netcdf-c/ncgen/util.c

670 lines
14 KiB
C
Raw Normal View History

2010-06-03 21:24:43 +08:00
/*********************************************************************
2018-12-07 06:40:43 +08:00
* Copyright 2018, UCAR/Unidata
2010-06-03 21:24:43 +08:00
* See netcdf/COPYRIGHT file for copying and redistribution conditions.
* $Header: /upc/share/CVS/netcdf-3/ncgen/util.c,v 1.4 2010/04/14 22:04:59 dmh Exp $
*********************************************************************/
#include "includes.h"
/* Track primitive symbol instances (initialized in ncgen.y) */
Symbol* primsymbols[PRIMNO];
char*
append(const char* s1, const char* s2)
{
int len = (s1?strlen(s1):0)+(s2?strlen(s2):0);
2017-10-31 05:52:08 +08:00
char* result = (char*)ecalloc(len+1);
2010-06-03 21:24:43 +08:00
result[0] = '\0';
if(s1) strcat(result,s1);
if(s2) strcat(result,s2);
return result;
}
unsigned int
chartohex(char c)
{
switch (c) {
case '0': case '1': case '2': case '3': case '4':
case '5': case '6': case '7': case '8': case '9':
return (c - '0');
case 'A': case 'B': case 'C':
case 'D': case 'E': case 'F':
return (c - 'A') + 0x0a;
case 'a': case 'b': case 'c':
case 'd': case 'e': case 'f':
return (c - 'a') + 0x0a;
}
return 0;
}
/*
* For generated Fortran, change 'e' to 'd' in exponent of double precision
* constants.
*/
void
expe2d(
char *cp) /* string containing double constant */
{
char *expchar = strrchr(cp,'e');
if (expchar) {
*expchar = 'd';
}
}
/* Returns non-zero if n is a power of 2, 0 otherwise */
int
pow2(
int n)
{
int m = n;
int p = 1;
while (m > 0) {
m /= 2;
p *= 2;
}
return p == 2*n;
}
/*
* Remove trailing zeros (after decimal point) but not trailing decimal
* point from ss, a string representation of a floating-point number that
* might include an exponent part.
*/
void
tztrim(
char *ss /* returned string representing dd */
)
{
char *cp, *ep;
2014-08-12 03:21:01 +08:00
2010-06-03 21:24:43 +08:00
cp = ss;
if (*cp == '-')
cp++;
while(isdigit((int)*cp) || *cp == '.')
cp++;
if (*--cp == '.')
return;
ep = cp+1;
while (*cp == '0')
cp--;
cp++;
if (cp == ep)
return;
while (*ep)
*cp++ = *ep++;
*cp = '\0';
return;
}
Fix more memory leaks in netcdf-c library This is a follow up to PR https://github.com/Unidata/netcdf-c/pull/1173 Sorry that it is so big, but leak suppression can be complex. This PR fixes all remaining memory leaks -- as determined by -fsanitize=address, and with the exceptions noted below. Unfortunately. there remains a significant leak that I cannot solve. It involves vlens, and it is unclear if the leak is occurring in the netcdf-c library or the HDF5 library. I have added a check_PROGRAM to the ncdump directory to show the problem. The program is called tst_vlen_demo.c To exercise it, build the netcdf library with -fsanitize=address enabled. Then go into ncdump and do a "make clean check". This should build tst_vlen_demo without actually executing it. Then do the command "./tst_vlen_demo" to see the output of the memory checker. Note the the lost malloc is deep in the HDF5 library (in H5Tvlen.c). I am temporarily working around this error in the following way. 1. I modified several test scripts to not execute known vlen tests that fail as described above. 2. Added an environment variable called NC_VLEN_NOTEST. If set, then those specific tests are suppressed. This should mean that the --disable-utilities option to ./configure should not need to be set to get a memory leak clean build. This should allow for detection of any new leaks. Note: I used an environment variable rather than a ./configure option to control the vlen tests. This is because it is temporary (I hope) and because it is a bit tricky for shell scripts to access ./configure options. Finally, as before, this only been tested with netcdf-4 and hdf5 support.
2018-11-16 01:00:38 +08:00
static void
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.
2020-06-29 08:02:47 +08:00
clearSpecialdata(Specialdata* data)
Fix more memory leaks in netcdf-c library This is a follow up to PR https://github.com/Unidata/netcdf-c/pull/1173 Sorry that it is so big, but leak suppression can be complex. This PR fixes all remaining memory leaks -- as determined by -fsanitize=address, and with the exceptions noted below. Unfortunately. there remains a significant leak that I cannot solve. It involves vlens, and it is unclear if the leak is occurring in the netcdf-c library or the HDF5 library. I have added a check_PROGRAM to the ncdump directory to show the problem. The program is called tst_vlen_demo.c To exercise it, build the netcdf library with -fsanitize=address enabled. Then go into ncdump and do a "make clean check". This should build tst_vlen_demo without actually executing it. Then do the command "./tst_vlen_demo" to see the output of the memory checker. Note the the lost malloc is deep in the HDF5 library (in H5Tvlen.c). I am temporarily working around this error in the following way. 1. I modified several test scripts to not execute known vlen tests that fail as described above. 2. Added an environment variable called NC_VLEN_NOTEST. If set, then those specific tests are suppressed. This should mean that the --disable-utilities option to ./configure should not need to be set to get a memory leak clean build. This should allow for detection of any new leaks. Note: I used an environment variable rather than a ./configure option to control the vlen tests. This is because it is temporary (I hope) and because it is a bit tricky for shell scripts to access ./configure options. Finally, as before, this only been tested with netcdf-4 and hdf5 support.
2018-11-16 01:00:38 +08:00
{
if(data == NULL) return;
reclaimdatalist(data->_Fillvalue);
if(data->_ChunkSizes)
efree(data->_ChunkSizes);
Add support for multiple filters per variable. re: https://github.com/Unidata/netcdf-c/issues/1584 Support has been added for multiple filters per variable. This affects a number of components in netcdf. The new APIs are documented in NUG/filters.md. The primary changes are: * A set of new functions are provided (see __include/netcdf_filter.h__). - Obtain a list of the filters associated with a variable - Obtain the parameters for a specific filter. * The existing __nc_inq_var_filter__ function now returns info about the first defined filter. * The utilities (ncgen, ncdump, and nccopy) now support an extended format for specifying a sequence of filters. The general form is __<filter>|<filter>..._. * The ncdump **_Filter** attribute now dumps a list of all the filters associated with a variable using the above new format. * Filter specifications can now use a filter name instead of number for filters known to the netcdf library, which in turn is taken from the HDF5 filter registration page. * New errors are defined: NC_EFILTER and NC_ENOFILTER. The latter is returned if an attempt is made to access an unknown filter. * Internally, the dispatch table has been extended to add a function to handle all of the filter functions. * New, filter-related, tests were added to nc_test4. * A new plugin was added to the plugins directory to help with testing. Notes: 1. The shuffle and fletcher32 filters are not part of the multifilter system. Misc. changes: 1. A debug module was added to libhdf5 to help catch error locations.
2020-02-17 03:59:33 +08:00
if(data->_Filters) {
int i;
for(i=0;i<data->nfilters;i++) {
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.
2020-06-29 08:02:47 +08:00
NC_Filterspec* f = (NC_Filterspec*)data->_Filters[i];
ncaux_filterspec_free(f);
Add support for multiple filters per variable. re: https://github.com/Unidata/netcdf-c/issues/1584 Support has been added for multiple filters per variable. This affects a number of components in netcdf. The new APIs are documented in NUG/filters.md. The primary changes are: * A set of new functions are provided (see __include/netcdf_filter.h__). - Obtain a list of the filters associated with a variable - Obtain the parameters for a specific filter. * The existing __nc_inq_var_filter__ function now returns info about the first defined filter. * The utilities (ncgen, ncdump, and nccopy) now support an extended format for specifying a sequence of filters. The general form is __<filter>|<filter>..._. * The ncdump **_Filter** attribute now dumps a list of all the filters associated with a variable using the above new format. * Filter specifications can now use a filter name instead of number for filters known to the netcdf library, which in turn is taken from the HDF5 filter registration page. * New errors are defined: NC_EFILTER and NC_ENOFILTER. The latter is returned if an attempt is made to access an unknown filter. * Internally, the dispatch table has been extended to add a function to handle all of the filter functions. * New, filter-related, tests were added to nc_test4. * A new plugin was added to the plugins directory to help with testing. Notes: 1. The shuffle and fletcher32 filters are not part of the multifilter system. Misc. changes: 1. A debug module was added to libhdf5 to help catch error locations.
2020-02-17 03:59:33 +08:00
}
efree(data->_Filters);
}
2010-06-03 21:24:43 +08:00
}
void
freeSymbol(Symbol* sym)
{
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.
2020-06-29 08:02:47 +08:00
if(sym == NULL) return;
2010-06-03 21:24:43 +08:00
switch (sym->objectclass) {
Fix more memory leaks in netcdf-c library This is a follow up to PR https://github.com/Unidata/netcdf-c/pull/1173 Sorry that it is so big, but leak suppression can be complex. This PR fixes all remaining memory leaks -- as determined by -fsanitize=address, and with the exceptions noted below. Unfortunately. there remains a significant leak that I cannot solve. It involves vlens, and it is unclear if the leak is occurring in the netcdf-c library or the HDF5 library. I have added a check_PROGRAM to the ncdump directory to show the problem. The program is called tst_vlen_demo.c To exercise it, build the netcdf library with -fsanitize=address enabled. Then go into ncdump and do a "make clean check". This should build tst_vlen_demo without actually executing it. Then do the command "./tst_vlen_demo" to see the output of the memory checker. Note the the lost malloc is deep in the HDF5 library (in H5Tvlen.c). I am temporarily working around this error in the following way. 1. I modified several test scripts to not execute known vlen tests that fail as described above. 2. Added an environment variable called NC_VLEN_NOTEST. If set, then those specific tests are suppressed. This should mean that the --disable-utilities option to ./configure should not need to be set to get a memory leak clean build. This should allow for detection of any new leaks. Note: I used an environment variable rather than a ./configure option to control the vlen tests. This is because it is temporary (I hope) and because it is a bit tricky for shell scripts to access ./configure options. Finally, as before, this only been tested with netcdf-4 and hdf5 support.
2018-11-16 01:00:38 +08:00
case NC_VAR:
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.
2020-06-29 08:02:47 +08:00
clearSpecialdata(&sym->var.special);
Fix more memory leaks in netcdf-c library This is a follow up to PR https://github.com/Unidata/netcdf-c/pull/1173 Sorry that it is so big, but leak suppression can be complex. This PR fixes all remaining memory leaks -- as determined by -fsanitize=address, and with the exceptions noted below. Unfortunately. there remains a significant leak that I cannot solve. It involves vlens, and it is unclear if the leak is occurring in the netcdf-c library or the HDF5 library. I have added a check_PROGRAM to the ncdump directory to show the problem. The program is called tst_vlen_demo.c To exercise it, build the netcdf library with -fsanitize=address enabled. Then go into ncdump and do a "make clean check". This should build tst_vlen_demo without actually executing it. Then do the command "./tst_vlen_demo" to see the output of the memory checker. Note the the lost malloc is deep in the HDF5 library (in H5Tvlen.c). I am temporarily working around this error in the following way. 1. I modified several test scripts to not execute known vlen tests that fail as described above. 2. Added an environment variable called NC_VLEN_NOTEST. If set, then those specific tests are suppressed. This should mean that the --disable-utilities option to ./configure should not need to be set to get a memory leak clean build. This should allow for detection of any new leaks. Note: I used an environment variable rather than a ./configure option to control the vlen tests. This is because it is temporary (I hope) and because it is a bit tricky for shell scripts to access ./configure options. Finally, as before, this only been tested with netcdf-4 and hdf5 support.
2018-11-16 01:00:38 +08:00
listfree(sym->var.attributes);
break;
case NC_TYPE:
if(sym->typ.econst)
reclaimconstant(sym->typ.econst);
if(sym->typ._Fillvalue)
reclaimdatalist(sym->typ._Fillvalue);
2010-06-03 21:24:43 +08:00
break;
Fix more memory leaks in netcdf-c library This is a follow up to PR https://github.com/Unidata/netcdf-c/pull/1173 Sorry that it is so big, but leak suppression can be complex. This PR fixes all remaining memory leaks -- as determined by -fsanitize=address, and with the exceptions noted below. Unfortunately. there remains a significant leak that I cannot solve. It involves vlens, and it is unclear if the leak is occurring in the netcdf-c library or the HDF5 library. I have added a check_PROGRAM to the ncdump directory to show the problem. The program is called tst_vlen_demo.c To exercise it, build the netcdf library with -fsanitize=address enabled. Then go into ncdump and do a "make clean check". This should build tst_vlen_demo without actually executing it. Then do the command "./tst_vlen_demo" to see the output of the memory checker. Note the the lost malloc is deep in the HDF5 library (in H5Tvlen.c). I am temporarily working around this error in the following way. 1. I modified several test scripts to not execute known vlen tests that fail as described above. 2. Added an environment variable called NC_VLEN_NOTEST. If set, then those specific tests are suppressed. This should mean that the --disable-utilities option to ./configure should not need to be set to get a memory leak clean build. This should allow for detection of any new leaks. Note: I used an environment variable rather than a ./configure option to control the vlen tests. This is because it is temporary (I hope) and because it is a bit tricky for shell scripts to access ./configure options. Finally, as before, this only been tested with netcdf-4 and hdf5 support.
2018-11-16 01:00:38 +08:00
case NC_GRP:
if(sym->file.filename)
efree(sym->file.filename);
2010-06-03 21:24:43 +08:00
break;
default: break;
2014-08-12 03:21:01 +08:00
}
Fix more memory leaks in netcdf-c library This is a follow up to PR https://github.com/Unidata/netcdf-c/pull/1173 Sorry that it is so big, but leak suppression can be complex. This PR fixes all remaining memory leaks -- as determined by -fsanitize=address, and with the exceptions noted below. Unfortunately. there remains a significant leak that I cannot solve. It involves vlens, and it is unclear if the leak is occurring in the netcdf-c library or the HDF5 library. I have added a check_PROGRAM to the ncdump directory to show the problem. The program is called tst_vlen_demo.c To exercise it, build the netcdf library with -fsanitize=address enabled. Then go into ncdump and do a "make clean check". This should build tst_vlen_demo without actually executing it. Then do the command "./tst_vlen_demo" to see the output of the memory checker. Note the the lost malloc is deep in the HDF5 library (in H5Tvlen.c). I am temporarily working around this error in the following way. 1. I modified several test scripts to not execute known vlen tests that fail as described above. 2. Added an environment variable called NC_VLEN_NOTEST. If set, then those specific tests are suppressed. This should mean that the --disable-utilities option to ./configure should not need to be set to get a memory leak clean build. This should allow for detection of any new leaks. Note: I used an environment variable rather than a ./configure option to control the vlen tests. This is because it is temporary (I hope) and because it is a bit tricky for shell scripts to access ./configure options. Finally, as before, this only been tested with netcdf-4 and hdf5 support.
2018-11-16 01:00:38 +08:00
/* Universal */
if(sym->name) efree(sym->name);
if(sym->fqn) efree(sym->fqn);
listfree(sym->prefix);
if(sym->data)
reclaimdatalist(sym->data);
listfree(sym->subnodes);
2010-06-03 21:24:43 +08:00
efree(sym);
}
char* nctypenames[17] = {
"NC_NAT",
"NC_BYTE", "NC_CHAR", "NC_SHORT", "NC_INT",
"NC_FLOAT", "NC_DOUBLE",
"NC_UBYTE", "NC_USHORT", "NC_UINT",
"NC_INT64", "NC_UINT64",
"NC_STRING",
"NC_VLEN", "NC_OPAQUE", "NC_ENUM", "NC_COMPOUND"
};
char* nctypenamesextend[9] = {
"NC_GRP", "NC_DIM", "NC_VAR", "NC_ATT", "NC_TYPE",
"NC_ECONST","NC_FIELD", "NC_ARRAY","NC_PRIM"
};
char*
nctypename(nc_type nctype)
{
char* s;
if(nctype >= NC_NAT && nctype <= NC_COMPOUND)
return nctypenames[nctype];
if(nctype >= NC_GRP && nctype <= NC_PRIM)
return nctypenamesextend[(nctype - NC_GRP)];
if(nctype == NC_FILLVALUE) return "NC_FILL";
2013-07-11 04:53:50 +08:00
if(nctype == NC_NIL) return "NC_NIL";
2014-08-12 03:21:01 +08:00
s = poolalloc(128);
2010-06-03 21:24:43 +08:00
sprintf(s,"NC_<%d>",nctype);
return s;
}
/* These are the augmented NC_ values (0 based from NC_GRP)*/
2014-08-12 03:21:01 +08:00
char* ncclassnames[9] = {
"NC_GRP", "NC_DIM", "NC_VAR", "NC_ATT",
"NC_TYP", "NC_ECONST", "NC_FIELD", "NC_ARRAY",
2010-06-03 21:24:43 +08:00
"NC_PRIM"
};
char*
ncclassname(nc_class ncc)
{
char* s;
if(ncc >= NC_NAT && ncc <= NC_COMPOUND)
return nctypename((nc_type)ncc);
if(ncc == NC_FILLVALUE) return "NC_FILL";
if(ncc >= NC_GRP && ncc <= NC_PRIM)
return ncclassnames[ncc - NC_GRP];
2014-08-12 03:21:01 +08:00
s = poolalloc(128);
2010-06-03 21:24:43 +08:00
sprintf(s,"NC_<%d>",ncc);
return s;
}
int ncsizes[17] = {
0,
1,1,2,4,
4,8,
1,2,4,
8,8,
sizeof(char*),
sizeof(nc_vlen_t),
0,0,0
};
int
ncsize(nc_type nctype)
{
if(nctype >= NC_NAT && nctype <= NC_COMPOUND)
return ncsizes[nctype];
return 0;
}
int
hasunlimited(Dimset* dimset)
{
int i;
for(i=0;i<dimset->ndims;i++) {
Symbol* dim = dimset->dimsyms[i];
if(dim->dim.declsize == NC_UNLIMITED) return 1;
}
return 0;
}
/* return 1 if first dimension is unlimited*/
int
isunlimited0(Dimset* dimset)
{
return (dimset->ndims > 0 && dimset->dimsyms[0]->dim.declsize == NC_UNLIMITED);
}
/* True only if dim[0] is unlimited all rest are bounded*/
/* or all are bounded*/
int
classicunlimited(Dimset* dimset)
{
int i;
int last = -1;
for(i=0;i<dimset->ndims;i++) {
Symbol* dim = dimset->dimsyms[i];
if(dim->dim.declsize == NC_UNLIMITED) last = i;
}
return (last < 1);
}
/* True only iff no dimension is unlimited*/
int
isbounded(Dimset* dimset)
{
int i;
for(i=0;i<dimset->ndims;i++) {
Symbol* dim = dimset->dimsyms[i];
if(dim->dim.declsize == NC_UNLIMITED) return 0;
}
return 1;
}
2015-11-20 04:44:07 +08:00
int
signedtype(nc_type nctype)
{
switch (nctype) {
case NC_BYTE:
case NC_SHORT:
case NC_INT:
case NC_INT64:
return nctype;
case NC_UBYTE: return NC_BYTE;
case NC_USHORT: return NC_SHORT;
case NC_UINT: return NC_INT;
case NC_UINT64: return NC_INT64;
default: break;
}
return nctype;
}
int
unsignedtype(nc_type nctype)
{
switch (nctype) {
case NC_UBYTE:
case NC_USHORT:
case NC_UINT:
case NC_UINT64:
return nctype;
case NC_BYTE: return NC_UBYTE;
case NC_SHORT: return NC_USHORT;
case NC_INT: return NC_UINT;
case NC_INT64: return NC_UINT64;
default: break;
}
return nctype;
}
int
isinttype(nc_type nctype)
{
return (nctype != NC_CHAR)
&& ((nctype >= NC_BYTE && nctype <= NC_INT)
|| (nctype >= NC_UBYTE && nctype <= NC_UINT64));
}
int
isuinttype(nc_type t)
{
return isinttype(t)
&& t >= NC_UBYTE
&& t <= NC_UINT64
&& t != NC_INT64;
}
int
isfloattype(nc_type nctype)
{
return (nctype == NC_FLOAT || nctype <= NC_DOUBLE);
}
2010-06-03 21:24:43 +08:00
int
isclassicprim(nc_type nctype)
{
return (nctype >= NC_BYTE && nctype <= NC_DOUBLE)
;
}
int
isclassicprimplus(nc_type nctype)
{
return (nctype >= NC_BYTE && nctype <= NC_DOUBLE)
|| (nctype == NC_STRING)
;
}
int
isprim(nc_type nctype)
{
return (nctype >= NC_BYTE && nctype <= NC_STRING)
;
}
int
isprimplus(nc_type nctype)
{
return (nctype >= NC_BYTE && nctype <= NC_STRING)
|| (nctype == NC_ECONST)
|| (nctype == NC_OPAQUE)
;
}
void
collectpath(Symbol* grp, List* grpstack)
{
while(grp != NULL) {
listpush(grpstack,(void*)grp);
2010-06-03 21:24:43 +08:00
grp = grp->container;
}
}
#ifdef USE_NETCDF4
/* Result is pool'd*/
char*
prefixtostring(List* prefix, char* separator)
{
int slen=0;
int plen;
int i;
char* result;
if(prefix == NULL) return pooldup("");
plen = prefixlen(prefix);
if(plen == 0) { /* root prefix*/
slen=0;
/* slen += strlen(separator);*/
slen++; /* for null terminator*/
result = poolalloc(slen);
result[0] = '\0';
/*strcat(result,separator);*/
} else {
for(i=0;i<plen;i++) {
Symbol* sym = (Symbol*)listget(prefix,i);
slen += (strlen(separator)+strlen(sym->name));
}
slen++; /* for null terminator*/
result = poolalloc(slen);
result[0] = '\0';
for(i=0;i<plen;i++) {
Symbol* sym = (Symbol*)listget(prefix,i);
strcat(result,separator);
strcat(result,sym->name); /* append "/<prefix[i]>"*/
}
2014-08-12 03:21:01 +08:00
}
2010-06-03 21:24:43 +08:00
return result;
}
#endif
/* Result is pool'd*/
char*
fullname(Symbol* sym)
{
2014-08-12 03:21:01 +08:00
#ifdef USE_NETCDF4
2010-06-03 21:24:43 +08:00
char* s1;
char* result;
char* prefix;
prefix = prefixtostring(sym->prefix,PATHSEPARATOR);
s1 = poolcat(prefix,PATHSEPARATOR);
result = poolcat(s1,sym->name);
return result;
#else
return nulldup(sym->name);
#endif
}
int
prefixeq(List* x1, List* x2)
{
Symbol** l1;
2014-08-12 03:21:01 +08:00
Symbol** l2;
2010-06-03 21:24:43 +08:00
int len,i;
if((len=listlength(x1)) != listlength(x2)) return 0;
l1=(Symbol**)listcontents(x1);
l2=(Symbol**)listcontents(x2);
for(i=0;i<len;i++) {
if(strcmp(l1[i]->name,l2[i]->name) != 0) return 0;
}
return 1;
}
List*
prefixdup(List* prefix)
{
List* dupseq;
int i;
if(prefix == NULL) return listnew();
dupseq = listnew();
listsetalloc(dupseq,listlength(prefix));
for(i=0;i<listlength(prefix);i++) listpush(dupseq,listget(prefix,i));
2014-08-12 03:21:01 +08:00
return dupseq;
2010-06-03 21:24:43 +08:00
}
/*
Many of the generate routines need to construct
heap strings for short periods. Remembering to
free such space is error prone, so provide a
pseudo-GC to handle these short term requests.
The idea is to have a fixed size pool
tracking malloc requests and automatically
releasing when the pool gets full.
*/
/* Max number of allocated pool items*/
#define POOLMAX 100
static char* pool[POOLMAX];
static int poolindex = -1;
#define POOL_DEFAULT 256
char*
poolalloc(size_t length)
{
if(poolindex == -1) { /* initialize*/
memset((void*)pool,0,sizeof(pool));
poolindex = 0;
}
if(poolindex == POOLMAX) poolindex=0;
if(length == 0) length = POOL_DEFAULT;
if(pool[poolindex] != NULL) efree(pool[poolindex]);
2017-10-31 05:52:08 +08:00
pool[poolindex] = (char*)ecalloc(length);
2010-06-03 21:24:43 +08:00
return pool[poolindex++];
}
char*
pooldup(const char* s)
2010-06-03 21:24:43 +08:00
{
char* sdup = poolalloc(strlen(s)+1);
strncpy(sdup,s,(strlen(s)+1));
2010-06-03 21:24:43 +08:00
return sdup;
}
char*
poolcat(const char* s1, const char* s2)
{
int len1, len2;
char* cat;
if(s1 == NULL && s2 == NULL) return NULL;
len1 = (s1?strlen(s1):0);
len2 = (s2?strlen(s2):0);
cat = poolalloc(len1+len2+1);
cat[0] = '\0';
if(s1 != NULL) strcat(cat,s1);
if(s2 != NULL) strcat(cat,s2);
return cat;
}
/* Result is malloc'd*/
unsigned char*
makebytestring(char* s, size_t* lenp)
{
unsigned char* bytes;
unsigned char* b;
size_t slen = strlen(s); /* # nibbles */
size_t blen = slen/2; /* # bytes */
2010-06-03 21:24:43 +08:00
int i;
ASSERT((slen%2) == 0);
2014-08-12 03:21:01 +08:00
ASSERT(blen > 0);
2017-10-31 05:52:08 +08:00
bytes = (unsigned char*)ecalloc(blen);
2010-06-03 21:24:43 +08:00
b = bytes;
for(i=0;i<slen;i+=2) {
unsigned int digit1 = chartohex(*s++);
unsigned int digit2 = chartohex(*s++);
unsigned int byte = (digit1 << 4) | digit2;
2014-08-12 03:21:01 +08:00
*b++ = byte;
2010-06-03 21:24:43 +08:00
}
if(lenp) *lenp = blen;
return bytes;
}
int
getpadding(int offset, int alignment)
{
int rem = (alignment==0?0:(offset % alignment));
int pad = (rem==0?0:(alignment - rem));
return pad;
}
static void
reclaimSymbols(void)
2010-06-03 21:24:43 +08:00
{
Fix more memory leaks in netcdf-c library This is a follow up to PR https://github.com/Unidata/netcdf-c/pull/1173 Sorry that it is so big, but leak suppression can be complex. This PR fixes all remaining memory leaks -- as determined by -fsanitize=address, and with the exceptions noted below. Unfortunately. there remains a significant leak that I cannot solve. It involves vlens, and it is unclear if the leak is occurring in the netcdf-c library or the HDF5 library. I have added a check_PROGRAM to the ncdump directory to show the problem. The program is called tst_vlen_demo.c To exercise it, build the netcdf library with -fsanitize=address enabled. Then go into ncdump and do a "make clean check". This should build tst_vlen_demo without actually executing it. Then do the command "./tst_vlen_demo" to see the output of the memory checker. Note the the lost malloc is deep in the HDF5 library (in H5Tvlen.c). I am temporarily working around this error in the following way. 1. I modified several test scripts to not execute known vlen tests that fail as described above. 2. Added an environment variable called NC_VLEN_NOTEST. If set, then those specific tests are suppressed. This should mean that the --disable-utilities option to ./configure should not need to be set to get a memory leak clean build. This should allow for detection of any new leaks. Note: I used an environment variable rather than a ./configure option to control the vlen tests. This is because it is temporary (I hope) and because it is a bit tricky for shell scripts to access ./configure options. Finally, as before, this only been tested with netcdf-4 and hdf5 support.
2018-11-16 01:00:38 +08:00
int i;
for(i=0;i<listlength(symlist);i++) {
Symbol* sym = listget(symlist,i);
freeSymbol(sym);
2010-06-03 21:24:43 +08:00
}
}
void
cleanup()
{
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.
2020-06-29 08:02:47 +08:00
reclaimSymbols();
listfree(symlist);
listfree(grpdefs);
listfree(dimdefs);
listfree(attdefs);
listfree(gattdefs);
listfree(xattdefs);
listfree(typdefs);
listfree(vardefs);
filldatalist->readonly = 0;
freedatalist(filldatalist);
2010-06-03 21:24:43 +08:00
}
/* compute the total n-dimensional size as 1 long array;
if stop == 0, then stop = dimset->ndims.
*/
2010-06-03 21:24:43 +08:00
size_t
crossproduct(Dimset* dimset, int start, int stop)
2010-06-03 21:24:43 +08:00
{
size_t totalsize = 1;
int i;
for(i=start;i<stop;i++) {
totalsize = totalsize * dimset->dimsyms[i]->dim.declsize;
2010-06-03 21:24:43 +08:00
}
2014-08-12 03:21:01 +08:00
return totalsize;
2010-06-03 21:24:43 +08:00
}
/* Do the "complement" of crossproduct;
2010-06-03 21:24:43 +08:00
compute the total n-dimensional size of an array
starting at 0 thru the 'last' array index.
stop if we encounter an unlimited dimension
*/
size_t
prefixarraylength(Dimset* dimset, int last)
{
return crossproduct(dimset,0,last+1);
2010-06-03 21:24:43 +08:00
}
#ifdef USE_HDF5
2010-06-03 21:24:43 +08:00
extern int H5Eprint1(FILE * stream);
2014-08-12 03:21:01 +08:00
#endif
2010-06-03 21:24:43 +08:00
void
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.
2020-06-29 08:02:47 +08:00
check_err(const int stat, const int line, const char* file, const char* func)
{
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.
2020-06-29 08:02:47 +08:00
check_err2(stat,-1,line,file,func);
}
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.
2020-06-29 08:02:47 +08:00
void check_err2(const int stat, const int cdlline, const int line, const char* file, const char* func)
{
2010-06-03 21:24:43 +08:00
if (stat != NC_NOERR) {
if(cdlline >= 0)
fprintf(stderr, "ncgen: cdl line %d; %s\n", cdlline, nc_strerror(stat));
else
fprintf(stderr, "ncgen: %s\n", nc_strerror(stat));
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.
2020-06-29 08:02:47 +08:00
fprintf(stderr, "\t(%s:%s:%d)\n", file,func,line);
#ifdef USE_HDF5
2010-06-03 21:24:43 +08:00
H5Eprint1(stderr);
2014-08-12 03:21:01 +08:00
#endif
2010-06-03 21:24:43 +08:00
fflush(stderr);
2017-11-01 04:03:57 +08:00
finalize_netcdf(1);
2010-06-03 21:24:43 +08:00
}
}
/**
Find the index of the first unlimited
dimension at or after 'start'.
If no unlimited exists, return |dimset|
*/
int
findunlimited(Dimset* dimset, int start)
{
for(;start<dimset->ndims;start++) {
if(dimset->dimsyms[start]->dim.isunlimited)
return start;
}
return dimset->ndims;
}
/**
Find the index of the last unlimited
dimension.
If no unlimited exists, return |dimset|
*/
int
findlastunlimited(Dimset* dimset)
{
int i;
for(i=dimset->ndims-1;i>=0;i--) {
if(dimset->dimsyms[i]->dim.isunlimited)
return i;
}
return dimset->ndims;
}
/**
Count the number of unlimited dimensions.
*/
int
countunlimited(Dimset* dimset)
{
int i, count;
for(count=0,i=dimset->ndims-1;i>=0;i--) {
if(dimset->dimsyms[i]->dim.isunlimited)
count++;
}
return count;
}
/* Return standard format string */
const char *
kind_string(int kind)
{
switch (kind) {
case 1: return "classic";
case 2: return "64-bit offset";
case 3: return "netCDF-4";
case 4: return "netCDF-4 classic model";
default:
derror("Unknown format index: %d\n",kind);
}
return NULL;
}
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.
2020-06-29 08:02:47 +08:00