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-rw-r--r--hl/src/H5DO.c81
-rw-r--r--hl/src/H5DOpublic.h6
-rw-r--r--hl/test/test_dset_opt.c461
-rw-r--r--src/H5D.c40
-rw-r--r--src/H5Dchunk.c282
-rw-r--r--src/H5Dio.c149
-rw-r--r--src/H5Dpkg.h3
-rw-r--r--src/H5Dpublic.h6
-rw-r--r--src/H5Pdxpl.c28
9 files changed, 898 insertions, 158 deletions
diff --git a/hl/src/H5DO.c b/hl/src/H5DO.c
index 8db6768..22d40fc 100644
--- a/hl/src/H5DO.c
+++ b/hl/src/H5DO.c
@@ -32,7 +32,7 @@
* Return: Non-negative on success/Negative on failure
*
* Programmer: Raymond Lu
- * 30 July 2012
+ * 30 July 2012
*
*-------------------------------------------------------------------------
*/
@@ -60,7 +60,7 @@ H5DOwrite_chunk(hid_t dset_id, hid_t dxpl_id, uint32_t filters, const hsize_t *o
/* If the user passed in a default DXPL, create one to pass to H5Dwrite() */
if(H5P_DEFAULT == dxpl_id) {
- if((dxpl_id = H5Pcreate(H5P_DATASET_XFER)) < 0)
+ if((dxpl_id = H5Pcreate(H5P_DATASET_XFER)) < 0)
goto done;
created_dxpl = TRUE;
} /* end if */
@@ -87,16 +87,87 @@ done:
if(H5Pclose(dxpl_id) < 0)
ret_value = FAIL;
} /* end if */
- else
+ else {
/* Reset the direct write flag on user DXPL */
+ do_direct_write = FALSE;
if(H5Pset(dxpl_id, H5D_XFER_DIRECT_CHUNK_WRITE_FLAG_NAME, &do_direct_write) < 0)
ret_value = FAIL;
+ }
return(ret_value);
} /* end H5DOwrite_chunk() */
-/*
+/*-------------------------------------------------------------------------
+ * Function: H5DOread_chunk
+ *
+ * Purpose: Reads an entire chunk from the file directly.
+ *
+ * Return: Non-negative on success/Negative on failure
+ *
+ * Programmer: Matthew Strong (GE Healthcare)
+ * 14 February 2016
+ *
+ *---------------------------------------------------------------------------
+ */
+herr_t
+H5DOread_chunk(hid_t dset_id, hid_t dxpl_id, const hsize_t *offset, uint32_t *filters,
+ void *buf)
+{
+ hbool_t created_dxpl = FALSE; /* Whether we created a DXPL */
+ hbool_t do_direct_read = TRUE; /* Flag for direct writes */
+ herr_t ret_value = FAIL; /* Return value */
+
+ /* Check arguments */
+ if(dset_id < 0)
+ goto done;
+ if(!buf)
+ goto done;
+ if(!offset)
+ goto done;
+ if(!filters)
+ goto done;
+
+ /* If the user passed in a default DXPL, create one to pass to H5Dwrite() */
+ if(H5P_DEFAULT == dxpl_id) {
+ if((dxpl_id = H5Pcreate(H5P_DATASET_XFER)) < 0)
+ goto done;
+ created_dxpl = TRUE;
+ } /* end if */
+
+ /* Set direct write parameters */
+ if(H5Pset(dxpl_id, H5D_XFER_DIRECT_CHUNK_READ_FLAG_NAME, &do_direct_read) < 0)
+ goto done;
+ if(H5Pset(dxpl_id, H5D_XFER_DIRECT_CHUNK_READ_OFFSET_NAME, &offset) < 0)
+ goto done;
+
+ /* Read chunk */
+ if(H5Dread(dset_id, 0, H5S_ALL, H5S_ALL, dxpl_id, buf) < 0)
+ goto done;
+ /* Get the filter mask */
+ if(H5Pget(dxpl_id, H5D_XFER_DIRECT_CHUNK_READ_FILTERS_NAME, filters) < 0)
+ goto done;
+
+ /* Indicate success */
+ ret_value = SUCCEED;
+
+done:
+ if(created_dxpl) {
+ if(H5Pclose(dxpl_id) < 0)
+ ret_value = FAIL;
+ } /* end if */
+ else {
+ /* Reset the direct read flag on user DXPL */
+ do_direct_read = FALSE;
+ if(H5Pset(dxpl_id, H5D_XFER_DIRECT_CHUNK_READ_FLAG_NAME, &do_direct_read) < 0)
+ ret_value = FAIL;
+ }
+
+ return(ret_value);
+} /* end H5DOread_chunk() */
+
+
+/*-------------------------------------------------------------------------
* Function: H5DOappend()
*
* Purpose: To append elements to a dataset.
@@ -122,6 +193,8 @@ done:
* ret_value = FAIL;
* goto done;
* }
+ *
+ *-------------------------------------------------------------------------
*/
herr_t
H5DOappend(hid_t dset_id, hid_t dxpl_id, unsigned axis, size_t extension,
diff --git a/hl/src/H5DOpublic.h b/hl/src/H5DOpublic.h
index ce0d32e..d5c8de4 100644
--- a/hl/src/H5DOpublic.h
+++ b/hl/src/H5DOpublic.h
@@ -28,6 +28,12 @@ extern "C" {
H5_HLDLL herr_t H5DOwrite_chunk(hid_t dset_id, hid_t dxpl_id, uint32_t filters,
const hsize_t *offset, size_t data_size, const void *buf);
+H5_HLDLL herr_t H5DOread_chunk(hid_t dset_id, /*in*/
+ hid_t dxpl_id, /*in*/
+ const hsize_t *offset, /*in*/
+ uint32_t *filters, /*out*/
+ void *buf); /*out*/
+
H5_HLDLL herr_t H5DOappend(hid_t dset_id, hid_t dxpl_id, unsigned axis,
size_t extension, hid_t memtype, const void *buf);
diff --git a/hl/test/test_dset_opt.c b/hl/test/test_dset_opt.c
index 03c467a..d3a6b5c 100644
--- a/hl/test/test_dset_opt.c
+++ b/hl/test/test_dset_opt.c
@@ -76,11 +76,10 @@ const H5Z_class2_t H5Z_BOGUS2[1] = {{
/*-------------------------------------------------------------------------
* Function: test_direct_chunk_write
*
- * Purpose: Test the basic functionality of H5DOwrite_chunk
+ * Purpose: Test the basic functionality of H5DOwrite_chunk/H5DOread_chunk
*
* Return: Success: 0
- *
- * Failure: 1
+ * Failure: 1
*
* Programmer: Raymond Lu
* 30 November 2012
@@ -103,24 +102,31 @@ test_direct_chunk_write (hid_t file)
int i, j, n;
unsigned filter_mask = 0;
+ unsigned read_filter_mask = 0;
int direct_buf[CHUNK_NX][CHUNK_NY];
int check_chunk[CHUNK_NX][CHUNK_NY];
hsize_t offset[2] = {0, 0};
size_t buf_size = CHUNK_NX*CHUNK_NY*sizeof(int);
const Bytef *z_src = (const Bytef*)(direct_buf);
- Bytef *z_dst; /*destination buffer */
+ Bytef *z_dst; /*destination buffer */
uLongf z_dst_nbytes = (uLongf)DEFLATE_SIZE_ADJUST(buf_size);
uLong z_src_nbytes = (uLong)buf_size;
- int aggression = 9; /* Compression aggression setting */
- void *outbuf = NULL; /* Pointer to new buffer */
+ int aggression = 9; /* Compression aggression setting */
+ void *outbuf = NULL; /* Pointer to new buffer */
+
+ /* For H5DOread_chunk() */
+ void *readbuf = NULL; /* Buffer for reading data */
+ const Bytef *pt_readbuf; /* Point to the buffer for data read */
+ hsize_t read_chunk_nbytes; /* Size of chunk on disk */
+ int read_dst_buf[CHUNK_NX][CHUNK_NY]; /* Buffer to hold un-compressed data */
hsize_t start[2]; /* Start of hyperslab */
hsize_t stride[2]; /* Stride of hyperslab */
hsize_t count[2]; /* Block count */
hsize_t block[2]; /* Block sizes */
- TESTING("basic functionality of H5DOwrite_chunk");
+ TESTING("basic functionality of H5DOwrite_chunk/H5DOread_chunk");
/*
* Create the data space with unlimited dimensions.
@@ -151,26 +157,76 @@ test_direct_chunk_write (hid_t file)
cparms, H5P_DEFAULT)) < 0)
goto error;
- /* Initialize the dataset */
- for(i = n = 0; i < NX; i++)
- for(j = 0; j < NY; j++)
- data[i][j] = n++;
-
if((dxpl = H5Pcreate(H5P_DATASET_XFER)) < 0)
goto error;
+ HDmemset(data, 0, sizeof(data));
+ /* Initialize data for the first chunk */
+ for(i = n = 0; i < CHUNK_NX; i++)
+ for(j = 0; j < CHUNK_NY; j++)
+ data[i][j] = n++;
+
/*
- * Write the data for the dataset. It should stay in the chunk cache.
- * It will be evicted from the cache by the H5DOwrite_chunk calls.
- */
+ * Write the data for the dataset. */
if((status = H5Dwrite(dataset, H5T_NATIVE_INT, H5S_ALL, H5S_ALL,
dxpl, data)) < 0)
goto error;
+ if(H5Fflush(dataset, H5F_SCOPE_LOCAL) < 0)
+ goto error;
+
+ if(H5Dclose(dataset) < 0)
+ goto error;
+
+ if((dataset = H5Dopen2(file, DATASETNAME1, H5P_DEFAULT)) < 0)
+ goto error;
+
+ offset[0] = offset[1] = 0;
+
+ /* Get the size of the compressed chunk */
+ ret = H5Dget_chunk_storage_size(dataset, offset, &read_chunk_nbytes);
+
+ readbuf = HDmalloc(read_chunk_nbytes);
+ pt_readbuf = (const Bytef *)readbuf;
+
+ /* Test to use H5DOread_chunk() to read the chunk back */
+ if((status = H5DOread_chunk(dataset, H5P_DEFAULT, offset, &read_filter_mask, readbuf)) < 0)
+ goto error;
+
+ /* uncompress(Bytef *dest, uLongf *destLen, const Bytef *source, uLong sourceLen) */
+ ret = uncompress((Bytef *)read_dst_buf, (uLongf *)&buf_size, pt_readbuf, (uLong)read_chunk_nbytes);
+
+ /* Check for various zlib errors */
+ if(Z_BUF_ERROR == ret) {
+ HDfprintf(stderr, "error: not enough room in output buffer");
+ goto error;
+ } else if(Z_MEM_ERROR == ret) {
+ HDfprintf(stderr, "error: not enough memory");
+ goto error;
+ } else if(Z_OK != ret) {
+ HDfprintf(stderr, "error: corrupted input data");
+ goto error;
+ }
+
+ /* Check that the values read are the same as the values written */
+ for(i = 0; i < CHUNK_NX; i++) {
+ for(j = 0; j < CHUNK_NY; j++) {
+ if(data[i][j] != read_dst_buf[i][j]) {
+ printf(" 1. Read different values than written.");
+ printf(" At index %d,%d\n", i, j);
+ printf(" data=%d, read_dst_buf=%d\n", data[i][j], read_dst_buf[i][j]);
+ goto error;
+ }
+ }
+ }
+
+ if(readbuf)
+ HDfree(readbuf);
+
/* Initialize data for one chunk */
for(i = n = 0; i < CHUNK_NX; i++)
for(j = 0; j < CHUNK_NY; j++)
- direct_buf[i][j] = n++;
+ direct_buf[i][j] = n++;
/* Allocate output (compressed) buffer */
outbuf = HDmalloc(z_dst_nbytes);
@@ -181,18 +237,18 @@ test_direct_chunk_write (hid_t file)
/* Check for various zlib errors */
if(Z_BUF_ERROR == ret) {
- fprintf(stderr, "overflow");
+ HDfprintf(stderr, "overflow");
goto error;
} else if(Z_MEM_ERROR == ret) {
- fprintf(stderr, "deflate memory error");
+ HDfprintf(stderr, "deflate memory error");
goto error;
} else if(Z_OK != ret) {
- fprintf(stderr, "other deflate error");
+ HDfprintf(stderr, "other deflate error");
goto error;
}
- /* Write the compressed chunk data repeatedly to cover all the chunks in the
- * dataset, using the direct writing function. */
+ /* Write the compressed chunk data repeatedly to cover all the chunks in the
+ * dataset, using the direct writing function. */
for(i=0; i<NX/CHUNK_NX; i++) {
for(j=0; j<NY/CHUNK_NY; j++) {
status = H5DOwrite_chunk(dataset, dxpl, filter_mask, offset, z_dst_nbytes, outbuf);
@@ -205,7 +261,7 @@ test_direct_chunk_write (hid_t file)
if(outbuf)
HDfree(outbuf);
- if(H5Fflush(dataset, H5F_SCOPE_LOCAL) < 0)
+ if(H5Fflush(dataset, H5F_SCOPE_LOCAL) < 0)
goto error;
if(H5Dclose(dataset) < 0)
@@ -214,6 +270,59 @@ test_direct_chunk_write (hid_t file)
if((dataset = H5Dopen2(file, DATASETNAME1, H5P_DEFAULT)) < 0)
goto error;
+ offset[0] = CHUNK_NX;
+ offset[1] = CHUNK_NY;
+
+ /* Get the size of the compressed chunk */
+ ret = H5Dget_chunk_storage_size(dataset, offset, &read_chunk_nbytes);
+
+ if(read_chunk_nbytes != (hsize_t)z_dst_nbytes) {
+ HDfprintf(stderr, "Read/write chunk size not the same.");
+ goto error;
+ }
+
+ readbuf = HDmalloc(read_chunk_nbytes);
+ pt_readbuf = (const Bytef *)readbuf;
+
+ /* Test to use H5DOread_chunk() to read the chunk back */
+ if((status = H5DOread_chunk(dataset, H5P_DEFAULT, offset, &read_filter_mask, readbuf)) < 0)
+ goto error;
+
+ if(read_filter_mask != filter_mask) {
+ HDfprintf(stderr, " Read/write filter mask not the same.");
+ goto error;
+ }
+
+ /* uncompress(Bytef *dest, uLongf *destLen, const Bytef *source, uLong sourceLen) */
+ ret = uncompress((Bytef *)read_dst_buf, (uLongf *)&buf_size, pt_readbuf, (uLong)read_chunk_nbytes);
+
+ /* Check for various zlib errors */
+ if(Z_BUF_ERROR == ret) {
+ HDfprintf(stderr, "error: not enough room in output buffer");
+ goto error;
+ } else if(Z_MEM_ERROR == ret) {
+ HDfprintf(stderr, "error: not enough memory");
+ goto error;
+ } else if(Z_OK != ret) {
+ HDfprintf(stderr, "error: corrupted input data");
+ goto error;
+ }
+
+ /* Check that the values read are the same as the values written */
+ for(i = 0; i < CHUNK_NX; i++) {
+ for(j = 0; j < CHUNK_NY; j++) {
+ if(direct_buf[i][j] != read_dst_buf[i][j]) {
+ printf(" 1. Read different values than written.");
+ printf(" At index %d,%d\n", i, j);
+ printf(" direct_buf=%d, read_dst_buf=%d\n", direct_buf[i][j], read_dst_buf[i][j]);
+ goto error;
+ }
+ }
+ }
+
+ if(readbuf)
+ HDfree(readbuf);
+
/*
* Select hyperslab for one chunk in the file
*/
@@ -224,7 +333,7 @@ test_direct_chunk_write (hid_t file)
if((status = H5Sselect_hyperslab(dataspace, H5S_SELECT_SET, start, stride, count, block)) < 0)
goto error;
- /* Read the chunk back */
+ /* Test to use H5Dread() to read the chunk back */
if((status = H5Dread(dataset, H5T_NATIVE_INT, mem_space, dataspace, H5P_DEFAULT, check_chunk)) < 0)
goto error;
@@ -234,38 +343,40 @@ test_direct_chunk_write (hid_t file)
if(direct_buf[i][j] != check_chunk[i][j]) {
printf(" 1. Read different values than written.");
printf(" At index %d,%d\n", i, j);
- printf(" direct_buf=%d, check_chunk=%d\n", direct_buf[i][j], check_chunk[i][j]);
+ printf(" direct_buf=%d, check_chunk=%d\n", direct_buf[i][j], check_chunk[i][j]);
goto error;
}
}
}
+
/* Reinitialize different data for one chunk */
for(i = 0; i < CHUNK_NX; i++)
for(j = 0; j < CHUNK_NY; j++)
- direct_buf[i][j] = i + j;
+ direct_buf[i][j] = i + j;
/* Allocate output (compressed) buffer */
outbuf = HDmalloc(z_dst_nbytes);
z_dst = (Bytef *)outbuf;
+
/* Perform compression from the source to the destination buffer */
ret = compress2(z_dst, &z_dst_nbytes, z_src, z_src_nbytes, aggression);
/* Check for various zlib errors */
if(Z_BUF_ERROR == ret) {
- fprintf(stderr, "overflow");
+ HDfprintf(stderr, "overflow");
goto error;
} else if(Z_MEM_ERROR == ret) {
- fprintf(stderr, "deflate memory error");
+ HDfprintf(stderr, "deflate memory error");
goto error;
} else if(Z_OK != ret) {
- fprintf(stderr, "other deflate error");
+ HDfprintf(stderr, "other deflate error");
goto error;
}
- /* Rewrite the compressed chunk data repeatedly to cover all the chunks in the
- * dataset, using the direct writing function. */
+ /* Rewrite the compressed chunk data repeatedly to cover all the chunks in the
+ * dataset, using the direct writing function. */
offset[0] = offset[1] = 0;
for(i=0; i<NX/CHUNK_NX; i++) {
for(j=0; j<NY/CHUNK_NY; j++) {
@@ -279,7 +390,7 @@ test_direct_chunk_write (hid_t file)
if(outbuf)
HDfree(outbuf);
- if(H5Fflush(dataset, H5F_SCOPE_LOCAL) < 0)
+ if(H5Fflush(dataset, H5F_SCOPE_LOCAL) < 0)
goto error;
if(H5Dclose(dataset) < 0)
@@ -288,7 +399,60 @@ test_direct_chunk_write (hid_t file)
if((dataset = H5Dopen2(file, DATASETNAME1, H5P_DEFAULT)) < 0)
goto error;
- /* Read the chunk back */
+ offset[0] = CHUNK_NX;
+ offset[1] = CHUNK_NY;
+
+ /* Get the size of the compressed chunk */
+ ret = H5Dget_chunk_storage_size(dataset, offset, &read_chunk_nbytes);
+
+ if(read_chunk_nbytes != (hsize_t)z_dst_nbytes) {
+ HDfprintf(stderr, "Read/write chunk size not the same.");
+ goto error;
+ }
+
+ readbuf = HDmalloc(read_chunk_nbytes);
+ pt_readbuf = (const Bytef *)readbuf;
+
+ /* Test to use H5DOread_chunk() to read the chunk back */
+ if((status = H5DOread_chunk(dataset, H5P_DEFAULT, offset, &read_filter_mask, readbuf)) < 0)
+ goto error;
+
+ if(read_filter_mask != filter_mask) {
+ HDfprintf(stderr, " Read/write filter mask not the same.");
+ goto error;
+ }
+
+ /* uncompress(Bytef *dest, uLongf *destLen, const Bytef *source, uLong sourceLen) */
+ ret = uncompress((Bytef *)read_dst_buf, (uLongf *)&buf_size, pt_readbuf, (uLong)read_chunk_nbytes);
+
+ /* Check for various zlib errors */
+ if(Z_BUF_ERROR == ret) {
+ HDfprintf(stderr, "error: not enough room in output buffer");
+ goto error;
+ } else if(Z_MEM_ERROR == ret) {
+ HDfprintf(stderr, "error: not enough memory");
+ goto error;
+ } else if(Z_OK != ret) {
+ HDfprintf(stderr, "error: corrupted input data");
+ goto error;
+ }
+
+ /* Check that the values read are the same as the values written */
+ for(i = 0; i < CHUNK_NX; i++) {
+ for(j = 0; j < CHUNK_NY; j++) {
+ if(direct_buf[i][j] != read_dst_buf[i][j]) {
+ printf(" 1. Read different values than written.");
+ printf(" At index %d,%d\n", i, j);
+ printf(" direct_buf=%d, my_buf=%d\n", direct_buf[i][j], read_dst_buf[i][j]);
+ goto error;
+ }
+ }
+ }
+
+ if(readbuf)
+ HDfree(readbuf);
+
+ /* Test to use H5Dread() to read the chunk back */
if((status = H5Dread(dataset, H5T_NATIVE_INT, mem_space, dataspace, H5P_DEFAULT, check_chunk)) < 0)
goto error;
@@ -298,7 +462,7 @@ test_direct_chunk_write (hid_t file)
if(direct_buf[i][j] != check_chunk[i][j]) {
printf(" 2. Read different values than written.");
printf(" At index %d,%d\n", i, j);
- printf(" direct_buf=%d, check_chunk=%d\n", direct_buf[i][j], check_chunk[i][j]);
+ printf(" direct_buf=%d, check_chunk=%d\n", direct_buf[i][j], check_chunk[i][j]);
goto error;
}
}
@@ -312,7 +476,7 @@ test_direct_chunk_write (hid_t file)
H5Sclose(dataspace);
H5Pclose(cparms);
H5Pclose(dxpl);
-
+
PASSED();
return 0;
@@ -327,6 +491,8 @@ error:
if(outbuf)
HDfree(outbuf);
+ if(readbuf)
+ HDfree(readbuf);
return 1;
}
@@ -335,12 +501,11 @@ error:
/*-------------------------------------------------------------------------
* Function: test_skip_compress_write1
*
- * Purpose: Test skipping compression filter when it is the only filter
+ * Purpose: Test skipping compression filter when it is the only filter
* for the dataset
*
* Return: Success: 0
- *
- * Failure: 1
+ * Failure: 1
*
* Programmer: Raymond Lu
* 30 November 2012
@@ -360,6 +525,7 @@ test_skip_compress_write1(hid_t file)
int i, j, n;
unsigned filter_mask = 0;
+ unsigned read_filter_mask = 0;
int direct_buf[CHUNK_NX][CHUNK_NY];
int check_chunk[CHUNK_NX][CHUNK_NY];
hsize_t offset[2] = {0, 0};
@@ -371,7 +537,7 @@ test_skip_compress_write1(hid_t file)
hsize_t count[2]; /* Block count */
hsize_t block[2]; /* Block sizes */
- TESTING("skipping compression filter for H5DOwrite_chunk");
+ TESTING("skipping compression filter for H5DOwrite_chunk/H5DOread_chunk");
/*
* Create the data space with unlimited dimensions.
@@ -408,7 +574,7 @@ test_skip_compress_write1(hid_t file)
/* Initialize data for one chunk */
for(i = n = 0; i < CHUNK_NX; i++)
for(j = 0; j < CHUNK_NY; j++) {
- direct_buf[i][j] = n++;
+ direct_buf[i][j] = n++;
}
/* write the uncompressed chunk data repeatedly to dataset, using the direct writing function.
@@ -430,6 +596,30 @@ test_skip_compress_write1(hid_t file)
if((dataset = H5Dopen2(file, DATASETNAME2, H5P_DEFAULT)) < 0)
goto error;
+ /* Use H5DOread_chunk() to read the uncompressed data */
+ if((status = H5DOread_chunk(dataset, dxpl, offset, &read_filter_mask, check_chunk)) < 0)
+ goto error;
+
+ if(read_filter_mask != filter_mask) {
+ HDfprintf(stderr, " Read/write filter mask not the same.");
+ goto error;
+ }
+
+ /* Check that the values read are the same as the values written */
+ for(i = 0; i < CHUNK_NX; i++) {
+ for(j = 0; j < CHUNK_NY; j++) {
+ if(direct_buf[i][j] != check_chunk[i][j]) {
+ printf(" 1. Read different values than written.");
+ printf(" At index %d,%d\n", i, j);
+ printf(" direct_buf=%d, check_chunk=%d\n", direct_buf[i][j], check_chunk[i][j]);
+ goto error;
+ }
+ }
+ }
+
+ /* Clear the buffer */
+ HDmemset(check_chunk, 0, buf_size);
+
/*
* Select hyperslab for the chunk just written in the file
*/
@@ -440,7 +630,7 @@ test_skip_compress_write1(hid_t file)
if((status = H5Sselect_hyperslab(dataspace, H5S_SELECT_SET, start, stride, count, block)) < 0)
goto error;
- /* Read the chunk back */
+ /* Use H5Dread() to read the chunk back */
if((status = H5Dread(dataset, H5T_NATIVE_INT, mem_space, dataspace, H5P_DEFAULT, check_chunk)) < 0)
goto error;
@@ -483,9 +673,9 @@ error:
/*-------------------------------------------------------------------------
* Function: filter_bogus1
*
- * Purpose: A bogus filte that adds ADD_ON to the original value
+ * Purpose: A bogus filter that adds ADD_ON to the original value
*
- * Return: Success: Data chunk size
+ * Return: Success: Data chunk size
*
* Programmer: Raymond Lu
* 30 November 2012
@@ -558,12 +748,11 @@ filter_bogus2(unsigned int flags, size_t H5_ATTR_UNUSED cd_nelmts,
/*-------------------------------------------------------------------------
* Function: test_skip_compress_write2
*
- * Purpose: Test skipping compression filter when there are three filters
+ * Purpose: Test skipping compression filter when there are three filters
* for the dataset
*
- * Return: Success: 0
- *
- * Failure: 1
+ * Return: Success: 0
+ * Failure: 1
*
* Programmer: Raymond Lu
* 30 November 2012
@@ -583,6 +772,7 @@ test_skip_compress_write2(hid_t file)
int i, j, n;
unsigned filter_mask = 0;
+ unsigned read_filter_mask = 0;
int origin_direct_buf[CHUNK_NX][CHUNK_NY];
int direct_buf[CHUNK_NX][CHUNK_NY];
int check_chunk[CHUNK_NX][CHUNK_NY];
@@ -618,10 +808,10 @@ test_skip_compress_write2(hid_t file)
/* Register and enable first bogus filter */
if(H5Zregister (H5Z_BOGUS1) < 0)
- goto error;
+ goto error;
if(H5Pset_filter(cparms, H5Z_FILTER_BOGUS1, 0, (size_t)0, NULL) < 0)
- goto error;
+ goto error;
/* Enable compression filter */
if((status = H5Pset_deflate( cparms, (unsigned) aggression)) < 0)
@@ -629,10 +819,10 @@ test_skip_compress_write2(hid_t file)
/* Register and enable second bogus filter */
if(H5Zregister (H5Z_BOGUS2) < 0)
- goto error;
+ goto error;
if(H5Pset_filter(cparms, H5Z_FILTER_BOGUS2, 0, (size_t)0, NULL) < 0)
- goto error;
+ goto error;
/*
* Create a new dataset within the file using cparms
@@ -648,9 +838,9 @@ test_skip_compress_write2(hid_t file)
/* Initialize data for one chunk. Apply operations of two bogus filters to the chunk */
for(i = n = 0; i < CHUNK_NX; i++)
for(j = 0; j < CHUNK_NY; j++) {
- origin_direct_buf[i][j] = n++;
- direct_buf[i][j] = (origin_direct_buf[i][j] + ADD_ON) * FACTOR;
- }
+ origin_direct_buf[i][j] = n++;
+ direct_buf[i][j] = (origin_direct_buf[i][j] + ADD_ON) * FACTOR;
+ }
/* write the uncompressed chunk data repeatedly to dataset, using the direct writing function.
* Indicate skipping the compression filter but keep the other two bogus filters */
@@ -672,6 +862,35 @@ test_skip_compress_write2(hid_t file)
if((dataset = H5Dopen2(file, DATASETNAME3, H5P_DEFAULT)) < 0)
goto error;
+ /* Use H5DOread_chunk() to read the uncompressed data */
+ if((status = H5DOread_chunk(dataset, dxpl, offset, &read_filter_mask, check_chunk)) < 0)
+ goto error;
+
+ if(read_filter_mask != filter_mask) {
+ HDfprintf(stderr, " Read/write filter mask not the same.");
+ goto error;
+ }
+
+ /* De-compress the operations of the two bogus filters to the chunk */
+ for(i = n = 0; i < CHUNK_NX; i++)
+ for(j = 0; j < CHUNK_NY; j++)
+ check_chunk[i][j] = (check_chunk[i][j]/FACTOR) - ADD_ON;
+
+ /* Check that the values read are the same as the values written */
+ for(i = 0; i < CHUNK_NX; i++) {
+ for(j = 0; j < CHUNK_NY; j++) {
+ if(origin_direct_buf[i][j] != check_chunk[i][j]) {
+ printf(" 1. Read different values than written.");
+ printf(" At index %d,%d\n", i, j);
+ printf(" origin_direct_buf=%d, check_chunk=%d\n", origin_direct_buf[i][j], check_chunk[i][j]);
+ goto error;
+ }
+ }
+ }
+
+ /* Clear the buffer */
+ HDmemset(check_chunk, 0, buf_size);
+
/*
* Select hyperslab for one chunk in the file
*/
@@ -682,7 +901,7 @@ test_skip_compress_write2(hid_t file)
if((status = H5Sselect_hyperslab(dataspace, H5S_SELECT_SET, start, stride, count, block)) < 0)
goto error;
- /* Read the chunk back */
+ /* Use H5Dread() to read the chunk back */
if((status = H5Dread(dataset, H5T_NATIVE_INT, mem_space, dataspace, H5P_DEFAULT, check_chunk)) < 0)
goto error;
@@ -725,11 +944,10 @@ error:
/*-------------------------------------------------------------------------
* Function: test_data_conv
*
- * Purpose: Test data conversion
- *
- * Return: Success: 0
+ * Purpose: Test data conversion
*
- * Failure: 1
+ * Return: Success: 0
+ * Failure: 1
*
* Programmer: Raymond Lu
* 30 November 2012
@@ -740,10 +958,10 @@ static int
test_data_conv(hid_t file)
{
typedef struct {
- int a, b, c[4], d, e;
+ int a, b, c[4], d, e;
} src_type_t;
typedef struct {
- int a, c[4], e;
+ int a, c[4], e;
} dst_type_t;
hid_t dataspace = -1, dataset = -1;
@@ -761,6 +979,8 @@ test_data_conv(hid_t file)
unsigned filter_mask = 0;
src_type_t direct_buf[CHUNK_NX][CHUNK_NY];
dst_type_t check_chunk[CHUNK_NX][CHUNK_NY];
+ src_type_t read_chunk[CHUNK_NX][CHUNK_NY]; /* For H5DOread_chunk */
+
hsize_t offset[2] = {0, 0};
size_t buf_size = CHUNK_NX*CHUNK_NY*sizeof(src_type_t);
@@ -769,7 +989,7 @@ test_data_conv(hid_t file)
hsize_t count[2]; /* Block count */
hsize_t block[2]; /* Block sizes */
- TESTING("data conversion for H5DOwrite_chunk");
+ TESTING("data conversion for H5DOwrite_chunk/H5DOread_chunk");
/*
* Create the data space with unlimited dimensions.
@@ -854,6 +1074,36 @@ test_data_conv(hid_t file)
if((dataset = H5Dopen2(file, DATASETNAME4, H5P_DEFAULT)) < 0)
goto error;
+ /* Use H5DOread_chunk() to read the uncompressed data */
+ if((status = H5DOread_chunk(dataset, dxpl, offset, &filter_mask, read_chunk)) < 0)
+ goto error;
+
+ /* Check that the values read are the same as the values written */
+ for(i = 0; i < CHUNK_NX; i++) {
+ for(j = 0; j < CHUNK_NY; j++) {
+ if ((direct_buf[i][j]).a != (read_chunk[i][j]).a ||
+ (direct_buf[i][j]).b != (read_chunk[i][j]).b ||
+ (direct_buf[i][j]).c[0] != (read_chunk[i][j]).c[0] ||
+ (direct_buf[i][j]).c[1] != (read_chunk[i][j]).c[1] ||
+ (direct_buf[i][j]).c[2] != (read_chunk[i][j]).c[2] ||
+ (direct_buf[i][j]).c[3] != (read_chunk[i][j]).c[3] ||
+ (direct_buf[i][j]).d != (read_chunk[i][j]).d ||
+ (direct_buf[i][j]).e != (read_chunk[i][j]).e) {
+ printf(" 1. Read different values than written.");
+ printf(" At index %d,%d\n", i, j);
+ printf(" src={a=%d, b=%d, c=[%d,%d,%d,%d], d=%d, e=%d\n",
+ (direct_buf[i][j]).a, (direct_buf[i][j]).b, (direct_buf[i][j]).c[0], (direct_buf[i][j]).c[1],
+ (direct_buf[i][j]).c[2], (direct_buf[i][j]).c[3], (direct_buf[i][j]).d, (direct_buf[i][j]).e);
+ printf(" dst={a=%d, b=%d, c=[%d,%d,%d,%d], d=%d, e=%d\n",
+ (read_chunk[i][j]).a, (read_chunk[i][j]).b, (read_chunk[i][j]).c[0], (read_chunk[i][j]).c[1],
+ (read_chunk[i][j]).c[2], (read_chunk[i][j]).c[3], (read_chunk[i][j]).d, (read_chunk[i][j]).e);
+
+ goto error;
+ }
+ }
+ }
+
+
/*
* Select hyperslab for the chunk just written in the file
*/
@@ -879,14 +1129,14 @@ test_data_conv(hid_t file)
(direct_buf[i][j]).e != (check_chunk[i][j]).e) {
printf(" 1. Read different values than written.");
printf(" At index %d,%d\n", i, j);
- printf(" src={a=%d, b=%d, c=[%d,%d,%d,%d], d=%d, e=%d\n",
+ printf(" src={a=%d, b=%d, c=[%d,%d,%d,%d], d=%d, e=%d\n",
(direct_buf[i][j]).a, (direct_buf[i][j]).b, (direct_buf[i][j]).c[0], (direct_buf[i][j]).c[1],
(direct_buf[i][j]).c[2], (direct_buf[i][j]).c[3], (direct_buf[i][j]).d, (direct_buf[i][j]).e);
- printf(" dst={a=%d, c=[%d,%d,%d,%d], e=%d\n",
+ printf(" dst={a=%d, c=[%d,%d,%d,%d], e=%d\n",
(check_chunk[i][j]).a, (check_chunk[i][j]).c[0], (check_chunk[i][j]).c[1], (check_chunk[i][j]).c[2],
(check_chunk[i][j]).c[3], (check_chunk[i][j]).e);
- goto error;
+ goto error;
}
}
}
@@ -923,11 +1173,10 @@ error:
/*-------------------------------------------------------------------------
* Function: test_invalid_parameters
*
- * Purpose: Test invalid parameters for H5DOwrite_chunk
- *
- * Return: Success: 0
+ * Purpose: Test invalid parameters for H5DOwrite_chunk and H5DOread_chunk
*
- * Failure: 1
+ * Return: Success: 0
+ * Failure: 1
*
* Programmer: Raymond Lu
* 30 November 2012
@@ -951,7 +1200,9 @@ test_invalid_parameters(hid_t file)
size_t buf_size = CHUNK_NX*CHUNK_NY*sizeof(int);
int aggression = 9; /* Compression aggression setting */
- TESTING("invalid parameters for H5DOwrite_chunk");
+ hsize_t chunk_nbytes; /* Chunk size */
+
+ TESTING("invalid parameters for H5DOwrite_chunk/H5DOread_chunk");
/*
* Create the data space with unlimited dimensions.
@@ -969,7 +1220,7 @@ test_invalid_parameters(hid_t file)
goto error;
/*
- * Create a new contiguous dataset to verify H5DOwrite_chunk doesn't work
+ * Create a new contiguous dataset to verify H5DOwrite_chunk/H5DOread_chunk doesn't work
*/
if((dataset = H5Dcreate2(file, DATASETNAME5, H5T_NATIVE_INT, dataspace, H5P_DEFAULT,
cparms, H5P_DEFAULT)) < 0)
@@ -981,8 +1232,8 @@ test_invalid_parameters(hid_t file)
/* Initialize data for one chunk */
for(i = n = 0; i < CHUNK_NX; i++)
for(j = 0; j < CHUNK_NY; j++) {
- direct_buf[i][j] = n++;
- }
+ direct_buf[i][j] = n++;
+ }
/* Try to write the chunk data to contiguous dataset. It should fail */
offset[0] = CHUNK_NX;
@@ -993,6 +1244,18 @@ test_invalid_parameters(hid_t file)
goto error;
} H5E_END_TRY;
+ /* Try to get chunk size for a contiguous dataset. It should fail */
+ H5E_BEGIN_TRY {
+ if((status = H5Dget_chunk_storage_size(dataset, offset, &chunk_nbytes)) != FAIL)
+ goto error;
+ } H5E_END_TRY;
+
+ /* Try to H5DOread_chunk from the contiguous dataset. It should fail */
+ H5E_BEGIN_TRY {
+ if((status = H5DOread_chunk(dataset, dxpl, offset, &filter_mask, direct_buf)) != FAIL)
+ goto error;
+ } H5E_END_TRY;
+
if(H5Dclose(dataset) < 0)
goto error;
@@ -1011,25 +1274,40 @@ test_invalid_parameters(hid_t file)
cparms, H5P_DEFAULT)) < 0)
goto error;
- /* Check invalid dataset ID */
+ /* Check invalid dataset ID for H5DOwrite_chunk and H5DOread_chunk */
H5E_BEGIN_TRY {
if((status = H5DOwrite_chunk((hid_t)-1, dxpl, filter_mask, offset, buf_size, direct_buf)) != FAIL)
goto error;
} H5E_END_TRY;
- /* Check invalid DXPL ID */
+ H5E_BEGIN_TRY {
+ if((status = H5DOread_chunk((hid_t)-1, dxpl, offset, &filter_mask, direct_buf)) != FAIL)
+ goto error;
+ } H5E_END_TRY;
+
+ /* Check invalid DXPL ID for H5DOwrite_chunk and H5DOread_chunk */
H5E_BEGIN_TRY {
if((status = H5DOwrite_chunk(dataset, (hid_t)-1, filter_mask, offset, buf_size, direct_buf)) != FAIL)
goto error;
} H5E_END_TRY;
- /* Check invalid OFFSET */
+ H5E_BEGIN_TRY {
+ if((status = H5DOread_chunk(dataset, (hid_t)-1, offset, &filter_mask, direct_buf)) != FAIL)
+ goto error;
+ } H5E_END_TRY;
+
+ /* Check invalid OFFSET for H5DOwrite_chunk and H5DOread_chunk */
H5E_BEGIN_TRY {
if((status = H5DOwrite_chunk(dataset, dxpl, filter_mask, NULL, buf_size, direct_buf)) != FAIL)
goto error;
} H5E_END_TRY;
- /* Check when OFFSET is out of dataset range */
+ H5E_BEGIN_TRY {
+ if((status = H5DOread_chunk(dataset, dxpl, NULL, &filter_mask, direct_buf)) != FAIL)
+ goto error;
+ } H5E_END_TRY;
+
+ /* Check when OFFSET is out of dataset range for H5DOwrite_chunk and H5DOread_chunk */
offset[0] = NX + 1;
offset[1] = NY;
H5E_BEGIN_TRY {
@@ -1037,7 +1315,12 @@ test_invalid_parameters(hid_t file)
goto error;
} H5E_END_TRY;
- /* Check when OFFSET is not on chunk boundary */
+ H5E_BEGIN_TRY {
+ if((status = H5DOread_chunk(dataset, dxpl, offset, &filter_mask, direct_buf)) != FAIL)
+ goto error;
+ } H5E_END_TRY;
+
+ /* Check when OFFSET is not on chunk boundary for H5DOwrite_chunk and H5DOread_chunk */
offset[0] = CHUNK_NX;
offset[1] = CHUNK_NY + 1;
H5E_BEGIN_TRY {
@@ -1045,7 +1328,12 @@ test_invalid_parameters(hid_t file)
goto error;
} H5E_END_TRY;
- /* Check invalid buffer size */
+ H5E_BEGIN_TRY {
+ if((status = H5DOread_chunk(dataset, dxpl, offset, &filter_mask, direct_buf)) != FAIL)
+ goto error;
+ } H5E_END_TRY;
+
+ /* Check invalid buffer size for H5DOwrite_chunk only */
offset[0] = CHUNK_NX;
offset[1] = CHUNK_NY;
buf_size = 0;
@@ -1054,13 +1342,18 @@ test_invalid_parameters(hid_t file)
goto error;
} H5E_END_TRY;
- /* Check invalid data buffer */
+ /* Check invalid data buffer for H5DOwrite_chunk and H5DOread_chunk */
buf_size = CHUNK_NX*CHUNK_NY*sizeof(int);
H5E_BEGIN_TRY {
if((status = H5DOwrite_chunk(dataset, dxpl, filter_mask, offset, buf_size, NULL)) != FAIL)
goto error;
} H5E_END_TRY;
+ H5E_BEGIN_TRY {
+ if((status = H5DOread_chunk(dataset, dxpl, offset, &filter_mask, NULL)) != FAIL)
+ goto error;
+ } H5E_END_TRY;
+
if(H5Dclose(dataset) < 0)
goto error;
@@ -1090,11 +1383,11 @@ error:
/*-------------------------------------------------------------------------
* Function: Main function
*
- * Purpose: Test direct chunk write function H5DOwrite_chunk
- *
- * Return: Success: 0
+ * Purpose: Test direct chunk write function H5DOwrite_chunk and
+ * chunk direct read function H5DOread_chunk
*
- * Failure: 1
+ * Return: Success: 0
+ * Failure: 1
*
* Programmer: Raymond Lu
* 30 November 2012
@@ -1112,7 +1405,7 @@ int main( void )
if((file_id = H5Fcreate(FILE_NAME, H5F_ACC_TRUNC, H5P_DEFAULT, H5P_DEFAULT)) < 0)
goto error;
- /* Test direct chunk write */
+ /* Test direct chunk write and direct chunk read */
#ifdef H5_HAVE_FILTER_DEFLATE
nerrors += test_direct_chunk_write(file_id);
#endif /* H5_HAVE_FILTER_DEFLATE */
diff --git a/src/H5D.c b/src/H5D.c
index 6f69ee4..a6de952 100644
--- a/src/H5D.c
+++ b/src/H5D.c
@@ -1087,3 +1087,43 @@ done:
FUNC_LEAVE_API(ret_value)
} /* H5Dget_chunk_index_type() */
+
+/*-------------------------------------------------------------------------
+ * Function: H5Dget_chunk_storage_size
+ *
+ * Purpose: Returns the size of an allocated chunk.
+ *
+ * Return: Non-negative on success, negative on failure
+ *
+ * Programmer: Matthew Strong (GE Healthcare)
+ * 20 October 2016
+ *
+ *-------------------------------------------------------------------------
+ */
+herr_t
+H5Dget_chunk_storage_size(hid_t dset_id, const hsize_t *offset, hsize_t *chunk_nbytes)
+{
+ H5D_t *dset = NULL;
+ herr_t ret_value = SUCCEED;
+
+ FUNC_ENTER_API(FAIL)
+ H5TRACE3("e", "i*h*h", dset_id, offset, chunk_nbytes);
+
+ /* Check arguments */
+ if(NULL == (dset = (H5D_t *)H5I_object_verify(dset_id, H5I_DATASET)))
+ HGOTO_ERROR(H5E_ARGS, H5E_BADTYPE, FAIL, "not a dataset")
+ if( NULL == offset )
+ HGOTO_ERROR(H5E_ARGS, H5E_BADVALUE, FAIL, "invalid argument (null)")
+ if( NULL == chunk_nbytes )
+ HGOTO_ERROR(H5E_ARGS, H5E_BADVALUE, FAIL, "invalid argument (null)")
+
+ if(H5D_CHUNKED != dset->shared->layout.type)
+ HGOTO_ERROR(H5E_ARGS, H5E_BADTYPE, FAIL, "not a chunked dataset")
+
+ /* Call private function */
+ if(H5D__get_chunk_storage_size(dset, H5P_DATASET_XFER_DEFAULT, offset, chunk_nbytes) < 0)
+ HGOTO_ERROR(H5E_DATASET, H5E_CANTGET, FAIL, "can't get storage size of chunk")
+
+done:
+ FUNC_LEAVE_API(ret_value);
+}
diff --git a/src/H5Dchunk.c b/src/H5Dchunk.c
index ce684a0..4905a70 100644
--- a/src/H5Dchunk.c
+++ b/src/H5Dchunk.c
@@ -303,6 +303,9 @@ static herr_t H5D__chunk_collective_fill(const H5D_t *dset, hid_t dxpl_id,
H5D_chunk_coll_info_t *chunk_info, size_t chunk_size, const void *fill_buf);
#endif /* H5_HAVE_PARALLEL */
+static int
+H5D__chunk_dump_index_cb(const H5D_chunk_rec_t *chunk_rec, void *_udata);
+
/*********************/
/* Package Variables */
/*********************/
@@ -369,8 +372,7 @@ H5FL_EXTERN(H5S_sel_iter_t);
/*-------------------------------------------------------------------------
* Function: H5D__chunk_direct_write
*
- * Purpose: Internal routine to write a chunk
- * directly into the file.
+ * Purpose: Internal routine to write a chunk directly into the file.
*
* Return: Non-negative on success/Negative on failure
*
@@ -408,7 +410,7 @@ H5D__chunk_direct_write(const H5D_t *dset, hid_t dxpl_id, uint32_t filters,
/* Allocate dataspace and initialize it if it hasn't been. */
if(!(*layout->ops->is_space_alloc)(&layout->storage)) {
- /* Allocate storage */
+ /* Allocate storage */
if(H5D__alloc_storage(&io_info, H5D_ALLOC_WRITE, FALSE, NULL) < 0)
HGOTO_ERROR(H5E_DATASET, H5E_CANTINIT, FAIL, "unable to initialize storage")
}
@@ -465,7 +467,7 @@ H5D__chunk_direct_write(const H5D_t *dset, hid_t dxpl_id, uint32_t filters,
HGOTO_ERROR(H5E_DATASET, H5E_CANTGET, FAIL, "can't fill dxpl cache")
if(H5D__chunk_cache_evict(dset, io_info.md_dxpl_id, dxpl_cache, rdcc->slot[udata.idx_hint], FALSE) < 0)
- HGOTO_ERROR(H5E_DATASET, H5E_CANTREMOVE, FAIL, "unable to evict chunk")
+ HGOTO_ERROR(H5E_DATASET, H5E_CANTREMOVE, FAIL, "unable to evict chunk")
} /* end if */
/* Write the data to the file */
@@ -491,6 +493,244 @@ done:
/*-------------------------------------------------------------------------
+ * Function: H5D__chunk_direct_read
+ *
+ * Purpose: Internal routine to read a chunk directly from the file.
+ *
+ * Return: Non-negative on success/Negative on failure
+ *
+ * Programmer: Matthew Strong (GE Healthcare)
+ * 14 February 2016
+ *
+ *-------------------------------------------------------------------------
+ */
+herr_t
+H5D__chunk_direct_read(const H5D_t *dset, hid_t dxpl_id, hsize_t *offset,
+ uint32_t* filters, void *buf)
+{
+ const H5O_layout_t *layout = &(dset->shared->layout); /* Dataset layout */
+ const H5D_rdcc_t *rdcc = &(dset->shared->cache.chunk); /* raw data chunk cache */
+ H5D_chunk_ud_t udata; /* User data for querying chunk info */
+ hsize_t scaled[H5S_MAX_RANK]; /* Scaled coordinates for this chunk */
+ H5D_io_info_t io_info; /* to hold the dset and two dxpls (meta and raw data) */
+ H5D_dxpl_cache_t _dxpl_cache; /* Data transfer property cache buffer */
+ H5D_dxpl_cache_t *dxpl_cache = &_dxpl_cache; /* Data transfer property cache */
+ hbool_t md_dxpl_generated = FALSE; /* bool to indicate whether we should free the md_dxpl_id at exit */
+ herr_t ret_value = SUCCEED; /* Return value */
+
+ FUNC_ENTER_STATIC_TAG(dxpl_id, dset->oloc.addr, FAIL)
+
+ /* Check args */
+ HDassert(dset && H5D_CHUNKED == layout->type);
+ HDassert(offset);
+ HDassert(filters);
+ HDassert(buf);
+
+ io_info.dset = dset;
+ io_info.raw_dxpl_id = dxpl_id;
+ io_info.md_dxpl_id = dxpl_id;
+
+ /* set the dxpl IO type for sanity checking at the FD layer */
+#ifdef H5_DEBUG_BUILD
+ if(H5D_set_io_info_dxpls(&io_info, dxpl_id) < 0)
+ HGOTO_ERROR(H5E_DATASET, H5E_CANTCOPY, FAIL, "can't set metadata and raw data dxpls")
+ md_dxpl_generated = TRUE;
+#endif /* H5_DEBUG_BUILD */
+
+ /* Allocate dataspace and initialize it if it hasn't been. */
+ if(!(*layout->ops->is_space_alloc)(&layout->storage))
+ HGOTO_ERROR(H5E_DATASET, H5E_CANTINIT, FAIL, "storage is not initialized")
+
+ /* Calculate the index of this chunk */
+ H5VM_chunk_scaled(dset->shared->ndims, offset, layout->u.chunk.dim, scaled);
+ scaled[dset->shared->ndims] = 0;
+
+ /* Reset fields about the chunk we are looking for */
+ udata.filter_mask = 0;
+ udata.chunk_block.offset = HADDR_UNDEF;
+ udata.chunk_block.length = 0;
+ udata.idx_hint = UINT_MAX;
+
+ /* Find out the file address of the chunk */
+ if(H5D__chunk_lookup(dset, io_info.md_dxpl_id, scaled, &udata) < 0)
+ HGOTO_ERROR(H5E_DATASET, H5E_CANTGET, FAIL, "error looking up chunk address")
+
+ /* Sanity check */
+ HDassert((H5F_addr_defined(udata.chunk_block.offset) && udata.chunk_block.length > 0) ||
+ (!H5F_addr_defined(udata.chunk_block.offset) && udata.chunk_block.length == 0));
+
+ /* Check if the requested chunk exists in the chunk cache */
+ if(UINT_MAX != udata.idx_hint) {
+ H5D_rdcc_ent_t *ent = rdcc->slot[udata.idx_hint];
+
+ /* Sanity checks */
+ HDassert(udata.idx_hint < rdcc->nslots);
+ HDassert(rdcc->slot[udata.idx_hint]);
+
+ /* If the cached chunk is dirty, it must be flushed to get accurate size */
+ if( ent->dirty == TRUE ) {
+
+ /* Fill the DXPL cache values for later use */
+ if(H5D__get_dxpl_cache(io_info.raw_dxpl_id, &dxpl_cache) < 0)
+ HGOTO_ERROR(H5E_DATASET, H5E_CANTGET, FAIL, "can't fill dxpl cache")
+
+ /* Flush the chunk to disk and clear the cache entry */
+ if(H5D__chunk_cache_evict(dset, io_info.md_dxpl_id, dxpl_cache, rdcc->slot[udata.idx_hint], TRUE) < 0)
+ HGOTO_ERROR(H5E_DATASET, H5E_CANTREMOVE, FAIL, "unable to evict chunk")
+
+ /* Reset fields about the chunk we are looking for */
+ udata.filter_mask = 0;
+ udata.chunk_block.offset = HADDR_UNDEF;
+ udata.chunk_block.length = 0;
+ udata.idx_hint = UINT_MAX;
+
+ /* Get the new file address / chunk size after flushing */
+ if(H5D__chunk_lookup(dset, io_info.md_dxpl_id, scaled, &udata) < 0)
+ HGOTO_ERROR(H5E_DATASET, H5E_CANTGET, FAIL, "error looking up chunk address")
+ }
+ }
+
+ /* Make sure the address of the chunk is returned. */
+ if(!H5F_addr_defined(udata.chunk_block.offset))
+ HGOTO_ERROR(H5E_DATASET, H5E_CANTGET, FAIL, "chunk address isn't defined")
+
+ /* Read the chunk data into the supplied buffer */
+ if(H5F_block_read(dset->oloc.file, H5FD_MEM_DRAW, udata.chunk_block.offset, udata.chunk_block.length, io_info.raw_dxpl_id, buf) < 0)
+ HGOTO_ERROR(H5E_IO, H5E_READERROR, FAIL, "unable to read raw data chunk")
+
+ /* Return the filter mask */
+ *filters = udata.filter_mask;
+
+done:
+#ifdef H5_DEBUG_BUILD
+ if(md_dxpl_generated && H5I_dec_ref(io_info.md_dxpl_id) < 0)
+ HDONE_ERROR(H5E_DATASET, H5E_CANTDEC, FAIL, "can't close metadata dxpl")
+#endif /* H5_DEBUG_BUILD */
+ FUNC_LEAVE_NOAPI(ret_value)
+} /* end H5D__chunk_direct_read() */
+
+
+/*-------------------------------------------------------------------------
+ * Function: H5D__get_chunk_storage_size
+ *
+ * Purpose: Internal routine to read the storage size of a chunk on disk.
+ *
+ * Return: Non-negative on success/Negative on failure
+ *
+ * Programmer: Matthew Strong (GE Healthcare)
+ * 20 October 2016
+ *
+ *-------------------------------------------------------------------------
+ */
+herr_t
+H5D__get_chunk_storage_size(H5D_t *dset, hid_t dxpl_id, const hsize_t *offset, hsize_t *storage_size)
+{
+ const H5O_layout_t *layout = &(dset->shared->layout); /* Dataset layout */
+ const H5D_rdcc_t *rdcc = &(dset->shared->cache.chunk); /* raw data chunk cache */
+ hsize_t scaled[H5S_MAX_RANK]; /* Scaled coordinates for this chunk */
+ H5D_io_info_t io_info; /* to hold the dset and two dxpls (meta and raw data) */
+ H5D_chunk_ud_t udata; /* User data for querying chunk info */
+ H5D_dxpl_cache_t _dxpl_cache; /* Data transfer property cache buffer */
+ H5D_dxpl_cache_t *dxpl_cache = &_dxpl_cache; /* Data transfer property cache */
+ hbool_t md_dxpl_generated = FALSE; /* bool to indicate whether we should free the md_dxpl_id at exit */
+ herr_t ret_value = SUCCEED; /* Return value */
+
+ FUNC_ENTER_STATIC_TAG(dxpl_id, dset->oloc.addr, FAIL)
+
+ /* Check args */
+ HDassert(dset && H5D_CHUNKED == layout->type);
+ HDassert(offset);
+ HDassert(storage_size);
+
+ io_info.dset = dset;
+ io_info.raw_dxpl_id = dxpl_id;
+ io_info.md_dxpl_id = dxpl_id;
+
+ /* set the dxpl IO type for sanity checking at the FD layer */
+#ifdef H5_DEBUG_BUILD
+ if(H5D_set_io_info_dxpls(&io_info, dxpl_id) < 0)
+ HGOTO_ERROR(H5E_DATASET, H5E_CANTCOPY, FAIL, "can't set metadata and raw data dxpls")
+ md_dxpl_generated = TRUE;
+#endif /* H5_DEBUG_BUILD */
+
+ /* Allocate dataspace and initialize it if it hasn't been. */
+ if(!(*layout->ops->is_space_alloc)(&layout->storage)) {
+ *storage_size = 0;
+ HGOTO_DONE(SUCCEED)
+ }
+
+ /* Calculate the index of this chunk */
+ H5VM_chunk_scaled(dset->shared->ndims, offset, layout->u.chunk.dim, scaled);
+ scaled[dset->shared->ndims] = 0;
+
+ /* Reset fields about the chunk we are looking for */
+ udata.chunk_block.offset = HADDR_UNDEF;
+ udata.chunk_block.length = 0;
+ udata.idx_hint = UINT_MAX;
+
+ /* Find out the file address of the chunk */
+ if(H5D__chunk_lookup(dset, io_info.md_dxpl_id, scaled, &udata) < 0)
+ HGOTO_ERROR(H5E_DATASET, H5E_CANTGET, FAIL, "error looking up chunk address")
+
+ /* Sanity check */
+ HDassert((H5F_addr_defined(udata.chunk_block.offset) && udata.chunk_block.length > 0) ||
+ (!H5F_addr_defined(udata.chunk_block.offset) && udata.chunk_block.length == 0));
+
+ /* The requested chunk is not in cache or on disk */
+ if(!H5F_addr_defined(udata.chunk_block.offset) && UINT_MAX == udata.idx_hint)
+ HGOTO_ERROR(H5E_DATASET, H5E_CANTGET, FAIL, "chunk storage is not allocated")
+
+ /* Check if there are filters registered to the dataset */
+ if( dset->shared->dcpl_cache.pline.nused > 0 ) {
+ /* Check if the requested chunk exists in the chunk cache */
+ if(UINT_MAX != udata.idx_hint) {
+ /* Sanity checks */
+ HDassert(udata.idx_hint < rdcc->nslots);
+ HDassert(rdcc->slot[udata.idx_hint]);
+ H5D_rdcc_ent_t *ent = rdcc->slot[udata.idx_hint];
+
+ /* If the cached chunk is dirty, it must be flushed to get accurate size */
+ if( ent->dirty == TRUE ) {
+ /* Fill the DXPL cache values for later use */
+ if(H5D__get_dxpl_cache(dxpl_id, &dxpl_cache) < 0)
+ HGOTO_ERROR(H5E_DATASET, H5E_CANTGET, FAIL, "can't fill dxpl cache")
+
+ /* Flush the chunk to disk and clear the cache entry */
+ if(H5D__chunk_cache_evict(dset, io_info.md_dxpl_id, dxpl_cache, rdcc->slot[udata.idx_hint], TRUE) < 0)
+ HGOTO_ERROR(H5E_DATASET, H5E_CANTREMOVE, FAIL, "unable to evict chunk")
+
+ /* Reset fields about the chunk we are looking for */
+ udata.chunk_block.offset = HADDR_UNDEF;
+ udata.chunk_block.length = 0;
+ udata.idx_hint = UINT_MAX;
+
+ /* Get the new file address / chunk size after flushing */
+ if(H5D__chunk_lookup(dset, io_info.md_dxpl_id, scaled, &udata) < 0)
+ HGOTO_ERROR(H5E_DATASET, H5E_CANTGET, FAIL, "error looking up chunk address")
+ }
+ }
+
+ /* Make sure the address of the chunk is returned. */
+ if(!H5F_addr_defined(udata.chunk_block.offset))
+ HGOTO_ERROR(H5E_DATASET, H5E_CANTGET, FAIL, "chunk address isn't defined")
+
+ /* Return the chunk size on disk */
+ *storage_size = udata.chunk_block.length;
+ }
+ /* There are no filters registered, return the chunk size from the storage layout */
+ else
+ *storage_size = dset->shared->layout.u.chunk.size;
+
+done:
+#ifdef H5_DEBUG_BUILD
+ if(md_dxpl_generated && H5I_dec_ref(io_info.md_dxpl_id) < 0)
+ HDONE_ERROR(H5E_DATASET, H5E_CANTDEC, FAIL, "can't close metadata dxpl")
+#endif /* H5_DEBUG_BUILD */
+ FUNC_LEAVE_NOAPI(ret_value)
+} /* H5D__get_chunk_storage_size */
+
+
+/*-------------------------------------------------------------------------
* Function: H5D__chunk_set_info_real
*
* Purpose: Internal routine to set the information about chunks for a dataset
@@ -519,22 +759,22 @@ H5D__chunk_set_info_real(H5O_layout_chunk_t *layout, unsigned ndims,
/* Compute the # of chunks in dataset dimensions */
for(u = 0, layout->nchunks = 1, layout->max_nchunks = 1; u < ndims; u++) {
/* Round up to the next integer # of chunks, to accomodate partial chunks */
- layout->chunks[u] = ((curr_dims[u] + layout->dim[u]) - 1) / layout->dim[u];
+ layout->chunks[u] = ((curr_dims[u] + layout->dim[u]) - 1) / layout->dim[u];
if(H5S_UNLIMITED == max_dims[u])
layout->max_chunks[u] = H5S_UNLIMITED;
else
layout->max_chunks[u] = ((max_dims[u] + layout->dim[u]) - 1) / layout->dim[u];
/* Accumulate the # of chunks */
- layout->nchunks *= layout->chunks[u];
- layout->max_nchunks *= layout->max_chunks[u];
+ layout->nchunks *= layout->chunks[u];
+ layout->max_nchunks *= layout->max_chunks[u];
} /* end for */
/* Get the "down" sizes for each dimension */
if(H5VM_array_down(ndims, layout->chunks, layout->down_chunks) < 0)
HGOTO_ERROR(H5E_DATASET, H5E_CANTSET, FAIL, "can't compute 'down' chunk size value")
if(H5VM_array_down(ndims, layout->max_chunks, layout->max_down_chunks) < 0)
- HGOTO_ERROR(H5E_DATASET, H5E_CANTSET, FAIL, "can't compute 'down' chunk size value")
+ HGOTO_ERROR(H5E_DATASET, H5E_CANTSET, FAIL, "can't compute 'down' chunk size value")
done:
FUNC_LEAVE_NOAPI(ret_value)
@@ -2383,14 +2623,14 @@ H5D__chunk_dest(H5D_t *dset, hid_t dxpl_id)
/* Flush all the cached chunks */
for(ent = rdcc->head; ent; ent = next) {
- next = ent->next;
- if(H5D__chunk_cache_evict(dset, dxpl_id, dxpl_cache, ent, TRUE) < 0)
- nerrors++;
+ next = ent->next;
+ if(H5D__chunk_cache_evict(dset, dxpl_id, dxpl_cache, ent, TRUE) < 0)
+ nerrors++;
} /* end for */
/* Continue even if there are failures. */
if(nerrors)
- HDONE_ERROR(H5E_IO, H5E_CANTFLUSH, FAIL, "unable to flush one or more raw data chunks")
+ HDONE_ERROR(H5E_IO, H5E_CANTFLUSH, FAIL, "unable to flush one or more raw data chunks")
/* Release cache structures */
if(rdcc->slot)
@@ -2997,27 +3237,27 @@ H5D__chunk_cache_evict(const H5D_t *dset, hid_t dxpl_id, const H5D_dxpl_cache_t
HDassert(ent->idx < rdcc->nslots);
if(flush) {
- /* Flush */
- if(H5D__chunk_flush_entry(dset, dxpl_id, dxpl_cache, ent, TRUE) < 0)
- HDONE_ERROR(H5E_IO, H5E_WRITEERROR, FAIL, "cannot flush indexed storage buffer")
+ /* Flush */
+ if(H5D__chunk_flush_entry(dset, dxpl_id, dxpl_cache, ent, TRUE) < 0)
+ HDONE_ERROR(H5E_IO, H5E_WRITEERROR, FAIL, "cannot flush indexed storage buffer")
} /* end if */
else {
/* Don't flush, just free chunk */
- if(ent->chunk != NULL)
- ent->chunk = (uint8_t *)H5D__chunk_mem_xfree(ent->chunk,
+ if(ent->chunk != NULL)
+ ent->chunk = (uint8_t *)H5D__chunk_mem_xfree(ent->chunk,
((ent->edge_chunk_state & H5D_RDCC_DISABLE_FILTERS) ? NULL
: &(dset->shared->dcpl_cache.pline)));
} /* end else */
/* Unlink from list */
if(ent->prev)
- ent->prev->next = ent->next;
+ ent->prev->next = ent->next;
else
- rdcc->head = ent->next;
+ rdcc->head = ent->next;
if(ent->next)
- ent->next->prev = ent->prev;
+ ent->next->prev = ent->prev;
else
- rdcc->tail = ent->prev;
+ rdcc->tail = ent->prev;
ent->prev = ent->next = NULL;
/* Unlink from temporary list */
diff --git a/src/H5Dio.c b/src/H5Dio.c
index dfd3f17..572e6cf 100644
--- a/src/H5Dio.c
+++ b/src/H5Dio.c
@@ -125,9 +125,13 @@ H5Dread(hid_t dset_id, hid_t mem_type_id, hid_t mem_space_id,
hid_t file_space_id, hid_t plist_id, void *buf/*out*/)
{
H5D_t *dset = NULL;
- const H5S_t *mem_space = NULL;
- const H5S_t *file_space = NULL;
- herr_t ret_value = SUCCEED; /* Return value */
+ const H5S_t *mem_space = NULL;
+ const H5S_t *file_space = NULL;
+ H5P_genplist_t *plist; /* Property list pointer */
+ hsize_t *direct_offset = NULL;
+ hbool_t direct_read = FALSE;
+ uint32_t direct_filters = 0;
+ herr_t ret_value = SUCCEED; /* Return value */
FUNC_ENTER_API(FAIL)
H5TRACE6("e", "iiiiix", dset_id, mem_type_id, mem_space_id, file_space_id,
@@ -135,28 +139,29 @@ H5Dread(hid_t dset_id, hid_t mem_type_id, hid_t mem_space_id,
/* check arguments */
if(NULL == (dset = (H5D_t *)H5I_object_verify(dset_id, H5I_DATASET)))
- HGOTO_ERROR(H5E_ARGS, H5E_BADTYPE, FAIL, "not a dataset")
+ HGOTO_ERROR(H5E_ARGS, H5E_BADTYPE, FAIL, "not a dataset")
if(NULL == dset->oloc.file)
- HGOTO_ERROR(H5E_ARGS, H5E_BADTYPE, FAIL, "not a dataset")
+ HGOTO_ERROR(H5E_ARGS, H5E_BADTYPE, FAIL, "not a dataset")
if(mem_space_id < 0 || file_space_id < 0)
HGOTO_ERROR(H5E_ARGS, H5E_BADTYPE, FAIL, "not a data space")
if(H5S_ALL != mem_space_id) {
- if(NULL == (mem_space = (const H5S_t *)H5I_object_verify(mem_space_id, H5I_DATASPACE)))
- HGOTO_ERROR(H5E_ARGS, H5E_BADTYPE, FAIL, "not a data space")
+ if(NULL == (mem_space = (const H5S_t *)H5I_object_verify(mem_space_id, H5I_DATASPACE)))
+ HGOTO_ERROR(H5E_ARGS, H5E_BADTYPE, FAIL, "not a data space")
- /* Check for valid selection */
- if(H5S_SELECT_VALID(mem_space) != TRUE)
- HGOTO_ERROR(H5E_DATASPACE, H5E_BADRANGE, FAIL, "selection+offset not within extent")
+ /* Check for valid selection */
+ if(H5S_SELECT_VALID(mem_space) != TRUE)
+ HGOTO_ERROR(H5E_DATASPACE, H5E_BADRANGE, FAIL, "selection+offset not within extent")
} /* end if */
+
if(H5S_ALL != file_space_id) {
- if(NULL == (file_space = (const H5S_t *)H5I_object_verify(file_space_id, H5I_DATASPACE)))
- HGOTO_ERROR(H5E_ARGS, H5E_BADTYPE, FAIL, "not a data space")
+ if(NULL == (file_space = (const H5S_t *)H5I_object_verify(file_space_id, H5I_DATASPACE)))
+ HGOTO_ERROR(H5E_ARGS, H5E_BADTYPE, FAIL, "not a data space")
- /* Check for valid selection */
- if(H5S_SELECT_VALID(file_space) != TRUE)
- HGOTO_ERROR(H5E_DATASPACE, H5E_BADRANGE, FAIL, "selection+offset not within extent")
+ /* Check for valid selection */
+ if(H5S_SELECT_VALID(file_space) != TRUE)
+ HGOTO_ERROR(H5E_DATASPACE, H5E_BADRANGE, FAIL, "selection+offset not within extent")
} /* end if */
/* Get the default dataset transfer property list if the user didn't provide one */
@@ -166,9 +171,55 @@ H5Dread(hid_t dset_id, hid_t mem_type_id, hid_t mem_space_id,
if(TRUE != H5P_isa_class(plist_id, H5P_DATASET_XFER))
HGOTO_ERROR(H5E_ARGS, H5E_BADTYPE, FAIL, "not xfer parms")
- /* read raw data */
- if(H5D__read(dset, mem_type_id, mem_space, file_space, plist_id, buf/*out*/) < 0)
- HGOTO_ERROR(H5E_DATASET, H5E_READERROR, FAIL, "can't read data")
+ /* Get the dataset transfer property list */
+ if(NULL == (plist = (H5P_genplist_t *)H5I_object(plist_id)))
+ HGOTO_ERROR(H5E_ARGS, H5E_BADTYPE, FAIL, "not a dataset transfer property list")
+
+ /* Retrieve the 'direct read' flag */
+ if(H5P_get(plist, H5D_XFER_DIRECT_CHUNK_READ_FLAG_NAME, &direct_read) < 0)
+ HGOTO_ERROR(H5E_PLIST, H5E_CANTGET, FAIL, "error getting flag for direct chunk read")
+
+ if(direct_read) {
+ unsigned u;
+ hsize_t dims[H5O_LAYOUT_NDIMS];
+ hsize_t internal_offset[H5O_LAYOUT_NDIMS];
+
+ if(H5D_CHUNKED != dset->shared->layout.type)
+ HGOTO_ERROR(H5E_ARGS, H5E_BADTYPE, FAIL, "not a chunked dataset")
+
+ /* Get the direct chunk offset property */
+ if(H5P_get(plist, H5D_XFER_DIRECT_CHUNK_READ_OFFSET_NAME, &direct_offset) < 0)
+ HGOTO_ERROR(H5E_PLIST, H5E_CANTGET, FAIL, "error getting direct offset from xfer properties")
+
+ /* The library's chunking code requires the offset terminates with a zero. So transfer the
+ * offset array to an internal offset array */
+ for(u = 0; u < dset->shared->ndims; u++) {
+ /* Make sure the offset doesn't exceed the dataset's dimensions */
+ if(direct_offset[u] > dset->shared->curr_dims[u])
+ HGOTO_ERROR(H5E_DATASPACE, H5E_BADTYPE, FAIL, "offset exceeds dimensions of dataset")
+
+ /* Make sure the offset fall right on a chunk's boundary */
+ if(direct_offset[u] % dset->shared->layout.u.chunk.dim[u])
+ HGOTO_ERROR(H5E_DATASPACE, H5E_BADTYPE, FAIL, "offset doesn't fall on chunks's boundary")
+
+ internal_offset[u] = direct_offset[u];
+ } /* end for */
+
+ /* Terminate the offset with a zero */
+ internal_offset[dset->shared->ndims] = 0;
+
+ /* Read the raw chunk */
+ if(H5D__chunk_direct_read(dset, plist_id, internal_offset, &direct_filters, buf) < 0)
+ HGOTO_ERROR(H5E_DATASET, H5E_READERROR, FAIL, "can't read chunk directly")
+ /* Set the chunk filter mask property */
+ if(H5P_set(plist, H5D_XFER_DIRECT_CHUNK_READ_FILTERS_NAME, &direct_filters) < 0)
+ HGOTO_ERROR(H5E_PLIST, H5E_CANTGET, FAIL, "error setting filter mask xfer property")
+ }
+ else {
+ /* read raw data */
+ if(H5D__read(dset, mem_type_id, mem_space, file_space, plist_id, buf/*out*/) < 0)
+ HGOTO_ERROR(H5E_DATASET, H5E_READERROR, FAIL, "can't read data")
+ }
done:
FUNC_LEAVE_API(ret_value)
@@ -245,28 +296,28 @@ H5Dwrite(hid_t dset_id, hid_t mem_type_id, hid_t mem_space_id,
/* Check dataspace selections if this is not a direct write */
if(!direct_write) {
if(mem_space_id < 0 || file_space_id < 0)
- HGOTO_ERROR(H5E_ARGS, H5E_BADTYPE, FAIL, "not a dataspace")
-
- if(H5S_ALL != mem_space_id) {
- if(NULL == (mem_space = (const H5S_t *)H5I_object_verify(mem_space_id, H5I_DATASPACE)))
- HGOTO_ERROR(H5E_ARGS, H5E_BADTYPE, FAIL, "not a dataspace")
-
- /* Check for valid selection */
- if(H5S_SELECT_VALID(mem_space) != TRUE)
- HGOTO_ERROR(H5E_DATASPACE, H5E_BADRANGE, FAIL, "memory selection+offset not within extent")
- } /* end if */
- if(H5S_ALL != file_space_id) {
- if(NULL == (file_space = (const H5S_t *)H5I_object_verify(file_space_id, H5I_DATASPACE)))
- HGOTO_ERROR(H5E_ARGS, H5E_BADTYPE, FAIL, "not a dataspace")
-
- /* Check for valid selection */
- if(H5S_SELECT_VALID(file_space) != TRUE)
- HGOTO_ERROR(H5E_DATASPACE, H5E_BADRANGE, FAIL, "file selection+offset not within extent")
- } /* end if */
+ HGOTO_ERROR(H5E_ARGS, H5E_BADTYPE, FAIL, "not a dataspace")
+
+ if(H5S_ALL != mem_space_id) {
+ if(NULL == (mem_space = (const H5S_t *)H5I_object_verify(mem_space_id, H5I_DATASPACE)))
+ HGOTO_ERROR(H5E_ARGS, H5E_BADTYPE, FAIL, "not a dataspace")
+
+ /* Check for valid selection */
+ if(H5S_SELECT_VALID(mem_space) != TRUE)
+ HGOTO_ERROR(H5E_DATASPACE, H5E_BADRANGE, FAIL, "memory selection+offset not within extent")
+ } /* end if */
+ if(H5S_ALL != file_space_id) {
+ if(NULL == (file_space = (const H5S_t *)H5I_object_verify(file_space_id, H5I_DATASPACE)))
+ HGOTO_ERROR(H5E_ARGS, H5E_BADTYPE, FAIL, "not a dataspace")
+
+ /* Check for valid selection */
+ if(H5S_SELECT_VALID(file_space) != TRUE)
+ HGOTO_ERROR(H5E_DATASPACE, H5E_BADRANGE, FAIL, "file selection+offset not within extent")
+ } /* end if */
}
if(H5D__pre_write(dset, direct_write, mem_type_id, mem_space, file_space, dxpl_id, buf) < 0)
- HGOTO_ERROR(H5E_DATASET, H5E_WRITEERROR, FAIL, "can't prepare for writing data")
+ HGOTO_ERROR(H5E_DATASET, H5E_WRITEERROR, FAIL, "can't prepare for writing data")
done:
FUNC_LEAVE_API(ret_value)
@@ -300,15 +351,15 @@ H5D__pre_write(H5D_t *dset, hbool_t direct_write, hid_t mem_type_id,
uint32_t direct_filters;
hsize_t *direct_offset;
uint32_t direct_datasize;
- hsize_t internal_offset[H5O_LAYOUT_NDIMS];
- unsigned u; /* Local index variable */
+ hsize_t internal_offset[H5O_LAYOUT_NDIMS];
+ unsigned u; /* Local index variable */
/* Get the dataset transfer property list */
if(NULL == (plist = (H5P_genplist_t *)H5I_object(dxpl_id)))
HGOTO_ERROR(H5E_ARGS, H5E_BADTYPE, FAIL, "not a dataset transfer property list")
if(H5D_CHUNKED != dset->shared->layout.type)
- HGOTO_ERROR(H5E_ARGS, H5E_BADTYPE, FAIL, "not a chunked dataset")
+ HGOTO_ERROR(H5E_ARGS, H5E_BADTYPE, FAIL, "not a chunked dataset")
/* Retrieve parameters for direct chunk write */
if(H5P_get(plist, H5D_XFER_DIRECT_CHUNK_WRITE_FILTERS_NAME, &direct_filters) < 0)
@@ -318,19 +369,19 @@ H5D__pre_write(H5D_t *dset, hbool_t direct_write, hid_t mem_type_id,
if(H5P_get(plist, H5D_XFER_DIRECT_CHUNK_WRITE_DATASIZE_NAME, &direct_datasize) < 0)
HGOTO_ERROR(H5E_PLIST, H5E_CANTGET, FAIL, "error getting data size for direct chunk write")
- /* The library's chunking code requires the offset terminates with a zero. So transfer the
+ /* The library's chunking code requires the offset terminates with a zero. So transfer the
* offset array to an internal offset array */
- for(u = 0; u < dset->shared->ndims; u++) {
- /* Make sure the offset doesn't exceed the dataset's dimensions */
+ for(u = 0; u < dset->shared->ndims; u++) {
+ /* Make sure the offset doesn't exceed the dataset's dimensions */
if(direct_offset[u] > dset->shared->curr_dims[u])
- HGOTO_ERROR(H5E_DATASPACE, H5E_BADTYPE, FAIL, "offset exceeds dimensions of dataset")
+ HGOTO_ERROR(H5E_DATASPACE, H5E_BADTYPE, FAIL, "offset exceeds dimensions of dataset")
/* Make sure the offset fall right on a chunk's boundary */
- if(direct_offset[u] % dset->shared->layout.u.chunk.dim[u])
- HGOTO_ERROR(H5E_DATASPACE, H5E_BADTYPE, FAIL, "offset doesn't fall on chunks's boundary")
+ if(direct_offset[u] % dset->shared->layout.u.chunk.dim[u])
+ HGOTO_ERROR(H5E_DATASPACE, H5E_BADTYPE, FAIL, "offset doesn't fall on chunks's boundary")
- internal_offset[u] = direct_offset[u];
- } /* end for */
+ internal_offset[u] = direct_offset[u];
+ } /* end for */
/* Terminate the offset with a zero */
internal_offset[dset->shared->ndims] = 0;
@@ -342,7 +393,7 @@ H5D__pre_write(H5D_t *dset, hbool_t direct_write, hid_t mem_type_id,
else { /* Normal write */
/* write raw data */
if(H5D__write(dset, mem_type_id, mem_space, file_space, dxpl_id, buf) < 0)
- HGOTO_ERROR(H5E_DATASET, H5E_WRITEERROR, FAIL, "can't write data")
+ HGOTO_ERROR(H5E_DATASET, H5E_WRITEERROR, FAIL, "can't write data")
} /* end else */
done:
diff --git a/src/H5Dpkg.h b/src/H5Dpkg.h
index 8a4711f..b123b81 100644
--- a/src/H5Dpkg.h
+++ b/src/H5Dpkg.h
@@ -578,6 +578,7 @@ H5_DLL herr_t H5D__get_space_status(H5D_t *dset, H5D_space_status_t *allocation,
H5_DLL herr_t H5D__alloc_storage(const H5D_io_info_t *io_info, H5D_time_alloc_t time_alloc,
hbool_t full_overwrite, hsize_t old_dim[]);
H5_DLL herr_t H5D__get_storage_size(H5D_t *dset, hid_t dxpl_id, hsize_t *storage_size);
+H5_DLL herr_t H5D__get_chunk_storage_size(H5D_t *dset, hid_t dxpl_id, const hsize_t *offset, hsize_t *storage_size);
H5_DLL haddr_t H5D__get_offset(const H5D_t *dset);
H5_DLL void *H5D__vlen_get_buf_size_alloc(size_t size, void *info);
H5_DLL herr_t H5D__vlen_get_buf_size(void *elem, hid_t type_id, unsigned ndim,
@@ -685,6 +686,8 @@ H5_DLL herr_t H5D__chunk_delete(H5F_t *f, hid_t dxpl_id, H5O_t *oh,
H5O_storage_t *store);
H5_DLL herr_t H5D__chunk_direct_write(const H5D_t *dset, hid_t dxpl_id, uint32_t filters,
hsize_t *offset, uint32_t data_size, const void *buf);
+H5_DLL herr_t H5D__chunk_direct_read(const H5D_t *dset, hid_t dxpl_id, hsize_t *offset,
+ uint32_t *filters, void *buf);
#ifdef H5D_CHUNK_DEBUG
H5_DLL herr_t H5D__chunk_stats(const H5D_t *dset, hbool_t headers);
#endif /* H5D_CHUNK_DEBUG */
diff --git a/src/H5Dpublic.h b/src/H5Dpublic.h
index fe408b2..baa844a 100644
--- a/src/H5Dpublic.h
+++ b/src/H5Dpublic.h
@@ -40,6 +40,11 @@
#define H5D_XFER_DIRECT_CHUNK_WRITE_FILTERS_NAME "direct_chunk_filters"
#define H5D_XFER_DIRECT_CHUNK_WRITE_OFFSET_NAME "direct_chunk_offset"
#define H5D_XFER_DIRECT_CHUNK_WRITE_DATASIZE_NAME "direct_chunk_datasize"
+
+/* Property names for H5LTDdirect_chunk_read */
+#define H5D_XFER_DIRECT_CHUNK_READ_FLAG_NAME "direct_chunk_read_flag"
+#define H5D_XFER_DIRECT_CHUNK_READ_OFFSET_NAME "direct_chunk_read_offset"
+#define H5D_XFER_DIRECT_CHUNK_READ_FILTERS_NAME "direct_chunk_read_filters"
/*******************/
/* Public Typedefs */
@@ -146,6 +151,7 @@ H5_DLL hid_t H5Dget_type(hid_t dset_id);
H5_DLL hid_t H5Dget_create_plist(hid_t dset_id);
H5_DLL hid_t H5Dget_access_plist(hid_t dset_id);
H5_DLL hsize_t H5Dget_storage_size(hid_t dset_id);
+H5_DLL herr_t H5Dget_chunk_storage_size(hid_t dset_id, const hsize_t *offset, hsize_t *chunk_bytes);
H5_DLL haddr_t H5Dget_offset(hid_t dset_id);
H5_DLL herr_t H5Dread(hid_t dset_id, hid_t mem_type_id, hid_t mem_space_id,
hid_t file_space_id, hid_t plist_id, void *buf/*out*/);
diff --git a/src/H5Pdxpl.c b/src/H5Pdxpl.c
index fdb402f..3c53c15 100644
--- a/src/H5Pdxpl.c
+++ b/src/H5Pdxpl.c
@@ -169,6 +169,13 @@
#define H5D_XFER_DIRECT_CHUNK_WRITE_OFFSET_DEF NULL
#define H5D_XFER_DIRECT_CHUNK_WRITE_DATASIZE_SIZE sizeof(uint32_t)
#define H5D_XFER_DIRECT_CHUNK_WRITE_DATASIZE_DEF 0
+/* Definitions for properties of direct chunk read */
+#define H5D_XFER_DIRECT_CHUNK_READ_FLAG_SIZE sizeof(hbool_t)
+#define H5D_XFER_DIRECT_CHUNK_READ_FLAG_DEF FALSE
+#define H5D_XFER_DIRECT_CHUNK_READ_FILTERS_SIZE sizeof(uint32_t)
+#define H5D_XFER_DIRECT_CHUNK_READ_FILTERS_DEF 0
+#define H5D_XFER_DIRECT_CHUNK_READ_OFFSET_SIZE sizeof(hsize_t *)
+#define H5D_XFER_DIRECT_CHUNK_READ_OFFSET_DEF NULL
/* Ring type - private property */
#define H5AC_XFER_RING_SIZE sizeof(unsigned)
#define H5AC_XFER_RING_DEF H5AC_RING_USER
@@ -293,6 +300,9 @@ static const hbool_t H5D_def_direct_chunk_flag_g = H5D_XFER_DIRECT_CHUNK_WRITE_F
static const uint32_t H5D_def_direct_chunk_filters_g = H5D_XFER_DIRECT_CHUNK_WRITE_FILTERS_DEF; /* Default value for the filters of direct chunk write */
static const hsize_t *H5D_def_direct_chunk_offset_g = H5D_XFER_DIRECT_CHUNK_WRITE_OFFSET_DEF; /* Default value for the offset of direct chunk write */
static const uint32_t H5D_def_direct_chunk_datasize_g = H5D_XFER_DIRECT_CHUNK_WRITE_DATASIZE_DEF; /* Default value for the datasize of direct chunk write */
+static const hbool_t direct_chunk_read_flag = H5D_XFER_DIRECT_CHUNK_READ_FLAG_DEF; /* Default value for the flag of direct chunk read */
+static const hsize_t *direct_chunk_read_offset = H5D_XFER_DIRECT_CHUNK_READ_OFFSET_DEF; /* Default value for the offset of direct chunk read */
+static const uint32_t direct_chunk_read_filters = H5D_XFER_DIRECT_CHUNK_READ_FILTERS_DEF; /* Default value for the filters of direct chunk read */
static const H5AC_ring_t H5D_ring_g = H5AC_XFER_RING_DEF; /* Default value for the cache entry ring type */
#ifdef H5_DEBUG_BUILD
static const H5FD_dxpl_type_t H5D_dxpl_type_g = H5FD_NOIO_DXPL; /* Default value for the dxpl type */
@@ -497,6 +507,24 @@ H5P__dxfr_reg_prop(H5P_genclass_t *pclass)
NULL, NULL, NULL, NULL, NULL, NULL, NULL, NULL, NULL) < 0)
HGOTO_ERROR(H5E_PLIST, H5E_CANTINSERT, FAIL, "can't insert property into class")
+ /* Register the property of flag for direct chunk read */
+ /* (Note: this property should not have an encode/decode callback) */
+ if(H5P_register_real(pclass, H5D_XFER_DIRECT_CHUNK_READ_FLAG_NAME, H5D_XFER_DIRECT_CHUNK_READ_FLAG_SIZE, &direct_chunk_read_flag,
+ NULL, NULL, NULL, NULL, NULL, NULL, NULL, NULL, NULL) < 0)
+ HGOTO_ERROR(H5E_PLIST, H5E_CANTINSERT, FAIL, "can't insert property into class")
+
+ /* Register the property of filter for direct chunk read */
+ /* (Note: this property should not have an encode/decode callback) */
+ if(H5P_register_real(pclass, H5D_XFER_DIRECT_CHUNK_READ_FILTERS_NAME, H5D_XFER_DIRECT_CHUNK_READ_FILTERS_SIZE, &direct_chunk_read_filters,
+ NULL, NULL, NULL, NULL, NULL, NULL, NULL, NULL, NULL) < 0)
+ HGOTO_ERROR(H5E_PLIST, H5E_CANTINSERT, FAIL, "can't insert property into class")
+
+ /* Register the property of offset for direct chunk read */
+ /* (Note: this property should not have an encode/decode callback) */
+ if(H5P_register_real(pclass, H5D_XFER_DIRECT_CHUNK_READ_OFFSET_NAME, H5D_XFER_DIRECT_CHUNK_READ_OFFSET_SIZE, &direct_chunk_read_offset,
+ NULL, NULL, NULL, NULL, NULL, NULL, NULL, NULL, NULL) < 0)
+ HGOTO_ERROR(H5E_PLIST, H5E_CANTINSERT, FAIL, "can't insert property into class")
+
/* Register the ring property (private) */
if(H5P_register_real(pclass, H5AC_RING_NAME, H5AC_XFER_RING_SIZE, &H5D_ring_g,
NULL, NULL, NULL, H5AC_XFER_RING_ENC, H5AC_XFER_RING_DEC,
generated by cgit v0.12 at 2024-07-04 20:31:21 (GMT)