netcdf-c/plugins/H5Zmisc.c
Dennis Heimbigner df3636b959 Mitigate S3 test interference + Unlimited Dimensions in NCZarr
This PR started as an attempt to add unlimited dimensions to NCZarr.
It did that, but this exposed significant problems with test interference.
So this PR is mostly about fixing -- well mitigating anyway -- test
interference.

The problem of test interference is now documented in the document docs/internal.md.
The solutions implemented here are also describe in that document.
The solution is somewhat fragile but multiple cleanup mechanisms
are provided. Note that this feature requires that the
AWS command line utility must be installed.

## Unlimited Dimensions.
The existing NCZarr extensions to Zarr are modified to support unlimited dimensions.
NCzarr extends the Zarr meta-data for the ".zgroup" object to include netcdf-4 model extensions. This information is stored in ".zgroup" as dictionary named "_nczarr_group".
Inside "_nczarr_group", there is a key named "dims" that stores information about netcdf-4 named dimensions. The value of "dims" is a dictionary whose keys are the named dimensions. The value associated with each dimension name has one of two forms
Form 1 is a special case of form 2, and is kept for backward compatibility. Whenever a new file is written, it uses format 1 if possible, otherwise format 2.
* Form 1: An integer representing the size of the dimension, which is used for simple named dimensions.
* Form 2: A dictionary with the following keys and values"
   - "size" with an integer value representing the (current) size of the dimension.
   - "unlimited" with a value of either "1" or "0" to indicate if this dimension is an unlimited dimension.

For Unlimited dimensions, the size is initially zero, and as variables extend the length of that dimension, the size value for the dimension increases.
That dimension size is shared by all arrays referencing that dimension, so if one array extends an unlimited dimension, it is implicitly extended for all other arrays that reference that dimension.
This is the standard semantics for unlimited dimensions.

Adding unlimited dimensions required a number of other changes to the NCZarr code-base. These included the following.
* Did a partial refactor of the slice handling code in zwalk.c to clean it up.
* Added a number of tests for unlimited dimensions derived from the same test in nc_test4.
* Added several NCZarr specific unlimited tests; more are needed.
* Add test of endianness.

## Misc. Other Changes
* Modify libdispatch/ncs3sdk_aws.cpp to optionally support use of the
   AWS Transfer Utility mechanism. This is controlled by the
   ```#define TRANSFER```` command in that file. It defaults to being disabled.
* Parameterize both the standard Unidata S3 bucket (S3TESTBUCKET) and the netcdf-c test data prefix (S3TESTSUBTREE).
* Fixed an obscure memory leak in ncdump.
* Removed some obsolete unit testing code and test cases.
* Uncovered a bug in the netcdf-c handling of big-endian floats and doubles. Have not fixed yet. See tst_h5_endians.c.
* Renamed some nczarr_tests testcases to avoid name conflicts with nc_test4.
* Modify the semantics of zmap\#ncsmap_write to only allow total rewrite of objects.
* Modify the semantics of zodom to properly handle stride > 1.
* Add a truncate operation to the libnczarr zmap code.
2023-09-26 16:56:48 -06:00

292 lines
8.3 KiB
C

#include "config.h"
#include <stdlib.h>
#include <string.h>
#include <assert.h>
#include <stdio.h>
#include <sys/types.h>
#include "h5misc.h"
#include "netcdf_aux.h"
/* WARNING:
Starting with HDF5 version 1.10.x, the plugin code MUST be
careful when using the standard *malloc()*, *realloc()*, and
*free()* function.
In the event that the code is allocating, reallocating, for
free'ing memory that either came from or will be exported to the
calling HDF5 library, then one MUST use the corresponding HDF5
functions *H5allocate_memory()*, *H5resize_memory()*,
*H5free_memory()* [5] to avoid memory failures.
Additionally, if your filter code leaks memory, then the HDF5 library
will generate an error.
*/
#undef DEBUG
/* The C standard apparently defines all floating point constants as double;
we rely on that in this code.
*/
#define DBLVAL 12345678.12345678
static htri_t H5Z_test_can_apply(hid_t dcpl_id, hid_t type_id, hid_t space_id);
static size_t H5Z_filter_test(unsigned int flags, size_t cd_nelmts,
const unsigned int cd_values[], size_t nbytes,
size_t *buf_size, void **buf);
static int paramcheck(size_t nparams, const unsigned int* params, struct All* extracted);
static void mismatch(const char* which);
const H5Z_class2_t H5Z_TEST[1] = {{
H5Z_CLASS_T_VERS, /* H5Z_class_t version */
(H5Z_filter_t)(H5Z_FILTER_TEST), /* Filter id number */
1, /* encoder_present flag (set to true) */
1, /* decoder_present flag (set to true) */
"test", /* Filter name for debugging */
(H5Z_can_apply_func_t)H5Z_test_can_apply, /* The "can apply" callback */
NULL, /* The "set local" callback */
(H5Z_func_t)H5Z_filter_test, /* The actual filter function */
}};
/* External Discovery Functions */
DLLEXPORT
H5PL_type_t
H5PLget_plugin_type(void)
{
return H5PL_TYPE_FILTER;
}
DLLEXPORT
const void*
H5PLget_plugin_info(void)
{
return H5Z_TEST;
}
/* Make this explicit */
/*
* The "can_apply" callback returns positive a valid combination, zero for an
* invalid combination and negative for an error.
*/
static htri_t
H5Z_test_can_apply(hid_t dcpl_id, hid_t type_id, hid_t space_id)
{
return 1; /* Assume it can always apply */
}
/*
This filter does some verification
that the parameters passed to the filter
are correct. Specifically, that endian-ness
is correct. As a filter, it is the identify
function, passing input to output unchanged.
It also prints out the size of each chunk.
Test cases format:
1.The first param is the test index i.e. which test to execute.
2. The remaining parameters are those for the test chosen in #1
*/
static size_t
H5Z_filter_test(unsigned int flags, size_t cd_nelmts,
const unsigned int cd_values[], size_t nbytes,
size_t *buf_size, void **buf)
{
void* newbuf;
unsigned int testcase = 0;
size_t size = 1024 * sizeof(float) * 2;
struct All values;
if(cd_nelmts == 0)
goto fail;
testcase = cd_values[0];
switch (testcase) {
case TC_PARAMS:
if(!paramcheck(cd_nelmts,cd_values,&values))
goto fail;
break;
case TC_ODDSIZE:
/* Print out the chunk size */
fprintf(stderr,"nbytes = %lld chunk size = %lld\n",(long long)nbytes,(long long)*buf_size);
fflush(stderr);
break;
default: break;
}
if (flags & H5Z_FLAG_REVERSE) { /* Decompress */
if(testcase == TC_EXPANDED) {
int i;
float* b = (float*)*buf;
fprintf(stderr,"TC_EXPANDED: decompress: nbytes=%u buf_size=%u xdata[0..8]=|",(unsigned)nbytes,(unsigned)*buf_size);
for(i=0;i<8;i++) {
fprintf(stderr," %u",(int)(b[1024+i]));
}
fprintf(stderr,"|\n");
/* Replace buffer */
newbuf = H5allocate_memory(*buf_size,0);
if(newbuf == NULL) abort();
memcpy(newbuf,*buf,*buf_size);
} else {
/* Replace buffer */
newbuf = H5allocate_memory(*buf_size,0);
if(newbuf == NULL) abort();
memcpy(newbuf,*buf,*buf_size);
}
/* reclaim old buffer */
H5free_memory(*buf);
*buf = newbuf;
} else { /* (flags & H5Z_FLAG_REVERSE) Compress */
if(testcase == TC_EXPANDED) {
int i;
float* b;
#if 0
fprintf(stderr,"TC_EXPANDED: compress: nbytes=%u buf_size=%u size=%u\n",(unsigned)nbytes,(unsigned)*buf_size,(unsigned)size);
#endif
/* Replace buffer with one that is bigger than the input size */
newbuf = H5allocate_memory(size,0);
if(newbuf == NULL) abort();
b = (float*)newbuf;
for(i=0;i<1024*2;i++) {
b[i] = (float)(17+i);
}
memcpy(newbuf,*buf,*buf_size);
*buf_size = size;
} else {
/* Replace buffer */
newbuf = H5allocate_memory(*buf_size,0);
if(newbuf == NULL) abort();
memcpy(newbuf,*buf,*buf_size);
}
/* reclaim old buffer */
H5free_memory(*buf);
*buf = newbuf;
}
return *buf_size;
fail:
return 0;
}
static void
extract1(void* field, size_t size, const unsigned int* params)
{
union {
unsigned long long ll;
unsigned char char8[8];
unsigned param[2];
} u;
unsigned char b = 0;
unsigned short s = 0;
unsigned int i = 0;
unsigned char* bp = 0;
unsigned short* sp = NULL;
unsigned int* ip = NULL;
unsigned long long* llp = NULL;
memset(&u,0,sizeof(u));
switch (size) {
case 1:
b = (unsigned char)(params[0]);
bp = (unsigned char*)field;
*bp = b;
break;
case 2:
s = (unsigned short)(params[0]);
sp = (unsigned short*)field;
*sp = s;
break;
case 4:
i = (unsigned)(params[0]);
ip = (unsigned*)field;
*ip = i;
break;
case 8:
u.param[0] = params[0];
u.param[1] = params[1];
ncaux_h5filterspec_fix8(u.char8,0);
llp = (unsigned long long*)field;
*llp = u.ll;
break;
default: fprintf(stderr,"insert: unexpected size: %u\n",(unsigned)size); abort();
}
}
static void
extractparams(size_t nparams, const unsigned int* params, struct All* all)
{
size_t offset = 0;
extract1(&all->tbyte,sizeof(all->tbyte),&params[offset]); offset += 1;
extract1(&all->tubyte,sizeof(all->tubyte),&params[offset]); offset += 1;
extract1(&all->tshort,sizeof(all->tshort),&params[offset]); offset += 1;
extract1(&all->tushort,sizeof(all->tushort),&params[offset]); offset += 1;
extract1(&all->tint,sizeof(all->tint),&params[offset]); offset += 1;
extract1(&all->tuint,sizeof(all->tuint),&params[offset]); offset += 1;
extract1(&all->tfloat32,sizeof(all->tfloat32),&params[offset]); offset += 1;
extract1(&all->tint64,sizeof(all->tint64),&params[offset]); offset += 2*1;
extract1(&all->tuint64,sizeof(all->tuint64),&params[offset]); offset += 2*1;
extract1(&all->tfloat64,sizeof(all->tfloat64),&params[offset]); offset += 2*1;
}
/* Verify values of the parameters */
static int
paramcheck(size_t nparams, const unsigned int* params, struct All* extracted)
{
struct All all;
memset(&all,0,sizeof(all));
if(nparams != NPARAMS) {
fprintf(stderr,"Incorrect number of parameters: expected=%ld sent=%ld\n",(unsigned long)NPARAMS,(unsigned long)nparams);
goto fail;
}
/* Convert numeric params to instance of struct All */
extractparams(nparams-1, &params[1], &all);
if(extracted) *extracted = all;
/* verify */
if(all.tbyte != spec.tbyte) mismatch("tbyte");
if(all.tubyte != spec.tubyte) mismatch("tubyte");
if(all.tshort != spec.tshort) mismatch("tshort");
if(all.tushort != spec.tushort) mismatch("tushort");
if(all.tint != spec.tint) mismatch("tint");
if(all.tuint != spec.tuint) mismatch("tuint");
if(all.tfloat32 != spec.tfloat32) mismatch("tfloat32");
if(all.tint64 != spec.tint64) mismatch("tint64");
if(all.tuint64 != spec.tuint64) mismatch("tuint64");
if(all.tfloat64 != spec.tfloat64) mismatch("tfloat64");
#ifdef DEBUG
{
size_t i;
fprintf(stderr,"bigendian=%d nparams=%d params=\n",bigendian,nparams);
for(i=0;i<nparams;i++) {
fprintf(stderr,"[%d] %ud %d %f\n", (unsigned int)i, params[i],(signed int)params[i],*(float*)&params[i]);
}
fflush(stderr);
}
#endif
return 1;
fail:
return 0;
}
static void
mismatch(const char* which)
{
fprintf(stderr,"mismatch: %s\n",which);
fflush(stderr);
}