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[svn-r353] Changes since 19980414

Browse Source 
----------------------

./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❌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.
This commit is contained in:
Robb Matzke 1998-04-17 16:29:43 -05:00
parent b59ab36893
commit 011457075e
46 changed files with 2900 additions and 901 deletions
Show Stats Download Patch File Download Diff File Expand all files Collapse all files

5
MANIFEST
View File

@ -42,6 +42,7 @@
./html/Big.html
./html/CodeReview.html
./html/Coding.html
./html/Compression.html
./html/Datasets.html
./html/Dataspaces.html
./html/Datatypes.html
@ -152,6 +153,7 @@
./src/H5MMprivate.h
./src/H5MMpublic.h
./src/H5O.c
./src/H5Ocomp.c
./src/H5Ocont.c
./src/H5Odtype.c
./src/H5Oefl.c
@ -177,6 +179,9 @@
./src/H5Tpublic.h
./src/H5V.c
./src/H5Vprivate.h
./src/H5Z.c
./src/H5Zprivate.h
./src/H5Zpublic.h
./src/H5config.h.in
./src/H5detect.c
./src/H5private.h

214
configure vendored
View File

@ -1036,10 +1036,56 @@ EOF
else
echo "$ac_t""no" 1>&6
fi
echo $ac_n "checking for compress2 in -lz""... $ac_c" 1>&6
echo "configure:1041: checking for compress2 in -lz" >&5
ac_lib_var=`echo z'_'compress2 | sed 'y%./+-%__p_%'`
if eval "test \"`echo '$''{'ac_cv_lib_$ac_lib_var'+set}'`\" = set"; then
echo $ac_n "(cached) $ac_c" 1>&6
else
ac_save_LIBS="$LIBS"
LIBS="-lz $LIBS"
cat > conftest.$ac_ext <<EOF
#line 1049 "configure"
#include "confdefs.h"
/* Override any gcc2 internal prototype to avoid an error. */
/* We use char because int might match the return type of a gcc2
builtin and then its argument prototype would still apply. */
char compress2();
int main() {
compress2()
; return 0; }
EOF
if { (eval echo configure:1060: \"$ac_link\") 1>&5; (eval $ac_link) 2>&5; } && test -s conftest; then
rm -rf conftest*
eval "ac_cv_lib_$ac_lib_var=yes"
else
echo "configure: failed program was:" >&5
cat conftest.$ac_ext >&5
rm -rf conftest*
eval "ac_cv_lib_$ac_lib_var=no"
fi
rm -f conftest*
LIBS="$ac_save_LIBS"
fi
if eval "test \"`echo '$ac_cv_lib_'$ac_lib_var`\" = yes"; then
echo "$ac_t""yes" 1>&6
ac_tr_lib=HAVE_LIB`echo z | sed -e 's/[^a-zA-Z0-9_]/_/g' \
-e 'y/abcdefghijklmnopqrstuvwxyz/ABCDEFGHIJKLMNOPQRSTUVWXYZ/'`
cat >> confdefs.h <<EOF
#define $ac_tr_lib 1
EOF
LIBS="-lz $LIBS"
else
echo "$ac_t""no" 1>&6
fi
echo $ac_n "checking how to run the C preprocessor""... $ac_c" 1>&6
echo "configure:1043: checking how to run the C preprocessor" >&5
echo "configure:1089: checking how to run the C preprocessor" >&5
# On Suns, sometimes $CPP names a directory.
if test -n "$CPP" && test -d "$CPP"; then
CPP=
@ -1054,13 +1100,13 @@ else
# On the NeXT, cc -E runs the code through the compiler's parser,
# not just through cpp.
cat > conftest.$ac_ext <<EOF
#line 1058 "configure"
#line 1104 "configure"
#include "confdefs.h"
#include <assert.h>
Syntax Error
EOF
ac_try="$ac_cpp conftest.$ac_ext >/dev/null 2>conftest.out"
{ (eval echo configure:1064: \"$ac_try\") 1>&5; (eval $ac_try) 2>&5; }
{ (eval echo configure:1110: \"$ac_try\") 1>&5; (eval $ac_try) 2>&5; }
ac_err=`grep -v '^ *+' conftest.out`
if test -z "$ac_err"; then
:
@ -1071,13 +1117,13 @@ else
rm -rf conftest*
CPP="${CC-cc} -E -traditional-cpp"
cat > conftest.$ac_ext <<EOF
#line 1075 "configure"
#line 1121 "configure"
#include "confdefs.h"
#include <assert.h>
Syntax Error
EOF
ac_try="$ac_cpp conftest.$ac_ext >/dev/null 2>conftest.out"
{ (eval echo configure:1081: \"$ac_try\") 1>&5; (eval $ac_try) 2>&5; }
{ (eval echo configure:1127: \"$ac_try\") 1>&5; (eval $ac_try) 2>&5; }
ac_err=`grep -v '^ *+' conftest.out`
if test -z "$ac_err"; then
:
@ -1100,12 +1146,12 @@ fi
echo "$ac_t""$CPP" 1>&6
echo $ac_n "checking for ANSI C header files""... $ac_c" 1>&6
echo "configure:1104: checking for ANSI C header files" >&5
echo "configure:1150: checking for ANSI C header files" >&5
if eval "test \"`echo '$''{'ac_cv_header_stdc'+set}'`\" = set"; then
echo $ac_n "(cached) $ac_c" 1>&6
else
cat > conftest.$ac_ext <<EOF
#line 1109 "configure"
#line 1155 "configure"
#include "confdefs.h"
#include <stdlib.h>
#include <stdarg.h>
@ -1113,7 +1159,7 @@ else
#include <float.h>
EOF
ac_try="$ac_cpp conftest.$ac_ext >/dev/null 2>conftest.out"
{ (eval echo configure:1117: \"$ac_try\") 1>&5; (eval $ac_try) 2>&5; }
{ (eval echo configure:1163: \"$ac_try\") 1>&5; (eval $ac_try) 2>&5; }
ac_err=`grep -v '^ *+' conftest.out`
if test -z "$ac_err"; then
rm -rf conftest*
@ -1130,7 +1176,7 @@ rm -f conftest*
if test $ac_cv_header_stdc = yes; then
# SunOS 4.x string.h does not declare mem*, contrary to ANSI.
cat > conftest.$ac_ext <<EOF
#line 1134 "configure"
#line 1180 "configure"
#include "confdefs.h"
#include <string.h>
EOF
@ -1148,7 +1194,7 @@ fi
if test $ac_cv_header_stdc = yes; then
# ISC 2.0.2 stdlib.h does not declare free, contrary to ANSI.
cat > conftest.$ac_ext <<EOF
#line 1152 "configure"
#line 1198 "configure"
#include "confdefs.h"
#include <stdlib.h>
EOF
@ -1169,7 +1215,7 @@ if test "$cross_compiling" = yes; then
:
else
cat > conftest.$ac_ext <<EOF
#line 1173 "configure"
#line 1219 "configure"
#include "confdefs.h"
#include <ctype.h>
#define ISLOWER(c) ('a' <= (c) && (c) <= 'z')
@ -1180,7 +1226,7 @@ if (XOR (islower (i), ISLOWER (i)) || toupper (i) != TOUPPER (i)) exit(2);
exit (0); }
EOF
if { (eval echo configure:1184: \"$ac_link\") 1>&5; (eval $ac_link) 2>&5; } && test -s conftest && (./conftest; exit) 2>/dev/null
if { (eval echo configure:1230: \"$ac_link\") 1>&5; (eval $ac_link) 2>&5; } && test -s conftest && (./conftest; exit) 2>/dev/null
then
:
else
@ -1203,21 +1249,21 @@ EOF
fi
for ac_hdr in unistd.h
for ac_hdr in unistd.h zlib.h
do
ac_safe=`echo "$ac_hdr" | sed 'y%./+-%__p_%'`
echo $ac_n "checking for $ac_hdr""... $ac_c" 1>&6
echo "configure:1211: checking for $ac_hdr" >&5
echo "configure:1257: checking for $ac_hdr" >&5
if eval "test \"`echo '$''{'ac_cv_header_$ac_safe'+set}'`\" = set"; then
echo $ac_n "(cached) $ac_c" 1>&6
else
cat > conftest.$ac_ext <<EOF
#line 1216 "configure"
#line 1262 "configure"
#include "confdefs.h"
#include <$ac_hdr>
EOF
ac_try="$ac_cpp conftest.$ac_ext >/dev/null 2>conftest.out"
{ (eval echo configure:1221: \"$ac_try\") 1>&5; (eval $ac_try) 2>&5; }
{ (eval echo configure:1267: \"$ac_try\") 1>&5; (eval $ac_try) 2>&5; }
ac_err=`grep -v '^ *+' conftest.out`
if test -z "$ac_err"; then
rm -rf conftest*
@ -1246,12 +1292,12 @@ done
echo $ac_n "checking for off_t""... $ac_c" 1>&6
echo "configure:1250: checking for off_t" >&5
echo "configure:1296: checking for off_t" >&5
if eval "test \"`echo '$''{'ac_cv_type_off_t'+set}'`\" = set"; then
echo $ac_n "(cached) $ac_c" 1>&6
else
cat > conftest.$ac_ext <<EOF
#line 1255 "configure"
#line 1301 "configure"
#include "confdefs.h"
#include <sys/types.h>
#if STDC_HEADERS
@ -1279,12 +1325,12 @@ EOF
fi
echo $ac_n "checking for size_t""... $ac_c" 1>&6
echo "configure:1283: checking for size_t" >&5
echo "configure:1329: checking for size_t" >&5
if eval "test \"`echo '$''{'ac_cv_type_size_t'+set}'`\" = set"; then
echo $ac_n "(cached) $ac_c" 1>&6
else
cat > conftest.$ac_ext <<EOF
#line 1288 "configure"
#line 1334 "configure"
#include "confdefs.h"
#include <sys/types.h>
#if STDC_HEADERS
@ -1312,14 +1358,14 @@ EOF
fi
echo $ac_n "checking whether byte ordering is bigendian""... $ac_c" 1>&6
echo "configure:1316: checking whether byte ordering is bigendian" >&5
echo "configure:1362: checking whether byte ordering is bigendian" >&5
if eval "test \"`echo '$''{'ac_cv_c_bigendian'+set}'`\" = set"; then
echo $ac_n "(cached) $ac_c" 1>&6
else
ac_cv_c_bigendian=unknown
# See if sys/param.h defines the BYTE_ORDER macro.
cat > conftest.$ac_ext <<EOF
#line 1323 "configure"
#line 1369 "configure"
#include "confdefs.h"
#include <sys/types.h>
#include <sys/param.h>
@ -1330,11 +1376,11 @@ int main() {
#endif
; return 0; }
EOF
if { (eval echo configure:1334: \"$ac_compile\") 1>&5; (eval $ac_compile) 2>&5; }; then
if { (eval echo configure:1380: \"$ac_compile\") 1>&5; (eval $ac_compile) 2>&5; }; then
rm -rf conftest*
# It does; now see whether it defined to BIG_ENDIAN or not.
cat > conftest.$ac_ext <<EOF
#line 1338 "configure"
#line 1384 "configure"
#include "confdefs.h"
#include <sys/types.h>
#include <sys/param.h>
@ -1345,7 +1391,7 @@ int main() {
#endif
; return 0; }
EOF
if { (eval echo configure:1349: \"$ac_compile\") 1>&5; (eval $ac_compile) 2>&5; }; then
if { (eval echo configure:1395: \"$ac_compile\") 1>&5; (eval $ac_compile) 2>&5; }; then
rm -rf conftest*
ac_cv_c_bigendian=yes
else
@ -1365,7 +1411,7 @@ if test "$cross_compiling" = yes; then
{ echo "configure: error: can not run test program while cross compiling" 1>&2; exit 1; }
else
cat > conftest.$ac_ext <<EOF
#line 1369 "configure"
#line 1415 "configure"
#include "confdefs.h"
main () {
/* Are we little or big endian? From Harbison&Steele. */
@ -1378,7 +1424,7 @@ main () {
exit (u.c[sizeof (long) - 1] == 1);
}
EOF
if { (eval echo configure:1382: \"$ac_link\") 1>&5; (eval $ac_link) 2>&5; } && test -s conftest && (./conftest; exit) 2>/dev/null
if { (eval echo configure:1428: \"$ac_link\") 1>&5; (eval $ac_link) 2>&5; } && test -s conftest && (./conftest; exit) 2>/dev/null
then
ac_cv_c_bigendian=no
else
@ -1402,7 +1448,7 @@ EOF
fi
echo $ac_n "checking size of short""... $ac_c" 1>&6
echo "configure:1406: checking size of short" >&5
echo "configure:1452: checking size of short" >&5
if eval "test \"`echo '$''{'ac_cv_sizeof_short'+set}'`\" = set"; then
echo $ac_n "(cached) $ac_c" 1>&6
else
@ -1410,7 +1456,7 @@ else
ac_cv_sizeof_short=2
else
cat > conftest.$ac_ext <<EOF
#line 1414 "configure"
#line 1460 "configure"
#include "confdefs.h"
#include <stdio.h>
main()
@ -1421,7 +1467,7 @@ main()
exit(0);
}
EOF
if { (eval echo configure:1425: \"$ac_link\") 1>&5; (eval $ac_link) 2>&5; } && test -s conftest && (./conftest; exit) 2>/dev/null
if { (eval echo configure:1471: \"$ac_link\") 1>&5; (eval $ac_link) 2>&5; } && test -s conftest && (./conftest; exit) 2>/dev/null
then
ac_cv_sizeof_short=`cat conftestval`
else
@ -1441,7 +1487,7 @@ EOF
echo $ac_n "checking size of int""... $ac_c" 1>&6
echo "configure:1445: checking size of int" >&5
echo "configure:1491: checking size of int" >&5
if eval "test \"`echo '$''{'ac_cv_sizeof_int'+set}'`\" = set"; then
echo $ac_n "(cached) $ac_c" 1>&6
else
@ -1449,7 +1495,7 @@ else
ac_cv_sizeof_int=4
else
cat > conftest.$ac_ext <<EOF
#line 1453 "configure"
#line 1499 "configure"
#include "confdefs.h"
#include <stdio.h>
main()
@ -1460,7 +1506,7 @@ main()
exit(0);
}
EOF
if { (eval echo configure:1464: \"$ac_link\") 1>&5; (eval $ac_link) 2>&5; } && test -s conftest && (./conftest; exit) 2>/dev/null
if { (eval echo configure:1510: \"$ac_link\") 1>&5; (eval $ac_link) 2>&5; } && test -s conftest && (./conftest; exit) 2>/dev/null
then
ac_cv_sizeof_int=`cat conftestval`
else
@ -1480,7 +1526,7 @@ EOF
echo $ac_n "checking size of long""... $ac_c" 1>&6
echo "configure:1484: checking size of long" >&5
echo "configure:1530: checking size of long" >&5
if eval "test \"`echo '$''{'ac_cv_sizeof_long'+set}'`\" = set"; then
echo $ac_n "(cached) $ac_c" 1>&6
else
@ -1488,7 +1534,7 @@ else
ac_cv_sizeof_long=4
else
cat > conftest.$ac_ext <<EOF
#line 1492 "configure"
#line 1538 "configure"
#include "confdefs.h"
#include <stdio.h>
main()
@ -1499,7 +1545,7 @@ main()
exit(0);
}
EOF
if { (eval echo configure:1503: \"$ac_link\") 1>&5; (eval $ac_link) 2>&5; } && test -s conftest && (./conftest; exit) 2>/dev/null
if { (eval echo configure:1549: \"$ac_link\") 1>&5; (eval $ac_link) 2>&5; } && test -s conftest && (./conftest; exit) 2>/dev/null
then
ac_cv_sizeof_long=`cat conftestval`
else
@ -1519,7 +1565,7 @@ EOF
echo $ac_n "checking size of long long""... $ac_c" 1>&6
echo "configure:1523: checking size of long long" >&5
echo "configure:1569: checking size of long long" >&5
if eval "test \"`echo '$''{'ac_cv_sizeof_long_long'+set}'`\" = set"; then
echo $ac_n "(cached) $ac_c" 1>&6
else
@ -1527,7 +1573,7 @@ else
ac_cv_sizeof_long_long=8
else
cat > conftest.$ac_ext <<EOF
#line 1531 "configure"
#line 1577 "configure"
#include "confdefs.h"
#include <stdio.h>
main()
@ -1538,7 +1584,7 @@ main()
exit(0);
}
EOF
if { (eval echo configure:1542: \"$ac_link\") 1>&5; (eval $ac_link) 2>&5; } && test -s conftest && (./conftest; exit) 2>/dev/null
if { (eval echo configure:1588: \"$ac_link\") 1>&5; (eval $ac_link) 2>&5; } && test -s conftest && (./conftest; exit) 2>/dev/null
then
ac_cv_sizeof_long_long=`cat conftestval`
else
@ -1558,7 +1604,7 @@ EOF
echo $ac_n "checking size of float""... $ac_c" 1>&6
echo "configure:1562: checking size of float" >&5
echo "configure:1608: checking size of float" >&5
if eval "test \"`echo '$''{'ac_cv_sizeof_float'+set}'`\" = set"; then
echo $ac_n "(cached) $ac_c" 1>&6
else
@ -1566,7 +1612,7 @@ else
ac_cv_sizeof_float=4
else
cat > conftest.$ac_ext <<EOF
#line 1570 "configure"
#line 1616 "configure"
#include "confdefs.h"
#include <stdio.h>
main()
@ -1577,7 +1623,7 @@ main()
exit(0);
}
EOF
if { (eval echo configure:1581: \"$ac_link\") 1>&5; (eval $ac_link) 2>&5; } && test -s conftest && (./conftest; exit) 2>/dev/null
if { (eval echo configure:1627: \"$ac_link\") 1>&5; (eval $ac_link) 2>&5; } && test -s conftest && (./conftest; exit) 2>/dev/null
then
ac_cv_sizeof_float=`cat conftestval`
else
@ -1597,7 +1643,7 @@ EOF
echo $ac_n "checking size of double""... $ac_c" 1>&6
echo "configure:1601: checking size of double" >&5
echo "configure:1647: checking size of double" >&5
if eval "test \"`echo '$''{'ac_cv_sizeof_double'+set}'`\" = set"; then
echo $ac_n "(cached) $ac_c" 1>&6
else
@ -1605,7 +1651,7 @@ else
ac_cv_sizeof_double=8
else
cat > conftest.$ac_ext <<EOF
#line 1609 "configure"
#line 1655 "configure"
#include "confdefs.h"
#include <stdio.h>
main()
@ -1616,7 +1662,7 @@ main()
exit(0);
}
EOF
if { (eval echo configure:1620: \"$ac_link\") 1>&5; (eval $ac_link) 2>&5; } && test -s conftest && (./conftest; exit) 2>/dev/null
if { (eval echo configure:1666: \"$ac_link\") 1>&5; (eval $ac_link) 2>&5; } && test -s conftest && (./conftest; exit) 2>/dev/null
then
ac_cv_sizeof_double=`cat conftestval`
else
@ -1636,7 +1682,7 @@ EOF
echo $ac_n "checking size of size_t""... $ac_c" 1>&6
echo "configure:1640: checking size of size_t" >&5
echo "configure:1686: checking size of size_t" >&5
if eval "test \"`echo '$''{'ac_cv_sizeof_size_t'+set}'`\" = set"; then
echo $ac_n "(cached) $ac_c" 1>&6
else
@ -1644,7 +1690,7 @@ else
ac_cv_sizeof_size_t=4
else
cat > conftest.$ac_ext <<EOF
#line 1648 "configure"
#line 1694 "configure"
#include "confdefs.h"
#include <stdio.h>
main()
@ -1655,7 +1701,7 @@ main()
exit(0);
}
EOF
if { (eval echo configure:1659: \"$ac_link\") 1>&5; (eval $ac_link) 2>&5; } && test -s conftest && (./conftest; exit) 2>/dev/null
if { (eval echo configure:1705: \"$ac_link\") 1>&5; (eval $ac_link) 2>&5; } && test -s conftest && (./conftest; exit) 2>/dev/null
then
ac_cv_sizeof_size_t=`cat conftestval`
else
@ -1678,7 +1724,7 @@ cat >>confdefs.h <<\EOF
#include <sys/types.h> /*for off_t definition*/
EOF
echo $ac_n "checking size of off_t""... $ac_c" 1>&6
echo "configure:1682: checking size of off_t" >&5
echo "configure:1728: checking size of off_t" >&5
if eval "test \"`echo '$''{'ac_cv_sizeof_off_t'+set}'`\" = set"; then
echo $ac_n "(cached) $ac_c" 1>&6
else
@ -1686,7 +1732,7 @@ else
ac_cv_sizeof_off_t=4
else
cat > conftest.$ac_ext <<EOF
#line 1690 "configure"
#line 1736 "configure"
#include "confdefs.h"
#include <stdio.h>
main()
@ -1697,7 +1743,7 @@ main()
exit(0);
}
EOF
if { (eval echo configure:1701: \"$ac_link\") 1>&5; (eval $ac_link) 2>&5; } && test -s conftest && (./conftest; exit) 2>/dev/null
if { (eval echo configure:1747: \"$ac_link\") 1>&5; (eval $ac_link) 2>&5; } && test -s conftest && (./conftest; exit) 2>/dev/null
then
ac_cv_sizeof_off_t=`cat conftestval`
else
@ -1724,7 +1770,7 @@ if test "${enable_hsizet+set}" = set; then
fi
echo $ac_n "checking for sizeof hsize_t and hssize_t""... $ac_c" 1>&6
echo "configure:1728: checking for sizeof hsize_t and hssize_t" >&5
echo "configure:1774: checking for sizeof hsize_t and hssize_t" >&5
case $HSIZET in
no|small)
echo "$ac_t""small" 1>&6
@ -1739,15 +1785,15 @@ EOF
esac
for ac_func in getpwuid gethostname system
for ac_func in getpwuid gethostname system getrusage
do
echo $ac_n "checking for $ac_func""... $ac_c" 1>&6
echo "configure:1746: checking for $ac_func" >&5
echo "configure:1792: checking for $ac_func" >&5
if eval "test \"`echo '$''{'ac_cv_func_$ac_func'+set}'`\" = set"; then
echo $ac_n "(cached) $ac_c" 1>&6
else
cat > conftest.$ac_ext <<EOF
#line 1751 "configure"
#line 1797 "configure"
#include "confdefs.h"
/* System header to define __stub macros and hopefully few prototypes,
which can conflict with char $ac_func(); below. */
@ -1770,7 +1816,7 @@ $ac_func();
; return 0; }
EOF
if { (eval echo configure:1774: \"$ac_link\") 1>&5; (eval $ac_link) 2>&5; } && test -s conftest; then
if { (eval echo configure:1820: \"$ac_link\") 1>&5; (eval $ac_link) 2>&5; } && test -s conftest; then
rm -rf conftest*
eval "ac_cv_func_$ac_func=yes"
else
@ -1796,24 +1842,24 @@ done
cat > conftest.$ac_ext <<EOF
#line 1800 "configure"
#line 1846 "configure"
#include "confdefs.h"
#include<sys/types.h>
int main() {
off64_t n = 0;
; return 0; }
EOF
if { (eval echo configure:1807: \"$ac_compile\") 1>&5; (eval $ac_compile) 2>&5; }; then
if { (eval echo configure:1853: \"$ac_compile\") 1>&5; (eval $ac_compile) 2>&5; }; then
rm -rf conftest*
for ac_func in lseek64 fseek64
do
echo $ac_n "checking for $ac_func""... $ac_c" 1>&6
echo "configure:1812: checking for $ac_func" >&5
echo "configure:1858: checking for $ac_func" >&5
if eval "test \"`echo '$''{'ac_cv_func_$ac_func'+set}'`\" = set"; then
echo $ac_n "(cached) $ac_c" 1>&6
else
cat > conftest.$ac_ext <<EOF
#line 1817 "configure"
#line 1863 "configure"
#include "confdefs.h"
/* System header to define __stub macros and hopefully few prototypes,
which can conflict with char $ac_func(); below. */
@ -1836,7 +1882,7 @@ $ac_func();
; return 0; }
EOF
if { (eval echo configure:1840: \"$ac_link\") 1>&5; (eval $ac_link) 2>&5; } && test -s conftest; then
if { (eval echo configure:1886: \"$ac_link\") 1>&5; (eval $ac_link) 2>&5; } && test -s conftest; then
rm -rf conftest*
eval "ac_cv_func_$ac_func=yes"
else
@ -1871,12 +1917,12 @@ rm -f conftest*
echo $ac_n "checking for working const""... $ac_c" 1>&6
echo "configure:1875: checking for working const" >&5
echo "configure:1921: checking for working const" >&5
if eval "test \"`echo '$''{'ac_cv_c_const'+set}'`\" = set"; then
echo $ac_n "(cached) $ac_c" 1>&6
else
cat > conftest.$ac_ext <<EOF
#line 1880 "configure"
#line 1926 "configure"
#include "confdefs.h"
int main() {
@ -1925,7 +1971,7 @@ ccp = (char const *const *) p;
; return 0; }
EOF
if { (eval echo configure:1929: \"$ac_compile\") 1>&5; (eval $ac_compile) 2>&5; }; then
if { (eval echo configure:1975: \"$ac_compile\") 1>&5; (eval $ac_compile) 2>&5; }; then
rm -rf conftest*
ac_cv_c_const=yes
else
@ -1946,21 +1992,21 @@ EOF
fi
echo $ac_n "checking for inline""... $ac_c" 1>&6
echo "configure:1950: checking for inline" >&5
echo "configure:1996: checking for inline" >&5
if eval "test \"`echo '$''{'ac_cv_c_inline'+set}'`\" = set"; then
echo $ac_n "(cached) $ac_c" 1>&6
else
ac_cv_c_inline=no
for ac_kw in inline __inline__ __inline; do
cat > conftest.$ac_ext <<EOF
#line 1957 "configure"
#line 2003 "configure"
#include "confdefs.h"
int main() {
} $ac_kw foo() {
; return 0; }
EOF
if { (eval echo configure:1964: \"$ac_compile\") 1>&5; (eval $ac_compile) 2>&5; }; then
if { (eval echo configure:2010: \"$ac_compile\") 1>&5; (eval $ac_compile) 2>&5; }; then
rm -rf conftest*
ac_cv_c_inline=$ac_kw; break
else
@ -1987,16 +2033,16 @@ esac
echo $ac_n "checking for __attribute__ extension""... $ac_c" 1>&6
echo "configure:1991: checking for __attribute__ extension" >&5
echo "configure:2037: checking for __attribute__ extension" >&5
cat > conftest.$ac_ext <<EOF
#line 1993 "configure"
#line 2039 "configure"
#include "confdefs.h"
int main() {
int __attribute__((unused)) f(void){return 1;}
; return 0; }
EOF
if { (eval echo configure:2000: \"$ac_compile\") 1>&5; (eval $ac_compile) 2>&5; }; then
if { (eval echo configure:2046: \"$ac_compile\") 1>&5; (eval $ac_compile) 2>&5; }; then
rm -rf conftest*
cat >> confdefs.h <<\EOF
#define HAVE_ATTRIBUTE 1
@ -2012,16 +2058,16 @@ fi
rm -f conftest*
echo $ac_n "checking for __FUNCTION__ extension""... $ac_c" 1>&6
echo "configure:2016: checking for __FUNCTION__ extension" >&5
echo "configure:2062: checking for __FUNCTION__ extension" >&5
cat > conftest.$ac_ext <<EOF
#line 2018 "configure"
#line 2064 "configure"
#include "confdefs.h"
int main() {
int f(void){return __FUNCTION__;}
; return 0; }
EOF
if { (eval echo configure:2025: \"$ac_compile\") 1>&5; (eval $ac_compile) 2>&5; }; then
if { (eval echo configure:2071: \"$ac_compile\") 1>&5; (eval $ac_compile) 2>&5; }; then
rm -rf conftest*
cat >> confdefs.h <<\EOF
#define HAVE_FUNCTION 1
@ -2037,7 +2083,7 @@ fi
rm -f conftest*
echo $ac_n "checking for debug flags""... $ac_c" 1>&6
echo "configure:2041: checking for debug flags" >&5;
echo "configure:2087: checking for debug flags" >&5;
# Check whether --enable-debug or --disable-debug was given.
if test "${enable_debug+set}" = set; then
enableval="$enable_debug"
@ -2045,9 +2091,9 @@ if test "${enable_debug+set}" = set; then
fi
all_packages="ac,b,d,e,f,g,hg,hl,i,mf,mm,o,p,s,t,v"
all_packages="ac,b,d,e,f,g,hg,hl,i,mf,mm,o,p,s,t,v,z"
if test X = "X$DEBUG_PKG" -o Xyes = "X$DEBUG_PKG"; then
DEBUG_PKG=ac,b,d,e,f,g,hg,i,mm,p,s,t,v
DEBUG_PKG=ac,b,d,e,f,g,hg,i,mm,p,s,t,v,z
CPPFLAGS="$CPPFLAGS -UNDEBUG"
echo "$ac_t""default ($DEBUG_PKG)" 1>&6
elif test Xall = "X$DEBUG_PKG"; then
@ -2075,7 +2121,7 @@ if test "${enable_parallel+set}" = set; then
fi
echo $ac_n "checking for parallel support""... $ac_c" 1>&6
echo "configure:2079: checking for parallel support" >&5;
echo "configure:2125: checking for parallel support" >&5;
@ -2102,7 +2148,7 @@ EOF
CFLAGS="$CFLAGS $MPI_LIB"
RUNTEST="$RUNTEST"
echo $ac_n "checking for main in -lmpi""... $ac_c" 1>&6
echo "configure:2106: checking for main in -lmpi" >&5
echo "configure:2152: checking for main in -lmpi" >&5
ac_lib_var=`echo mpi'_'main | sed 'y%./+-%__p_%'`
if eval "test \"`echo '$''{'ac_cv_lib_$ac_lib_var'+set}'`\" = set"; then
echo $ac_n "(cached) $ac_c" 1>&6
@ -2110,14 +2156,14 @@ else
ac_save_LIBS="$LIBS"
LIBS="-lmpi $LIBS"
cat > conftest.$ac_ext <<EOF
#line 2114 "configure"
#line 2160 "configure"
#include "confdefs.h"
int main() {
main()
; return 0; }
EOF
if { (eval echo configure:2121: \"$ac_link\") 1>&5; (eval $ac_link) 2>&5; } && test -s conftest; then
if { (eval echo configure:2167: \"$ac_link\") 1>&5; (eval $ac_link) 2>&5; } && test -s conftest; then
rm -rf conftest*
eval "ac_cv_lib_$ac_lib_var=yes"
else
@ -2144,7 +2190,7 @@ else
echo "$ac_t""no" 1>&6
fi
echo $ac_n "checking for main in -lmpio""... $ac_c" 1>&6
echo "configure:2148: checking for main in -lmpio" >&5
echo "configure:2194: checking for main in -lmpio" >&5
ac_lib_var=`echo mpio'_'main | sed 'y%./+-%__p_%'`
if eval "test \"`echo '$''{'ac_cv_lib_$ac_lib_var'+set}'`\" = set"; then
echo $ac_n "(cached) $ac_c" 1>&6
@ -2152,14 +2198,14 @@ else
ac_save_LIBS="$LIBS"
LIBS="-lmpio $LIBS"
cat > conftest.$ac_ext <<EOF
#line 2156 "configure"
#line 2202 "configure"
#include "confdefs.h"
int main() {
main()
; return 0; }
EOF
if { (eval echo configure:2163: \"$ac_link\") 1>&5; (eval $ac_link) 2>&5; } && test -s conftest; then
if { (eval echo configure:2209: \"$ac_link\") 1>&5; (eval $ac_link) 2>&5; } && test -s conftest; then
rm -rf conftest*
eval "ac_cv_lib_$ac_lib_var=yes"
else

10
configure.in
View File

@ -126,13 +126,13 @@ dnl ----------------------------------------------------------------------
dnl Check for libraries. (none required yet)
dnl
AC_CHECK_LIB(coug, main) dnl ...for ASCI/Red
AC_CHECK_LIB(z, compress2)
dnl ----------------------------------------------------------------------
dnl Check for header files.
dnl
AC_HEADER_STDC
AC_CHECK_HEADERS(unistd.h)
AC_CHECK_HEADERS(unistd.h zlib.h)
dnl ----------------------------------------------------------------------
@ -176,7 +176,7 @@ esac
dnl ----------------------------------------------------------------------
dnl Check for functions.
dnl
AC_CHECK_FUNCS(getpwuid gethostname system)
AC_CHECK_FUNCS(getpwuid gethostname system getrusage)
AC_TRY_COMPILE([#include<sys/types.h>],
[off64_t n = 0;],
@ -214,9 +214,9 @@ AC_ARG_ENABLE(debug,
is most packages.],
DEBUG_PKG=$enableval)
all_packages="ac,b,d,e,f,g,hg,hl,i,mf,mm,o,p,s,t,v"
all_packages="ac,b,d,e,f,g,hg,hl,i,mf,mm,o,p,s,t,v,z"
if test X = "X$DEBUG_PKG" -o Xyes = "X$DEBUG_PKG"; then
DEBUG_PKG=ac,b,d,e,f,g,hg,i,mm,p,s,t,v
DEBUG_PKG=ac,b,d,e,f,g,hg,i,mm,p,s,t,v,z
CPPFLAGS="$CPPFLAGS -UNDEBUG"
AC_MSG_RESULT(default ($DEBUG_PKG))
elif test Xall = "X$DEBUG_PKG"; then

105
src/H5.c
View File

@ -38,6 +38,8 @@ static char RcsId[] = "@(#)$Revision$";
#include <ctype.h>
#include <errno.h>
#include <stdarg.h>
#include <sys/time.h>
#include <sys/resource.h>
/* private headers */
#include <H5private.h> /*library */
@ -478,7 +480,7 @@ HDfprintf (FILE *stream, const char *fmt, ...)
if ('.'==*s) {
s++;
if (isdigit (*s)) {
prec = (int)strtol (s+1, &rest, 10);
prec = (int)strtol (s, &rest, 10);
s = rest;
} else if ('*'==*s) {
prec = va_arg (ap, int);
@ -576,6 +578,7 @@ HDfprintf (FILE *stream, const char *fmt, ...)
long double x = va_arg (ap, long double);
n = fprintf (stream, template, x);
}
break;
case 'a':
if (1) {
@ -738,3 +741,103 @@ HDstrtoll (const char *s, const char **rest, int base)
if (rest) *rest = s;
return acc;
}
/*-------------------------------------------------------------------------
* Function: H5_timer_reset
*
* Purpose: Resets the timer struct to zero. Use this to reset a timer
* that's being used as an accumulator for summing times.
*
* Return: void
*
* Programmer: Robb Matzke
* Thursday, April 16, 1998
*
* Modifications:
*
*-------------------------------------------------------------------------
*/
void
H5_timer_reset (H5_timer_t *timer)
{
assert (timer);
HDmemset (timer, 0, sizeof *timer);
}
/*-------------------------------------------------------------------------
* Function: H5_timer_begin
*
* Purpose: Initialize a timer to time something.
*
* Return: void
*
* Programmer: Robb Matzke
* Thursday, April 16, 1998
*
* Modifications:
*
*-------------------------------------------------------------------------
*/
void
H5_timer_begin (H5_timer_t *timer)
{
#ifdef HAVE_GETRUSAGE
struct rusage rusage;
#endif
struct timeval etime;
assert (timer);
#ifdef HAVE_GETRUSAGE
getrusage (RUSAGE_SELF, &rusage);
timer->utime = rusage.ru_utime.tv_sec + rusage.ru_utime.tv_usec/1e6;
timer->stime = rusage.ru_stime.tv_sec + rusage.ru_stime.tv_usec/1e6;
#else
timer->utime = 0.0;
timer->stime = 0.0;
#endif
gettimeofday (&etime, NULL);
timer->etime = etime.tv_sec + etime.tv_usec/1e6;
}
/*-------------------------------------------------------------------------
* Function: H5_timer_end
*
* Purpose: This function should be called at the end of a timed region.
* The SUM is an optional pointer which will accumulate times.
* TMS is the same struct that was passed to H5_timer_start().
* On return, TMS will contain total times for the timed region.
*
* Return: void
*
* Programmer: Robb Matzke
* Thursday, April 16, 1998
*
* Modifications:
*
*-------------------------------------------------------------------------
*/
void
H5_timer_end (H5_timer_t *sum/*in,out*/, H5_timer_t *timer/*in,out*/)
{
H5_timer_t now;
assert (timer);
H5_timer_begin (&now);
timer->utime = now.utime - timer->utime;
timer->stime = now.stime - timer->stime;
timer->etime = now.etime - timer->etime;
if (sum) {
sum->utime += timer->utime;
sum->stime += timer->stime;
sum->etime += timer->etime;
}
}

10
src/H5AC.c
View File

@ -838,9 +838,11 @@ H5AC_debug(H5F_t *f)
FUNC_ENTER(H5AC_debug, FAIL);
fprintf(stderr, "H5AC: cache diagnostics for %s\n", f->name);
fprintf(stderr, " %18s %8s %8s %8s %8s+%-8s\n",
"", "Hits", "Misses", "MissRate", "Inits", "Flushes");
fprintf(stderr, "H5AC: cache statistics for file %s\n", f->name);
fprintf(stderr, " %-18s %8s %8s %8s %8s+%-8s\n",
"Layer", "Hits", "Misses", "MissRate", "Inits", "Flushes");
fprintf(stderr, " %-18s %8s %8s %8s %8s-%-8s\n",
"-----", "----", "------", "--------", "-----", "-------");
for (i = H5AC_BT_ID; i < H5AC_NTYPES; i++) {
@ -876,7 +878,7 @@ H5AC_debug(H5F_t *f)
} else {
sprintf(ascii, "%7.2f%%", miss_rate);
}
fprintf(stderr, " %18s: %8u %8u %7s %8u%+-9ld\n", s,
fprintf(stderr, " %-18s %8u %8u %7s %8u%+-9ld\n", s,
cache->diagnostics[i].nhits,
cache->diagnostics[i].nmisses,
ascii,

60
src/H5B.c
View File

@ -1022,7 +1022,7 @@ H5B_insert_helper(H5F_t *f, const haddr_t *addr, const H5B_class_t *type,
uint8 *lt_key, hbool_t *lt_key_changed,
uint8 *md_key, void *udata,
uint8 *rt_key, hbool_t *rt_key_changed,
haddr_t *new_node /*out */ )
haddr_t *new_node/*out*/)
{
H5B_t *bt = NULL, *twin = NULL, *tmp_bt = NULL;
intn lt = 0, idx = -1, rt, cmp = -1;
@ -1097,10 +1097,9 @@ H5B_insert_helper(H5F_t *f, const haddr_t *addr, const H5B_class_t *type,
idx = 0;
if (type->follow_min) {
if ((my_ins = (type->insert) (f, bt->child + idx,
bt->key[idx].nkey, lt_key_changed,
md_key, udata,
bt->key[idx + 1].nkey, rt_key_changed,
if ((my_ins = (type->insert) (f, bt->child+idx, bt->key[idx].nkey,
lt_key_changed, md_key, udata,
bt->key[idx+1].nkey, rt_key_changed,
&child_addr/*out*/)) < 0) {
HGOTO_ERROR(H5E_BTREE, H5E_CANTINSERT, H5B_INS_ERROR,
"unable to insert first leaf node");
@ -1119,11 +1118,11 @@ H5B_insert_helper(H5F_t *f, const haddr_t *addr, const H5B_class_t *type,
HGOTO_ERROR(H5E_BTREE, H5E_CANTDECODE, H5B_INS_ERROR,
"unable to decode key");
}
if ((my_ins = H5B_insert_helper(f, bt->child + idx, type,
if ((my_ins = H5B_insert_helper(f, bt->child+idx, type,
bt->key[idx].nkey, lt_key_changed,
md_key, udata,
bt->key[idx + 1].nkey, rt_key_changed,
&child_addr /*out */ )) < 0) {
md_key, udata, bt->key[idx+1].nkey,
rt_key_changed,
&child_addr/*out*/))<0) {
HGOTO_ERROR(H5E_BTREE, H5E_CANTINSERT, H5B_INS_ERROR,
"can't insert minimum subtree");
}
@ -1138,11 +1137,10 @@ H5B_insert_helper(H5F_t *f, const haddr_t *addr, const H5B_class_t *type,
HGOTO_ERROR(H5E_BTREE, H5E_CANTDECODE, H5B_INS_ERROR,
"unable to decode key");
}
if ((my_ins = (type->insert) (f, bt->child + idx,
bt->key[idx].nkey, lt_key_changed,
md_key, udata,
bt->key[idx + 1].nkey, rt_key_changed,
&child_addr /*out */ )) < 0) {
if ((my_ins = (type->insert) (f, bt->child+idx, bt->key[idx].nkey,
lt_key_changed, md_key, udata,
bt->key[idx+1].nkey, rt_key_changed,
&child_addr/*out*/)) < 0) {
HGOTO_ERROR(H5E_BTREE, H5E_CANTINSERT, H5B_INS_ERROR,
"can't insert minimum leaf node");
}
@ -1176,11 +1174,11 @@ H5B_insert_helper(H5F_t *f, const haddr_t *addr, const H5B_class_t *type,
HGOTO_ERROR(H5E_BTREE, H5E_CANTDECODE, H5B_INS_ERROR,
"unable to decode key");
}
if ((my_ins = H5B_insert_helper(f, bt->child + idx, type,
if ((my_ins = H5B_insert_helper(f, bt->child+idx, type,
bt->key[idx].nkey, lt_key_changed,
md_key, udata,
bt->key[idx + 1].nkey, rt_key_changed,
&child_addr /*out */ )) < 0) {
md_key, udata, bt->key[idx+1].nkey,
rt_key_changed,
&child_addr/*out*/)) < 0) {
HGOTO_ERROR(H5E_BTREE, H5E_CANTINSERT, H5B_INS_ERROR,
"can't insert maximum subtree");
}
@ -1195,11 +1193,10 @@ H5B_insert_helper(H5F_t *f, const haddr_t *addr, const H5B_class_t *type,
HGOTO_ERROR(H5E_BTREE, H5E_CANTDECODE, H5B_INS_ERROR,
"unable to decode key");
}
if ((my_ins = (type->insert) (f, bt->child + idx,
bt->key[idx].nkey, lt_key_changed,
md_key, udata,
bt->key[idx + 1].nkey, rt_key_changed,
&child_addr /*out */ )) < 0) {
if ((my_ins = (type->insert) (f, bt->child+idx, bt->key[idx].nkey,
lt_key_changed, md_key, udata,
bt->key[idx+1].nkey, rt_key_changed,
&child_addr/*out*/)) < 0) {
HGOTO_ERROR(H5E_BTREE, H5E_CANTINSERT, H5B_INS_ERROR,
"can't insert maximum leaf node");
}
@ -1248,11 +1245,10 @@ H5B_insert_helper(H5F_t *f, const haddr_t *addr, const H5B_class_t *type,
* Follow a branch out of this node to a leaf node of some other type.
*/
assert(idx >= 0 && idx < bt->nchildren);
if ((my_ins = (type->insert) (f, bt->child + idx,
bt->key[idx].nkey, lt_key_changed,
md_key, udata,
bt->key[idx + 1].nkey, rt_key_changed,
&child_addr /*out */ )) < 0) {
if ((my_ins = (type->insert) (f, bt->child+idx, bt->key[idx].nkey,
lt_key_changed, md_key, udata,
bt->key[idx+1].nkey, rt_key_changed,
&child_addr/*out*/)) < 0) {
HGOTO_ERROR(H5E_BTREE, H5E_CANTINSERT, H5B_INS_ERROR,
"can't insert leaf node");
}
@ -1531,7 +1527,7 @@ H5B_nodesize(H5F_t *f, const H5B_class_t *type,
*-------------------------------------------------------------------------
*/
herr_t
H5B_debug(H5F_t *f, const haddr_t *addr, FILE * stream, intn indent,
H5B_debug(H5F_t *f, const haddr_t *addr, FILE *stream, intn indent,
intn fwidth, const H5B_class_t *type, void *udata)
{
H5B_t *bt = NULL;
@ -1599,6 +1595,12 @@ H5B_debug(H5F_t *f, const haddr_t *addr, FILE * stream, intn indent,
"Address:");
H5F_addr_print(stream, bt->child + i);
fprintf(stream, "\n");
H5B_decode_key(f, bt, i);
if (type->debug_key) {
(type->debug_key)(stream, indent+3, MAX (0, fwidth-3),
bt->key[i].nkey, udata);
}
}
FUNC_LEAVE(SUCCEED);

1
src/H5Bprivate.h
View File

@ -86,6 +86,7 @@ typedef struct H5B_class_t {
herr_t (*list) (H5F_t*, const haddr_t*, void*); /*walk leaf nodes*/
herr_t (*decode) (H5F_t*, struct H5B_t*, uint8*, void*);
herr_t (*encode) (H5F_t*, struct H5B_t*, uint8*, void*);
herr_t (*debug_key)(FILE*, intn, intn, const void*, const void*);
} H5B_class_t;
/*

66
src/H5D.c
View File

@ -17,16 +17,17 @@ static char RcsId[] = "@(#)$Revision$";
/* $Id$ */
#include <H5private.h> /* Generic Functions */
#include <H5Iprivate.h> /* IDs */
#include <H5Iprivate.h> /* IDs */
#include <H5ACprivate.h> /* Cache */
#include <H5Dprivate.h> /* Dataset functions */
#include <H5Eprivate.h> /* Error handling */
#include <H5Gprivate.h> /* Group headers */
#include <H5HLprivate.h> /* Name heap */
#include <H5HLprivate.h> /* Name heap */
#include <H5MFprivate.h> /* File space allocation header */
#include <H5MMprivate.h> /* Memory management */
#include <H5Oprivate.h> /* Object headers */
#include <H5Pprivate.h> /* Property lists */
#include <H5Zprivate.h> /* Data compression */
#define PABLO_MASK H5D_mask
@ -55,10 +56,17 @@ const H5D_create_t H5D_create_dflt = {
1, 1, 1, 1, 1, 1, 1, 1, /*...are quite useless. Larger chunks..*/
1, 1, 1, 1, 1, 1, 1, 1, /*...produce fewer, but larger I/O......*/
1, 1, 1, 1, 1, 1, 1, 1}, /*...requests. */
/* External file list */
{H5F_ADDR_UNDEF, /* External file list heap address */
0, /*...slots allocated */
0, /*...slots used */
NULL} /*...slot array */
NULL}, /*...slot array */
/* Compression */
{H5Z_NONE, /* No compression */
0, /*...flags */
0, NULL} /*...client data */
};
/* Default dataset transfer property list */
@ -741,6 +749,11 @@ H5D_create(H5G_t *loc, const char *name, const H5T_t *type, const H5S_t *space,
assert (type);
assert (space);
assert (create_parms);
if (H5Z_NONE!=create_parms->compress.method &&
H5D_CHUNKED!=create_parms->layout) {
HGOTO_ERROR (H5E_DATASET, H5E_BADVALUE, NULL,
"compression can only be used with chunked layout");
}
/* Initialize the dataset object */
new_dset = H5MM_xcalloc(1, sizeof(H5D_t));
@ -829,9 +842,17 @@ H5D_create(H5G_t *loc, const char *name, const H5T_t *type, const H5S_t *space,
new_dset->type) < 0 ||
H5S_modify(&(new_dset->ent), new_dset->space) < 0) {
HGOTO_ERROR(H5E_DATASET, H5E_CANTINIT, NULL,
"can't update type or space header messages");
"unable to update type or space header messages");
}
/* Update the compression message */
if (H5Z_NONE!=new_dset->create_parms->compress.method &&
H5O_modify (&(new_dset->ent), H5O_COMPRESS, 0, H5O_FLAG_CONSTANT,
&(new_dset->create_parms->compress))<0) {
HGOTO_ERROR (H5E_DATASET, H5E_CANTINIT, NULL,
"unable to update compression header message");
}
/*
* Initialize storage. We assume that external storage is already
* initialized by the caller, or at least will be before I/O is
@ -1111,6 +1132,9 @@ H5D_read(H5D_t *dataset, const H5T_t *mem_type, const H5S_t *mem_space,
size_t target_size; /*desired buffer size */
size_t request_nelmts; /*requested strip mine */
H5T_bkg_t need_bkg; /*type of background buf*/
#ifdef H5T_DEBUG
H5_timer_t timer;
#endif
#ifdef HAVE_PARALLEL
int access_mode_saved = -1;
#endif
@ -1210,6 +1234,7 @@ H5D_read(H5D_t *dataset, const H5T_t *mem_type, const H5S_t *mem_space,
H5T_conv_noop==tconv_func &&
NULL!=sconv_func->read) {
status = (sconv_func->read)(dataset->ent.file, &(dataset->layout),
&(dataset->create_parms->compress),
&(dataset->create_parms->efl),
H5T_get_size (dataset->type), file_space,
mem_space, buf/*out*/);
@ -1296,6 +1321,7 @@ H5D_read(H5D_t *dataset, const H5T_t *mem_type, const H5S_t *mem_space,
* if necessary.
*/
if ((sconv_func->fgath)(dataset->ent.file, &(dataset->layout),
&(dataset->create_parms->compress),
&(dataset->create_parms->efl),
H5T_get_size (dataset->type), file_space,
&numbering, smine_start, smine_nelmts,
@ -1314,14 +1340,19 @@ H5D_read(H5D_t *dataset, const H5T_t *mem_type, const H5S_t *mem_space,
/*
* Perform data type conversion.
*/
#ifdef H5T_DEBUG
H5T_timer_begin (&timer, cdata);
#endif
cdata->command = H5T_CONV_CONV;
cdata->ncalls++;
if ((tconv_func)(src_id, dst_id, cdata, smine_nelmts, tconv_buf,
bkg_buf)<0) {
status = (tconv_func)(src_id, dst_id, cdata, smine_nelmts, tconv_buf,
bkg_buf);
#ifdef H5T_DEBUG
H5T_timer_end (&timer, cdata, smine_nelmts);
#endif
if (status<0) {
HGOTO_ERROR(H5E_DATASET, H5E_CANTINIT, FAIL,
"data type conversion failed");
}
cdata->nelmts += smine_nelmts;
/*
* Scatter the data into memory.
@ -1396,6 +1427,9 @@ H5D_write(H5D_t *dataset, const H5T_t *mem_type, const H5S_t *mem_space,
size_t target_size; /*desired buffer size */
size_t request_nelmts; /*requested strip mine */
H5T_bkg_t need_bkg; /*type of background buf*/
#ifdef H5T_DEBUG
H5_timer_t timer;
#endif
#ifdef HAVE_PARALLEL
int access_mode_saved = -1;
#endif
@ -1495,6 +1529,7 @@ H5D_write(H5D_t *dataset, const H5T_t *mem_type, const H5S_t *mem_space,
H5T_conv_noop==tconv_func &&
NULL!=sconv_func->write) {
status = (sconv_func->write)(dataset->ent.file, &(dataset->layout),
&(dataset->create_parms->compress),
&(dataset->create_parms->efl),
H5T_get_size (dataset->type), file_space,
mem_space, buf);
@ -1588,6 +1623,7 @@ H5D_write(H5D_t *dataset, const H5T_t *mem_type, const H5S_t *mem_space,
if ((H5D_OPTIMIZE_PIPE && H5T_BKG_YES==need_bkg) ||
(!H5D_OPTIMIZE_PIPE && need_bkg)) {
if ((sconv_func->fgath)(dataset->ent.file, &(dataset->layout),
&(dataset->create_parms->compress),
&(dataset->create_parms->efl),
H5T_get_size (dataset->type), file_space,
&numbering, smine_start, smine_nelmts,
@ -1600,19 +1636,25 @@ H5D_write(H5D_t *dataset, const H5T_t *mem_type, const H5S_t *mem_space,
/*
* Perform data type conversion.
*/
#ifdef H5T_DEBUG
H5T_timer_begin (&timer, cdata);
#endif
cdata->command = H5T_CONV_CONV;
cdata->ncalls++;
if ((tconv_func) (src_id, dst_id, cdata, smine_nelmts, tconv_buf,
bkg_buf)<0) {
status = (tconv_func) (src_id, dst_id, cdata, smine_nelmts, tconv_buf,
bkg_buf);
#ifdef H5T_DEBUG
H5T_timer_end (&timer, cdata, smine_nelmts);
#endif
if (status<0) {
HGOTO_ERROR(H5E_DATASET, H5E_CANTINIT, FAIL,
"data type conversion failed");
}
cdata->nelmts += smine_nelmts;
/*
* Scatter the data out to the file.
*/
if ((sconv_func->fscat)(dataset->ent.file, &(dataset->layout),
&(dataset->create_parms->compress),
&(dataset->create_parms->efl),
H5T_get_size (dataset->type), file_space,
&numbering, smine_start, smine_nelmts,

785
src/H5Distore.c
View File

@ -14,17 +14,9 @@
#include <H5Oprivate.h>
#include <H5Vprivate.h>
typedef enum H5F_isop_t {
H5F_ISTORE_READ, /*read from file to memory */
H5F_ISTORE_WRITE /*write from memory to file */
} H5F_isop_t;
/* Does the array domain include negative indices? */
#undef H5F_ISTORE_NEGATIVE_DOMAIN
#define PABLO_MASK H5F_istore_mask
/* Interface initialization */
#define PABLO_MASK H5F_istore_mask
static hbool_t interface_initialize_g = FALSE;
#define INTERFACE_INIT NULL
@ -48,13 +40,8 @@ static herr_t H5F_istore_decode_key(H5F_t *f, H5B_t *bt, uint8 *raw,
void *_key);
static herr_t H5F_istore_encode_key(H5F_t *f, H5B_t *bt, uint8 *raw,
void *_key);
static herr_t H5F_istore_copy_hyperslab(H5F_t *f, const H5O_layout_t *layout,
H5F_isop_t op,
const hssize_t offset_f[],
const hsize_t size[],
const hssize_t offset_m[],
const hsize_t size_m[],
void *buf);
static herr_t H5F_istore_debug_key (FILE *stream, intn indent, intn fwidth,
const void *key, const void *udata);
/*
* B-tree key. A key contains the minimum logical N-dimensional address and
@ -68,12 +55,11 @@ static herr_t H5F_istore_copy_hyperslab(H5F_t *f, const H5O_layout_t *layout,
* Only the first few values of the OFFSET and SIZE fields are actually
* stored on disk, depending on the dimensionality.
*
* The storage file address is part of the B-tree and not part of the key.
* The chunk's file address is part of the B-tree and not part of the key.
*/
typedef struct H5F_istore_key_t {
uintn file_number; /*external file number */
hsize_t nbytes; /*size of stored data */
hssize_t offset[H5O_LAYOUT_NDIMS]; /*logical offset to start*/
hsize_t size[H5O_LAYOUT_NDIMS]; /*logical chunk size */
} H5F_istore_key_t;
typedef struct H5F_istore_ud1_t {
@ -97,6 +83,7 @@ H5B_class_t H5B_ISTORE[1] = {{
NULL, /*list */
H5F_istore_decode_key, /*decode */
H5F_istore_encode_key, /*encode */
H5F_istore_debug_key, /*debug */
}};
@ -128,9 +115,8 @@ H5F_istore_sizeof_rkey(H5F_t __unused__ *f, const void *_udata)
assert(udata);
assert(udata->mesg.ndims > 0 && udata->mesg.ndims <= H5O_LAYOUT_NDIMS);
nbytes = 4 + /*external file number */
udata->mesg.ndims * 4 + /*dimension indices */
udata->mesg.ndims * 4; /*dimension sizes */
nbytes = 4 + /*storage size */
udata->mesg.ndims * 4; /*dimension indices */
return nbytes;
}
@ -157,7 +143,7 @@ H5F_istore_decode_key(H5F_t __unused__ *f, H5B_t *bt, uint8 *raw, void *_key)
{
H5F_istore_key_t *key = (H5F_istore_key_t *) _key;
intn i;
intn ndims = (intn)(bt->sizeof_rkey/8);
intn ndims = (intn)((bt->sizeof_rkey-4)/4);
FUNC_ENTER(H5F_istore_decode_key, FAIL);
@ -169,11 +155,9 @@ H5F_istore_decode_key(H5F_t __unused__ *f, H5B_t *bt, uint8 *raw, void *_key)
assert(ndims > 0 && ndims <= H5O_LAYOUT_NDIMS);
/* decode */
UINT32DECODE(raw, key->file_number);
assert(0 == key->file_number);
UINT32DECODE (raw, key->nbytes);
for (i = 0; i < ndims; i++) {
UINT32DECODE(raw, key->offset[i]);
UINT32DECODE(raw, key->size[i]);
}
FUNC_LEAVE(SUCCEED);
@ -200,7 +184,7 @@ static herr_t
H5F_istore_encode_key(H5F_t __unused__ *f, H5B_t *bt, uint8 *raw, void *_key)
{
H5F_istore_key_t *key = (H5F_istore_key_t *) _key;
intn ndims = (intn)(bt->sizeof_rkey / 8);
intn ndims = (intn)((bt->sizeof_rkey-4) / 4);
intn i;
FUNC_ENTER(H5F_istore_encode_key, FAIL);
@ -213,16 +197,54 @@ H5F_istore_encode_key(H5F_t __unused__ *f, H5B_t *bt, uint8 *raw, void *_key)
assert(ndims > 0 && ndims <= H5O_LAYOUT_NDIMS);
/* encode */
UINT32ENCODE(raw, key->file_number);
assert(0 == key->file_number);
UINT32ENCODE (raw, key->nbytes);
for (i = 0; i < ndims; i++) {
UINT32ENCODE(raw, key->offset[i]);
UINT32ENCODE(raw, key->size[i]);
}
FUNC_LEAVE(SUCCEED);
}
/*-------------------------------------------------------------------------
* Function: H5F_istore_debug_key
*
* Purpose: Prints a key.
*
* Return: Success: SUCCEED
*
* Failure: FAIL
*
* Programmer: Robb Matzke
* Thursday, April 16, 1998
*
* Modifications:
*
*-------------------------------------------------------------------------
*/
static herr_t
H5F_istore_debug_key (FILE *stream, intn indent, intn fwidth,
const void *_key, const void *_udata)
{
const H5F_istore_key_t *key = (const H5F_istore_key_t *)_key;
const H5F_istore_ud1_t *udata = (const H5F_istore_ud1_t *)_udata;
int i;
FUNC_ENTER (H5F_istore_debug_key, FAIL);
assert (key);
HDfprintf (stream, "%*s%-*s %Hd bytes\n", indent, "", fwidth,
"Chunk size:", key->nbytes);
HDfprintf (stream, "%*s%-*s {", indent, "", fwidth,
"Logical offset:");
for (i=0; i<udata->mesg.ndims; i++) {
HDfprintf (stream, "%s%Hd", i?", ":"", key->offset[i]);
}
fputs ("}\n", stream);
FUNC_LEAVE (SUCCEED);
}
/*-------------------------------------------------------------------------
* Function: H5F_istore_cmp2
@ -352,7 +374,6 @@ H5F_istore_new_node(H5F_t *f, H5B_ins_t op,
H5F_istore_key_t *lt_key = (H5F_istore_key_t *) _lt_key;
H5F_istore_key_t *rt_key = (H5F_istore_key_t *) _rt_key;
H5F_istore_ud1_t *udata = (H5F_istore_ud1_t *) _udata;
hsize_t nbytes;
intn i;
FUNC_ENTER(H5F_istore_new_node, FAIL);
@ -366,37 +387,34 @@ H5F_istore_new_node(H5F_t *f, H5B_ins_t op,
assert(addr);
/* Allocate new storage */
nbytes = H5V_vector_reduce_product(udata->mesg.ndims, udata->key.size);
assert(nbytes > 0);
if (H5MF_alloc(f, H5MF_RAW, nbytes, addr /*out */ ) < 0) {
assert (udata->key.nbytes > 0);
if (H5MF_alloc(f, H5MF_RAW, udata->key.nbytes, addr /*out */ ) < 0) {
HRETURN_ERROR(H5E_IO, H5E_CANTINIT, FAIL,
"couldn't allocate new file storage");
}
udata->addr = *addr;
udata->key.file_number = 0;
lt_key->file_number = udata->key.file_number;
if (H5B_INS_LEFT != op)
rt_key->file_number = 0;
/* Initialize the key(s) */
for (i = 0; i < udata->mesg.ndims; i++) {
/*
* The left key describes the storage of the UDATA chunk being
* inserted into the tree.
*/
assert(udata->key.size[i] > 0);
/*
* The left key describes the storage of the UDATA chunk being
* inserted into the tree.
*/
lt_key->nbytes = udata->key.nbytes;
for (i=0; i<udata->mesg.ndims; i++) {
lt_key->offset[i] = udata->key.offset[i];
lt_key->size[i] = udata->key.size[i];
}
/*
* The right key might already be present. If not, then add
* a zero-width chunk.
*/
if (H5B_INS_LEFT != op) {
assert (udata->key.size[i] < MAX_HSSIZET);
/*
* The right key might already be present. If not, then add a zero-width
* chunk.
*/
if (H5B_INS_LEFT != op) {
rt_key->nbytes = 0;
for (i=0; i<udata->mesg.ndims; i++) {
assert (udata->mesg.dim[i] < MAX_HSSIZET);
assert (udata->key.offset[i]+(hssize_t)(udata->mesg.dim[i]) >
udata->key.offset[i]);
rt_key->offset[i] = udata->key.offset[i] +
(hssize_t)udata->key.size[i];
rt_key->size[i] = 0;
(hssize_t)(udata->mesg.dim[i]);
}
}
@ -445,12 +463,10 @@ H5F_istore_found(H5F_t __unused__ *f, const haddr_t *addr,
/* Initialize return values */
udata->addr = *addr;
udata->key.file_number = lt_key->file_number;
assert(0 == lt_key->file_number);
udata->key.nbytes = lt_key->nbytes;
assert (lt_key->nbytes>0);
for (i = 0; i < udata->mesg.ndims; i++) {
udata->key.offset[i] = lt_key->offset[i];
udata->key.size[i] = lt_key->size[i];
assert(lt_key->size[i] > 0);
}
FUNC_LEAVE(SUCCEED);
@ -500,7 +516,6 @@ H5F_istore_insert(H5F_t *f, const haddr_t *addr, void *_lt_key,
H5F_istore_ud1_t *udata = (H5F_istore_ud1_t *) _udata;
intn i, cmp;
H5B_ins_t ret_value = H5B_INS_ERROR;
hsize_t nbytes;
FUNC_ENTER(H5F_istore_insert, H5B_INS_ERROR);
@ -523,46 +538,61 @@ H5F_istore_insert(H5F_t *f, const haddr_t *addr, void *_lt_key,
assert("HDF5 INTERNAL ERROR -- see rpm" && 0);
HRETURN_ERROR(H5E_STORAGE, H5E_UNSUPPORTED, H5B_INS_ERROR,
"internal error");
} else if (H5V_hyper_eq(udata->mesg.ndims,
udata->key.offset, udata->key.size,
lt_key->offset, lt_key->size)) {
} else if (H5V_vector_eq_s (udata->mesg.ndims,
udata->key.offset, lt_key->offset) &&
lt_key->nbytes>0) {
/*
* Already exists. Just return the info.
* Already exists. If the new size is not the same as the old size
* then we should reallocate storage.
*/
#if 1
if (lt_key->nbytes != udata->key.nbytes) {
if (H5MF_realloc (f, H5MF_RAW, lt_key->nbytes, addr,
udata->key.nbytes, new_node/*out*/)<0) {
HRETURN_ERROR (H5E_STORAGE, H5E_WRITEERROR, H5B_INS_ERROR,
"unable to reallocate chunk storage");
}
lt_key->nbytes = udata->key.nbytes;
*lt_key_changed = TRUE;
udata->addr = *new_node;
ret_value = H5B_INS_CHANGE;
} else {
udata->addr = *addr;
ret_value = H5B_INS_NOOP;
}
#else
assert (lt_key->nbytes == udata->key.nbytes);
assert (!H5F_addr_defined (&(udata->addr)) ||
H5F_addr_eq (&(udata->addr), addr));
udata->addr = *addr;
udata->key.file_number = lt_key->file_number;
ret_value = H5B_INS_NOOP;
#endif
} else if (H5V_hyper_disjointp(udata->mesg.ndims,
lt_key->offset, lt_key->size,
udata->key.offset, udata->key.size)) {
lt_key->offset, udata->mesg.dim,
udata->key.offset, udata->mesg.dim)) {
assert(H5V_hyper_disjointp(udata->mesg.ndims,
rt_key->offset, rt_key->size,
udata->key.offset, udata->key.size));
rt_key->offset, udata->mesg.dim,
udata->key.offset, udata->mesg.dim));
/*
* Split this node, inserting the new new node to the right of the
* current node. The MD_KEY is where the split occurs.
*/
md_key->file_number = udata->key.file_number;
for (i=0, nbytes=1; i<udata->mesg.ndims; i++) {
md_key->nbytes = udata->key.nbytes;
for (i=0; i<udata->mesg.ndims; i++) {
assert(0 == udata->key.offset[i] % udata->mesg.dim[i]);
assert(udata->key.size[i] == udata->mesg.dim[i]);
md_key->offset[i] = udata->key.offset[i];
md_key->size[i] = udata->key.size[i];
nbytes *= udata->key.size[i];
}
/*
* Allocate storage for the new chunk
*/
if (H5MF_alloc(f, H5MF_RAW, nbytes, new_node /*out */ ) < 0) {
if (H5MF_alloc(f, H5MF_RAW, udata->key.nbytes, new_node/*out*/)<0) {
HRETURN_ERROR(H5E_IO, H5E_CANTINIT, H5B_INS_ERROR,
"file allocation failed");
}
udata->addr = *new_node;
udata->key.file_number = 0;
ret_value = H5B_INS_RIGHT;
} else {
@ -574,223 +604,6 @@ H5F_istore_insert(H5F_t *f, const haddr_t *addr, void *_lt_key,
FUNC_LEAVE(ret_value);
}
/*-------------------------------------------------------------------------
* Function: H5F_istore_copy_hyperslab
*
* Purpose: Reads or writes a hyperslab to disk depending on whether OP
* is H5F_ISTORE_READ or H5F_ISTORE_WRITE. The hyperslab
* storage is described with ISTORE and exists in file F. The
* file hyperslab begins at location OFFSET_F[] (an N-dimensional
* point in the domain in terms of elements) in the file and
* OFFSET_M[] in memory pointed to by BUF. Its size is SIZE[]
* elements. The dimensionality of memory is assumed to be the
* same as the file and the total size of the multi-dimensional
* memory buffer is SIZE_M[].
*
* The slowest varying dimension is always listed first in the
* various offset and size arrays.
*
* A `chunk' is a hyperslab of the disk array which is stored
* contiguously. I/O occurs in units of chunks where the size of
* a chunk is determined by the alignment constraints specified
* in ISTORE.
*
* Return: Success: SUCCEED
*
* Failure: FAIL
*
* Programmer: Robb Matzke
* Friday, October 17, 1997
*
* Modifications:
*
*-------------------------------------------------------------------------
*/
static herr_t
H5F_istore_copy_hyperslab(H5F_t *f, const H5O_layout_t *layout, H5F_isop_t op,
const hssize_t offset_f[], const hsize_t size[],
const hssize_t offset_m[], const hsize_t size_m[],
void *buf/*in or out*/)
{
intn i, carry;
hsize_t idx_cur[H5O_LAYOUT_NDIMS];
hsize_t idx_min[H5O_LAYOUT_NDIMS];
hsize_t idx_max[H5O_LAYOUT_NDIMS];
hsize_t sub_size[H5O_LAYOUT_NDIMS];
hssize_t offset_wrt_chunk[H5O_LAYOUT_NDIMS];
hssize_t sub_offset_m[H5O_LAYOUT_NDIMS];
size_t chunk_size;
hsize_t acc;
uint8 *chunk = NULL;
H5F_istore_ud1_t udata;
herr_t status;
herr_t ret_value = FAIL;
FUNC_ENTER(H5F_istore_copy_hyperslab, FAIL);
/* check args */
assert(f);
assert(layout && H5D_CHUNKED == layout->type);
assert(H5F_addr_defined(&(layout->addr)));
assert(layout->ndims > 0 && layout->ndims <= H5O_LAYOUT_NDIMS);
assert(H5F_ISTORE_READ == op || H5F_ISTORE_WRITE == op);
assert(size);
assert(size_m);
assert(buf);
#ifndef NDEBUG
for (i=0; i<layout->ndims; i++) {
assert(size_m[i] > 0); /*destination must exist */
/*hyperslab must fit in BUF */
assert((offset_m?offset_m[i]:0) + size[i] <= size_m[i]);
assert(layout->dim[i] > 0);
}
#endif
/*
* As a special case of H5F_ISTORE_READ, if the source is aligned on
* a chunk boundary and is the same size as a chunk, and the destination
* is the same size as a chunk, then instead of reading into a temporary
* buffer and then into the destination, we read directly into the
* destination.
*/
if (H5F_ISTORE_READ==op) {
for (i=0, acc=1; i<layout->ndims; i++) {
if (offset_f[i] % layout->dim[i]) break; /*src not aligned*/
if (size[i]!=layout->dim[i]) break; /*src not a chunk*/
if (size_m[i]!=layout->dim[i]) break; /*dst not a chunk*/
udata.key.offset[i] = offset_f[i];
udata.key.size[i] = layout->dim[i];
acc *= layout->dim[i];
}
chunk_size = acc;
assert ((hsize_t)chunk_size==acc);
if (i==layout->ndims) {
udata.mesg = *layout;
H5F_addr_undef (&(udata.addr));
udata.key.file_number = 0;
status = H5B_find (f, H5B_ISTORE, &(layout->addr), &udata);
if (status>=0 && H5F_addr_defined (&(udata.addr))) {
assert (0==udata.key.file_number);
if (H5F_block_read (f, &(udata.addr), (hsize_t)chunk_size,
buf)<0) {
HGOTO_ERROR (H5E_IO, H5E_READERROR, FAIL,
"unable to read raw storage chunk");
}
} else {
HDmemset (buf, 0, chunk_size);
}
HRETURN (SUCCEED);
}
}
/*
* This is the general case. We set up multi-dimensional counters
* (idx_min, idx_max, and idx_cur) and loop through the chunks copying
* each chunk into a temporary buffer, compressing or decompressing, and
* then copying it to it's destination.
*/
for (i=0; i<layout->ndims; i++) {
idx_min[i] = (offset_f?offset_f[i]:0) / layout->dim[i];
idx_max[i] = ((offset_f?offset_f[i]:0) + size[i]-1) / layout->dim[i]+1;
idx_cur[i] = idx_min[i];
}
/* Allocate buffers */
for (i=0, chunk_size=1; i<layout->ndims; i++) {
chunk_size *= layout->dim[i];
}
chunk = H5MM_xmalloc(chunk_size);
/* Initialize non-changing part of udata */
udata.mesg = *layout;
/* Loop over all chunks */
while (1) {
/* Read/Write chunk or create it if it doesn't exist */
udata.mesg.ndims = layout->ndims;
H5F_addr_undef(&(udata.addr));
udata.key.file_number = 0;
for (i=0; i<layout->ndims; i++) {
/* The location and size of the chunk being accessed */
assert (layout->dim[i] < MAX_HSSIZET);
udata.key.offset[i] = idx_cur[i] * (hssize_t)(layout->dim[i]);
udata.key.size[i] = layout->dim[i];
/* The offset and size wrt the chunk */
offset_wrt_chunk[i] = MAX((offset_f?offset_f[i]:0),
udata.key.offset[i]) -
udata.key.offset[i];
sub_size[i] = MIN((idx_cur[i] + 1) * layout->dim[i],
(offset_f ? offset_f[i] : 0) + size[i]) -
(udata.key.offset[i] + offset_wrt_chunk[i]);
/* Offset into mem buffer */
sub_offset_m[i] = udata.key.offset[i] + offset_wrt_chunk[i] +
(offset_m ? offset_m[i] : 0) -
(offset_f ? offset_f[i] : 0);
}
if (H5F_ISTORE_WRITE == op) {
status = H5B_insert(f, H5B_ISTORE, &(layout->addr), &udata);
assert(status >= 0);
} else {
status = H5B_find(f, H5B_ISTORE, &(layout->addr), &udata);
}
/*
* If the operation is reading from the disk or if we are writing a
* partial chunk then load the chunk from disk.
*/
if (H5F_ISTORE_READ == op ||
!H5V_vector_zerop_s(layout->ndims, offset_wrt_chunk) ||
!H5V_vector_eq_u(layout->ndims, sub_size, udata.key.size)) {
if (status>=0 && H5F_addr_defined(&(udata.addr))) {
assert(0==udata.key.file_number);
if (H5F_block_read(f, &(udata.addr), (hsize_t)chunk_size,
chunk) < 0) {
HGOTO_ERROR(H5E_IO, H5E_READERROR, FAIL,
"unable to read raw storage chunk");
}
} else {
HDmemset(chunk, 0, chunk_size);
}
}
/* Transfer data to/from the chunk */
if (H5F_ISTORE_WRITE==op) {
H5V_hyper_copy(layout->ndims, sub_size,
udata.key.size, offset_wrt_chunk, chunk,
size_m, sub_offset_m, buf);
assert(0 == udata.key.file_number);
if (H5F_block_write(f, &(udata.addr), (hsize_t)chunk_size,
chunk) < 0) {
HGOTO_ERROR(H5E_IO, H5E_WRITEERROR, FAIL,
"unable to write raw storage chunk");
}
} else {
H5V_hyper_copy(layout->ndims, sub_size,
size_m, sub_offset_m, (void *)buf,
udata.key.size, offset_wrt_chunk, chunk);
}
/* Increment indices */
for (i=layout->ndims-1, carry=1; i>=0 && carry; --i) {
if (++idx_cur[i]>=idx_max[i]) idx_cur[i] = idx_min[i];
else carry = 0;
}
if (carry) break;
}
ret_value = SUCCEED;
done:
chunk = H5MM_xfree(chunk);
FUNC_LEAVE(ret_value);
}
/*-------------------------------------------------------------------------
* Function: H5F_istore_read
@ -811,23 +624,183 @@ H5F_istore_copy_hyperslab(H5F_t *f, const H5O_layout_t *layout, H5F_isop_t op,
*/
herr_t
H5F_istore_read(H5F_t *f, const H5O_layout_t *layout,
const hssize_t offset[], const hsize_t size[], void *buf)
const H5O_compress_t *comp, const hssize_t offset_f[],
const hsize_t size[], void *buf)
{
hssize_t offset_m[H5O_LAYOUT_NDIMS];
hsize_t size_m[H5O_LAYOUT_NDIMS];
intn i, carry;
hsize_t idx_cur[H5O_LAYOUT_NDIMS];
hsize_t idx_min[H5O_LAYOUT_NDIMS];
hsize_t idx_max[H5O_LAYOUT_NDIMS];
hsize_t sub_size[H5O_LAYOUT_NDIMS];
hssize_t offset_wrt_chunk[H5O_LAYOUT_NDIMS];
hssize_t sub_offset_m[H5O_LAYOUT_NDIMS];
size_t chunk_size;
uint8 *chunk=NULL, *compressed=NULL;
H5F_istore_ud1_t udata;
herr_t status;
herr_t ret_value = FAIL;
FUNC_ENTER(H5F_istore_read, FAIL);
/* Check args */
assert(f);
assert(layout && H5D_CHUNKED == layout->type);
assert(layout->ndims > 0 && layout->ndims <= H5O_LAYOUT_NDIMS);
assert(size);
assert(buf);
assert (f);
assert (layout && H5D_CHUNKED==layout->type);
assert (layout->ndims>0 && layout->ndims<=H5O_LAYOUT_NDIMS);
assert (H5F_addr_defined(&(layout->addr)));
assert (offset_f);
assert (size);
assert (buf);
if (H5F_istore_copy_hyperslab(f, layout, H5F_ISTORE_READ,
offset, size, H5V_ZERO, size, buf) < 0) {
HRETURN_ERROR(H5E_IO, H5E_READERROR, FAIL,
"hyperslab output failure");
/*
* For now, a hyperslab of the file must be read into an array in
* memory.We do not yet support reading into a hyperslab of memory.
*/
for (i=0; i<layout->ndims; i++) {
offset_m[i] = 0;
size_m[i] = size[i];
}
FUNC_LEAVE(SUCCEED);
#ifndef NDEBUG
for (i=0; i<layout->ndims; i++) {
assert (offset_f[i]>=0); /*negative offsets not supported*/
assert (offset_m[i]>=0); /*negative offsets not supported*/
assert (size[i]<MAX_SIZET);
assert(offset_m[i]+(hssize_t)size[i]<=(hssize_t)size_m[i]);
assert(layout->dim[i]>0);
}
#endif
/* Determine the chunk size and allocate buffers */
for (i=0, chunk_size=1; i<layout->ndims; i++) {
chunk_size *= layout->dim[i];
}
chunk = H5MM_xmalloc(chunk_size);
if (comp && H5Z_NONE!=comp->method) {
compressed = H5MM_xmalloc (chunk_size);
}
/*
* As a special case if the source is aligned on a chunk boundary and is
* the same size as a chunk, and the destination is the same size as a
* chunk, then instead of reading into a temporary buffer and then into
* the destination, we read directly into the destination.
*/
for (i=0; i<layout->ndims; i++) {
if (offset_f[i] % layout->dim[i]) break; /*src not aligned*/
if (size[i]!=layout->dim[i]) break; /*src not a chunk*/
if (size_m[i]!=layout->dim[i]) break; /*dst not a chunk*/
udata.key.offset[i] = offset_f[i];
}
if (i==layout->ndims) {
udata.mesg = *layout;
H5F_addr_undef (&(udata.addr));
status = H5B_find (f, H5B_ISTORE, &(layout->addr), &udata);
if (status>=0 && H5F_addr_defined (&(udata.addr))) {
if (compressed && udata.key.nbytes<chunk_size) {
if (H5F_block_read (f, &(udata.addr), udata.key.nbytes,
compressed)<0) {
HGOTO_ERROR (H5E_IO, H5E_READERROR, FAIL,
"unable to read raw storage chunk");
}
if (chunk_size!=H5Z_uncompress (comp, udata.key.nbytes,
compressed, chunk_size, buf)) {
HGOTO_ERROR (H5E_IO, H5E_READERROR, FAIL,
"unable to uncompress raw storage chunk");
}
} else {
assert (udata.key.nbytes==chunk_size);
if (H5F_block_read (f, &(udata.addr), chunk_size, buf)<0) {
HGOTO_ERROR (H5E_IO, H5E_READERROR, FAIL,
"unable to read raw storage chunk");
}
}
} else {
HDmemset (buf, 0, chunk_size);
}
HGOTO_DONE (SUCCEED);
}
/*
* This is the general case. We set up multi-dimensional counters
* (idx_min, idx_max, and idx_cur) and loop through the chunks compressing
* or copying each chunk into a temporary buffer, and then copying it to
* it's destination.
*/
for (i=0; i<layout->ndims; i++) {
idx_min[i] = offset_f[i] / layout->dim[i];
idx_max[i] = (offset_f[i]+size[i]-1) / layout->dim[i] + 1;
idx_cur[i] = idx_min[i];
}
/* Initialize non-changing part of udata */
udata.mesg = *layout;
/* Loop over all chunks */
while (1) {
for (i=0; i<layout->ndims; i++) {
/* The location and size of the chunk being accessed */
assert (layout->dim[i] < MAX_HSSIZET);
udata.key.offset[i] = idx_cur[i] * (hssize_t)(layout->dim[i]);
/* The offset and size wrt the chunk */
offset_wrt_chunk[i] = MAX(offset_f[i], udata.key.offset[i]) -
udata.key.offset[i];
sub_size[i] = MIN((idx_cur[i]+1)*layout->dim[i],
offset_f[i]+size[i]) -
(udata.key.offset[i] + offset_wrt_chunk[i]);
/* Offset into mem buffer */
sub_offset_m[i] = udata.key.offset[i] + offset_wrt_chunk[i] +
offset_m[i] - offset_f[i];
}
/* Read chunk */
H5F_addr_undef(&(udata.addr));
status = H5B_find(f, H5B_ISTORE, &(layout->addr), &udata);
if (status>=0 && H5F_addr_defined(&(udata.addr))) {
if (compressed && udata.key.nbytes<chunk_size) {
if (H5F_block_read (f, &(udata.addr), udata.key.nbytes,
compressed)<0) {
HGOTO_ERROR (H5E_IO, H5E_READERROR, FAIL,
"unable to read raw storage chunk");
}
if (chunk_size!=H5Z_uncompress (comp, udata.key.nbytes,
compressed, chunk_size,
chunk)) {
HGOTO_ERROR (H5E_IO, H5E_READERROR, FAIL,
"unable to uncompress data");
}
} else {
assert (udata.key.nbytes == chunk_size);
if (H5F_block_read(f, &(udata.addr), chunk_size, chunk) < 0) {
HGOTO_ERROR(H5E_IO, H5E_READERROR, FAIL,
"unable to read raw storage chunk");
}
}
} else {
HDmemset(chunk, 0, chunk_size);
}
/* Transfer data from the chunk buffer to the application */
H5V_hyper_copy(layout->ndims, sub_size, size_m, sub_offset_m,
(void *)buf, layout->dim, offset_wrt_chunk, chunk);
/* Increment indices */
for (i=layout->ndims-1, carry=1; i>=0 && carry; --i) {
if (++idx_cur[i]>=idx_max[i]) idx_cur[i] = idx_min[i];
else carry = 0;
}
if (carry) break;
}
ret_value = SUCCEED;
done:
H5MM_xfree(chunk);
H5MM_xfree (compressed);
FUNC_LEAVE(ret_value);
}
@ -850,25 +823,174 @@ H5F_istore_read(H5F_t *f, const H5O_layout_t *layout,
*/
herr_t
H5F_istore_write(H5F_t *f, const H5O_layout_t *layout,
const hssize_t offset[], const hsize_t size[],
const void *buf)
const H5O_compress_t *comp, const hssize_t offset_f[],
const hsize_t size[], const void *buf)
{
hssize_t offset_m[H5O_LAYOUT_NDIMS];
hsize_t size_m[H5O_LAYOUT_NDIMS];
intn i, carry;
hsize_t idx_cur[H5O_LAYOUT_NDIMS];
hsize_t idx_min[H5O_LAYOUT_NDIMS];
hsize_t idx_max[H5O_LAYOUT_NDIMS];
hsize_t sub_size[H5O_LAYOUT_NDIMS];
hssize_t offset_wrt_chunk[H5O_LAYOUT_NDIMS];
hssize_t sub_offset_m[H5O_LAYOUT_NDIMS];
hsize_t chunk_size, nbytes;
uint8 *chunk=NULL, *compressed=NULL, *outbuf;
H5F_istore_ud1_t udata;
herr_t ret_value = FAIL;
FUNC_ENTER(H5F_istore_write, FAIL);
/* Check args */
assert(f);
assert(layout && H5D_CHUNKED == layout->type);
assert(layout->ndims > 0 && layout->ndims <= H5O_LAYOUT_NDIMS);
assert(layout && H5D_CHUNKED==layout->type);
assert(layout->ndims>0 && layout->ndims<=H5O_LAYOUT_NDIMS);
assert(H5F_addr_defined(&(layout->addr)));
assert (offset_f);
assert(size);
assert(buf);
if (H5F_istore_copy_hyperslab(f, layout, H5F_ISTORE_WRITE,
offset, size, H5V_ZERO, size,
(void*)buf) < 0) {
HRETURN_ERROR(H5E_IO, H5E_WRITEERROR, FAIL,
"hyperslab output failure");
/*
* For now the source must not be a hyperslab. It must be an entire
* memory buffer.
*/
for (i=0; i<layout->ndims; i++) {
offset_m[i] = 0;
size_m[i] = size[i];
}
FUNC_LEAVE(SUCCEED);
#ifndef NDEBUG
for (i=0; i<layout->ndims; i++) {
assert (offset_f[i]>=0); /*negative offsets not supported*/
assert (offset_m[i]>=0); /*negative offsets not supported*/
assert(size[i]<MAX_SIZET);
assert(offset_m[i]+(hssize_t)size[i]<=(hssize_t)size_m[i]);
assert(layout->dim[i]>0);
}
#endif
/*
* This is the general case. We set up multi-dimensional counters
* (idx_min, idx_max, and idx_cur) and loop through the chunks copying
* each chunk into a temporary buffer, compressing or decompressing, and
* then copying it to it's destination.
*/
for (i=0; i<layout->ndims; i++) {
idx_min[i] = offset_f[i] / layout->dim[i];
idx_max[i] = (offset_f[i]+size[i]-1) / layout->dim[i] + 1;
idx_cur[i] = idx_min[i];
}
/* Allocate buffers */
for (i=0, chunk_size=1; i<layout->ndims; i++) {
chunk_size *= layout->dim[i];
}
chunk = H5MM_xmalloc(chunk_size);
if (comp && H5Z_NONE!=comp->method) {
compressed = H5MM_xmalloc (chunk_size);
}
/* Initialize non-changing part of udata */
udata.mesg = *layout;
/* Loop over all chunks */
while (1) {
for (i=0; i<layout->ndims; i++) {
/* The location and size of the chunk being accessed */
assert (layout->dim[i] < MAX_HSSIZET);
udata.key.offset[i] = idx_cur[i] * (hssize_t)(layout->dim[i]);
/* The offset and size wrt the chunk */
offset_wrt_chunk[i] = MAX(offset_f[i], udata.key.offset[i]) -
udata.key.offset[i];
sub_size[i] = MIN((idx_cur[i]+1)*layout->dim[i],
offset_f[i]+size[i]) -
(udata.key.offset[i] + offset_wrt_chunk[i]);
/* Offset into mem buffer */
sub_offset_m[i] = udata.key.offset[i] + offset_wrt_chunk[i] +
offset_m[i] - offset_f[i];
}
/*
* If we are writing a partial chunk then load the chunk from disk
* and uncompress it if it exists.
*/
if (!H5V_vector_zerop_s(layout->ndims, offset_wrt_chunk) ||
!H5V_vector_eq_u(layout->ndims, sub_size, layout->dim)) {
if (H5B_find (f, H5B_ISTORE, &(layout->addr), &udata)>=0 &&
H5F_addr_defined (&(udata.addr))) {
if (compressed && udata.key.nbytes<chunk_size) {
if (H5F_block_read(f, &(udata.addr), udata.key.nbytes,
compressed)<0) {
HGOTO_ERROR(H5E_IO, H5E_READERROR, FAIL,
"unable to read raw storage chunk");
}
if (chunk_size!=H5Z_uncompress (comp, udata.key.nbytes,
compressed, chunk_size,
chunk)) {
HGOTO_ERROR (H5E_IO, H5E_READERROR, FAIL,
"unable to uncompress data");
}
} else {
assert (chunk_size==udata.key.nbytes);
if (H5F_block_read(f, &(udata.addr), udata.key.nbytes,
chunk)<0) {
HGOTO_ERROR(H5E_IO, H5E_READERROR, FAIL,
"unable to read raw storage chunk");
}
}
} else {
HDmemset(chunk, 0, chunk_size);
}
}
/* Transfer data to the chunk */
H5V_hyper_copy(layout->ndims, sub_size,
layout->dim, offset_wrt_chunk, chunk,
size_m, sub_offset_m, buf);
/* Compress the chunk */
if (compressed &&
(nbytes=H5Z_compress (comp, chunk_size, chunk, compressed)) &&
nbytes<chunk_size) {
outbuf = compressed;
} else {
outbuf = chunk;
nbytes = chunk_size;
}
/*
* Create the chunk it if it doesn't exist, or reallocate the chunk
* if its size changed. Then write the data into the file.
*/
H5F_addr_undef(&(udata.addr));
udata.key.nbytes = nbytes;
if (H5B_insert(f, H5B_ISTORE, &(layout->addr), &udata)<0) {
HGOTO_ERROR (H5E_IO, H5E_WRITEERROR, FAIL,
"unable to allocate chunk");
}
if (H5F_block_write(f, &(udata.addr), nbytes, outbuf) < 0) {
HGOTO_ERROR(H5E_IO, H5E_WRITEERROR, FAIL,
"unable to write raw storage chunk");
}
/* Increment indices */
for (i=layout->ndims-1, carry=1; i>=0 && carry; --i) {
if (++idx_cur[i]>=idx_max[i]) idx_cur[i] = idx_min[i];
else carry = 0;
}
if (carry) break;
}
ret_value = SUCCEED;
done:
H5MM_xfree(chunk);
H5MM_xfree (compressed);
FUNC_LEAVE(ret_value);
}
@ -921,3 +1043,36 @@ H5F_istore_create(H5F_t *f, H5O_layout_t *layout /*out */ )
FUNC_LEAVE(SUCCEED);
}
/*-------------------------------------------------------------------------
* Function: H5F_istore_debug
*
* Purpose: Debugs a B-tree node for indexed raw data storage.
*
* Return: Success: SUCCEED
*
* Failure: FAIL
*
* Programmer: Robb Matzke
* Thursday, April 16, 1998
*
* Modifications:
*
*-------------------------------------------------------------------------
*/
herr_t
H5F_istore_debug(H5F_t *f, const haddr_t *addr, FILE * stream, intn indent,
intn fwidth, int ndims)
{
H5F_istore_ud1_t udata;
FUNC_ENTER (H5F_istore_debug, FAIL);
HDmemset (&udata, 0, sizeof udata);
udata.mesg.ndims = ndims;
H5B_debug (f, addr, stream, indent, fwidth, H5B_ISTORE, &udata);
FUNC_LEAVE (SUCCEED);
}

1
src/H5Dprivate.h
View File

@ -46,6 +46,7 @@ typedef struct H5D_create_t {
intn chunk_ndims; /*chunk dimensionality */
hsize_t chunk_size[32]; /*chunk size if chunked storage */
H5O_efl_t efl; /*external file list */
H5O_compress_t compress; /*data compression parameters */
} H5D_create_t;
/* Dataset transfer property list */

39
src/H5Dpublic.h
View File

@ -1,13 +1,13 @@
/****************************************************************************
* NCSA HDF *
* Software Development Group *
* National Center for Supercomputing Applications *
* University of Illinois at Urbana-Champaign *
* 605 E. Springfield, Champaign IL 61820 *
* *
* For conditions of distribution and use, see the accompanying *
* hdf/COPYING file. *
* *
* NCSA HDF *
* Software Development Group *
* National Center for Supercomputing Applications *
* University of Illinois at Urbana-Champaign *
* 605 E. Springfield, Champaign IL 61820 *
* *
* For conditions of distribution and use, see the accompanying *
* hdf/COPYING file. *
* *
****************************************************************************/
/*
@ -22,38 +22,39 @@
/* Values for the H5D_LAYOUT property */
typedef enum H5D_layout_t {
H5D_LAYOUT_ERROR = -1,
H5D_LAYOUT_ERROR = -1,
H5D_COMPACT = 0, /*raw data is very small */
H5D_CONTIGUOUS = 1, /*the default */
H5D_CHUNKED = 2, /*slow and fancy */
H5D_COMPACT = 0, /*raw data is very small */
H5D_CONTIGUOUS = 1, /*the default */
H5D_CHUNKED = 2, /*slow and fancy */
H5D_NLAYOUTS = 3 /*this one must be last! */
H5D_NLAYOUTS = 3 /*this one must be last! */
} H5D_layout_t;
#ifdef HAVE_PARALLEL
/* Values for the data transfer property */
typedef enum H5D_transfer_t {
H5D_XFER_INDEPENDENT, /*Independent data transfer */
H5D_XFER_COLLECTIVE /*Collective data transfer */
H5D_XFER_INDEPENDENT, /*Independent data transfer */
H5D_XFER_COLLECTIVE /*Collective data transfer */
} H5D_transfer_t;
#endif
#ifdef __cplusplus
extern "C" {
#endif
hid_t H5Dcreate (hid_t file_id, const char *name, hid_t type_id,
hid_t space_id, hid_t create_parms_id);
hid_t space_id, hid_t create_parms_id);
hid_t H5Dopen (hid_t file_id, const char *name);
herr_t H5Dclose (hid_t dataset_id);
hid_t H5Dget_space (hid_t dataset_id);
hid_t H5Dget_type (hid_t dataset_id);
hid_t H5Dget_create_plist (hid_t dataset_id);
herr_t H5Dread (hid_t dataset_id, hid_t mem_type_id, hid_t mem_space_id,
hid_t file_space_id, hid_t xfer_parms_id, void *buf/*out*/);
hid_t file_space_id, hid_t xfer_parms_id, void *buf/*out*/);
herr_t H5Dwrite (hid_t dataset_id, hid_t mem_type_id, hid_t mem_space_id,
hid_t file_space_id, hid_t xfer_parms_id, const void *buf);
hid_t file_space_id, hid_t xfer_parms_id, const void *buf);
herr_t H5Dextend (hid_t dataset_id, const hsize_t *size);
#ifdef __cplusplus

1
src/H5E.c
View File

@ -54,6 +54,7 @@ static const H5E_major_mesg_t H5E_major_mesg_g[] = {
{H5E_DATASET, "Dataset interface"},
{H5E_STORAGE, "Data storage layer"},
{H5E_TEMPLATE, "Property list interface"},
{H5E_COMP, "Data compression layer"},
{H5E_EFL, "External file list"},
};

1
src/H5Epublic.h
View File

@ -46,6 +46,7 @@ typedef enum H5E_major_t {
H5E_DATASET, /*Dataset */
H5E_STORAGE, /*data storage */
H5E_TEMPLATE, /*Property lists */
H5E_COMP, /*Data compression */
H5E_EFL /*External file list */
} H5E_major_t;

33
src/H5Farray.c
View File

@ -112,7 +112,7 @@ H5F_arr_create (H5F_t *f, struct H5O_layout_t *layout/*in,out*/)
*/
herr_t
H5F_arr_read (H5F_t *f, const struct H5O_layout_t *layout,
const struct H5O_efl_t *efl,
const struct H5O_compress_t *comp, const struct H5O_efl_t *efl,
const hsize_t _hslab_size[], const hsize_t mem_size[],
const hssize_t mem_offset[], const hssize_t file_offset[],
void *_buf/*out*/)
@ -173,6 +173,14 @@ H5F_arr_read (H5F_t *f, const struct H5O_layout_t *layout,
"negative offsets are not valid");
}
}
/*
* Compression cannot be used for contiguous data.
*/
if (comp && H5Z_NONE!=comp->method) {
HRETURN_ERROR (H5E_IO, H5E_READERROR, FAIL,
"compression is not allowed for contiguous data");
}
/*
* Calculate the strides needed to walk through the array on disk
@ -270,7 +278,8 @@ printf("nelmts=%lu, min=%lu, max=%lu\n", temp, min, max);
"unable to copy into a proper hyperslab");
}
}
if (H5F_istore_read (f, layout, file_offset, hslab_size, buf)<0) {
if (H5F_istore_read (f, layout, comp, file_offset, hslab_size,
buf)<0) {
HRETURN_ERROR (H5E_IO, H5E_READERROR, FAIL, "chunked read failed");
}
break;
@ -313,9 +322,10 @@ printf("nelmts=%lu, min=%lu, max=%lu\n", temp, min, max);
*/
herr_t
H5F_arr_write (H5F_t *f, const struct H5O_layout_t *layout,
const struct H5O_efl_t *efl, const hsize_t _hslab_size[],
const hsize_t mem_size[], const hssize_t mem_offset[],
const hssize_t file_offset[], const void *_buf)
const struct H5O_compress_t *comp, const struct H5O_efl_t *efl,
const hsize_t _hslab_size[], const hsize_t mem_size[],
const hssize_t mem_offset[], const hssize_t file_offset[],
const void *_buf)
{
const uint8 *buf = (const uint8 *)_buf; /*cast for arithmetic */
hssize_t file_stride[H5O_LAYOUT_NDIMS]; /*strides through file */
@ -369,10 +379,18 @@ H5F_arr_write (H5F_t *f, const struct H5O_layout_t *layout,
*/
for (i=0; i<ndims; i++) {
if (mem_offset[i]<0 || file_offset[i]<0) {
HRETURN_ERROR (H5E_IO, H5E_READERROR, FAIL,
HRETURN_ERROR (H5E_IO, H5E_WRITEERROR, FAIL,
"negative offsets are not valid");
}
}
/*
* Compression cannot be used for contiguous data
*/
if (comp && H5Z_NONE!=comp->method) {
HRETURN_ERROR (H5E_IO, H5E_WRITEERROR, FAIL,
"compression is not allowed for contiguous data");
}
/*
* Calculate the strides needed to walk through the array on disk.
@ -471,7 +489,8 @@ printf("nelmts=%lu, min=%lu, max=%lu\n", temp, min, max);
"unable to copy from a proper hyperslab");
}
}
if (H5F_istore_write (f, layout, file_offset, hslab_size, buf)<0) {
if (H5F_istore_write (f, layout, comp, file_offset, hslab_size,
buf)<0) {
HRETURN_ERROR (H5E_IO, H5E_WRITEERROR, FAIL,
"chunked write failed");
}

785
src/H5Fistore.c
View File

@ -14,17 +14,9 @@
#include <H5Oprivate.h>
#include <H5Vprivate.h>
typedef enum H5F_isop_t {
H5F_ISTORE_READ, /*read from file to memory */
H5F_ISTORE_WRITE /*write from memory to file */
} H5F_isop_t;
/* Does the array domain include negative indices? */
#undef H5F_ISTORE_NEGATIVE_DOMAIN
#define PABLO_MASK H5F_istore_mask
/* Interface initialization */
#define PABLO_MASK H5F_istore_mask
static hbool_t interface_initialize_g = FALSE;
#define INTERFACE_INIT NULL
@ -48,13 +40,8 @@ static herr_t H5F_istore_decode_key(H5F_t *f, H5B_t *bt, uint8 *raw,
void *_key);
static herr_t H5F_istore_encode_key(H5F_t *f, H5B_t *bt, uint8 *raw,
void *_key);
static herr_t H5F_istore_copy_hyperslab(H5F_t *f, const H5O_layout_t *layout,
H5F_isop_t op,
const hssize_t offset_f[],
const hsize_t size[],
const hssize_t offset_m[],
const hsize_t size_m[],
void *buf);
static herr_t H5F_istore_debug_key (FILE *stream, intn indent, intn fwidth,
const void *key, const void *udata);
/*
* B-tree key. A key contains the minimum logical N-dimensional address and
@ -68,12 +55,11 @@ static herr_t H5F_istore_copy_hyperslab(H5F_t *f, const H5O_layout_t *layout,
* Only the first few values of the OFFSET and SIZE fields are actually
* stored on disk, depending on the dimensionality.
*
* The storage file address is part of the B-tree and not part of the key.
* The chunk's file address is part of the B-tree and not part of the key.
*/
typedef struct H5F_istore_key_t {
uintn file_number; /*external file number */
hsize_t nbytes; /*size of stored data */
hssize_t offset[H5O_LAYOUT_NDIMS]; /*logical offset to start*/
hsize_t size[H5O_LAYOUT_NDIMS]; /*logical chunk size */
} H5F_istore_key_t;
typedef struct H5F_istore_ud1_t {
@ -97,6 +83,7 @@ H5B_class_t H5B_ISTORE[1] = {{
NULL, /*list */
H5F_istore_decode_key, /*decode */
H5F_istore_encode_key, /*encode */
H5F_istore_debug_key, /*debug */
}};
@ -128,9 +115,8 @@ H5F_istore_sizeof_rkey(H5F_t __unused__ *f, const void *_udata)
assert(udata);
assert(udata->mesg.ndims > 0 && udata->mesg.ndims <= H5O_LAYOUT_NDIMS);
nbytes = 4 + /*external file number */
udata->mesg.ndims * 4 + /*dimension indices */
udata->mesg.ndims * 4; /*dimension sizes */
nbytes = 4 + /*storage size */
udata->mesg.ndims * 4; /*dimension indices */
return nbytes;
}
@ -157,7 +143,7 @@ H5F_istore_decode_key(H5F_t __unused__ *f, H5B_t *bt, uint8 *raw, void *_key)
{
H5F_istore_key_t *key = (H5F_istore_key_t *) _key;
intn i;
intn ndims = (intn)(bt->sizeof_rkey/8);
intn ndims = (intn)((bt->sizeof_rkey-4)/4);
FUNC_ENTER(H5F_istore_decode_key, FAIL);
@ -169,11 +155,9 @@ H5F_istore_decode_key(H5F_t __unused__ *f, H5B_t *bt, uint8 *raw, void *_key)
assert(ndims > 0 && ndims <= H5O_LAYOUT_NDIMS);
/* decode */
UINT32DECODE(raw, key->file_number);
assert(0 == key->file_number);
UINT32DECODE (raw, key->nbytes);
for (i = 0; i < ndims; i++) {
UINT32DECODE(raw, key->offset[i]);
UINT32DECODE(raw, key->size[i]);
}
FUNC_LEAVE(SUCCEED);
@ -200,7 +184,7 @@ static herr_t
H5F_istore_encode_key(H5F_t __unused__ *f, H5B_t *bt, uint8 *raw, void *_key)
{
H5F_istore_key_t *key = (H5F_istore_key_t *) _key;
intn ndims = (intn)(bt->sizeof_rkey / 8);
intn ndims = (intn)((bt->sizeof_rkey-4) / 4);
intn i;
FUNC_ENTER(H5F_istore_encode_key, FAIL);
@ -213,16 +197,54 @@ H5F_istore_encode_key(H5F_t __unused__ *f, H5B_t *bt, uint8 *raw, void *_key)
assert(ndims > 0 && ndims <= H5O_LAYOUT_NDIMS);
/* encode */
UINT32ENCODE(raw, key->file_number);
assert(0 == key->file_number);
UINT32ENCODE (raw, key->nbytes);
for (i = 0; i < ndims; i++) {
UINT32ENCODE(raw, key->offset[i]);
UINT32ENCODE(raw, key->size[i]);
}
FUNC_LEAVE(SUCCEED);
}
/*-------------------------------------------------------------------------
* Function: H5F_istore_debug_key
*
* Purpose: Prints a key.
*
* Return: Success: SUCCEED
*
* Failure: FAIL
*
* Programmer: Robb Matzke
* Thursday, April 16, 1998
*
* Modifications:
*
*-------------------------------------------------------------------------
*/
static herr_t
H5F_istore_debug_key (FILE *stream, intn indent, intn fwidth,
const void *_key, const void *_udata)
{
const H5F_istore_key_t *key = (const H5F_istore_key_t *)_key;
const H5F_istore_ud1_t *udata = (const H5F_istore_ud1_t *)_udata;
int i;
FUNC_ENTER (H5F_istore_debug_key, FAIL);
assert (key);
HDfprintf (stream, "%*s%-*s %Hd bytes\n", indent, "", fwidth,
"Chunk size:", key->nbytes);
HDfprintf (stream, "%*s%-*s {", indent, "", fwidth,
"Logical offset:");
for (i=0; i<udata->mesg.ndims; i++) {
HDfprintf (stream, "%s%Hd", i?", ":"", key->offset[i]);
}
fputs ("}\n", stream);
FUNC_LEAVE (SUCCEED);
}
/*-------------------------------------------------------------------------
* Function: H5F_istore_cmp2
@ -352,7 +374,6 @@ H5F_istore_new_node(H5F_t *f, H5B_ins_t op,
H5F_istore_key_t *lt_key = (H5F_istore_key_t *) _lt_key;
H5F_istore_key_t *rt_key = (H5F_istore_key_t *) _rt_key;
H5F_istore_ud1_t *udata = (H5F_istore_ud1_t *) _udata;
hsize_t nbytes;
intn i;
FUNC_ENTER(H5F_istore_new_node, FAIL);
@ -366,37 +387,34 @@ H5F_istore_new_node(H5F_t *f, H5B_ins_t op,
assert(addr);
/* Allocate new storage */
nbytes = H5V_vector_reduce_product(udata->mesg.ndims, udata->key.size);
assert(nbytes > 0);
if (H5MF_alloc(f, H5MF_RAW, nbytes, addr /*out */ ) < 0) {
assert (udata->key.nbytes > 0);
if (H5MF_alloc(f, H5MF_RAW, udata->key.nbytes, addr /*out */ ) < 0) {
HRETURN_ERROR(H5E_IO, H5E_CANTINIT, FAIL,
"couldn't allocate new file storage");
}
udata->addr = *addr;
udata->key.file_number = 0;
lt_key->file_number = udata->key.file_number;
if (H5B_INS_LEFT != op)
rt_key->file_number = 0;
/* Initialize the key(s) */
for (i = 0; i < udata->mesg.ndims; i++) {
/*
* The left key describes the storage of the UDATA chunk being
* inserted into the tree.
*/
assert(udata->key.size[i] > 0);
/*
* The left key describes the storage of the UDATA chunk being
* inserted into the tree.
*/
lt_key->nbytes = udata->key.nbytes;
for (i=0; i<udata->mesg.ndims; i++) {
lt_key->offset[i] = udata->key.offset[i];
lt_key->size[i] = udata->key.size[i];
}
/*
* The right key might already be present. If not, then add
* a zero-width chunk.
*/
if (H5B_INS_LEFT != op) {
assert (udata->key.size[i] < MAX_HSSIZET);
/*
* The right key might already be present. If not, then add a zero-width
* chunk.
*/
if (H5B_INS_LEFT != op) {
rt_key->nbytes = 0;
for (i=0; i<udata->mesg.ndims; i++) {
assert (udata->mesg.dim[i] < MAX_HSSIZET);
assert (udata->key.offset[i]+(hssize_t)(udata->mesg.dim[i]) >
udata->key.offset[i]);
rt_key->offset[i] = udata->key.offset[i] +
(hssize_t)udata->key.size[i];
rt_key->size[i] = 0;
(hssize_t)(udata->mesg.dim[i]);
}
}
@ -445,12 +463,10 @@ H5F_istore_found(H5F_t __unused__ *f, const haddr_t *addr,
/* Initialize return values */
udata->addr = *addr;
udata->key.file_number = lt_key->file_number;
assert(0 == lt_key->file_number);
udata->key.nbytes = lt_key->nbytes;
assert (lt_key->nbytes>0);
for (i = 0; i < udata->mesg.ndims; i++) {
udata->key.offset[i] = lt_key->offset[i];
udata->key.size[i] = lt_key->size[i];
assert(lt_key->size[i] > 0);
}
FUNC_LEAVE(SUCCEED);
@ -500,7 +516,6 @@ H5F_istore_insert(H5F_t *f, const haddr_t *addr, void *_lt_key,
H5F_istore_ud1_t *udata = (H5F_istore_ud1_t *) _udata;
intn i, cmp;
H5B_ins_t ret_value = H5B_INS_ERROR;
hsize_t nbytes;
FUNC_ENTER(H5F_istore_insert, H5B_INS_ERROR);
@ -523,46 +538,61 @@ H5F_istore_insert(H5F_t *f, const haddr_t *addr, void *_lt_key,
assert("HDF5 INTERNAL ERROR -- see rpm" && 0);
HRETURN_ERROR(H5E_STORAGE, H5E_UNSUPPORTED, H5B_INS_ERROR,
"internal error");
} else if (H5V_hyper_eq(udata->mesg.ndims,
udata->key.offset, udata->key.size,
lt_key->offset, lt_key->size)) {
} else if (H5V_vector_eq_s (udata->mesg.ndims,
udata->key.offset, lt_key->offset) &&
lt_key->nbytes>0) {
/*
* Already exists. Just return the info.
* Already exists. If the new size is not the same as the old size
* then we should reallocate storage.
*/
#if 1
if (lt_key->nbytes != udata->key.nbytes) {
if (H5MF_realloc (f, H5MF_RAW, lt_key->nbytes, addr,
udata->key.nbytes, new_node/*out*/)<0) {
HRETURN_ERROR (H5E_STORAGE, H5E_WRITEERROR, H5B_INS_ERROR,
"unable to reallocate chunk storage");
}
lt_key->nbytes = udata->key.nbytes;
*lt_key_changed = TRUE;
udata->addr = *new_node;
ret_value = H5B_INS_CHANGE;
} else {
udata->addr = *addr;
ret_value = H5B_INS_NOOP;
}
#else
assert (lt_key->nbytes == udata->key.nbytes);
assert (!H5F_addr_defined (&(udata->addr)) ||
H5F_addr_eq (&(udata->addr), addr));
udata->addr = *addr;
udata->key.file_number = lt_key->file_number;
ret_value = H5B_INS_NOOP;
#endif
} else if (H5V_hyper_disjointp(udata->mesg.ndims,
lt_key->offset, lt_key->size,
udata->key.offset, udata->key.size)) {
lt_key->offset, udata->mesg.dim,
udata->key.offset, udata->mesg.dim)) {
assert(H5V_hyper_disjointp(udata->mesg.ndims,
rt_key->offset, rt_key->size,
udata->key.offset, udata->key.size));
rt_key->offset, udata->mesg.dim,
udata->key.offset, udata->mesg.dim));
/*
* Split this node, inserting the new new node to the right of the
* current node. The MD_KEY is where the split occurs.
*/
md_key->file_number = udata->key.file_number;
for (i=0, nbytes=1; i<udata->mesg.ndims; i++) {
md_key->nbytes = udata->key.nbytes;
for (i=0; i<udata->mesg.ndims; i++) {
assert(0 == udata->key.offset[i] % udata->mesg.dim[i]);
assert(udata->key.size[i] == udata->mesg.dim[i]);
md_key->offset[i] = udata->key.offset[i];
md_key->size[i] = udata->key.size[i];
nbytes *= udata->key.size[i];
}
/*
* Allocate storage for the new chunk
*/
if (H5MF_alloc(f, H5MF_RAW, nbytes, new_node /*out */ ) < 0) {
if (H5MF_alloc(f, H5MF_RAW, udata->key.nbytes, new_node/*out*/)<0) {
HRETURN_ERROR(H5E_IO, H5E_CANTINIT, H5B_INS_ERROR,
"file allocation failed");
}
udata->addr = *new_node;
udata->key.file_number = 0;
ret_value = H5B_INS_RIGHT;
} else {
@ -574,223 +604,6 @@ H5F_istore_insert(H5F_t *f, const haddr_t *addr, void *_lt_key,
FUNC_LEAVE(ret_value);
}
/*-------------------------------------------------------------------------
* Function: H5F_istore_copy_hyperslab
*
* Purpose: Reads or writes a hyperslab to disk depending on whether OP
* is H5F_ISTORE_READ or H5F_ISTORE_WRITE. The hyperslab
* storage is described with ISTORE and exists in file F. The
* file hyperslab begins at location OFFSET_F[] (an N-dimensional
* point in the domain in terms of elements) in the file and
* OFFSET_M[] in memory pointed to by BUF. Its size is SIZE[]
* elements. The dimensionality of memory is assumed to be the
* same as the file and the total size of the multi-dimensional
* memory buffer is SIZE_M[].
*
* The slowest varying dimension is always listed first in the
* various offset and size arrays.
*
* A `chunk' is a hyperslab of the disk array which is stored
* contiguously. I/O occurs in units of chunks where the size of
* a chunk is determined by the alignment constraints specified
* in ISTORE.
*
* Return: Success: SUCCEED
*
* Failure: FAIL
*
* Programmer: Robb Matzke
* Friday, October 17, 1997
*
* Modifications:
*
*-------------------------------------------------------------------------
*/
static herr_t
H5F_istore_copy_hyperslab(H5F_t *f, const H5O_layout_t *layout, H5F_isop_t op,
const hssize_t offset_f[], const hsize_t size[],
const hssize_t offset_m[], const hsize_t size_m[],
void *buf/*in or out*/)
{
intn i, carry;
hsize_t idx_cur[H5O_LAYOUT_NDIMS];
hsize_t idx_min[H5O_LAYOUT_NDIMS];
hsize_t idx_max[H5O_LAYOUT_NDIMS];
hsize_t sub_size[H5O_LAYOUT_NDIMS];
hssize_t offset_wrt_chunk[H5O_LAYOUT_NDIMS];
hssize_t sub_offset_m[H5O_LAYOUT_NDIMS];
size_t chunk_size;
hsize_t acc;
uint8 *chunk = NULL;
H5F_istore_ud1_t udata;
herr_t status;
herr_t ret_value = FAIL;
FUNC_ENTER(H5F_istore_copy_hyperslab, FAIL);
/* check args */
assert(f);
assert(layout && H5D_CHUNKED == layout->type);
assert(H5F_addr_defined(&(layout->addr)));
assert(layout->ndims > 0 && layout->ndims <= H5O_LAYOUT_NDIMS);
assert(H5F_ISTORE_READ == op || H5F_ISTORE_WRITE == op);
assert(size);
assert(size_m);
assert(buf);
#ifndef NDEBUG
for (i=0; i<layout->ndims; i++) {
assert(size_m[i] > 0); /*destination must exist */
/*hyperslab must fit in BUF */
assert((offset_m?offset_m[i]:0) + size[i] <= size_m[i]);
assert(layout->dim[i] > 0);
}
#endif
/*
* As a special case of H5F_ISTORE_READ, if the source is aligned on
* a chunk boundary and is the same size as a chunk, and the destination
* is the same size as a chunk, then instead of reading into a temporary
* buffer and then into the destination, we read directly into the
* destination.
*/
if (H5F_ISTORE_READ==op) {
for (i=0, acc=1; i<layout->ndims; i++) {
if (offset_f[i] % layout->dim[i]) break; /*src not aligned*/
if (size[i]!=layout->dim[i]) break; /*src not a chunk*/
if (size_m[i]!=layout->dim[i]) break; /*dst not a chunk*/
udata.key.offset[i] = offset_f[i];
udata.key.size[i] = layout->dim[i];
acc *= layout->dim[i];
}
chunk_size = acc;
assert ((hsize_t)chunk_size==acc);
if (i==layout->ndims) {
udata.mesg = *layout;
H5F_addr_undef (&(udata.addr));
udata.key.file_number = 0;
status = H5B_find (f, H5B_ISTORE, &(layout->addr), &udata);
if (status>=0 && H5F_addr_defined (&(udata.addr))) {
assert (0==udata.key.file_number);
if (H5F_block_read (f, &(udata.addr), (hsize_t)chunk_size,
buf)<0) {
HGOTO_ERROR (H5E_IO, H5E_READERROR, FAIL,
"unable to read raw storage chunk");
}
} else {
HDmemset (buf, 0, chunk_size);
}
HRETURN (SUCCEED);
}
}
/*
* This is the general case. We set up multi-dimensional counters
* (idx_min, idx_max, and idx_cur) and loop through the chunks copying
* each chunk into a temporary buffer, compressing or decompressing, and
* then copying it to it's destination.
*/
for (i=0; i<layout->ndims; i++) {
idx_min[i] = (offset_f?offset_f[i]:0) / layout->dim[i];
idx_max[i] = ((offset_f?offset_f[i]:0) + size[i]-1) / layout->dim[i]+1;
idx_cur[i] = idx_min[i];
}
/* Allocate buffers */
for (i=0, chunk_size=1; i<layout->ndims; i++) {
chunk_size *= layout->dim[i];
}
chunk = H5MM_xmalloc(chunk_size);
/* Initialize non-changing part of udata */
udata.mesg = *layout;
/* Loop over all chunks */
while (1) {
/* Read/Write chunk or create it if it doesn't exist */
udata.mesg.ndims = layout->ndims;
H5F_addr_undef(&(udata.addr));
udata.key.file_number = 0;
for (i=0; i<layout->ndims; i++) {
/* The location and size of the chunk being accessed */
assert (layout->dim[i] < MAX_HSSIZET);
udata.key.offset[i] = idx_cur[i] * (hssize_t)(layout->dim[i]);
udata.key.size[i] = layout->dim[i];
/* The offset and size wrt the chunk */
offset_wrt_chunk[i] = MAX((offset_f?offset_f[i]:0),
udata.key.offset[i]) -
udata.key.offset[i];
sub_size[i] = MIN((idx_cur[i] + 1) * layout->dim[i],
(offset_f ? offset_f[i] : 0) + size[i]) -
(udata.key.offset[i] + offset_wrt_chunk[i]);
/* Offset into mem buffer */
sub_offset_m[i] = udata.key.offset[i] + offset_wrt_chunk[i] +
(offset_m ? offset_m[i] : 0) -
(offset_f ? offset_f[i] : 0);
}
if (H5F_ISTORE_WRITE == op) {
status = H5B_insert(f, H5B_ISTORE, &(layout->addr), &udata);
assert(status >= 0);
} else {
status = H5B_find(f, H5B_ISTORE, &(layout->addr), &udata);
}
/*
* If the operation is reading from the disk or if we are writing a
* partial chunk then load the chunk from disk.
*/
if (H5F_ISTORE_READ == op ||
!H5V_vector_zerop_s(layout->ndims, offset_wrt_chunk) ||
!H5V_vector_eq_u(layout->ndims, sub_size, udata.key.size)) {
if (status>=0 && H5F_addr_defined(&(udata.addr))) {
assert(0==udata.key.file_number);
if (H5F_block_read(f, &(udata.addr), (hsize_t)chunk_size,
chunk) < 0) {
HGOTO_ERROR(H5E_IO, H5E_READERROR, FAIL,
"unable to read raw storage chunk");
}
} else {
HDmemset(chunk, 0, chunk_size);
}
}
/* Transfer data to/from the chunk */
if (H5F_ISTORE_WRITE==op) {
H5V_hyper_copy(layout->ndims, sub_size,
udata.key.size, offset_wrt_chunk, chunk,
size_m, sub_offset_m, buf);
assert(0 == udata.key.file_number);
if (H5F_block_write(f, &(udata.addr), (hsize_t)chunk_size,
chunk) < 0) {
HGOTO_ERROR(H5E_IO, H5E_WRITEERROR, FAIL,
"unable to write raw storage chunk");
}
} else {
H5V_hyper_copy(layout->ndims, sub_size,
size_m, sub_offset_m, (void *)buf,
udata.key.size, offset_wrt_chunk, chunk);
}
/* Increment indices */
for (i=layout->ndims-1, carry=1; i>=0 && carry; --i) {
if (++idx_cur[i]>=idx_max[i]) idx_cur[i] = idx_min[i];
else carry = 0;
}
if (carry) break;
}
ret_value = SUCCEED;
done:
chunk = H5MM_xfree(chunk);
FUNC_LEAVE(ret_value);
}
/*-------------------------------------------------------------------------
* Function: H5F_istore_read
@ -811,23 +624,183 @@ H5F_istore_copy_hyperslab(H5F_t *f, const H5O_layout_t *layout, H5F_isop_t op,
*/
herr_t
H5F_istore_read(H5F_t *f, const H5O_layout_t *layout,
const hssize_t offset[], const hsize_t size[], void *buf)
const H5O_compress_t *comp, const hssize_t offset_f[],
const hsize_t size[], void *buf)
{
hssize_t offset_m[H5O_LAYOUT_NDIMS];
hsize_t size_m[H5O_LAYOUT_NDIMS];
intn i, carry;
hsize_t idx_cur[H5O_LAYOUT_NDIMS];
hsize_t idx_min[H5O_LAYOUT_NDIMS];
hsize_t idx_max[H5O_LAYOUT_NDIMS];
hsize_t sub_size[H5O_LAYOUT_NDIMS];
hssize_t offset_wrt_chunk[H5O_LAYOUT_NDIMS];
hssize_t sub_offset_m[H5O_LAYOUT_NDIMS];
size_t chunk_size;
uint8 *chunk=NULL, *compressed=NULL;
H5F_istore_ud1_t udata;
herr_t status;
herr_t ret_value = FAIL;
FUNC_ENTER(H5F_istore_read, FAIL);
/* Check args */
assert(f);
assert(layout && H5D_CHUNKED == layout->type);
assert(layout->ndims > 0 && layout->ndims <= H5O_LAYOUT_NDIMS);
assert(size);
assert(buf);
assert (f);
assert (layout && H5D_CHUNKED==layout->type);
assert (layout->ndims>0 && layout->ndims<=H5O_LAYOUT_NDIMS);
assert (H5F_addr_defined(&(layout->addr)));
assert (offset_f);
assert (size);
assert (buf);
if (H5F_istore_copy_hyperslab(f, layout, H5F_ISTORE_READ,
offset, size, H5V_ZERO, size, buf) < 0) {
HRETURN_ERROR(H5E_IO, H5E_READERROR, FAIL,
"hyperslab output failure");
/*
* For now, a hyperslab of the file must be read into an array in
* memory.We do not yet support reading into a hyperslab of memory.
*/
for (i=0; i<layout->ndims; i++) {
offset_m[i] = 0;
size_m[i] = size[i];
}
FUNC_LEAVE(SUCCEED);
#ifndef NDEBUG
for (i=0; i<layout->ndims; i++) {
assert (offset_f[i]>=0); /*negative offsets not supported*/
assert (offset_m[i]>=0); /*negative offsets not supported*/
assert (size[i]<MAX_SIZET);
assert(offset_m[i]+(hssize_t)size[i]<=(hssize_t)size_m[i]);
assert(layout->dim[i]>0);
}
#endif
/* Determine the chunk size and allocate buffers */
for (i=0, chunk_size=1; i<layout->ndims; i++) {
chunk_size *= layout->dim[i];
}
chunk = H5MM_xmalloc(chunk_size);
if (comp && H5Z_NONE!=comp->method) {
compressed = H5MM_xmalloc (chunk_size);
}
/*
* As a special case if the source is aligned on a chunk boundary and is
* the same size as a chunk, and the destination is the same size as a
* chunk, then instead of reading into a temporary buffer and then into
* the destination, we read directly into the destination.
*/
for (i=0; i<layout->ndims; i++) {
if (offset_f[i] % layout->dim[i]) break; /*src not aligned*/
if (size[i]!=layout->dim[i]) break; /*src not a chunk*/
if (size_m[i]!=layout->dim[i]) break; /*dst not a chunk*/
udata.key.offset[i] = offset_f[i];
}
if (i==layout->ndims) {
udata.mesg = *layout;
H5F_addr_undef (&(udata.addr));
status = H5B_find (f, H5B_ISTORE, &(layout->addr), &udata);
if (status>=0 && H5F_addr_defined (&(udata.addr))) {
if (compressed && udata.key.nbytes<chunk_size) {
if (H5F_block_read (f, &(udata.addr), udata.key.nbytes,
compressed)<0) {
HGOTO_ERROR (H5E_IO, H5E_READERROR, FAIL,
"unable to read raw storage chunk");
}
if (chunk_size!=H5Z_uncompress (comp, udata.key.nbytes,
compressed, chunk_size, buf)) {
HGOTO_ERROR (H5E_IO, H5E_READERROR, FAIL,
"unable to uncompress raw storage chunk");
}
} else {
assert (udata.key.nbytes==chunk_size);
if (H5F_block_read (f, &(udata.addr), chunk_size, buf)<0) {
HGOTO_ERROR (H5E_IO, H5E_READERROR, FAIL,
"unable to read raw storage chunk");
}
}
} else {
HDmemset (buf, 0, chunk_size);
}
HGOTO_DONE (SUCCEED);
}
/*
* This is the general case. We set up multi-dimensional counters
* (idx_min, idx_max, and idx_cur) and loop through the chunks compressing
* or copying each chunk into a temporary buffer, and then copying it to
* it's destination.
*/
for (i=0; i<layout->ndims; i++) {
idx_min[i] = offset_f[i] / layout->dim[i];
idx_max[i] = (offset_f[i]+size[i]-1) / layout->dim[i] + 1;
idx_cur[i] = idx_min[i];
}
/* Initialize non-changing part of udata */
udata.mesg = *layout;
/* Loop over all chunks */
while (1) {
for (i=0; i<layout->ndims; i++) {
/* The location and size of the chunk being accessed */
assert (layout->dim[i] < MAX_HSSIZET);
udata.key.offset[i] = idx_cur[i] * (hssize_t)(layout->dim[i]);
/* The offset and size wrt the chunk */
offset_wrt_chunk[i] = MAX(offset_f[i], udata.key.offset[i]) -
udata.key.offset[i];
sub_size[i] = MIN((idx_cur[i]+1)*layout->dim[i],
offset_f[i]+size[i]) -
(udata.key.offset[i] + offset_wrt_chunk[i]);
/* Offset into mem buffer */
sub_offset_m[i] = udata.key.offset[i] + offset_wrt_chunk[i] +
offset_m[i] - offset_f[i];
}
/* Read chunk */
H5F_addr_undef(&(udata.addr));
status = H5B_find(f, H5B_ISTORE, &(layout->addr), &udata);
if (status>=0 && H5F_addr_defined(&(udata.addr))) {
if (compressed && udata.key.nbytes<chunk_size) {
if (H5F_block_read (f, &(udata.addr), udata.key.nbytes,
compressed)<0) {
HGOTO_ERROR (H5E_IO, H5E_READERROR, FAIL,
"unable to read raw storage chunk");
}
if (chunk_size!=H5Z_uncompress (comp, udata.key.nbytes,
compressed, chunk_size,
chunk)) {
HGOTO_ERROR (H5E_IO, H5E_READERROR, FAIL,
"unable to uncompress data");
}
} else {
assert (udata.key.nbytes == chunk_size);
if (H5F_block_read(f, &(udata.addr), chunk_size, chunk) < 0) {
HGOTO_ERROR(H5E_IO, H5E_READERROR, FAIL,
"unable to read raw storage chunk");
}
}
} else {
HDmemset(chunk, 0, chunk_size);
}
/* Transfer data from the chunk buffer to the application */
H5V_hyper_copy(layout->ndims, sub_size, size_m, sub_offset_m,
(void *)buf, layout->dim, offset_wrt_chunk, chunk);
/* Increment indices */
for (i=layout->ndims-1, carry=1; i>=0 && carry; --i) {
if (++idx_cur[i]>=idx_max[i]) idx_cur[i] = idx_min[i];
else carry = 0;
}
if (carry) break;
}
ret_value = SUCCEED;
done:
H5MM_xfree(chunk);
H5MM_xfree (compressed);
FUNC_LEAVE(ret_value);
}
@ -850,25 +823,174 @@ H5F_istore_read(H5F_t *f, const H5O_layout_t *layout,
*/
herr_t
H5F_istore_write(H5F_t *f, const H5O_layout_t *layout,
const hssize_t offset[], const hsize_t size[],
const void *buf)
const H5O_compress_t *comp, const hssize_t offset_f[],
const hsize_t size[], const void *buf)
{
hssize_t offset_m[H5O_LAYOUT_NDIMS];
hsize_t size_m[H5O_LAYOUT_NDIMS];
intn i, carry;
hsize_t idx_cur[H5O_LAYOUT_NDIMS];
hsize_t idx_min[H5O_LAYOUT_NDIMS];
hsize_t idx_max[H5O_LAYOUT_NDIMS];
hsize_t sub_size[H5O_LAYOUT_NDIMS];
hssize_t offset_wrt_chunk[H5O_LAYOUT_NDIMS];
hssize_t sub_offset_m[H5O_LAYOUT_NDIMS];
hsize_t chunk_size, nbytes;
uint8 *chunk=NULL, *compressed=NULL, *outbuf;
H5F_istore_ud1_t udata;
herr_t ret_value = FAIL;
FUNC_ENTER(H5F_istore_write, FAIL);
/* Check args */
assert(f);
assert(layout && H5D_CHUNKED == layout->type);
assert(layout->ndims > 0 && layout->ndims <= H5O_LAYOUT_NDIMS);
assert(layout && H5D_CHUNKED==layout->type);
assert(layout->ndims>0 && layout->ndims<=H5O_LAYOUT_NDIMS);
assert(H5F_addr_defined(&(layout->addr)));
assert (offset_f);
assert(size);
assert(buf);
if (H5F_istore_copy_hyperslab(f, layout, H5F_ISTORE_WRITE,
offset, size, H5V_ZERO, size,
(void*)buf) < 0) {
HRETURN_ERROR(H5E_IO, H5E_WRITEERROR, FAIL,
"hyperslab output failure");
/*
* For now the source must not be a hyperslab. It must be an entire
* memory buffer.
*/
for (i=0; i<layout->ndims; i++) {
offset_m[i] = 0;
size_m[i] = size[i];
}
FUNC_LEAVE(SUCCEED);
#ifndef NDEBUG
for (i=0; i<layout->ndims; i++) {
assert (offset_f[i]>=0); /*negative offsets not supported*/
assert (offset_m[i]>=0); /*negative offsets not supported*/
assert(size[i]<MAX_SIZET);
assert(offset_m[i]+(hssize_t)size[i]<=(hssize_t)size_m[i]);
assert(layout->dim[i]>0);
}
#endif
/*
* This is the general case. We set up multi-dimensional counters
* (idx_min, idx_max, and idx_cur) and loop through the chunks copying
* each chunk into a temporary buffer, compressing or decompressing, and
* then copying it to it's destination.
*/
for (i=0; i<layout->ndims; i++) {
idx_min[i] = offset_f[i] / layout->dim[i];
idx_max[i] = (offset_f[i]+size[i]-1) / layout->dim[i] + 1;
idx_cur[i] = idx_min[i];
}
/* Allocate buffers */
for (i=0, chunk_size=1; i<layout->ndims; i++) {
chunk_size *= layout->dim[i];
}
chunk = H5MM_xmalloc(chunk_size);
if (comp && H5Z_NONE!=comp->method) {
compressed = H5MM_xmalloc (chunk_size);
}
/* Initialize non-changing part of udata */
udata.mesg = *layout;
/* Loop over all chunks */
while (1) {
for (i=0; i<layout->ndims; i++) {
/* The location and size of the chunk being accessed */
assert (layout->dim[i] < MAX_HSSIZET);
udata.key.offset[i] = idx_cur[i] * (hssize_t)(layout->dim[i]);
/* The offset and size wrt the chunk */
offset_wrt_chunk[i] = MAX(offset_f[i], udata.key.offset[i]) -
udata.key.offset[i];
sub_size[i] = MIN((idx_cur[i]+1)*layout->dim[i],
offset_f[i]+size[i]) -
(udata.key.offset[i] + offset_wrt_chunk[i]);
/* Offset into mem buffer */
sub_offset_m[i] = udata.key.offset[i] + offset_wrt_chunk[i] +
offset_m[i] - offset_f[i];
}
/*
* If we are writing a partial chunk then load the chunk from disk
* and uncompress it if it exists.
*/
if (!H5V_vector_zerop_s(layout->ndims, offset_wrt_chunk) ||
!H5V_vector_eq_u(layout->ndims, sub_size, layout->dim)) {
if (H5B_find (f, H5B_ISTORE, &(layout->addr), &udata)>=0 &&
H5F_addr_defined (&(udata.addr))) {
if (compressed && udata.key.nbytes<chunk_size) {
if (H5F_block_read(f, &(udata.addr), udata.key.nbytes,
compressed)<0) {
HGOTO_ERROR(H5E_IO, H5E_READERROR, FAIL,
"unable to read raw storage chunk");
}
if (chunk_size!=H5Z_uncompress (comp, udata.key.nbytes,
compressed, chunk_size,
chunk)) {
HGOTO_ERROR (H5E_IO, H5E_READERROR, FAIL,
"unable to uncompress data");
}
} else {
assert (chunk_size==udata.key.nbytes);
if (H5F_block_read(f, &(udata.addr), udata.key.nbytes,
chunk)<0) {
HGOTO_ERROR(H5E_IO, H5E_READERROR, FAIL,
"unable to read raw storage chunk");
}
}
} else {
HDmemset(chunk, 0, chunk_size);
}
}
/* Transfer data to the chunk */
H5V_hyper_copy(layout->ndims, sub_size,
layout->dim, offset_wrt_chunk, chunk,
size_m, sub_offset_m, buf);
/* Compress the chunk */
if (compressed &&
(nbytes=H5Z_compress (comp, chunk_size, chunk, compressed)) &&
nbytes<chunk_size) {
outbuf = compressed;
} else {
outbuf = chunk;
nbytes = chunk_size;
}
/*
* Create the chunk it if it doesn't exist, or reallocate the chunk
* if its size changed. Then write the data into the file.
*/
H5F_addr_undef(&(udata.addr));
udata.key.nbytes = nbytes;
if (H5B_insert(f, H5B_ISTORE, &(layout->addr), &udata)<0) {
HGOTO_ERROR (H5E_IO, H5E_WRITEERROR, FAIL,
"unable to allocate chunk");
}
if (H5F_block_write(f, &(udata.addr), nbytes, outbuf) < 0) {
HGOTO_ERROR(H5E_IO, H5E_WRITEERROR, FAIL,
"unable to write raw storage chunk");
}
/* Increment indices */
for (i=layout->ndims-1, carry=1; i>=0 && carry; --i) {
if (++idx_cur[i]>=idx_max[i]) idx_cur[i] = idx_min[i];
else carry = 0;
}
if (carry) break;
}
ret_value = SUCCEED;
done:
H5MM_xfree(chunk);
H5MM_xfree (compressed);
FUNC_LEAVE(ret_value);
}
@ -921,3 +1043,36 @@ H5F_istore_create(H5F_t *f, H5O_layout_t *layout /*out */ )
FUNC_LEAVE(SUCCEED);
}
/*-------------------------------------------------------------------------
* Function: H5F_istore_debug
*
* Purpose: Debugs a B-tree node for indexed raw data storage.
*
* Return: Success: SUCCEED
*
* Failure: FAIL
*
* Programmer: Robb Matzke
* Thursday, April 16, 1998
*
* Modifications:
*
*-------------------------------------------------------------------------
*/
herr_t
H5F_istore_debug(H5F_t *f, const haddr_t *addr, FILE * stream, intn indent,
intn fwidth, int ndims)
{
H5F_istore_ud1_t udata;
FUNC_ENTER (H5F_istore_debug, FAIL);
HDmemset (&udata, 0, sizeof udata);
udata.mesg.ndims = ndims;
H5B_debug (f, addr, stream, indent, fwidth, H5B_ISTORE, &udata);
FUNC_LEAVE (SUCCEED);
}

2
src/H5Flow.c
View File

@ -586,7 +586,7 @@ H5F_addr_cmp(const haddr_t *a1, const haddr_t *a2)
*-------------------------------------------------------------------------
*/
void
H5F_addr_undef(haddr_t *addr /*out */ )
H5F_addr_undef(haddr_t *addr/*out*/)
{
assert(addr);

7
src/H5Fprivate.h
View File

@ -462,6 +462,7 @@ typedef struct H5F_t {
struct H5O_layout_t; /*forward decl for prototype arguments */
struct H5O_efl_t; /*forward decl for prototype arguments */
struct H5O_compress_t; /*forward decl for prototype arguments */
/* library variables */
extern const H5F_create_t H5F_create_dflt;
@ -476,14 +477,18 @@ H5F_t *H5F_open(const char *name, uintn flags,
herr_t H5F_close(H5F_t *f);
herr_t H5F_debug(H5F_t *f, const haddr_t *addr, FILE * stream, intn indent,
intn fwidth);
herr_t H5F_istore_debug(H5F_t *f, const haddr_t *addr, FILE * stream,
intn indent, intn fwidth, int ndims);
/* Functions that operate on array storage */
herr_t H5F_arr_create(H5F_t *f, struct H5O_layout_t *layout /*in,out*/);
herr_t H5F_arr_read (H5F_t *f, const struct H5O_layout_t *layout,
const struct H5O_compress_t *comp,
const struct H5O_efl_t *efl, const hsize_t _hslab_size[],
const hsize_t mem_size[], const hssize_t mem_offset[],
const hssize_t file_offset[], void *_buf/*out*/);
herr_t H5F_arr_write (H5F_t *f, const struct H5O_layout_t *layout,
const struct H5O_compress_t *comp,
const struct H5O_efl_t *efl, const hsize_t _hslab_size[],
const hsize_t mem_size[], const hssize_t mem_offset[],
const hssize_t file_offset[], const void *_buf);
@ -491,9 +496,11 @@ herr_t H5F_arr_write (H5F_t *f, const struct H5O_layout_t *layout,
/* Functions that operate on indexed storage */
herr_t H5F_istore_create(H5F_t *f, struct H5O_layout_t *layout /*in,out*/);
herr_t H5F_istore_read(H5F_t *f, const struct H5O_layout_t *layout,
const struct H5O_compress_t *comp,
const hssize_t offset[], const hsize_t size[],
void *buf /*out */ );
herr_t H5F_istore_write(H5F_t *f, const struct H5O_layout_t *layout,
const struct H5O_compress_t *comp,
const hssize_t offset[], const hsize_t size[],
const void *buf);

1
src/H5Gnode.c
View File

@ -82,6 +82,7 @@ H5B_class_t H5B_SNODE[1] = {{
H5G_node_iterate, /*list */
H5G_node_decode_key, /*decode */
H5G_node_encode_key, /*encode */
NULL, /*debug key */
}};
/* Interface initialization */

86
src/H5MF.c
View File

@ -128,3 +128,89 @@ H5MF_free(H5F_t __unused__ *f, const haddr_t *addr, hsize_t size)
FUNC_LEAVE(SUCCEED);
}
/*-------------------------------------------------------------------------
* Function: H5MF_realloc
*
* Purpose: Changes the size of an allocated chunk, possibly moving it to
* a new address. The chunk to change is at address ORIG_ADDR
* and is exactly ORIG_SIZE bytes (if these are zero and undef
* then this function acts like H5MF_alloc). The new size will
* be NEW_SIZE and its address is returned though NEW_ADDR (if
* NEW_SIZE is zero then this function acts like H5MF_free and
* an undefined address is returned for NEW_ADDR).
*
* If the new size is less than the old size then the new
* address will be the same as the old address (except for the
* special case where the new size is zero).
*
* If the new size is more than the old size then most likely a
* new address will be returned. However, under certain
* circumstances the library may return the same address.
*
* Return: Success: SUCCEED
*
* Failure: FAIL
*
* Programmer: Robb Matzke
* Thursday, April 16, 1998
*
* Modifications:
*
*-------------------------------------------------------------------------
*/
herr_t
H5MF_realloc (H5F_t *f, intn op, hsize_t orig_size, const haddr_t *orig_addr,
hsize_t new_size, haddr_t *new_addr/*out*/)
{
FUNC_ENTER (H5MF_realloc, FAIL);
if (0==orig_size) {
/* Degenerate to H5MF_alloc() */
assert (!H5F_addr_defined (orig_addr));
if (new_size>0) {
if (H5MF_alloc (f, op, new_size, new_addr/*out*/)<0) {
HRETURN_ERROR (H5E_RESOURCE, H5E_CANTINIT, FAIL,
"unable to allocate new file memory");
}
} else {
H5F_addr_undef (new_addr);
}
} else if (0==new_size) {
/* Degenerate to H5MF_free() */
assert (H5F_addr_defined (orig_addr));
if (H5MF_free (f, orig_addr, orig_size)<0) {
HRETURN_ERROR (H5E_RESOURCE, H5E_CANTINIT, FAIL,
"unable to free old file memory");
}
H5F_addr_undef (new_addr);
} else if (new_size > orig_size) {
/* Size is getting larger */
if (H5MF_alloc (f, op, new_size, new_addr/*out*/)<0) {
HRETURN_ERROR (H5E_RESOURCE, H5E_CANTINIT, FAIL,
"unable to allocate new file memory");
}
if (H5MF_free (f, orig_addr, orig_size)<0) {
HRETURN_ERROR (H5E_RESOURCE, H5E_CANTINIT, FAIL,
"unable to free old file memory");
}
} else {
/* New size is not larger */
#ifdef H5MF_DEBUG
if (new_size<orig_size) {
HDfprintf (stderr, "H5MF: realloc lost %Hd bytes\n",
orig_size-new_size);
}
#endif
*new_addr = *orig_addr;
}
FUNC_LEAVE (SUCCEED);
}

4
src/H5MFprivate.h
View File

@ -39,4 +39,8 @@
*/
herr_t H5MF_alloc (H5F_t *f, intn, hsize_t size, haddr_t *addr/*out*/);
herr_t H5MF_free (H5F_t *f, const haddr_t *addr, hsize_t size);
herr_t H5MF_realloc (H5F_t *f, intn op, hsize_t orig_size,
const haddr_t *orig_addr, hsize_t new_size,
haddr_t *new_addr/*out*/);
#endif

15
src/H5MM.c
View File

@ -169,19 +169,8 @@ H5MM_xstrdup(const char *s)
*-------------------------------------------------------------------------
*/
void *
H5MM_xfree(const void *mem)
H5MM_xfree(void *mem)
{
/*
* free(3) takes a non-const pointer as an argument even though
* conceptually the argument could be a constant because by time
* free() mucks with it's contents, it should already be free :-)
* Instead of passing a const arg to free, which generates a
* compiler warning, we cast it to a non-const arg first. With
* gcc, this results in a warning only if -Wcast-qual is turned on.
*/
void *non_const_mem = (void *) mem;
if (mem)
HDfree(non_const_mem);
if (mem) HDfree(mem);
return NULL;
}

2
src/H5MMprivate.h
View File

@ -29,5 +29,5 @@ void *H5MM_xmalloc (size_t size);
void *H5MM_xcalloc (intn n, size_t size);
void *H5MM_xrealloc (void *mem, size_t size);
char *H5MM_xstrdup (const char *s);
void *H5MM_xfree (const void *mem);
void *H5MM_xfree (void *mem);
#endif

2
src/H5O.c
View File

@ -61,7 +61,7 @@ static const H5O_class_t *const message_type_g[] = {
H5O_LAYOUT, /*0x0008 Data Layout */
NULL, /*0x0009 Not assigned */
NULL, /*0x000A Not assigned */
NULL, /*0x000B Data storage -- compressed object */
H5O_COMPRESS, /*0x000B Data storage -- compressed object */
NULL, /*0x000C Attribute list */
H5O_NAME, /*0x000D Object name */
NULL, /*0x000E Object modification date and time */

291
src/H5Ocomp.c Normal file
View File

@ -0,0 +1,291 @@
/*
* Copyright (C) 1998 NCSA
* All rights reserved.
*
* Programmer: Robb Matzke <matzke@llnl.gov>
* Wednesday, April 15, 1998
*
* Purpose: Data compression message.
*/
#include <H5private.h>
#include <H5Eprivate.h>
#include <H5MMprivate.h>
#include <H5Oprivate.h>
#define PABLO_MASK H5O_comp_mask
/* PRIVATE PROTOTYPES */
static herr_t H5O_comp_encode (H5F_t *f, uint8 *p, const void *mesg);
static void *H5O_comp_decode (H5F_t *f, const uint8 *p, H5HG_t *hobj);
static void *H5O_comp_copy (const void *_mesg, void *_dest);
static size_t H5O_comp_size (H5F_t *f, const void *_mesg);
static herr_t H5O_comp_reset (void *_mesg);
static herr_t H5O_comp_debug (H5F_t *f, const void *_mesg,
FILE * stream, intn indent, intn fwidth);
/* This message derives from H5O */
const H5O_class_t H5O_COMPRESS[1] = {{
H5O_COMPRESS_ID, /* message id number */
"compression", /* message name for debugging */
sizeof(H5O_compress_t), /* native message size */
H5O_comp_decode, /* decode message */
H5O_comp_encode, /* encode message */
H5O_comp_copy, /* copy the native value */
H5O_comp_size, /* size of raw message */
H5O_comp_reset, /* reset method */
NULL, /* share method */
H5O_comp_debug, /* debug the message */
}};
/* Interface initialization */
static hbool_t interface_initialize_g = FALSE;
#define INTERFACE_INIT NULL
/*-------------------------------------------------------------------------
* Function: H5O_comp_decode
*
* Purpose: Decodes a compression message.
*
* Return: Success: Ptr to the native message.
*
* Failure: NULL
*
* Programmer: Robb Matzke
* Wednesday, April 15, 1998
*
* Modifications:
*
*-------------------------------------------------------------------------
*/
static void *
H5O_comp_decode(H5F_t __unused__ *f, const uint8 *p, H5HG_t __unused__ *hobj)
{
H5O_compress_t *comp = NULL;
FUNC_ENTER(H5O_comp_decode, NULL);
/* check args */
assert(p);
/* Decode */
comp = H5MM_xcalloc(1, sizeof *comp);
comp->method = *p++;
comp->flags = *p++;
UINT16DECODE (p, comp->cd_size);
if (comp->cd_size>0) {
comp->client_data = H5MM_xmalloc (comp->cd_size);
HDmemcpy (comp->client_data, p, comp->cd_size);
}
FUNC_LEAVE(comp);
}
/*-------------------------------------------------------------------------
* Function: H5O_comp_encode
*
* Purpose: Encodes message MESG into buffer P.
*
* Return: Success: SUCCEED
*
* Failure: FAIL
*
* Programmer: Robb Matzke
* Wednesday, April 15, 1998
*
* Modifications:
*
*-------------------------------------------------------------------------
*/
static herr_t
H5O_comp_encode (H5F_t __unused__ *f, uint8 *p/*out*/, const void *mesg)
{
const H5O_compress_t *comp = (const H5O_compress_t*)mesg;
FUNC_ENTER (H5O_comp_encode, FAIL);
/* Check args */
assert (p);
assert (mesg);
*p++ = comp->method;
*p++ = comp->flags;
UINT16ENCODE (p, comp->cd_size);
if (comp->cd_size) {
HDmemcpy (p, comp->client_data, comp->cd_size);
}
FUNC_LEAVE (SUCCEED);
}
/*-------------------------------------------------------------------------
* Function: H5O_comp_copy
*
* Purpose: Copies a compression message from SRC to DST allocating DST
* if necessary. If DST is already allocated then we assume
* that it isn't initialized.
*
* Return: Success: Ptr to DST or allocated result.
*
* Failure: NULL
*
* Programmer: Robb Matzke
* Wednesday, April 15, 1998
*
* Modifications:
*
*-------------------------------------------------------------------------
*/
static void *
H5O_comp_copy (const void *_src, void *_dst/*out*/)
{
const H5O_compress_t *src = (const H5O_compress_t *)_src;
H5O_compress_t *dst = (H5O_compress_t *)_dst;
FUNC_ENTER (H5O_comp_copy, NULL);
if (!dst) dst = H5MM_xmalloc (sizeof *dst);
*dst = *src;
if (src->cd_size>0) {
dst->client_data = H5MM_xmalloc (src->cd_size);
HDmemcpy (dst->client_data, src->client_data, src->cd_size);
}
FUNC_LEAVE (dst);
}
/*-------------------------------------------------------------------------
* Function: H5O_comp_size
*
* Purpose: Determines the size of a raw compression message.
*
* Return: Success: Size of message.
*
* Failure: zero
*
* Programmer: Robb Matzke
* Wednesday, April 15, 1998
*
* Modifications:
*
*-------------------------------------------------------------------------
*/
static size_t
H5O_comp_size (H5F_t __unused__ *f, const void *mesg)
{
const H5O_compress_t *comp = (const H5O_compress_t*)mesg;
FUNC_ENTER (H5O_comp_size, 0);
FUNC_LEAVE (4+comp->cd_size);
}
/*-------------------------------------------------------------------------
* Function: H5O_comp_reset
*
* Purpose: Resets a compression message by freeing the client data and
* setting all fields to zero. The MESG buffer is not freed.
*
* Return: Success: SUCCEED
*
* Failure: FAIL
*
* Programmer: Robb Matzke
* Wednesday, April 15, 1998
*
* Modifications:
*
*-------------------------------------------------------------------------
*/
static herr_t
H5O_comp_reset (void *mesg)
{
H5O_compress_t *comp = (H5O_compress_t*)mesg;
FUNC_ENTER (H5O_comp_reset, FAIL);
assert (comp);
H5MM_xfree (comp->client_data);
HDmemset (comp, 0, sizeof *comp);
FUNC_LEAVE (SUCCEED);
}
/*-------------------------------------------------------------------------
* Function: H5O_comp_debug
*
* Purpose: Prints debugging information for compression message MESG on
* output stream STREAM. Each line is indented INDENT
* characters and the field name takes up FWIDTH characters.
*
* Return: Success: SUCCEED
*
* Failure: FAIL
*
* Programmer: Robb Matzke
* Wednesday, April 15, 1998
*
* Modifications:
*
*-------------------------------------------------------------------------
*/
static herr_t
H5O_comp_debug (H5F_t __unused__ *f, const void *mesg, FILE *stream,
intn indent, intn fwidth)
{
const H5O_compress_t *comp = (const H5O_compress_t *)mesg;
size_t i, j;
FUNC_ENTER(H5O_comp_debug, FAIL);
/* check args */
assert(f);
assert(comp);
assert(stream);
assert(indent >= 0);
assert(fwidth >= 0);
fprintf (stream, "%*s%-*s %d\n", indent, "", fwidth,
"Method:",
(int)(comp->method));
fprintf (stream, "%*s%-*s 0x%02x\n", indent, "", fwidth,
"Flags:",
(unsigned)(comp->flags));
fprintf (stream, "%*s%-*s %lu\n", indent, "", fwidth,
"Size of client data:",
(unsigned long)(comp->cd_size));
if (comp->cd_size>0) {
fprintf (stream, "%*s%s\n", indent, "", "Client Data:");
for (i=0; i<comp->cd_size; i+=16) {
fprintf (stream, "%*s%04d: ", indent+3, "", i);
for (j=0; j<16; j++) {
if (8==j) putc (' ', stream);
if (i+j<comp->cd_size) {
fprintf (stream, "%02x ", comp->client_data[i+j]);
} else {
fputs (" ", stream);
}
}
for (j=0; j<16 && i+j<comp->cd_size; j++) {
if (8==j) putc (' ', stream);
if (comp->client_data[i+j]>' ' &&
comp->client_data[i+j]<='~') {
putc (comp->client_data[i+j], stream);
} else {
putc ('.', stream);
}
putc ('\n', stream);
}
}
} else {
fprintf (stream, "%*s%-*s None\n", indent, "", fwidth, "Client Data:");
}
FUNC_LEAVE(SUCCEED);
}

14
src/H5Oprivate.h
View File

@ -26,6 +26,7 @@
#include <H5HGprivate.h>
#include <H5Tprivate.h>
#include <H5Sprivate.h>
#include <H5Zprivate.h>
/*
* Align messages on 8-byte boundaries because we would like to copy the
@ -165,6 +166,19 @@ typedef struct H5O_layout_t {
hsize_t dim[H5O_LAYOUT_NDIMS]; /*size of data or chunk */
} H5O_layout_t;
/*
* Compression message.
*/
#define H5O_COMPRESS_ID 0x000b
extern const H5O_class_t H5O_COMPRESS[1];
typedef struct H5O_compress_t {
H5Z_method_t method; /*algorithm ID */
uintn flags; /*flags */
size_t cd_size; /*client data size */
uint8 *client_data; /*client data passed to algorithm */
} H5O_compress_t;
/*
* Object name message.
*/

173
src/H5P.c
View File

@ -942,7 +942,7 @@ H5Pget_chunk(hid_t tid, int max_ndims, hsize_t dim[]/*out*/)
if (H5P_DATASET_CREATE != H5Pget_class(tid) ||
NULL == (tmpl = H5I_object(tid))) {
HRETURN_ERROR(H5E_ARGS, H5E_BADTYPE, FAIL,
"not a dataset creation template");
"not a dataset creation property list");
}
if (H5D_CHUNKED != tmpl->layout) {
HRETURN_ERROR(H5E_ARGS, H5E_BADVALUE, FAIL,
@ -1847,7 +1847,178 @@ H5Pget_preserve (hid_t plist_id)
FUNC_LEAVE (plist->need_bkg?TRUE:FALSE);
}
/*-------------------------------------------------------------------------
* Function: H5Pset_compression
*
* Purpose: Sets the compression method in a dataset creation property
* list. This sets default values for the compression
* attributes by setting the flags to zero and supplying no
* compression client data. It's probably better to use
* specific compression initialization functions like
* H5Pset_deflate().
*
* Return: Success: SUCCEED
*
* Failure: FAIL
*
* Programmer: Robb Matzke
* Wednesday, April 15, 1998
*
* Modifications:
*
*-------------------------------------------------------------------------
*/
herr_t
H5Pset_compression (hid_t plist_id, H5Z_method_t method)
{
H5D_create_t *plist = NULL;
FUNC_ENTER (H5Pset_compression, FAIL);
/* Check arguments */
if (H5P_DATASET_CREATE!=H5Pget_class (plist_id) ||
NULL==(plist=H5I_object (plist_id))) {
HRETURN_ERROR (H5E_ARGS, H5E_BADTYPE, FAIL,
"not a dataset creation property list");
}
if (method<0 || method>H5Z_MAXVAL) {
HRETURN_ERROR (H5E_ARGS, H5E_BADVALUE, FAIL,
"invalid compression method");
}
/* Clear any previous compression method info, then set new value */
H5O_reset (H5O_COMPRESS, &(plist->compress));
plist->compress.method = method;
FUNC_LEAVE (SUCCEED);
}
/*-------------------------------------------------------------------------
* Function: H5Pget_compression
*
* Purpose: Gets the compression method information from a dataset
* creation property list.
*
* Return: Success: Compression method.
*
* Failure: FAIL
*
* Programmer: Robb Matzke
* Wednesday, April 15, 1998
*
* Modifications:
*
*-------------------------------------------------------------------------
*/
H5Z_method_t
H5Pget_compression (hid_t plist_id)
{
H5D_create_t *plist = NULL;
FUNC_ENTER (H5Pget_compression, FAIL);
/* Check arguments */
if (H5P_DATASET_CREATE!=H5Pget_class (plist_id) ||
NULL==(plist=H5I_object (plist_id))) {
HRETURN_ERROR (H5E_ARGS, H5E_BADTYPE, FAIL,
"not a dataset creation property list");
}
FUNC_LEAVE (plist->compress.method);
}
/*-------------------------------------------------------------------------
* Function: H5Pset_deflate
*
* Purpose: Sets the compression method for a dataset creation property
* list to H5D_COMPRESS_DEFLATE and the compression level to
* LEVEL which should be a value between zero and nine,
* inclusive. Lower compression levels are faster but result in
* less compression. This is the same algorithm as used by the
* GNU gzip program.
*
* Return: Success: SUCCEED
*
* Failure: FAIL
*
* Programmer: Robb Matzke
* Wednesday, April 15, 1998
*
* Modifications:
*
*-------------------------------------------------------------------------
*/
herr_t
H5Pset_deflate (hid_t plist_id, int level)
{
H5D_create_t *plist = NULL;
FUNC_ENTER (H5Pset_deflate, FAIL);
/* Check arguments */
if (H5P_DATASET_CREATE!=H5Pget_class (plist_id) ||
NULL==(plist=H5I_object (plist_id))) {
HRETURN_ERROR (H5E_ARGS, H5E_BADTYPE, FAIL,
"not a dataset creation property list");
}
if (level<0 || level>9) {
HRETURN_ERROR (H5E_ARGS, H5E_BADVALUE, FAIL,
"invalid deflate level");
}
/* Clear previous compression parameters */
H5O_reset (H5O_COMPRESS, &(plist->compress));
plist->compress.method = H5Z_DEFLATE;
plist->compress.flags = level;
FUNC_LEAVE (SUCCEED);
}
/*-------------------------------------------------------------------------
* Function: H5Pget_deflate
*
* Purpose: Returns the deflate compression level from a dataset creation
* property list that uses that method.
*
* Return: Success: A value between zero and nine, inclusive.
* Smaller values indicate faster compression
* while higher values indicate better
* compression ratios.
*
* Failure: FAIL
*
* Programmer: Robb Matzke
* Wednesday, April 15, 1998
*
* Modifications:
*
*-------------------------------------------------------------------------
*/
int
H5Pget_deflate (hid_t plist_id)
{
H5D_create_t *plist = NULL;
FUNC_ENTER (H5Pget_deflate, FAIL);
/* Check arguments */
if (H5P_DATASET_CREATE!=H5Pget_class (plist_id) ||
NULL==(plist=H5I_object (plist_id))) {
HRETURN_ERROR (H5E_ARGS, H5E_BADTYPE, FAIL,
"not a dataset creation property list");
}
if (H5Z_DEFLATE!=plist->compress.method) {
HRETURN_ERROR (H5E_ARGS, H5E_BADVALUE, FAIL,
"deflate method is not being used");
}
FUNC_LEAVE (plist->compress.flags % 10);
}
#ifdef HAVE_PARALLEL

5
src/H5Ppublic.h
View File

@ -25,6 +25,7 @@
#include <H5Ipublic.h>
#include <H5Dpublic.h>
#include <H5Fpublic.h>
#include <H5Zpublic.h>
/* Template classes */
typedef enum H5P_class_t {
@ -87,6 +88,10 @@ herr_t H5Pset_buffer (hid_t plist_id, size_t size, void *tconv, void *bkg);
size_t H5Pget_buffer (hid_t plist_id, void **tconv/*out*/, void **bkg/*out*/);
herr_t H5Pset_preserve (hid_t plist_id, hbool_t status);
int H5Pget_preserve (hid_t plist_id);
herr_t H5Pset_compression (hid_t plist_id, H5Z_method_t method);
H5Z_method_t H5Pget_compression (hid_t plist_id);
herr_t H5Pset_deflate (hid_t plist_id, int level);
int H5Pget_deflate (hid_t plist_id);
#ifdef HAVE_PARALLEL
herr_t H5Pset_mpi (hid_t tid, MPI_Comm comm, MPI_Info info);

8
src/H5Sprivate.h
View File

@ -70,6 +70,7 @@ typedef struct H5S_tconv_t {
/* Gather elements from disk to type conversion buffer */
size_t (*fgath)(H5F_t *f, const struct H5O_layout_t *layout,
const struct H5O_compress_t *comp,
const struct H5O_efl_t *efl, size_t elmt_size,
const H5S_t *file_space, const H5S_number_t *numbering,
size_t start, size_t nelmts, void *tconv_buf/*out*/);
@ -86,18 +87,21 @@ typedef struct H5S_tconv_t {
/* Scatter elements from type conversion buffer to disk */
herr_t (*fscat)(H5F_t *f, const struct H5O_layout_t *layout,
const struct H5O_compress_t *compress,
const struct H5O_efl_t *efl, size_t elmt_size,
const H5S_t *file_space, const H5S_number_t *numbering,
size_t start, size_t nelmts, const void *tconv_buf);
/* Read from file to application w/o intermediate scratch buffer */
herr_t (*read)(H5F_t *f, const struct H5O_layout_t *layout,
const struct H5O_compress_t *comp,
const struct H5O_efl_t *efl, size_t elmt_size,
const H5S_t *file_space, const H5S_t *mem_space,
void *buf/*out*/);
/* Write directly from app buffer to file */
herr_t (*write)(H5F_t *f, const struct H5O_layout_t *layout,
const struct H5O_compress_t *comp,
const struct H5O_efl_t *efl, size_t elmt_size,
const H5S_t *file_space, const H5S_t *mem_space,
const void *buf);
@ -125,6 +129,7 @@ size_t H5S_simp_init (const struct H5O_layout_t *layout,
const H5S_t *mem_space, const H5S_t *file_space,
size_t desired_nelmts, H5S_number_t *numbering/*out*/);
size_t H5S_simp_fgath (H5F_t *f, const struct H5O_layout_t *layout,
const struct H5O_compress_t *comp,
const struct H5O_efl_t *efl, size_t elmt_size,
const H5S_t *file_space, const H5S_number_t *numbering,
size_t start, size_t nelmts, void *tconv_buf/*out*/);
@ -135,14 +140,17 @@ size_t H5S_simp_mgath (const void *buf, size_t elmt_size,
const H5S_t *mem_space, const H5S_number_t *numbering,
size_t start, size_t nelmts, void *tconv_buf/*out*/);
herr_t H5S_simp_fscat (H5F_t *f, const struct H5O_layout_t *layout,
const struct H5O_compress_t *comp,
const struct H5O_efl_t *efl, size_t elmt_size,
const H5S_t *file_space, const H5S_number_t *numbering,
size_t start, size_t nelmts, const void *tconv_buf);
herr_t H5S_simp_read (H5F_t *f, const struct H5O_layout_t *layout,
const struct H5O_compress_t *comp,
const struct H5O_efl_t *efl, size_t elmt_size,
const H5S_t *file_space, const H5S_t *mem_space,
void *buf/*out*/);
herr_t H5S_simp_write (H5F_t *f, const struct H5O_layout_t *layout,
const struct H5O_compress_t *comp,
const struct H5O_efl_t *efl, size_t elmt_size,
const H5S_t *file_space, const H5S_t *mem_space,
const void *buf);

24
src/H5Ssimp.c
View File

@ -124,7 +124,7 @@ H5S_simp_init (const struct H5O_layout_t __unused__ *layout,
*/
size_t
H5S_simp_fgath (H5F_t *f, const struct H5O_layout_t *layout,
const struct H5O_efl_t *efl,
const struct H5O_compress_t *comp, const struct H5O_efl_t *efl,
size_t elmt_size, const H5S_t *file_space,
const H5S_number_t __unused__ *numbering,
size_t start, size_t nelmts, void *buf/*out*/)
@ -184,7 +184,7 @@ H5S_simp_fgath (H5F_t *f, const struct H5O_layout_t *layout,
/*
* Gather from file.
*/
if (H5F_arr_read (f, layout, efl, hsize, hsize, zero, file_offset,
if (H5F_arr_read (f, layout, comp, efl, hsize, hsize, zero, file_offset,
buf/*out*/)<0) {
HRETURN_ERROR (H5E_DATASPACE, H5E_READERROR, 0, "read error");
}
@ -408,7 +408,7 @@ H5S_simp_mgath (const void *buf, size_t elmt_size,
*/
herr_t
H5S_simp_fscat (H5F_t *f, const struct H5O_layout_t *layout,
const struct H5O_efl_t *efl,
const struct H5O_compress_t *comp, const struct H5O_efl_t *efl,
size_t elmt_size, const H5S_t *file_space,
const H5S_number_t __unused__ *numbering,
size_t start, size_t nelmts, const void *buf)
@ -468,7 +468,7 @@ H5S_simp_fscat (H5F_t *f, const struct H5O_layout_t *layout,
/*
* Scatter to file.
*/
if (H5F_arr_write (f, layout, efl, hsize, hsize, zero,
if (H5F_arr_write (f, layout, comp, efl, hsize, hsize, zero,
file_offset, buf)<0) {
HRETURN_ERROR (H5E_DATASPACE, H5E_WRITEERROR, FAIL, "write error");
}
@ -499,9 +499,9 @@ H5S_simp_fscat (H5F_t *f, const struct H5O_layout_t *layout,
*/
herr_t
H5S_simp_read (H5F_t *f, const struct H5O_layout_t *layout,
const struct H5O_efl_t *efl, size_t elmt_size,
const H5S_t *file_space, const H5S_t *mem_space,
void *buf/*out*/)
const struct H5O_compress_t *comp, const struct H5O_efl_t *efl,
size_t elmt_size, const H5S_t *file_space,
const H5S_t *mem_space, void *buf/*out*/)
{
hssize_t file_offset[H5O_LAYOUT_NDIMS];
hsize_t hslab_size[H5O_LAYOUT_NDIMS];
@ -573,7 +573,7 @@ H5S_simp_read (H5F_t *f, const struct H5O_layout_t *layout,
mem_offset[file_space->u.simple.rank] = 0;
/* Read the hyperslab */
if (H5F_arr_read (f, layout, efl, hslab_size,
if (H5F_arr_read (f, layout, comp, efl, hslab_size,
mem_size, mem_offset, file_offset, buf)<0) {
HRETURN_ERROR (H5E_IO, H5E_READERROR, FAIL, "unable to read dataset");
}
@ -604,9 +604,9 @@ H5S_simp_read (H5F_t *f, const struct H5O_layout_t *layout,
*/
herr_t
H5S_simp_write (H5F_t *f, const struct H5O_layout_t *layout,
const struct H5O_efl_t *efl, size_t elmt_size,
const H5S_t *file_space, const H5S_t *mem_space,
const void *buf)
const struct H5O_compress_t *comp, const struct H5O_efl_t *efl,
size_t elmt_size, const H5S_t *file_space,
const H5S_t *mem_space, const void *buf)
{
hssize_t file_offset[H5O_LAYOUT_NDIMS];
hsize_t hslab_size[H5O_LAYOUT_NDIMS];
@ -678,7 +678,7 @@ H5S_simp_write (H5F_t *f, const struct H5O_layout_t *layout,
mem_offset[file_space->u.simple.rank] = 0;
/* Write the hyperslab */
if (H5F_arr_write (f, layout, efl, hslab_size,
if (H5F_arr_write (f, layout, comp, efl, hslab_size,
mem_size, mem_offset, file_offset, buf)<0) {
HRETURN_ERROR (H5E_IO, H5E_WRITEERROR, FAIL,
"unable to write dataset");

133
src/H5T.c
View File

@ -231,15 +231,17 @@ H5T_init_interface(void)
* Register conversion functions beginning with the most general and
* ending with the most specific.
*/
if (H5Tregister_soft(H5T_INTEGER, H5T_INTEGER, H5T_conv_order) < 0) {
if (H5Tregister_soft("ibo", H5T_INTEGER, H5T_INTEGER,
H5T_conv_order) < 0) {
HRETURN_ERROR(H5E_DATATYPE, H5E_CANTINIT, FAIL,
"unable to register conversion function");
}
if (H5Tregister_soft(H5T_FLOAT, H5T_FLOAT, H5T_conv_order) < 0) {
if (H5Tregister_soft("fbo", H5T_FLOAT, H5T_FLOAT, H5T_conv_order) < 0) {
HRETURN_ERROR(H5E_DATATYPE, H5E_CANTINIT, FAIL,
"unable to register conversion function");
}
if (H5Tregister_soft (H5T_COMPOUND, H5T_COMPOUND, H5T_conv_struct)<0) {
if (H5Tregister_soft ("struct", H5T_COMPOUND, H5T_COMPOUND,
H5T_conv_struct)<0) {
HRETURN_ERROR (H5E_DATATYPE, H5E_CANTINIT, FAIL,
"unable to register conversion function");
}
@ -268,10 +270,14 @@ H5T_init_interface(void)
static void
H5T_term_interface(void)
{
int i;
intn i;
H5T_path_t *path = NULL;
H5T_cdata_t *pcdata = NULL;
H5T_conv_t cfunc = NULL;
#ifdef H5T_DEBUG
intn nprint=0;
hsize_t nbytes;
#endif
/* Unregister all conversion functions */
for (i=0; i<H5T_npath_g; i++) {
@ -286,6 +292,29 @@ H5T_term_interface(void)
#endif
H5E_clear(); /*ignore the error*/
}
#ifdef H5T_DEBUG
if (0==nprint++) {
HDfprintf (stderr, "H5T: type conversion statistics "
"accumulated over life of library:\n");
HDfprintf (stderr, " %-*s %8s/%-5s %8s %8s %8s %15s\n",
H5T_NAMELEN-1, "Name", "Elmts", "Calls", "User",
"System", "Elapsed", "Bandwidth");
HDfprintf (stderr, " %-*s %8s-%-5s %8s %8s %8s %15s\n",
H5T_NAMELEN-1, "----", "-----", "-----", "----",
"------", "-------", "---------");
}
nbytes = MAX (H5T_get_size (path->src), H5T_get_size (path->dst));
nbytes *= path->cdata.stats->nelmts;
HDfprintf (stderr, " %-*s %8Hd/%-5d %8.2f %8.2f %8.2f %15g\n",
H5T_NAMELEN-1, path->name,
path->cdata.stats->nelmts,
path->cdata.stats->ncalls,
path->cdata.stats->timer.utime,
path->cdata.stats->timer.stime,
path->cdata.stats->timer.etime,
nbytes / path->cdata.stats->timer.etime);
#endif
H5MM_xfree (path->cdata.stats);
}
}
@ -2276,7 +2305,7 @@ H5Tis_shared (hid_t loc_id, hid_t type_id)
*-------------------------------------------------------------------------
*/
herr_t
H5Tregister_hard(hid_t src_id, hid_t dst_id, H5T_conv_t func)
H5Tregister_hard(const char *name, hid_t src_id, hid_t dst_id, H5T_conv_t func)
{
H5T_t *src = NULL;
H5T_t *dst = NULL;
@ -2286,6 +2315,10 @@ H5Tregister_hard(hid_t src_id, hid_t dst_id, H5T_conv_t func)
FUNC_ENTER(H5Tregister_hard, FAIL);
/* Check args */
if (!name || !*name) {
HRETURN_ERROR (H5E_ARGS, H5E_BADTYPE, FAIL,
"conversion must have a name for debugging");
}
if (H5_DATATYPE != H5I_group(src_id) ||
NULL == (src = H5I_object(src_id)) ||
H5_DATATYPE != H5I_group(dst_id) ||
@ -2294,7 +2327,7 @@ H5Tregister_hard(hid_t src_id, hid_t dst_id, H5T_conv_t func)
}
/* Locate or create a new conversion path */
if (NULL == (path = H5T_path_find(src, dst, TRUE, func))) {
if (NULL == (path = H5T_path_find(name, src, dst, TRUE, func))) {
HRETURN_ERROR(H5E_DATATYPE, H5E_CANTINIT, FAIL,
"unable to locate/allocate conversion path");
}
@ -2334,7 +2367,8 @@ H5Tregister_hard(hid_t src_id, hid_t dst_id, H5T_conv_t func)
*-------------------------------------------------------------------------
*/
herr_t
H5Tregister_soft(H5T_class_t src_cls, H5T_class_t dst_cls, H5T_conv_t func)
H5Tregister_soft(const char *name, H5T_class_t src_cls, H5T_class_t dst_cls,
H5T_conv_t func)
{
intn i;
hid_t src_id, dst_id;
@ -2343,6 +2377,10 @@ H5Tregister_soft(H5T_class_t src_cls, H5T_class_t dst_cls, H5T_conv_t func)
FUNC_ENTER(H5Tregister_soft, FAIL);
/* Check args */
if (!name || !*name) {
HRETURN_ERROR (H5E_ARGS, H5E_BADTYPE, FAIL,
"conversion must have a name for debugging");
}
if (src_cls < 0 || src_cls >= H5T_NCLASSES ||
dst_cls < 0 || dst_cls >= H5T_NCLASSES) {
HRETURN_ERROR(H5E_ARGS, H5E_BADVALUE, FAIL,
@ -2359,6 +2397,8 @@ H5Tregister_soft(H5T_class_t src_cls, H5T_class_t dst_cls, H5T_conv_t func)
H5T_soft_g = H5MM_xrealloc(H5T_soft_g,
H5T_asoft_g * sizeof(H5T_soft_t));
}
HDstrncpy (H5T_soft_g[H5T_nsoft_g].name, name, H5T_NAMELEN);
H5T_soft_g[H5T_nsoft_g].name[H5T_NAMELEN-1] = '\0';
H5T_soft_g[H5T_nsoft_g].src = src_cls;
H5T_soft_g[H5T_nsoft_g].dst = dst_cls;
H5T_soft_g[H5T_nsoft_g].func = func;
@ -2387,6 +2427,7 @@ H5Tregister_soft(H5T_class_t src_cls, H5T_class_t dst_cls, H5T_conv_t func)
HDmemset (&cdata, 0, sizeof cdata);
cdata.command = H5T_CONV_INIT;
cdata.stats = H5MM_xcalloc (1, sizeof(H5T_stats_t));
if ((func) (src_id, dst_id, &cdata, 0, NULL, NULL) >= 0) {
/*
* Free resources used by the previous conversion function. We
@ -2403,9 +2444,14 @@ H5Tregister_soft(H5T_class_t src_cls, H5T_class_t dst_cls, H5T_conv_t func)
#endif
H5E_clear();
}
H5MM_xfree (path->cdata.stats);
}
HDstrncpy (path->name, name, H5T_NAMELEN);
path->name[H5T_NAMELEN-1] = '\0';
path->func = func;
path->cdata = cdata;
} else {
H5MM_xfree (cdata.stats);
}
/* Release temporary atoms */
@ -2475,6 +2521,7 @@ H5Tunregister(H5T_conv_t func)
#endif
H5E_clear();
}
H5MM_xfree (path->cdata.stats);
HDmemset (&(path->cdata), 0, sizeof(H5T_cdata_t));
/*
@ -2500,8 +2547,10 @@ H5Tunregister(H5T_conv_t func)
}
path->cdata.command = H5T_CONV_INIT;
path->cdata.stats = H5MM_xcalloc (1, sizeof(H5T_stats_t));
if ((H5T_soft_g[j].func)(src_id, dst_id, &(path->cdata),
0, NULL, NULL) >= 0) {
HDstrcpy (path->name, H5T_soft_g[j].name);
path->func = H5T_soft_g[j].func;
} else {
H5E_clear();
@ -3348,6 +3397,9 @@ H5T_cmp(const H5T_t *dt1, const H5T_t *dt2)
* H5T_BKG_YES then a pointer to the H5T_conv_noop() function is
* returned.
*
* NAME is assigned to the conversion path if the path is
* created. The name is only for debugging.
*
* Return: Success: A pointer to an appropriate conversion
* function. The PCDATA argument is initialized
* to point to type conversion data which should
@ -3378,9 +3430,8 @@ H5T_find(const H5T_t *src, const H5T_t *dst, H5T_bkg_t need_bkg,
HRETURN(H5T_conv_noop);
}
/* Find it */
if (NULL == (path = H5T_path_find(src, dst, TRUE, NULL))) {
if (NULL == (path = H5T_path_find(NULL, src, dst, TRUE, NULL))) {
HRETURN_ERROR(H5E_DATATYPE, H5E_CANTINIT, NULL,
"unable to create conversion path");
}
@ -3403,6 +3454,8 @@ H5T_find(const H5T_t *src, const H5T_t *dst, H5T_bkg_t need_bkg,
* is created. If FUNC is non-null then it is registered as the
* hard function for that path.
*
* If a path is created then NAME is used for debugging.
*
* Return: Success: Pointer to the path, valid until the path
* database is modified.
*
@ -3416,8 +3469,8 @@ H5T_find(const H5T_t *src, const H5T_t *dst, H5T_bkg_t need_bkg,
*-------------------------------------------------------------------------
*/
H5T_path_t *
H5T_path_find(const H5T_t *src, const H5T_t *dst, hbool_t create,
H5T_conv_t func)
H5T_path_find(const char *name, const H5T_t *src, const H5T_t *dst,
hbool_t create, H5T_conv_t func)
{
intn lt = 0; /*left edge (inclusive) */
intn rt = H5T_npath_g; /*right edge (exclusive) */
@ -3471,9 +3524,12 @@ H5T_path_find(const H5T_t *src, const H5T_t *dst, hbool_t create,
/* Associate a function with the path if possible */
if (func) {
HDstrncpy (path->name, name, H5T_NAMELEN);
path->name[H5T_NAMELEN-1] = '\0';
path->func = func;
path->is_hard = TRUE;
path->cdata.command = H5T_CONV_INIT;
path->cdata.stats = H5MM_xcalloc (1, sizeof(H5T_stats_t));
if ((src_id=H5I_register(H5_DATATYPE, H5T_copy(path->src))) < 0 ||
(dst_id=H5I_register(H5_DATATYPE, H5T_copy(path->dst))) < 0) {
HRETURN_ERROR(H5E_DATATYPE, H5E_CANTREGISTER, NULL,
@ -3503,11 +3559,13 @@ H5T_path_find(const H5T_t *src, const H5T_t *dst, hbool_t create,
"unable to register conv types for query");
}
path->cdata.command = H5T_CONV_INIT;
path->cdata.stats = H5MM_xcalloc (1, sizeof(H5T_stats_t));
if ((H5T_soft_g[i].func) (src_id, dst_id, &(path->cdata),
H5T_CONV_INIT, NULL, NULL) < 0) {
HDmemset (&(path->cdata), 0, sizeof(H5T_cdata_t));
H5E_clear(); /*ignore the error*/
} else {
HDstrcpy (path->name, H5T_soft_g[i].name);
path->func = H5T_soft_g[i].func;
}
H5I_dec_ref(src_id);
@ -3518,6 +3576,59 @@ H5T_path_find(const H5T_t *src, const H5T_t *dst, hbool_t create,
FUNC_LEAVE(path);
}
/*-------------------------------------------------------------------------
* Function: H5T_timer_begin
*
* Purpose: Start a timer for a data type conversion.
*
* Return: void
*
* Programmer: Robb Matzke
* Friday, April 17, 1998
*
* Modifications:
*
*-------------------------------------------------------------------------
*/
void
H5T_timer_begin (H5_timer_t *timer, H5T_cdata_t *cdata)
{
assert (timer);
assert (cdata);
assert (cdata->stats);
H5_timer_begin (timer);
}
/*-------------------------------------------------------------------------
* Function: H5T_timer_end
*
* Purpose: Ends a timer for a data type conversion
*
* Return: void
*
* Programmer: Robb Matzke
* Friday, April 17, 1998
*
* Modifications:
*
*-------------------------------------------------------------------------
*/
void
H5T_timer_end (H5_timer_t *timer, H5T_cdata_t *cdata, size_t nelmts)
{
assert (timer);
assert (cdata);
assert (cdata->stats);
H5_timer_end (&(cdata->stats->timer), timer);
cdata->stats->ncalls++;
cdata->stats->nelmts += nelmts;
}
/*-------------------------------------------------------------------------
* Function: H5T_debug
*

24
src/H5Tconv.c
View File

@ -62,14 +62,8 @@ H5T_conv_noop(hid_t __unused__ src_id, hid_t __unused__ dst_id,
case H5T_CONV_FREE:
/* Nothing to free */
#ifdef H5T_DEBUG
if (cdata->ncalls>0) {
fprintf (stderr, "H5T: H5T_conv_noop statistics...\n");
fprintf (stderr, " Number of calls: %lu\n", cdata->ncalls);
fprintf (stderr, " Data points converted: %lu\n", cdata->nelmts);
}
#endif
break;
default:
HRETURN_ERROR (H5E_DATATYPE, H5E_UNSUPPORTED, FAIL,
"unknown conversion command");
@ -173,13 +167,6 @@ H5T_conv_order(hid_t src_id, hid_t dst_id, H5T_cdata_t *cdata, size_t nelmts,
case H5T_CONV_FREE:
/* Free private data */
#ifdef H5T_DEBUG
if (cdata->ncalls>0) {
fprintf (stderr, "H5T: H5T_conv_order statistics...\n");
fprintf (stderr, " Number of calls: %lu\n", cdata->ncalls);
fprintf (stderr, " Data points converted: %lu\n", cdata->nelmts);
}
#endif
break;
default:
@ -396,13 +383,6 @@ H5T_conv_struct(hid_t src_id, hid_t dst_id, H5T_cdata_t *cdata, size_t nelmts,
/*
* Free the private conversion data.
*/
#ifdef H5T_DEBUG
if (cdata->ncalls>0) {
fprintf (stderr, "H5T: H5T_conv_struct statistics...\n");
fprintf (stderr, " Number of calls: %lu\n", cdata->ncalls);
fprintf (stderr, " Data points converted: %lu\n", cdata->nelmts);
}
#endif
H5MM_xfree (priv->src2dst);
H5MM_xfree (priv->src_memb_id);
H5MM_xfree (priv->dst_memb_id);

17
src/H5Tpkg.h
View File

@ -26,6 +26,8 @@
#include <H5HGprivate.h>
#include <H5Tprivate.h>
#define H5T_NAMELEN 10 /*length of debugging name buffer */
typedef struct H5T_atomic_t {
H5T_order_t order; /*byte order */
size_t prec; /*precision in bits */
@ -84,6 +86,7 @@ typedef struct H5T_member_t {
/* The data type conversion database */
typedef struct H5T_path_t {
char name[H5T_NAMELEN]; /*name for debugging only */
H5T_t *src; /*source data type ID */
H5T_t *dst; /*destination data type ID */
H5T_conv_t func; /*data conversion function */
@ -93,14 +96,24 @@ typedef struct H5T_path_t {
/* The master list of soft conversion functions */
typedef struct H5T_soft_t {
char name[H5T_NAMELEN]; /*name for debugging only */
H5T_class_t src; /*source data type class */
H5T_class_t dst; /*destination data type class */
H5T_conv_t func; /*the conversion function */
} H5T_soft_t;
/* Statistics about a conversion function */
typedef struct H5T_stats_t {
uintn ncalls; /*num calls to conversion function */
#ifdef H5T_DEBUG
hsize_t nelmts; /*total data points converted */
H5_timer_t timer; /*total time for conversion */
#endif
} H5T_stats_t;
/* Function prototypes for H5T package scope */
H5T_path_t *H5T_path_find (const H5T_t *src, const H5T_t *dst,
hbool_t create, H5T_conv_t func);
H5T_path_t *H5T_path_find (const char *name, const H5T_t *src,
const H5T_t *dst, hbool_t create, H5T_conv_t func);
/* Conversion functions */
herr_t H5T_conv_order (hid_t src_id, hid_t dst_id, H5T_cdata_t *cdata,

2
src/H5Tprivate.h
View File

@ -45,6 +45,8 @@ herr_t H5T_pack (H5T_t *dt);
herr_t H5T_debug (H5T_t *dt, FILE * stream);
H5T_conv_t H5T_find (const H5T_t *src, const H5T_t *dst, H5T_bkg_t need_bkg,
H5T_cdata_t **pcdata/*out*/);
void H5T_timer_begin (H5_timer_t *timer, H5T_cdata_t *cdata);
void H5T_timer_end (H5_timer_t *timer, H5T_cdata_t *cdata, size_t nelmts);
/*
* This conversion function is here so we can determine whether a conversion

9
src/H5Tpublic.h
View File

@ -111,9 +111,8 @@ typedef struct H5T_cdata_t {
H5T_cmd_t command;/*what should the conversion function do? */
H5T_bkg_t need_bkg;/*is the background buffer needed? */
hbool_t recalc; /*recalculate private data */
unsigned long ncalls; /*number of calls to conversion function */
unsigned long nelmts; /*total number of data points converted */
void *priv; /*private data */
struct H5T_stats_t *stats; /*statistics for the conversion */
} H5T_cdata_t;
/* All data type conversion functions are... */
@ -232,8 +231,10 @@ herr_t H5Tset_cset (hid_t type_id, H5T_cset_t cset);
herr_t H5Tset_strpad (hid_t type_id, H5T_str_t strpad);
/* Type conversion database */
herr_t H5Tregister_hard (hid_t src_id, hid_t dst_id, H5T_conv_t func);
herr_t H5Tregister_soft (H5T_class_t src, H5T_class_t dst, H5T_conv_t func);
herr_t H5Tregister_hard (const char *name, hid_t src_id, hid_t dst_id,
H5T_conv_t func);
herr_t H5Tregister_soft (const char *name, H5T_class_t src, H5T_class_t dst,
H5T_conv_t func);
herr_t H5Tunregister (H5T_conv_t func);
H5T_conv_t H5Tfind (hid_t src_id, hid_t dst_id, H5T_cdata_t **pcdata);

501
src/H5Z.c Normal file
View File

@ -0,0 +1,501 @@
/*
* Copyright (C) 1998 NCSA
* All rights reserved.
*
* Programmer: Robb Matzke <matzke@llnl.gov>
* Thursday, April 16, 1998
*
* Purpose: Functions for data compression.
*/
#include <H5private.h>
#include <H5Eprivate.h>
#include <H5MMprivate.h>
#include <H5Oprivate.h>
#include <H5Zprivate.h>
#ifdef HAVE_ZLIB_H
# include <zlib.h>
#endif
/* Interface initialization */
#define PABLO_MASK H5Z_mask
#define INTERFACE_INIT H5Z_init_interface
static intn interface_initialize_g = FALSE;
static herr_t H5Z_init_interface (void);
static void H5Z_term_interface (void);
/*
* The compression table maps compression method number to a struct that
* contains pointers to the compress and uncompress methods along with timing
* statistics.
*/
typedef struct H5Z_class_t {
char *name; /*method name for debugging */
H5Z_func_t compress; /*compression function */
H5Z_func_t uncompress; /*uncompression function */
#ifdef H5Z_DEBUG
struct {
hsize_t nbytes; /*bytes compressed including overruns */
hsize_t over; /*bytes of overrun */
H5_timer_t timer; /*total compression time inc. overruns */
hsize_t failed; /*bytes of failure (not overruns) */
} comp;
struct {
hsize_t nbytes; /*bytes uncompressed, including overruns*/
hsize_t over; /*bytes of overrun */
H5_timer_t timer; /*total uncompression time */
hsize_t failed; /*bytes of failure (not overruns) */
} uncomp;
#endif
} H5Z_class_t;
static H5Z_class_t H5Z_g[H5Z_MAXVAL+1];
/* Compression and uncompression methods */
static size_t H5Z_zlib_c (unsigned int flags, size_t __unused__ cd_size,
const void __unused__ *client_data,
size_t src_nbytes, const void *_src,
size_t dst_nbytes, void *dst/*out*/);
static size_t H5Z_zlib_u (unsigned int flags, size_t __unused__ cd_size,
const void __unused__ *client_data,
size_t src_nbytes, const void *_src,
size_t dst_nbytes, void *dst/*out*/);
/*-------------------------------------------------------------------------
* Function: H5Z_init_interface
*
* Purpose: Initializes the data compression layer.
*
* Return: Success: SUCCEED
*
* Failure: FAIL
*
* Programmer: Robb Matzke
* Thursday, April 16, 1998
*
* Modifications:
*
*-------------------------------------------------------------------------
*/
static herr_t
H5Z_init_interface (void)
{
FUNC_ENTER (H5Z_init_interface, FAIL);
H5_add_exit (H5Z_term_interface);
H5Z_register (H5Z_NONE, "none", NULL, NULL);
H5Z_register (H5Z_DEFLATE, "deflate", H5Z_zlib_c, H5Z_zlib_u);
FUNC_LEAVE (SUCCEED);
}
/*-------------------------------------------------------------------------
* Function: H5Z_term_interface
*
* Purpose: Terminate the H5Z layer.
*
* Return: void
*
* Programmer: Robb Matzke
* Thursday, April 16, 1998
*
* Modifications:
*
*-------------------------------------------------------------------------
*/
static void
H5Z_term_interface (void)
{
#ifdef H5Z_DEBUG
int i, nprint=0;
char name[16];
for (i=0; i<=H5Z_MAXVAL; i++) {
if (H5Z_g[i].comp.nbytes || H5Z_g[i].uncomp.nbytes) {
if (0==nprint++) {
HDfprintf (stderr, "H5Z: compression statistics accumulated "
"over life of library:\n");
HDfprintf (stderr, " %-10s %8s %8s %8s %8s %8s %8s %9s\n",
"Method", "Total", "Overrun", "Errors", "User",
"System", "Elapsed", "Bandwidth");
HDfprintf (stderr, " %-10s %8s %8s %8s %8s %8s %8s %9s\n",
"------", "-----", "-------", "------", "----",
"------", "-------", "---------");
}
sprintf (name, "%s-c", H5Z_g[i].name);
HDfprintf (stderr,
" %-12s %8Hd %8Hd %8Hd %8.2f %8.2f %8.2f ",
name,
H5Z_g[i].comp.nbytes,
H5Z_g[i].comp.over,
H5Z_g[i].comp.failed,
H5Z_g[i].comp.timer.utime,
H5Z_g[i].comp.timer.stime,
H5Z_g[i].comp.timer.etime);
if (H5Z_g[i].comp.timer.etime>0) {
HDfprintf (stderr, "%9.3e\n",
H5Z_g[i].comp.nbytes / H5Z_g[i].comp.timer.etime);
} else {
HDfprintf (stderr, "%9s\n", "NaN");
}
sprintf (name, "%s-u", H5Z_g[i].name);
HDfprintf (stderr,
" %-12s %8Hd %8Hd %8Hd %8.2f %8.2f %8.2f ",
name,
H5Z_g[i].uncomp.nbytes,
H5Z_g[i].uncomp.over,
H5Z_g[i].uncomp.failed,
H5Z_g[i].uncomp.timer.utime,
H5Z_g[i].uncomp.timer.stime,
H5Z_g[i].uncomp.timer.etime);
if (H5Z_g[i].uncomp.timer.etime>0) {
HDfprintf (stderr, "%9.3e\n",
H5Z_g[i].uncomp.nbytes/H5Z_g[i].uncomp.timer.etime);
} else {
HDfprintf (stderr, "%9s\n", "NaN");
}
}
}
#endif
}
/*-------------------------------------------------------------------------
* Function: H5Zregister
*
* Purpose: This function registers new compression and uncompression
* methods for a method number. The NAME argument is used for
* debugging and may be the null pointer. Either or both of
* CFUNC (the compression function) and UFUNC (the uncompression
* method) may be null pointers.
*
* The statistics associated with a method number are not reset
* by this function; they accumulate over the life of the
* library.
*
* Return: Success: SUCCEED
*
* Failure: FAIL
*
* Programmer: Robb Matzke
* Thursday, April 16, 1998
*
* Modifications:
*
*-------------------------------------------------------------------------
*/
herr_t
H5Zregister (H5Z_method_t method, const char *name, H5Z_func_t cfunc,
H5Z_func_t ufunc)
{
FUNC_ENTER (H5Zregister, FAIL);
/* Check args */
if (method<0 || method>H5Z_MAXVAL) {
HRETURN_ERROR (H5E_ARGS, H5E_BADVALUE, FAIL,
"invalid data compression method number");
}
if (method<16) {
HRETURN_ERROR (H5E_ARGS, H5E_BADVALUE, FAIL,
"unable to modify predefined compression methods");
}
/* Do it */
if (H5Z_register (method, name, cfunc, ufunc)<0) {
HRETURN_ERROR (H5E_COMP, H5E_CANTINIT, FAIL,
"unable to register compression methods");
}
FUNC_LEAVE (SUCCEED);
}
/*-------------------------------------------------------------------------
* Function: H5Z_compress
*
* Purpose: Compress NBYTES from SRC into at most NBYTES of DST.
*
* Return: Success: Number of bytes in DST
*
* Failure: 0 if the DST buffer overflowed or something
* else went wrong.
*
* Programmer: Robb Matzke
* Thursday, April 16, 1998
*
* Modifications:
*
*-------------------------------------------------------------------------
*/
size_t
H5Z_compress (const H5O_compress_t *comp, size_t nbytes, const void *src,
void *dst/*out*/)
{
size_t ret_value = 0;
H5Z_method_t method = comp ? comp->method : H5Z_NONE;
H5Z_func_t cfunc = NULL;
#ifdef H5Z_DEBUG
intn over = 0;
H5_timer_t timer;
#endif
FUNC_ENTER (H5Z_compress, 0);
#ifdef H5Z_DEBUG
H5_timer_begin (&timer);
#endif
if (H5Z_NONE==method) {
/* No compression method */
HGOTO_DONE (0);
} else if (NULL==(cfunc=H5Z_g[method].compress)) {
/* No compress function */
HGOTO_ERROR (H5E_COMP, H5E_UNSUPPORTED, 0,
"compression method is not supported");
} else if (0==(ret_value=(cfunc)(comp->flags, comp->cd_size,
comp->client_data, nbytes,
src, nbytes, dst))) {
/* Compress failed */
HGOTO_ERROR (H5E_COMP, H5E_CANTINIT, 0, "compression failed");
} else if (ret_value>=nbytes) {
/* Output is not smaller than input */
#ifdef H5Z_DEBUG
H5Z_g[method].comp.over += 1;
over = 1;
#endif
HGOTO_DONE (0);
}
done:
#ifdef H5Z_DEBUG
H5Z_g[method].comp.nbytes += nbytes;
if (0==ret_value && !over) H5Z_g[method].comp.failed += nbytes;
H5_timer_end (&(H5Z_g[method].comp.timer), &timer);
#endif
FUNC_LEAVE (ret_value);
}
/*-------------------------------------------------------------------------
* Function: H5Z_uncompress
*
* Purpose: Uncompress SRC_NBYTES from SRC into at most DST_NBYTES of
* DST.
*
* Return: Success: Number of bytes in DST buffer.
*
* Failure: 0 if the uncompression failed or DST wasn't
* big enough to hold the result.
*
* Programmer: Robb Matzke
* Thursday, April 16, 1998
*
* Modifications:
*
*-------------------------------------------------------------------------
*/
size_t
H5Z_uncompress (const H5O_compress_t *comp, size_t src_nbytes, const void *src,
size_t dst_nbytes, void *dst/*out*/)
{
size_t ret_value = 0;
H5Z_func_t ufunc = NULL;
H5Z_method_t method = comp ? comp->method : H5Z_NONE;
#ifdef H5Z_DEBUG
H5_timer_t timer;
#endif
FUNC_ENTER (H5Z_uncompress, 0);
#ifdef H5Z_DEBUG
H5_timer_begin (&timer);
#endif
if (H5Z_NONE==method) {
/* No compression method */
assert (src_nbytes<=dst_nbytes);
HDmemcpy (dst, src, src_nbytes);
ret_value = src_nbytes;
} else if (src_nbytes==dst_nbytes) {
/* Data is not compressed */
#ifdef H5Z_DEBUG
H5Z_g[method].uncomp.over += src_nbytes;
#endif
HDmemcpy (dst, src, src_nbytes);
ret_value = src_nbytes;
} else if (NULL==(ufunc=H5Z_g[method].uncompress)) {
/* No uncompress function */
HGOTO_ERROR (H5E_COMP, H5E_UNSUPPORTED, 0,
"uncompression method is not supported");
} else if (0==(ret_value=(ufunc)(comp->flags, comp->cd_size,
comp->client_data, src_nbytes,
src, dst_nbytes, dst))) {
/* Uncompress failed */
HGOTO_ERROR (H5E_COMP, H5E_CANTINIT, 0, "uncompression failed");
}
done:
#ifdef H5Z_DEBUG
H5Z_g[method].uncomp.nbytes += dst_nbytes;
if (0==ret_value) H5Z_g[method].uncomp.failed += dst_nbytes;
H5_timer_end (&(H5Z_g[method].uncomp.timer), &timer);
#endif
FUNC_LEAVE (ret_value);
}
/*-------------------------------------------------------------------------
* Function: H5Z_register
*
* Purpose: Same as the public version except this one allows compression
* methods to be set for predefined method numbers <16.
*
* Return: Success: SUCCEED
*
* Failure: FAIL
*
* Programmer: Robb Matzke
* Thursday, April 16, 1998
*
* Modifications:
*
*-------------------------------------------------------------------------
*/
herr_t
H5Z_register (H5Z_method_t method, const char *name, H5Z_func_t cfunc,
H5Z_func_t ufunc)
{
FUNC_ENTER (H5Z_register, FAIL);
assert (method>=0 && method<=H5Z_MAXVAL);
H5MM_xfree (H5Z_g[method].name);
H5Z_g[method].name = H5MM_xstrdup (name);
H5Z_g[method].compress = cfunc;
H5Z_g[method].uncompress = ufunc;
FUNC_LEAVE (SUCCEED);
}
/*-------------------------------------------------------------------------
* Function: H5Z_zlib_c
*
* Purpose: Compress SRC_NBYTES bytes from SRC into at most DST_NBYTES of
* DST using the compression level as specified in FLAGS.
*
* Return: Success: Number of bytes compressed into DST limited
* by DST_NBYTES.
*
* Failure: 0
*
* Programmer: Robb Matzke
* Thursday, April 16, 1998
*
* Modifications:
*
*-------------------------------------------------------------------------
*/
static size_t
H5Z_zlib_c (unsigned int flags, size_t __unused__ cd_size,
const void __unused__ *client_data, size_t src_nbytes,
const void *src, size_t dst_nbytes, void *dst/*out*/)
{
size_t ret_value = 0;
#ifdef HAVE_ZLIB_H
const Bytef *z_src = (const Bytef*)src;
Bytef *z_dst = (Bytef*)dst;
uLongf z_dst_nbytes = (uLongf)dst_nbytes;
uLong z_src_nbytes = (uLong)src_nbytes;
int level = flags % 10;
int status;
#endif
FUNC_ENTER (H5Z_zlib_c, 0);
#if defined(HAVE_LIBZ) && defined (HAVE_ZLIB_H)
status = compress2 (z_dst, &z_dst_nbytes, z_src, z_src_nbytes, level);
if (Z_BUF_ERROR==status) {
ret_value = dst_nbytes;
} else if (Z_MEM_ERROR==status) {
HGOTO_ERROR (H5E_COMP, H5E_CANTINIT, 0, "deflate memory error");
} else if (Z_OK!=status) {
HGOTO_ERROR (H5E_COMP, H5E_CANTINIT, 0, "deflate error");
} else {
ret_value = z_dst_nbytes;
}
#else
HGOTO_ERROR (H5E_COMP, H5E_UNSUPPORTED, 0,
"hdf5 was not compiled with zlib-1.0.2 or better");
#endif
done:
FUNC_LEAVE (ret_value);
}
/*-------------------------------------------------------------------------
* Function: H5Z_zlib_u
*
* Purpose: Uncompress SRC_NBYTES from SRC into at most DST_NBYTES of
* DST.
*
* Return: Success: Number of bytes returned in DST.
*
* Failure: 0
*
* Programmer: Robb Matzke
* Thursday, April 16, 1998
*
* Modifications:
*
*-------------------------------------------------------------------------
*/
static size_t
H5Z_zlib_u (unsigned int __unused__ flags, size_t __unused__ cd_size,
const void __unused__ *client_data, size_t src_nbytes,
const void *src, size_t dst_nbytes, void *dst/*out*/)
{
size_t ret_value = 0;
#ifdef HAVE_ZLIB_H
const Bytef *z_src = (const Bytef*)src;
Bytef *z_dst = (Bytef*)dst;
uLongf z_dst_nbytes = (uLongf)dst_nbytes;
uLong z_src_nbytes = (uLong)src_nbytes;
int status;
#endif
FUNC_ENTER (H5Z_zlib_u, 0);
#if defined(HAVE_LIBZ) && defined (HAVE_ZLIB_H)
status = uncompress (z_dst, &z_dst_nbytes, z_src, z_src_nbytes);
if (Z_BUF_ERROR==status) {
HGOTO_ERROR (H5E_COMP, H5E_CANTINIT, 0,
"deflate destination buffer was too small");
} else if (Z_MEM_ERROR==status) {
HGOTO_ERROR (H5E_COMP, H5E_CANTINIT, 0, "deflate memory error");
} else if (Z_DATA_ERROR==status) {
HGOTO_ERROR (H5E_COMP, H5E_CANTINIT, 0, "deflate corrupted data");
} else if (Z_OK!=status) {
HGOTO_ERROR (H5E_COMP, H5E_CANTINIT, 0, "deflate error");
}
ret_value = z_dst_nbytes;
#else
HGOTO_ERROR (H5E_COMP, H5E_UNSUPPORTED, 0,
"hdf5 was not compiled with zlib-1.0.2 or better");
#endif
done:
FUNC_LEAVE (ret_value);
}

23
src/H5Zprivate.h Normal file
View File

@ -0,0 +1,23 @@
/*
* Copyright (C) 1998 NCSA
* All rights reserved.
*
* Programmer: Robb Matzke <matzke@llnl.gov>
* Thursday, April 16, 1998
*/
#ifndef _H5Zprivate_H
#define _H5Zprivate_H
#include <H5Zpublic.h>
struct H5O_compress_t; /*forward decl*/
herr_t H5Z_register (H5Z_method_t method, const char *name,
H5Z_func_t compress, H5Z_func_t uncompress);
size_t H5Z_compress (const struct H5O_compress_t *compress, size_t nbytes,
const void *src, void *dst/*out*/);
size_t H5Z_uncompress (const struct H5O_compress_t *compress,
size_t src_nbytes, const void *src, size_t dst_nbytes,
void *dst/*out*/);
#endif

69
src/H5Zpublic.h Normal file
View File

@ -0,0 +1,69 @@
/*
* Copyright (C) 1998 NCSA
* All rights reserved.
*
* Programmer: Robb Matzke <matzke@llnl.gov>
* Thursday, April 16, 1998
*/
#ifndef _H5Zpublic_H
#define _H5Zpublic_H
/*
* Compression methods. Method zero means no compression. Methods 1 through
* 15 are defined by the library. Methods 16-255 are user-defined.
*/
typedef int H5Z_method_t;
#define H5Z_NONE 0 /*no compression, must be zero */
#define H5Z_DEFLATE 1 /*deflation like gzip */
#define H5Z_RES_2 2 /*reserved for internal use */
#define H5Z_RES_3 3 /*reserved for internal use */
#define H5Z_RES_4 4 /*reserved for internal use */
#define H5Z_RES_5 5 /*reserved for internal use */
#define H5Z_RES_6 6 /*reserved for internal use */
#define H5Z_RES_7 7 /*reserved for internal use */
#define H5Z_RES_8 8 /*reserved for internal use */
#define H5Z_RES_9 9 /*reserved for internal use */
#define H5Z_RES_10 10 /*reserved for internal use */
#define H5Z_RES_11 11 /*reserved for internal use */
#define H5Z_RES_12 12 /*reserved for internal use */
#define H5Z_RES_13 13 /*reserved for internal use */
#define H5Z_RES_14 14 /*reserved for internal use */
#define H5Z_RES_15 15 /*reserved for internal use */
/* user-defined 16-255 */
#define H5Z_MAXVAL 255 /*maximum compression method ID */
/*
* A compression function takes some configuration data which comes from the
* compression message, namely FLAGS, CD_SIZE, and CLIENT_DATA. It should
* read SRC_NBYTES from SRC and compress them into at most DST_NBYTES of DST.
* If the compressed data would be larger than DST_NBYTES the function should
* return a value greater than or equal to DST_NBYTES. On failure the
* function may return zero.
*
* The uncompression function is the inverse of compression and takes the
* same arguments. The SRC_NBYTES argument is the number of compressed bytes
* in SRC. The function should uncompress SRC into DST. For redundancy,
* DST_NBYTES contains the size of the DST buffer although if the algorithm
* is operating properly and the file has not been corrupted the uncompressed
* data will never be larger than DST_NBYTES. The function should return the
* number of bytes in the DST buffer or zero on failure. Failure includes
* the overflow of the DST buffer.
*/
typedef size_t (*H5Z_func_t)(unsigned int flags, size_t cd_size,
const void *client_data, size_t src_nbytes,
const void *src, size_t dst_nbytes,
void *dst/*out*/);
#ifdef __cplusplus
extern "C" {
#endif
herr_t H5Zregister (H5Z_method_t method, const char *name, H5Z_func_t compress,
H5Z_func_t uncompress);
#ifdef __cplusplus
}
#endif
#endif

9
src/H5config.h.in
View File

@ -64,6 +64,9 @@
/* Define if you have the getpwuid function. */
#undef HAVE_GETPWUID
/* Define if you have the getrusage function. */
#undef HAVE_GETRUSAGE
/* Define if you have the lseek64 function. */
#undef HAVE_LSEEK64
@ -73,6 +76,9 @@
/* Define if you have the <unistd.h> header file. */
#undef HAVE_UNISTD_H
/* Define if you have the <zlib.h> header file. */
#undef HAVE_ZLIB_H
/* Define if you have the coug library (-lcoug). */
#undef HAVE_LIBCOUG
@ -81,3 +87,6 @@
/* Define if you have the mpio library (-lmpio). */
#undef HAVE_LIBMPIO
/* Define if you have the z library (-lz). */
#undef HAVE_LIBZ

13
src/H5private.h
View File

@ -205,6 +205,19 @@ typedef struct {
# define CONSTR(VAR,STR) static const char VAR[]=STR
#endif
/*
* Data types and functions for timing certain parts of the library.
*/
typedef struct {
double utime; /*user time */
double stime; /*system time */
double etime; /*elapsed wall-clock time */
} H5_timer_t;
void H5_timer_reset (H5_timer_t *timer);
void H5_timer_begin (H5_timer_t *timer);
void H5_timer_end (H5_timer_t *sum/*in,out*/, H5_timer_t *timer/*in,out*/);
/*
* Redefine all the POSIX functions. We should never see a POSIX
* function (or any other non-HDF5 function) in the source!

12
src/Makefile.in
View File

@ -18,10 +18,10 @@ PARALLEL_SRC=H5Fmpio.c
LIB_SRC=H5.c H5AC.c H5B.c H5D.c H5E.c H5F.c H5Farray.c H5Fcore.c H5Ffamily.c \
H5Fistore.c H5Flow.c H5Fsec2.c H5Fsplit.c H5Fstdio.c H5G.c H5Gent.c \
H5Gnode.c H5Gstab.c H5HG.c H5HL.c H5I.c H5MF.c H5MM.c H5O.c H5Ocont.c \
H5Odtype.c H5Oefl.c H5Olayout.c H5Oname.c H5Onull.c H5Osdspace.c \
H5Oshared.c H5Ostab.c H5P.c H5S.c H5Ssimp.c H5T.c H5Tconv.c H5Tinit.c \
H5V.c @PARALLEL_SRC@
H5Gnode.c H5Gstab.c H5HG.c H5HL.c H5I.c H5MF.c H5MM.c H5O.c H5Ocomp.c \
H5Ocont.c H5Odtype.c H5Oefl.c H5Olayout.c H5Oname.c H5Onull.c \
H5Osdspace.c H5Oshared.c H5Ostab.c H5P.c H5S.c H5Ssimp.c H5T.c \
H5Tconv.c H5Tinit.c H5V.c H5Z.c @PARALLEL_SRC@
LIB_OBJ=$(LIB_SRC:.c=.o)
@ -36,13 +36,13 @@ PROG_OBJ=$(PROG_SRC:.c=.o)
PUB_HDR=H5public.h H5ACpublic.h H5Bpublic.h H5Ppublic.h H5Dpublic.h \
H5Epublic.h H5Fpublic.h H5Gpublic.h H5HGpublic.h H5HLpublic.h \
H5Ipublic.h H5MFpublic.h H5MMpublic.h H5Opublic.h H5Spublic.h \
H5Tpublic.h H5config.h hdf5.h
H5Tpublic.h H5Zpublic.h H5config.h hdf5.h
# Other header files (not to be installed)...
PRIVATE_HDR=H5private.h H5ACprivate.h H5Bprivate.h H5Pprivate.h H5Dprivate.h \
H5Eprivate.h H5Fprivate.h H5Gprivate.h H5Gpkg.h H5HGprivate.h \
H5HLprivate.h H5Iprivate.h H5MFprivate.h H5MMprivate.h H5Oprivate.h \
H5Sprivate.h H5Tprivate.h H5Tpkg.h H5Vprivate.h
H5Sprivate.h H5Tprivate.h H5Tpkg.h H5Vprivate.h H5Zprivate.h
# Number format detection
H5Tinit.c: H5detect

11
src/debug.c
View File

@ -26,6 +26,7 @@
#define INDENT 3
#define VCOL 50
/*-------------------------------------------------------------------------
* Function: main
@ -51,7 +52,7 @@ main(int argc, char *argv[])
H5F_t *f;
haddr_t addr;
uint8 sig[16];
intn i;
intn i, ndims;
herr_t status = SUCCEED;
haddr_t extra;
@ -123,12 +124,18 @@ main(int argc, char *argv[])
* subclass. The subclass identifier is the byte immediately
* after the B-tree signature.
*/
H5B_subid_t subtype = (H5B_subid_t)sig[H5B_SIZEOF_MAGIC];
H5B_subid_t subtype = (H5B_subid_t)sig[H5B_SIZEOF_MAGIC];
switch (subtype) {
case H5B_SNODE_ID:
status = H5G_node_debug(f, &addr, stdout, 0, VCOL, &extra);
break;
case H5B_ISTORE_ID:
ndims = (int)extra.offset;
status = H5F_istore_debug (f, &addr, stdout, 0, VCOL, ndims);
break;
default:
fprintf(stderr, "Unknown B-tree subtype %u\n", (unsigned) (subtype));
HDexit(4);

25
src/h5ls.c
View File

@ -44,7 +44,7 @@ list (hid_t group, const char *name, void __unused__ *op_data)
hid_t (*func)(void*);
void *edata;
int i;
char linkval[512];
char buf[512];
H5G_stat_t statbuf;
/* Disable error reporting */
@ -52,19 +52,20 @@ list (hid_t group, const char *name, void __unused__ *op_data)
H5Eset_auto (NULL, NULL);
/* Print info about each name */
printf ("%-30s", name);
printf ("%-25s ", name);
if (H5Gstat (group, name, TRUE, &statbuf)>=0) {
printf ("FILE={%lu,%lu}, OID={%lu,%lu} ",
statbuf.fileno[0], statbuf.fileno[1],
statbuf.objno[0], statbuf.objno[1]);
sprintf (buf, "%lu:%lu:%lu:%lu",
statbuf.fileno[1], statbuf.fileno[0],
statbuf.objno[1], statbuf.objno[0]);
printf ("%-20s ", buf);
}
if ((obj=H5Dopen (group, name))>=0) {
hsize_t size[64];
hid_t space = H5Dget_space (obj);
int ndims = H5Sget_dims (space, size);
printf (" Dataset {");
printf ("Dataset {");
for (i=0; i<ndims; i++) {
HDfprintf (stdout, "%s%Hu", i?", ":"", size[i]);
}
@ -72,15 +73,15 @@ list (hid_t group, const char *name, void __unused__ *op_data)
H5Dclose (space);
H5Dclose (obj);
} else if ((obj=H5Gopen (group, name))>=0) {
printf (" Group\n");
printf ("Group\n");
H5Gclose (obj);
} else if (H5Gget_linkval (group, name, sizeof(linkval), linkval)>=0) {
if (NULL==HDmemchr (linkval, 0, sizeof(linkval))) {
strcpy (linkval+sizeof(linkval)-4, "...");
} else if (H5Gget_linkval (group, name, sizeof(buf), buf)>=0) {
if (NULL==HDmemchr (buf, 0, sizeof(buf))) {
strcpy (buf+sizeof(buf)-4, "...");
}
printf (" -> %s\n", linkval);
printf (" -> %s\n", buf);
} else {
printf (" Unknown Type\n");
printf ("Unknown Type\n");
}
/* Restore error reporting */

2
src/hdf5.h
View File

@ -34,4 +34,6 @@
#include <H5Ppublic.h> /* Property lists */
#include <H5Spublic.h> /* Dataspaces */
#include <H5Tpublic.h> /* Datatypes */
#include <H5Zpublic.h> /* Data compression */
#endif

44
test/.distdep
View File

@ -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 \

145
test/dsets.c
View File

@ -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);

12
test/istore.c
View File

@ -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();