diff options
| -rw-r--r-- | src/H5F.c | 21 | ||||
| -rw-r--r-- | src/H5FDdpss.c | 36 | ||||
| -rw-r--r-- | src/H5FDfamily.c | 1 | ||||
| -rw-r--r-- | src/H5FDgass.c | 37 | ||||
| -rw-r--r-- | src/H5FDlog.c | 1 | ||||
| -rw-r--r-- | src/H5FDmulti.c | 32 | ||||
| -rw-r--r-- | src/H5FDpublic.h | 10 | ||||
| -rw-r--r-- | src/H5FDsec2.c | 1 | ||||
| -rw-r--r-- | src/H5FDsrb.c | 36 | ||||
| -rw-r--r-- | src/H5FDstdio.c | 1 | ||||
| -rw-r--r-- | src/H5FDstream.c | 36 | ||||
| -rw-r--r-- | src/H5Farray.c | 298 | ||||
| -rw-r--r-- | src/H5Fprivate.h | 11 | ||||
| -rw-r--r-- | src/H5P.c | 84 | ||||
| -rw-r--r-- | src/H5Ppublic.h | 2 |
15 files changed, 580 insertions, 27 deletions
@@ -264,6 +264,7 @@ H5F_init_interface(void) H5F_access_dflt.alignment = 1; /*no alignment*/ H5F_access_dflt.gc_ref = 0; /*don't garbage-collect references*/ H5F_access_dflt.meta_block_size = 2048; /* set metadata block allocations to 2KB */ + H5F_access_dflt.sieve_buf_size = 64*1024; /* set sieve buffer allocation to 64KB */ H5F_access_dflt.driver_id = H5FD_SEC2; /*default driver*/ H5F_access_dflt.driver_info = NULL; /*driver file access properties*/ @@ -522,6 +523,7 @@ H5Fget_access_plist(hid_t file_id) _fapl.alignment = f->shared->alignment; _fapl.gc_ref = f->shared->gc_ref; _fapl.meta_block_size = f->shared->lf->def_meta_block_size; + _fapl.sieve_buf_size = f->shared->sieve_buf_size; _fapl.driver_id = f->shared->lf->driver_id; _fapl.driver_info = NULL; /*just for now */ @@ -761,6 +763,7 @@ H5F_new(H5F_file_t *shared, hid_t fcpl_id, hid_t fapl_id) f->shared->threshold = fapl->threshold; f->shared->alignment = fapl->alignment; f->shared->gc_ref = fapl->gc_ref; + f->shared->sieve_buf_size = fapl->sieve_buf_size; #ifdef H5_HAVE_PARALLEL /* @@ -854,6 +857,12 @@ H5F_dest(H5F_t *f) } f->shared->cwfs = H5MM_xfree (f->shared->cwfs); + /* Free the data sieve buffer, if it's been allocated */ + if(f->shared->sieve_buf) { + assert(f->shared->sieve_dirty==0); /* The buffer had better be flushed... */ + f->shared->sieve_buf = H5MM_xfree (f->shared->sieve_buf); + } /* end if */ + /* Destroy file creation properties */ H5P_close(f->shared->fcpl); @@ -1670,6 +1679,18 @@ H5F_flush(H5F_t *f, H5F_scope_t scope, hbool_t invalidate, } } + /* flush the data sieve buffer, if we have a dirty one */ + if(!alloc_only && f->shared->sieve_buf && f->shared->sieve_dirty) { + /* Write dirty data sieve buffer to file */ + if (H5F_block_write(f, H5FD_MEM_DRAW, f->shared->sieve_loc, f->shared->sieve_size, H5P_DEFAULT, f->shared->sieve_buf)<0) { + HRETURN_ERROR(H5E_IO, H5E_WRITEERROR, FAIL, + "block write failed"); + } + + /* Reset sieve buffer dirty flag */ + f->shared->sieve_dirty=0; + } /* end if */ + /* flush the entire raw data cache */ if (!alloc_only && H5F_istore_flush (f, invalidate)<0) { HRETURN_ERROR(H5E_CACHE, H5E_CANTFLUSH, FAIL, diff --git a/src/H5FDdpss.c b/src/H5FDdpss.c index 7a03ffe..26ede02 100644 --- a/src/H5FDdpss.c +++ b/src/H5FDdpss.c @@ -114,6 +114,7 @@ typedef struct H5FD_dpss_t { static H5FD_t *H5FD_dpss_open (const char *name, unsigned flags, hid_t UNUSED fapl_id, haddr_t maxaddr); static herr_t H5FD_dpss_close (H5FD_t *_file); +static herr_t H5FD_dpss_query(const H5FD_t *_f1, unsigned long *flags); static haddr_t H5FD_dpss_get_eoa (H5FD_t *_file); static herr_t H5FD_dpss_set_eoa (H5FD_t *_file, haddr_t addr); static haddr_t H5FD_dpss_get_eof (H5FD_t *_file); @@ -139,7 +140,7 @@ static const H5FD_class_t H5FD_dpss_g = { H5FD_dpss_open, /* open */ H5FD_dpss_close, /* close */ NULL, /* cmp */ - NULL, /*query */ + H5FD_dpss_query, /*query */ NULL, /* alloc */ NULL, /* free */ H5FD_dpss_get_eoa, /* get_eoa */ @@ -394,6 +395,39 @@ H5FD_dpss_close (H5FD_t *_file) /*------------------------------------------------------------------------- + * Function: H5FD_dpss_query + * + * Purpose: Set the flags that this VFL driver is capable of supporting. + * (listed in H5FDpublic.h) + * + * Return: Success: non-negative + * + * Failure: negative + * + * Programmer: Quincey Koziol + * Tuesday, September 26, 2000 + * + * Modifications: + * + *------------------------------------------------------------------------- + */ +static herr_t +H5FD_dpss_query(const UNUSED H5FD_t *_f, unsigned long *flags /* out */) +{ + herr_t ret_value=SUCCEED; + + FUNC_ENTER(H5FD_dpss_query, FAIL); + + /* Set the VFL feature flags that this driver supports */ + if(flags) { + *flags|=H5FD_FEAT_DATA_SIEVE; /* OK to perform data sieving for faster raw data reads & writes */ + } /* end if */ + + FUNC_LEAVE(ret_value); +} + + +/*------------------------------------------------------------------------- * Function: H5FD_dpss_get_eoa * * Purpose: Gets the end-of-address marker for the file. The EOA marker diff --git a/src/H5FDfamily.c b/src/H5FDfamily.c index 1c456a4..6f12863 100644 --- a/src/H5FDfamily.c +++ b/src/H5FDfamily.c @@ -637,6 +637,7 @@ H5FD_family_query(const UNUSED H5FD_t *_f, unsigned long *flags /* out */) if(flags) { *flags|=H5FD_FEAT_AGGREGATE_METADATA; /* OK to aggregate metadata allocations */ *flags|=H5FD_FEAT_ACCUMULATE_METADATA; /* OK to accumulate metadata for faster writes */ + *flags|=H5FD_FEAT_DATA_SIEVE; /* OK to perform data sieving for faster raw data reads & writes */ } /* end if */ FUNC_LEAVE(ret_value); diff --git a/src/H5FDgass.c b/src/H5FDgass.c index e500d8e..7d8ac9c 100644 --- a/src/H5FDgass.c +++ b/src/H5FDgass.c @@ -100,6 +100,7 @@ typedef struct H5FD_gass_t { static H5FD_t *H5FD_gass_open(const char *name, unsigned flags, hid_t fapl_id, haddr_t maxaddr); static herr_t H5FD_gass_close(H5FD_t *_file); +static herr_t H5FD_gass_query(const H5FD_t *_f1, unsigned long *flags); static haddr_t H5FD_gass_get_eoa(H5FD_t *_file); static herr_t H5FD_gass_set_eoa(H5FD_t *_file, haddr_t addr); static haddr_t H5FD_gass_get_eof(H5FD_t *_file); @@ -129,8 +130,8 @@ static const H5FD_class_t H5FD_gass_g = { NULL, /*dxpl_free */ H5FD_gass_open, /*open */ H5FD_gass_close, /*close */ - NULL, /*query */ NULL, /*cmp */ + H5FD_gass_query, /*query */ NULL, /*alloc */ NULL, /*free */ H5FD_gass_get_eoa, /*get_eoa */ @@ -432,6 +433,40 @@ H5FD_gass_close (H5FD_t *_file) } + +/*------------------------------------------------------------------------- + * Function: H5FD_gass_query + * + * Purpose: Set the flags that this VFL driver is capable of supporting. + * (listed in H5FDpublic.h) + * + * Return: Success: non-negative + * + * Failure: negative + * + * Programmer: Quincey Koziol + * Tuesday, September 26, 2000 + * + * Modifications: + * + *------------------------------------------------------------------------- + */ +static herr_t +H5FD_gass_query(const UNUSED H5FD_t *_f, unsigned long *flags /* out */) +{ + herr_t ret_value=SUCCEED; + + FUNC_ENTER(H5FD_gass_query, FAIL); + + /* Set the VFL feature flags that this driver supports */ + if(flags) { + *flags|=H5FD_FEAT_DATA_SIEVE; /* OK to perform data sieving for faster raw data reads & writes */ + } /* end if */ + + FUNC_LEAVE(ret_value); +} + + /*------------------------------------------------------------------------- * Function: H5FD_gass_get_eoa * diff --git a/src/H5FDlog.c b/src/H5FDlog.c index 148f3ef..1fc7c5c 100644 --- a/src/H5FDlog.c +++ b/src/H5FDlog.c @@ -646,6 +646,7 @@ H5FD_log_query(const UNUSED H5FD_t *_f, unsigned long *flags /* out */) if(flags) { *flags|=H5FD_FEAT_AGGREGATE_METADATA; /* OK to aggregate metadata allocations */ *flags|=H5FD_FEAT_ACCUMULATE_METADATA; /* OK to accumulate metadata for faster writes */ + *flags|=H5FD_FEAT_DATA_SIEVE; /* OK to perform data sieving for faster raw data reads & writes */ } /* end if */ FUNC_LEAVE(ret_value); diff --git a/src/H5FDmulti.c b/src/H5FDmulti.c index b77a695..68fa26a 100644 --- a/src/H5FDmulti.c +++ b/src/H5FDmulti.c @@ -115,6 +115,7 @@ static H5FD_t *H5FD_multi_open(const char *name, unsigned flags, hid_t fapl_id, haddr_t maxaddr); static herr_t H5FD_multi_close(H5FD_t *_file); static int H5FD_multi_cmp(const H5FD_t *_f1, const H5FD_t *_f2); +static herr_t H5FD_multi_query(const H5FD_t *_f1, unsigned long *flags); static haddr_t H5FD_multi_get_eoa(H5FD_t *_file); static herr_t H5FD_multi_set_eoa(H5FD_t *_file, haddr_t eoa); static haddr_t H5FD_multi_get_eof(H5FD_t *_file); @@ -144,7 +145,7 @@ static const H5FD_class_t H5FD_multi_g = { H5FD_multi_open, /*open */ H5FD_multi_close, /*close */ H5FD_multi_cmp, /*cmp */ - NULL, /*query */ + H5FD_multi_query, /*query */ H5FD_multi_alloc, /*alloc */ H5FD_multi_free, /*free */ H5FD_multi_get_eoa, /*get_eoa */ @@ -1300,6 +1301,35 @@ H5FD_multi_cmp(const H5FD_t *_f1, const H5FD_t *_f2) /*------------------------------------------------------------------------- + * Function: H5FD_multi_query + * + * Purpose: Set the flags that this VFL driver is capable of supporting. + * (listed in H5FDpublic.h) + * + * Return: Success: non-negative + * + * Failure: negative + * + * Programmer: Quincey Koziol + * Tuesday, September 26, 2000 + * + * Modifications: + * + *------------------------------------------------------------------------- + */ +static herr_t +H5FD_multi_query(const H5FD_t *_f, unsigned long *flags /* out */) +{ + /* Set the VFL feature flags that this driver supports */ + if(flags) { + *flags|=H5FD_FEAT_DATA_SIEVE; /* OK to perform data sieving for faster raw data reads & writes */ + } /* end if */ + + return(0); +} + + +/*------------------------------------------------------------------------- * Function: H5FD_multi_get_eoa * * Purpose: Returns the end-of-address marker for the file. The EOA diff --git a/src/H5FDpublic.h b/src/H5FDpublic.h index 8971590..b1185fa 100644 --- a/src/H5FDpublic.h +++ b/src/H5FDpublic.h @@ -75,7 +75,7 @@ typedef enum H5FD_mem_t { /* Define VFL driver features that can be enabled on a per-driver basis */ -/* These are returned queried with the 'query' function pointer in H5FD_class_t */ +/* These are returned with the 'query' function pointer in H5FD_class_t */ /* * Defining the H5FD_FEAT_AGGREGATE_METADATA for a VFL driver means that * the library will attempt to allocate a larger block for metadata and @@ -89,6 +89,14 @@ typedef enum H5FD_mem_t { * 'write' routine. */ #define H5FD_FEAT_ACCUMULATE_METADATA 0x00000002 + /* + * Defining the H5FD_FEAT_DATA_SIEVE for a VFL driver means that + * the library will attempt to cache raw data as it is read from/written to + * a file in a "data seive" buffer. See Rajeev Thakur's papers: + * http://www.mcs.anl.gov/~thakur/papers/romio-coll.ps.gz + * http://www.mcs.anl.gov/~thakur/papers/mpio-high-perf.ps.gz + */ +#define H5FD_FEAT_DATA_SIEVE 0x00000004 /* Forward declaration */ diff --git a/src/H5FDsec2.c b/src/H5FDsec2.c index 6222964..ee38f55 100644 --- a/src/H5FDsec2.c +++ b/src/H5FDsec2.c @@ -416,6 +416,7 @@ H5FD_sec2_query(const UNUSED H5FD_t *_f, unsigned long *flags /* out */) if(flags) { *flags|=H5FD_FEAT_AGGREGATE_METADATA; /* OK to aggregate metadata allocations */ *flags|=H5FD_FEAT_ACCUMULATE_METADATA; /* OK to accumulate metadata for faster writes */ + *flags|=H5FD_FEAT_DATA_SIEVE; /* OK to perform data sieving for faster raw data reads & writes */ } /* end if */ FUNC_LEAVE(ret_value); diff --git a/src/H5FDsrb.c b/src/H5FDsrb.c index af75b1e..bfc5f13 100644 --- a/src/H5FDsrb.c +++ b/src/H5FDsrb.c @@ -56,6 +56,7 @@ static hid_t H5FD_SRB_g = 0; static H5FD_t *H5FD_srb_open(const char *name, unsigned flags, hid_t fapl_id, haddr_t maxaddr); static herr_t H5FD_srb_close(H5FD_t *_file); +static herr_t H5FD_srb_query(const H5FD_t *_f1, unsigned long *flags); static haddr_t H5FD_srb_get_eoa(H5FD_t *_file); static herr_t H5FD_srb_set_eoa(H5FD_t *_file, haddr_t addr); static haddr_t H5FD_srb_get_eof(H5FD_t *_file); @@ -99,7 +100,7 @@ static const H5FD_class_t H5FD_srb_g = { H5FD_srb_open, /*open */ H5FD_srb_close, /*close */ NULL, /*cmp */ - NULL, /*query */ + H5FD_srb_query, /*query */ NULL, /*alloc */ NULL, /*free */ H5FD_srb_get_eoa, /*get_eoa */ @@ -361,6 +362,39 @@ H5FD_srb_close(H5FD_t *_file) FUNC_LEAVE(SUCCEED); } + +/*------------------------------------------------------------------------- + * Function: H5FD_srb_query + * + * Purpose: Set the flags that this VFL driver is capable of supporting. + * (listed in H5FDpublic.h) + * + * Return: Success: non-negative + * + * Failure: negative + * + * Programmer: Quincey Koziol + * Tuesday, September 26, 2000 + * + * Modifications: + * + *------------------------------------------------------------------------- + */ +static herr_t +H5FD_srb_query(const UNUSED H5FD_t *_f, unsigned long *flags /* out */) +{ + herr_t ret_value=SUCCEED; + + FUNC_ENTER(H5FD_srb_query, FAIL); + + /* Set the VFL feature flags that this driver supports */ + if(flags) { + *flags|=H5FD_FEAT_DATA_SIEVE; /* OK to perform data sieving for faster raw data reads & writes */ + } /* end if */ + + FUNC_LEAVE(ret_value); +} + /*------------------------------------------------------------------------- * Function: H5FD_srb_get_eoa * diff --git a/src/H5FDstdio.c b/src/H5FDstdio.c index 5461996..28b32a7 100644 --- a/src/H5FDstdio.c +++ b/src/H5FDstdio.c @@ -437,6 +437,7 @@ H5FD_stdio_query(const H5FD_t *_f, unsigned long *flags /* out */) if(flags) { *flags|=H5FD_FEAT_AGGREGATE_METADATA; /* OK to aggregate metadata allocations */ *flags|=H5FD_FEAT_ACCUMULATE_METADATA; /* OK to accumulate metadata for faster writes */ + *flags|=H5FD_FEAT_DATA_SIEVE; /* OK to perform data sieving for faster raw data reads & writes */ } /* end if */ return(0); diff --git a/src/H5FDstream.c b/src/H5FDstream.c index cd0e6e6..ba07ae4 100644 --- a/src/H5FDstream.c +++ b/src/H5FDstream.c @@ -108,6 +108,7 @@ static H5FD_t *H5FD_stream_open (const char *name, unsigned flags, hid_t fapl_id, haddr_t maxaddr); static herr_t H5FD_stream_flush (H5FD_t *_stream); static herr_t H5FD_stream_close (H5FD_t *_stream); +static herr_t H5FD_stream_query(const H5FD_t *_f1, unsigned long *flags); static haddr_t H5FD_stream_get_eoa (H5FD_t *_stream); static herr_t H5FD_stream_set_eoa (H5FD_t *_stream, haddr_t addr); static haddr_t H5FD_stream_get_eof (H5FD_t *_stream); @@ -134,8 +135,8 @@ static const H5FD_class_t H5FD_stream_g = NULL, /* dxpl_free */ H5FD_stream_open, /* open */ H5FD_stream_close, /* close */ - NULL, /* query */ NULL, /* cmp */ + H5FD_stream_query, /*query */ NULL, /* alloc */ NULL, /* free */ H5FD_stream_get_eoa, /* get_eoa */ @@ -753,6 +754,39 @@ static herr_t H5FD_stream_close (H5FD_t *_stream) /*------------------------------------------------------------------------- + * Function: H5FD_stream_query + * + * Purpose: Set the flags that this VFL driver is capable of supporting. + * (listed in H5FDpublic.h) + * + * Return: Success: non-negative + * + * Failure: negative + * + * Programmer: Quincey Koziol + * Tuesday, September 26, 2000 + * + * Modifications: + * + *------------------------------------------------------------------------- + */ +static herr_t +H5FD_stream_query(const UNUSED H5FD_t *_f, unsigned long *flags /* out */) +{ + herr_t ret_value=SUCCEED; + + FUNC_ENTER(H5FD_stream_query, FAIL); + + /* Set the VFL feature flags that this driver supports */ + if(flags) { + *flags|=H5FD_FEAT_DATA_SIEVE; /* OK to perform data sieving for faster raw data reads & writes */ + } /* end if */ + + FUNC_LEAVE(ret_value); +} + + +/*------------------------------------------------------------------------- * Function: H5FD_stream_get_eoa * * Purpose: Gets the end-of-address marker for the file. The EOA marker diff --git a/src/H5Farray.c b/src/H5Farray.c index db23acc..e581315 100644 --- a/src/H5Farray.c +++ b/src/H5Farray.c @@ -15,8 +15,10 @@ #include <H5Dprivate.h> #include <H5Eprivate.h> #include <H5Fprivate.h> +#include <H5FDprivate.h> /*file driver */ #include <H5Iprivate.h> #include <H5MFprivate.h> +#include <H5MMprivate.h> /*memory management */ #include <H5Oprivate.h> #include <H5Pprivate.h> #include <H5Vprivate.h> @@ -138,6 +140,7 @@ H5F_arr_read(H5F_t *f, hid_t dxpl_id, const struct H5O_layout_t *layout, size_t nelmts, z; /*number of elements */ intn ndims; /*stride dimensionality */ haddr_t addr; /*address in file */ + haddr_t eof; /*end of file address */ intn i, j; /*counters */ hbool_t carray; /*carry for subtraction */ #ifdef H5_HAVE_PARALLEL @@ -286,19 +289,147 @@ H5F_arr_read(H5F_t *f, hid_t dxpl_id, const struct H5O_layout_t *layout, z<nelmts; z++, xfer_parms->gather_reads--) { #else +#ifdef QAK +printf("%s: nelmts=%d, addr=%lu, elmt_size=%lu\n",FUNC,(int)nelmts,(unsigned long)addr,(unsigned long)elmt_size); +printf("%s: sieve_buf=%p, sieve_loc=%lu, sieve_size=%lu, sieve_buf_size=%lu, sieve_dirty=%u\n",FUNC,f->shared->sieve_buf,(unsigned long)f->shared->sieve_loc,(unsigned long)f->shared->sieve_size,(unsigned long)f->shared->sieve_buf_size,(unsigned)f->shared->sieve_dirty); +printf("%s: feature_flags=%lx\n",FUNC,(unsigned long)f->shared->lf->feature_flags); +#endif /* QAK */ for (z=0; z<nelmts; z++) { #endif - /* Read from file */ - if (efl && efl->nused>0) { - if (H5O_efl_read(f, efl, addr, elmt_size, buf)<0) { - HRETURN_ERROR(H5E_IO, H5E_READERROR, FAIL, - "external data read failed"); - } - } else if (H5F_block_read(f, addr, elmt_size, dxpl_id, buf)<0) { - HRETURN_ERROR(H5E_IO, H5E_READERROR, FAIL, - "block read failed"); - } + /* Read directly from file if the dataset is in an external file */ + /* Note: We can't use data sieve buffers for datasets in external files + * because the 'addr' of all external files is set to 0 (above) and + * all datasets in external files would alias to the same set of + * file offsets, totally mixing up the data sieve buffer information. -QAK + */ + if (efl && efl->nused>0) { + if (H5O_efl_read(f, efl, addr, elmt_size, buf)<0) { + HRETURN_ERROR(H5E_IO, H5E_READERROR, FAIL, + "external data read failed"); + } + } else { + /* Check if data sieving is enabled */ + if(f->shared->lf->feature_flags&H5FD_FEAT_DATA_SIEVE) { + /* Try reading from the data sieve buffer */ + if(f->shared->sieve_buf) { + /* If entire read is within the sieve buffer, read it from the buffer */ + if((addr>=f->shared->sieve_loc && addr<(f->shared->sieve_loc+f->shared->sieve_size)) + && ((addr+elmt_size-1)>=f->shared->sieve_loc && (addr+elmt_size-1)<(f->shared->sieve_loc+f->shared->sieve_size))) { + /* Grab the data out of the buffer */ + HDmemcpy(buf,f->shared->sieve_buf+(addr-f->shared->sieve_loc),elmt_size); + } /* end if */ + /* Entire request is not within this data sieve buffer */ + else { + /* Check if we can actually hold the I/O request in the sieve buffer */ + if(elmt_size>f->shared->sieve_buf_size) { + /* Check for any overlap with the current sieve buffer */ + if((f->shared->sieve_loc>=addr && f->shared->sieve_loc<(addr+elmt_size)) + || ((f->shared->sieve_loc+f->shared->sieve_size-1)>=addr && (f->shared->sieve_loc+f->shared->sieve_size-1)<(addr+elmt_size))) { + /* Flush the sieve buffer, if it's dirty */ + if(f->shared->sieve_dirty) { + /* Write to file */ + if (H5F_block_write(f, H5FD_MEM_DRAW, f->shared->sieve_loc, f->shared->sieve_size, dxpl_id, f->shared->sieve_buf)<0) { + HRETURN_ERROR(H5E_IO, H5E_WRITEERROR, FAIL, + "block write failed"); + } + + /* Reset sieve buffer dirty flag */ + f->shared->sieve_dirty=0; + } /* end if */ + } /* end if */ + + /* Read directly into the user's buffer */ + if (H5F_block_read(f, addr, elmt_size, dxpl_id, buf)<0) { + HRETURN_ERROR(H5E_IO, H5E_READERROR, FAIL, + "block read failed"); + } + } /* end if */ + /* Element size fits within the buffer size */ + else { + /* Flush the sieve buffer if it's dirty */ + if(f->shared->sieve_dirty) { + /* Write to file */ + if (H5F_block_write(f, H5FD_MEM_DRAW, f->shared->sieve_loc, f->shared->sieve_size, dxpl_id, f->shared->sieve_buf)<0) { + HRETURN_ERROR(H5E_IO, H5E_WRITEERROR, FAIL, + "block write failed"); + } + + /* Reset sieve buffer dirty flag */ + f->shared->sieve_dirty=0; + } /* end if */ + + /* Determine the new sieve buffer size & location */ + f->shared->sieve_loc=addr; + + /* Make certain we don't read off the end of the file */ + if (HADDR_UNDEF==(eof=H5FD_get_eof(f->shared->lf))) { + HRETURN_ERROR(H5E_FILE, H5E_CANTOPENFILE, NULL, + "unable to determine file size"); + } + f->shared->sieve_size=MIN(eof-addr,f->shared->sieve_buf_size); + + /* Read the new sieve buffer */ + if (H5F_block_read(f, f->shared->sieve_loc, f->shared->sieve_size, dxpl_id, f->shared->sieve_buf)<0) { + HRETURN_ERROR(H5E_IO, H5E_READERROR, FAIL, + "block read failed"); + } + + /* Reset sieve buffer dirty flag */ + f->shared->sieve_dirty=0; + + /* Grab the data out of the buffer (must be first piece of data in buffer ) */ + HDmemcpy(buf,f->shared->sieve_buf,elmt_size); + } /* end else */ + } /* end else */ + } /* end if */ + /* No data sieve buffer yet, go allocate one */ + else { + /* Check if we can actually hold the I/O request in the sieve buffer */ + if(elmt_size>f->shared->sieve_buf_size) { + if (H5F_block_read(f, addr, elmt_size, dxpl_id, buf)<0) { + HRETURN_ERROR(H5E_IO, H5E_READERROR, FAIL, + "block read failed"); + } + } /* end if */ + else { + /* Allocate room for the data sieve buffer */ + if (NULL==(f->shared->sieve_buf=H5MM_malloc(f->shared->sieve_buf_size))) { + HRETURN_ERROR(H5E_RESOURCE, H5E_NOSPACE, NULL, + "memory allocation failed"); + } + + /* Determine the new sieve buffer size & location */ + f->shared->sieve_loc=addr; + + /* Make certain we don't read off the end of the file */ + if (HADDR_UNDEF==(eof=H5FD_get_eof(f->shared->lf))) { + HRETURN_ERROR(H5E_FILE, H5E_CANTOPENFILE, NULL, + "unable to determine file size"); + } + f->shared->sieve_size=MIN(eof-addr,f->shared->sieve_buf_size); + + /* Read the new sieve buffer */ + if (H5F_block_read(f, f->shared->sieve_loc, f->shared->sieve_size, dxpl_id, f->shared->sieve_buf)<0) { + HRETURN_ERROR(H5E_IO, H5E_READERROR, FAIL, + "block read failed"); + } + + /* Reset sieve buffer dirty flag */ + f->shared->sieve_dirty=0; + + /* Grab the data out of the buffer (must be first piece of data in buffer ) */ + HDmemcpy(buf,f->shared->sieve_buf,elmt_size); + } /* end else */ + } /* end else */ + } /* end if */ + else { + if (H5F_block_read(f, addr, elmt_size, dxpl_id, buf)<0) { + HRETURN_ERROR(H5E_IO, H5E_READERROR, FAIL, + "block read failed"); + } + } /* end else */ + } /* end else */ /* Decrement indices and advance pointers */ for (j=ndims-1, carray=TRUE; j>=0 && carray; --j) { @@ -318,8 +449,7 @@ H5F_arr_read(H5F_t *f, hid_t dxpl_id, const struct H5O_layout_t *layout, */ if (efl && efl->nused>0) { HRETURN_ERROR(H5E_IO, H5E_UNSUPPORTED, FAIL, - "chunking and external files are mutually " - "exclusive"); + "chunking and external files are mutually exclusive"); } for (i=0; i<layout->ndims; i++) { if (0!=mem_offset[i] || hslab_size[i]!=mem_size[i]) { @@ -395,6 +525,7 @@ H5F_arr_write(H5F_t *f, hid_t dxpl_id, const struct H5O_layout_t *layout, size_t nelmts, z; /*number of elements */ intn ndims; /*dimensionality */ haddr_t addr; /*address in file */ + haddr_t eof; /*end of file address */ intn i, j; /*counters */ hbool_t carray; /*carry for subtraction */ #ifdef H5_HAVE_PARALLEL @@ -535,14 +666,141 @@ H5F_arr_write(H5F_t *f, hid_t dxpl_id, const struct H5O_layout_t *layout, /* Write to file */ if (efl && efl->nused>0) { - if (H5O_efl_write(f, efl, addr, elmt_size, buf)<0) { - HRETURN_ERROR(H5E_IO, H5E_READERROR, FAIL, - "external data write failed"); - } - } else if (H5F_block_write(f, H5FD_MEM_DRAW, addr, elmt_size, dxpl_id, buf)<0) { - HRETURN_ERROR(H5E_IO, H5E_WRITEERROR, FAIL, - "block write failed"); - } + if (H5O_efl_write(f, efl, addr, elmt_size, buf)<0) { + HRETURN_ERROR(H5E_IO, H5E_READERROR, FAIL, + "external data write failed"); + } + } else { + /* Check if data sieving is enabled */ + if(f->shared->lf->feature_flags&H5FD_FEAT_DATA_SIEVE) { + /* Try writing to the data sieve buffer */ + if(f->shared->sieve_buf) { + /* If entire write is within the sieve buffer, write it to the buffer */ + if((addr>=f->shared->sieve_loc && addr<(f->shared->sieve_loc+f->shared->sieve_size)) + && ((addr+elmt_size-1)>=f->shared->sieve_loc && (addr+elmt_size-1)<(f->shared->sieve_loc+f->shared->sieve_size))) { + /* Grab the data out of the buffer */ + HDmemcpy(f->shared->sieve_buf+(addr-f->shared->sieve_loc),buf,elmt_size); + + /* Set sieve buffer dirty flag */ + f->shared->sieve_dirty=1; + + } /* end if */ + /* Entire request is not within this data sieve buffer */ + else { + /* Check if we can actually hold the I/O request in the sieve buffer */ + if(elmt_size>f->shared->sieve_buf_size) { + /* Check for any overlap with the current sieve buffer */ + if((f->shared->sieve_loc>=addr && f->shared->sieve_loc<(addr+elmt_size)) + || ((f->shared->sieve_loc+f->shared->sieve_size-1)>=addr && (f->shared->sieve_loc+f->shared->sieve_size-1)<(addr+elmt_size))) { + /* Flush the sieve buffer, if it's dirty */ + if(f->shared->sieve_dirty) { + /* Write to file */ + if (H5F_block_write(f, H5FD_MEM_DRAW, f->shared->sieve_loc, f->shared->sieve_size, dxpl_id, f->shared->sieve_buf)<0) { + HRETURN_ERROR(H5E_IO, H5E_WRITEERROR, FAIL, + "block write failed"); + } + + /* Reset sieve buffer dirty flag */ + f->shared->sieve_dirty=0; + } /* end if */ + + /* Force the sieve buffer to be re-read the next time */ + f->shared->sieve_loc=HADDR_UNDEF; + f->shared->sieve_size=0; + } /* end if */ + + /* Write directly from the user's buffer */ + if (H5F_block_write(f, H5FD_MEM_DRAW, addr, elmt_size, dxpl_id, buf)<0) { + HRETURN_ERROR(H5E_IO, H5E_WRITEERROR, FAIL, + "block write failed"); + } + } /* end if */ + /* Element size fits within the buffer size */ + else { + /* Flush the sieve buffer if it's dirty */ + if(f->shared->sieve_dirty) { + /* Write to file */ + if (H5F_block_write(f, H5FD_MEM_DRAW, f->shared->sieve_loc, f->shared->sieve_size, dxpl_id, f->shared->sieve_buf)<0) { + HRETURN_ERROR(H5E_IO, H5E_WRITEERROR, FAIL, + "block write failed"); + } + + /* Reset sieve buffer dirty flag */ + f->shared->sieve_dirty=0; + } /* end if */ + + /* Determine the new sieve buffer size & location */ + f->shared->sieve_loc=addr; + + /* Make certain we don't read off the end of the file */ + if (HADDR_UNDEF==(eof=H5FD_get_eof(f->shared->lf))) { + HRETURN_ERROR(H5E_FILE, H5E_CANTOPENFILE, NULL, + "unable to determine file size"); + } + f->shared->sieve_size=MIN(eof-addr,f->shared->sieve_buf_size); + + /* Read the new sieve buffer */ + if (H5F_block_read(f, f->shared->sieve_loc, f->shared->sieve_size, dxpl_id, f->shared->sieve_buf)<0) { + HRETURN_ERROR(H5E_IO, H5E_READERROR, FAIL, + "block read failed"); + } + + /* Grab the data out of the buffer (must be first piece of data in buffer) */ + HDmemcpy(f->shared->sieve_buf,buf,elmt_size); + + /* Set sieve buffer dirty flag */ + f->shared->sieve_dirty=1; + + } /* end else */ + } /* end else */ + } /* end if */ + /* No data sieve buffer yet, go allocate one */ + else { + /* Check if we can actually hold the I/O request in the sieve buffer */ + if(elmt_size>f->shared->sieve_buf_size) { + if (H5F_block_write(f, H5FD_MEM_DRAW, addr, elmt_size, dxpl_id, buf)<0) { + HRETURN_ERROR(H5E_IO, H5E_WRITEERROR, FAIL, + "block write failed"); + } + } /* end if */ + else { + /* Allocate room for the data sieve buffer */ + if (NULL==(f->shared->sieve_buf=H5MM_malloc(f->shared->sieve_buf_size))) { + HRETURN_ERROR(H5E_RESOURCE, H5E_NOSPACE, NULL, + "memory allocation failed"); + } + + /* Determine the new sieve buffer size & location */ + f->shared->sieve_loc=addr; + + /* Make certain we don't read off the end of the file */ + if (HADDR_UNDEF==(eof=H5FD_get_eof(f->shared->lf))) { + HRETURN_ERROR(H5E_FILE, H5E_CANTOPENFILE, NULL, + "unable to determine file size"); + } + f->shared->sieve_size=MIN(eof-addr,f->shared->sieve_buf_size); + + /* Read the new sieve buffer */ + if (H5F_block_read(f, f->shared->sieve_loc, f->shared->sieve_size, dxpl_id, f->shared->sieve_buf)<0) { + HRETURN_ERROR(H5E_IO, H5E_READERROR, FAIL, + "block read failed"); + } + + /* Grab the data out of the buffer (must be first piece of data in buffer) */ + HDmemcpy(f->shared->sieve_buf,buf,elmt_size); + + /* Set sieve buffer dirty flag */ + f->shared->sieve_dirty=1; + } /* end else */ + } /* end else */ + } /* end if */ + else { + if (H5F_block_write(f, H5FD_MEM_DRAW, addr, elmt_size, dxpl_id, buf)<0) { + HRETURN_ERROR(H5E_IO, H5E_WRITEERROR, FAIL, + "block write failed"); + } + } /* end else */ + } /* end else */ /* Decrement indices and advance pointers */ for (j=ndims-1, carray=TRUE; j>=0 && carray; --j) { diff --git a/src/H5Fprivate.h b/src/H5Fprivate.h index 19b65b4..e8e36e4 100644 --- a/src/H5Fprivate.h +++ b/src/H5Fprivate.h @@ -254,7 +254,8 @@ typedef struct H5F_access_t { double rdcc_w0; /* Preempt read chunks first? [0.0..1.0]*/ hsize_t threshold; /* Threshold for alignment */ hsize_t alignment; /* Alignment */ - size_t meta_block_size; /* Minimum metadata allocation block size (when aggregating metadata allocations */ + size_t meta_block_size; /* Minimum metadata allocation block size (when aggregating metadata allocations) */ + hsize_t sieve_buf_size; /* Maximum sieve buffer size (when data sieving is allowed by file driver) */ uintn gc_ref; /* Garbage-collect references? */ hid_t driver_id; /* File driver ID */ void *driver_info; /* File driver specific information */ @@ -328,6 +329,14 @@ typedef struct H5F_file_t { struct H5G_t *root_grp; /* Open root group */ intn ncwfs; /* Num entries on cwfs list */ struct H5HG_heap_t **cwfs; /* Global heap cache */ + + /* Data Sieve Buffering fields */ + unsigned char *sieve_buf; /* Buffer to hold data sieve buffer */ + haddr_t sieve_loc; /* File location (offset) of the data sieve buffer */ + hsize_t sieve_size; /* Size of the data sieve buffer used (in bytes) */ + hsize_t sieve_buf_size; /* Size of the data sieve buffer allocated (in bytes) */ + unsigned sieve_dirty; /* Flag to indicate that the data sieve buffer is dirty */ + H5F_rdcc_t rdcc; /* Raw data chunk cache */ } H5F_file_t; @@ -2991,6 +2991,90 @@ H5Pget_meta_block_size(hid_t fapl_id, hsize_t *size/*out*/) } +/*------------------------------------------------------------------------- + * Function: H5Pset_sieve_buf_size + * + * Purpose: Sets the maximum size of the data seive buffer used for file + * drivers which are capable of using data sieving. The data sieve + * buffer is used when performing I/O on datasets in the file. Using a + * buffer which is large anough to hold several pieces of the dataset + * being read in for hyperslab selections boosts performance by quite a + * bit. + * + * The default value is set to 64KB, indicating that file I/O for raw data + * reads and writes will occur in at least 64KB blocks. + * Setting the value to 0 with this API function will turn off the + * data sieving, even if the VFL driver attempts to use that strategy. + * + * Return: Non-negative on success/Negative on failure + * + * Programmer: Quincey Koziol + * Thursday, September 21, 2000 + * + * Modifications: + * + *------------------------------------------------------------------------- + */ +herr_t +H5Pset_sieve_buf_size(hid_t fapl_id, hsize_t size) +{ + H5F_access_t *fapl = NULL; + + FUNC_ENTER (H5Pset_sieve_buf_size, FAIL); + H5TRACE2("e","ih",fapl_id,size); + + /* Check args */ + if (H5P_FILE_ACCESS != H5P_get_class (fapl_id) || + NULL == (fapl = H5I_object (fapl_id))) { + HRETURN_ERROR (H5E_ARGS, H5E_BADTYPE, FAIL, + "not a file access property list"); + } + + /* Set values */ + fapl->sieve_buf_size = size; + + FUNC_LEAVE (SUCCEED); +} /* end H5Pset_sieve_buf_size() */ + + +/*------------------------------------------------------------------------- + * Function: H5Pget_sieve_buf_size + * + * Purpose: Returns the current settings for the data sieve buffer size + * property from a file access property list. + * + * Return: Non-negative on success/Negative on failure + * + * Programmer: Quincey Koziol + * Thursday, September 21, 2000 + * + * Modifications: + * + *------------------------------------------------------------------------- + */ +herr_t +H5Pget_sieve_buf_size(hid_t fapl_id, hsize_t *size/*out*/) +{ + H5F_access_t *fapl = NULL; + + FUNC_ENTER (H5Pget_sieve_buf_size, FAIL); + H5TRACE2("e","ix",fapl_id,size); + + /* Check args */ + if (H5P_FILE_ACCESS != H5P_get_class (fapl_id) || + NULL == (fapl = H5I_object (fapl_id))) { + HRETURN_ERROR (H5E_ARGS, H5E_BADTYPE, FAIL, + "not a file access property list"); + } + + /* Get values */ + if (size) + *size = fapl->sieve_buf_size; + + FUNC_LEAVE (SUCCEED); +} /* end H5Pget_sieve_buf_size() */ + + /*-------------------------------------------------------------------------- NAME H5P_copy_prop diff --git a/src/H5Ppublic.h b/src/H5Ppublic.h index 3d2b253..49c2563 100644 --- a/src/H5Ppublic.h +++ b/src/H5Ppublic.h @@ -181,6 +181,8 @@ __DLL__ herr_t H5Pget_vlen_mem_manager(hid_t plist_id, void **free_info); __DLL__ herr_t H5Pset_meta_block_size(hid_t fapl_id, hsize_t size); __DLL__ herr_t H5Pget_meta_block_size(hid_t fapl_id, hsize_t *size/*out*/); +__DLL__ herr_t H5Pset_sieve_buf_size(hid_t fapl_id, hsize_t size); +__DLL__ herr_t H5Pget_sieve_buf_size(hid_t fapl_id, hsize_t *size/*out*/); #ifdef __cplusplus } |