netcdf-c/ncdump/tst_netcdf4.sh

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#!/bin/sh
# This shell script tests ncdump for netcdf-4
# Ed Hartnett, Dennis Heimbigner, Ward Fisher
Primary change: add dap4 support Specific changes: 1. Add dap4 code: libdap4 and dap4_test. Note that until the d4ts server problem is solved, dap4 is turned off. 2. Modify various files to support dap4 flags: configure.ac, Makefile.am, CMakeLists.txt, etc. 3. Add nc_test/test_common.sh. This centralizes the handling of the locations of various things in the build tree: e.g. where is ncgen.exe located. See nc_test/test_common.sh for details. 4. Modify .sh files to use test_common.sh 5. Obsolete separate oc2 by moving it to be part of netcdf-c. This means replacing code with netcdf-c equivalents. 5. Add --with-testserver to configure.ac to allow override of the servers to be used for --enable-dap-remote-tests. 6. There were multiple versions of nctypealignment code. Try to centralize in libdispatch/doffset.c and include/ncoffsets.h 7. Add a unit test for the ncuri code because of its complexity. 8. Move the findserver code out of libdispatch and into a separate, self contained program in ncdap_test and dap4_test. 9. Move the dispatch header files (nc{3,4}dispatch.h) to .../include because they are now shared by modules. 10. Revamp the handling of TOPSRCDIR and TOPBUILDDIR for shell scripts. 11. Make use of MREMAP if available 12. Misc. minor changes e.g. - #include <config.h> -> #include "config.h" - Add some no-install headers to /include - extern -> EXTERNL and vice versa as needed - misc header cleanup - clean up checking for misc. unix vs microsoft functions 13. Change copyright decls in some files to point to LICENSE file. 14. Add notes to RELEASENOTES.md
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if test "x$srcdir" = x ; then srcdir=`pwd`; fi
Primary change: add dap4 support Specific changes: 1. Add dap4 code: libdap4 and dap4_test. Note that until the d4ts server problem is solved, dap4 is turned off. 2. Modify various files to support dap4 flags: configure.ac, Makefile.am, CMakeLists.txt, etc. 3. Add nc_test/test_common.sh. This centralizes the handling of the locations of various things in the build tree: e.g. where is ncgen.exe located. See nc_test/test_common.sh for details. 4. Modify .sh files to use test_common.sh 5. Obsolete separate oc2 by moving it to be part of netcdf-c. This means replacing code with netcdf-c equivalents. 5. Add --with-testserver to configure.ac to allow override of the servers to be used for --enable-dap-remote-tests. 6. There were multiple versions of nctypealignment code. Try to centralize in libdispatch/doffset.c and include/ncoffsets.h 7. Add a unit test for the ncuri code because of its complexity. 8. Move the findserver code out of libdispatch and into a separate, self contained program in ncdap_test and dap4_test. 9. Move the dispatch header files (nc{3,4}dispatch.h) to .../include because they are now shared by modules. 10. Revamp the handling of TOPSRCDIR and TOPBUILDDIR for shell scripts. 11. Make use of MREMAP if available 12. Misc. minor changes e.g. - #include <config.h> -> #include "config.h" - Add some no-install headers to /include - extern -> EXTERNL and vice versa as needed - misc header cleanup - clean up checking for misc. unix vs microsoft functions 13. Change copyright decls in some files to point to LICENSE file. 14. Add notes to RELEASENOTES.md
2017-03-09 08:01:10 +08:00
. ../test_common.sh
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set -e
There was a request to extend the provenance information stored in the _NCProperties attribute to allow two things: 1. capture of additional library dependencies (over and above hdf5) 2. Recognition of non-netcdf libraries that create netcdf-4 format files. To this end, the _NCProperties format has been extended to be and arbitrary set of key=value pairs separated by commas. This new format has version = 2, and uses commas as the pair separator. Thus the general form is: _NCProperties = "version=2,key1=value,key2=value2..." ; This new version is accompanied by a new ./configure option of the form --with-ncproperties="key1=value1,key2=value2..." that specifies pairs to add to the _NCProperties attribute for all files created with that netcdf library. At this point, what is missing is some programmatic way to specify either all the pairs or additional pairs to the _NCProperties attribute. Not sure of the best way to do this. Builders using non-netcdf libraries can specify whatever they want in the key value pairs (as long as the version=2 is specified first). By convention, the primary library is expected to be the the first pair after the leading version=2 pair, but this is convention only and is neither required nor enforced. Related changes: 1. Fixed the tests that check _NCProperties to properly operate with version=2. 2. When reading a version 1 _NCProperties attribute, convert it to look like a version 2 attribute. 2. Added some version 2 tests to ncdump/tst_fileinfo.c and ncdump/tst_fileinfo.sh Misc Changes: 1. Fix minor problem in ncdap_test/testurl.sh where a parameter to buildurl needed to be quoted. 2. Minor fix to ncgen to swap switches -H and -h to be consistent with other utilities. 3. Document the -M flag in nccopy usage() and the nccopy man page. 4. Modify a test case to use the nccopy -M flag.
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# Remove the version information from _NCProperties
cleanncprops() {
src="$1"
dst="$2"
rm -f $dst
cat $src \
This PR adds EXPERIMENTAL support for accessing data in the cloud using a variant of the Zarr protocol and storage format. This enhancement is generically referred to as "NCZarr". The data model supported by NCZarr is netcdf-4 minus the user-defined types and the String type. In this sense it is similar to the CDF-5 data model. More detailed information about enabling and using NCZarr is described in the document NUG/nczarr.md and in a [Unidata Developer's blog entry](https://www.unidata.ucar.edu/blogs/developer/en/entry/overview-of-zarr-support-in). WARNING: this code has had limited testing, so do use this version for production work. Also, performance improvements are ongoing. Note especially the following platform matrix of successful tests: Platform | Build System | S3 support ------------------------------------ Linux+gcc | Automake | yes Linux+gcc | CMake | yes Visual Studio | CMake | no Additionally, and as a consequence of the addition of NCZarr, major changes have been made to the Filter API. NOTE: NCZarr does not yet support filters, but these changes are enablers for that support in the future. Note that it is possible (probable?) that there will be some accidental reversions if the changes here did not correctly mimic the existing filter testing. In any case, previously filter ids and parameters were of type unsigned int. In order to support the more general zarr filter model, this was all converted to char*. The old HDF5-specific, unsigned int operations are still supported but they are wrappers around the new, char* based nc_filterx_XXX functions. This entailed at least the following changes: 1. Added the files libdispatch/dfilterx.c and include/ncfilter.h 2. Some filterx utilities have been moved to libdispatch/daux.c 3. A new entry, "filter_actions" was added to the NCDispatch table and the version bumped. 4. An overly complex set of structs was created to support funnelling all of the filterx operations thru a single dispatch "filter_actions" entry. 5. Move common code to from libhdf5 to libsrc4 so that it is accessible to nczarr. Changes directly related to Zarr: 1. Modified CMakeList.txt and configure.ac to support both C and C++ -- this is in support of S3 support via the awd-sdk libraries. 2. Define a size64_t type to support nczarr. 3. More reworking of libdispatch/dinfermodel.c to support zarr and to regularize the structure of the fragments section of a URL. Changes not directly related to Zarr: 1. Make client-side filter registration be conditional, with default off. 2. Hack include/nc4internal.h to make some flags added by Ed be unique: e.g. NC_CREAT, NC_INDEF, etc. 3. cleanup include/nchttp.h and libdispatch/dhttp.c. 4. Misc. changes to support compiling under Visual Studio including: * Better testing under windows for dirent.h and opendir and closedir. 5. Misc. changes to the oc2 code to support various libcurl CURLOPT flags and to centralize error reporting. 6. By default, suppress the vlen tests that have unfixed memory leaks; add option to enable them. 7. Make part of the nc_test/test_byterange.sh test be contingent on remotetest.unidata.ucar.edu being accessible. Changes Left TO-DO: 1. fix provenance code, it is too HDF5 specific.
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| sed -e '/:_Endianness/d' \
| sed -e 's/_SuperblockVersion = [12]/_SuperblockVersion = 0/' \
There was a request to extend the provenance information stored in the _NCProperties attribute to allow two things: 1. capture of additional library dependencies (over and above hdf5) 2. Recognition of non-netcdf libraries that create netcdf-4 format files. To this end, the _NCProperties format has been extended to be and arbitrary set of key=value pairs separated by commas. This new format has version = 2, and uses commas as the pair separator. Thus the general form is: _NCProperties = "version=2,key1=value,key2=value2..." ; This new version is accompanied by a new ./configure option of the form --with-ncproperties="key1=value1,key2=value2..." that specifies pairs to add to the _NCProperties attribute for all files created with that netcdf library. At this point, what is missing is some programmatic way to specify either all the pairs or additional pairs to the _NCProperties attribute. Not sure of the best way to do this. Builders using non-netcdf libraries can specify whatever they want in the key value pairs (as long as the version=2 is specified first). By convention, the primary library is expected to be the the first pair after the leading version=2 pair, but this is convention only and is neither required nor enforced. Related changes: 1. Fixed the tests that check _NCProperties to properly operate with version=2. 2. When reading a version 1 _NCProperties attribute, convert it to look like a version 2 attribute. 2. Added some version 2 tests to ncdump/tst_fileinfo.c and ncdump/tst_fileinfo.sh Misc Changes: 1. Fix minor problem in ncdap_test/testurl.sh where a parameter to buildurl needed to be quoted. 2. Minor fix to ncgen to swap switches -H and -h to be consistent with other utilities. 3. Document the -M flag in nccopy usage() and the nccopy man page. 4. Modify a test case to use the nccopy -M flag.
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| sed -e 's/\(netcdflibversion\|netcdf\)=.*|/\1=NNNN|/' \
| sed -e 's/\(hdf5libversion\|hdf5\)=.*"/\1=HHHH"/' \
| grep -v '_NCProperties' \
There was a request to extend the provenance information stored in the _NCProperties attribute to allow two things: 1. capture of additional library dependencies (over and above hdf5) 2. Recognition of non-netcdf libraries that create netcdf-4 format files. To this end, the _NCProperties format has been extended to be and arbitrary set of key=value pairs separated by commas. This new format has version = 2, and uses commas as the pair separator. Thus the general form is: _NCProperties = "version=2,key1=value,key2=value2..." ; This new version is accompanied by a new ./configure option of the form --with-ncproperties="key1=value1,key2=value2..." that specifies pairs to add to the _NCProperties attribute for all files created with that netcdf library. At this point, what is missing is some programmatic way to specify either all the pairs or additional pairs to the _NCProperties attribute. Not sure of the best way to do this. Builders using non-netcdf libraries can specify whatever they want in the key value pairs (as long as the version=2 is specified first). By convention, the primary library is expected to be the the first pair after the leading version=2 pair, but this is convention only and is neither required nor enforced. Related changes: 1. Fixed the tests that check _NCProperties to properly operate with version=2. 2. When reading a version 1 _NCProperties attribute, convert it to look like a version 2 attribute. 2. Added some version 2 tests to ncdump/tst_fileinfo.c and ncdump/tst_fileinfo.sh Misc Changes: 1. Fix minor problem in ncdap_test/testurl.sh where a parameter to buildurl needed to be quoted. 2. Minor fix to ncgen to swap switches -H and -h to be consistent with other utilities. 3. Document the -M flag in nccopy usage() and the nccopy man page. 4. Modify a test case to use the nccopy -M flag.
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| cat >$dst
}
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ERR() {
RES=$?
if [ $RES -ne 0 ]; then
echo "Error found: $RES"
exit $RES
fi
}
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echo ""
echo "*** Testing ncgen and ncdump for netCDF-4 format."
${NCGEN} -k nc4 -b -o tst_netcdf4_c0_4.nc ${ncgenc04} ;ERR
${NCDUMP} -n c1 tst_netcdf4_c0_4.nc | sed 's/e+0/e+/g' > tst_netcdf4_c1_4.cdl ; ERR
diff -b tst_netcdf4_c1_4.cdl $srcdir/ref_ctest1_nc4.cdl ; ERR
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echo "*** Creating test output tst_netcdf4_c0.nc."
${NCGEN} -k nc7 -b -o tst_netcdf4_c0.nc ${ncgenc0} ; ERR
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echo "*** Testing that program tst_h_rdc0 can read tst_netcdf4_c0.nc."
${execdir}/tst_h_rdc0 ; ERR
echo "*** Running tst_create_files.c to create test files."
${execdir}/tst_create_files ; ERR
echo "*** Testing tst_create_files output for netCDF-4 features."
${NCDUMP} tst_solar_1.nc | sed 's/e+0/e+/g' > tst_solar_1.cdl ; ERR
diff -b tst_solar_1.cdl $srcdir/ref_tst_solar_1.cdl ; ERR
${NCDUMP} tst_solar_2.nc | sed 's/e+0/e+/g' > tst_solar_2.cdl ; ERR
diff -b tst_solar_2.cdl $srcdir/ref_tst_solar_2.cdl ; ERR
if test -f tst_roman_szip_simple.nc; then
echo "*** Testing szip compression."
${NCDUMP} tst_roman_szip_simple.nc | sed 's/e+0/e+/g' > tst_roman_szip_simple.cdl ; ERR
diff -b tst_roman_szip_simple.cdl $srcdir/ref_roman_szip_simple.cdl ; ERR
${NCDUMP} tst_roman_szip_unlim.nc | sed 's/e+0/e+/g' > tst_roman_szip_unlim.cdl ; ERR
diff -b tst_roman_szip_unlim.cdl $srcdir/ref_roman_szip_unlim.cdl ; ERR
fi
echo "*** Running tst_group_data.c to create test files."
${execdir}/tst_group_data ; ERR
${NCDUMP} tst_group_data.nc | sed 's/e+0/e+/g' > tst_group_data.cdl ; ERR
diff -b tst_group_data.cdl $srcdir/ref_tst_group_data.cdl ; ERR
echo "*** Testing -v option with absolute name and groups..."
${NCDUMP} -v g2/g3/var tst_group_data.nc | sed 's/e+0/e+/g' > tst_group_data.cdl ; ERR
diff -b tst_group_data.cdl $srcdir/ref_tst_group_data_v23.cdl ; ERR
echo "*** Testing -v option with relative name and groups..."
${NCDUMP} -v var,var2 tst_group_data.nc | sed 's/e+0/e+/g' > tst_group_data.cdl ; ERR
diff -b tst_group_data.cdl $srcdir/ref_tst_group_data.cdl ; ERR
echo "*** Running tst_enum_data.c to create test files."
${execdir}/tst_enum_data ; ERR
${NCDUMP} tst_enum_data.nc | sed 's/e+0/e+/g' > tst_enum_data.cdl ; ERR
diff -b tst_enum_data.cdl $srcdir/ref_tst_enum_data.cdl ; ERR
echo "*** Running tst_enum_undef.c to create test files."
${execdir}/tst_enum_undef ; ERR
${NCDUMP} tst_enum_undef.nc | sed 's/e+0/e+/g' > tst_enum_undef.cdl ; ERR
diff -b tst_enum_undef.cdl $srcdir/ref_tst_enum_undef.cdl ; ERR
echo "*** Running tst_opaque_data.c to create test files."
${execdir}/tst_opaque_data ; ERR
${NCDUMP} tst_opaque_data.nc | sed 's/e+0/e+/g' > tst_opaque_data.cdl ; ERR
diff -b tst_opaque_data.cdl $srcdir/ref_tst_opaque_data.cdl ; ERR
echo "*** Running tst_comp.c to create test files."
${execdir}/tst_comp ; ERR
${NCDUMP} tst_comp.nc | sed 's/e+0/e+/g' > tst_comp.cdl ; ERR
diff -b tst_comp.cdl $srcdir/ref_tst_comp.cdl ; ERR
echo "*** Running tst_nans.c to create test files."
${execdir}/tst_nans ; ERR
${NCDUMP} tst_nans.nc | sed 's/e+0/e+/g' > tst_nans.cdl ; ERR
diff -b tst_nans.cdl $srcdir/ref_tst_nans.cdl ; ERR
echo "*** Running tst_special_atts.c to create test files."
${execdir}/tst_special_atts ; ERR
There was a request to extend the provenance information stored in the _NCProperties attribute to allow two things: 1. capture of additional library dependencies (over and above hdf5) 2. Recognition of non-netcdf libraries that create netcdf-4 format files. To this end, the _NCProperties format has been extended to be and arbitrary set of key=value pairs separated by commas. This new format has version = 2, and uses commas as the pair separator. Thus the general form is: _NCProperties = "version=2,key1=value,key2=value2..." ; This new version is accompanied by a new ./configure option of the form --with-ncproperties="key1=value1,key2=value2..." that specifies pairs to add to the _NCProperties attribute for all files created with that netcdf library. At this point, what is missing is some programmatic way to specify either all the pairs or additional pairs to the _NCProperties attribute. Not sure of the best way to do this. Builders using non-netcdf libraries can specify whatever they want in the key value pairs (as long as the version=2 is specified first). By convention, the primary library is expected to be the the first pair after the leading version=2 pair, but this is convention only and is neither required nor enforced. Related changes: 1. Fixed the tests that check _NCProperties to properly operate with version=2. 2. When reading a version 1 _NCProperties attribute, convert it to look like a version 2 attribute. 2. Added some version 2 tests to ncdump/tst_fileinfo.c and ncdump/tst_fileinfo.sh Misc Changes: 1. Fix minor problem in ncdap_test/testurl.sh where a parameter to buildurl needed to be quoted. 2. Minor fix to ncgen to swap switches -H and -h to be consistent with other utilities. 3. Document the -M flag in nccopy usage() and the nccopy man page. 4. Modify a test case to use the nccopy -M flag.
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${NCDUMP} -c -s tst_special_atts.nc > tst_special_atts.cdl ; ERR
cleanncprops tst_special_atts.cdl tst_special_atts.tmp
cleanncprops $srcdir/ref_tst_special_atts.cdl ref_tst_special_atts.tmp
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echo "*** comparing tst_special_atts.cdl with ref_tst_special_atts.cdl..."
There was a request to extend the provenance information stored in the _NCProperties attribute to allow two things: 1. capture of additional library dependencies (over and above hdf5) 2. Recognition of non-netcdf libraries that create netcdf-4 format files. To this end, the _NCProperties format has been extended to be and arbitrary set of key=value pairs separated by commas. This new format has version = 2, and uses commas as the pair separator. Thus the general form is: _NCProperties = "version=2,key1=value,key2=value2..." ; This new version is accompanied by a new ./configure option of the form --with-ncproperties="key1=value1,key2=value2..." that specifies pairs to add to the _NCProperties attribute for all files created with that netcdf library. At this point, what is missing is some programmatic way to specify either all the pairs or additional pairs to the _NCProperties attribute. Not sure of the best way to do this. Builders using non-netcdf libraries can specify whatever they want in the key value pairs (as long as the version=2 is specified first). By convention, the primary library is expected to be the the first pair after the leading version=2 pair, but this is convention only and is neither required nor enforced. Related changes: 1. Fixed the tests that check _NCProperties to properly operate with version=2. 2. When reading a version 1 _NCProperties attribute, convert it to look like a version 2 attribute. 2. Added some version 2 tests to ncdump/tst_fileinfo.c and ncdump/tst_fileinfo.sh Misc Changes: 1. Fix minor problem in ncdap_test/testurl.sh where a parameter to buildurl needed to be quoted. 2. Minor fix to ncgen to swap switches -H and -h to be consistent with other utilities. 3. Document the -M flag in nccopy usage() and the nccopy man page. 4. Modify a test case to use the nccopy -M flag.
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diff -b tst_special_atts.tmp ref_tst_special_atts.tmp ; ERR
# This creates a memory leak
if test 0 = 1 ; then
Fix various problem around VLEN's re: https://github.com/Unidata/netcdf-c/issues/541 re: https://github.com/Unidata/netcdf-c/issues/1208 re: https://github.com/Unidata/netcdf-c/issues/2078 re: https://github.com/Unidata/netcdf-c/issues/2041 re: https://github.com/Unidata/netcdf-c/issues/2143 For a long time, there have been known problems with the management of complex types containing VLENs. This also involves the string type because it is stored as a VLEN of chars. This PR (mostly) fixes this problem. But note that it adds new functions to netcdf.h (see below) and this may require bumping the .so number. These new functions can be removed, if desired, in favor of functions in netcdf_aux.h, but netcdf.h seems the better place for them because they are intended as alternatives to the nc_free_vlen and nc_free_string functions already in netcdf.h. The term complex type refers to any type that directly or transitively references a VLEN type. So an array of VLENS, a compound with a VLEN field, and so on. In order to properly handle instances of these complex types, it is necessary to have function that can recursively walk instances of such types to perform various actions on them. The term "deep" is also used to mean recursive. At the moment, the two operations needed by the netcdf library are: * free'ing an instance of the complex type * copying an instance of the complex type. The current library does only shallow free and shallow copy of complex types. This means that only the top level is properly free'd or copied, but deep internal blocks in the instance are not touched. Note that the term "vector" will be used to mean a contiguous (in memory) sequence of instances of some type. Given an array with, say, dimensions 2 X 3 X 4, this will be stored in memory as a vector of length 2*3*4=24 instances. The use cases are primarily these. ## nc_get_vars Suppose one is reading a vector of instances using nc_get_vars (or nc_get_vara or nc_get_var, etc.). These functions will return the vector in the top-level memory provided. All interior blocks (form nested VLEN or strings) will have been dynamically allocated. After using this vector of instances, it is necessary to free (aka reclaim) the dynamically allocated memory, otherwise a memory leak occurs. So, the recursive reclaim function is used to walk the returned instance vector and do a deep reclaim of the data. Currently functions are defined in netcdf.h that are supposed to handle this: nc_free_vlen(), nc_free_vlens(), and nc_free_string(). Unfortunately, these functions only do a shallow free, so deeply nested instances are not properly handled by them. Note that internally, the provided data is immediately written so there is no need to copy it. But the caller may need to reclaim the data it passed into the function. ## nc_put_att Suppose one is writing a vector of instances as the data of an attribute using, say, nc_put_att. Internally, the incoming attribute data must be copied and stored so that changes/reclamation of the input data will not affect the attribute. Again, the code inside the netcdf library does only shallow copying rather than deep copy. As a result, one sees effects such as described in Github Issue https://github.com/Unidata/netcdf-c/issues/2143. Also, after defining the attribute, it may be necessary for the user to free the data that was provided as input to nc_put_att(). ## nc_get_att Suppose one is reading a vector of instances as the data of an attribute using, say, nc_get_att. Internally, the existing attribute data must be copied and returned to the caller, and the caller is responsible for reclaiming the returned data. Again, the code inside the netcdf library does only shallow copying rather than deep copy. So this can lead to memory leaks and errors because the deep data is shared between the library and the user. # Solution The solution is to build properly recursive reclaim and copy functions and use those as needed. These recursive functions are defined in libdispatch/dinstance.c and their signatures are defined in include/netcdf.h. For back compatibility, corresponding "ncaux_XXX" functions are defined in include/netcdf_aux.h. ```` int nc_reclaim_data(int ncid, nc_type xtypeid, void* memory, size_t count); int nc_reclaim_data_all(int ncid, nc_type xtypeid, void* memory, size_t count); int nc_copy_data(int ncid, nc_type xtypeid, const void* memory, size_t count, void* copy); int nc_copy_data_all(int ncid, nc_type xtypeid, const void* memory, size_t count, void** copyp); ```` There are two variants. The first two, nc_reclaim_data() and nc_copy_data(), assume the top-level vector is managed by the caller. For reclaim, this is so the user can use, for example, a statically allocated vector. For copy, it assumes the user provides the space into which the copy is stored. The second two, nc_reclaim_data_all() and nc_copy_data_all(), allows the functions to manage the top-level. So for nc_reclaim_data_all, the top level is assumed to be dynamically allocated and will be free'd by nc_reclaim_data_all(). The nc_copy_data_all() function will allocate the top level and return a pointer to it to the user. The user can later pass that pointer to nc_reclaim_data_all() to reclaim the instance(s). # Internal Changes The netcdf-c library internals are changed to use the proper reclaim and copy functions. It turns out that the places where these functions are needed is quite pervasive in the netcdf-c library code. Using these functions also allows some simplification of the code since the stdata and vldata fields of NC_ATT_INFO are no longer needed. Currently this is commented out using the SEPDATA \#define macro. When any bugs are largely fixed, all this code will be removed. # Known Bugs 1. There is still one known failure that has not been solved. All the failures revolve around some variant of this .cdl file. The proximate cause of failure is the use of a VLEN FillValue. ```` netcdf x { types: float(*) row_of_floats ; dimensions: m = 5 ; variables: row_of_floats ragged_array(m) ; row_of_floats ragged_array:_FillValue = {-999} ; data: ragged_array = {10, 11, 12, 13, 14}, {20, 21, 22, 23}, {30, 31, 32}, {40, 41}, _ ; } ```` When a solution is found, I will either add it to this PR or post a new PR. # Related Changes * Mark nc_free_vlen(s) as deprecated in favor of ncaux_reclaim_data. * Remove the --enable-unfixed-memory-leaks option. * Remove the NC_VLENS_NOTEST code that suppresses some vlen tests. * Document this change in docs/internal.md * Disable the tst_vlen_data test in ncdump/tst_nccopy4.sh. * Mark types as fixed size or not (transitively) to optimize the reclaim and copy functions. # Misc. Changes * Make Doxygen process libdispatch/daux.c * Make sure the NC_ATT_INFO_T.container field is set.
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echo "*** Running tst_vlen_data.c to create test files."
if ! ${execdir}/tst_vlen_data ; then if test $? != 027 ; then ERR; fi; fi
${NCDUMP} tst_vlen_data.nc | sed 's/e+0/e+/g' > tst_vlen_data.cdl ; ERR
diff -b tst_vlen_data.cdl $srcdir/ref_tst_vlen_data.cdl ; ERR
fi
Fix various problem around VLEN's re: https://github.com/Unidata/netcdf-c/issues/541 re: https://github.com/Unidata/netcdf-c/issues/1208 re: https://github.com/Unidata/netcdf-c/issues/2078 re: https://github.com/Unidata/netcdf-c/issues/2041 re: https://github.com/Unidata/netcdf-c/issues/2143 For a long time, there have been known problems with the management of complex types containing VLENs. This also involves the string type because it is stored as a VLEN of chars. This PR (mostly) fixes this problem. But note that it adds new functions to netcdf.h (see below) and this may require bumping the .so number. These new functions can be removed, if desired, in favor of functions in netcdf_aux.h, but netcdf.h seems the better place for them because they are intended as alternatives to the nc_free_vlen and nc_free_string functions already in netcdf.h. The term complex type refers to any type that directly or transitively references a VLEN type. So an array of VLENS, a compound with a VLEN field, and so on. In order to properly handle instances of these complex types, it is necessary to have function that can recursively walk instances of such types to perform various actions on them. The term "deep" is also used to mean recursive. At the moment, the two operations needed by the netcdf library are: * free'ing an instance of the complex type * copying an instance of the complex type. The current library does only shallow free and shallow copy of complex types. This means that only the top level is properly free'd or copied, but deep internal blocks in the instance are not touched. Note that the term "vector" will be used to mean a contiguous (in memory) sequence of instances of some type. Given an array with, say, dimensions 2 X 3 X 4, this will be stored in memory as a vector of length 2*3*4=24 instances. The use cases are primarily these. ## nc_get_vars Suppose one is reading a vector of instances using nc_get_vars (or nc_get_vara or nc_get_var, etc.). These functions will return the vector in the top-level memory provided. All interior blocks (form nested VLEN or strings) will have been dynamically allocated. After using this vector of instances, it is necessary to free (aka reclaim) the dynamically allocated memory, otherwise a memory leak occurs. So, the recursive reclaim function is used to walk the returned instance vector and do a deep reclaim of the data. Currently functions are defined in netcdf.h that are supposed to handle this: nc_free_vlen(), nc_free_vlens(), and nc_free_string(). Unfortunately, these functions only do a shallow free, so deeply nested instances are not properly handled by them. Note that internally, the provided data is immediately written so there is no need to copy it. But the caller may need to reclaim the data it passed into the function. ## nc_put_att Suppose one is writing a vector of instances as the data of an attribute using, say, nc_put_att. Internally, the incoming attribute data must be copied and stored so that changes/reclamation of the input data will not affect the attribute. Again, the code inside the netcdf library does only shallow copying rather than deep copy. As a result, one sees effects such as described in Github Issue https://github.com/Unidata/netcdf-c/issues/2143. Also, after defining the attribute, it may be necessary for the user to free the data that was provided as input to nc_put_att(). ## nc_get_att Suppose one is reading a vector of instances as the data of an attribute using, say, nc_get_att. Internally, the existing attribute data must be copied and returned to the caller, and the caller is responsible for reclaiming the returned data. Again, the code inside the netcdf library does only shallow copying rather than deep copy. So this can lead to memory leaks and errors because the deep data is shared between the library and the user. # Solution The solution is to build properly recursive reclaim and copy functions and use those as needed. These recursive functions are defined in libdispatch/dinstance.c and their signatures are defined in include/netcdf.h. For back compatibility, corresponding "ncaux_XXX" functions are defined in include/netcdf_aux.h. ```` int nc_reclaim_data(int ncid, nc_type xtypeid, void* memory, size_t count); int nc_reclaim_data_all(int ncid, nc_type xtypeid, void* memory, size_t count); int nc_copy_data(int ncid, nc_type xtypeid, const void* memory, size_t count, void* copy); int nc_copy_data_all(int ncid, nc_type xtypeid, const void* memory, size_t count, void** copyp); ```` There are two variants. The first two, nc_reclaim_data() and nc_copy_data(), assume the top-level vector is managed by the caller. For reclaim, this is so the user can use, for example, a statically allocated vector. For copy, it assumes the user provides the space into which the copy is stored. The second two, nc_reclaim_data_all() and nc_copy_data_all(), allows the functions to manage the top-level. So for nc_reclaim_data_all, the top level is assumed to be dynamically allocated and will be free'd by nc_reclaim_data_all(). The nc_copy_data_all() function will allocate the top level and return a pointer to it to the user. The user can later pass that pointer to nc_reclaim_data_all() to reclaim the instance(s). # Internal Changes The netcdf-c library internals are changed to use the proper reclaim and copy functions. It turns out that the places where these functions are needed is quite pervasive in the netcdf-c library code. Using these functions also allows some simplification of the code since the stdata and vldata fields of NC_ATT_INFO are no longer needed. Currently this is commented out using the SEPDATA \#define macro. When any bugs are largely fixed, all this code will be removed. # Known Bugs 1. There is still one known failure that has not been solved. All the failures revolve around some variant of this .cdl file. The proximate cause of failure is the use of a VLEN FillValue. ```` netcdf x { types: float(*) row_of_floats ; dimensions: m = 5 ; variables: row_of_floats ragged_array(m) ; row_of_floats ragged_array:_FillValue = {-999} ; data: ragged_array = {10, 11, 12, 13, 14}, {20, 21, 22, 23}, {30, 31, 32}, {40, 41}, _ ; } ```` When a solution is found, I will either add it to this PR or post a new PR. # Related Changes * Mark nc_free_vlen(s) as deprecated in favor of ncaux_reclaim_data. * Remove the --enable-unfixed-memory-leaks option. * Remove the NC_VLENS_NOTEST code that suppresses some vlen tests. * Document this change in docs/internal.md * Disable the tst_vlen_data test in ncdump/tst_nccopy4.sh. * Mark types as fixed size or not (transitively) to optimize the reclaim and copy functions. # Misc. Changes * Make Doxygen process libdispatch/daux.c * Make sure the NC_ATT_INFO_T.container field is set.
2022-01-09 09:30:00 +08:00
#echo ""
#echo "*** Testing ncdump on file with corrupted header "
#rm -f ./ignore_tst_netcdf4
#if ${NCDUMP} ${srcdir}/ref_test_corrupt_magic.nc > ./ignore_tst_netcdf4 2>&1 ; then
#echo "***Fail: ncdump should have failed on ref_test_corrupt_magic.nc"
#else
#echo "***XFail: ncdump properly failed on ref_test_corrupt_magic.nc"
#fi
#rm -fr ./ignore_tst_netcdf4
re e-support UBS-599337 re pull request https://github.com/Unidata/netcdf-c/pull/405 re pull request https://github.com/Unidata/netcdf-c/pull/446 Notes: 1. This branch is a cleanup of the magic.dmh branch. 2. magic.dmh was originally merged, but caused problems with parallel IO. It was re-issued as pull request https://github.com/Unidata/netcdf-c/pull/446. 3. This branch + pull request replace any previous pull requests and magic.dmh branch. Given an otherwise valid netCDF file that has a corrupted header, the netcdf library currently crashes. Instead, it should return NC_ENOTNC. Additionally, the NC_check_file_type code does not do the forward search required by hdf5 files. It currently only looks at file position 0 instead of 512, 1024, 2048,... Also, it turns out that the HDF4 magic number is assumed to always be at the beginning of the file (unlike HDF5). The change is localized to libdispatch/dfile.c See https://support.hdfgroup.org/release4/doc/DSpec_html/DS.pdf Also, it turns out that the code in NC_check_file_type is duplicated (mostly) in the function libsrc4/nc4file.c#nc_check_for_hdf. This branch does the following. 1. Make NC_check_file_type return NC_ENOTNC instead of crashing. 2. Remove nc_check_for_hdf and centralize all file format checking NC_check_file_type. 3. Add proper forward search for HDF5 files (but not HDF4 files) to look for the magic number at offsets of 0, 512, 1024... 4. Add test tst_hdf5_offset.sh. This tests that hdf5 files with an offset are properly recognized. It does so by prefixing a legal file with some number of zero bytes: 512, 1024, etc. 5. Off-topic: Added -N flag to ncdump to force a specific output dataset name.
2017-10-25 06:25:09 +08:00
2018-05-15 22:24:27 +08:00
# This should work, but does not. See github issue 982.
#echo "*** creating tst_output_irish_rover.cdl from ref_tst_irish_rover.nc..."
#${NCDUMP} ref_tst_irish_rover.nc > tst_output_irish_rover.cdl
There was a request to extend the provenance information stored in the _NCProperties attribute to allow two things: 1. capture of additional library dependencies (over and above hdf5) 2. Recognition of non-netcdf libraries that create netcdf-4 format files. To this end, the _NCProperties format has been extended to be and arbitrary set of key=value pairs separated by commas. This new format has version = 2, and uses commas as the pair separator. Thus the general form is: _NCProperties = "version=2,key1=value,key2=value2..." ; This new version is accompanied by a new ./configure option of the form --with-ncproperties="key1=value1,key2=value2..." that specifies pairs to add to the _NCProperties attribute for all files created with that netcdf library. At this point, what is missing is some programmatic way to specify either all the pairs or additional pairs to the _NCProperties attribute. Not sure of the best way to do this. Builders using non-netcdf libraries can specify whatever they want in the key value pairs (as long as the version=2 is specified first). By convention, the primary library is expected to be the the first pair after the leading version=2 pair, but this is convention only and is neither required nor enforced. Related changes: 1. Fixed the tests that check _NCProperties to properly operate with version=2. 2. When reading a version 1 _NCProperties attribute, convert it to look like a version 2 attribute. 2. Added some version 2 tests to ncdump/tst_fileinfo.c and ncdump/tst_fileinfo.sh Misc Changes: 1. Fix minor problem in ncdap_test/testurl.sh where a parameter to buildurl needed to be quoted. 2. Minor fix to ncgen to swap switches -H and -h to be consistent with other utilities. 3. Document the -M flag in nccopy usage() and the nccopy man page. 4. Modify a test case to use the nccopy -M flag.
2018-08-26 11:44:41 +08:00
rm -f *.tmp
2010-06-03 21:24:43 +08:00
echo "*** All ncgen and ncdump test output for netCDF-4 format passed!"
exit 0