[svn-r353] Changes since 19980414

----------------------

./html/Compression.html          [NEW]
./html/Datasets.html
./html/H5.format.html
./html/H5.user.html
        Documented compression.  A couple of the H5P functions aren't
        quite implemented yet but they're coming soon...

./src/H5Dprivate.h
./src/H5E.c
./src/H5Epublic.h
./src/H5Farray.c
./src/H5Fistore.c
./src/H5Fprivate.h
./src/H5MF.c
./src/H5MFprivate.h
./src/H5O.c
./src/H5Ocomp.c         [NEW]
./src/H5Oprivate.h
./src/H5P.c
./src/H5Ppublic.h
./src/H5Sprivate.h
./src/H5Ssimp.c
./src/H5Z.c             [NEW]
./src/H5Zprivate.h      [NEW]
./src/H5Zpublic.h       [NEW]
./src/Makefile.in
./src/hdf5.h
./test/dsets.c
./test/istore.c
        Compression is now mostly working.  Don't try to open a
        compressed dataset though because the compression message
        won't be read.

./html/Datatypes.html
./html/H5.api.html
./src/H5.c
./src/H5private.h
./src/H5D.c
./src/H5T.c
./src/H5Tconv.c
./src/H5Tpkg.h
./src/H5Tprivate.h
./src/H5Tpublic.h
        Added timing support.  When compiled with H5T_DEBUG defined
        the library will print conversion bandwidths when the library
        closes.  The H5Tregister functions take a string as the first
        argument so the statistics output is meaningful.

./MANIFEST
        Added new files.

./configure.in
./src/H5config.h.in
        Check for getrusage().  Check for compress2() in libz.a and
        the zlib.h header file.  Added `z' to the debug list.

./src/H5B.c
./src/H5Bprivate.h
./src/H5Gnode.c
./src/debug.c
        Cleaned up some indentation and added support to print istore
        B-trees.  From the debugger, give the B-tree address and the
        dimensionality from the layout message of the object header.

./src/h5ls.c
        The oid is printed as  w:x:y:z where w and x are the file ID
        and y and z are the OID within the file.  You can give z or
        y*2^32+z as an argument to the debugger to print the object
        header for the object.

./src/H5AC.c
        Cleaned up statistics and made them match those reported by
        H5T and H5Z.

./src/H5MM.c
./src/H5MMprivate.h
./src/H5Fistore.c
        Finally got rid of a couple of long-standing const cast
        warnings.

3 files changed, 179 insertions, 22 deletions

diff --git a/test/.distdep b/test/.distdep
index cbe325d..e7c7b05 100644
--- a/test/.distdep
+++ b/test/.distdep
@@ -3,9 +3,7 @@ testhdf5.o: \
    testhdf5.h \
    ../src/H5private.h \
    ../src/H5public.h \
-   ../src/H5config.h \
-   ../src/H5Eprivate.h \
-   ../src/H5Epublic.h
+   ../src/H5config.h
 tfile.o: \
    tfile.c \
    testhdf5.h \
@@ -19,7 +17,8 @@ tfile.o: \
    ../src/H5Bpublic.h \
    ../src/H5Fprivate.h \
    ../src/H5Fpublic.h \
-   ../src/H5Pprivate.h
+   ../src/H5Pprivate.h \
+   ../src/H5Ppublic.h
 theap.o: \
    theap.c \
    testhdf5.h \
@@ -36,7 +35,8 @@ theap.o: \
    ../src/H5Fpublic.h \
    ../src/H5Pprivate.h \
    ../src/H5Ppublic.h \
-   ../src/H5Dpublic.h
+   ../src/H5Dpublic.h \
+   ../src/H5Zpublic.h
 tmeta.o: \
    tmeta.c \
    testhdf5.h \
@@ -44,7 +44,8 @@ tmeta.o: \
    ../src/H5public.h \
    ../src/H5config.h \
    ../src/H5Eprivate.h \
-   ../src/H5Epublic.h
+   ../src/H5Epublic.h \
+   ../src/H5Ipublic.h
 tohdr.o: \
    tohdr.c \
    testhdf5.h \
@@ -62,6 +63,7 @@ tohdr.o: \
    ../src/H5Pprivate.h \
    ../src/H5Ppublic.h \
    ../src/H5Dpublic.h \
+   ../src/H5Zpublic.h \
    ../src/H5Gprivate.h \
    ../src/H5Gpublic.h \
    ../src/H5Bprivate.h \
@@ -91,6 +93,7 @@ tstab.o: \
    ../src/H5Pprivate.h \
    ../src/H5Ppublic.h \
    ../src/H5Dpublic.h \
+   ../src/H5Zpublic.h \
    ../src/H5Gprivate.h \
    ../src/H5Gpublic.h \
    ../src/H5Bprivate.h \
@@ -125,7 +128,11 @@ th5s.o: \
    ../src/H5HGprivate.h \
    ../src/H5HGpublic.h \
    ../src/H5Tprivate.h \
-   ../src/H5Tpublic.h
+   ../src/H5Tpublic.h \
+   ../src/H5Zprivate.h \
+   ../src/H5Zpublic.h \
+   ../src/H5Pprivate.h \
+   ../src/H5Ppublic.h
 dtypes.o: \
    dtypes.c \
    ../src/hdf5.h \
@@ -144,6 +151,7 @@ dtypes.o: \
    ../src/H5MMpublic.h \
    ../src/H5Opublic.h \
    ../src/H5Ppublic.h \
+   ../src/H5Zpublic.h \
    ../src/H5Spublic.h \
    ../src/H5Tpublic.h \
    ../src/H5Iprivate.h \
@@ -167,6 +175,7 @@ istore.o: \
    ../src/H5Ppublic.h \
    ../src/H5Dpublic.h \
    ../src/H5Fpublic.h \
+   ../src/H5Zpublic.h \
    ../src/H5Fprivate.h \
    ../src/H5Gprivate.h \
    ../src/H5Gpublic.h \
@@ -180,8 +189,7 @@ istore.o: \
    ../src/H5HGpublic.h \
    ../src/H5Tprivate.h \
    ../src/H5Tpublic.h \
-   ../src/H5Sprivate.h \
-   ../src/H5Spublic.h
+   ../src/H5Sprivate.h
 dsets.o: \
    dsets.c \
    ../src/hdf5.h \
@@ -200,6 +208,7 @@ dsets.o: \
    ../src/H5MMpublic.h \
    ../src/H5Opublic.h \
    ../src/H5Ppublic.h \
+   ../src/H5Zpublic.h \
    ../src/H5Spublic.h \
    ../src/H5Tpublic.h
 cmpd_dset.o: \
@@ -220,7 +229,9 @@ cmpd_dset.o: \
    ../src/H5MMpublic.h \
    ../src/H5Opublic.h \
    ../src/H5Ppublic.h \
-   ../src/H5Spublic.h
+   ../src/H5Zpublic.h \
+   ../src/H5Spublic.h \
+   ../src/H5Tpublic.h
 extend.o: \
    extend.c \
    ../src/hdf5.h \
@@ -239,7 +250,7 @@ extend.o: \
    ../src/H5MMpublic.h \
    ../src/H5Opublic.h \
    ../src/H5Ppublic.h \
-   ../src/H5Spublic.h
+   ../src/H5Zpublic.h
 external.o: \
    external.c \
    ../src/hdf5.h \
@@ -258,6 +269,7 @@ external.o: \
    ../src/H5MMpublic.h \
    ../src/H5Opublic.h \
    ../src/H5Ppublic.h \
+   ../src/H5Zpublic.h \
    ../src/H5Spublic.h \
    ../src/H5Tpublic.h
 iopipe.o: \
@@ -278,6 +290,7 @@ iopipe.o: \
    ../src/H5MMpublic.h \
    ../src/H5Opublic.h \
    ../src/H5Ppublic.h \
+   ../src/H5Zpublic.h \
    ../src/H5Spublic.h \
    ../src/H5Tpublic.h
 gheap.o: \
@@ -295,7 +308,8 @@ gheap.o: \
    ../src/H5Bprivate.h \
    ../src/H5Bpublic.h \
    ../src/H5HGprivate.h \
-   ../src/H5HGpublic.h
+   ../src/H5HGpublic.h \
+   ../src/H5Pprivate.h
 shtype.o: \
    shtype.c \
    ../src/hdf5.h \
@@ -314,7 +328,7 @@ shtype.o: \
    ../src/H5MMpublic.h \
    ../src/H5Opublic.h \
    ../src/H5Ppublic.h \
-   ../src/H5Spublic.h
+   ../src/H5Zpublic.h
 big.o: \
    big.c \
    ../src/hdf5.h \
@@ -333,8 +347,10 @@ big.o: \
    ../src/H5MMpublic.h \
    ../src/H5Opublic.h \
    ../src/H5Ppublic.h \
+   ../src/H5Zpublic.h \
    ../src/H5Spublic.h \
-   ../src/H5Tpublic.h
+   ../src/H5Tpublic.h \
+   ../src/H5private.h
 links.o: \
    links.c \
    ../src/hdf5.h \
diff --git a/test/dsets.c b/test/dsets.c
index bf4b75f..fab1f75 100644
--- a/test/dsets.c
+++ b/test/dsets.c
@@ -35,6 +35,7 @@
 #define DSET_CHUNKED_NAME	"chunked"
 #define DSET_SIMPLE_IO_NAME	"simple_io"
 #define DSET_TCONV_NAME		"tconv"
+#define DSET_COMPRESS_NAME	"compressed"
 
 
 /*-------------------------------------------------------------------------
@@ -89,6 +90,7 @@ test_create(hid_t file)
     void	*client_data = NULL;
 
     printf("%-70s", "Testing create/open/close");
+    fflush (stdout);
 
     /* Create the data space */
     dims[0] = 256;
@@ -202,6 +204,7 @@ test_simple_io(hid_t file)
     void		*tconv_buf = NULL;
 
     printf("%-70s", "Testing simple I/O");
+    fflush (stdout);
 
     /* Initialize the dataset */
     for (i = n = 0; i < 100; i++) {
@@ -290,7 +293,8 @@ test_tconv(hid_t file)
     assert (in);
 
     printf("%-70s", "Testing data type conversion");
-
+    fflush (stdout);
+    
     /* Initialize the dataset */
     for (i = 0; i < 1000000; i++) {
 	out[i*4+0] = 0x11;
@@ -346,6 +350,132 @@ test_tconv(hid_t file)
     puts(" PASSED");
     return 0;
 }
+
+
+/*-------------------------------------------------------------------------
+ * Function:	test_compression
+ *
+ * Purpose:	Tests dataset compression.
+ *
+ * Return:	Success:	0
+ *
+ *		Failure:	-1
+ *
+ * Programmer:	Robb Matzke
+ *              Wednesday, April 15, 1998
+ *
+ * Modifications:
+ *
+ *-------------------------------------------------------------------------
+ */
+static herr_t
+test_compression(hid_t file)
+{
+    hid_t		dataset, space, xfer, dc;
+    herr_t		status;
+    int			points[100][200], check[100][200];
+    int			i, j, n;
+    hsize_t		dims[2], chunk_size[2];
+    void		*tconv_buf = NULL;
+
+    printf("%-70s", "Testing compression");
+    fflush (stdout);
+    
+    /* Initialize the dataset */
+    for (i = n = 0; i < 100; i++) {
+	for (j = 0; j < 100; j++) {
+	    points[i][j] = n++;
+	}
+    }
+
+    /* Create the data space */
+    dims[0] = 100;
+    dims[1] = 200;
+    space = H5Screate_simple(2, dims, NULL);
+    assert(space>=0);
+
+    /* Create a small conversion buffer to test strip mining */
+    tconv_buf = malloc (1000);
+    xfer = H5Pcreate (H5P_DATASET_XFER);
+    assert (xfer>=0);
+    status = H5Pset_buffer (xfer, 1000, tconv_buf, NULL);
+    assert (status>=0);
+
+    /* Use chunked storage with compression */
+    dc = H5Pcreate (H5P_DATASET_CREATE);
+    chunk_size[0] = 2;
+    chunk_size[1] = 25;
+    H5Pset_chunk (dc, 2, chunk_size);
+    H5Pset_deflate (dc, 6);
+
+    /* Create the dataset */
+    dataset = H5Dcreate(file, DSET_COMPRESS_NAME, H5T_NATIVE_INT, space, dc);
+    assert(dataset >= 0);
+
+    /* Write the data to the dataset */
+    status = H5Dwrite(dataset, H5T_NATIVE_INT, H5S_ALL, H5S_ALL,
+		      xfer, points);
+    if (status<0) goto error;
+
+    /* Read the dataset back */
+    status = H5Dread(dataset, H5T_NATIVE_INT, H5S_ALL, H5S_ALL,
+		     xfer, check);
+    if (status<0) goto error;
+
+    /* Check that the values read are the same as the values written */
+    for (i = 0; i < 100; i++) {
+	for (j = 0; j < 200; j++) {
+	    if (points[i][j] != check[i][j]) {
+		puts("*FAILED*");
+		printf("   Read different values than written.\n");
+		printf("   At index %d,%d\n", i, j);
+		goto error;
+	    }
+	}
+    }
+
+    /*
+     * Write some random data to the dataset, hopefully causing chunks to be
+     * reallocated as they grow.
+     */
+    for (i=0; i<100; i++) {
+	for (j=0; j<100; j++) {
+	    points[i][j] = rand ();
+	}
+    }
+    status = H5Dwrite (dataset, H5T_NATIVE_INT, H5S_ALL, H5S_ALL,
+		       xfer, points);
+    if (status<0) goto error;
+
+
+    /* Read the dataset back and check it */
+    status = H5Dread(dataset, H5T_NATIVE_INT, H5S_ALL, H5S_ALL,
+		     xfer, check);
+    if (status<0) goto error;
+
+    /* Check that the values read are the same as the values written */
+    for (i = 0; i < 100; i++) {
+	for (j = 0; j < 200; j++) {
+	    if (points[i][j] != check[i][j]) {
+		puts("*FAILED*");
+		printf("   Read different values than written.\n");
+		printf("   At index %d,%d\n", i, j);
+		goto error;
+	    }
+	}
+    }
+
+    
+    
+
+    H5Dclose(dataset);
+
+    puts(" PASSED");
+    return 0;
+
+  error:
+    return -1;
+}
 
 /*-------------------------------------------------------------------------
  * Function:	main
@@ -366,7 +496,7 @@ test_tconv(hid_t file)
 int
 main(void)
 {
-    hid_t		    file;
+    hid_t		    file, grp;
     herr_t		    status;
     int			    nerrors = 0;
 
@@ -377,9 +507,15 @@ main(void)
     H5Eset_auto (display_error_cb, NULL);
 
     unlink("dataset.h5");
-    file = H5Fcreate("dataset.h5", H5F_ACC_TRUNC, H5P_DEFAULT, H5P_DEFAULT);
+    file = H5Fcreate("dataset.h5", H5F_ACC_TRUNC|H5F_ACC_DEBUG,
+		     H5P_DEFAULT, H5P_DEFAULT);
     assert(file >= 0);
 
+    /* Cause the library to emit initial messages */
+    grp = H5Gcreate (file, "emit diagnostics", 0);
+    H5Gclose (grp);
+    
+
     status = test_create(file);
     nerrors += status < 0 ? 1 : 0;
 
@@ -388,6 +524,9 @@ main(void)
 
     status = test_tconv(file);
     nerrors += status < 0 ? 1 : 0;
+    
+    status = test_compression(file);
+    nerrors += status < 0 ? 1 : 0;
 
     status = H5Fclose(file);
 
diff --git a/test/istore.c b/test/istore.c
index fa90b55..9dc4de2 100644
--- a/test/istore.c
+++ b/test/istore.c
@@ -316,7 +316,8 @@ test_extend(H5F_t *f, const char *prefix,
 	memset(buf, (signed)(128+ctr), (size_t)nelmts);
 
 	/* Write to disk */
-	if (H5F_arr_write(f, &layout, NULL, size, size, zero, offset, buf)<0) {
+	if (H5F_arr_write(f, &layout, NULL, NULL, size, size, zero, offset,
+			  buf)<0) {
 	    puts("*FAILED*");
 	    if (!isatty(1)) {
 		AT();
@@ -326,7 +327,7 @@ test_extend(H5F_t *f, const char *prefix,
 	}
 	/* Read from disk */
 	memset(check, 0xff, (size_t)nelmts);
-	if (H5F_arr_read(f, &layout, NULL, size, size, zero, offset,
+	if (H5F_arr_read(f, &layout, NULL, NULL, size, size, zero, offset,
 			 check)<0) {
 	    puts("*FAILED*");
 	    if (!isatty(1)) {
@@ -362,8 +363,8 @@ test_extend(H5F_t *f, const char *prefix,
 
     /* Now read the entire array back out and check it */
     memset(buf, 0xff, nx * ny * nz);
-    if (H5F_arr_read(f, &layout, NULL, whole_size, whole_size, zero, zero,
-		     buf)<0) {
+    if (H5F_arr_read(f, &layout, NULL, NULL, whole_size, whole_size, zero,
+		     zero, buf)<0) {
 	puts("*FAILED*");
 	if (!isatty(1)) {
 	    AT();
@@ -486,7 +487,8 @@ test_sparse(H5F_t *f, const char *prefix, size_t nblocks,
 	memset(buf, (signed)(128+ctr), nx * ny * nz);
 
 	/* write to disk */
-	if (H5F_arr_write(f, &layout, NULL, size, size, zero, offset, buf)<0) {
+	if (H5F_arr_write(f, &layout, NULL, NULL, size, size, zero, offset,
+			  buf)<0) {
 	    puts("*FAILED*");
 	    if (!isatty(1)) {
 		AT();