diff options
| -rw-r--r-- | release_docs/RELEASE.txt | 7 | ||||
| -rw-r--r-- | src/H5Dcontig.c | 2 | ||||
| -rw-r--r-- | src/H5Distore.c | 2 | ||||
| -rw-r--r-- | src/H5F.c | 55 | ||||
| -rw-r--r-- | src/H5Fcontig.c | 2 | ||||
| -rw-r--r-- | src/H5Fistore.c | 2 | ||||
| -rw-r--r-- | src/H5Fpkg.h | 2 | ||||
| -rw-r--r-- | test/Makefile.in | 9 | ||||
| -rw-r--r-- | test/tmisc.c | 237 |
9 files changed, 300 insertions, 18 deletions
diff --git a/release_docs/RELEASE.txt b/release_docs/RELEASE.txt index 3b04d42..1d6b2ec 100644 --- a/release_docs/RELEASE.txt +++ b/release_docs/RELEASE.txt @@ -56,6 +56,9 @@ Bug Fixes since HDF5-1.6.0 release Library ------- + - Corrected bug in sieve buffer code which could cause loss of data + when a small dataset was created and deleted in quick succession. + QAK - 2003/08/27 - Corrected bug in H5Gget_objname_by_idx which was not allowing NULL for the name when just querying for the object name's length. QAK - 2003/08/25 @@ -91,7 +94,7 @@ Bug Fixes since HDF5-1.6.0 release Configuration ------------- - Fixed the error that caused "make install" to fail because of the - macro definition syntax of "prefix?=..." AKC - 2003/07/22 + macro definition syntax of "prefix?=..." AKC - 2003/07/22 Performance ------------- @@ -99,7 +102,7 @@ Bug Fixes since HDF5-1.6.0 release Tools ----- - Fixed a segmentation fault of h5diff when percentage option is used. - AKC - 2003/08/27 + AKC - 2003/08/27 - Switched away from tools using internal "fixtype" function(s) to use H5Tget_native_type() internally. QAK - 2003/08/25 diff --git a/src/H5Dcontig.c b/src/H5Dcontig.c index 6445d19..7867be7 100644 --- a/src/H5Dcontig.c +++ b/src/H5Dcontig.c @@ -346,7 +346,7 @@ H5F_contig_delete(H5F_t *f, hid_t dxpl_id, const struct H5O_layout_t *layout) size *= layout->dim[u]; /* Check for overlap with the sieve buffer and reset it */ - if (H5F_sieve_overlap_clear(f, layout->addr, size)<0) + if (H5F_sieve_overlap_clear(f, dxpl_id, layout->addr, size)<0) HGOTO_ERROR(H5E_OHDR, H5E_CANTFREE, FAIL, "unable to clear sieve buffer"); /* Free the file space for the chunk */ diff --git a/src/H5Distore.c b/src/H5Distore.c index 913278a..828a971 100644 --- a/src/H5Distore.c +++ b/src/H5Distore.c @@ -2675,7 +2675,7 @@ H5F_istore_remove(H5F_t *f, hid_t dxpl_id, haddr_t addr, void *_lt_key /*in,out FUNC_ENTER_NOAPI(H5F_istore_remove,H5B_INS_ERROR); /* Check for overlap with the sieve buffer and reset it */ - if (H5F_sieve_overlap_clear(f, addr, (hsize_t)lt_key->nbytes)<0) + if (H5F_sieve_overlap_clear(f, dxpl_id, addr, (hsize_t)lt_key->nbytes)<0) HGOTO_ERROR(H5E_OHDR, H5E_CANTFREE, H5B_INS_ERROR, "unable to clear sieve buffer"); /* Remove raw data chunk from file */ @@ -4224,7 +4224,7 @@ H5F_addr_pack(H5F_t UNUSED *f, haddr_t *addr_p/*out*/, *------------------------------------------------------------------------- */ herr_t -H5F_sieve_overlap_clear(H5F_t *f, haddr_t addr, hsize_t size) +H5F_sieve_overlap_clear(H5F_t *f, hid_t dxpl_id, haddr_t addr, hsize_t size) { herr_t ret_value=SUCCEED; /* Return value */ @@ -4235,10 +4235,55 @@ H5F_sieve_overlap_clear(H5F_t *f, haddr_t addr, hsize_t size) /* Check for the address range overlapping with the sieve buffer */ if(H5F_addr_overlap(f->shared->sieve_loc,f->shared->sieve_size,addr,size)) { - /* Reset sieve information */ - f->shared->sieve_loc=HADDR_UNDEF; - f->shared->sieve_size=0; - f->shared->sieve_dirty=0; + /* Check if only part of the sieve buffer is being invalidated */ + if(size<f->shared->sieve_size) { + /* Check if the portion to invalidate is at the end */ + if((f->shared->sieve_loc+f->shared->sieve_size)==(addr+size)) { + /* Just shorten the buffer */ + f->shared->sieve_size-=size; + } /* end if */ + /* Check if the portion to invalidate is at the beginning */ + else if(f->shared->sieve_loc==addr) { + /* Advance the start of the sieve buffer (on disk) and shorten the buffer */ + f->shared->sieve_loc+=size; + f->shared->sieve_size-=size; + + /* Move the retained information in the buffer down */ + HDmemcpy(f->shared->sieve_buf,f->shared->sieve_buf+size,f->shared->sieve_size); + } /* end elif */ + /* Portion to invalidate is in middle */ + else { + size_t invalid_size; /* Portion of sieve buffer to invalidate */ + + /* Write out portion at the beginning of the buffer, if buffer is dirty */ + if(f->shared->sieve_dirty) { + size_t start_size; /* Portion of sieve buffer to write */ + + /* Compute size of block at beginning of buffer */ + start_size=(addr-f->shared->sieve_loc); + + /* Write to file */ + if (H5F_block_write(f, H5FD_MEM_DRAW, f->shared->sieve_loc, start_size, dxpl_id, f->shared->sieve_buf)<0) + HGOTO_ERROR(H5E_IO, H5E_WRITEERROR, FAIL, "block write failed"); + } /* end if */ + + /* Compute size of block to invalidate */ + invalid_size=((addr+size)-f->shared->sieve_loc); + + /* Advance the start of the sieve buffer (on disk) and shorten the buffer */ + f->shared->sieve_loc+=invalid_size; + f->shared->sieve_size-=invalid_size; + + /* Move the retained information in the buffer down */ + HDmemcpy(f->shared->sieve_buf,f->shared->sieve_buf+invalid_size,f->shared->sieve_size); + } /* end else */ + } /* end if */ + else { + /* Reset sieve information */ + f->shared->sieve_loc=HADDR_UNDEF; + f->shared->sieve_size=0; + f->shared->sieve_dirty=0; + } /* end else */ } /* end if */ done: diff --git a/src/H5Fcontig.c b/src/H5Fcontig.c index 6445d19..7867be7 100644 --- a/src/H5Fcontig.c +++ b/src/H5Fcontig.c @@ -346,7 +346,7 @@ H5F_contig_delete(H5F_t *f, hid_t dxpl_id, const struct H5O_layout_t *layout) size *= layout->dim[u]; /* Check for overlap with the sieve buffer and reset it */ - if (H5F_sieve_overlap_clear(f, layout->addr, size)<0) + if (H5F_sieve_overlap_clear(f, dxpl_id, layout->addr, size)<0) HGOTO_ERROR(H5E_OHDR, H5E_CANTFREE, FAIL, "unable to clear sieve buffer"); /* Free the file space for the chunk */ diff --git a/src/H5Fistore.c b/src/H5Fistore.c index 913278a..828a971 100644 --- a/src/H5Fistore.c +++ b/src/H5Fistore.c @@ -2675,7 +2675,7 @@ H5F_istore_remove(H5F_t *f, hid_t dxpl_id, haddr_t addr, void *_lt_key /*in,out FUNC_ENTER_NOAPI(H5F_istore_remove,H5B_INS_ERROR); /* Check for overlap with the sieve buffer and reset it */ - if (H5F_sieve_overlap_clear(f, addr, (hsize_t)lt_key->nbytes)<0) + if (H5F_sieve_overlap_clear(f, dxpl_id, addr, (hsize_t)lt_key->nbytes)<0) HGOTO_ERROR(H5E_OHDR, H5E_CANTFREE, H5B_INS_ERROR, "unable to clear sieve buffer"); /* Remove raw data chunk from file */ diff --git a/src/H5Fpkg.h b/src/H5Fpkg.h index 1ae333d..631d482 100644 --- a/src/H5Fpkg.h +++ b/src/H5Fpkg.h @@ -198,7 +198,7 @@ H5_DLL void H5F_encode_length_unusual(const H5F_t *f, uint8_t **p, uint8_t *l); H5_DLL herr_t H5F_mountpoint(struct H5G_entry_t *find/*in,out*/); H5_DLL herr_t H5F_debug(H5F_t *f, hid_t dxpl_id, haddr_t addr, FILE * stream, int indent, int fwidth); -H5_DLL herr_t H5F_sieve_overlap_clear(H5F_t *f, haddr_t addr, hsize_t size); +H5_DLL herr_t H5F_sieve_overlap_clear(H5F_t *f, hid_t dxpl_id, haddr_t addr, hsize_t size); /* Functions that operate on indexed storage */ H5_DLL herr_t H5F_istore_init (H5F_t *f); diff --git a/test/Makefile.in b/test/Makefile.in index 2041f35..fe33968 100644 --- a/test/Makefile.in +++ b/test/Makefile.in @@ -56,12 +56,13 @@ MOSTLYCLEAN=cmpd_dset.h5 compact_dataset.h5 dataset.h5 extend.h5 istore.h5 \ tselect.h5 mtime.h5 unlink.h5 fillval_[0-9].h5 fillval.raw \ mount_[0-9].h5 testmeta.h5 ttime.h5 trefer[1-3].h5 tvltypes.h5 \ tvlstr.h5 flush.h5 enum1.h5 titerate.h5 ttsafe.h5 tarray1.h5 \ - tgenprop.h5 tmisc.h5 tmisc2a.h5 tmisc2b.h5 tmisc3.h5 tmisc4a.h5 \ + tgenprop.h5 tmisc1.h5 tmisc2a.h5 tmisc2b.h5 tmisc3.h5 tmisc4a.h5 \ tmisc4b.h5 tmisc5.h5 tmisc6.h5 tmisc7.h5 tmisc8.h5 tmisc9.h5 \ tmisc10.h5 tmisc11.h5 tmisc12.h5 tmisc13a.h5 tmisc13b.h5 \ - set_extent_read.h5 set_extent_create.h5 getname.h5 getname1.h5 \ - getname2.h5 getname3.h5 sec2_file.h5 family_file000[0-3][0-9].h5 \ - multi_file-[rs].h5 core_file new_move_[ab].h5 ntypes.h5 dangle.h5 + tmisc14.h5 set_extent_read.h5 set_extent_create.h5 getname.h5 \ + getname1.h5 getname2.h5 getname3.h5 sec2_file.h5 \ + family_file000[0-3][0-9].h5 multi_file-[rs].h5 core_file \ + new_move_[ab].h5 ntypes.h5 dangle.h5 CLEAN=$(TIMINGS) diff --git a/test/tmisc.c b/test/tmisc.c index 8884120..ba255ba 100644 --- a/test/tmisc.c +++ b/test/tmisc.c @@ -28,7 +28,7 @@ #include "testhdf5.h" /* Definitions for misc. test #1 */ -#define MISC1_FILE "tmisc.h5" +#define MISC1_FILE "tmisc1.h5" #define MISC1_VAL (13417386) /* 0xccbbaa */ #define MISC1_VAL2 (15654348) /* 0xeeddcc */ #define MISC1_DSET_NAME "/scalar_set" @@ -184,6 +184,13 @@ typedef struct unsigned m13_data[MISC13_DIM1][MISC13_DIM2]; /* Data to write to dataset */ unsigned m13_rdata[MISC13_DIM1][MISC13_DIM2]; /* Data read from dataset */ +/* Definitions for misc. test #14 */ +#define MISC14_FILE "tmisc14.h5" +#define MISC14_DSET1_NAME "Dataset1" +#define MISC14_DSET2_NAME "Dataset2" +#define MISC14_DSET3_NAME "Dataset3" +#define MISC14_METADATA_SIZE 4096 + /**************************************************************** ** ** test_misc1(): test unlinking a dataset from a group and immediately @@ -2330,7 +2337,231 @@ test_misc13(void) /* Verify file contents are still correct */ verify_file(MISC13_FILE_2,(hsize_t)MISC13_USERBLOCK_SIZE,1); -} +} /* end test_misc13() */ + +/**************************************************************** +** +** test_misc14(): Test that file contents can be "slid down" by +** inserting a user block in front of an existing file. +** +****************************************************************/ +static void +test_misc14(void) +{ + hid_t file_id; /* File ID */ + hid_t fapl; /* File access property list ID */ + hid_t DataSpace; /* Dataspace ID */ + hid_t Dataset1; /* Dataset ID #1 */ + hid_t Dataset2; /* Dataset ID #2 */ + hid_t Dataset3; /* Dataset ID #3 */ + double data1 = 5.0; /* Data to write for dataset #1 */ + double data2 = 10.0; /* Data to write for dataset #2 */ + double data3 = 15.0; /* Data to write for dataset #3 */ + double rdata; /* Data read in */ + herr_t ret; /* Generic return value */ + + /* Test creating two datasets and deleting the second */ + + /* Increase the metadata block size */ + /* (This makes certain that all the data blocks are allocated together) */ + fapl=H5Pcreate(H5P_FILE_ACCESS); + CHECK(fapl, FAIL, "H5Pcreate"); + + ret=H5Pset_meta_block_size(fapl,(hsize_t)MISC14_METADATA_SIZE); + CHECK(ret, FAIL, "H5Pset_meta_block_size"); + + /* Create dataspace to use */ + DataSpace = H5Screate(H5S_SCALAR); + CHECK(DataSpace, FAIL, "H5Screate"); + + /* Open the file */ + file_id = H5Fcreate(MISC14_FILE, H5F_ACC_TRUNC, H5P_DEFAULT, fapl); + CHECK(file_id, FAIL, "H5Fcreate"); + + /* Create first dataset & write data */ + Dataset1 = H5Dcreate(file_id, MISC14_DSET1_NAME, H5T_NATIVE_DOUBLE, DataSpace, H5P_DEFAULT); + CHECK(Dataset1, FAIL, "H5Dcreate"); + + ret = H5Dwrite(Dataset1, H5T_NATIVE_DOUBLE, H5S_ALL, H5S_ALL, H5P_DEFAULT, &data1); + CHECK(ret, FAIL, "H5Dwrite"); + + /* Create second dataset (to be unlinked). */ + Dataset2 = H5Dcreate(file_id, MISC14_DSET2_NAME, H5T_NATIVE_DOUBLE, DataSpace, H5P_DEFAULT); + CHECK(Dataset2, FAIL, "H5Dcreate"); + + ret = H5Dwrite(Dataset2, H5T_NATIVE_DOUBLE, H5S_ALL, H5S_ALL, H5P_DEFAULT, &data2); + CHECK(ret, FAIL, "H5Dwrite"); + + /* Check data from first dataset */ + ret = H5Dread(Dataset1, H5T_NATIVE_DOUBLE, H5S_ALL, H5S_ALL, H5P_DEFAULT, &rdata); + CHECK(ret, FAIL, "H5Dread"); + if(rdata!=data1) { + num_errs++; + printf("Error on line %d: data1!=rdata\n",__LINE__); + } /* end if */ + + /* Unlink second dataset */ + ret = H5Gunlink(file_id, MISC14_DSET2_NAME); + CHECK(ret, FAIL, "H5Gunlink"); + + /* Close second dataset */ + ret = H5Dclose(Dataset2); + CHECK(ret, FAIL, "H5Dclose"); + + /* Verify the data from dataset #1 */ + ret = H5Dread(Dataset1, H5T_NATIVE_DOUBLE, H5S_ALL, H5S_ALL, H5P_DEFAULT, &rdata); + CHECK(ret, FAIL, "H5Dread"); + if(rdata!=data1) { + num_errs++; + printf("Error on line %d: data1!=rdata\n",__LINE__); + } /* end if */ + + /* Close first dataset */ + ret = H5Dclose(Dataset1); + CHECK(ret, FAIL, "H5Dclose"); + + /* Close the file */ + ret = H5Fclose (file_id); + CHECK(ret, FAIL, "H5Fclose"); + + /* Test creating two datasets and deleting the first */ + + /* Open the file */ + file_id = H5Fcreate(MISC14_FILE, H5F_ACC_TRUNC, H5P_DEFAULT, fapl); + CHECK(file_id, FAIL, "H5Fcreate"); + + /* Create first dataset & write data */ + Dataset1 = H5Dcreate(file_id, MISC14_DSET1_NAME, H5T_NATIVE_DOUBLE, DataSpace, H5P_DEFAULT); + CHECK(Dataset1, FAIL, "H5Dcreate"); + + ret = H5Dwrite(Dataset1, H5T_NATIVE_DOUBLE, H5S_ALL, H5S_ALL, H5P_DEFAULT, &data1); + CHECK(ret, FAIL, "H5Dwrite"); + + /* Create second dataset */ + Dataset2 = H5Dcreate(file_id, MISC14_DSET2_NAME, H5T_NATIVE_DOUBLE, DataSpace, H5P_DEFAULT); + CHECK(Dataset2, FAIL, "H5Dcreate"); + + ret = H5Dwrite(Dataset2, H5T_NATIVE_DOUBLE, H5S_ALL, H5S_ALL, H5P_DEFAULT, &data2); + CHECK(ret, FAIL, "H5Dwrite"); + + /* Check data from second dataset */ + ret = H5Dread(Dataset2, H5T_NATIVE_DOUBLE, H5S_ALL, H5S_ALL, H5P_DEFAULT, &rdata); + CHECK(ret, FAIL, "H5Dread"); + if(rdata!=data2) { + num_errs++; + printf("Error on line %d: data2!=rdata\n",__LINE__); + } /* end if */ + + /* Unlink first dataset */ + ret = H5Gunlink(file_id, MISC14_DSET1_NAME); + CHECK(ret, FAIL, "H5Gunlink"); + + /* Close first dataset */ + ret = H5Dclose(Dataset1); + CHECK(ret, FAIL, "H5Dclose"); + + /* Verify the data from dataset #2 */ + ret = H5Dread(Dataset2, H5T_NATIVE_DOUBLE, H5S_ALL, H5S_ALL, H5P_DEFAULT, &rdata); + CHECK(ret, FAIL, "H5Dread"); + if(rdata!=data2) { + num_errs++; + printf("Error on line %d: data2!=rdata\n",__LINE__); + } /* end if */ + + /* Close second dataset */ + ret = H5Dclose(Dataset2); + CHECK(ret, FAIL, "H5Dclose"); + + /* Close the file */ + ret = H5Fclose (file_id); + CHECK(ret, FAIL, "H5Fclose"); + + /* Test creating three datasets and deleting the second */ + + /* Open the file */ + file_id = H5Fcreate(MISC14_FILE, H5F_ACC_TRUNC, H5P_DEFAULT, fapl); + CHECK(file_id, FAIL, "H5Fcreate"); + + /* Create first dataset & write data */ + Dataset1 = H5Dcreate(file_id, MISC14_DSET1_NAME, H5T_NATIVE_DOUBLE, DataSpace, H5P_DEFAULT); + CHECK(Dataset1, FAIL, "H5Dcreate"); + + ret = H5Dwrite(Dataset1, H5T_NATIVE_DOUBLE, H5S_ALL, H5S_ALL, H5P_DEFAULT, &data1); + CHECK(ret, FAIL, "H5Dwrite"); + + /* Create second dataset */ + Dataset2 = H5Dcreate(file_id, MISC14_DSET2_NAME, H5T_NATIVE_DOUBLE, DataSpace, H5P_DEFAULT); + CHECK(Dataset2, FAIL, "H5Dcreate"); + + ret = H5Dwrite(Dataset2, H5T_NATIVE_DOUBLE, H5S_ALL, H5S_ALL, H5P_DEFAULT, &data2); + CHECK(ret, FAIL, "H5Dwrite"); + + /* Create third dataset */ + Dataset3 = H5Dcreate(file_id, MISC14_DSET3_NAME, H5T_NATIVE_DOUBLE, DataSpace, H5P_DEFAULT); + CHECK(Dataset2, FAIL, "H5Dcreate"); + + ret = H5Dwrite(Dataset3, H5T_NATIVE_DOUBLE, H5S_ALL, H5S_ALL, H5P_DEFAULT, &data3); + CHECK(ret, FAIL, "H5Dwrite"); + + /* Check data from first dataset */ + ret = H5Dread(Dataset1, H5T_NATIVE_DOUBLE, H5S_ALL, H5S_ALL, H5P_DEFAULT, &rdata); + CHECK(ret, FAIL, "H5Dread"); + if(rdata!=data1) { + num_errs++; + printf("Error on line %d: data1!=rdata\n",__LINE__); + } /* end if */ + + /* Check data from third dataset */ + ret = H5Dread(Dataset3, H5T_NATIVE_DOUBLE, H5S_ALL, H5S_ALL, H5P_DEFAULT, &rdata); + CHECK(ret, FAIL, "H5Dread"); + if(rdata!=data3) { + num_errs++; + printf("Error on line %d: data3!=rdata\n",__LINE__); + } /* end if */ + + /* Unlink second dataset */ + ret = H5Gunlink(file_id, MISC14_DSET2_NAME); + CHECK(ret, FAIL, "H5Gunlink"); + + /* Close second dataset */ + ret = H5Dclose(Dataset2); + CHECK(ret, FAIL, "H5Dclose"); + + /* Verify the data from dataset #1 */ + ret = H5Dread(Dataset1, H5T_NATIVE_DOUBLE, H5S_ALL, H5S_ALL, H5P_DEFAULT, &rdata); + CHECK(ret, FAIL, "H5Dread"); + if(rdata!=data1) { + num_errs++; + printf("Error on line %d: data1!=rdata\n",__LINE__); + } /* end if */ + + /* Verify the data from dataset #3 */ + ret = H5Dread(Dataset3, H5T_NATIVE_DOUBLE, H5S_ALL, H5S_ALL, H5P_DEFAULT, &rdata); + CHECK(ret, FAIL, "H5Dread"); + if(rdata!=data3) { + num_errs++; + printf("Error on line %d: data3!=rdata\n",__LINE__); + } /* end if */ + + /* Close first dataset */ + ret = H5Dclose(Dataset1); + CHECK(ret, FAIL, "H5Dclose"); + + /* Close third dataset */ + ret = H5Dclose(Dataset3); + CHECK(ret, FAIL, "H5Dclose"); + + /* Close the file */ + ret = H5Fclose (file_id); + CHECK(ret, FAIL, "H5Fclose"); + + /* Close shared objects (dataspace & fapl) */ + ret = H5Sclose (DataSpace); + CHECK(ret, FAIL, "H5Sclose"); + ret = H5Pclose (fapl); + CHECK(ret, FAIL, "H5Pclose"); + +} /* end test_misc14() */ /**************************************************************** ** @@ -2356,6 +2587,7 @@ test_misc(void) test_misc11(); /* Test for all properties of a file creation property list being stored */ test_misc12(); /* Test VL-strings in chunked datasets operating correctly */ test_misc13(); /* Test that a user block can be insert in front of file contents */ + test_misc14(); /* Test that deleted dataset's data is removed from sieve buffer correctly */ } /* test_misc() */ @@ -2393,4 +2625,5 @@ cleanup_misc(void) HDremove(MISC12_FILE); HDremove(MISC13_FILE_1); HDremove(MISC13_FILE_2); + HDremove(MISC14_FILE); } |