char *grp_name, int
         fprintf(stderr, "Error: %s> H5Dwrite failed.\n", fname1);
         status = FAIL;
         goto out;
-    } 
+    }
     H5Dclose(did_comp);
 
     /* Write data to compound 9 dataset buffer */
@@ -3966,7 +3967,7 @@ static int test_comp_vlen_strings(const char *fname1, const char *grp_name, int
         fprintf(stderr, "Error: %s> H5Dwrite failed.\n", fname1);
         status = FAIL;
         goto out;
-    } 
+    }
 
 
     H5Dclose(did_comp);
@@ -4049,7 +4050,7 @@ test_enums(const char *fname)
     int         enum_val  = -1;
 
     /* The data in the two arrays cover the following cases:
-     *   
+     *
      *   V = valid enum value, I = invalid enum value
      *
      *   0:  I-I (same value)
@@ -4083,7 +4084,7 @@ test_enums(const char *fname)
     /*-----------------------------------------------------------------------
      * Create enum types
      *---------------------------------------------------------------------*/
- 
+
     tid = H5Tenum_create(H5T_NATIVE_INT);
     enum_val = 0;
     status = H5Tenum_insert(tid, "YIN", &enum_val);
@@ -4093,7 +4094,7 @@ test_enums(const char *fname)
     /*-----------------------------------------------------------------------
      * Create datasets containing enum data.
      *---------------------------------------------------------------------*/
- 
+
     status = write_dset(fid, 1, &dims, "dset1", tid, data1);
     status = write_dset(fid, 1, &dims, "dset2", tid, data2);
 
@@ -4105,7 +4106,7 @@ out:
         H5Fclose(fid);
     if(tid)
         H5Tclose(tid);
-    
+
     return status;
 }
 
diff --git a/tools/h5diff/testfiles/h5diff_17.txt b/tools/h5diff/testfiles/h5diff_17.txt
index 5e48dae..4906a2a 100644
--- a/tools/h5diff/testfiles/h5diff_17.txt
+++ b/tools/h5diff/testfiles/h5diff_17.txt
@@ -22,6 +22,7 @@ file1     file2
     x           /g1/fp16       
     x           /g1/fp17       
     x           /g1/fp18       
+    x           /g1/fp18_COPY  
     x           /g1/fp19       
     x           /g1/fp19_COPY  
     x           /g1/fp2        
diff --git a/tools/h5diff/testfiles/h5diff_basic1.h5 b/tools/h5diff/testfiles/h5diff_basic1.h5
index d97017e..e1396be 100644
--- a/tools/h5diff/testfiles/h5diff_basic1.h5
+++ b/tools/h5diff/testfiles/h5diff_basic1.h5
diff --git a/tools/h5diff/testh5diff.sh b/tools/h5diff/testh5diff.sh
index b33e691..fcfcc14 100755
--- a/tools/h5diff/testh5diff.sh
+++ b/tools/h5diff/testh5diff.sh
@@ -629,6 +629,10 @@ TOOLTEST h5diff_609.txt -d 200 h5diff_basic1.h5 h5diff_basic2.h5 g1/dset3 g1/dse
 # 6.10: number smaller than smallest difference
 TOOLTEST h5diff_610.txt -d 1 h5diff_basic1.h5 h5diff_basic2.h5 g1/dset3 g1/dset4
 
+# 6.11: test (NaN == NaN) must be true based on our documentation -- XCAO
+TOOLTEST h5diff_609.txt -d "0.0001" h5diff_basic1.h5 h5diff_basic1.h5 g1/fp18 g1/fp18_COPY
+TOOLTEST h5diff_609.txt --use-system-epsilon h5diff_basic1.h5 h5diff_basic1.h5 g1/fp18 g1/fp18_COPY
+
 
 # ##############################################################################
 # # -p
diff --git a/tools/h5repack/h5repack_copy.c b/tools/h5repack/h5repack_copy.c
index 5153cc4..0e9d1dd 100644
--- a/tools/h5repack/h5repack_copy.c
+++ b/tools/h5repack/h5repack_copy.c
@@ -808,6 +808,11 @@ int do_copy_objects(hid_t fidin,
                                 goto error;
                         }
 
+                        /* unset the unlimimted dimensions, which cannot be applied to layout other than chunked. */ 
+                        if (options->layout_g != H5D_CHUNKED) {
+                             H5Sset_extent_simple( f_space_id, rank, dims, NULL );
+                        }
+
                         /*-------------------------------------------------------------------------
                         * create the output dataset;
                         * disable error checking in case the dataset cannot be created with the
diff --git a/tools/h5repack/testfiles/h5repack_layout.h5 b/tools/h5repack/testfiles/h5repack_layout.h5
index 5772a31..2cc44b1 100644
--- a/tools/h5repack/testfiles/h5repack_layout.h5
+++ b/tools/h5repack/testfiles/h5repack_layout.h5
diff --git a/tools/lib/h5diff_array.c b/tools/lib/h5diff_array.c
index 6c5744f..ecfc238 100644
--- a/tools/lib/h5diff_array.c
+++ b/tools/lib/h5diff_array.c
@@ -234,11 +234,11 @@ hsize_t diff_array( void *_mem1,
     size = H5Tget_size( m_type );
     type_class = H5Tget_class(m_type);
 
-    /* Fast comparison first for atomic type by memcmp(). 
+    /* Fast comparison first for atomic type by memcmp().
      * It is OK not to list non-atomic type here because it will not be caught
-     * by the confition, but it gives more clarity for code planning 
+     * by the condition, but it gives more clarity for code planning
      */
-    if (type_class != H5T_REFERENCE && 
+    if (type_class != H5T_REFERENCE &&
         type_class != H5T_COMPOUND &&
         type_class != H5T_STRING &&
         type_class != H5T_VLEN &&
@@ -269,7 +269,6 @@ hsize_t diff_array( void *_mem1,
     */
 
     case H5T_FLOAT:
-
         if (H5Tequal(m_type, H5T_NATIVE_FLOAT))
             nfound=diff_float(mem1,mem2,nelmts,hyper_start,rank,dims,acc,pos,options,name1,name2,&ph);
         else if (H5Tequal(m_type, H5T_NATIVE_DOUBLE))
@@ -427,11 +426,11 @@ hsize_t diff_datum(void       *_mem1,
     type_size = H5Tget_size( m_type );
     type_class = H5Tget_class(m_type);
 
-    /* Fast comparison first for atomic type by memcmp(). 
+    /* Fast comparison first for atomic type by memcmp().
      * It is OK not to list non-atomic type here because it will not be caught
-     * by the confition, but it gives more clarity for code planning 
+     * by the confition, but it gives more clarity for code planning
      */
-    if (type_class != H5T_REFERENCE && 
+    if (type_class != H5T_REFERENCE &&
         type_class != H5T_COMPOUND &&
         type_class != H5T_STRING &&
         type_class != H5T_VLEN &&
@@ -513,10 +512,10 @@ hsize_t diff_datum(void       *_mem1,
                 size2 = H5Tget_size(m_type);
             }
 
-            /* 
+            /*
              * compare for shorter string
-             * TODO: this code need to be improved to handle the difference 
-             *       of length of strings. 
+             * TODO: this code need to be improved to handle the difference
+             *       of length of strings.
              *       For now mimic the previous way.
              */
             if(size1 < size2)
@@ -622,7 +621,7 @@ hsize_t diff_datum(void       *_mem1,
             char enum_name2[1024];
 
             herr_t err1;
-            herr_t err2; 
+            herr_t err2;
 
             /* disable error reporting */
             H5E_BEGIN_TRY {
@@ -1946,8 +1945,8 @@ hsize_t diff_datum(void       *_mem1,
                     }
 
                 }
-                /* one is NaN, assume difference */
-                else if ( isnan1==1 || isnan2==1)
+                /* only one is NaN, assume difference */
+                else if (isnan1==1 && isnan2==0  || isnan1==0 && isnan2==1)
                 {
                     if ( print_data(options) )
                     {
@@ -2009,8 +2008,8 @@ hsize_t diff_datum(void       *_mem1,
                         }
 
                 }
-                /* one is NaN, assume difference */
-                else if ( isnan1==1 || isnan2==1)
+                /* only one is NaN, assume difference */
+                else if (isnan1==1 && isnan2==0  || isnan1==0 && isnan2==1)
                 {
                     if ( print_data(options) )
                     {
@@ -2075,8 +2074,8 @@ hsize_t diff_datum(void       *_mem1,
                         }
 
                 }
-                /* one is NaN, assume difference */
-                else if ( isnan1==1 || isnan2==1)
+                /* only one is NaN, assume difference */
+                else if (isnan1==1 && isnan2==0  || isnan1==0 && isnan2==1)
                 {
                     if ( print_data(options) )
                     {
@@ -2131,7 +2130,6 @@ hsize_t diff_datum(void       *_mem1,
             */
             if (options->d && !options->p)
             {
-
                /*-------------------------------------------------------------------------
                 * detect NaNs
                 *-------------------------------------------------------------------------
@@ -2158,8 +2156,8 @@ hsize_t diff_datum(void       *_mem1,
                     }
 
                 }
-                /* one is NaN, assume difference */
-                else if ( isnan1==1 || isnan2==1)
+                /* only one is NaN, assume difference */
+                else if (isnan1==1 && isnan2==0  || isnan1==0 && isnan2==1)
                 {
                     if ( print_data(options) )
                     {
@@ -2223,8 +2221,8 @@ hsize_t diff_datum(void       *_mem1,
                         }
 
                 }
-                /* one is NaN, assume difference */
-                else if ( isnan1==1 || isnan2==1)
+                /* only one is NaN, assume difference */
+                else if (isnan1==1 && isnan2==0  || isnan1==0 && isnan2==1)
                 {
                     if ( print_data(options) )
                     {
@@ -2289,8 +2287,8 @@ hsize_t diff_datum(void       *_mem1,
                         }
 
                 }
-                /* one is NaN, assume difference */
-                else if ( isnan1==1 || isnan2==1)
+                /* only one is NaN, assume difference */
+                else if (isnan1==1 && isnan2==0  || isnan1==0 && isnan2==1)
                 {
                     if ( print_data(options) )
                     {
@@ -2299,7 +2297,6 @@ hsize_t diff_datum(void       *_mem1,
                         parallel_print(F_FORMAT,temp1_double,temp2_double,ABS(temp1_double-temp2_double));
                     }
                     nfound++;
-
                 }
             }
 
@@ -2373,8 +2370,18 @@ hsize_t diff_datum(void       *_mem1,
                         }
                         nfound++;
                     }
-
                 } /* NaN */
+                /* only one is NaN, assume difference */
+                else if (isnan1==1 && isnan2==0  || isnan1==0 && isnan2==1)
+                {
+                    if ( print_data(options) )
+                    {
+                        print_pos(ph,0,i,acc,pos,rank,dims,obj1,obj2);
+                        parallel_print(SPACES);
+                        parallel_print(F_FORMAT,temp1_double,temp2_double,ABS(temp1_double-temp2_double));
+                    }
+                    nfound++;
+                }
             }
 
            /*-------------------------------------------------------------------------
@@ -2428,7 +2435,18 @@ hsize_t diff_datum(void       *_mem1,
                         }
 
                 } /* NaN */
-            }
+                /* only one is NaN, assume difference */
+                else if (isnan1==1 && isnan2==0  || isnan1==0 && isnan2==1)
+                {
+                    if ( print_data(options) )
+                    {
+                        print_pos(ph,0,i,acc,pos,rank,dims,obj1,obj2);
+                        parallel_print(SPACES);
+                        parallel_print(F_FORMAT,temp1_double,temp2_double,ABS(temp1_double-temp2_double));
+                    }
+                    nfound++;
+                }
+           }
 
            /*-------------------------------------------------------------------------
             * -d and -p
@@ -2482,6 +2500,17 @@ hsize_t diff_datum(void       *_mem1,
                         }
 
                 } /* NaN */
+                /* only one is NaN, assume difference */
+                else if (isnan1==1 && isnan2==0  || isnan1==0 && isnan2==1)
+                {
+                    if ( print_data(options) )
+                    {
+                        print_pos(ph,0,i,acc,pos,rank,dims,obj1,obj2);
+                        parallel_print(SPACES);
+                        parallel_print(F_FORMAT,temp1_double,temp2_double,ABS(temp1_double-temp2_double));
+                    }
+                    nfound++;
+                }
             }
 
            /*-------------------------------------------------------------------------
@@ -2973,8 +3002,8 @@ hsize_t diff_float(unsigned char *mem1,
                     nfound++;
                 }
             }
-            /* one is NaN, assume difference */
-            else if ( isnan1==1 || isnan2==1)
+            /* only one is NaN, assume difference */
+            else if (isnan1==1 && isnan2==0  || isnan1==0 && isnan2==1)
             {
                 if ( print_data(options) )
                 {
@@ -3045,8 +3074,8 @@ hsize_t diff_float(unsigned char *mem1,
                         nfound++;
                     }
             }
-            /* one is NaN, assume difference */
-            else if ( isnan1==1 || isnan2==1)
+            /* only one is NaN, assume difference */
+            else if (isnan1==1 && isnan2==0  || isnan1==0 && isnan2==1)
             {
                 if ( print_data(options) )
                 {
@@ -3120,8 +3149,8 @@ hsize_t diff_float(unsigned char *mem1,
                     }
 
             }
-            /* one is NaN, assume difference */
-            else if ( isnan1==1 || isnan2==1)
+            /* only one is NaN, assume difference */
+            else if (isnan1==1 && isnan2==0  || isnan1==0 && isnan2==1)
             {
                 if ( print_data(options) )
                 {
@@ -3210,7 +3239,6 @@ hsize_t diff_double(unsigned char *mem1,
     int         isnan1=0;
     int         isnan2=0;
 
-
  /*-------------------------------------------------------------------------
   * -d and !-p
   *-------------------------------------------------------------------------
@@ -3247,8 +3275,8 @@ hsize_t diff_double(unsigned char *mem1,
                     nfound++;
                 }
             }
-            /* one is NaN, assume difference */
-            else if ( isnan1==1 || isnan2==1)
+            /* only one is NaN, assume difference */
+            else if (isnan1==1 && isnan2==0  || isnan1==0 && isnan2==1)
             {
                 if ( print_data(options) )
                 {
@@ -3319,8 +3347,8 @@ hsize_t diff_double(unsigned char *mem1,
                         nfound++;
                     }
             }
-            /* one is NaN, assume difference */
-            else if ( isnan1==1 || isnan2==1)
+            /* only one is NaN, assume difference */
+            else if (isnan1==1 && isnan2==0  || isnan1==0 && isnan2==1)
             {
                 if ( print_data(options) )
                 {
@@ -3394,8 +3422,8 @@ hsize_t diff_double(unsigned char *mem1,
                     }
 
             }
-            /* one is NaN, assume difference */
-            else if ( isnan1==1 || isnan2==1)
+            /* only one is NaN, assume difference */
+            else if (isnan1==1 && isnan2==0  || isnan1==0 && isnan2==1)
             {
                 if ( print_data(options) )
                 {
@@ -3530,8 +3558,8 @@ hsize_t diff_ldouble(unsigned char *mem1,
                     nfound++;
                 }
             }
-            /* one is NaN, assume difference */
-            else if ( isnan1==1 || isnan2==1)
+            /* only one is NaN, assume difference */
+            else if (isnan1==1 && isnan2==0  || isnan1==0 && isnan2==1)
             {
                 if ( print_data(options) )
                 {
@@ -3602,8 +3630,8 @@ hsize_t diff_ldouble(unsigned char *mem1,
                         nfound++;
                     }
             }
-            /* one is NaN, assume difference */
-            else if ( isnan1==1 || isnan2==1)
+            /* only one is NaN, assume difference */
+            else if (isnan1==1 && isnan2==0  || isnan1==0 && isnan2==1)
             {
                 if ( print_data(options) )
                 {
@@ -3677,8 +3705,8 @@ hsize_t diff_ldouble(unsigned char *mem1,
                     }
 
             }
-            /* one is NaN, assume difference */
-            else if ( isnan1==1 || isnan2==1)
+            /* only one is NaN, assume difference */
+            else if (isnan1==1 && isnan2==0  || isnan1==0 && isnan2==1)
             {
                 if ( print_data(options) )
                 {
@@ -6107,13 +6135,13 @@ static void set_comp_members(hid_t tid, mcomp_t *members)
     members->flags = HDcalloc(members->n, sizeof(unsigned char));
     members->offsets = HDcalloc(members->n, sizeof(size_t));
     members->m = HDcalloc(members->n, sizeof(mcomp_t *));
-   
-    for (i=0; i< members->n; i++) 
+
+    for (i=0; i< members->n; i++)
     {
          members->ids[i] = H5Tget_member_type( tid, i );
          members->flags[i] = H5Tis_variable_str( members->ids[i] );
          members->offsets[i] = H5Tget_member_offset( tid, i );
-         if (H5Tget_class( members->ids[i])==H5T_COMPOUND) 
+         if (H5Tget_class( members->ids[i])==H5T_COMPOUND)
          {
               members->m[i] = (mcomp_t *)HDmalloc(sizeof(mcomp_t));
               set_comp_members(members->ids[i], members->m[i]);
@@ -6126,16 +6154,16 @@ static void set_comp_members(hid_t tid, mcomp_t *members)
  * added to improve performance for compound datasets
  * clean and close compound members.
  */
-static void free_comp_members(mcomp_t *members) 
+static void free_comp_members(mcomp_t *members)
 {
     int i;
 
     if (!members || members->n<=0 || !members->ids)
         return;
 
-    for (i=0; i<members->n; i++) 
+    for (i=0; i<members->n; i++)
     {
-        if (members->m[i]) 
+        if (members->m[i])
         {
             free_comp_members(members->m[i]);
             HDfree(members->m[i]);
diff --git a/tools/lib/h5diff_dset.c b/tools/lib/h5diff_dset.c
index 230e7bb..c26c766 100644
--- a/tools/lib/h5diff_dset.c
+++ b/tools/lib/h5diff_dset.c
@@ -327,7 +327,7 @@ hsize_t diff_datasetid( hid_t did1,
         can_compare=0;
         options->not_cmp=1;
     }
-    
+
     /* Check if type is either VLEN-data or VLEN-string to reclaim any
      * VLEN memory buffer later */
     if( TRUE == h5tools_detect_vlen(m_tid1) )
@@ -390,7 +390,6 @@ hsize_t diff_datasetid( hid_t did1,
         * read/compare
         *-------------------------------------------------------------------------
         */
-
         need = (size_t)(nelmts1 * m_size1);  /* bytes needed */
         if(need < H5TOOLS_MALLOCSIZE) {
             buf1 = HDmalloc(need);
@@ -562,7 +561,7 @@ error:
     if (buf1!=NULL)
     {
         /* reclaim any VL memory, if necessary */
-        if(vl_data) 
+        if(vl_data)
             H5Dvlen_reclaim(m_tid1, sid1, H5P_DEFAULT, buf1);
         free(buf1);
         buf1=NULL;
@@ -570,7 +569,7 @@ error:
     if (buf2!=NULL)
     {
         /* reclaim any VL memory, if necessary */
-        if(vl_data) 
+        if(vl_data)
             H5Dvlen_reclaim(m_tid2, sid2, H5P_DEFAULT, buf2);
         free(buf2);
         buf2=NULL;