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authorJonathan Kim <jkm@hdfgroup.org>2010-11-02 16:39:42 (GMT)
committerJonathan Kim <jkm@hdfgroup.org>2010-11-02 16:39:42 (GMT)
commite45cfcb9ee17bcfd6e777514f0488f67f2521c83 (patch)
tree3301d806f4fa887eff2ee176b4921956f9bc1a11
parent584735fb9889d89096a245b4a91894b83b6b7d18 (diff)
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hdf5-e45cfcb9ee17bcfd6e777514f0488f67f2521c83.tar.gz
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[svn-r19712] Purpose:
Fixed h5diff to handle variable-length strings in a compound dataset correctly. Also variable-length string array in a compound dataset. Bug #1989. Description: Garbage values were displayed when h5diff compared variable-length strings (or string array) in a compound type dataset. Tested: jam (linux32-LE), amani (linux64-LE), heiwa (linuxppc64-BE), tejeda (Mac32)
-rw-r--r--MANIFEST2
-rw-r--r--release_docs/RELEASE.txt5
-rw-r--r--tools/h5diff/CMakeLists.txt11
-rw-r--r--tools/h5diff/h5diffgentest.c298
-rw-r--r--tools/h5diff/testfiles/h5diff_530.txt11
-rw-r--r--tools/h5diff/testfiles/h5diff_comp_vl_strs.h5bin0 -> 8504 bytes
-rw-r--r--tools/lib/h5diff_array.c106
-rw-r--r--windows/tools/h5diff/testh5diff.bat8
8 files changed, 411 insertions, 30 deletions
diff --git a/MANIFEST b/MANIFEST
index 708d708..c8aa72d 100644
--- a/MANIFEST
+++ b/MANIFEST
@@ -1634,6 +1634,7 @@
./tools/h5diff/testfiles/h5diff_516.txt
./tools/h5diff/testfiles/h5diff_517.txt
./tools/h5diff/testfiles/h5diff_518.txt
+./tools/h5diff/testfiles/h5diff_530.txt
./tools/h5diff/testfiles/h5diff_attr1.h5
./tools/h5diff/testfiles/h5diff_attr2.h5
@@ -1665,6 +1666,7 @@
./tools/h5diff/testfiles/h5diff_exclude1-2.h5
./tools/h5diff/testfiles/h5diff_exclude2-1.h5
./tools/h5diff/testfiles/h5diff_exclude2-2.h5
+./tools/h5diff/testfiles/h5diff_comp_vl_strs.h5
#test files for h5repack
diff --git a/release_docs/RELEASE.txt b/release_docs/RELEASE.txt
index c43de9c..4f513c0 100644
--- a/release_docs/RELEASE.txt
+++ b/release_docs/RELEASE.txt
@@ -474,6 +474,11 @@ Bug Fixes since HDF5-1.8.0 release
Tools
-----
+ - Fixed h5diff to handle variable-length strings in a compound dataset
+ correctly. (also variable-length string array in a compound dataset)
+ Garbage values were displayed when h5diff compared multiple
+ variable-length strings in a compound type dataset.
+ Bug#1989 (JKM 2010/10/28)
- Fixed h5copy to fail gracefully when copying object to non-exist
group without -p option. Bug#2040 (JKM 2010/10/18)
- Fixed to compare member objects and groups recursively when two
diff --git a/tools/h5diff/CMakeLists.txt b/tools/h5diff/CMakeLists.txt
index a784ae7..b86a804 100644
--- a/tools/h5diff/CMakeLists.txt
+++ b/tools/h5diff/CMakeLists.txt
@@ -147,6 +147,7 @@ IF (BUILD_TESTING)
h5diff_516.txt
h5diff_517.txt
h5diff_518.txt
+ h5diff_530.txt
h5diff_600.txt
h5diff_601.txt
h5diff_603.txt
@@ -209,6 +210,7 @@ IF (BUILD_TESTING)
h5diff_exclude1-2.h5
h5diff_exclude2-1.h5
h5diff_exclude2-2.h5
+ h5diff_comp_vl_strs.h5
)
FOREACH (txt_file ${HDF5_REFERENCE_FILES})
@@ -326,6 +328,8 @@ IF (BUILD_TESTING)
# different structure and obj names
SET (EXCLUDE_FILE2_1 h5diff_exclude2-1.h5)
SET (EXCLUDE_FILE2_2 h5diff_exclude2-2.h5)
+ # compound type with multiple vlen string types
+ SET (COMP_VL_STRS_FILE h5diff_comp_vl_strs.h5)
# Remove any output file left over from previous test run
ADD_TEST (
@@ -540,6 +544,8 @@ IF (BUILD_TESTING)
h5diff_517.out.err
h5diff_518.out
h5diff_518.out.err
+ h5diff_530.out
+ h5diff_530.out.err
h5diff_600.out
h5diff_600.out.err
h5diff_601.out
@@ -1057,6 +1063,11 @@ ADD_H5_TEST (h5diff_483 1 -v --exclude-path "/group1" ${EXCLUDE_FILE2_1} ${EXCLU
# Exclude from group compare
ADD_H5_TEST (h5diff_484 0 -v --exclude-path "/dset3" ${EXCLUDE_FILE1_1} ${EXCLUDE_FILE1_2} /group1)
+# ##############################################################################
+# # diff various multiple vlen and fixed strings in a compound type dataset
+# ##############################################################################
+ADD_H5_TEST (h5diff_530 0 -v ${COMP_VL_STRS_FILE} ${COMP_VL_STRS_FILE})
+
ENDIF (BUILD_TESTING)
diff --git a/tools/h5diff/h5diffgentest.c b/tools/h5diff/h5diffgentest.c
index d66f821..fd4f2a9 100644
--- a/tools/h5diff/h5diffgentest.c
+++ b/tools/h5diff/h5diffgentest.c
@@ -68,6 +68,8 @@
/* different structure and obj names */
#define EXCLUDE_FILE2_1 "h5diff_exclude2-1.h5"
#define EXCLUDE_FILE2_2 "h5diff_exclude2-2.h5"
+/* compound type with multiple vlen string types */
+#define COMP_VL_STRS_FILE "h5diff_comp_vl_strs.h5"
#define UIMAX 4294967295u /*Maximum value for a variable of type unsigned int */
#define STR_SIZE 3
@@ -116,6 +118,7 @@ static int test_group_recurse(const char *fname1, const char *fname2);
static int test_group_recurse2();
static int test_exclude_obj1(const char *fname1, const char *fname2);
static int test_exclude_obj2(const char *fname1, const char *fname2);
+static int test_comp_vlen_strings(const char *fname1);
/* called by test_attributes() and test_datasets() */
static void write_attr_in(hid_t loc_id,const char* dset_name,hid_t fid,int make_diffs);
@@ -171,6 +174,9 @@ int main(void)
test_exclude_obj1(EXCLUDE_FILE1_1, EXCLUDE_FILE1_2);
test_exclude_obj2(EXCLUDE_FILE2_1, EXCLUDE_FILE2_2);
+ /* diff various multiple vlen and fixlen string types in a compound dataset */
+ test_comp_vlen_strings(COMP_VL_STRS_FILE );
+
return 0;
}
@@ -2919,6 +2925,298 @@ out:
}
/*-------------------------------------------------------------------------
+*
+* Purpose: Create test files for multiple variable length string/string array
+* along with fixed length string/string array types in
+* a compound type dataset.
+*
+* Programmer: Jonathan Kim (Oct, 26, 2010)
+*
+*-------------------------------------------------------------------------*/
+#define STR_RANK 1
+#define VLSTR1_DIM 1
+#define FLSTR2_SIZE 21
+#define FLSTR2_DIM 1
+#define VLSTRARRY3_DIM 3
+#define FLSTRARRY4_DIM 3
+#define FLSTRARRY4_SIZE 30
+#define COMP_RANK 1
+#define COMP_DIM 1
+static int test_comp_vlen_strings(const char *fname1)
+{
+ int i;
+
+ hid_t fid1; /* file id */
+
+ /* compound datatype */
+ typedef struct comp_t
+ {
+ char *str1; /* vlen string */
+ char *str1_again; /* vlen string */
+ char str2[FLSTR2_SIZE]; /* fixed len string */
+ char str2_again[FLSTR2_SIZE]; /* fixed len string */
+ char *str3[VLSTRARRY3_DIM]; /* vlen string array */
+ char *str3_again[VLSTRARRY3_DIM]; /* vlen string array */
+ char str4[FLSTRARRY4_DIM][FLSTRARRY4_SIZE]; /* fixed len string array */
+ char str4_again[FLSTRARRY4_DIM][FLSTRARRY4_SIZE]; /* fixed len string array */
+ } comp_t;
+
+ /* vlen string1 */
+ hid_t sid_str1=0; /* dataspace ID */
+ hid_t tid_str1=0; /* datatype ID */
+ hid_t did_str1=0; /* dataset ID */
+ const char vlstr1_buf[]= {
+ "Variable length string"
+ };
+ hsize_t dims_str1[] = {VLSTR1_DIM};
+
+ /* fixlen string2 */
+ hid_t sid_str2=0; /* dataspace ID */
+ hid_t tid_str2=0; /* datatype ID */
+ hid_t did_str2=0; /* dataset ID */
+ const char flstr2_buf[FLSTR2_SIZE]= {
+ "Fixed length string"
+ };
+ hsize_t dims_str2[] = {FLSTR2_DIM};
+
+ /* vlen string3 array */
+ hid_t sid_str3=0; /* dataspace ID */
+ hid_t tid_str3=0; /* datatype ID */
+ hid_t tid_str3_array=0; /* datatype ID */
+ hid_t did_str3=0; /* dataset ID */
+ const char *vlstr3_buf[VLSTRARRY3_DIM]= {
+ "1 - Variable length string Array",
+ "2 - Testing variable length string array in compound type",
+ "3 - Four score and seven\n years ago our forefathers brought forth on this continent a new nation,"
+ };
+ hsize_t dims_str3[] = {VLSTRARRY3_DIM};
+
+ /* fixlen string array 4 */
+ hid_t sid_str4=0; /* dataspace ID */
+ hid_t tid_str4=0; /* datatype ID */
+ hid_t tid_str4_array=0; /* datatype ID */
+ hid_t did_str4=0; /* dataset ID */
+ const char *flstr4_buf[FLSTRARRY4_DIM]= {
+ "1 - Fixed length string Array",
+ "2 - Fixed length string Array",
+ "3 - Fixed length string Array"
+ };
+ hsize_t dims_str4[] = {FLSTRARRY4_DIM};
+
+ /*------------------------------------------
+ * compound dataset
+ *------------------------------------------*/
+ hid_t sid_comp=0; /* dataspace ID */
+ hid_t tid_comp=0; /* datatype ID */
+ hid_t did_comp=0; /* dataset ID */
+ hsize_t dims_comp[] = {COMP_DIM};
+ herr_t status = SUCCEED;
+
+ /* make compound strings data */
+ comp_t comp_buf;
+
+ /* copy string1 type to compound buffer */
+ comp_buf.str1 = comp_buf.str1_again = vlstr1_buf;
+ /* copy string2 type to compound buffer */
+ HDstrcpy(comp_buf.str2, flstr2_buf);
+ HDstrcpy(comp_buf.str2_again, flstr2_buf);
+ /* copy string3 type to compound buffer */
+ for (i=0; i < VLSTRARRY3_DIM; i++)
+ comp_buf.str3[i] = comp_buf.str3_again[i] = vlstr3_buf[i];
+ /* copy string4 type to compound buffer */
+ for (i=0; i < FLSTRARRY4_DIM; i++)
+ {
+ HDstrcpy(comp_buf.str4[i], flstr4_buf[i]);
+ HDstrcpy(comp_buf.str4_again[i], flstr4_buf[i]);
+ }
+
+ /*-----------------------------------------------------------------------
+ * Create file(s)
+ *------------------------------------------------------------------------*/
+ fid1 = H5Fcreate (fname1, H5F_ACC_TRUNC, H5P_DEFAULT, H5P_DEFAULT);
+ if (fid1 < 0)
+ {
+ fprintf(stderr, "Error: %s> H5Fcreate failed.\n", fname1);
+ status = FAIL;
+ goto out;
+ }
+
+ /*-----------------------------------------------------------------------
+ * Variable length String1 - Create space and type
+ *------------------------------------------------------------------------*/
+ sid_str1 = H5Screate_simple(STR_RANK, dims_str1, NULL);
+ if (sid_str1 < 0)
+ {
+ fprintf(stderr, "Error: %s> H5Screate_simple failed.\n", fname1);
+ status = FAIL;
+ goto out;
+ }
+
+ tid_str1 = H5Tcopy(H5T_C_S1);
+ status = H5Tset_size(tid_str1, H5T_VARIABLE);
+ if (status < 0)
+ {
+ fprintf(stderr, "Error: %s> H5Tset_size failed.\n", fname1);
+ status = FAIL;
+ goto out;
+ }
+
+ /*-----------------------------------------------------------------------
+ * Fixed length String2 - Create space and type
+ *------------------------------------------------------------------------*/
+ sid_str2 = H5Screate_simple(STR_RANK, dims_str2, NULL);
+ if (sid_str2 < 0)
+ {
+ fprintf(stderr, "Error: %s> H5Screate_simple failed.\n", fname1);
+ status = FAIL;
+ goto out;
+ }
+
+ tid_str2 = H5Tcopy(H5T_C_S1);
+ status = H5Tset_size(tid_str2, FLSTR2_SIZE);
+ if (status < 0)
+ {
+ fprintf(stderr, "Error: %s> H5Tset_size failed.\n", fname1);
+ status = FAIL;
+ goto out;
+ }
+
+ /*-----------------------------------------------------------------------
+ * Fixed length String3 array - Create space and type
+ *------------------------------------------------------------------------*/
+ sid_str3 = H5Screate_simple(STR_RANK, dims_str3, NULL);
+ if (sid_str3 < 0)
+ {
+ fprintf(stderr, "Error: %s> H5Screate_simple failed.\n", fname1);
+ status = FAIL;
+ goto out;
+ }
+
+ tid_str3 = H5Tcopy(H5T_C_S1);
+ status = H5Tset_size(tid_str3, H5T_VARIABLE);
+ if (status < 0)
+ {
+ fprintf(stderr, "Error: %s> H5Tset_size failed.\n", fname1);
+ status = FAIL;
+ goto out;
+ }
+
+ /* Create the array data type for the string array */
+ tid_str3_array = H5Tarray_create2(tid_str3, COMP_RANK, dims_str3);
+ if (tid_str3_array < 0)
+ {
+ fprintf(stderr, "Error: %s> H5Tarray_create2 failed.\n", fname1);
+ status = FAIL;
+ goto out;
+ }
+
+ /*-----------------------------------------------------------------------
+ * Variable length String4 array - Create space and type
+ *------------------------------------------------------------------------*/
+ sid_str4 = H5Screate_simple(STR_RANK, dims_str4, NULL);
+ if (sid_str4 < 0)
+ {
+ fprintf(stderr, "Error: %s> H5Screate_simple failed.\n", fname1);
+ status = FAIL;
+ goto out;
+ }
+
+ tid_str4 = H5Tcopy(H5T_C_S1);
+ status = H5Tset_size(tid_str4, FLSTRARRY4_SIZE);
+ if (status < 0)
+ {
+ fprintf(stderr, "Error: %s> H5Tset_size failed.\n", fname1);
+ status = FAIL;
+ goto out;
+ }
+ /* Create the array data type for the string array */
+ tid_str4_array = H5Tarray_create2(tid_str4, COMP_RANK, dims_str4);
+ if (tid_str4_array < 0)
+ {
+ fprintf(stderr, "Error: %s> H5Tarray_create2 failed.\n", fname1);
+ status = FAIL;
+ goto out;
+ }
+
+ /*-------------------------------------------------------------------------
+ * Compound dataset
+ *------------------------------------------------------------------------*/
+ sid_comp = H5Screate_simple(COMP_RANK, dims_comp, NULL);
+ if (sid_comp < 0)
+ {
+ fprintf(stderr, "Error: %s> H5Screate_simple failed.\n", fname1);
+ status = FAIL;
+ goto out;
+ }
+ tid_comp = H5Tcreate (H5T_COMPOUND, sizeof(comp_t));
+ H5Tinsert(tid_comp, "VLEN_STR1", HOFFSET(comp_t, str1), tid_str1 );
+ H5Tinsert(tid_comp, "VLEN_STR2", HOFFSET(comp_t, str1_again), tid_str1 );
+ H5Tinsert(tid_comp, "FIXLEN_STR1", HOFFSET(comp_t, str2), tid_str2 );
+ H5Tinsert(tid_comp, "FIXLEN_STR2", HOFFSET(comp_t, str2_again), tid_str2 );
+ H5Tinsert(tid_comp, "VLEN_STR_ARRAY1", HOFFSET(comp_t, str3), tid_str3_array);
+ H5Tinsert(tid_comp, "VLEN_STR_ARRAY2", HOFFSET(comp_t, str3_again), tid_str3_array);
+ H5Tinsert(tid_comp, "FIXLEN_STR_ARRAY1", HOFFSET(comp_t, str4), tid_str4_array);
+ H5Tinsert(tid_comp, "FIXLEN_STR_ARRAY2", HOFFSET(comp_t, str4_again), tid_str4_array);
+
+ /* Write data to compound dataset buffer */
+ did_comp = H5Dcreate2(fid1, "Compound_dset", tid_comp, sid_comp, H5P_DEFAULT, H5P_DEFAULT, H5P_DEFAULT);
+ status = H5Dwrite(did_comp, tid_comp, H5S_ALL, H5S_ALL, H5P_DEFAULT, &comp_buf);
+ if (status < 0)
+ {
+ fprintf(stderr, "Error: %s> H5Dwrite failed.\n", fname1);
+ status = FAIL;
+ goto out;
+ }
+out:
+ /*-----------------------------------------------------------------------
+ * Close
+ *-----------------------------------------------------------------------*/
+ if(fid1)
+ H5Fclose(fid1);
+ /* string1 */
+ if(tid_str1)
+ H5Tclose(tid_str1);
+ if(did_str1)
+ H5Dclose(did_str1);
+ if(sid_str1)
+ H5Sclose(sid_str1);
+ /* string2 */
+ if(tid_str2)
+ H5Tclose(tid_str2);
+ if(did_str2)
+ H5Dclose(did_str2);
+ if(sid_str2)
+ H5Sclose(sid_str2);
+ /* string3 */
+ if(tid_str3)
+ H5Tclose(tid_str3);
+ if(tid_str3_array)
+ H5Tclose(tid_str3_array);
+ if(did_str3)
+ H5Dclose(did_str3);
+ if(sid_str3)
+ H5Sclose(sid_str3);
+ /* string4 */
+ if(tid_str4)
+ H5Tclose(tid_str4);
+ if(tid_str4_array)
+ H5Tclose(tid_str4_array);
+ if(did_str4)
+ H5Dclose(did_str4);
+ if(sid_str4)
+ H5Sclose(sid_str4);
+ /* compound */
+ if(tid_comp)
+ H5Tclose(tid_comp);
+ if(did_comp)
+ H5Dclose(did_comp);
+ if(sid_comp)
+ H5Sclose(sid_comp);
+
+ return status;
+}
+
+/*-------------------------------------------------------------------------
* Function: write_attr_in
*
* Purpose: write attributes in LOC_ID (dataset, group, named datatype)
diff --git a/tools/h5diff/testfiles/h5diff_530.txt b/tools/h5diff/testfiles/h5diff_530.txt
new file mode 100644
index 0000000..6f7e08f
--- /dev/null
+++ b/tools/h5diff/testfiles/h5diff_530.txt
@@ -0,0 +1,11 @@
+
+file1 file2
+---------------------------------------
+ x x /
+ x x /Compound_dset
+
+group : </> and </>
+0 differences found
+dataset: </Compound_dset> and </Compound_dset>
+0 differences found
+EXIT CODE: 0
diff --git a/tools/h5diff/testfiles/h5diff_comp_vl_strs.h5 b/tools/h5diff/testfiles/h5diff_comp_vl_strs.h5
new file mode 100644
index 0000000..348cfee
--- /dev/null
+++ b/tools/h5diff/testfiles/h5diff_comp_vl_strs.h5
Binary files differ
diff --git a/tools/lib/h5diff_array.c b/tools/lib/h5diff_array.c
index dc3c9fb..6005ed8 100644
--- a/tools/lib/h5diff_array.c
+++ b/tools/lib/h5diff_array.c
@@ -447,21 +447,43 @@ hsize_t diff_datum(void *_mem1,
{
offset = H5Tget_member_offset(m_type, (unsigned)j);
memb_type = H5Tget_member_type(m_type, (unsigned)j);
- nfound+=diff_datum(
- mem1+offset,
- mem2+offset,
- memb_type,
- i,
- rank,
- dims,
- acc,
- pos,
- options,
- obj1,
- obj2,
- container1_id,
- container2_id,
- ph);
+ /* if member type is vlen string */
+ if(H5Tis_variable_str(memb_type))
+ {
+ nfound+=diff_datum(
+ ((unsigned char**)mem1)[j],
+ ((unsigned char**)mem2)[j],
+ memb_type,
+ i,
+ rank,
+ dims,
+ acc,
+ pos,
+ options,
+ obj1,
+ obj2,
+ container1_id,
+ container2_id,
+ ph);
+ }
+ else
+ {
+ nfound+=diff_datum(
+ mem1+offset,
+ mem2+offset,
+ memb_type,
+ i,
+ rank,
+ dims,
+ acc,
+ pos,
+ options,
+ obj1,
+ obj2,
+ container1_id,
+ container2_id,
+ ph);
+ }
H5Tclose(memb_type);
}
break;
@@ -631,21 +653,45 @@ hsize_t diff_datum(void *_mem1,
for (u = 0, nelmts = 1; u <ndims; u++)
nelmts *= adims[u];
for (u = 0; u < nelmts; u++)
- nfound+=diff_datum(
- mem1 + u * size,
- mem2 + u * size, /* offset */
- memb_type,
- i, /* index position */
- rank,
- dims,
- acc,
- pos,
- options,
- obj1,
- obj2,
- container1_id,
- container2_id,
- ph);
+ {
+ /* if member type is vlen string */
+ if(H5Tis_variable_str(memb_type))
+ {
+ nfound+=diff_datum(
+ ((unsigned char**)mem1)[u],
+ ((unsigned char**)mem2)[u],
+ memb_type,
+ i, /* index position */
+ rank,
+ dims,
+ acc,
+ pos,
+ options,
+ obj1,
+ obj2,
+ container1_id,
+ container2_id,
+ ph);
+ }
+ else
+ {
+ nfound+=diff_datum(
+ mem1 + u * size,
+ mem2 + u * size, /* offset */
+ memb_type,
+ i, /* index position */
+ rank,
+ dims,
+ acc,
+ pos,
+ options,
+ obj1,
+ obj2,
+ container1_id,
+ container2_id,
+ ph);
+ }
+ }
H5Tclose(memb_type);
}
break;
diff --git a/windows/tools/h5diff/testh5diff.bat b/windows/tools/h5diff/testh5diff.bat
index 29be753..f745c42 100644
--- a/windows/tools/h5diff/testh5diff.bat
+++ b/windows/tools/h5diff/testh5diff.bat
@@ -58,6 +58,7 @@ set srcexclude1_1=h5diff_exclude1-1.h5
set srcexclude1_2=h5diff_exclude1-2.h5
set srcexclude2_1=h5diff_exclude2-1.h5
set srcexclude2_2=h5diff_exclude2-2.h5
+set src_comp_vl_strs=h5diff_comp_vl_strs.h5
set file1=%indir%\h5diff_basic1.h5
set file2=%indir%\h5diff_basic2.h5
@@ -89,6 +90,7 @@ set exclude1_1=%indir%\h5diff_exclude1-1.h5
set exclude1_2=%indir%\h5diff_exclude1-2.h5
set exclude2_1=%indir%\h5diff_exclude2-1.h5
set exclude2_2=%indir%\h5diff_exclude2-2.h5
+set comp_vl_strs=%indir%\h5diff_comp_vl_strs.h5
rem The tool name
@@ -853,6 +855,12 @@ rem ############################################################################
call :testing %h5diff% -v --exclude-path "/dset3" %srcexclude1_1% %srcexclude1_2% /group1
call :tooltest h5diff_484.txt -v --exclude-path "/dset3" %exclude1_1% %exclude1_2% /group1
+ rem ##############################################################################
+ rem # diff various multiple vlen and fixed strings in a compound type dataset
+ rem ##############################################################################
+ call :testing %h5diff% -v %src_comp_vl_strs% %src_comp_vl_strs%
+ call :tooltest h5diff_530.txt -v %comp_vl_strs% %comp_vl_strs%
+
rem #######################################################################
rem # END