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e8955b876c
hdf5/tools/h5repack/h5repack.sh.in
Jonathan Kim e8955b876c [svn-r23407] Purpose: 
HDFFV-8214 - h5repack failed converting small chunked dataset (size < 1K) to contiguous layout.

Description:
  h5repack failed converting small chunked dataset (size < 1K) to contiguous layout.
  The first case was when chunk dim is bigger than the dataset dim (at leat one), h5repack failed with displaying error stacks.
  The other case is when chunk dim is smaller than the dataset dim, h5repack failed to change layout.

    
Tested: 
    jam (linux32-LE), koala (linux64-LE), ostrich (linuxppc64-BE), emu (solaris-BE),fred (mac64-LE), Windows (32-LE cmake), cmake (jam)
2013-03-20 15:33:33 -05:00

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#! /bin/sh
#
# Copyright by The HDF Group.
# Copyright by the Board of Trustees of the University of Illinois.
# All rights reserved.
#
# This file is part of HDF5. The full HDF5 copyright notice, including
# terms governing use, modification, and redistribution, is contained in
# the files COPYING and Copyright.html. COPYING can be found at the root
# of the source code distribution tree; Copyright.html can be found at the
# root level of an installed copy of the electronic HDF5 document set and
# is linked from the top-level documents page. It can also be found at
# http://hdfgroup.org/HDF5/doc/Copyright.html. If you do not have
# access to either file, you may request a copy from help@hdfgroup.org.
#
# Tests for the h5repack tool
#
# Modification:
# Pedro Vicente Nunes, 11/15/2006
# Added $FILEN variables for file names
#
srcdir=@srcdir@
USE_FILTER_SZIP="@USE_FILTER_SZIP@"
USE_FILTER_DEFLATE="@USE_FILTER_DEFLATE@"
USE_FILTER_SHUFFLE="@USE_FILTER_SHUFFLE@"
USE_FILTER_FLETCHER32="@USE_FILTER_FLETCHER32@"
USE_FILTER_NBIT="@USE_FILTER_NBIT@"
USE_FILTER_SCALEOFFSET="@USE_FILTER_SCALEOFFSET@"
TESTNAME=h5repack
EXIT_SUCCESS=0
EXIT_FAILURE=1
H5REPACK=h5repack # The tool name
H5REPACK_BIN=`pwd`/$H5REPACK # The path of the tool binary
H5DIFF=../h5diff/h5diff # The h5diff tool name
H5DIFF_BIN=`pwd`/$H5DIFF # The path of the h5diff tool binary
H5DUMP=../h5dump/h5dump # The h5dump tool name
H5DUMP_BIN=`pwd`/$H5DUMP # The path of the h5dump tool binary
GREP='grep'
CP='cp'
DIRNAME='dirname'
LS='ls'
AWK='awk'
H5DETECTSZIP=testh5repack_detect_szip
H5DETECTSZIP_BIN=`pwd`/$H5DETECTSZIP
nerrors=0
verbose=yes
# source dirs
SRC_TOOLS="$srcdir/.."
SRC_TOOLS_TESTFILES="$SRC_TOOLS/testfiles"
# testfiles source dirs for tools
SRC_H5LS_TESTFILES="$SRC_TOOLS_TESTFILES"
SRC_H5DUMP_TESTFILES="$SRC_TOOLS_TESTFILES"
SRC_H5DIFF_TESTFILES="$SRC_TOOLS/h5diff/testfiles"
SRC_H5COPY_TESTFILES="$SRC_TOOLS/h5copy/testfiles"
SRC_H5REPACK_TESTFILES="$SRC_TOOLS/h5repack/testfiles"
SRC_H5JAM_TESTFILES="$SRC_TOOLS/h5jam/testfiles"
SRC_H5STAT_TESTFILES="$SRC_TOOLS/h5stat/testfiles"
SRC_H5IMPORT_TESTFILES="$SRC_TOOLS/h5import/testfiles"
TESTDIR=./testfiles
test -d $TESTDIR || mkdir $TESTDIR
######################################################################
# test files
# --------------------------------------------------------------------
# All the test files copy from source directory to test directory
# NOTE: Keep this framework to add/remove test files.
# Any test files from other tools can be used in this framework.
# This list are also used for checking exist.
# Comment '#' without space can be used.
# --------------------------------------------------------------------
LIST_HDF5_TEST_FILES="
$SRC_H5REPACK_TESTFILES/h5repack_attr.h5
$SRC_H5REPACK_TESTFILES/h5repack_attr_refs.h5
$SRC_H5REPACK_TESTFILES/h5repack_deflate.h5
$SRC_H5REPACK_TESTFILES/h5repack_early.h5
$SRC_H5REPACK_TESTFILES/h5repack_ext.h5
$SRC_H5REPACK_TESTFILES/h5repack_fill.h5
$SRC_H5REPACK_TESTFILES/h5repack_filters.h5
$SRC_H5REPACK_TESTFILES/h5repack_fletcher.h5
$SRC_H5REPACK_TESTFILES/h5repack_hlink.h5
$SRC_H5REPACK_TESTFILES/h5repack_layout.h5
$SRC_H5REPACK_TESTFILES/h5repack_layouto.h5
$SRC_H5REPACK_TESTFILES/h5repack_layout2.h5
$SRC_H5REPACK_TESTFILES/h5repack_layout3.h5
$SRC_H5REPACK_TESTFILES/h5repack_named_dtypes.h5
$SRC_H5REPACK_TESTFILES/h5repack_nbit.h5
$SRC_H5REPACK_TESTFILES/h5repack_objs.h5
$SRC_H5REPACK_TESTFILES/h5repack_refs.h5
$SRC_H5REPACK_TESTFILES/h5repack_shuffle.h5
$SRC_H5REPACK_TESTFILES/h5repack_soffset.h5
$SRC_H5REPACK_TESTFILES/h5repack_szip.h5
$SRC_H5DIFF_TESTFILES/h5diff_attr1.h5
$SRC_TOOLS_TESTFILES/tfamily00000.h5
$SRC_TOOLS_TESTFILES/tfamily00001.h5
$SRC_TOOLS_TESTFILES/tfamily00002.h5
$SRC_TOOLS_TESTFILES/tfamily00003.h5
$SRC_TOOLS_TESTFILES/tfamily00004.h5
$SRC_TOOLS_TESTFILES/tfamily00005.h5
$SRC_TOOLS_TESTFILES/tfamily00006.h5
$SRC_TOOLS_TESTFILES/tfamily00007.h5
$SRC_TOOLS_TESTFILES/tfamily00008.h5
$SRC_TOOLS_TESTFILES/tfamily00009.h5
$SRC_TOOLS_TESTFILES/tfamily00010.h5
"
LIST_OTHER_TEST_FILES="
$SRC_H5REPACK_TESTFILES/h5repack_ext.bin
$SRC_H5REPACK_TESTFILES/ublock.bin
$SRC_H5REPACK_TESTFILES/h5repack.info
$SRC_TOOLS_TESTFILES/h5repack_filters.h5.ddl
"
#
# copy test files and expected output files from source dirs to test dir
#
COPY_TESTFILES="$LIST_HDF5_TEST_FILES $LIST_OTHER_TEST_FILES"
COPY_TESTFILES_TO_TESTDIR()
{
# copy test files. Used -f to make sure get a new copy
for tstfile in $COPY_TESTFILES
do
# ignore '#' comment
echo $tstfile | tr -d ' ' | grep '^#' > /dev/null
RET=$?
if [ $RET -eq 1 ]; then
# skip cp if srcdir is same as destdir
# this occurs when build/test performed in source dir and
# make cp fail
SDIR=`$DIRNAME $tstfile`
INODE_SDIR=`$LS -i -d $SDIR | $AWK -F' ' '{print $1}'`
INODE_DDIR=`$LS -i -d $TESTDIR | $AWK -F' ' '{print $1}'`
if [ "$INODE_SDIR" != "$INODE_DDIR" ]; then
$CP -f $tstfile $TESTDIR
if [ $? -ne 0 ]; then
echo "Error: FAILED to copy $tstfile ."
# Comment out this to CREATE expected file
exit $EXIT_FAILURE
fi
fi
fi
done
}
# Print a $* message left justified in a field of 70 characters
#
MESSAGE() {
SPACES=" "
echo "$* $SPACES" | cut -c1-70 | tr -d '\012'
}
# Print a line-line message left justified in a field of 70 characters
# beginning with the word "Testing".
#
TESTING() {
MESSAGE "Testing $*"
}
# Print a line-line message left justified in a field of 70 characters
# beginning with the word "Verifying".
#
VERIFY() {
MESSAGE "Verifying $*"
}
# Print a message that a test has been skipped (because a required filter
# was unavailable)
SKIP() {
TESTING $H5REPACK $@
echo " -SKIP-"
}
# Call the h5diff tool
#
DIFFTEST()
{
VERIFY h5diff output $@
(
$RUNSERIAL $H5DIFF_BIN -q "$@"
)
RET=$?
if [ $RET != 0 ] ; then
echo "*FAILED*"
nerrors="`expr $nerrors + 1`"
else
echo " PASSED"
fi
}
# Call h5repack
#
# call TOOLTEST_MAIN and delete $output file
TOOLTEST()
{
echo $@
infile=$TESTDIR/$2
outfile=$TESTDIR/out-$1.$2
shift
shift
# Run test.
TESTING $H5REPACK $@
(
$RUNSERIAL $H5REPACK_BIN "$@" $infile $outfile
)
RET=$?
if [ $RET != 0 ] ; then
echo "*FAILED*"
nerrors="`expr $nerrors + 1`"
else
echo " PASSED"
DIFFTEST $infile $outfile
fi
rm -f $outfile
}
#------------------------------------------
# Verifying layouts of a dataset
VERIFY_LAYOUT_DSET()
{
layoutfile=$TESTDIR/layout-$1.$2
dset=$3
expectlayout=$4
infile=$TESTDIR/$2
outfile=$TESTDIR/out-$1.$2
shift
shift
shift
shift
$RUNSERIAL $H5REPACK_BIN "$@" $infile $outfile
RET=$?
if [ $RET != 0 ] ; then
echo "*FAILED*"
nerrors="`expr $nerrors + 1`"
else
echo " PASSED"
DIFFTEST $infile $outfile
fi
#---------------------------------
# check the layout from a dataset
VERIFY "a dataset layout"
(
$RUNSERIAL $H5DUMP_BIN -d $dset -pH $outfile > $layoutfile
)
$GREP $expectlayout $layoutfile > /dev/null
if [ $? -eq 0 ]; then
echo " PASSED"
else
echo " FAILED"
fi
# clean up tmp files
rm -f $outfile
rm -f $layoutfile
}
#----------------------------------------
# Verifying layouts from entire file
VERIFY_LAYOUT_ALL()
{
outfile=$TESTDIR/out-$1.$2
layoutfile=$TESTDIR/layout-$1.$2
expectlayout=$3
shift
shift
shift
$RUNSERIAL $H5REPACK_BIN "$@" $infile $outfile
RET=$?
if [ $RET != 0 ] ; then
echo "*FAILED*"
nerrors="`expr $nerrors + 1`"
else
echo " PASSED"
DIFFTEST $infile $outfile
fi
#---------------------------------
# check the layout from a dataset
# check if the other layouts still exsit
VERIFY "layouts"
(
# if CONTIGUOUS
if [ $expectlayout = "CONTIGUOUS" ]; then
TESTING $H5DUMP_BIN -pH $outfile
(
$RUNSERIAL $H5DUMP_BIN -pH $outfile > $layoutfile
)
$GREP "COMPACT" $layoutfile > /dev/null
if [ $? -eq 0 ]; then
echo " FAILED"
else
$GREP "CHUNKED" $layoutfile > /dev/null
if [ $? -eq 0 ]; then
echo " FAILED"
else
echo " PASSED"
fi
fi
else
# if COMPACT
if [ $expectlayout = "COMPACT" ]; then
TESTING $H5DUMP_BIN -pH $outfile
(
$RUNSERIAL $H5DUMP_BIN -pH $outfile > $layoutfile
)
$GREP "CHUNKED" $layoutfile > /dev/null
if [ $? -eq 0 ]; then
echo " FAILED"
else
$GREP "CONTIGUOUS" $layoutfile > /dev/null
if [ $? -eq 0 ]; then
echo " FAILED"
else
echo " PASSED"
fi
fi
else
# if CHUNKED
if [ $expectlayout = "CHUNKED" ]; then
TESTING $H5DUMP_BIN -pH $outfile
(
$RUNSERIAL $H5DUMP_BIN -pH $outfile > $layoutfile
)
$GREP "CONTIGUOUS" $layoutfile > /dev/null
if [ $? -eq 0 ]; then
echo " FAILED"
else
$GREP "COMPACT" $layoutfile > /dev/null
if [ $? -eq 0 ]; then
echo " FAILED"
else
echo " PASSED"
fi
fi
fi
fi
fi
)
# clean up tmp files
rm -f $outfile
rm -f $layoutfile
}
# same as TOOLTEST, but it uses the old syntax -i input_file -o output_file
#
TOOLTEST0()
{
infile=$TESTDIR/$2
outfile=$TESTDIR/out-$1.$2
shift
shift
# Run test.
TESTING $H5REPACK $@
(
$RUNSERIAL $H5REPACK_BIN -i $infile -o $outfile "$@"
)
RET=$?
if [ $RET != 0 ] ; then
echo "*FAILED*"
nerrors="`expr $nerrors + 1`"
else
echo " PASSED"
DIFFTEST $infile $outfile
fi
rm -f $outfile
}
# same as TOOLTEST, but it uses without -i -o options
# used to test the family driver, where these files reside
#
TOOLTEST1()
{
infile=$TESTDIR/$2
outfile=$TESTDIR/out-$1.$2
shift
shift
# Run test.
TESTING $H5REPACK $@
(
$RUNSERIAL $H5REPACK_BIN "$@" $infile $outfile
)
RET=$?
if [ $RET != 0 ] ; then
echo "*FAILED*"
nerrors="`expr $nerrors + 1`"
else
echo " PASSED"
DIFFTEST $infile $outfile
fi
rm -f $outfile
}
# This is same as TOOLTEST() with comparing display output
# from -v option
#
TOOLTESTV()
{
expect="$TESTDIR/$2.ddl"
actual="$TESTDIR/`basename $2 .ddl`.out"
actual_err="$TESTDIR/`basename $2 .ddl`.err"
infile=$TESTDIR/$2
outfile=$TESTDIR/out-$1.$2
shift
shift
# Run test.
TESTING $H5REPACK $@
(
$RUNSERIAL $H5REPACK_BIN "$@" $infile $outfile
) >$actual 2>$actual_err
RET=$?
if [ $RET != 0 ] ; then
echo "*FAILED*"
nerrors="`expr $nerrors + 1`"
else
echo " PASSED"
DIFFTEST $infile $outfile
fi
# display output compare
STDOUT_FILTER $actual
cat $actual_err >> $actual
VERIFY output from $H5REPACK $@
if cmp -s $expect $actual; then
echo " PASSED"
else
echo "*FAILED*"
echo " Expected result (*.ddl) differs from actual result (*.out)"
nerrors="`expr $nerrors + 1`"
test yes = "$verbose" && diff -c $expect $actual |sed 's/^/ /'
fi
rm -f $actual $actual_err
rm -f $outfile
}
# TOOLTEST_META:
# Test metadata block size option.
# Reason to create a function here is to localize all special steps related to
# metadata block size option in one place. This is a quick solution. More
# thought out solution needed when there is more time.
#
# $1: test input file
# $2:$: metadata options (either "-M size" or "--metadata_block_size=size")
#
# Algorithm:
# Run it once without the metadata option ($2-$);
# Save the result output file;
# Run it second time with the metadata option;
# Verify the output file of second run is larger than the one of 1st run.
TOOLTEST_META()
{
infile=$TESTDIR/$2
outfile=$TESTDIR/out-$1.$2
shift
shift
# Run test.
TESTING $H5REPACK $@
(
$RUNSERIAL $H5REPACK_BIN $infile $outfile
)
RET=$?
if [ $RET != 0 ] ; then
echo "*FAILED*"
nerrors="`expr $nerrors + 1`"
else
echo " PASSED"
DIFFTEST $infile $outfile
fi
# get the size of the first output file
size1=`wc -c $outfile | cut -d' ' -f1`
# 2nd run with metadata option
# Run test.
TESTING $H5REPACK $@
(
$RUNSERIAL $H5REPACK_BIN "$@" $infile $outfile
)
RET=$?
if [ $RET != 0 ] ; then
echo "*FAILED*"
nerrors="`expr $nerrors + 1`"
else
echo " PASSED"
DIFFTEST $infile $outfile
fi
# get the size of the second output file
size2=`wc -c $outfile | cut -d' ' -f1`
# verify sizes.
MESSAGE "Verify the sizes of both output files ($size1 vs $size2)"
if [ $size1 -lt $size2 ]; then
# pass
echo " PASSED"
else
#fail
echo "*FAILED*"
fi
rm -f $outfile
}
# This is different from $srcdir/../../bin/output_filter.sh
STDOUT_FILTER() {
result_file=$1
tmp_file=/tmp/h5test_tmp_$$
# Filter name of files.
cp $result_file $tmp_file
sed -e '/^Opening file/d' -e '/^Making file/d' \
< $tmp_file > $result_file
# cleanup
rm -f $tmp_file
}
#
# The tests
# We use the files generated by h5repacktst
# Each run generates "<file>.out.h5" and the tool h5diff is used to
# compare the input and output files
#
# the tests are the same as the program h5repacktst, but run from the CLI
#
# See which filters are usable (and skip tests for filters we
# don't have). Do this by searching H5pubconf.h to see which
# filters are defined.
# detect whether the encoder is present.
USE_FILTER_SZIP_ENCODER="no";
if test $USE_FILTER_SZIP = "yes"; then
USE_FILTER_SZIP_ENCODER=`$RUNSERIAL $H5DETECTSZIP_BIN`
fi
##############################################################################
### T H E T E S T S
##############################################################################
# prepare for test
COPY_TESTFILES_TO_TESTDIR
# copy files (these files have no filters)
TOOLTEST fill h5repack_fill.h5
TOOLTEST objs h5repack_objs.h5
TOOLTEST attr h5repack_attr.h5
TOOLTEST hlink h5repack_hlink.h5
TOOLTEST layout h5repack_layout.h5
TOOLTEST early h5repack_early.h5
# use h5repack_layout.h5 to write some filters (this file has no filters)
# gzip with individual object
arg="h5repack_layout.h5 -f dset1:GZIP=1 -l dset1:CHUNK=20x10"
if test $USE_FILTER_DEFLATE != "yes" ; then
SKIP $arg
else
TOOLTEST gzip_individual $arg
fi
# gzip for all
arg="h5repack_layout.h5 -f GZIP=1"
if test $USE_FILTER_DEFLATE != "yes" ; then
SKIP $arg
else
TOOLTEST gzip_all $arg
fi
# szip with individual object
arg="h5repack_layout.h5 -f dset2:SZIP=8,EC -l dset2:CHUNK=20x10"
if test $USE_FILTER_SZIP_ENCODER != "yes" -o $USE_FILTER_SZIP != "yes" ; then
SKIP $arg
else
TOOLTEST szip_individual $arg
fi
# szip for all
arg="h5repack_layout.h5 -f SZIP=8,NN"
if test $USE_FILTER_SZIP_ENCODER != "yes" -o $USE_FILTER_SZIP != "yes" ; then
SKIP $arg
else
TOOLTEST szip_all $arg
fi
# shuffle with individual object
arg="h5repack_layout.h5 -f dset2:SHUF -l dset2:CHUNK=20x10"
if test $USE_FILTER_SHUFFLE != "yes" ; then
SKIP $arg
else
TOOLTEST shuffle_individual $arg
fi
# shuffle for all
arg="h5repack_layout.h5 -f SHUF"
if test $USE_FILTER_SHUFFLE != "yes" ; then
SKIP $arg
else
TOOLTEST shuffle_all $arg
fi
# fletcher32 with individual object
arg="h5repack_layout.h5 -f dset2:FLET -l dset2:CHUNK=20x10"
if test $USE_FILTER_FLETCHER32 != "yes" ; then
SKIP $arg
else
TOOLTEST fletcher_individual $arg
fi
# fletcher32 for all
arg="h5repack_layout.h5 -f FLET"
if test $USE_FILTER_FLETCHER32 != "yes" ; then
SKIP $arg
else
TOOLTEST fletcher_all $arg
fi
# all filters
arg="h5repack_layout.h5 -f dset2:SHUF -f dset2:FLET -f dset2:SZIP=8,NN -f dset2:GZIP=1 -l dset2:CHUNK=20x10"
if test $USE_FILTER_SZIP_ENCODER != "yes" -o $USE_FILTER_SZIP != "yes" -o $USE_FILTER_SHUFFLE != "yes" -o $USE_FILTER_FLETCHER32 != "yes" -o $USE_FILTER_DEFLATE != "yes" ; then
SKIP $arg
else
TOOLTEST all_filters $arg
fi
# verbose gzip with individual object
arg="h5repack_filters.h5 -v -f /dset_deflate:GZIP=9"
if test $USE_FILTER_DEFLATE != "yes" ; then
SKIP $arg
else
# compare output
TOOLTESTV gzip_verbose_filters $arg
fi
###########################################################
# the following tests assume the input files have filters
###########################################################
# szip copy
arg="h5repack_szip.h5"
if test $USE_FILTER_SZIP_ENCODER != "yes" -o $USE_FILTER_SZIP != "yes" ; then
SKIP $arg
else
TOOLTEST szip_copy $arg
fi
# szip remove
arg="h5repack_szip.h5 --filter=dset_szip:NONE"
if test $USE_FILTER_SZIP_ENCODER != "yes" -o $USE_FILTER_SZIP != "yes" ; then
SKIP $arg
else
TOOLTEST szip_remove $arg
fi
# deflate copy
arg="h5repack_deflate.h5"
if test $USE_FILTER_DEFLATE != "yes" ; then
SKIP $arg
else
TOOLTEST deflate_copy $arg
fi
# deflate remove
arg="h5repack_deflate.h5 -f dset_deflate:NONE"
if test $USE_FILTER_DEFLATE != "yes" ; then
SKIP $arg
else
TOOLTEST deflate_remove $arg
fi
# shuffle copy
arg="h5repack_shuffle.h5"
if test $USE_FILTER_SHUFFLE != "yes" ; then
SKIP $arg
else
TOOLTEST shuffle_copy $arg
fi
# shuffle remove
arg="h5repack_shuffle.h5 -f dset_shuffle:NONE"
if test $USE_FILTER_SHUFFLE != "yes" ; then
SKIP $arg
else
TOOLTEST shuffle_remove $arg
fi
# fletcher32 copy
arg="h5repack_fletcher.h5"
if test $USE_FILTER_FLETCHER32 != "yes" ; then
SKIP $arg
else
TOOLTEST fletcher_copy $arg
fi
# fletcher32 remove
arg="h5repack_fletcher.h5 -f dset_fletcher32:NONE"
if test $USE_FILTER_FLETCHER32 != "yes" ; then
SKIP $arg
else
TOOLTEST fletcher_remove $arg
fi
# nbit copy
arg="h5repack_nbit.h5"
if test $USE_FILTER_NBIT != "yes" ; then
SKIP $arg
else
TOOLTEST nbit_copy $arg
fi
# nbit remove
arg="h5repack_nbit.h5 -f dset_nbit:NONE"
if test $USE_FILTER_NBIT != "yes" ; then
SKIP $arg
else
TOOLTEST nbit_remove $arg
fi
# nbit add
arg="h5repack_nbit.h5 -f dset_int31:NBIT"
if test $USE_FILTER_NBIT != "yes" ; then
SKIP $arg
else
TOOLTEST nbit_add $arg
fi
# scaleoffset copy
arg="h5repack_soffset.h5"
if test $USE_FILTER_SCALEOFFSET != "yes" ; then
SKIP $arg
else
TOOLTEST scale_copy $arg
fi
# scaleoffset add
arg="h5repack_soffset.h5 -f dset_none:SOFF=31,IN"
if test $USE_FILTER_SCALEOFFSET != "yes" ; then
SKIP $arg
else
TOOLTEST scale_add $arg
fi
# scaleoffset remove
arg="h5repack_soffset.h5 -f dset_scaleoffset:NONE"
if test $USE_FILTER_SCALEOFFSET != "yes" ; then
SKIP $arg
else
TOOLTEST scale_remove $arg
fi
# remove all filters
arg="h5repack_filters.h5 -f NONE"
if test $USE_FILTER_FLETCHER32 != "yes" -o $USE_FILTER_DEFLATE != "yes" -o $USE_FILTER_SZIP != "yes" -o $USE_FILTER_SZIP_ENCODER != "yes" -o $USE_FILTER_SHUFFLE != "yes" -o $USE_FILTER_NBIT != "yes" -o $USE_FILTER_SCALEOFFSET != "yes" ; then
SKIP $arg
else
TOOLTEST remove_all $arg
fi
#filter conversions
arg="h5repack_deflate.h5 -f dset_deflate:SZIP=8,NN"
if test $USE_FILTER_SZIP_ENCODER != "yes" -o $USE_FILTER_SZIP != "yes" -o $USE_FILTER_DEFLATE != "yes" ; then
SKIP $arg
else
TOOLTEST deflate_convert $arg
fi
arg="h5repack_szip.h5 -f dset_szip:GZIP=1"
if test $USE_FILTER_SZIP != "yes" -o $USE_FILTER_SZIP_ENCODER != "yes" -o $USE_FILTER_DEFLATE != "yes" ; then
SKIP $arg
else
TOOLTEST szip_convert $arg
fi
#limit
arg="h5repack_layout.h5 -f GZIP=1 -m 1024"
if test $USE_FILTER_DEFLATE != "yes" ; then
SKIP $arg
else
TOOLTEST deflate_limit $arg
fi
#file
arg="h5repack_layout.h5 -e $TESTDIR/h5repack.info"
if test $USE_FILTER_DEFLATE != "yes" ; then
SKIP $arg
else
TOOLTEST deflate_file $arg
fi
#########################################################
# layout options (these files have no filters)
#########################################################
VERIFY_LAYOUT_DSET dset2_chunk_20x10 h5repack_layout.h5 dset2 CHUNKED --layout dset2:CHUNK=20x10
VERIFY_LAYOUT_ALL chunk_20x10 h5repack_layout.h5 CHUNKED -l CHUNK=20x10
VERIFY_LAYOUT_DSET dset2_conti h5repack_layout.h5 dset2 CONTIGUOUS -l dset2:CONTI
VERIFY_LAYOUT_ALL conti h5repack_layout.h5 CONTIGUOUS -l CONTI
VERIFY_LAYOUT_DSET dset2_compa h5repack_layout.h5 dset2 COMPACT -l dset2:COMPA
VERIFY_LAYOUT_ALL compa h5repack_layout.h5 COMPACT -l COMPA
################################################################
# layout conversions (file has no filters)
###############################################################
VERIFY_LAYOUT_DSET dset_compa_conti h5repack_layout.h5 dset_compact CONTIGUOUS -l dset_compact:CONTI
VERIFY_LAYOUT_DSET dset_compa_chunk h5repack_layout.h5 dset_compact CHUNKED -l dset_compact:CHUNK=2x5
VERIFY_LAYOUT_DSET dset_compa_compa h5repack_layout.h5 dset_compact COMPACT -l dset_compact:COMPA
VERIFY_LAYOUT_DSET dset_conti_compa h5repack_layout.h5 dset_contiguous COMPACT -l dset_contiguous:COMPA
VERIFY_LAYOUT_DSET dset_conti_chunk h5repack_layout.h5 dset_contiguous CHUNKED -l dset_contiguous:CHUNK=3x6
VERIFY_LAYOUT_DSET dset_conti_conti h5repack_layout.h5 dset_contiguous CONTIGUOUS -l dset_contiguous:CONTI
VERIFY_LAYOUT_DSET chunk_compa h5repack_layout.h5 dset_chunk COMPACT -l dset_chunk:COMPA
VERIFY_LAYOUT_DSET chunk_conti h5repack_layout.h5 dset_chunk CONTIGUOUS -l dset_chunk:CONTI
VERIFY_LAYOUT_DSET chunk_18x13 h5repack_layout.h5 dset_chunk CHUNKED -l dset_chunk:CHUNK=18x13
# test convert small size dataset ( < 1k) to compact layout without -m
VERIFY_LAYOUT_DSET contig_small_compa h5repack_layout2.h5 contig_small COMPACT -l contig_small:COMPA
VERIFY_LAYOUT_DSET contig_small_fixed_compa h5repack_layout2.h5 chunked_small_fixed COMPACT -l chunked_small_fixed:COMPA
#---------------------------------------------------------------------------
# Test file contains chunked datasets (need multiple dsets) with
# unlimited max dims. (HDFFV-7933)
# Use first dset to test.
#---------------------------------------------------------------------------
# chunk to chunk - specify chunk dim bigger than any current dim
VERIFY_LAYOUT_DSET chunk2chunk h5repack_layout3.h5 chunk_unlimit1 CHUNK -l chunk_unlimit1:CHUNK=100x300
# chunk to contiguous
VERIFY_LAYOUT_DSET chunk2conti h5repack_layout3.h5 chunk_unlimit1 CONTI -l chunk_unlimit1:CONTI
# chunk to compact - convert big dataset (should be > 64k) for this purpose,
# should remain as original layout (chunk)
VERIFY_LAYOUT_DSET chunk2compa h5repack_layout3.h5 chunk_unlimit1 CHUNK -l chunk_unlimit1:COMPA
#--------------------------------------------------------------------------
# Test -f for some specific cases. Chunked dataset with unlimited max dims.
# (HDFFV-8012)
#--------------------------------------------------------------------------
# - should not fail
# - should not change max dims from unlimit
# chunk dim is bigger than dataset dim. ( dset size < 64k )
VERIFY_LAYOUT_DSET error1 h5repack_layout3.h5 chunk_unlimit1 H5S_UNLIMITED -f chunk_unlimit1:NONE
# chunk dim is bigger than dataset dim. ( dset size > 64k )
VERIFY_LAYOUT_DSET error2 h5repack_layout3.h5 chunk_unlimit2 H5S_UNLIMITED -f chunk_unlimit2:NONE
# chunk dims are smaller than dataset dims. ( dset size < 64k )
#TOOLTEST_MAIN h5repack_layout3.h5 -f chunk_unlimit3:NONE
VERIFY_LAYOUT_DSET error3 h5repack_layout3.h5 chunk_unlimit3 H5S_UNLIMITED -f chunk_unlimit3:NONE
# file input - should not fail
TOOLTEST error4 h5repack_layout3.h5 -f NONE
#--------------------------------------------------------------------------
# Test base: Convert CHUNK to CONTI for a chunked dataset with small dataset
# (dset size < 64K) and with unlimited max dims on a condition as follow.
# (HDFFV-8214)
#--------------------------------------------------------------------------
# chunk dim is bigger than dataset dim. should succeed.
VERIFY_LAYOUT_DSET ckdim_biger h5repack_layout3.h5 chunk_unlimit2 CONTI -l chunk_unlimit2:CONTI
# chunk dim is smaller than dataset dim. should succeed.
VERIFY_LAYOUT_DSET ckdim_smaller h5repack_layout3.h5 chunk_unlimit3 CONTI -l chunk_unlimit3:CONTI
# Native option
# Do not use FILE1, as the named dtype will be converted to native, and h5diff will
# report a difference.
TOOLTEST native_fill h5repack_fill.h5 -n
TOOLTEST native_attr h5repack_attr.h5 -n
# latest file format with long switches. use FILE4=h5repack_layout.h5 (no filters)
arg="h5repack_layout.h5 --layout CHUNK=20x10 --filter GZIP=1 --minimum=10 --native --latest --compact=8 --indexed=6 --ssize=8[:dtype]"
if test $USE_FILTER_DEFLATE != "yes" ; then
SKIP $arg
else
VERIFY_LAYOUT_ALL layout_long_switches h5repack_layout.h5 CHUNKED --layout CHUNK=20x10 --filter GZIP=1 --minimum=10 --native --latest --compact=8 --indexed=6 --ssize=8[:dtype]
fi
# latest file format with short switches. use FILE4=h5repack_layout.h5 (no filters)
arg="h5repack_layout.h5 -l CHUNK=20x10 -f GZIP=1 -m 10 -n -L -c 8 -d 6 -s 8[:dtype]"
if test $USE_FILTER_DEFLATE != "yes" ; then
SKIP $arg
else
VERIFY_LAYOUT_ALL layout_short_switches h5repack_layout.h5 CHUNKED -l CHUNK=20x10 -f GZIP=1 -m 10 -n -L -c 8 -d 6 -s 8[:dtype]
fi
# several global filters
arg="h5repack_layout.h5 --filter GZIP=1 --filter SHUF"
if test $USE_FILTER_DEFLATE != "yes" -o $USE_FILTER_SHUFFLE != "yes" ; then
SKIP $arg
else
TOOLTEST global_filters $arg
fi
# syntax of -i infile -o outfile
# latest file format with short switches. use FILE4=h5repack_layout.h5 (no filters)
arg="h5repack_layout.h5 -l CHUNK=20x10 -f GZIP=1 -m 10 -n -L -c 8 -d 6 -s 8[:dtype]"
if test $USE_FILTER_DEFLATE != "yes" ; then
SKIP $arg
else
TOOLTEST0 old_style_layout_short_switches $arg
fi
# add a userblock to file
arg="h5repack_objs.h5 -u $TESTDIR/ublock.bin -b 2048"
TOOLTEST add_userblock $arg
# add alignment
arg="h5repack_objs.h5 -t 1 -a 1 "
TOOLTEST add_alignment $arg
# Check repacking file with old version of layout message (should get upgraded
# to new version and be readable, etc.)
TOOLTEST pgrade_layout h5repack_layouto.h5
# test for datum size > H5TOOLS_MALLOCSIZE
TOOLTEST gt_mallocsize h5repack_objs.h5 -f GZIP=1
# Check repacking file with committed datatypes in odd configurations
TOOLTEST committed_dt h5repack_named_dtypes.h5
# tests family driver (file is located in common testfiles folder, uses TOOLTEST1
TOOLTEST1 family tfamily%05d.h5
# test various references (bug 1814 and 1726)
TOOLTEST bug1814 h5repack_refs.h5
# test attribute with various references (bug1797 / HDFFV-5932)
# the references in attribute of compund or vlen datatype
TOOLTEST HDFFV-5932 h5repack_attr_refs.h5
# Add test for memory leak in attirbute. This test is verified by CTEST.
# 1. leak from vlen string
# 2. leak from compound type without reference member
# (HDFFV-7840, )
# Note: this test is experimental for sharing test file among tools
TOOLTEST HDFFV-7840 h5diff_attr1.h5
# tests for metadata block size option
TOOLTEST_META meta_short h5repack_layout.h5 -M 8192
TOOLTEST_META meta_long h5repack_layout.h5 --metadata_block_size=8192
if test $nerrors -eq 0 ; then
echo "All $TESTNAME tests passed."
exit $EXIT_SUCCESS
else
echo "$TESTNAME tests failed with $nerrors errors."
exit $EXIT_FAILURE
fi
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