From 002b1494b79e2fd638a0676745c340a9a9e9d8e7 Mon Sep 17 00:00:00 2001 From: Robb Matzke Date: Wed, 5 Aug 1998 17:22:59 -0500 Subject: [svn-r569] Changes since 19980731 ---------------------- ./bin/release Added ./Makefile to the distribution again -- it got lost in the changes last week although it isn't all that important a file since it gets clobbered by configure anyway. ./bin/trace ./doc/html/Filters.html ./doc/html/H5.format.html ./doc/html/H5.user.html ./src/H5.c ./src/H5D.c ./src/H5Dprivate.h ./src/H5E.c ./src/H5Epublic.h ./src/H5Farray.c ./src/H5Fistore.c ./src/H5Fprivate.h ./src/H5O.c ./src/H5Ocomp.c ./src/H5Oprivate.h ./src/H5P.c ./src/H5Ppublic.h ./src/H5Sall.c ./src/H5Shyper.c ./src/H5Spoint.c ./src/H5Sprivate.h ./src/H5Ssimp.c ./src/H5Z.c ./src/H5Zprivate.h ./src/H5Zpublic.h ./src/hdf5.h ./test/dsets.c ./tools/h5ls.c Added the data filter pipeline, a generalization of the compression stuff which allows things like checksums, encryption, compression, performance monitoring, etc. See ./doc/html/Filters.html for details -- it replaces the Compression.html doc. ./src/H5T.c Cleaned up debugging output. ./config/linux Added checks for egcs and pgcc and changed optimization flags for the compilers. ./src/H5G.c ./tools/h5dump.c Fixed compiler warnings in these files and others. ./configure.in ./src/H5private.h ./test/mtime.c Added a check for difftime() and defined HDdifftime() to do something else on systems that don't have difftime(). --- bin/release | 6 +- bin/snapshot | 5 +- bin/trace | 2 +- config/linux | 28 +- configure | 2 +- configure.in | 2 +- doc/html/H5.format.html | 205 +++++++++------ doc/html/H5.user.html | 6 +- src/.distdep | 46 ++-- src/H5.c | 95 +++++-- src/H5D.c | 60 +++-- src/H5Distore.c | 283 ++++++++++++--------- src/H5Dprivate.h | 2 +- src/H5E.c | 4 +- src/H5Epublic.h | 2 +- src/H5Farray.c | 27 +- src/H5Fistore.c | 283 ++++++++++++--------- src/H5Fprivate.h | 12 +- src/H5G.c | 2 +- src/H5O.c | 2 +- src/H5Ocomp.c | 380 ++++++++++++++++++--------- src/H5Oprivate.h | 25 +- src/H5P.c | 260 ++++++++++++------- src/H5Ppublic.h | 16 +- src/H5Sall.c | 10 +- src/H5Shyper.c | 101 +++++--- src/H5Spoint.c | 11 +- src/H5Sprivate.h | 114 +++++---- src/H5Ssimp.c | 16 +- src/H5Z.c | 665 ++++++++++++++++++++++++++++-------------------- src/H5Zprivate.h | 15 +- src/H5Zpublic.h | 77 +++--- src/H5config.h.in | 3 + src/H5private.h | 5 + src/hdf5.h | 2 +- test/.distdep | 3 +- test/dsets.c | 33 +-- test/mtime.c | 4 +- tools/h5ls.c | 28 +- tools/h5tools.c | 8 +- 40 files changed, 1721 insertions(+), 1129 deletions(-) diff --git a/bin/release b/bin/release index f4a11dd..8c1e5aa 100755 --- a/bin/release +++ b/bin/release @@ -91,7 +91,11 @@ echo "This is hdf5-$VERS released on `date`" >README.x tail -n +2 >README.x mv README.x README test "$verbose" && echo " Running tar..." 1>&2 -(cd ..; tar cf x.tar `sed s+^.+hdf5-$VERS+ hdf5-$VERS/MANIFEST` || exit 1) +( \ + cd ..; \ + tar cf x.tar hdf5-$VERS/Makefile \ + `sed s+^.+hdf5-$VERS+ hdf5-$VERS/MANIFEST` || exit 1 \ +) # Compress for comp in $methods; do diff --git a/bin/snapshot b/bin/snapshot index 2bb7876..31a7fa3 100755 --- a/bin/snapshot +++ b/bin/snapshot @@ -1,5 +1,6 @@ #!/bin/sh set -x +date # # This script should be run nightly from cron. It checks out hdf5 # from the CVS source tree and compares it against the previous @@ -33,8 +34,8 @@ cvs -Q co -d ${COMPARE}/current hdf5 || exit 1 # Compare it with the previous version. if [ -d ${COMPARE}/previous ]; then - if (diff -r -I H5_VERS_RELEASE -I " released on " \ - ${COMPARE}/previous ${COMPARE}/current >/dev/null); then + if (diff -r -I H5_VERS_RELEASE -I " released on " --exclude CVS \ + ${COMPARE}/previous ${COMPARE}/current); then update=no else update=yes diff --git a/bin/trace b/bin/trace index 3ab902e..4dab596 100755 --- a/bin/trace +++ b/bin/trace @@ -55,7 +55,7 @@ $Source = ""; "H5T_overflow_t" => "x", "H5Z_func_t" => "x", "size_t" => "z", - "H5Z_method_t" => "Zm", + "H5Z_filter_t" => "Zf", "ssize_t" => "Zs", ); diff --git a/config/linux b/config/linux index ff79283..3766079 100644 --- a/config/linux +++ b/config/linux @@ -18,15 +18,24 @@ case `$CC -v 2>&1 |tail -1 |sed 's/gcc version //'` in echo " | code generation may be wrong on some platforms.|" echo " +------------------------------------------------+" sleep 5 + CCVENDOR=gcc ;; 2.8.*) - CFLAGS="$CFLAGS -Wundef -Wsign-compare" + CFLAGS="$CFLAGS -Wsign-compare" + CCVENDOR=gcc + ;; + egcs-*) + CFLAGS="$CFLAGS -Wsign-compare" + CCVENDOR=egcs + ;; + pgcc-*) + CFLAGS="$CFLAGS -Wsign-compare" + CCVENDOR=pgcc ;; esac # What must *always* be present for things to compile correctly? CFLAGS="$CFLAGS -ansi" -#CPPFLAGS="$CPPFLAGS -I." # What compiler flags should be used for code development? DEBUG_CFLAGS="-g -fverbose-asm" @@ -34,8 +43,19 @@ DEBUG_CPPFLAGS="-DH5F_OPT_SEEK=0 -DH5F_LOW_DFLT=H5F_LOW_SEC2" # What compiler flags should be used for building a production # library? -PROD_CFLAGS="-mcpu=pentiumpro -march=pentiumpro -O3 -finline-functions -malign-double -fomit-frame-pointer -fschedule-insns2" -PROD_CPPFLAGS= +if [ "gcc" = "$CCVENDOR" ]; then + PROD_CFLAGS="-mcpu=pentiumpro -march=pentiumpro -O3 -finline-functions -malign-double -fomit-frame-pointer -fschedule-insns2" + PROD_CPPFLAGS= +elif [ "egcs" = "$CCVENDOR" ]; then + PROD_CFLAGS="-mcpu=pentiumpro -march=pentiumpro -O6 -malign-double" + PROD_CPPFLAGS= +elif [ "pgcc" = "$CCVENDOR" ]; then + PROD_CFLAGS="-mcpu=pentiumpro -march=pentiumpro -O6 -malign-double" + PROD_CPPFLAGS= +else + PROD_CFLAGS= + PROD_CPPFLAGS= +fi # What compiler flags enable code profiling? PROFILE_CFLAGS=-pg diff --git a/configure b/configure index 0dbfde1..a75d147 100755 --- a/configure +++ b/configure @@ -2115,7 +2115,7 @@ else fi done -for ac_func in gettimeofday BSDgettimeofday +for ac_func in gettimeofday BSDgettimeofday difftime do echo $ac_n "checking for $ac_func""... $ac_c" 1>&6 echo "configure:2122: checking for $ac_func" >&5 diff --git a/configure.in b/configure.in index 4128971..c7486b7 100644 --- a/configure.in +++ b/configure.in @@ -213,7 +213,7 @@ dnl ---------------------------------------------------------------------- dnl Check for functions. dnl AC_CHECK_FUNCS(getpwuid gethostname system getrusage fork waitpid) -AC_CHECK_FUNCS(gettimeofday BSDgettimeofday) +AC_CHECK_FUNCS(gettimeofday BSDgettimeofday difftime) AC_TRY_COMPILE([#include], [off64_t n = 0;], diff --git a/doc/html/H5.format.html b/doc/html/H5.format.html index 7813856..fff60db 100644 --- a/doc/html/H5.format.html +++ b/doc/html/H5.format.html @@ -54,8 +54,8 @@ Name: Reserved - not assigned yet
  • Name: Reserved - not assigned yet -
  • - Name: Data Storage - Compressed +
  • + Name: Data Storage - Filter Pipeline
  • Name: Attribute
  • @@ -2433,18 +2433,20 @@
    1. The array can be stored in one contiguous area of the file. The layout requires that the size of the array be constant and - does not permit chunking or compression. The message stores - the total size of the array and the offset of an element from - the beginning of the storage area is computed as in C. + does not permit chunking, compression, checksums, encryption, + etc. The message stores the total size of the array and the + offset of an element from the beginning of the storage area is + computed as in C.
    2. The array domain can be regularly decomposed into chunks and each chunk is allocated separately. This layout supports - arbitrary element traversals and compression and the chunks - can be distributed across external raw data files (these - features are described in other messages). The message stores - the size of a chunk instead of the size of the entire array; - the size of the entire array can be calculated by traversing - the B-tree that stores the chunk addresses. + arbitrary element traversals, compression, encryption, and + checksums, and the chunks can be distributed across external + raw data files (these features are described in other + messages). The message stores the size of a chunk instead of + the size of the entire array; the size of the entire array can + be calculated by traversing the B-tree that stores the chunk + addresses.

    @@ -2555,22 +2557,21 @@ Format of Data: N/A

    -

    Name: Data Storage - Compressed

    +

    Name: Data Storage - Filter Pipeline

    Type: 0x000B
    Length: varies
    Status: Optional, may not be repeated. - -

    Purpose and Description: Compressed objects are - datasets which are stored in an HDF file after they have been - compressed. The encoding algorithm and its parameters are - stored in a Compression Message in the object header of the - dataset. + +

    Purpose and Description: This message describes the + filter pipeline which should be applied to the data stream by + providing filter identification numbers, flags, a name, an + client data.

    @@ -2581,13 +2582,17 @@ - - - + + + - + + + + +
    - Compression Message + Filter Pipeline Message
    MethodFlagsClient Data SizeVersionNumber of FiltersReserved

    Client Data

    		Reserved

    Filter List
    @@ -2601,106 +2606,138 @@ - Method - The compression method is a value between zero and 255, - inclusive, that is used as a index into a compression - method lookup table. The value zero indicates no - compression. The values one through 15, inclusive, are - reserved for methods defined by NCSA. All other values - are user-defined compression methods. + Version + The version number for this message. This document + describes version one. - Flags - Eight bits of flags which are passed to the compression - algorithm. There meaning depends on the compression - method. + Number of Filters + The total number of filters described by this + message. The maximum possible number of filters in a + message is 32. - Client Data Size - The size in bytes of the optional Client Data - field. + Filter List + A description of each filter. A filter description + appears in the next table. + + - - Client Data - Additional information needed by the compression method - can be stored in this field. The data will be passed to - the compression algorithm as a void pointer. +

    +

    + + + + + + + + + + + + + + + + + + + + + + + + + + + + + +
    + Filter Pipeline Message +
    bytebytebytebyte
    Filter IdentificationName Length
    FlagsClient Data Number of Values

    Name


    Client Data

    Padding
    -

    Sometimes additional redundancy can be added to the data before - it's compressed to result in a better compression ratio. The - library doesn't specifically support modeling methods to add - redundancy, but the effect can be achieved through the use of - user-defined data types. - -

    The library uses the following compression methods. +

    - - - + + + - - + + - - + + - - - + + - - +
    +
    bit 1 +
    If set then the filter is an optional filter. + During output, if an optional filter fails it will be + silently removed from the pipeline. +
    - - + + - - + + - - + + - - + +
    0No compression: The blocks of data are stored in - their raw format.
    Field NameDescription
    1Deflation: This is the same algorithm used by - GNU gzip which is a combination Huffman and LZ77 - dictionary encoder. The libz library version - 1.1.2 or later must be available.Filter IdentificationThis is a unique (except in the case of testing) + identifier for the filter. Values from zero through 255 + are reserved for filters defined by the NCSA HDF5 + library. Values 256 through 511 have been set aside for + use when developing/testing new filters. The remaining + values are allocated to specific filters by contacting the + HDF5 Development + Team.
    2Run length encoding: Not implemented yet.Name LengthEach filter has an optional null-terminated ASCII name + and this field holds the length of the name including the + null termination padded with nulls to be a multiple of + eight. If the filter has no name then a value of zero is + stored in this field.
    3Adaptive Huffman: Not implemented yet.
    FlagsThe flags indicate certain properties for a filter. The + bit values defined so far are: -
    4Adaptive Arithmetic: Not implemented yet.
    5LZ78 Dictionary Encoding: Not implemented yet.Client Data Number of ValuesEach filter can store a few integer values to control + how the filter operates. The number of entries in the + Client Data array is stored in this field.
    6Adaptive Lempel-Ziv: Similar to Unix - compress. Not implemented yet.NameIf the Name Length field is non-zero then it will + contain the size of this field, a multiple of eight. This + field contains a null-terminated, ASCII character + string to serve as a comment/name for the filter.
    7-15Reserved for future use.Client DataThis is an array of four-byte integers which will be + passed to the filter function. The Client Data Number of + Values determines the number of elements in the + array.
    16-255User-defined.PaddingFour bytes of zeros are added to the message at this + point if the Client Data Number of Values field contains + an odd number.
    -

    The compression is applied independently to each chunk of - storage (after data space and data type conversions). If the - compression is unable to make the chunk smaller than it would - normally be, the chunk is stored without compression. At the - library's discretion, chunks which fail the compression can also - be stored in their raw format. - -

    Name: Attribute

    Type: 0x000C
    @@ -3255,7 +3292,7 @@ data-type.
    Quincey Koziol
    Robb Matzke
    -Last modified: Fri Jul 24 15:10:57 EDT 1998 +Last modified: Tue Aug 4 10:04:40 EDT 1998 diff --git a/doc/html/H5.user.html b/doc/html/H5.user.html index dc1232a..c090922 100644 --- a/doc/html/H5.user.html +++ b/doc/html/H5.user.html @@ -28,6 +28,8 @@ A guide to the H5P interface.
  • Error handling - A guide to the H5E interface. +
  • Filters - + A guide to the H5Z interface.
  • Caching - A guide for meta and raw data caching.
  • API Tracing - @@ -44,8 +46,6 @@ A description of HDF5 version numbers.
  • I/O Pipeline - A description of the raw data I/O pipeline. -
  • Compression - - A guide to the use of compression for datasets.
  • Working with external files - A guide to the use of multiple files with HDF5.
  • Large Datasets - @@ -66,7 +66,7 @@
    Quincey Koziol
    Robb Matzke
    -Last modified: Wed Jul 8 14:10:50 EDT 1998 +Last modified: Wed Aug 5 17:02:57 EDT 1998 diff --git a/src/.distdep b/src/.distdep index 15be2c8..88b4253 100644 --- a/src/.distdep +++ b/src/.distdep @@ -819,6 +819,29 @@ H5P.o: \ H5Eprivate.h \ H5Epublic.h \ H5MMprivate.h +H5S.o: \ + H5S.c \ + H5private.h \ + H5public.h \ + H5config.h \ + H5Iprivate.h \ + H5Ipublic.h \ + H5Eprivate.h \ + H5Epublic.h \ + H5MMprivate.h \ + H5MMpublic.h \ + H5Oprivate.h \ + H5Opublic.h \ + H5Fprivate.h \ + H5Fpublic.h \ + H5Dpublic.h \ + H5Gprivate.h \ + H5Gpublic.h \ + H5Bprivate.h \ + H5Bpublic.h \ + H5HGprivate.h \ + H5HGpublic.h \ + H5Tprivate.h H5Sall.o: \ H5Sall.c \ H5private.h \ @@ -1084,26 +1107,3 @@ H5Z.o: \ H5Spublic.h \ H5Zprivate.h \ H5Zpublic.h -H5S.o: \ - H5S.c \ - H5private.h \ - H5public.h \ - H5config.h \ - H5Iprivate.h \ - H5Ipublic.h \ - H5Eprivate.h \ - H5Epublic.h \ - H5MMprivate.h \ - H5MMpublic.h \ - H5Oprivate.h \ - H5Opublic.h \ - H5Fprivate.h \ - H5Fpublic.h \ - H5Dpublic.h \ - H5Gprivate.h \ - H5Gpublic.h \ - H5Bprivate.h \ - H5Bpublic.h \ - H5HGprivate.h \ - H5HGpublic.h \ - H5Tprivate.h diff --git a/src/H5.c b/src/H5.c index 02b8f09..84e6018 100644 --- a/src/H5.c +++ b/src/H5.c @@ -55,7 +55,7 @@ FILE *fdopen(int fd, const char *mode); #include /*property lists */ #include /*data spaces */ #include /*data types */ -#include /*compression */ +#include /*filters */ #define PABLO_MASK H5_mask @@ -113,7 +113,7 @@ H5_init_library(void) /* Turn on tracing? */ const char *s = getenv ("HDF5_TRACE"); if (s && isdigit(*s)) { - int fd = HDstrtol (s, NULL, 0); + int fd = (int)HDstrtol (s, NULL, 0); H5_trace_g = HDfdopen (fd, "w"); } } @@ -795,7 +795,7 @@ HDstrtoll (const char *s, const char **rest, int base) (*s>='a' && *s<'a'+base-10) || (*s>='A' && *s<'A'+base-10)))) { if (!overflow) { - int64 digit; + int64 digit = 0; if (*s>='0' && *s<='9') digit = *s - '0'; else if (*s>='a' && *s<='z') digit = *s-'a'+10; else digit = *s-'A'+10; @@ -925,7 +925,74 @@ H5_timer_end (H5_timer_t *sum/*in,out*/, H5_timer_t *timer/*in,out*/) sum->etime += timer->etime; } } - + + +/*------------------------------------------------------------------------- + * Function: H5_bandwidth + * + * Purpose: Prints the bandwidth (bytes per second) in a field 10 + * characters wide widh four digits of precision like this: + * + * NaN If <=0 seconds + * 1234. TB/s + * 123.4 TB/s + * 12.34 GB/s + * 1.234 MB/s + * 4.000 kB/s + * 1.000 B/s + * 0.000 B/s If NBYTES==0 + * 1.2345e-10 For bandwidth less than 1 + * 6.7893e+94 For exceptionally large values + * 6.678e+106 For really big values + * + * Return: void + * + * Programmer: Robb Matzke + * Wednesday, August 5, 1998 + * + * Modifications: + * + *------------------------------------------------------------------------- + */ +void +H5_bandwidth(char *buf/*out*/, double nbytes, double nseconds) +{ + double bw; + + if (nseconds<=0.0) { + strcpy(buf, " NaN"); + } else { + bw = nbytes/nseconds; + if (bw==0.0) { + strcpy(buf, "0.000 B/s"); + } else if (bw<1.0) { + sprintf(buf, "%10.4e", bw); + } else if (bw<1024.0) { + sprintf(buf, "%05.4f", bw); + strcpy(buf+5, " B/s"); + } else if (bw<1024.0*1024.0) { + sprintf(buf, "%05.4f", bw/1024.0); + strcpy(buf+5, " kB/s"); + } else if (bw<1024.0*1024.0*1024.0) { + sprintf(buf, "%05.4f", bw/(1024.0*1024.0)); + strcpy(buf+5, " MB/s"); + } else if (bw<1024.0*1024.0*1024.0*1024.0) { + sprintf(buf, "%05.4f", + bw/(1024.0*1024.0*1024.0)); + strcpy(buf+5, " GB/s"); + } else if (bw<1024.0*1024.0*1024.0*1024.0*1024.0) { + sprintf(buf, "%05.4f", + bw/(1024.0*1024.0*1024.0*1024.0)); + strcpy(buf+5, " TB/s"); + } else { + sprintf(buf, "%10.4e", bw); + if (strlen(buf)>10) { + sprintf(buf, "%10.3e", bw); + } + } + } +} + /*------------------------------------------------------------------------- * Function: H5_trace @@ -989,7 +1056,7 @@ H5_trace (hbool_t returning, const char *func, const char *type, ...) for (ptr=0; '*'==*type; type++) ptr++; if ('['==*type) { if ('a'==type[1]) { - asize_idx = strtol(type+2, &rest, 10); + asize_idx = (int)strtol(type+2, &rest, 10); assert(']'==*rest); type = rest+1; } else { @@ -1959,7 +2026,7 @@ H5_trace (hbool_t returning, const char *func, const char *type, ...) case 'Z': switch (type[1]) { - case 'm': + case 'f': if (ptr) { if (vp) { fprintf (out, "0x%lx", (unsigned long)vp); @@ -1967,19 +2034,11 @@ H5_trace (hbool_t returning, const char *func, const char *type, ...) fprintf(out, "NULL"); } } else { - H5Z_method_t zmeth = va_arg (ap, H5Z_method_t); - if (zmeth<0) { - fprintf (out, "%d (range)", (int)zmeth); - } else if (H5Z_NONE==zmeth) { - fprintf (out, "H5Z_NONE"); - } else if (H5Z_DEFLATE==zmeth) { - fprintf (out, "H5Z_DEFLATE"); - } else if (zmeth /* Memory management */ #include /* Object headers */ #include /* Property lists */ -#include /* Data compression */ +#include /* Data filters */ #ifdef QAK int qak_debug=0; @@ -66,10 +66,8 @@ const H5D_create_t H5D_create_dflt = { 0, /*...slots used */ NULL}, /*...slot array */ - /* Compression */ - {H5Z_NONE, /* No compression */ - 0, /*...flags */ - 0, NULL} /*...client data */ + /* Filters */ + {0, 0, NULL} /* No filters in pipeline */ }; /* Default dataset transfer property list */ @@ -805,17 +803,17 @@ H5D_create(H5G_t *loc, const char *name, const H5T_t *type, const H5S_t *space, assert (space); assert (create_parms); #ifdef HAVE_PARALLEL - /* If MPIO is used, no compression support yet. */ + /* If MPIO is used, no filter support yet. */ if (f->shared->access_parms->driver == H5F_LOW_MPIO && - H5Z_NONE!=create_parms->compress.method){ + create_parms->pline.nfilters>0) { HGOTO_ERROR (H5E_DATASET, H5E_UNSUPPORTED, NULL, - "Parallel IO does not support compression yet"); + "Parallel IO does not support filters yet"); } #endif - if (H5Z_NONE!=create_parms->compress.method && + if (create_parms->pline.nfilters>0 && H5D_CHUNKED!=create_parms->layout) { HGOTO_ERROR (H5E_DATASET, H5E_BADVALUE, NULL, - "compression can only be used with chunked layout"); + "filters can only be used with chunked layout"); } /* Initialize the dataset object */ @@ -909,12 +907,12 @@ H5D_create(H5G_t *loc, const char *name, const H5T_t *type, const H5S_t *space, "unable to update type or space header messages"); } - /* Update the compression message */ - if (H5Z_NONE!=new_dset->create_parms->compress.method && - H5O_modify (&(new_dset->ent), H5O_COMPRESS, 0, H5O_FLAG_CONSTANT, - &(new_dset->create_parms->compress))<0) { + /* Update the filters message */ + if (new_dset->create_parms->pline.nfilters>0 && + H5O_modify (&(new_dset->ent), H5O_PLINE, 0, H5O_FLAG_CONSTANT, + &(new_dset->create_parms->pline))<0) { HGOTO_ERROR (H5E_DATASET, H5E_CANTINIT, NULL, - "unable to update compression header message"); + "unable to update filter header message"); } /* @@ -1065,21 +1063,21 @@ H5D_open(H5G_t *loc, const char *name) "unable to read data space info from dataset header"); } - /* Get the optional compression message */ - if (NULL==H5O_read (&(dataset->ent), H5O_COMPRESS, 0, - &(dataset->create_parms->compress))) { + /* Get the optional filters message */ + if (NULL==H5O_read (&(dataset->ent), H5O_PLINE, 0, + &(dataset->create_parms->pline))) { H5E_clear (); - HDmemset (&(dataset->create_parms->compress), 0, - sizeof(dataset->create_parms->compress)); + HDmemset (&(dataset->create_parms->pline), 0, + sizeof(dataset->create_parms->pline)); } #ifdef HAVE_PARALLEL f = H5G_fileof (loc); - /* If MPIO is used, no compression support yet. */ + /* If MPIO is used, no filter support yet. */ if (f->shared->access_parms->driver == H5F_LOW_MPIO && - H5Z_NONE!=dataset->create_parms->compress.method){ + dataset->create_parms->pline.nfilters>0){ HGOTO_ERROR (H5E_DATASET, H5E_UNSUPPORTED, NULL, - "Parallel IO does not support compression yet"); + "Parallel IO does not support filters yet"); } #endif @@ -1356,7 +1354,7 @@ H5D_read(H5D_t *dataset, const H5T_t *mem_type, const H5S_t *mem_space, if (H5T_conv_noop==tconv_func && NULL!=sconv_func.read) { status = (sconv_func.read)(dataset->ent.file, &(dataset->layout), - &(dataset->create_parms->compress), + &(dataset->create_parms->pline), &(dataset->create_parms->efl), H5T_get_size (dataset->type), file_space, mem_space, @@ -1376,7 +1374,7 @@ H5D_read(H5D_t *dataset, const H5T_t *mem_type, const H5S_t *mem_space, if (H5D_OPTIMIZE_PIPE && H5T_conv_noop==tconv_func && NULL!=sconv_func.read) { status = (sconv_func.read)(dataset->ent.file, &(dataset->layout), - &(dataset->create_parms->compress), + &(dataset->create_parms->pline), &(dataset->create_parms->efl), H5T_get_size (dataset->type), file_space, mem_space, xfer_parms->xfer_mode, @@ -1474,7 +1472,7 @@ H5D_read(H5D_t *dataset, const H5T_t *mem_type, const H5S_t *mem_space, * if necessary. */ if ((sconv_func.fgath)(dataset->ent.file, &(dataset->layout), - &(dataset->create_parms->compress), + &(dataset->create_parms->pline), &(dataset->create_parms->efl), H5T_get_size (dataset->type), file_space, &file_iter, smine_nelmts, xfer_parms->xfer_mode, @@ -1703,7 +1701,7 @@ H5D_write(H5D_t *dataset, const H5T_t *mem_type, const H5S_t *mem_space, NULL!=sconv_func.write) { status = (sconv_func.write)(dataset->ent.file, &(dataset->layout), - &(dataset->create_parms->compress), + &(dataset->create_parms->pline), &(dataset->create_parms->efl), H5T_get_size (dataset->type), file_space, mem_space, @@ -1724,7 +1722,7 @@ H5D_write(H5D_t *dataset, const H5T_t *mem_type, const H5S_t *mem_space, H5T_conv_noop==tconv_func && NULL!=sconv_func.write) { status = (sconv_func.write)(dataset->ent.file, &(dataset->layout), - &(dataset->create_parms->compress), + &(dataset->create_parms->pline), &(dataset->create_parms->efl), H5T_get_size (dataset->type), file_space, mem_space, xfer_parms->xfer_mode, buf); @@ -1842,7 +1840,7 @@ H5D_write(H5D_t *dataset, const H5T_t *mem_type, const H5S_t *mem_space, if ((H5D_OPTIMIZE_PIPE && H5T_BKG_YES==need_bkg) || (!H5D_OPTIMIZE_PIPE && need_bkg)) { if ((sconv_func.fgath)(dataset->ent.file, &(dataset->layout), - &(dataset->create_parms->compress), + &(dataset->create_parms->pline), &(dataset->create_parms->efl), H5T_get_size (dataset->type), file_space, &bkg_iter, smine_nelmts, xfer_parms->xfer_mode, @@ -1873,7 +1871,7 @@ H5D_write(H5D_t *dataset, const H5T_t *mem_type, const H5S_t *mem_space, * Scatter the data out to the file. */ if ((sconv_func.fscat)(dataset->ent.file, &(dataset->layout), - &(dataset->create_parms->compress), + &(dataset->create_parms->pline), &(dataset->create_parms->efl), H5T_get_size (dataset->type), file_space, &file_iter, smine_nelmts, @@ -2101,7 +2099,7 @@ H5D_allocate (H5D_t *dataset) if (H5F_istore_allocate(dataset->ent.file, (layout), space_dim, - &(dataset->create_parms->compress))==FAIL){ + &(dataset->create_parms->pline))==FAIL){ HRETURN(FAIL); } break; diff --git a/src/H5Distore.c b/src/H5Distore.c index a8b321b..21f90bc 100644 --- a/src/H5Distore.c +++ b/src/H5Distore.c @@ -33,12 +33,13 @@ typedef struct H5F_rdcc_ent_t { hbool_t locked; /*entry is locked in cache */ hbool_t dirty; /*needs to be written to disk? */ H5O_layout_t *layout; /*the layout message */ - H5O_compress_t *comp; /*compression message */ + H5O_pline_t *pline; /*filter pipeline message */ hssize_t offset[H5O_LAYOUT_NDIMS]; /*chunk name */ - size_t chunk_size; /*size of a chunk */ size_t rd_count; /*bytes remaining to be read */ size_t wr_count; /*bytes remaining to be written */ - uint8 *chunk; /*the uncompressed chunk data */ + size_t chunk_size; /*size of a chunk */ + size_t alloc_size; /*amount allocated for the chunk */ + uint8 *chunk; /*the unfiltered chunk data */ } H5F_rdcc_ent_t; /* Private prototypes */ @@ -83,8 +84,9 @@ static herr_t H5F_istore_get_addr (H5F_t *f, const H5O_layout_t *layout, * The chunk's file address is part of the B-tree and not part of the key. */ typedef struct H5F_istore_key_t { - hsize_t nbytes; /*size of stored data */ + size_t nbytes; /*size of stored data */ hssize_t offset[H5O_LAYOUT_NDIMS]; /*logical offset to start*/ + uintn filter_mask; /*excluded filters */ } H5F_istore_key_t; typedef struct H5F_istore_ud1_t { @@ -141,6 +143,7 @@ H5F_istore_sizeof_rkey(H5F_t __unused__ *f, const void *_udata) assert(udata->mesg.ndims > 0 && udata->mesg.ndims <= H5O_LAYOUT_NDIMS); nbytes = 4 + /*storage size */ + 4 + /*filter mask */ udata->mesg.ndims * 4; /*dimension indices */ return nbytes; @@ -180,7 +183,8 @@ H5F_istore_decode_key(H5F_t __unused__ *f, H5B_t *bt, uint8 *raw, void *_key) assert(ndims > 0 && ndims <= H5O_LAYOUT_NDIMS); /* decode */ - UINT32DECODE (raw, key->nbytes); + UINT32DECODE(raw, key->nbytes); + UINT32DECODE(raw, key->filter_mask); for (i = 0; i < ndims; i++) { UINT32DECODE(raw, key->offset[i]); } @@ -222,7 +226,8 @@ H5F_istore_encode_key(H5F_t __unused__ *f, H5B_t *bt, uint8 *raw, void *_key) assert(ndims > 0 && ndims <= H5O_LAYOUT_NDIMS); /* encode */ - UINT32ENCODE (raw, key->nbytes); + UINT32ENCODE(raw, key->nbytes); + UINT32ENCODE(raw, key->filter_mask); for (i = 0; i < ndims; i++) { UINT32ENCODE(raw, key->offset[i]); } @@ -258,10 +263,12 @@ H5F_istore_debug_key (FILE *stream, intn indent, intn fwidth, FUNC_ENTER (H5F_istore_debug_key, FAIL); assert (key); - HDfprintf (stream, "%*s%-*s %Hd bytes\n", indent, "", fwidth, - "Chunk size:", key->nbytes); - HDfprintf (stream, "%*s%-*s {", indent, "", fwidth, - "Logical offset:"); + HDfprintf(stream, "%*s%-*s %Zd bytes\n", indent, "", fwidth, + "Chunk size:", key->nbytes); + HDfprintf(stream, "%*s%-*s 0x%08x\n", indent, "", fwidth, + "Filter mask:", key->filter_mask); + HDfprintf(stream, "%*s%-*s {", indent, "", fwidth, + "Logical offset:"); for (i=0; imesg.ndims; i++) { HDfprintf (stream, "%s%Hd", i?", ":"", key->offset[i]); } @@ -429,6 +436,7 @@ H5F_istore_new_node(H5F_t *f, H5B_ins_t op, * inserted into the tree. */ lt_key->nbytes = udata->key.nbytes; + lt_key->filter_mask = udata->key.filter_mask; for (i=0; imesg.ndims; i++) { lt_key->offset[i] = udata->key.offset[i]; } @@ -439,6 +447,7 @@ H5F_istore_new_node(H5F_t *f, H5B_ins_t op, */ if (H5B_INS_LEFT != op) { rt_key->nbytes = 0; + rt_key->filter_mask = 0; for (i=0; imesg.ndims; i++) { assert (udata->mesg.dim[i] < MAX_HSSIZET); assert (udata->key.offset[i]+(hssize_t)(udata->mesg.dim[i]) > @@ -494,6 +503,7 @@ H5F_istore_found(H5F_t __unused__ *f, const haddr_t *addr, /* Initialize return values */ udata->addr = *addr; udata->key.nbytes = lt_key->nbytes; + udata->key.filter_mask = lt_key->filter_mask; assert (lt_key->nbytes>0); for (i = 0; i < udata->mesg.ndims; i++) { udata->key.offset[i] = lt_key->offset[i]; @@ -589,6 +599,7 @@ H5F_istore_insert(H5F_t *f, const haddr_t *addr, void *_lt_key, "unable to reallocate chunk storage"); } lt_key->nbytes = udata->key.nbytes; + lt_key->filter_mask = udata->key.filter_mask; *lt_key_changed = TRUE; udata->addr = *new_node; ret_value = H5B_INS_CHANGE; @@ -608,6 +619,7 @@ H5F_istore_insert(H5F_t *f, const haddr_t *addr, void *_lt_key, * current node. The MD_KEY is where the split occurs. */ md_key->nbytes = udata->key.nbytes; + md_key->filter_mask = udata->key.filter_mask; for (i=0; imesg.ndims; i++) { assert(0 == udata->key.offset[i] % udata->mesg.dim[i]); md_key->offset[i] = udata->key.offset[i]; @@ -677,7 +689,10 @@ H5F_istore_init (H5F_t *f) /*------------------------------------------------------------------------- * Function: H5F_istore_flush_entry * - * Purpose: Writes a chunk to disk. + * Purpose: Writes a chunk to disk. If RESET is non-zero then the + * entry is cleared -- it's slightly faster to flush a chunk if + * the RESET flag is turned on because it results in one fewer + * memory copy. * * Return: Success: SUCCEED * @@ -691,65 +706,106 @@ H5F_istore_init (H5F_t *f) *------------------------------------------------------------------------- */ static herr_t -H5F_istore_flush_entry (H5F_t *f, H5F_rdcc_ent_t *ent) +H5F_istore_flush_entry (H5F_t *f, H5F_rdcc_ent_t *ent, hbool_t reset) { - void *c_buf = NULL; /*temp compression buffer */ - void *out_ptr = NULL; /*ptr to output buffer */ - size_t nbytes; /*size of output buffer */ - herr_t ret_value = FAIL; /*return value */ - H5F_istore_ud1_t udata; /*pass through B-tree */ - intn i; + herr_t ret_value=FAIL; /*return value */ + H5F_istore_ud1_t udata; /*pass through B-tree */ + intn i; /*counters */ + void *buf=NULL; /*temporary buffer */ + size_t alloc; /*bytes allocated for BUF */ + hbool_t point_of_no_return = FALSE; FUNC_ENTER (H5F_istore_flush_entry, FAIL); - assert (ent); + assert(f); + assert(ent); assert (!ent->locked); - if (!ent->dirty) HRETURN (SUCCEED); - /* Should the chunk be compressed before writing it to disk? */ - if (ent->comp && H5Z_NONE!=ent->comp->method) { - if (NULL==(c_buf = H5MM_malloc (ent->chunk_size))) { - HGOTO_ERROR (H5E_RESOURCE, H5E_NOSPACE, FAIL, - "memory allocation failed for data compression"); + buf = ent->chunk; + if (ent->dirty) { + udata.mesg = *(ent->layout); + udata.key.filter_mask = 0; + H5F_addr_undef(&(udata.addr)); + udata.key.nbytes = ent->chunk_size; + for (i=0; ilayout->ndims; i++) { + udata.key.offset[i] = ent->offset[i]; } - nbytes = H5Z_compress (ent->comp, ent->chunk_size, ent->chunk, c_buf); - if (nbytes && nbyteschunk_size) { - out_ptr = c_buf; - } else { - out_ptr = ent->chunk; - nbytes = ent->chunk_size; + alloc = ent->alloc_size; + + /* Should the chunk be filtered before writing it to disk? */ + if (ent->pline && ent->pline->nfilters) { + if (!reset) { + /* + * Copy the chunk to a new buffer before running it through + * the pipeline because we'll want to save the original buffer + * for later. + */ + alloc = ent->chunk_size; + if (NULL==(buf = H5MM_malloc(alloc))) { + HGOTO_ERROR(H5E_RESOURCE, H5E_NOSPACE, FAIL, + "memory allocation failed for pipeline"); + } + HDmemcpy(buf, ent->chunk, ent->chunk_size); + } else { + /* + * If we are reseting and something goes wrong after this + * point then it's too late to recover because we may have + * destroyed the original data by calling H5Z_pipeline(). + * The only safe option is to continue with the reset + * even if we can't write the data to disk. + */ + point_of_no_return = TRUE; + } + if (H5Z_pipeline(f, ent->pline, 0, &(udata.key.filter_mask), + &(udata.key.nbytes), &alloc, &buf)<0) { + HGOTO_ERROR(H5E_PLINE, H5E_WRITEERROR, FAIL, + "output pipeline failed"); + } } - } else { - out_ptr = ent->chunk; - nbytes = ent->chunk_size; + + /* + * Create the chunk it if it doesn't exist, or reallocate the chunk if + * its size changed. Then write the data into the file. + */ + if (H5B_insert(f, H5B_ISTORE, &(ent->layout->addr), &udata)<0) { + HGOTO_ERROR (H5E_IO, H5E_WRITEERROR, FAIL, + "unable to allocate chunk"); + } + if (H5F_block_write (f, &(udata.addr), udata.key.nbytes, H5D_XFER_DFLT, + buf)<0) { + HGOTO_ERROR (H5E_IO, H5E_WRITEERROR, FAIL, + "unable to write raw data to file"); + } + + /* Mark cache entry as clean */ + ent->dirty = FALSE; + f->shared->rdcc.nflushes++; } - /* - * Create the chunk it if it doesn't exist, or reallocate the chunk if its - * size changed. Then write the data into the file. - */ - udata.mesg = *(ent->layout); - H5F_addr_undef(&(udata.addr)); - udata.key.nbytes = nbytes; - for (i=0; ilayout->ndims; i++) { - udata.key.offset[i] = ent->offset[i]; + /* Reset */ + if (reset) { + point_of_no_return = FALSE; + ent->layout = H5O_free(H5O_LAYOUT, ent->layout); + ent->pline = H5O_free(H5O_PLINE, ent->pline); + if (buf==ent->chunk) buf = NULL; + ent->chunk = H5MM_xfree(ent->chunk); } - if (H5B_insert(f, H5B_ISTORE, &(ent->layout->addr), &udata)<0) { - HGOTO_ERROR (H5E_IO, H5E_WRITEERROR, FAIL, - "unable to allocate chunk"); - } - if (H5F_block_write (f, &(udata.addr), nbytes, H5D_XFER_DFLT, out_ptr)<0) { - HGOTO_ERROR (H5E_IO, H5E_WRITEERROR, FAIL, - "unable to write raw data to file"); - } - - /* Mark cache entry as clean */ - ent->dirty = FALSE; - f->shared->rdcc.nflushes++; ret_value = SUCCEED; done: - H5MM_xfree (c_buf); + /* Free the temp buffer only if it's different than the entry chunk */ + if (buf!=ent->chunk) H5MM_xfree(buf); + + /* + * If we reached the point of no return then we have no choice but to + * reset the entry. This can only happen if RESET is true but the + * output pipeline failed. + */ + if (ret_value<0 && point_of_no_return) { + ent->layout = H5O_free(H5O_LAYOUT, ent->layout); + ent->pline = H5O_free(H5O_PLINE, ent->pline); + ent->chunk = H5MM_xfree(ent->chunk); + } FUNC_LEAVE (ret_value); } @@ -780,7 +836,7 @@ H5F_istore_flush (H5F_t *f) FUNC_ENTER (H5F_istore_flush, FAIL); for (i=0; inused; i++) { - if (H5F_istore_flush_entry (f, rdcc->slot+i)<0) { + if (H5F_istore_flush_entry (f, rdcc->slot+i, FALSE)<0) { nerrors++; } } @@ -791,18 +847,17 @@ H5F_istore_flush (H5F_t *f) FUNC_LEAVE (SUCCEED); } - /*------------------------------------------------------------------------- - * Function: H5F_istore_preempt + * Function: H5F_istore_preempt * - * Purpose: Preempts the specified entry from the cache, flushing it to - * disk if necessary. + * Purpose: Preempts the specified entry from the cache, flushing it to + * disk if necessary. * - * Return: Success: SUCCEED + * Return: Success: SUCCEED * - * Failure: FAIL + * Failure: FAIL * - * Programmer: Robb Matzke + * Programmer: Robb Matzke * Thursday, May 21, 1998 * * Modifications: @@ -812,21 +867,18 @@ H5F_istore_flush (H5F_t *f) static herr_t H5F_istore_preempt (H5F_t *f, intn idx) { - H5F_rdcc_t *rdcc = &(f->shared->rdcc); - H5F_rdcc_ent_t *ent = rdcc->slot + idx; + H5F_rdcc_t *rdcc = &(f->shared->rdcc); + H5F_rdcc_ent_t *ent = rdcc->slot + idx; FUNC_ENTER (H5F_istore_preempt, FAIL); assert (idx>=0 && idxnused); assert (!ent->locked); - if (ent->dirty) H5F_istore_flush_entry (f, ent); - H5O_free (H5O_LAYOUT, ent->layout); - H5O_free (H5O_COMPRESS, ent->comp); - H5MM_xfree (ent->chunk); + H5F_istore_flush_entry (f, ent, TRUE); + HDmemmove (rdcc->slot+idx, rdcc->slot+idx+1, + (rdcc->nused-idx) * sizeof(H5F_rdcc_ent_t)); rdcc->nused -= 1; rdcc->nbytes -= ent->chunk_size; - HDmemmove (rdcc->slot+idx, rdcc->slot+idx+1, - (rdcc->nused-idx) * sizeof(H5F_rdcc_ent_t)); FUNC_LEAVE (SUCCEED); } @@ -858,10 +910,10 @@ H5F_istore_dest (H5F_t *f) FUNC_ENTER (H5F_istore_dest, FAIL); for (i=rdcc->nused-1; i>=0; --i) { - if (H5F_istore_flush_entry (f, rdcc->slot+i)<0) { + if (H5F_istore_flush_entry (f, rdcc->slot+i, TRUE)<0) { nerrors++; } - if (H5F_istore_preempt (f, i)<0) { + if (H5F_istore_preempt(f, i)<0) { nerrors++; } } @@ -951,7 +1003,7 @@ H5F_istore_prune (H5F_t *f, size_t size) /*------------------------------------------------------------------------- * Function: H5F_istore_lock * - * Purpose: Return a pointer to an uncompressed chunk. The pointer + * Purpose: Return a pointer to a file chunk chunk. The pointer * points directly into the chunk cache and should not be freed * by the caller but will be valid until it is unlocked. The * input value IDX_HINT is used to speed up cache lookups and @@ -963,7 +1015,7 @@ H5F_istore_prune (H5F_t *f, size_t size) * for output functions that are about to overwrite the entire * chunk. * - * Return: Success: Ptr to an uncompressed chunk. + * Return: Success: Ptr to a file chunk. * * Failure: NULL * @@ -976,7 +1028,7 @@ H5F_istore_prune (H5F_t *f, size_t size) */ static void * H5F_istore_lock (H5F_t *f, const H5O_layout_t *layout, - const H5O_compress_t *comp, const hssize_t offset[], + const H5O_pline_t *pline, const hssize_t offset[], hbool_t relax, intn *idx_hint/*in,out*/) { H5F_rdcc_t *rdcc = &(f->shared->rdcc); @@ -984,8 +1036,9 @@ H5F_istore_lock (H5F_t *f, const H5O_layout_t *layout, intn i, j, found = -1; H5F_istore_ud1_t udata; /*B-tree pass-through */ size_t chunk_size=0; /*size of a chunk */ + size_t chunk_alloc=0; /*allocated chunk size */ herr_t status; /*func return status */ - void *chunk=NULL; /*the uncompressed chunk*/ + void *chunk=NULL; /*the file chunk */ void *temp=NULL; /*temporary chunk buffer*/ void *ret_value=NULL; /*return value */ @@ -1031,7 +1084,8 @@ H5F_istore_lock (H5F_t *f, const H5O_layout_t *layout, for (i=0, chunk_size=1; indims; i++) { chunk_size *= layout->dim[i]; } - if (NULL==(chunk=H5MM_malloc (chunk_size))) { + chunk_alloc = chunk_size; + if (NULL==(chunk=H5MM_malloc (chunk_alloc))) { HGOTO_ERROR (H5E_RESOURCE, H5E_NOSPACE, NULL, "memory allocation failed for raw data chunk"); } @@ -1045,39 +1099,30 @@ H5F_istore_lock (H5F_t *f, const H5O_layout_t *layout, udata.key.offset[i] = offset[i]; chunk_size *= layout->dim[i]; } + chunk_alloc = chunk_size; udata.mesg = *layout; H5F_addr_undef (&(udata.addr)); status = H5B_find (f, H5B_ISTORE, &(layout->addr), &udata); H5E_clear (); - if (NULL==(chunk = H5MM_malloc (chunk_size))) { + if (NULL==(chunk = H5MM_malloc (chunk_alloc))) { HGOTO_ERROR (H5E_RESOURCE, H5E_NOSPACE, NULL, "memory allocation failed for raw data chunk"); } if (status>=0 && H5F_addr_defined (&(udata.addr))) { /* - * The chunk exists on disk but might be compressed. Instead of - * allocating the exact size for the compressed chunk we allocate - * the entire chunk size -- it reduces strain on the malloc() - * subsystem. + * The chunk exists on disk. */ if (H5F_block_read (f, &(udata.addr), udata.key.nbytes, H5D_XFER_DFLT, chunk)<0) { HGOTO_ERROR (H5E_IO, H5E_READERROR, NULL, "unable to read raw data chunk"); } - if (udata.key.nbytesnmisses++; } else { @@ -1117,8 +1162,9 @@ H5F_istore_lock (H5F_t *f, const H5O_layout_t *layout, ent->locked = 0; ent->dirty = FALSE; ent->chunk_size = chunk_size; + ent->alloc_size = chunk_alloc; ent->layout = H5O_copy (H5O_LAYOUT, layout); - ent->comp = H5O_copy (H5O_COMPRESS, comp); + ent->pline = H5O_copy (H5O_PLINE, pline); for (i=0; indims; i++) { ent->offset[i] = offset[i]; } @@ -1191,7 +1237,7 @@ H5F_istore_lock (H5F_t *f, const H5O_layout_t *layout, */ static herr_t H5F_istore_unlock (H5F_t *f, const H5O_layout_t *layout, - const H5O_compress_t *comp, hbool_t dirty, + const H5O_pline_t *pline, hbool_t dirty, const hssize_t offset[], intn *idx_hint, uint8 *chunk, size_t naccessed) { @@ -1215,7 +1261,7 @@ H5F_istore_unlock (H5F_t *f, const H5O_layout_t *layout, /* * It's not in the cache, probably because it's too big. If it's * dirty then flush it to disk. In any case, free the chunk. - * Note: we have to copy the layout and compression messages so we + * Note: we have to copy the layout and filter messages so we * don't discard the `const' qualifier. */ if (dirty) { @@ -1223,17 +1269,16 @@ H5F_istore_unlock (H5F_t *f, const H5O_layout_t *layout, HDmemset (&x, 0, sizeof x); x.dirty = TRUE; x.layout = H5O_copy (H5O_LAYOUT, layout); - x.comp = H5O_copy (H5O_COMPRESS, comp); + x.pline = H5O_copy (H5O_PLINE, pline); for (i=0, x.chunk_size=1; indims; i++) { x.offset[i] = offset[i]; x.chunk_size *= layout->dim[i]; } x.chunk = chunk; - H5F_istore_flush_entry (f, &x); - H5O_free (H5O_LAYOUT, x.layout); - H5O_free (H5O_COMPRESS, x.comp); + H5F_istore_flush_entry (f, &x, TRUE); + } else { + H5MM_xfree (chunk); } - H5MM_xfree (chunk); } else { /* * It's in the cache so unlock it. @@ -1272,7 +1317,7 @@ H5F_istore_unlock (H5F_t *f, const H5O_layout_t *layout, */ herr_t H5F_istore_read(H5F_t *f, const H5O_layout_t *layout, - const H5O_compress_t *comp, const hssize_t offset_f[], + const H5O_pline_t *pline, const hssize_t offset_f[], const hsize_t size[], void *buf) { hssize_t offset_m[H5O_LAYOUT_NDIMS]; @@ -1375,7 +1420,7 @@ H5F_istore_read(H5F_t *f, const H5O_layout_t *layout, l.dim[i] = layout->dim[i]; l.addr = udata.addr; if (H5F_arr_read(f, &l, - comp, NULL /* no efl */, + pline, NULL /* no efl */, sub_size, size_m, sub_offset_m, offset_wrt_chunk, H5D_XFER_DFLT, buf)==FAIL){ @@ -1397,15 +1442,15 @@ H5F_istore_read(H5F_t *f, const H5O_layout_t *layout, * Lock the chunk, transfer data to the application, then unlock the * chunk. */ - if (NULL==(chunk=H5F_istore_lock (f, layout, comp, chunk_offset, + if (NULL==(chunk=H5F_istore_lock (f, layout, pline, chunk_offset, FALSE, &idx_hint))) { HRETURN_ERROR (H5E_IO, H5E_READERROR, FAIL, "unable to read raw data chunk"); } H5V_hyper_copy(layout->ndims, sub_size, size_m, sub_offset_m, (void*)buf, layout->dim, offset_wrt_chunk, chunk); - if (H5F_istore_unlock (f, layout, comp, FALSE, chunk_offset, &idx_hint, - chunk, naccessed)<0) { + if (H5F_istore_unlock (f, layout, pline, FALSE, chunk_offset, + &idx_hint, chunk, naccessed)<0) { HRETURN_ERROR (H5E_IO, H5E_READERROR, FAIL, "unable to unlock raw data chunk"); } @@ -1443,7 +1488,7 @@ H5F_istore_read(H5F_t *f, const H5O_layout_t *layout, */ herr_t H5F_istore_write(H5F_t *f, const H5O_layout_t *layout, - const H5O_compress_t *comp, const hssize_t offset_f[], + const H5O_pline_t *pline, const hssize_t offset_f[], const hsize_t size[], const void *buf) { hssize_t offset_m[H5O_LAYOUT_NDIMS]; @@ -1550,7 +1595,7 @@ H5F_istore_write(H5F_t *f, const H5O_layout_t *layout, l.dim[i] = layout->dim[i]; l.addr = udata.addr; if (H5F_arr_write(f, &l, - comp, NULL /* no efl */, + pline, NULL /* no efl */, sub_size, size_m, sub_offset_m, offset_wrt_chunk, H5D_XFER_DFLT, buf)==FAIL){ @@ -1571,7 +1616,7 @@ H5F_istore_write(H5F_t *f, const H5O_layout_t *layout, * Lock the chunk, copy from application to chunk, then unlock the * chunk. */ - if (NULL==(chunk=H5F_istore_lock (f, layout, comp, chunk_offset, + if (NULL==(chunk=H5F_istore_lock (f, layout, pline, chunk_offset, naccessed==chunk_size, &idx_hint))) { HRETURN_ERROR (H5E_IO, H5E_WRITEERROR, FAIL, @@ -1580,7 +1625,7 @@ H5F_istore_write(H5F_t *f, const H5O_layout_t *layout, H5V_hyper_copy(layout->ndims, sub_size, layout->dim, offset_wrt_chunk, chunk, size_m, sub_offset_m, buf); - if (H5F_istore_unlock (f, layout, comp, TRUE, chunk_offset, + if (H5F_istore_unlock (f, layout, pline, TRUE, chunk_offset, &idx_hint, chunk, naccessed)<0) { HRETURN_ERROR (H5E_IO, H5E_WRITEERROR, FAIL, "uanble to unlock raw data chunk"); @@ -1826,7 +1871,7 @@ H5F_istore_get_addr (H5F_t *f, const H5O_layout_t *layout, */ herr_t H5F_istore_allocate (H5F_t *f, const H5O_layout_t *layout, - const hsize_t *space_dim, const H5O_compress_t *comp) + const hsize_t *space_dim, const H5O_pline_t *pline) { intn i, carry; @@ -1846,7 +1891,7 @@ H5F_istore_allocate (H5F_t *f, const H5O_layout_t *layout, /* Check args */ assert(f); assert(space_dim); - assert(comp); + assert(pline); assert(layout && H5D_CHUNKED==layout->type); assert(layout->ndims>0 && layout->ndims<=H5O_LAYOUT_NDIMS); assert(H5F_addr_defined(&(layout->addr))); @@ -1885,13 +1930,13 @@ H5F_istore_allocate (H5F_t *f, const H5O_layout_t *layout, * Lock the chunk, copy from application to chunk, then unlock the * chunk. */ - if (NULL==(chunk=H5F_istore_lock (f, layout, comp, chunk_offset, + if (NULL==(chunk=H5F_istore_lock (f, layout, pline, chunk_offset, FALSE, &idx_hint))) { HRETURN_ERROR (H5E_IO, H5E_WRITEERROR, FAIL, "unable to read raw data chunk"); } - if (H5F_istore_unlock (f, layout, comp, TRUE, chunk_offset, &idx_hint, - chunk, chunk_size)<0) { + if (H5F_istore_unlock (f, layout, pline, TRUE, chunk_offset, + &idx_hint, chunk, chunk_size)<0) { HRETURN_ERROR (H5E_IO, H5E_WRITEERROR, FAIL, "uanble to unlock raw data chunk"); } diff --git a/src/H5Dprivate.h b/src/H5Dprivate.h index 12c95d6..b5f2d26 100644 --- a/src/H5Dprivate.h +++ b/src/H5Dprivate.h @@ -46,7 +46,7 @@ typedef struct H5D_create_t { intn chunk_ndims; /*chunk dimensionality */ hsize_t chunk_size[32]; /*chunk size if chunked storage */ H5O_efl_t efl; /*external file list */ - H5O_compress_t compress; /*data compression parameters */ + H5O_pline_t pline; /*data filter pipeline */ } H5D_create_t; /* Dataset transfer property list */ diff --git a/src/H5E.c b/src/H5E.c index eb02ba6..71f5187 100644 --- a/src/H5E.c +++ b/src/H5E.c @@ -55,7 +55,7 @@ static const H5E_major_mesg_t H5E_major_mesg_g[] = { {H5E_STORAGE, "Data storage layer"}, {H5E_TEMPLATE, "Property list interface"}, {H5E_ATTR, "Attribute layer"}, - {H5E_COMP, "Data compression layer"}, + {H5E_PLINE, "Data filters layer"}, {H5E_EFL, "External file list"}, }; @@ -85,7 +85,7 @@ static const H5E_minor_mesg_t H5E_minor_mesg_g[] = { {H5E_ALREADYINIT, "Object already initialized"}, {H5E_BADATOM, "Unable to find atom information (already closed?)"}, {H5E_CANTREGISTER, "Unable to register new atom"}, - {H5E_CANTFLUSH, "Unable to flush meta data from cache"}, + {H5E_CANTFLUSH, "Unable to flush data from cache"}, {H5E_CANTLOAD, "Unable to load meta data into cache"}, {H5E_PROTECT, "Protected meta data error"}, {H5E_NOTCACHED, "Meta data not currently cached"}, diff --git a/src/H5Epublic.h b/src/H5Epublic.h index d155e9a..64f0ff4 100644 --- a/src/H5Epublic.h +++ b/src/H5Epublic.h @@ -72,7 +72,7 @@ typedef enum H5E_major_t { H5E_STORAGE, /*data storage */ H5E_TEMPLATE, /*Property lists */ H5E_ATTR, /*Attribute */ - H5E_COMP, /*Data compression */ + H5E_PLINE, /*Data filters */ H5E_EFL /*External file list */ } H5E_major_t; diff --git a/src/H5Farray.c b/src/H5Farray.c index 25ce208..27ec922 100644 --- a/src/H5Farray.c +++ b/src/H5Farray.c @@ -114,7 +114,7 @@ H5F_arr_create (H5F_t *f, struct H5O_layout_t *layout/*in,out*/) */ herr_t H5F_arr_read (H5F_t *f, const struct H5O_layout_t *layout, - const struct H5O_compress_t *comp, const struct H5O_efl_t *efl, + const struct H5O_pline_t *pline, const struct H5O_efl_t *efl, const hsize_t _hslab_size[], const hsize_t mem_size[], const hssize_t mem_offset[], const hssize_t file_offset[], const H5D_transfer_t xfer_mode, void *_buf/*out*/) @@ -182,11 +182,11 @@ H5F_arr_read (H5F_t *f, const struct H5O_layout_t *layout, } /* - * Compression cannot be used for contiguous data. + * Filters cannot be used for contiguous data. */ - if (comp && H5Z_NONE!=comp->method) { + if (pline && pline->nfilters>0) { HRETURN_ERROR (H5E_IO, H5E_READERROR, FAIL, - "compression is not allowed for contiguous data"); + "filters are not allowed for contiguous data"); } /* @@ -286,7 +286,7 @@ H5F_arr_read (H5F_t *f, const struct H5O_layout_t *layout, "unable to copy into a proper hyperslab"); } } - if (H5F_istore_read (f, layout, comp, file_offset, hslab_size, + if (H5F_istore_read (f, layout, pline, file_offset, hslab_size, buf)<0) { HRETURN_ERROR (H5E_IO, H5E_READERROR, FAIL, "chunked read failed"); } @@ -332,10 +332,11 @@ H5F_arr_read (H5F_t *f, const struct H5O_layout_t *layout, */ herr_t H5F_arr_write (H5F_t *f, const struct H5O_layout_t *layout, - const struct H5O_compress_t *comp, const struct H5O_efl_t *efl, - const hsize_t _hslab_size[], const hsize_t mem_size[], - const hssize_t mem_offset[], const hssize_t file_offset[], - const H5D_transfer_t xfer_mode, const void *_buf) + const struct H5O_pline_t *pline, + const struct H5O_efl_t *efl, const hsize_t _hslab_size[], + const hsize_t mem_size[], const hssize_t mem_offset[], + const hssize_t file_offset[], const H5D_transfer_t xfer_mode, + const void *_buf) { const uint8 *buf = (const uint8 *)_buf; /*cast for arithmetic */ hssize_t file_stride[H5O_LAYOUT_NDIMS]; /*strides through file */ @@ -399,11 +400,11 @@ H5F_arr_write (H5F_t *f, const struct H5O_layout_t *layout, } /* - * Compression cannot be used for contiguous data + * Filters cannot be used for contiguous data */ - if (comp && H5Z_NONE!=comp->method) { + if (pline && pline->nfilters>0) { HRETURN_ERROR (H5E_IO, H5E_WRITEERROR, FAIL, - "compression is not allowed for contiguous data"); + "filters are not allowed for contiguous data"); } /* @@ -503,7 +504,7 @@ printf("nelmts=%lu, min=%lu, max=%lu\n", temp, min, max); "unable to copy from a proper hyperslab"); } } - if (H5F_istore_write (f, layout, comp, file_offset, hslab_size, + if (H5F_istore_write (f, layout, pline, file_offset, hslab_size, buf)<0) { HRETURN_ERROR (H5E_IO, H5E_WRITEERROR, FAIL, "chunked write failed"); diff --git a/src/H5Fistore.c b/src/H5Fistore.c index a8b321b..21f90bc 100644 --- a/src/H5Fistore.c +++ b/src/H5Fistore.c @@ -33,12 +33,13 @@ typedef struct H5F_rdcc_ent_t { hbool_t locked; /*entry is locked in cache */ hbool_t dirty; /*needs to be written to disk? */ H5O_layout_t *layout; /*the layout message */ - H5O_compress_t *comp; /*compression message */ + H5O_pline_t *pline; /*filter pipeline message */ hssize_t offset[H5O_LAYOUT_NDIMS]; /*chunk name */ - size_t chunk_size; /*size of a chunk */ size_t rd_count; /*bytes remaining to be read */ size_t wr_count; /*bytes remaining to be written */ - uint8 *chunk; /*the uncompressed chunk data */ + size_t chunk_size; /*size of a chunk */ + size_t alloc_size; /*amount allocated for the chunk */ + uint8 *chunk; /*the unfiltered chunk data */ } H5F_rdcc_ent_t; /* Private prototypes */ @@ -83,8 +84,9 @@ static herr_t H5F_istore_get_addr (H5F_t *f, const H5O_layout_t *layout, * The chunk's file address is part of the B-tree and not part of the key. */ typedef struct H5F_istore_key_t { - hsize_t nbytes; /*size of stored data */ + size_t nbytes; /*size of stored data */ hssize_t offset[H5O_LAYOUT_NDIMS]; /*logical offset to start*/ + uintn filter_mask; /*excluded filters */ } H5F_istore_key_t; typedef struct H5F_istore_ud1_t { @@ -141,6 +143,7 @@ H5F_istore_sizeof_rkey(H5F_t __unused__ *f, const void *_udata) assert(udata->mesg.ndims > 0 && udata->mesg.ndims <= H5O_LAYOUT_NDIMS); nbytes = 4 + /*storage size */ + 4 + /*filter mask */ udata->mesg.ndims * 4; /*dimension indices */ return nbytes; @@ -180,7 +183,8 @@ H5F_istore_decode_key(H5F_t __unused__ *f, H5B_t *bt, uint8 *raw, void *_key) assert(ndims > 0 && ndims <= H5O_LAYOUT_NDIMS); /* decode */ - UINT32DECODE (raw, key->nbytes); + UINT32DECODE(raw, key->nbytes); + UINT32DECODE(raw, key->filter_mask); for (i = 0; i < ndims; i++) { UINT32DECODE(raw, key->offset[i]); } @@ -222,7 +226,8 @@ H5F_istore_encode_key(H5F_t __unused__ *f, H5B_t *bt, uint8 *raw, void *_key) assert(ndims > 0 && ndims <= H5O_LAYOUT_NDIMS); /* encode */ - UINT32ENCODE (raw, key->nbytes); + UINT32ENCODE(raw, key->nbytes); + UINT32ENCODE(raw, key->filter_mask); for (i = 0; i < ndims; i++) { UINT32ENCODE(raw, key->offset[i]); } @@ -258,10 +263,12 @@ H5F_istore_debug_key (FILE *stream, intn indent, intn fwidth, FUNC_ENTER (H5F_istore_debug_key, FAIL); assert (key); - HDfprintf (stream, "%*s%-*s %Hd bytes\n", indent, "", fwidth, - "Chunk size:", key->nbytes); - HDfprintf (stream, "%*s%-*s {", indent, "", fwidth, - "Logical offset:"); + HDfprintf(stream, "%*s%-*s %Zd bytes\n", indent, "", fwidth, + "Chunk size:", key->nbytes); + HDfprintf(stream, "%*s%-*s 0x%08x\n", indent, "", fwidth, + "Filter mask:", key->filter_mask); + HDfprintf(stream, "%*s%-*s {", indent, "", fwidth, + "Logical offset:"); for (i=0; imesg.ndims; i++) { HDfprintf (stream, "%s%Hd", i?", ":"", key->offset[i]); } @@ -429,6 +436,7 @@ H5F_istore_new_node(H5F_t *f, H5B_ins_t op, * inserted into the tree. */ lt_key->nbytes = udata->key.nbytes; + lt_key->filter_mask = udata->key.filter_mask; for (i=0; imesg.ndims; i++) { lt_key->offset[i] = udata->key.offset[i]; } @@ -439,6 +447,7 @@ H5F_istore_new_node(H5F_t *f, H5B_ins_t op, */ if (H5B_INS_LEFT != op) { rt_key->nbytes = 0; + rt_key->filter_mask = 0; for (i=0; imesg.ndims; i++) { assert (udata->mesg.dim[i] < MAX_HSSIZET); assert (udata->key.offset[i]+(hssize_t)(udata->mesg.dim[i]) > @@ -494,6 +503,7 @@ H5F_istore_found(H5F_t __unused__ *f, const haddr_t *addr, /* Initialize return values */ udata->addr = *addr; udata->key.nbytes = lt_key->nbytes; + udata->key.filter_mask = lt_key->filter_mask; assert (lt_key->nbytes>0); for (i = 0; i < udata->mesg.ndims; i++) { udata->key.offset[i] = lt_key->offset[i]; @@ -589,6 +599,7 @@ H5F_istore_insert(H5F_t *f, const haddr_t *addr, void *_lt_key, "unable to reallocate chunk storage"); } lt_key->nbytes = udata->key.nbytes; + lt_key->filter_mask = udata->key.filter_mask; *lt_key_changed = TRUE; udata->addr = *new_node; ret_value = H5B_INS_CHANGE; @@ -608,6 +619,7 @@ H5F_istore_insert(H5F_t *f, const haddr_t *addr, void *_lt_key, * current node. The MD_KEY is where the split occurs. */ md_key->nbytes = udata->key.nbytes; + md_key->filter_mask = udata->key.filter_mask; for (i=0; imesg.ndims; i++) { assert(0 == udata->key.offset[i] % udata->mesg.dim[i]); md_key->offset[i] = udata->key.offset[i]; @@ -677,7 +689,10 @@ H5F_istore_init (H5F_t *f) /*------------------------------------------------------------------------- * Function: H5F_istore_flush_entry * - * Purpose: Writes a chunk to disk. + * Purpose: Writes a chunk to disk. If RESET is non-zero then the + * entry is cleared -- it's slightly faster to flush a chunk if + * the RESET flag is turned on because it results in one fewer + * memory copy. * * Return: Success: SUCCEED * @@ -691,65 +706,106 @@ H5F_istore_init (H5F_t *f) *------------------------------------------------------------------------- */ static herr_t -H5F_istore_flush_entry (H5F_t *f, H5F_rdcc_ent_t *ent) +H5F_istore_flush_entry (H5F_t *f, H5F_rdcc_ent_t *ent, hbool_t reset) { - void *c_buf = NULL; /*temp compression buffer */ - void *out_ptr = NULL; /*ptr to output buffer */ - size_t nbytes; /*size of output buffer */ - herr_t ret_value = FAIL; /*return value */ - H5F_istore_ud1_t udata; /*pass through B-tree */ - intn i; + herr_t ret_value=FAIL; /*return value */ + H5F_istore_ud1_t udata; /*pass through B-tree */ + intn i; /*counters */ + void *buf=NULL; /*temporary buffer */ + size_t alloc; /*bytes allocated for BUF */ + hbool_t point_of_no_return = FALSE; FUNC_ENTER (H5F_istore_flush_entry, FAIL); - assert (ent); + assert(f); + assert(ent); assert (!ent->locked); - if (!ent->dirty) HRETURN (SUCCEED); - /* Should the chunk be compressed before writing it to disk? */ - if (ent->comp && H5Z_NONE!=ent->comp->method) { - if (NULL==(c_buf = H5MM_malloc (ent->chunk_size))) { - HGOTO_ERROR (H5E_RESOURCE, H5E_NOSPACE, FAIL, - "memory allocation failed for data compression"); + buf = ent->chunk; + if (ent->dirty) { + udata.mesg = *(ent->layout); + udata.key.filter_mask = 0; + H5F_addr_undef(&(udata.addr)); + udata.key.nbytes = ent->chunk_size; + for (i=0; ilayout->ndims; i++) { + udata.key.offset[i] = ent->offset[i]; } - nbytes = H5Z_compress (ent->comp, ent->chunk_size, ent->chunk, c_buf); - if (nbytes && nbyteschunk_size) { - out_ptr = c_buf; - } else { - out_ptr = ent->chunk; - nbytes = ent->chunk_size; + alloc = ent->alloc_size; + + /* Should the chunk be filtered before writing it to disk? */ + if (ent->pline && ent->pline->nfilters) { + if (!reset) { + /* + * Copy the chunk to a new buffer before running it through + * the pipeline because we'll want to save the original buffer + * for later. + */ + alloc = ent->chunk_size; + if (NULL==(buf = H5MM_malloc(alloc))) { + HGOTO_ERROR(H5E_RESOURCE, H5E_NOSPACE, FAIL, + "memory allocation failed for pipeline"); + } + HDmemcpy(buf, ent->chunk, ent->chunk_size); + } else { + /* + * If we are reseting and something goes wrong after this + * point then it's too late to recover because we may have + * destroyed the original data by calling H5Z_pipeline(). + * The only safe option is to continue with the reset + * even if we can't write the data to disk. + */ + point_of_no_return = TRUE; + } + if (H5Z_pipeline(f, ent->pline, 0, &(udata.key.filter_mask), + &(udata.key.nbytes), &alloc, &buf)<0) { + HGOTO_ERROR(H5E_PLINE, H5E_WRITEERROR, FAIL, + "output pipeline failed"); + } } - } else { - out_ptr = ent->chunk; - nbytes = ent->chunk_size; + + /* + * Create the chunk it if it doesn't exist, or reallocate the chunk if + * its size changed. Then write the data into the file. + */ + if (H5B_insert(f, H5B_ISTORE, &(ent->layout->addr), &udata)<0) { + HGOTO_ERROR (H5E_IO, H5E_WRITEERROR, FAIL, + "unable to allocate chunk"); + } + if (H5F_block_write (f, &(udata.addr), udata.key.nbytes, H5D_XFER_DFLT, + buf)<0) { + HGOTO_ERROR (H5E_IO, H5E_WRITEERROR, FAIL, + "unable to write raw data to file"); + } + + /* Mark cache entry as clean */ + ent->dirty = FALSE; + f->shared->rdcc.nflushes++; } - /* - * Create the chunk it if it doesn't exist, or reallocate the chunk if its - * size changed. Then write the data into the file. - */ - udata.mesg = *(ent->layout); - H5F_addr_undef(&(udata.addr)); - udata.key.nbytes = nbytes; - for (i=0; ilayout->ndims; i++) { - udata.key.offset[i] = ent->offset[i]; + /* Reset */ + if (reset) { + point_of_no_return = FALSE; + ent->layout = H5O_free(H5O_LAYOUT, ent->layout); + ent->pline = H5O_free(H5O_PLINE, ent->pline); + if (buf==ent->chunk) buf = NULL; + ent->chunk = H5MM_xfree(ent->chunk); } - if (H5B_insert(f, H5B_ISTORE, &(ent->layout->addr), &udata)<0) { - HGOTO_ERROR (H5E_IO, H5E_WRITEERROR, FAIL, - "unable to allocate chunk"); - } - if (H5F_block_write (f, &(udata.addr), nbytes, H5D_XFER_DFLT, out_ptr)<0) { - HGOTO_ERROR (H5E_IO, H5E_WRITEERROR, FAIL, - "unable to write raw data to file"); - } - - /* Mark cache entry as clean */ - ent->dirty = FALSE; - f->shared->rdcc.nflushes++; ret_value = SUCCEED; done: - H5MM_xfree (c_buf); + /* Free the temp buffer only if it's different than the entry chunk */ + if (buf!=ent->chunk) H5MM_xfree(buf); + + /* + * If we reached the point of no return then we have no choice but to + * reset the entry. This can only happen if RESET is true but the + * output pipeline failed. + */ + if (ret_value<0 && point_of_no_return) { + ent->layout = H5O_free(H5O_LAYOUT, ent->layout); + ent->pline = H5O_free(H5O_PLINE, ent->pline); + ent->chunk = H5MM_xfree(ent->chunk); + } FUNC_LEAVE (ret_value); } @@ -780,7 +836,7 @@ H5F_istore_flush (H5F_t *f) FUNC_ENTER (H5F_istore_flush, FAIL); for (i=0; inused; i++) { - if (H5F_istore_flush_entry (f, rdcc->slot+i)<0) { + if (H5F_istore_flush_entry (f, rdcc->slot+i, FALSE)<0) { nerrors++; } } @@ -791,18 +847,17 @@ H5F_istore_flush (H5F_t *f) FUNC_LEAVE (SUCCEED); } - /*------------------------------------------------------------------------- - * Function: H5F_istore_preempt + * Function: H5F_istore_preempt * - * Purpose: Preempts the specified entry from the cache, flushing it to - * disk if necessary. + * Purpose: Preempts the specified entry from the cache, flushing it to + * disk if necessary. * - * Return: Success: SUCCEED + * Return: Success: SUCCEED * - * Failure: FAIL + * Failure: FAIL * - * Programmer: Robb Matzke + * Programmer: Robb Matzke * Thursday, May 21, 1998 * * Modifications: @@ -812,21 +867,18 @@ H5F_istore_flush (H5F_t *f) static herr_t H5F_istore_preempt (H5F_t *f, intn idx) { - H5F_rdcc_t *rdcc = &(f->shared->rdcc); - H5F_rdcc_ent_t *ent = rdcc->slot + idx; + H5F_rdcc_t *rdcc = &(f->shared->rdcc); + H5F_rdcc_ent_t *ent = rdcc->slot + idx; FUNC_ENTER (H5F_istore_preempt, FAIL); assert (idx>=0 && idxnused); assert (!ent->locked); - if (ent->dirty) H5F_istore_flush_entry (f, ent); - H5O_free (H5O_LAYOUT, ent->layout); - H5O_free (H5O_COMPRESS, ent->comp); - H5MM_xfree (ent->chunk); + H5F_istore_flush_entry (f, ent, TRUE); + HDmemmove (rdcc->slot+idx, rdcc->slot+idx+1, + (rdcc->nused-idx) * sizeof(H5F_rdcc_ent_t)); rdcc->nused -= 1; rdcc->nbytes -= ent->chunk_size; - HDmemmove (rdcc->slot+idx, rdcc->slot+idx+1, - (rdcc->nused-idx) * sizeof(H5F_rdcc_ent_t)); FUNC_LEAVE (SUCCEED); } @@ -858,10 +910,10 @@ H5F_istore_dest (H5F_t *f) FUNC_ENTER (H5F_istore_dest, FAIL); for (i=rdcc->nused-1; i>=0; --i) { - if (H5F_istore_flush_entry (f, rdcc->slot+i)<0) { + if (H5F_istore_flush_entry (f, rdcc->slot+i, TRUE)<0) { nerrors++; } - if (H5F_istore_preempt (f, i)<0) { + if (H5F_istore_preempt(f, i)<0) { nerrors++; } } @@ -951,7 +1003,7 @@ H5F_istore_prune (H5F_t *f, size_t size) /*------------------------------------------------------------------------- * Function: H5F_istore_lock * - * Purpose: Return a pointer to an uncompressed chunk. The pointer + * Purpose: Return a pointer to a file chunk chunk. The pointer * points directly into the chunk cache and should not be freed * by the caller but will be valid until it is unlocked. The * input value IDX_HINT is used to speed up cache lookups and @@ -963,7 +1015,7 @@ H5F_istore_prune (H5F_t *f, size_t size) * for output functions that are about to overwrite the entire * chunk. * - * Return: Success: Ptr to an uncompressed chunk. + * Return: Success: Ptr to a file chunk. * * Failure: NULL * @@ -976,7 +1028,7 @@ H5F_istore_prune (H5F_t *f, size_t size) */ static void * H5F_istore_lock (H5F_t *f, const H5O_layout_t *layout, - const H5O_compress_t *comp, const hssize_t offset[], + const H5O_pline_t *pline, const hssize_t offset[], hbool_t relax, intn *idx_hint/*in,out*/) { H5F_rdcc_t *rdcc = &(f->shared->rdcc); @@ -984,8 +1036,9 @@ H5F_istore_lock (H5F_t *f, const H5O_layout_t *layout, intn i, j, found = -1; H5F_istore_ud1_t udata; /*B-tree pass-through */ size_t chunk_size=0; /*size of a chunk */ + size_t chunk_alloc=0; /*allocated chunk size */ herr_t status; /*func return status */ - void *chunk=NULL; /*the uncompressed chunk*/ + void *chunk=NULL; /*the file chunk */ void *temp=NULL; /*temporary chunk buffer*/ void *ret_value=NULL; /*return value */ @@ -1031,7 +1084,8 @@ H5F_istore_lock (H5F_t *f, const H5O_layout_t *layout, for (i=0, chunk_size=1; indims; i++) { chunk_size *= layout->dim[i]; } - if (NULL==(chunk=H5MM_malloc (chunk_size))) { + chunk_alloc = chunk_size; + if (NULL==(chunk=H5MM_malloc (chunk_alloc))) { HGOTO_ERROR (H5E_RESOURCE, H5E_NOSPACE, NULL, "memory allocation failed for raw data chunk"); } @@ -1045,39 +1099,30 @@ H5F_istore_lock (H5F_t *f, const H5O_layout_t *layout, udata.key.offset[i] = offset[i]; chunk_size *= layout->dim[i]; } + chunk_alloc = chunk_size; udata.mesg = *layout; H5F_addr_undef (&(udata.addr)); status = H5B_find (f, H5B_ISTORE, &(layout->addr), &udata); H5E_clear (); - if (NULL==(chunk = H5MM_malloc (chunk_size))) { + if (NULL==(chunk = H5MM_malloc (chunk_alloc))) { HGOTO_ERROR (H5E_RESOURCE, H5E_NOSPACE, NULL, "memory allocation failed for raw data chunk"); } if (status>=0 && H5F_addr_defined (&(udata.addr))) { /* - * The chunk exists on disk but might be compressed. Instead of - * allocating the exact size for the compressed chunk we allocate - * the entire chunk size -- it reduces strain on the malloc() - * subsystem. + * The chunk exists on disk. */ if (H5F_block_read (f, &(udata.addr), udata.key.nbytes, H5D_XFER_DFLT, chunk)<0) { HGOTO_ERROR (H5E_IO, H5E_READERROR, NULL, "unable to read raw data chunk"); } - if (udata.key.nbytesnmisses++; } else { @@ -1117,8 +1162,9 @@ H5F_istore_lock (H5F_t *f, const H5O_layout_t *layout, ent->locked = 0; ent->dirty = FALSE; ent->chunk_size = chunk_size; + ent->alloc_size = chunk_alloc; ent->layout = H5O_copy (H5O_LAYOUT, layout); - ent->comp = H5O_copy (H5O_COMPRESS, comp); + ent->pline = H5O_copy (H5O_PLINE, pline); for (i=0; indims; i++) { ent->offset[i] = offset[i]; } @@ -1191,7 +1237,7 @@ H5F_istore_lock (H5F_t *f, const H5O_layout_t *layout, */ static herr_t H5F_istore_unlock (H5F_t *f, const H5O_layout_t *layout, - const H5O_compress_t *comp, hbool_t dirty, + const H5O_pline_t *pline, hbool_t dirty, const hssize_t offset[], intn *idx_hint, uint8 *chunk, size_t naccessed) { @@ -1215,7 +1261,7 @@ H5F_istore_unlock (H5F_t *f, const H5O_layout_t *layout, /* * It's not in the cache, probably because it's too big. If it's * dirty then flush it to disk. In any case, free the chunk. - * Note: we have to copy the layout and compression messages so we + * Note: we have to copy the layout and filter messages so we * don't discard the `const' qualifier. */ if (dirty) { @@ -1223,17 +1269,16 @@ H5F_istore_unlock (H5F_t *f, const H5O_layout_t *layout, HDmemset (&x, 0, sizeof x); x.dirty = TRUE; x.layout = H5O_copy (H5O_LAYOUT, layout); - x.comp = H5O_copy (H5O_COMPRESS, comp); + x.pline = H5O_copy (H5O_PLINE, pline); for (i=0, x.chunk_size=1; indims; i++) { x.offset[i] = offset[i]; x.chunk_size *= layout->dim[i]; } x.chunk = chunk; - H5F_istore_flush_entry (f, &x); - H5O_free (H5O_LAYOUT, x.layout); - H5O_free (H5O_COMPRESS, x.comp); + H5F_istore_flush_entry (f, &x, TRUE); + } else { + H5MM_xfree (chunk); } - H5MM_xfree (chunk); } else { /* * It's in the cache so unlock it. @@ -1272,7 +1317,7 @@ H5F_istore_unlock (H5F_t *f, const H5O_layout_t *layout, */ herr_t H5F_istore_read(H5F_t *f, const H5O_layout_t *layout, - const H5O_compress_t *comp, const hssize_t offset_f[], + const H5O_pline_t *pline, const hssize_t offset_f[], const hsize_t size[], void *buf) { hssize_t offset_m[H5O_LAYOUT_NDIMS]; @@ -1375,7 +1420,7 @@ H5F_istore_read(H5F_t *f, const H5O_layout_t *layout, l.dim[i] = layout->dim[i]; l.addr = udata.addr; if (H5F_arr_read(f, &l, - comp, NULL /* no efl */, + pline, NULL /* no efl */, sub_size, size_m, sub_offset_m, offset_wrt_chunk, H5D_XFER_DFLT, buf)==FAIL){ @@ -1397,15 +1442,15 @@ H5F_istore_read(H5F_t *f, const H5O_layout_t *layout, * Lock the chunk, transfer data to the application, then unlock the * chunk. */ - if (NULL==(chunk=H5F_istore_lock (f, layout, comp, chunk_offset, + if (NULL==(chunk=H5F_istore_lock (f, layout, pline, chunk_offset, FALSE, &idx_hint))) { HRETURN_ERROR (H5E_IO, H5E_READERROR, FAIL, "unable to read raw data chunk"); } H5V_hyper_copy(layout->ndims, sub_size, size_m, sub_offset_m, (void*)buf, layout->dim, offset_wrt_chunk, chunk); - if (H5F_istore_unlock (f, layout, comp, FALSE, chunk_offset, &idx_hint, - chunk, naccessed)<0) { + if (H5F_istore_unlock (f, layout, pline, FALSE, chunk_offset, + &idx_hint, chunk, naccessed)<0) { HRETURN_ERROR (H5E_IO, H5E_READERROR, FAIL, "unable to unlock raw data chunk"); } @@ -1443,7 +1488,7 @@ H5F_istore_read(H5F_t *f, const H5O_layout_t *layout, */ herr_t H5F_istore_write(H5F_t *f, const H5O_layout_t *layout, - const H5O_compress_t *comp, const hssize_t offset_f[], + const H5O_pline_t *pline, const hssize_t offset_f[], const hsize_t size[], const void *buf) { hssize_t offset_m[H5O_LAYOUT_NDIMS]; @@ -1550,7 +1595,7 @@ H5F_istore_write(H5F_t *f, const H5O_layout_t *layout, l.dim[i] = layout->dim[i]; l.addr = udata.addr; if (H5F_arr_write(f, &l, - comp, NULL /* no efl */, + pline, NULL /* no efl */, sub_size, size_m, sub_offset_m, offset_wrt_chunk, H5D_XFER_DFLT, buf)==FAIL){ @@ -1571,7 +1616,7 @@ H5F_istore_write(H5F_t *f, const H5O_layout_t *layout, * Lock the chunk, copy from application to chunk, then unlock the * chunk. */ - if (NULL==(chunk=H5F_istore_lock (f, layout, comp, chunk_offset, + if (NULL==(chunk=H5F_istore_lock (f, layout, pline, chunk_offset, naccessed==chunk_size, &idx_hint))) { HRETURN_ERROR (H5E_IO, H5E_WRITEERROR, FAIL, @@ -1580,7 +1625,7 @@ H5F_istore_write(H5F_t *f, const H5O_layout_t *layout, H5V_hyper_copy(layout->ndims, sub_size, layout->dim, offset_wrt_chunk, chunk, size_m, sub_offset_m, buf); - if (H5F_istore_unlock (f, layout, comp, TRUE, chunk_offset, + if (H5F_istore_unlock (f, layout, pline, TRUE, chunk_offset, &idx_hint, chunk, naccessed)<0) { HRETURN_ERROR (H5E_IO, H5E_WRITEERROR, FAIL, "uanble to unlock raw data chunk"); @@ -1826,7 +1871,7 @@ H5F_istore_get_addr (H5F_t *f, const H5O_layout_t *layout, */ herr_t H5F_istore_allocate (H5F_t *f, const H5O_layout_t *layout, - const hsize_t *space_dim, const H5O_compress_t *comp) + const hsize_t *space_dim, const H5O_pline_t *pline) { intn i, carry; @@ -1846,7 +1891,7 @@ H5F_istore_allocate (H5F_t *f, const H5O_layout_t *layout, /* Check args */ assert(f); assert(space_dim); - assert(comp); + assert(pline); assert(layout && H5D_CHUNKED==layout->type); assert(layout->ndims>0 && layout->ndims<=H5O_LAYOUT_NDIMS); assert(H5F_addr_defined(&(layout->addr))); @@ -1885,13 +1930,13 @@ H5F_istore_allocate (H5F_t *f, const H5O_layout_t *layout, * Lock the chunk, copy from application to chunk, then unlock the * chunk. */ - if (NULL==(chunk=H5F_istore_lock (f, layout, comp, chunk_offset, + if (NULL==(chunk=H5F_istore_lock (f, layout, pline, chunk_offset, FALSE, &idx_hint))) { HRETURN_ERROR (H5E_IO, H5E_WRITEERROR, FAIL, "unable to read raw data chunk"); } - if (H5F_istore_unlock (f, layout, comp, TRUE, chunk_offset, &idx_hint, - chunk, chunk_size)<0) { + if (H5F_istore_unlock (f, layout, pline, TRUE, chunk_offset, + &idx_hint, chunk, chunk_size)<0) { HRETURN_ERROR (H5E_IO, H5E_WRITEERROR, FAIL, "uanble to unlock raw data chunk"); } diff --git a/src/H5Fprivate.h b/src/H5Fprivate.h index b9d0c59..b230b06 100644 --- a/src/H5Fprivate.h +++ b/src/H5Fprivate.h @@ -493,7 +493,7 @@ typedef struct H5F_t { struct H5O_layout_t; /*forward decl for prototype arguments */ struct H5O_efl_t; /*forward decl for prototype arguments */ -struct H5O_compress_t; /*forward decl for prototype arguments */ +struct H5O_pline_t; /*forward decl for prototype arguments */ /* library variables */ extern const H5F_create_t H5F_create_dflt; @@ -514,13 +514,13 @@ herr_t H5F_istore_debug(H5F_t *f, const haddr_t *addr, FILE * stream, /* Functions that operate on array storage */ herr_t H5F_arr_create(H5F_t *f, struct H5O_layout_t *layout /*in,out*/); herr_t H5F_arr_read (H5F_t *f, const struct H5O_layout_t *layout, - const struct H5O_compress_t *comp, + const struct H5O_pline_t *pline, const struct H5O_efl_t *efl, const hsize_t _hslab_size[], const hsize_t mem_size[], const hssize_t mem_offset[], const hssize_t file_offset[], const H5D_transfer_t xfer_mode, void *_buf/*out*/); herr_t H5F_arr_write (H5F_t *f, const struct H5O_layout_t *layout, - const struct H5O_compress_t *comp, + const struct H5O_pline_t *pline, const struct H5O_efl_t *efl, const hsize_t _hslab_size[], const hsize_t mem_size[], const hssize_t mem_offset[], const hssize_t file_offset[], @@ -533,17 +533,17 @@ herr_t H5F_istore_dest (H5F_t *f); herr_t H5F_istore_stats (H5F_t *f, hbool_t headers); herr_t H5F_istore_create(H5F_t *f, struct H5O_layout_t *layout /*in,out*/); herr_t H5F_istore_read(H5F_t *f, const struct H5O_layout_t *layout, - const struct H5O_compress_t *comp, + const struct H5O_pline_t *pline, const hssize_t offset[], const hsize_t size[], void *buf /*out */ ); herr_t H5F_istore_write(H5F_t *f, const struct H5O_layout_t *layout, - const struct H5O_compress_t *comp, + const struct H5O_pline_t *pline, const hssize_t offset[], const hsize_t size[], const void *buf); herr_t H5F_istore_allocate (H5F_t *f, const struct H5O_layout_t *layout, const hsize_t *space_dim, - const struct H5O_compress_t *comp); + const struct H5O_pline_t *pline); /* Functions that operate on contiguous storage wrt boot block */ herr_t H5F_block_read(H5F_t *f, const haddr_t *addr, hsize_t size, diff --git a/src/H5G.c b/src/H5G.c index 75ce590..1bb00ef 100644 --- a/src/H5G.c +++ b/src/H5G.c @@ -2176,7 +2176,7 @@ H5G_get_comment(H5G_t *loc, const char *name, size_t bufsize, char *buf) retval = 0; } else { strncpy(buf, comment.s, bufsize); - retval = strlen(comment.s); + retval = (intn)strlen(comment.s); H5O_reset(H5O_NAME, &comment); } diff --git a/src/H5O.c b/src/H5O.c index c3bb495..70f5181 100644 --- a/src/H5O.c +++ b/src/H5O.c @@ -62,7 +62,7 @@ static const H5O_class_t *const message_type_g[] = { H5O_LAYOUT, /*0x0008 Data Layout */ NULL, /*0x0009 Not assigned */ NULL, /*0x000A Not assigned */ - H5O_COMPRESS, /*0x000B Data storage -- compressed object */ + H5O_PLINE, /*0x000B Data storage -- filter pipeline */ H5O_ATTR, /*0x000C Attribute list */ H5O_NAME, /*0x000D Object name */ H5O_MTIME, /*0x000E Object modification date and time */ diff --git a/src/H5Ocomp.c b/src/H5Ocomp.c index 3f341ea..a30eb6f 100644 --- a/src/H5Ocomp.c +++ b/src/H5Ocomp.c @@ -5,48 +5,49 @@ * Programmer: Robb Matzke * Wednesday, April 15, 1998 * - * Purpose: Data compression message. + * Purpose: Data filter pipeline message. */ #include #include #include #include -#define PABLO_MASK H5O_comp_mask +/* Interface initialization */ +#define PABLO_MASK H5O_pline_mask +static hbool_t interface_initialize_g = FALSE; +#define INTERFACE_INIT NULL -/* PRIVATE PROTOTYPES */ -static herr_t H5O_comp_encode (H5F_t *f, uint8 *p, const void *mesg); -static void *H5O_comp_decode (H5F_t *f, const uint8 *p, H5O_shared_t *sh); -static void *H5O_comp_copy (const void *_mesg, void *_dest); -static size_t H5O_comp_size (H5F_t *f, const void *_mesg); -static herr_t H5O_comp_reset (void *_mesg); -static herr_t H5O_comp_debug (H5F_t *f, const void *_mesg, - FILE * stream, intn indent, intn fwidth); +#define H5O_PLINE_VERSION 1 + +static herr_t H5O_pline_encode (H5F_t *f, uint8 *p, const void *mesg); +static void *H5O_pline_decode (H5F_t *f, const uint8 *p, H5O_shared_t *sh); +static void *H5O_pline_copy (const void *_mesg, void *_dest); +static size_t H5O_pline_size (H5F_t *f, const void *_mesg); +static herr_t H5O_pline_reset (void *_mesg); +static herr_t H5O_pline_debug (H5F_t *f, const void *_mesg, + FILE * stream, intn indent, intn fwidth); /* This message derives from H5O */ -const H5O_class_t H5O_COMPRESS[1] = {{ - H5O_COMPRESS_ID, /* message id number */ - "compression", /* message name for debugging */ - sizeof(H5O_compress_t), /* native message size */ - H5O_comp_decode, /* decode message */ - H5O_comp_encode, /* encode message */ - H5O_comp_copy, /* copy the native value */ - H5O_comp_size, /* size of raw message */ - H5O_comp_reset, /* reset method */ +const H5O_class_t H5O_PLINE[1] = {{ + H5O_PLINE_ID, /* message id number */ + "filter pipeline", /* message name for debugging */ + sizeof(H5O_pline_t), /* native message size */ + H5O_pline_decode, /* decode message */ + H5O_pline_encode, /* encode message */ + H5O_pline_copy, /* copy the native value */ + H5O_pline_size, /* size of raw message */ + H5O_pline_reset, /* reset method */ NULL, /* get share method */ NULL, /* set share method */ - H5O_comp_debug, /* debug the message */ + H5O_pline_debug, /* debug the message */ }}; -/* Interface initialization */ -static hbool_t interface_initialize_g = FALSE; -#define INTERFACE_INIT NULL /*------------------------------------------------------------------------- - * Function: H5O_comp_decode + * Function: H5O_pline_decode * - * Purpose: Decodes a compression message. + * Purpose: Decodes a filter pipeline message. * * Return: Success: Ptr to the native message. * @@ -60,46 +61,97 @@ static hbool_t interface_initialize_g = FALSE; *------------------------------------------------------------------------- */ static void * -H5O_comp_decode(H5F_t __unused__ *f, const uint8 *p, +H5O_pline_decode(H5F_t __unused__ *f, const uint8 *p, H5O_shared_t __unused__ *sh) { - H5O_compress_t *comp = NULL; + H5O_pline_t *pline = NULL; void *ret_value = NULL; + uintn version; + size_t i, j, n, name_length; - FUNC_ENTER(H5O_comp_decode, NULL); + FUNC_ENTER(H5O_pline_decode, NULL); /* check args */ assert(p); /* Decode */ - if (NULL==(comp = H5MM_calloc(sizeof *comp))) { + if (NULL==(pline = H5MM_calloc(sizeof *pline))) { HGOTO_ERROR (H5E_RESOURCE, H5E_NOSPACE, NULL, "memory allocation failed"); } - comp->method = *p++; - comp->flags = *p++; - UINT16DECODE (p, comp->cd_size); - - if (comp->cd_size>0) { - if (NULL==(comp->client_data = H5MM_malloc (comp->cd_size))) { - HGOTO_ERROR (H5E_RESOURCE, H5E_NOSPACE, NULL, - "memory allocation failed"); + version = *p++; + if (version!=H5O_PLINE_VERSION) { + HGOTO_ERROR(H5E_PLINE, H5E_CANTLOAD, NULL, + "bad version number for filter pipeline message"); + } + pline->nfilters = *p++; + if (pline->nfilters>32) { + HGOTO_ERROR(H5E_PLINE, H5E_CANTLOAD, NULL, + "filter pipeline message has too many filters"); + } + p += 6; /*reserved*/ + pline->nalloc = pline->nfilters; + pline->filter = H5MM_calloc(pline->nalloc*sizeof(pline->filter[0])); + if (NULL==pline->filter) { + HGOTO_ERROR(H5E_RESOURCE, H5E_NOSPACE, NULL, + "memory allocation failed"); + } + for (i=0; infilters; i++) { + UINT16DECODE(p, pline->filter[i].id); + UINT16DECODE(p, name_length); + if (name_length % 8) { + HGOTO_ERROR(H5E_PLINE, H5E_CANTLOAD, NULL, + "filter name length is not a multiple of eight"); + } + UINT16DECODE(p, pline->filter[i].flags); + UINT16DECODE(p, pline->filter[i].cd_nelmts); + if (name_length) { + /* + * Get the name, allocating an extra byte for an extra null + * terminator just in case there isn't one in the file (there + * should be, but to be safe...) + */ + pline->filter[i].name = H5MM_malloc(name_length+1); + memcpy(pline->filter[i].name, p, name_length); + pline->filter[i].name[name_length] = '\0'; + p += name_length; + } + if ((n=pline->filter[i].cd_nelmts)) { + /* + * Read the client data values and the padding + */ + pline->filter[i].cd_values = H5MM_malloc(n*sizeof(uintn)); + if (NULL==pline->filter[i].cd_values) { + HGOTO_ERROR(H5E_RESOURCE, H5E_NOSPACE, NULL, + "memory allocation failed for client data"); + } + for (j=0; jfilter[i].cd_nelmts; j++) { + UINT32DECODE(p, pline->filter[i].cd_values[j]); + } + if (pline->filter[i].cd_nelmts % 2) { + p += 4; /*padding*/ + } } - HDmemcpy (comp->client_data, p, comp->cd_size); } - ret_value = comp; + ret_value = pline; done: - if (NULL==ret_value && comp) { - H5MM_xfree (comp->client_data); - H5MM_xfree (comp); + if (NULL==ret_value && pline) { + if (pline->filter) { + for (i=0; infilters; i++) { + H5MM_xfree(pline->filter[i].name); + H5MM_xfree(pline->filter[i].cd_values); + } + H5MM_xfree(pline->filter); + } + H5MM_xfree(pline); } FUNC_LEAVE(ret_value); } /*------------------------------------------------------------------------- - * Function: H5O_comp_encode + * Function: H5O_pline_encode * * Purpose: Encodes message MESG into buffer P. * @@ -115,21 +167,47 @@ H5O_comp_decode(H5F_t __unused__ *f, const uint8 *p, *------------------------------------------------------------------------- */ static herr_t -H5O_comp_encode (H5F_t __unused__ *f, uint8 *p/*out*/, const void *mesg) +H5O_pline_encode (H5F_t __unused__ *f, uint8 *p/*out*/, const void *mesg) { - const H5O_compress_t *comp = (const H5O_compress_t*)mesg; + const H5O_pline_t *pline = (const H5O_pline_t*)mesg; + size_t i, j, name_length; - FUNC_ENTER (H5O_comp_encode, FAIL); + FUNC_ENTER (H5O_pline_encode, FAIL); /* Check args */ assert (p); assert (mesg); - *p++ = comp->method; - *p++ = comp->flags; - UINT16ENCODE (p, comp->cd_size); - if (comp->cd_size) { - HDmemcpy (p, comp->client_data, comp->cd_size); + *p++ = H5O_PLINE_VERSION; + *p++ = pline->nfilters; + *p++ = 0; /*reserved 1*/ + *p++ = 0; /*reserved 2*/ + *p++ = 0; /*reserved 3*/ + *p++ = 0; /*reserved 4*/ + *p++ = 0; /*reserved 5*/ + *p++ = 0; /*reserved 6*/ + + for (i=0; infilters; i++) { + if (pline->filter[i].name) { + name_length = strlen(pline->filter[i].name)+1; + } else { + name_length = 0; + } + UINT16ENCODE(p, pline->filter[i].id); + UINT16ENCODE(p, H5O_ALIGN(name_length)); + UINT16ENCODE(p, pline->filter[i].flags); + UINT16ENCODE(p, pline->filter[i].cd_nelmts); + if (name_length>0) { + memcpy(p, pline->filter[i].name, name_length); + p += name_length; + while (name_length++ % 8) *p++ = 0; + } + for (j=0; jfilter[i].cd_nelmts; j++) { + UINT32ENCODE(p, pline->filter[i].cd_values[j]); + } + if (pline->filter[i].cd_nelmts % 2) { + UINT32ENCODE(p, 0); + } } FUNC_LEAVE (SUCCEED); @@ -137,10 +215,10 @@ H5O_comp_encode (H5F_t __unused__ *f, uint8 *p/*out*/, const void *mesg) /*------------------------------------------------------------------------- - * Function: H5O_comp_copy + * Function: H5O_pline_copy * - * Purpose: Copies a compression message from SRC to DST allocating DST - * if necessary. If DST is already allocated then we assume + * Purpose: Copies a filter pipeline message from SRC to DST allocating + * DST if necessary. If DST is already allocated then we assume * that it isn't initialized. * * Return: Success: Ptr to DST or allocated result. @@ -155,34 +233,70 @@ H5O_comp_encode (H5F_t __unused__ *f, uint8 *p/*out*/, const void *mesg) *------------------------------------------------------------------------- */ static void * -H5O_comp_copy (const void *_src, void *_dst/*out*/) +H5O_pline_copy (const void *_src, void *_dst/*out*/) { - const H5O_compress_t *src = (const H5O_compress_t *)_src; - H5O_compress_t *dst = (H5O_compress_t *)_dst; + const H5O_pline_t *src = (const H5O_pline_t *)_src; + H5O_pline_t *dst = (H5O_pline_t *)_dst; + size_t i; + H5O_pline_t *ret_value = NULL; - FUNC_ENTER (H5O_comp_copy, NULL); + FUNC_ENTER (H5O_pline_copy, NULL); if (!dst && NULL==(dst = H5MM_malloc (sizeof *dst))) { HRETURN_ERROR (H5E_RESOURCE, H5E_NOSPACE, NULL, "memory allocation failed"); } + *dst = *src; - if (src->cd_size>0) { - if (NULL==(dst->client_data = H5MM_malloc (src->cd_size))) { - HRETURN_ERROR (H5E_RESOURCE, H5E_NOSPACE, NULL, - "memory allocation failed"); + dst->nalloc = dst->nfilters; + if (dst->nalloc>0) { + dst->filter = H5MM_calloc(dst->nalloc * sizeof(dst->filter[0])); + if (NULL==dst->filter) { + HGOTO_ERROR(H5E_RESOURCE, H5E_NOSPACE, NULL, + "memory allocation failed"); + } + } else { + dst->filter = NULL; + } + + for (i=0; infilters; i++) { + dst->filter[i] = src->filter[i]; + if (src->filter[i].name) { + dst->filter[i].name = H5MM_xstrdup(src->filter[i].name); + } + if (src->filter[i].cd_nelmts>0) { + dst->filter[i].cd_values = H5MM_malloc(src->filter[i].cd_nelmts* + sizeof(uintn)); + if (NULL==dst->filter[i].cd_values) { + HGOTO_ERROR (H5E_RESOURCE, H5E_NOSPACE, NULL, + "memory allocation failed"); + } + HDmemcpy (dst->filter[i].cd_values, src->filter[i].cd_values, + src->filter[i].cd_nelmts * sizeof(uintn)); } - HDmemcpy (dst->client_data, src->client_data, src->cd_size); } + ret_value = dst; - FUNC_LEAVE (dst); + done: + if (!ret_value && dst) { + if (dst->filter) { + for (i=0; infilters; i++) { + H5MM_xfree(dst->filter[i].name); + H5MM_xfree(dst->filter[i].cd_values); + } + H5MM_xfree(dst->filter); + } + if (!_dst) H5MM_xfree(dst); + } + + FUNC_LEAVE (ret_value); } /*------------------------------------------------------------------------- - * Function: H5O_comp_size + * Function: H5O_pline_size * - * Purpose: Determines the size of a raw compression message. + * Purpose: Determines the size of a raw filter pipeline message. * * Return: Success: Size of message. * @@ -196,20 +310,39 @@ H5O_comp_copy (const void *_src, void *_dst/*out*/) *------------------------------------------------------------------------- */ static size_t -H5O_comp_size (H5F_t __unused__ *f, const void *mesg) +H5O_pline_size (H5F_t __unused__ *f, const void *mesg) { - const H5O_compress_t *comp = (const H5O_compress_t*)mesg; - - FUNC_ENTER (H5O_comp_size, 0); - FUNC_LEAVE (4+comp->cd_size); + const H5O_pline_t *pline = (const H5O_pline_t*)mesg; + size_t i, size; + + FUNC_ENTER (H5O_pline_size, 0); + + size = 1 + /*version */ + 1 + /*number of filters */ + 6; /*reserved */ + + for (i=0; infilters; i++) { + size += 2 + /*filter identification number */ + 2 + /*name length */ + 2 + /*flags */ + 2; /*number of client data values */ + if (pline->filter[i].name) { + size_t n = strlen(pline->filter[i].name) + 1; + size += H5O_ALIGN(n); + } + size += pline->filter[i].cd_nelmts * 4; + if (pline->filter[i].cd_nelmts % 2) size += 4; + } + + FUNC_LEAVE (size); } /*------------------------------------------------------------------------- - * Function: H5O_comp_reset + * Function: H5O_pline_reset * - * Purpose: Resets a compression message by freeing the client data and - * setting all fields to zero. The MESG buffer is not freed. + * Purpose: Resets a filter pipeline message by clearing all filters. + * The MESG buffer is not freed. * * Return: Success: SUCCEED * @@ -223,25 +356,30 @@ H5O_comp_size (H5F_t __unused__ *f, const void *mesg) *------------------------------------------------------------------------- */ static herr_t -H5O_comp_reset (void *mesg) +H5O_pline_reset (void *mesg) { - H5O_compress_t *comp = (H5O_compress_t*)mesg; + H5O_pline_t *pline = (H5O_pline_t*)mesg; + size_t i; - FUNC_ENTER (H5O_comp_reset, FAIL); + FUNC_ENTER (H5O_pline_reset, FAIL); - assert (comp); - H5MM_xfree (comp->client_data); - HDmemset (comp, 0, sizeof *comp); + assert (pline); + for (i=0; infilters; i++) { + H5MM_xfree(pline->filter[i].name); + H5MM_xfree(pline->filter[i].cd_values); + } + H5MM_xfree(pline->filter); + HDmemset(pline, 0, sizeof *pline); FUNC_LEAVE (SUCCEED); } /*------------------------------------------------------------------------- - * Function: H5O_comp_debug + * Function: H5O_pline_debug * - * Purpose: Prints debugging information for compression message MESG on - * output stream STREAM. Each line is indented INDENT + * Purpose: Prints debugging information for filter pipeline message MESG + * on output stream STREAM. Each line is indented INDENT * characters and the field name takes up FWIDTH characters. * * Return: Success: SUCCEED @@ -256,56 +394,54 @@ H5O_comp_reset (void *mesg) *------------------------------------------------------------------------- */ static herr_t -H5O_comp_debug (H5F_t __unused__ *f, const void *mesg, FILE *stream, +H5O_pline_debug (H5F_t __unused__ *f, const void *mesg, FILE *stream, intn indent, intn fwidth) { - const H5O_compress_t *comp = (const H5O_compress_t *)mesg; - size_t i, j; + const H5O_pline_t *pline = (const H5O_pline_t *)mesg; + size_t i, j; - FUNC_ENTER(H5O_comp_debug, FAIL); + FUNC_ENTER(H5O_pline_debug, FAIL); /* check args */ assert(f); - assert(comp); + assert(pline); assert(stream); assert(indent >= 0); assert(fwidth >= 0); - fprintf (stream, "%*s%-*s %d\n", indent, "", fwidth, - "Method:", - (int)(comp->method)); - fprintf (stream, "%*s%-*s 0x%02x\n", indent, "", fwidth, - "Flags:", - (unsigned)(comp->flags)); - fprintf (stream, "%*s%-*s %lu\n", indent, "", fwidth, - "Size of client data:", - (unsigned long)(comp->cd_size)); - - if (comp->cd_size>0) { - fprintf (stream, "%*s%s\n", indent, "", "Client Data:"); - for (i=0; icd_size; i+=16) { - fprintf (stream, "%*s%04d: ", indent+3, "", i); - for (j=0; j<16; j++) { - if (8==j) putc (' ', stream); - if (i+jcd_size) { - fprintf (stream, "%02x ", comp->client_data[i+j]); - } else { - fputs (" ", stream); - } - } - for (j=0; j<16 && i+jcd_size; j++) { - if (8==j) putc (' ', stream); - if (comp->client_data[i+j]>' ' && - comp->client_data[i+j]<='~') { - putc (comp->client_data[i+j], stream); - } else { - putc ('.', stream); - } - putc ('\n', stream); - } + fprintf(stream, "%*s%-*s %lu/%lu\n", indent, "", fwidth, + "Number of filters:", + (unsigned long)(pline->nfilters), + (unsigned long)(pline->nalloc)); + + for (i=0; infilters; i++) { + char name[32]; + sprintf(name, "Filter at position %lu", (unsigned long)i); + fprintf(stream, "%*s%-*s\n", indent, "", fwidth, name); + fprintf(stream, "%*s%-*s 0x%04x\n", indent+3, "", MAX(0, fwidth-3), + "Filter identification:", + (unsigned)(pline->filter[i].id)); + if (pline->filter[i].name) { + fprintf(stream, "%*s%-*s \"%s\"\n", indent+3, "", MAX(0, fwidth-3), + "Filter name:", + pline->filter[i].name); + } else { + fprintf(stream, "%*s%-*s NONE\n", indent+3, "", MAX(0, fwidth-3), + "Filter name:"); + } + fprintf(stream, "%*s%-*s 0x%04x\n", indent+3, "", MAX(0, fwidth-3), + "Flags:", + (unsigned)(pline->filter[i].flags)); + fprintf(stream, "%*s%-*s %lu\n", indent+3, "", MAX(0, fwidth-3), + "Num CD values:", + (unsigned long)(pline->filter[i].cd_nelmts)); + for (j=0; jfilter[i].cd_nelmts; j++) { + char field_name[32]; + sprintf(field_name, "CD value %d", j); + fprintf(stream, "%*s%-*s %lu\n", indent+6, "", MAX(0, fwidth-6), + field_name, + (unsigned long)(pline->filter[i].cd_values[j])); } - } else { - fprintf (stream, "%*s%-*s None\n", indent, "", fwidth, "Client Data:"); } FUNC_LEAVE(SUCCEED); diff --git a/src/H5Oprivate.h b/src/H5Oprivate.h index 92ba11a..370603f 100644 --- a/src/H5Oprivate.h +++ b/src/H5Oprivate.h @@ -169,17 +169,22 @@ typedef struct H5O_layout_t { } H5O_layout_t; /* - * Compression message. + * Filter pipeline message. */ -#define H5O_COMPRESS_ID 0x000b -extern const H5O_class_t H5O_COMPRESS[1]; - -typedef struct H5O_compress_t { - H5Z_method_t method; /*algorithm ID */ - uintn flags; /*flags */ - size_t cd_size; /*client data size */ - uint8 *client_data; /*client data passed to algorithm */ -} H5O_compress_t; +#define H5O_PLINE_ID 0x000b +extern const H5O_class_t H5O_PLINE[1]; + +typedef struct H5O_pline_t { + size_t nfilters; /*num filters defined */ + size_t nalloc; /*num elements in `filter' array */ + struct { + H5Z_filter_t id; /*filter identification number */ + uintn flags; /*defn and invocation flags */ + char *name; /*optional filter name */ + size_t cd_nelmts; /*number of elements in cd_values[] */ + uintn *cd_values; /*client data values */ + } *filter; /*array of filters */ +} H5O_pline_t; /* * Attribute Message. diff --git a/src/H5P.c b/src/H5P.c index 904dfe2..a509486 100644 --- a/src/H5P.c +++ b/src/H5P.c @@ -2150,18 +2150,31 @@ H5Pget_preserve (hid_t plist_id) /*------------------------------------------------------------------------- - * Function: H5Pset_compression - * - * Purpose: Sets the compression method in a dataset creation property - * list. This sets default values for the compression - * attributes by setting the flags to zero and supplying no - * compression client data. It's probably better to use - * specific compression initialization functions like - * H5Pset_deflate(). - * - * The FLAGS, CD_SIZE, and CLIENT_DATA are copied to the - * property list and eventually to the file and passed to the - * compression functions. + * Function: H5Pset_filter + * + * Purpose: Adds the specified FILTER and corresponding properties to the + * end of the transient or permanent output filter pipeline + * depending on whether PLIST is a dataset creation or dataset + * transfer property list. The FLAGS argument specifies certain + * general properties of the filter and is documented below. + * The CD_VALUES is an array of CD_NELMTS integers which are + * auxiliary data for the filter. The integer vlues will be + * stored in the dataset object header as part of the filter + * information. + * + * The FLAGS argument is a bit vector of the following fields: + * + * H5Z_FLAG_OPTIONAL(0x0001) + * If this bit is set then the filter is optional. If the + * filter fails during an H5Dwrite() operation then the filter + * is just excluded from the pipeline for the chunk for which it + * failed; the filter will not participate in the pipeline + * during an H5Dread() of the chunk. If this bit is clear and + * the filter fails then the entire I/O operation fails. + * + * Note: This function currently supports only the permanent filter + * pipeline. That is, PLIST_ID must be a dataset creation + * property list. * * Return: Success: SUCCEED * @@ -2175,105 +2188,110 @@ H5Pget_preserve (hid_t plist_id) *------------------------------------------------------------------------- */ herr_t -H5Pset_compression (hid_t plist_id, H5Z_method_t method, unsigned int flags, - size_t cd_size, const void *client_data) +H5Pset_filter (hid_t plist_id, H5Z_filter_t filter, unsigned int flags, + size_t cd_nelmts, const unsigned int cd_values[/*cd_nelmts*/]) { H5D_create_t *plist = NULL; - FUNC_ENTER (H5Pset_compression, FAIL); - H5TRACE5("e","iZmIuzx",plist_id,method,flags,cd_size,client_data); + FUNC_ENTER (H5Pset_filter, FAIL); + H5TRACE5("e","iZfIuz*[a3]Iu",plist_id,filter,flags,cd_nelmts,cd_values); /* Check arguments */ + if (H5P_DATASET_XFER==H5P_get_class(plist_id)) { + HRETURN_ERROR(H5E_PLINE, H5E_UNSUPPORTED, FAIL, + "transient pipelines are not supported yet"); + } if (H5P_DATASET_CREATE!=H5P_get_class (plist_id) || NULL==(plist=H5I_object (plist_id))) { HRETURN_ERROR (H5E_ARGS, H5E_BADTYPE, FAIL, "not a dataset creation property list"); } - if (method<0 || method>H5Z_USERDEF_MAX) { + if (filter<0 || filter>H5Z_FILTER_MAX) { HRETURN_ERROR (H5E_ARGS, H5E_BADVALUE, FAIL, - "invalid compression method"); + "invalid filter identifier"); + } + if (flags & ~H5Z_FLAG_DEFMASK) { + HRETURN_ERROR(H5E_ARGS, H5E_BADVALUE, FAIL, + "invalid flags"); + } + if (cd_nelmts>0 && !cd_values) { + HRETURN_ERROR(H5E_ARGS, H5E_BADVALUE, FAIL, + "no client data values supplied"); } - /* Clear any previous compression method info, then set new value */ - H5O_reset (H5O_COMPRESS, &(plist->compress)); - plist->compress.method = method; - plist->compress.flags = flags; - plist->compress.cd_size = cd_size; - if (cd_size) { - if (NULL==(plist->compress.client_data = H5MM_malloc (cd_size))) { - HRETURN_ERROR (H5E_RESOURCE, H5E_NOSPACE, FAIL, - "memory allocation failed"); - } - HDmemcpy (plist->compress.client_data, client_data, cd_size); + /* Do it */ + if (H5Z_append(&(plist->pline), filter, flags, cd_nelmts, cd_values)<0) { + HRETURN_ERROR(H5E_PLINE, H5E_CANTINIT, FAIL, + "unable to add filter to pipeline"); } + FUNC_LEAVE (SUCCEED); } /*------------------------------------------------------------------------- - * Function: H5Pget_compression + * Function: H5Pget_nfilters + * + * Purpose: Returns the number of filters in the permanent or transient + * pipeline depending on whether PLIST_ID is a dataset creation + * or dataset transfer property list. In each pipeline the + * filters are numbered from zero through N-1 where N is the + * value returned by this function. During output to the file + * the filters of a pipeline are applied in increasing order + * (the inverse is true for input). * - * Purpose: Gets the compression method information from a dataset - * creation property list. The CLIENT_DATA buffer is initially - * CD_SIZE bytes. On return, CLIENT_DATA will be initialized - * with at most that many bytes, and CD_SIZE will contain the - * actual size of the client data, which might be larger than - * its original value. + * Note: Only permanent filters are supported at this time. * - * Return: Success: Compression method. + * Return: Success: Number of filters or zero if there are none. * * Failure: FAIL * * Programmer: Robb Matzke - * Wednesday, April 15, 1998 + * Tuesday, August 4, 1998 * * Modifications: * *------------------------------------------------------------------------- */ -H5Z_method_t -H5Pget_compression (hid_t plist_id, unsigned int *flags/*out*/, - size_t *cd_size/*in_out*/, void *client_data/*out*/) +int +H5Pget_nfilters (hid_t plist_id) { H5D_create_t *plist = NULL; - FUNC_ENTER (H5Pget_compression, FAIL); - H5TRACE4("Zm","ix*zx",plist_id,flags,cd_size,client_data); - - /* Check arguments */ - if (H5P_DATASET_CREATE!=H5P_get_class (plist_id) || - NULL==(plist=H5I_object (plist_id))) { - HRETURN_ERROR (H5E_ARGS, H5E_BADTYPE, FAIL, - "not a dataset creation property list"); - } + FUNC_ENTER(H5Pget_nfilters, FAIL); + H5TRACE1("Is","i",plist_id); - /* Output values */ - if (flags) *flags = plist->compress.flags; - if (cd_size) { - if (*cd_size>0 && client_data) { - HDmemcpy (client_data, plist->compress.client_data, - MIN(plist->compress.cd_size, *cd_size)); - } - *cd_size = plist->compress.cd_size; + if (H5P_DATASET_XFER==H5P_get_class(plist_id)) { + HRETURN_ERROR(H5E_PLINE, H5E_UNSUPPORTED, FAIL, + "transient pipelines are not supported yet"); + } + if (H5P_DATASET_CREATE!=H5P_get_class(plist_id) || + NULL==(plist=H5I_object(plist_id))) { + HRETURN_ERROR(H5E_ARGS, H5E_BADTYPE, FAIL, + "not a dataset creation property list"); } - FUNC_LEAVE (plist->compress.method); + FUNC_LEAVE(plist->pline.nfilters); } /*------------------------------------------------------------------------- - * Function: H5Pset_deflate - * - * Purpose: Sets the compression method for a dataset creation property - * list to H5D_COMPRESS_DEFLATE and the compression level to - * LEVEL which should be a value between zero and nine, - * inclusive. Lower compression levels are faster but result in - * less compression. This is the same algorithm as used by the - * GNU gzip program. - * - * Return: Success: SUCCEED - * - * Failure: FAIL + * Function: H5Pget_filter + * + * Purpose: This is the query counterpart of H5Pset_filter() and returns + * information about a particular filter number in a permanent + * or transient pipeline depending on whether PLIST_ID is a + * dataset creation or transfer property list. On input, + * CD_NELMTS indicates the number of entries in the CD_VALUES + * array allocated by the caller while on exit it contains the + * number of values defined by the filter. The IDX should be a + * value between zero and N-1 as described for H5Pget_nfilters() + * and the function will return failure if the filter number is + * out or range. + * + * Return: Success: Filter identification number. + * + * Failure: H5Z_FILTER_ERROR (-1) * * Programmer: Robb Matzke * Wednesday, April 15, 1998 @@ -2282,44 +2300,77 @@ H5Pget_compression (hid_t plist_id, unsigned int *flags/*out*/, * *------------------------------------------------------------------------- */ -herr_t -H5Pset_deflate (hid_t plist_id, int level) +H5Z_filter_t +H5Pget_filter (hid_t plist_id, int idx, unsigned int *flags/*out*/, + size_t *cd_nelmts/*in_out*/, unsigned cd_values[]/*out*/) { H5D_create_t *plist = NULL; + size_t i; + + FUNC_ENTER (H5Pget_filter, FAIL); + H5TRACE5("Zf","iIsx*zx",plist_id,idx,flags,cd_nelmts,cd_values); - FUNC_ENTER (H5Pset_deflate, FAIL); - H5TRACE2("e","iIs",plist_id,level); - /* Check arguments */ + if (H5P_DATASET_XFER==H5P_get_class(plist_id)) { + HRETURN_ERROR(H5E_PLINE, H5E_UNSUPPORTED, FAIL, + "transient filters are not supported yet"); + } if (H5P_DATASET_CREATE!=H5P_get_class (plist_id) || NULL==(plist=H5I_object (plist_id))) { HRETURN_ERROR (H5E_ARGS, H5E_BADTYPE, FAIL, "not a dataset creation property list"); } - if (level<0 || level>9) { - HRETURN_ERROR (H5E_ARGS, H5E_BADVALUE, FAIL, - "invalid deflate level"); + if (idx<0 || (size_t)idx>=plist->pline.nfilters) { + HRETURN_ERROR(H5E_ARGS, H5E_BADVALUE, FAIL, + "filter number is invalid"); + } + if (cd_nelmts || cd_values) { + if (cd_nelmts && *cd_nelmts>256) { + /* + * It's likely that users forget to initialize this on input, so + * we'll check that it has a reasonable value. The actual number + * is unimportant because the H5O layer will detect when a message + * is too large. + */ + HRETURN_ERROR(H5E_ARGS, H5E_BADVALUE, FAIL, + "probable uninitialized *cd_nelmts argument"); + } + if (cd_nelmts && *cd_nelmts>0 && !cd_values) { + HRETURN_ERROR(H5E_ARGS, H5E_BADVALUE, FAIL, + "client data values not supplied"); + } + /* + * If cd_nelmts is null but cd_values is non-null then just ignore + * cd_values + */ + if (!cd_nelmts) cd_values = NULL; } - /* Clear previous compression parameters */ - H5O_reset (H5O_COMPRESS, &(plist->compress)); - plist->compress.method = H5Z_DEFLATE; - plist->compress.flags = level; + /* Output values */ + if (flags) *flags = plist->pline.filter[idx].flags; + if (cd_values) { + for (i=0; ipline.filter[idx].cd_nelmts && i<*cd_nelmts; i++) { + cd_values[i] = plist->pline.filter[idx].cd_values[i]; + } + } + if (cd_nelmts) *cd_nelmts = plist->pline.filter[idx].cd_nelmts; - FUNC_LEAVE (SUCCEED); + FUNC_LEAVE (plist->pline.filter[idx].id); } /*------------------------------------------------------------------------- - * Function: H5Pget_deflate + * Function: H5Pset_deflate * - * Purpose: Returns the deflate compression level from a dataset creation - * property list that uses that method. + * Purpose: Sets the compression method for a permanent or transient + * filter pipeline (depending on whether PLIST_ID is a dataset + * creation or transfer property list) to H5Z_FILTER_DEFLATE + * and the compression level to LEVEL which should be a value + * between zero and nine, inclusive. Lower compression levels + * are faster but result in less compression. This is the same + * algorithm as used by the GNU gzip program. * - * Return: Success: A value between zero and nine, inclusive. - * Smaller values indicate faster compression - * while higher values indicate better - * compression ratios. + * Return: Success: SUCCEED * * Failure: FAIL * @@ -2330,26 +2381,37 @@ H5Pset_deflate (hid_t plist_id, int level) * *------------------------------------------------------------------------- */ -int -H5Pget_deflate (hid_t plist_id) +herr_t +H5Pset_deflate (hid_t plist_id, unsigned level) { H5D_create_t *plist = NULL; - FUNC_ENTER (H5Pget_deflate, FAIL); - H5TRACE1("Is","i",plist_id); - + FUNC_ENTER (H5Pset_deflate, FAIL); + H5TRACE2("e","iIu",plist_id,level); + /* Check arguments */ + if (H5P_DATASET_XFER==H5P_get_class(plist_id)) { + HRETURN_ERROR(H5E_PLINE, H5E_UNSUPPORTED, FAIL, + "transient filter pipelines are not supported yet"); + } if (H5P_DATASET_CREATE!=H5P_get_class (plist_id) || NULL==(plist=H5I_object (plist_id))) { HRETURN_ERROR (H5E_ARGS, H5E_BADTYPE, FAIL, "not a dataset creation property list"); } - if (H5Z_DEFLATE!=plist->compress.method) { + if (level>9) { HRETURN_ERROR (H5E_ARGS, H5E_BADVALUE, FAIL, - "deflate method is not being used"); + "invalid deflate level"); } - FUNC_LEAVE (plist->compress.flags % 10); + /* Add the filter */ + if (H5Z_append(&(plist->pline), H5Z_FILTER_DEFLATE, H5Z_FLAG_OPTIONAL, + 1, &level)<0) { + HRETURN_ERROR(H5E_PLINE, H5E_CANTINIT, FAIL, + "unable to add deflate filter to pipeline"); + } + + FUNC_LEAVE (SUCCEED); } diff --git a/src/H5Ppublic.h b/src/H5Ppublic.h index f39be45..c7de8f6 100644 --- a/src/H5Ppublic.h +++ b/src/H5Ppublic.h @@ -92,14 +92,14 @@ herr_t H5Pset_buffer (hid_t plist_id, size_t size, void *tconv, void *bkg); size_t H5Pget_buffer (hid_t plist_id, void **tconv/*out*/, void **bkg/*out*/); herr_t H5Pset_preserve (hid_t plist_id, hbool_t status); int H5Pget_preserve (hid_t plist_id); -herr_t H5Pset_compression (hid_t plist_id, H5Z_method_t method, - unsigned int flags, size_t cd_size, - const void *client_data); -H5Z_method_t H5Pget_compression (hid_t plist_id, unsigned int *flags/*out*/, - size_t *cd_size/*in,out*/, - void *client_data/*out*/); -herr_t H5Pset_deflate (hid_t plist_id, int level); -int H5Pget_deflate (hid_t plist_id); +herr_t H5Pset_filter (hid_t plist_id, H5Z_filter_t filter, unsigned int flags, + size_t cd_nelmts, const unsigned int c_values[]); +int H5Pget_nfilters(hid_t plist_id); +H5Z_filter_t H5Pget_filter(hid_t plist_id, int filter, + unsigned int *flags/*out*/, + size_t *cd_nelmts/*out*/, + unsigned cd_values[]/*out*/); +herr_t H5Pset_deflate (hid_t plist_id, unsigned aggression); herr_t H5Pset_cache (hid_t plist_id, int mdc_nelmts, size_t rdcc_nbytes, double rdcc_w0); herr_t H5Pget_cache (hid_t plist_id, int *mdc_nelmts, size_t *rdcc_nbytes, diff --git a/src/H5Sall.c b/src/H5Sall.c index 08d01c5..467ed2e 100644 --- a/src/H5Sall.c +++ b/src/H5Sall.c @@ -125,7 +125,7 @@ H5S_all_favail (const H5S_t *space, const H5S_sel_iter_t *sel_iter, size_t max) */ size_t H5S_all_fgath (H5F_t *f, const struct H5O_layout_t *layout, - const struct H5O_compress_t *comp, const struct H5O_efl_t *efl, + const struct H5O_pline_t *pline, const struct H5O_efl_t *efl, size_t elmt_size, const H5S_t *file_space, H5S_sel_iter_t *file_iter, size_t nelmts, const H5D_transfer_t xfer_mode, void *_buf/*out*/) @@ -181,7 +181,7 @@ H5S_all_fgath (H5F_t *f, const struct H5O_layout_t *layout, /* * Gather from file. */ - if (H5F_arr_read (f, layout, comp, efl, hsize, hsize, zero, file_offset, + if (H5F_arr_read (f, layout, pline, efl, hsize, hsize, zero, file_offset, xfer_mode, buf/*out*/)<0) { HRETURN_ERROR (H5E_DATASPACE, H5E_READERROR, 0, "read error"); } @@ -215,7 +215,7 @@ H5S_all_fgath (H5F_t *f, const struct H5O_layout_t *layout, */ herr_t H5S_all_fscat (H5F_t *f, const struct H5O_layout_t *layout, - const struct H5O_compress_t *comp, const struct H5O_efl_t *efl, + const struct H5O_pline_t *pline, const struct H5O_efl_t *efl, size_t elmt_size, const H5S_t *file_space, H5S_sel_iter_t *file_iter, size_t nelmts, const H5D_transfer_t xfer_mode, const void *_buf) @@ -267,7 +267,7 @@ H5S_all_fscat (H5F_t *f, const struct H5O_layout_t *layout, /* * Scatter to file. */ - if (H5F_arr_write (f, layout, comp, efl, hsize, hsize, zero, + if (H5F_arr_write (f, layout, pline, efl, hsize, hsize, zero, file_offset, xfer_mode, buf)<0) { HRETURN_ERROR (H5E_DATASPACE, H5E_WRITEERROR, FAIL, "write error"); } @@ -479,7 +479,7 @@ H5S_all_mscat (const void *_tconv_buf, size_t elmt_size, REVISION LOG --------------------------------------------------------------------------*/ herr_t -H5S_all_release (H5S_t *space) +H5S_all_release (H5S_t __unused__ *space) { FUNC_ENTER (H5S_all_release, FAIL); diff --git a/src/H5Shyper.c b/src/H5Shyper.c index ebf6cfe..5c6ddf3 100644 --- a/src/H5Shyper.c +++ b/src/H5Shyper.c @@ -23,7 +23,7 @@ static intn interface_initialize_g = FALSE; typedef struct { H5F_t *f; const struct H5O_layout_t *layout; - const struct H5O_compress_t *comp; + const struct H5O_pline_t *pline; const struct H5O_efl_t *efl; size_t elmt_size; const H5S_t *space; @@ -291,21 +291,29 @@ H5S_hyper_get_regions (size_t *num_regions, intn dim, size_t bound_count, ret_value[0].start=MAX(node->start[next_dim],pos[next_dim])+offset[next_dim]; ret_value[0].end=node->end[next_dim]+offset[next_dim]; #ifdef QAK - printf("%s: check 3.2, lo_bounds=%d, start=%d, hi_bounds=%d, end=%d\n", - FUNC, (int)node->start[next_dim], (int)ret_value[curr_reg].start, - (int)node->end[next_dim], (int)ret_value[curr_reg].end); + printf("%s: check 3.2, lo_bounds=%d, start=%d, " + "hi_bounds=%d, end=%d\n", + FUNC, (int)node->start[next_dim], + (int)ret_value[curr_reg].start, + (int)node->end[next_dim], + (int)ret_value[curr_reg].end); #endif /* QAK */ /* Increment the number of regions */ num_reg++; } else { #ifdef QAK - printf("%s: check 4.0, lo_bounds=%d, start=%d, hi_bounds=%d, end=%d\n", - FUNC, (int)node->start[next_dim], (int)ret_value[curr_reg].start, - (int)node->end[next_dim], (int)ret_value[curr_reg].end); + printf("%s: check 4.0, lo_bounds=%d, start=%d, " + "hi_bounds=%d, end=%d\n", + FUNC, (int)node->start[next_dim], + (int)ret_value[curr_reg].start, + (int)node->end[next_dim], + (int)ret_value[curr_reg].end); #endif /* QAK */ /* Enlarge array */ - ret_value=H5MM_realloc(ret_value,(sizeof(H5S_hyper_region_t)*(num_reg+1))); + ret_value=H5MM_realloc(ret_value, + (sizeof(H5S_hyper_region_t)* + (num_reg+1))); /* Initialize with new region */ ret_value[num_reg].start=node->start[next_dim]+offset[next_dim]; @@ -320,7 +328,8 @@ H5S_hyper_get_regions (size_t *num_regions, intn dim, size_t bound_count, /* Sort region list and eliminate duplicates if necessary */ if(num_reg>1) { - qsort(ret_value,num_reg,sizeof(H5S_hyper_region_t),H5S_hyper_compare_regions); + qsort(ret_value,num_reg,sizeof(H5S_hyper_region_t), + H5S_hyper_compare_regions); for(i=1,curr_reg=0,uniq_reg=1; iiter->hyp.pos, (fhyper_info->space->extent.u.simple.rank * sizeof(hssize_t))); + HDmemcpy(file_offset, fhyper_info->iter->hyp.pos, + (fhyper_info->space->extent.u.simple.rank * + sizeof(hssize_t))); file_offset[fhyper_info->space->extent.u.simple.rank]=0; /* Set the hyperslab size to copy */ hsize[0]=1; - H5V_array_fill(hsize, hsize, sizeof(hsize[0]), fhyper_info->space->extent.u.simple.rank); + H5V_array_fill(hsize, hsize, sizeof(hsize[0]), + fhyper_info->space->extent.u.simple.rank); hsize[fhyper_info->space->extent.u.simple.rank]=fhyper_info->elmt_size; /* Set the memory offset to the origin */ @@ -426,7 +438,8 @@ H5S_hyper_fread (intn dim, H5S_hyper_fhyper_info_t *fhyper_info) #ifdef QAK printf("%s: check 2.2, i=%d\n",FUNC,(int)i); #endif /* QAK */ - region_size=MIN(fhyper_info->nelmts, (regions[i].end-regions[i].start)+1); + region_size=MIN(fhyper_info->nelmts, + (regions[i].end-regions[i].start)+1); hsize[fhyper_info->space->extent.u.simple.rank-1]=region_size; file_offset[fhyper_info->space->extent.u.simple.rank-1]=regions[i].start; @@ -434,9 +447,12 @@ H5S_hyper_fread (intn dim, H5S_hyper_fhyper_info_t *fhyper_info) * Gather from file. */ if (H5F_arr_read (fhyper_info->f, fhyper_info->layout, - fhyper_info->comp, fhyper_info->efl, hsize, hsize, zero, - file_offset, fhyper_info->xfer_mode, fhyper_info->dst/*out*/)<0) { - HRETURN_ERROR (H5E_DATASPACE, H5E_READERROR, 0, "read error"); + fhyper_info->pline, fhyper_info->efl, + hsize, hsize, zero, file_offset, + fhyper_info->xfer_mode, + fhyper_info->dst/*out*/)<0) { + HRETURN_ERROR (H5E_DATASPACE, H5E_READERROR, 0, + "read error"); } #ifdef QAK printf("%s: check 2.3, region #%d\n",FUNC,(int)i); @@ -446,7 +462,8 @@ H5S_hyper_fread (intn dim, H5S_hyper_fhyper_info_t *fhyper_info) #endif /* QAK */ /* Advance the pointer in the buffer */ - fhyper_info->dst = ((uint8 *)fhyper_info->dst) + region_size*fhyper_info->elmt_size; + fhyper_info->dst = ((uint8 *)fhyper_info->dst) + + region_size*fhyper_info->elmt_size; /* Increment the number of elements read */ num_read+=region_size; @@ -458,7 +475,8 @@ H5S_hyper_fread (intn dim, H5S_hyper_fhyper_info_t *fhyper_info) if(region_size==(hsize_t)((regions[i].end-regions[i].start)+1)) fhyper_info->iter->hyp.pos[dim+1]=(-1); else - fhyper_info->iter->hyp.pos[dim+1] = regions[i].start + region_size; + fhyper_info->iter->hyp.pos[dim+1] = regions[i].start + + region_size; /* Decrement the iterator count */ fhyper_info->iter->hyp.elmt_left-=region_size; @@ -474,15 +492,17 @@ H5S_hyper_fread (intn dim, H5S_hyper_fhyper_info_t *fhyper_info) /* Step through each region in this dimension */ for(i=0; inelmts>0; i++) { /* Step through each location in each region */ - for(j=regions[i].start; j<=regions[i].end && fhyper_info->nelmts>0; j++) { + for(j=regions[i].start; + j<=regions[i].end && fhyper_info->nelmts>0; + j++) { #ifdef QAK printf("%s: check 4.0, dim=%d, location=%d\n",FUNC,dim,j); #endif /* QAK */ /* - * If we are moving to a new position in this dim, reset - * the next lower dim. location. - */ + * If we are moving to a new position in this dim, reset + * the next lower dim. location. + */ if(fhyper_info->iter->hyp.pos[dim]!=j) fhyper_info->iter->hyp.pos[dim+1]=(-1); @@ -527,7 +547,7 @@ H5S_hyper_fread (intn dim, H5S_hyper_fhyper_info_t *fhyper_info) */ size_t H5S_hyper_fgath (H5F_t *f, const struct H5O_layout_t *layout, - const struct H5O_compress_t *comp, + const struct H5O_pline_t *pline, const struct H5O_efl_t *efl, size_t elmt_size, const H5S_t *file_space, H5S_sel_iter_t *file_iter, size_t nelmts, const H5D_transfer_t xfer_mode, @@ -571,7 +591,7 @@ H5S_hyper_fgath (H5F_t *f, const struct H5O_layout_t *layout, /* Initialize parameter block for recursive calls */ fhyper_info.f=f; fhyper_info.layout=layout; - fhyper_info.comp=comp; + fhyper_info.pline=pline; fhyper_info.efl=efl; fhyper_info.elmt_size=elmt_size; fhyper_info.space=file_space; @@ -674,7 +694,7 @@ H5S_hyper_fwrite (intn dim, H5S_hyper_fhyper_info_t *fhyper_info) * Scatter from file. */ if (H5F_arr_write (fhyper_info->f, fhyper_info->layout, - fhyper_info->comp, fhyper_info->efl, + fhyper_info->pline, fhyper_info->efl, hsize, hsize, zero, file_offset, fhyper_info->xfer_mode, fhyper_info->src)<0) { @@ -758,7 +778,7 @@ H5S_hyper_fwrite (intn dim, H5S_hyper_fhyper_info_t *fhyper_info) */ herr_t H5S_hyper_fscat (H5F_t *f, const struct H5O_layout_t *layout, - const struct H5O_compress_t *comp, + const struct H5O_pline_t *pline, const struct H5O_efl_t *efl, size_t elmt_size, const H5S_t *file_space, H5S_sel_iter_t *file_iter, size_t nelmts, const H5D_transfer_t xfer_mode, @@ -803,7 +823,7 @@ H5S_hyper_fscat (H5F_t *f, const struct H5O_layout_t *layout, /* Initialize parameter block for recursive calls */ fhyper_info.f=f; fhyper_info.layout=layout; - fhyper_info.comp=comp; + fhyper_info.pline=pline; fhyper_info.efl=efl; fhyper_info.elmt_size=elmt_size; fhyper_info.space=file_space; @@ -889,24 +909,30 @@ H5S_hyper_mread (intn dim, H5S_hyper_fhyper_info_t *fhyper_info) /* Set up hyperslab I/O parameters which apply to all regions */ /* Set up the size of the memory space */ - HDmemcpy(mem_size, fhyper_info->space->extent.u.simple.size, fhyper_info->space->extent.u.simple.rank*sizeof(hsize_t)); + HDmemcpy(mem_size, fhyper_info->space->extent.u.simple.size, + fhyper_info->space->extent.u.simple.rank*sizeof(hsize_t)); mem_size[fhyper_info->space->extent.u.simple.rank]=fhyper_info->elmt_size; /* Copy the location of the region in the file */ - HDmemcpy(mem_offset, fhyper_info->iter->hyp.pos, (fhyper_info->space->extent.u.simple.rank * sizeof(hssize_t))); + HDmemcpy(mem_offset, fhyper_info->iter->hyp.pos, + (fhyper_info->space->extent.u.simple.rank * + sizeof(hssize_t))); mem_offset[fhyper_info->space->extent.u.simple.rank]=0; /* Set the hyperslab size to copy */ hsize[0]=1; - H5V_array_fill(hsize, hsize, sizeof(hsize[0]), fhyper_info->space->extent.u.simple.rank); + H5V_array_fill(hsize, hsize, sizeof(hsize[0]), + fhyper_info->space->extent.u.simple.rank); hsize[fhyper_info->space->extent.u.simple.rank]=fhyper_info->elmt_size; /* Set the memory offset to the origin */ - HDmemset (zero, 0, ((fhyper_info->space->extent.u.simple.rank+1)* sizeof(*zero))); + HDmemset (zero, 0, ((fhyper_info->space->extent.u.simple.rank+1)* + sizeof(*zero))); /* perform I/O on data from regions */ for(i=0; inelmts>0; i++) { - region_size=MIN(fhyper_info->nelmts, (regions[i].end-regions[i].start)+1); + region_size=MIN(fhyper_info->nelmts, + (regions[i].end-regions[i].start)+1); hsize[fhyper_info->space->extent.u.simple.rank-1]=region_size; mem_offset[fhyper_info->space->extent.u.simple.rank-1]=regions[i].start; #ifdef QAK @@ -925,7 +951,8 @@ H5S_hyper_mread (intn dim, H5S_hyper_fhyper_info_t *fhyper_info) } /* Advance the pointer in the buffer */ - fhyper_info->dst = ((uint8 *)fhyper_info->dst) + region_size*fhyper_info->elmt_size; + fhyper_info->dst = ((uint8 *)fhyper_info->dst) + + region_size*fhyper_info->elmt_size; /* Increment the number of elements read */ num_read+=region_size; @@ -954,15 +981,17 @@ H5S_hyper_mread (intn dim, H5S_hyper_fhyper_info_t *fhyper_info) /* Step through each region in this dimension */ for(i=0; inelmts>0; i++) { /* Step through each location in each region */ - for(j=regions[i].start; j<=regions[i].end && fhyper_info->nelmts>0; j++) { + for(j=regions[i].start; + j<=regions[i].end && fhyper_info->nelmts>0; + j++) { #ifdef QAK printf("%s: check 4.0, dim=%d, location=%d\n",FUNC,dim,j); #endif /* QAK */ /* - * If we are moving to a new position in this dim, reset - * the next lower dim. location. - */ + * If we are moving to a new position in this dim, reset + * the next lower dim. location. + */ if(fhyper_info->iter->hyp.pos[dim]!=j) fhyper_info->iter->hyp.pos[dim+1]=(-1); diff --git a/src/H5Spoint.c b/src/H5Spoint.c index d375e0d..cfde236 100644 --- a/src/H5Spoint.c +++ b/src/H5Spoint.c @@ -215,7 +215,7 @@ H5S_point_favail (const H5S_t __unused__ *space, const H5S_sel_iter_t *sel_iter, */ size_t H5S_point_fgath (H5F_t *f, const struct H5O_layout_t *layout, - const struct H5O_compress_t *comp, + const struct H5O_pline_t *pline, const struct H5O_efl_t *efl, size_t elmt_size, const H5S_t *file_space, H5S_sel_iter_t *file_iter, size_t nelmts, const H5D_transfer_t xfer_mode, @@ -259,7 +259,8 @@ H5S_point_fgath (H5F_t *f, const struct H5O_layout_t *layout, while(num_readpnt.elmt_left>0) { /* Copy the location of the point to get */ - HDmemcpy(file_offset, file_iter->pnt.curr->pnt,ndims*sizeof(hssize_t)); + HDmemcpy(file_offset, file_iter->pnt.curr->pnt, + ndims*sizeof(hssize_t)); file_offset[ndims] = 0; /* Add in the offset */ @@ -267,7 +268,7 @@ H5S_point_fgath (H5F_t *f, const struct H5O_layout_t *layout, file_offset[i] += file_space->select.offset[i]; /* Go read the point */ - if (H5F_arr_read (f, layout, comp, efl, hsize, hsize, zero, + if (H5F_arr_read (f, layout, pline, efl, hsize, hsize, zero, file_offset, xfer_mode, buf/*out*/)<0) { HRETURN_ERROR (H5E_DATASPACE, H5E_READERROR, 0, "read error"); } @@ -323,7 +324,7 @@ H5S_point_fgath (H5F_t *f, const struct H5O_layout_t *layout, */ herr_t H5S_point_fscat (H5F_t *f, const struct H5O_layout_t *layout, - const struct H5O_compress_t *comp, + const struct H5O_pline_t *pline, const struct H5O_efl_t *efl, size_t elmt_size, const H5S_t *file_space, H5S_sel_iter_t *file_iter, size_t nelmts, const H5D_transfer_t xfer_mode, @@ -395,7 +396,7 @@ H5S_point_fscat (H5F_t *f, const struct H5O_layout_t *layout, } #endif /* QAK */ /* Go write the point */ - if (H5F_arr_write (f, layout, comp, efl, hsize, hsize, zero, + if (H5F_arr_write (f, layout, pline, efl, hsize, hsize, zero, file_offset, xfer_mode, buf)<0) { HRETURN_ERROR (H5E_DATASPACE, H5E_WRITEERROR, 0, "write error"); } diff --git a/src/H5Sprivate.h b/src/H5Sprivate.h index 842c114..f7f398f 100644 --- a/src/H5Sprivate.h +++ b/src/H5Sprivate.h @@ -145,23 +145,26 @@ typedef struct H5S_t { typedef struct H5S_tconv_t { /* Initialize file element numbering information */ herr_t (*finit)(const struct H5O_layout_t *layout, const H5S_t *space, - H5S_sel_iter_t *iter); + H5S_sel_iter_t *iter); /* Initialize memory element numbering information */ herr_t (*minit)(const struct H5O_layout_t *layout, const H5S_t *space, - H5S_sel_iter_t *iter); + H5S_sel_iter_t *iter); /* Initialize background element numbering information */ herr_t (*binit)(const struct H5O_layout_t *layout, const H5S_t *space, - H5S_sel_iter_t *iter); + H5S_sel_iter_t *iter); - /* Figure out the optimal number of elements to transfer to/from the file */ + /* + * Figure out the optimal number of elements to transfer to/from the + * file. + */ size_t (*favail)(const H5S_t *file_space, const H5S_sel_iter_t *file_iter, - size_t max); + size_t max); /* Gather elements from disk to type conversion buffer */ size_t (*fgath)(H5F_t *f, const struct H5O_layout_t *layout, - const struct H5O_compress_t *comp, + const struct H5O_pline_t *pline, const struct H5O_efl_t *efl, size_t elmt_size, const H5S_t *file_space, H5S_sel_iter_t *file_iter, size_t nelmts, @@ -169,7 +172,7 @@ typedef struct H5S_tconv_t { /* Scatter elements from type conversion buffer to disk */ herr_t (*fscat)(H5F_t *f, const struct H5O_layout_t *layout, - const struct H5O_compress_t *compress, + const struct H5O_pline_t *pline, const struct H5O_efl_t *efl, size_t elmt_size, const H5S_t *file_space, H5S_sel_iter_t *file_iter, size_t nelmts, @@ -187,14 +190,14 @@ typedef struct H5S_tconv_t { /* Read from file to application w/o intermediate scratch buffer */ herr_t (*read)(H5F_t *f, const struct H5O_layout_t *layout, - const struct H5O_compress_t *comp, + const struct H5O_pline_t *pline, const struct H5O_efl_t *efl, size_t elmt_size, const H5S_t *file_space, const H5S_t *mem_space, const H5D_transfer_t xfer_mode, void *buf/*out*/); /* Write directly from app buffer to file */ herr_t (*write)(H5F_t *f, const struct H5O_layout_t *layout, - const struct H5O_compress_t *comp, + const struct H5O_pline_t *pline, const struct H5O_efl_t *efl, size_t elmt_size, const H5S_t *file_space, const H5S_t *mem_space, const H5D_transfer_t xfer_mode, const void *buf); @@ -236,7 +239,7 @@ size_t H5S_simp_init (const struct H5O_layout_t *layout, const H5S_t *mem_space, const H5S_t *file_space, size_t desired_nelmts); size_t H5S_simp_fgath (H5F_t *f, const struct H5O_layout_t *layout, - const struct H5O_compress_t *comp, + const struct H5O_pline_t *pline, const struct H5O_efl_t *efl, size_t elmt_size, const H5S_t *file_space, size_t start, size_t nelmts, @@ -248,18 +251,18 @@ size_t H5S_simp_mgath (const void *buf, size_t elmt_size, const H5S_t *mem_space, size_t start, size_t nelmts, void *tconv_buf/*out*/); herr_t H5S_simp_fscat (H5F_t *f, const struct H5O_layout_t *layout, - const struct H5O_compress_t *comp, + const struct H5O_pline_t *pline, const struct H5O_efl_t *efl, size_t elmt_size, const H5S_t *file_space, size_t start, size_t nelmts, const H5D_transfer_t xfer_mode, const void *tconv_buf); herr_t H5S_simp_read (H5F_t *f, const struct H5O_layout_t *layout, - const struct H5O_compress_t *comp, + const struct H5O_pline_t *pline, const struct H5O_efl_t *efl, size_t elmt_size, const H5S_t *file_space, const H5S_t *mem_space, const H5D_transfer_t xfer_mode, void *buf/*out*/); herr_t H5S_simp_write (H5F_t *f, const struct H5O_layout_t *layout, - const struct H5O_compress_t *comp, + const struct H5O_pline_t *pline, const struct H5O_efl_t *efl, size_t elmt_size, const H5S_t *file_space, const H5S_t *mem_space, const H5D_transfer_t xfer_mode, const void *buf); @@ -268,23 +271,25 @@ herr_t H5S_simp_write (H5F_t *f, const struct H5O_layout_t *layout, herr_t H5S_point_init (const struct H5O_layout_t *layout, const H5S_t *space, H5S_sel_iter_t *iter); size_t H5S_point_favail (const H5S_t *space, const H5S_sel_iter_t *iter, - size_t max); + size_t max); size_t H5S_point_fgath (H5F_t *f, const struct H5O_layout_t *layout, - const struct H5O_compress_t *comp, const struct H5O_efl_t *efl, - size_t elmt_size, const H5S_t *file_space, H5S_sel_iter_t *file_iter, - size_t nelmts, - const H5D_transfer_t xfer_mode, void *buf/*out*/); + const struct H5O_pline_t *pline, + const struct H5O_efl_t *efl, size_t elmt_size, + const H5S_t *file_space, H5S_sel_iter_t *file_iter, + size_t nelmts, const H5D_transfer_t xfer_mode, + void *buf/*out*/); herr_t H5S_point_fscat (H5F_t *f, const struct H5O_layout_t *layout, - const struct H5O_compress_t *comp, const struct H5O_efl_t *efl, - size_t elmt_size, const H5S_t *file_space, H5S_sel_iter_t *file_iter, - size_t nelmts, - const H5D_transfer_t xfer_mode, const void *buf); + const struct H5O_pline_t *pline, + const struct H5O_efl_t *efl, size_t elmt_size, + const H5S_t *file_space, H5S_sel_iter_t *file_iter, + size_t nelmts, const H5D_transfer_t xfer_mode, + const void *buf); size_t H5S_point_mgath (const void *_buf, size_t elmt_size, - const H5S_t *mem_space, H5S_sel_iter_t *mem_iter, - size_t nelmts, void *_tconv_buf/*out*/); + const H5S_t *mem_space, H5S_sel_iter_t *mem_iter, + size_t nelmts, void *_tconv_buf/*out*/); herr_t H5S_point_mscat (const void *_tconv_buf, size_t elmt_size, - const H5S_t *mem_space, H5S_sel_iter_t *mem_iter, - size_t nelmts, void *_buf/*out*/); + const H5S_t *mem_space, H5S_sel_iter_t *mem_iter, + size_t nelmts, void *_buf/*out*/); herr_t H5S_point_add (H5S_t *space, size_t num_elemn, const hssize_t **coord); herr_t H5S_point_release (H5S_t *space); hsize_t H5S_point_npoints (const H5S_t *space); @@ -295,23 +300,25 @@ hbool_t H5S_point_select_valid (const H5S_t *space); herr_t H5S_all_init (const struct H5O_layout_t *layout, const H5S_t *space, H5S_sel_iter_t *iter); size_t H5S_all_favail (const H5S_t *space, const H5S_sel_iter_t *iter, - size_t max); + size_t max); size_t H5S_all_fgath (H5F_t *f, const struct H5O_layout_t *layout, - const struct H5O_compress_t *comp, const struct H5O_efl_t *efl, - size_t elmt_size, const H5S_t *file_space, H5S_sel_iter_t *file_iter, - size_t nelmts, - const H5D_transfer_t xfer_mode, void *buf/*out*/); + const struct H5O_pline_t *pline, + const struct H5O_efl_t *efl, size_t elmt_size, + const H5S_t *file_space, H5S_sel_iter_t *file_iter, + size_t nelmts, const H5D_transfer_t xfer_mode, + void *buf/*out*/); herr_t H5S_all_fscat (H5F_t *f, const struct H5O_layout_t *layout, - const struct H5O_compress_t *comp, const struct H5O_efl_t *efl, - size_t elmt_size, const H5S_t *file_space, H5S_sel_iter_t *file_iter, - size_t nelmts, - const H5D_transfer_t xfer_mode, const void *buf); + const struct H5O_pline_t *pline, + const struct H5O_efl_t *efl, size_t elmt_size, + const H5S_t *file_space, H5S_sel_iter_t *file_iter, + size_t nelmts, const H5D_transfer_t xfer_mode, + const void *buf); size_t H5S_all_mgath (const void *_buf, size_t elmt_size, - const H5S_t *mem_space, H5S_sel_iter_t *mem_iter, - size_t nelmts, void *_tconv_buf/*out*/); + const H5S_t *mem_space, H5S_sel_iter_t *mem_iter, + size_t nelmts, void *_tconv_buf/*out*/); herr_t H5S_all_mscat (const void *_tconv_buf, size_t elmt_size, - const H5S_t *mem_space, H5S_sel_iter_t *mem_iter, - size_t nelmts, void *_buf/*out*/); + const H5S_t *mem_space, H5S_sel_iter_t *mem_iter, + size_t nelmts, void *_buf/*out*/); herr_t H5S_all_release (H5S_t *space); hsize_t H5S_all_npoints (const H5S_t *space); @@ -321,22 +328,25 @@ herr_t H5S_hyper_init (const struct H5O_layout_t *layout, size_t H5S_hyper_favail (const H5S_t *space, const H5S_sel_iter_t *iter, size_t max); size_t H5S_hyper_fgath (H5F_t *f, const struct H5O_layout_t *layout, - const struct H5O_compress_t *comp, const struct H5O_efl_t *efl, - size_t elmt_size, const H5S_t *file_space, H5S_sel_iter_t *file_iter, - size_t nelmts, - const H5D_transfer_t xfer_mode, void *buf/*out*/); + const struct H5O_pline_t *pline, + const struct H5O_efl_t *efl, size_t elmt_size, + const H5S_t *file_space, H5S_sel_iter_t *file_iter, + size_t nelmts, const H5D_transfer_t xfer_mode, + void *buf/*out*/); herr_t H5S_hyper_fscat (H5F_t *f, const struct H5O_layout_t *layout, - const struct H5O_compress_t *comp, const struct H5O_efl_t *efl, - size_t elmt_size, const H5S_t *file_space, H5S_sel_iter_t *file_iter, - size_t nelmts, - const H5D_transfer_t xfer_mode, const void *buf); + const struct H5O_pline_t *pline, + const struct H5O_efl_t *efl, size_t elmt_size, + const H5S_t *file_space, H5S_sel_iter_t *file_iter, + size_t nelmts, const H5D_transfer_t xfer_mode, + const void *buf); size_t H5S_hyper_mgath (const void *_buf, size_t elmt_size, - const H5S_t *mem_space, H5S_sel_iter_t *mem_iter, - size_t nelmts, void *_tconv_buf/*out*/); + const H5S_t *mem_space, H5S_sel_iter_t *mem_iter, + size_t nelmts, void *_tconv_buf/*out*/); herr_t H5S_hyper_mscat (const void *_tconv_buf, size_t elmt_size, - const H5S_t *mem_space, H5S_sel_iter_t *mem_iter, - size_t nelmts, void *_buf/*out*/); -herr_t H5S_hyper_add (H5S_t *space, const hssize_t *start, const hsize_t *size); + const H5S_t *mem_space, H5S_sel_iter_t *mem_iter, + size_t nelmts, void *_buf/*out*/); +herr_t H5S_hyper_add (H5S_t *space, const hssize_t *start, + const hsize_t *size); herr_t H5S_hyper_release (H5S_t *space); herr_t H5S_hyper_sel_iter_release (H5S_sel_iter_t *sel_iter); hsize_t H5S_hyper_npoints (const H5S_t *space); diff --git a/src/H5Ssimp.c b/src/H5Ssimp.c index e4a7c05..40981fb 100644 --- a/src/H5Ssimp.c +++ b/src/H5Ssimp.c @@ -121,7 +121,7 @@ H5S_simp_init (const struct H5O_layout_t __unused__ *layout, */ size_t H5S_simp_fgath (H5F_t *f, const struct H5O_layout_t *layout, - const struct H5O_compress_t *comp, const struct H5O_efl_t *efl, + const struct H5O_pline_t *pline, const struct H5O_efl_t *efl, size_t elmt_size, const H5S_t *file_space, size_t start, size_t nelmts, const H5D_transfer_t xfer_mode, void *buf/*out*/) @@ -180,7 +180,7 @@ H5S_simp_fgath (H5F_t *f, const struct H5O_layout_t *layout, /* * Gather from file. */ - if (H5F_arr_read (f, layout, comp, efl, hsize, hsize, zero, file_offset, + if (H5F_arr_read (f, layout, pline, efl, hsize, hsize, zero, file_offset, xfer_mode, buf/*out*/)<0) { HRETURN_ERROR (H5E_DATASPACE, H5E_READERROR, 0, "read error"); } @@ -402,7 +402,7 @@ H5S_simp_mgath (const void *buf, size_t elmt_size, */ herr_t H5S_simp_fscat (H5F_t *f, const struct H5O_layout_t *layout, - const struct H5O_compress_t *comp, const struct H5O_efl_t *efl, + const struct H5O_pline_t *pline, const struct H5O_efl_t *efl, size_t elmt_size, const H5S_t *file_space, size_t start, size_t nelmts, const H5D_transfer_t xfer_mode, const void *buf) @@ -461,7 +461,7 @@ H5S_simp_fscat (H5F_t *f, const struct H5O_layout_t *layout, /* * Scatter to file. */ - if (H5F_arr_write (f, layout, comp, efl, hsize, hsize, zero, + if (H5F_arr_write (f, layout, pline, efl, hsize, hsize, zero, file_offset, xfer_mode, buf)<0) { HRETURN_ERROR (H5E_DATASPACE, H5E_WRITEERROR, FAIL, "write error"); } @@ -494,7 +494,7 @@ H5S_simp_fscat (H5F_t *f, const struct H5O_layout_t *layout, */ herr_t H5S_simp_read (H5F_t *f, const struct H5O_layout_t *layout, - const struct H5O_compress_t *comp, const struct H5O_efl_t *efl, + const struct H5O_pline_t *pline, const struct H5O_efl_t *efl, size_t elmt_size, const H5S_t *file_space, const H5S_t *mem_space, const H5D_transfer_t xfer_mode, void *buf/*out*/) @@ -613,7 +613,7 @@ H5S_simp_read (H5F_t *f, const struct H5O_layout_t *layout, mem_offset[file_space->extent.u.simple.rank] = 0; /* Read the hyperslab */ - if (H5F_arr_read (f, layout, comp, efl, hslab_size, + if (H5F_arr_read (f, layout, pline, efl, hslab_size, mem_size, mem_offset, file_offset, xfer_mode, buf)<0) { HRETURN_ERROR (H5E_IO, H5E_READERROR, FAIL, "unable to read dataset"); } @@ -646,7 +646,7 @@ H5S_simp_read (H5F_t *f, const struct H5O_layout_t *layout, */ herr_t H5S_simp_write (H5F_t *f, const struct H5O_layout_t *layout, - const struct H5O_compress_t *comp, const struct H5O_efl_t *efl, + const struct H5O_pline_t *pline, const struct H5O_efl_t *efl, size_t elmt_size, const H5S_t *file_space, const H5S_t *mem_space, const H5D_transfer_t xfer_mode, const void *buf) @@ -765,7 +765,7 @@ H5S_simp_write (H5F_t *f, const struct H5O_layout_t *layout, mem_offset[file_space->extent.u.simple.rank] = 0; /* Write the hyperslab */ - if (H5F_arr_write (f, layout, comp, efl, hslab_size, + if (H5F_arr_write (f, layout, pline, efl, hslab_size, mem_size, mem_offset, file_offset, xfer_mode, buf)<0) { HRETURN_ERROR (H5E_IO, H5E_WRITEERROR, FAIL, "unable to write dataset"); diff --git a/src/H5Z.c b/src/H5Z.c index 386ea59..9919023 100644 --- a/src/H5Z.c +++ b/src/H5Z.c @@ -5,7 +5,7 @@ * Programmer: Robb Matzke * Thursday, April 16, 1998 * - * Purpose: Functions for data compression. + * Purpose: Functions for data filters. */ #include #include @@ -25,48 +25,39 @@ static herr_t H5Z_init_interface (void); static void H5Z_term_interface (void); /* - * The compression table maps compression method number to a struct that - * contains pointers to the compress and uncompress methods along with timing - * statistics. + * The filter table maps filter identification numbers to structs that + * contain a pointers to the filter function and timing statistics. */ typedef struct H5Z_class_t { - char *name; /*method name for debugging */ - H5Z_func_t compress; /*compression function */ - H5Z_func_t uncompress; /*uncompression function */ + H5Z_filter_t id; /*filter ID number */ + char *comment; /*comment for debugging */ + H5Z_func_t func; /*the filter function */ #ifdef H5Z_DEBUG struct { - hsize_t nbytes; /*bytes compressed including overruns */ - hsize_t over; /*bytes of overrun */ - H5_timer_t timer; /*total compression time inc. overruns */ - hsize_t failed; /*bytes of failure (not overruns) */ - } comp; - - struct { - hsize_t nbytes; /*bytes uncompressed, including overruns*/ - hsize_t over; /*bytes of overrun */ - H5_timer_t timer; /*total uncompression time */ - hsize_t failed; /*bytes of failure (not overruns) */ - } uncomp; + hsize_t total; /*total number of bytes processed */ + hsize_t errors; /*bytes of total attributable to errors */ + H5_timer_t timer; /*execution time including errors */ + } stats[2]; /*0=output, 1=input */ #endif } H5Z_class_t; -static H5Z_class_t H5Z_g[H5Z_USERDEF_MAX+1]; - -/* Compression and uncompression methods */ -static size_t H5Z_zlib_c (unsigned int flags, size_t __unused__ cd_size, - const void __unused__ *client_data, - size_t src_nbytes, const void *_src, - size_t dst_nbytes, void *dst/*out*/); -static size_t H5Z_zlib_u (unsigned int flags, size_t __unused__ cd_size, - const void __unused__ *client_data, - size_t src_nbytes, const void *_src, - size_t dst_nbytes, void *dst/*out*/); + +static size_t H5Z_table_alloc_g = 0; +static size_t H5Z_table_used_g = 0; +static H5Z_class_t *H5Z_table_g = NULL; + +static H5Z_class_t *H5Z_find(H5Z_filter_t id); + +/* Predefined filters */ +static size_t H5Z_filter_deflate(uintn flags, size_t cd_nelmts, + const uintn cd_values[], size_t nbytes, + size_t *buf_size, void **buf); /*------------------------------------------------------------------------- * Function: H5Z_init_interface * - * Purpose: Initializes the data compression layer. + * Purpose: Initializes the data filter layer. * * Return: Success: SUCCEED * @@ -83,11 +74,10 @@ static herr_t H5Z_init_interface (void) { FUNC_ENTER (H5Z_init_interface, FAIL); - H5_add_exit (H5Z_term_interface); - H5Z_register (H5Z_NONE, "none", NULL, NULL); - H5Z_register (H5Z_DEFLATE, "deflate", H5Z_zlib_c, H5Z_zlib_u); + H5Z_register (H5Z_FILTER_DEFLATE, "deflate", + H5Z_filter_deflate); FUNC_LEAVE (SUCCEED); } @@ -110,75 +100,69 @@ H5Z_init_interface (void) static void H5Z_term_interface (void) { + size_t i; + #ifdef H5Z_DEBUG - int i, nprint=0; - char name[16]; + int dir, nprint=0; + char comment[16], bandwidth[32]; + + for (i=0; i<=H5Z_table_used_g; i++) { + for (dir=0; dir<2; dir++) { + if (0==H5Z_table_g[i].stats[dir].total) continue; - for (i=0; i<=H5Z_USERDEF_MAX; i++) { - if (H5Z_g[i].comp.nbytes || H5Z_g[i].uncomp.nbytes) { if (0==nprint++) { - HDfprintf (stderr, "H5Z: compression statistics accumulated " + /* Print column headers */ + HDfprintf (stderr, "H5Z: filter statistics accumulated " "over life of library:\n"); - HDfprintf (stderr, " %-10s %10s %7s %7s %8s %8s %8s %9s\n", - "Method", "Total", "Overrun", "Errors", "User", + HDfprintf (stderr, " %-16s %10s %10s %8s %8s %8s %10s\n", + "Filter", "Total", "Errors", "User", "System", "Elapsed", "Bandwidth"); - HDfprintf (stderr, " %-10s %10s %7s %7s %8s %8s %8s %9s\n", - "------", "-----", "-------", "------", "----", + HDfprintf (stderr, " %-16s %10s %10s %8s %8s %8s %10s\n", + "------", "-----", "------", "----", "------", "-------", "---------"); } - sprintf (name, "%s-c", H5Z_g[i].name); - HDfprintf (stderr, - " %-12s %10Hd %7Hd %7Hd %8.2f %8.2f %8.2f ", - name, - H5Z_g[i].comp.nbytes, - H5Z_g[i].comp.over, - H5Z_g[i].comp.failed, - H5Z_g[i].comp.timer.utime, - H5Z_g[i].comp.timer.stime, - H5Z_g[i].comp.timer.etime); - if (H5Z_g[i].comp.timer.etime>0) { - HDfprintf (stderr, "%9.3e\n", - H5Z_g[i].comp.nbytes / H5Z_g[i].comp.timer.etime); - } else { - HDfprintf (stderr, "%9s\n", "NaN"); - } - - sprintf (name, "%s-u", H5Z_g[i].name); + + /* Truncate the comment to fit in the field */ + strncpy(comment, H5Z_table_g[i].comment, sizeof comment); + comment[sizeof(comment)-1] = '\0'; + + /* + * Format bandwidth to have four significant digits and units + * of `B/s', `kB/s', `MB/s', `GB/s', or `TB/s' or the word + * `Inf' if the elapsed time is zero. + */ + H5_bandwidth(bandwidth, + (double)(H5Z_table_g[i].stats[dir].total), + H5Z_table_g[i].stats[dir].timer.etime); + + /* Print the statistics */ HDfprintf (stderr, - " %-12s %10Hd %7Hd %7Hd %8.2f %8.2f %8.2f ", - name, - H5Z_g[i].uncomp.nbytes, - H5Z_g[i].uncomp.over, - H5Z_g[i].uncomp.failed, - H5Z_g[i].uncomp.timer.utime, - H5Z_g[i].uncomp.timer.stime, - H5Z_g[i].uncomp.timer.etime); - if (H5Z_g[i].uncomp.timer.etime>0) { - HDfprintf (stderr, "%9.3e\n", - H5Z_g[i].uncomp.nbytes/H5Z_g[i].uncomp.timer.etime); - } else { - HDfprintf (stderr, "%9s\n", "NaN"); - } + " %c%-15s %10Hd %10Hd %8.2f %8.2f %8.2f " + "%10s\n", dir?'<':'>', comment, + H5Z_table_g[i].stats[dir].total, + H5Z_table_g[i].stats[dir].errors, + H5Z_table_g[i].stats[dir].timer.utime, + H5Z_table_g[i].stats[dir].timer.stime, + H5Z_table_g[i].stats[dir].timer.etime, + bandwidth); } - H5MM_xfree (H5Z_g[i].name); } - HDmemset (H5Z_g, 0, sizeof H5Z_g); #endif + + /* Free the table */ + for (i=0; iH5Z_USERDEF_MAX) { + if (id<0 || id>H5Z_FILTER_MAX) { HRETURN_ERROR (H5E_ARGS, H5E_BADVALUE, FAIL, - "invalid data compression method number"); + "invalid filter identification number"); } - if (method<16) { + if (id<256) { HRETURN_ERROR (H5E_ARGS, H5E_BADVALUE, FAIL, - "unable to modify predefined compression methods"); + "unable to modify predefined filters"); + } + if (!func) { + HRETURN_ERROR(H5E_ARGS, H5E_BADVALUE, FAIL, + "no function specified"); } /* Do it */ - if (H5Z_register (method, name, cfunc, ufunc)<0) { - HRETURN_ERROR (H5E_COMP, H5E_CANTINIT, FAIL, - "unable to register compression methods"); + if (H5Z_register (id, comment, func)<0) { + HRETURN_ERROR (H5E_PLINE, H5E_CANTINIT, FAIL, + "unable to register filter"); } FUNC_LEAVE (SUCCEED); @@ -219,14 +206,14 @@ H5Zregister (H5Z_method_t method, const char *name, H5Z_func_t cfunc, /*------------------------------------------------------------------------- - * Function: H5Z_compress + * Function: H5Z_register * - * Purpose: Compress NBYTES from SRC into at most NBYTES of DST. + * Purpose: Same as the public version except this one allows filters + * to be set for predefined method numbers <256 * - * Return: Success: Number of bytes in DST + * Return: Success: SUCCEED * - * Failure: 0 if the DST buffer overflowed or something - * else went wrong. + * Failure: FAIL * * Programmer: Robb Matzke * Thursday, April 16, 1998 @@ -235,228 +222,294 @@ H5Zregister (H5Z_method_t method, const char *name, H5Z_func_t cfunc, * *------------------------------------------------------------------------- */ -size_t -H5Z_compress (const H5O_compress_t *comp, size_t nbytes, const void *src, - void *dst/*out*/) +herr_t +H5Z_register (H5Z_filter_t id, const char *comment, H5Z_func_t func) { - size_t ret_value = 0; - H5Z_method_t method = comp ? comp->method : H5Z_NONE; - H5Z_func_t cfunc = NULL; -#ifdef H5Z_DEBUG - intn over = 0; - H5_timer_t timer; -#endif + size_t i; - FUNC_ENTER (H5Z_compress, 0); + FUNC_ENTER (H5Z_register, FAIL); -#ifdef H5Z_DEBUG - H5_timer_begin (&timer); -#endif + assert (id>=0 && id<=H5Z_FILTER_MAX); - if (H5Z_NONE==method) { - /* No compression method */ - HGOTO_DONE (0); - - } else if (NULL==(cfunc=H5Z_g[method].compress)) { - /* No compress function */ - HGOTO_ERROR (H5E_COMP, H5E_UNSUPPORTED, 0, - "compression method is not supported"); - - } else if (0==(ret_value=(cfunc)(comp->flags, comp->cd_size, - comp->client_data, nbytes, - src, nbytes, dst))) { - /* Compress failed */ - HGOTO_ERROR (H5E_COMP, H5E_CANTINIT, 0, "compression failed"); - - } else if (ret_value>=nbytes) { - /* Output is not smaller than input */ -#ifdef H5Z_DEBUG - H5Z_g[method].comp.over += nbytes; - over = 1; -#endif - HGOTO_DONE (0); + /* Is the filter already registered? */ + for (i=0; i=H5Z_table_used_g) { + if (H5Z_table_used_g>=H5Z_table_alloc_g) { + size_t n = MAX(32, 2*H5Z_table_alloc_g); + H5Z_class_t *table = H5MM_realloc(H5Z_table_g, + n*sizeof(H5Z_class_t)); + if (!table) { + HRETURN_ERROR(H5E_RESOURCE, H5E_NOSPACE, FAIL, + "unable to extend filter table"); + } + H5Z_table_g = table; + H5Z_table_alloc_g = n; + } - done: -#ifdef H5Z_DEBUG - H5Z_g[method].comp.nbytes += nbytes; - if (0==ret_value && !over) H5Z_g[method].comp.failed += nbytes; - H5_timer_end (&(H5Z_g[method].comp.timer), &timer); -#endif - FUNC_LEAVE (ret_value); + /* Initialize */ + i = H5Z_table_used_g++; + HDmemset(H5Z_table_g+i, 0, sizeof(H5Z_class_t)); + H5Z_table_g[i].id = id; + H5Z_table_g[i].comment = H5MM_xstrdup(comment); + H5Z_table_g[i].func = func; + } else { + /* Replace old contents */ + H5MM_xfree(H5Z_table_g[i].comment); + H5Z_table_g[i].comment = H5MM_xstrdup(comment); + H5Z_table_g[i].func = func; + } + + FUNC_LEAVE (SUCCEED); } /*------------------------------------------------------------------------- - * Function: H5Z_uncompress + * Function: H5Z_append * - * Purpose: Uncompress SRC_NBYTES from SRC into at most DST_NBYTES of - * DST. + * Purpose: Append another filter to the specified pipeline. * - * Return: Success: Number of bytes in DST buffer. + * Return: Success: SUCCEED * - * Failure: 0 if the uncompression failed or DST wasn't - * big enough to hold the result. + * Failure: FAIL * * Programmer: Robb Matzke - * Thursday, April 16, 1998 + * Tuesday, August 4, 1998 * * Modifications: * *------------------------------------------------------------------------- */ -size_t -H5Z_uncompress (const H5O_compress_t *comp, size_t src_nbytes, const void *src, - size_t dst_nbytes, void *dst/*out*/) +herr_t +H5Z_append(H5O_pline_t *pline, H5Z_filter_t filter, uintn flags, + size_t cd_nelmts, const unsigned int cd_values[/*cd_nelmts*/]) { - size_t ret_value = 0; - H5Z_func_t ufunc = NULL; - H5Z_method_t method = comp ? comp->method : H5Z_NONE; -#ifdef H5Z_DEBUG - H5_timer_t timer; -#endif + size_t idx, i; - FUNC_ENTER (H5Z_uncompress, 0); - -#ifdef H5Z_DEBUG - H5_timer_begin (&timer); -#endif - - if (H5Z_NONE==method) { - /* No compression method */ - assert (src_nbytes<=dst_nbytes); - HDmemcpy (dst, src, src_nbytes); - ret_value = src_nbytes; - - } else if (src_nbytes==dst_nbytes) { - /* Data is not compressed */ -#ifdef H5Z_DEBUG - H5Z_g[method].uncomp.over += src_nbytes; -#endif - HDmemcpy (dst, src, src_nbytes); - ret_value = src_nbytes; - - } else if (NULL==(ufunc=H5Z_g[method].uncompress)) { - /* No uncompress function */ - HGOTO_ERROR (H5E_COMP, H5E_UNSUPPORTED, 0, - "uncompression method is not supported"); - - } else if (0==(ret_value=(ufunc)(comp->flags, comp->cd_size, - comp->client_data, src_nbytes, - src, dst_nbytes, dst))) { - /* Uncompress failed */ - HGOTO_ERROR (H5E_COMP, H5E_CANTINIT, 0, "uncompression failed"); + FUNC_ENTER(H5Z_append, FAIL); + assert(pline); + assert(filter>=0 && filter<=H5Z_FILTER_MAX); + assert(0==(flags & ~H5Z_FLAG_DEFMASK)); + assert(0==cd_nelmts || cd_values); + + /* + * Check filter limit. We do it here for early warnings although we may + * decide to relax this restriction in the future. + */ + if (pline->nfilters>=32) { + HRETURN_ERROR(H5E_PLINE, H5E_CANTINIT, FAIL, + "too many filters in pipeline"); } - done: -#ifdef H5Z_DEBUG - H5Z_g[method].uncomp.nbytes += dst_nbytes; - if (0==ret_value) H5Z_g[method].uncomp.failed += dst_nbytes; - H5_timer_end (&(H5Z_g[method].uncomp.timer), &timer); -#endif + /* Allocate additional space in the pipeline if it's full */ + if (pline->nfilters>=pline->nalloc) { + H5O_pline_t x; + x.nalloc = MAX(32, 2*pline->nalloc); + x.filter = H5MM_realloc(pline->filter, x.nalloc*sizeof(x.filter[0])); + if (NULL==x.filter) { + HRETURN_ERROR(H5E_RESOURCE, H5E_NOSPACE, FAIL, + "memory allocation failed for filter pipeline"); + } + pline->nalloc = x.nalloc; + pline->filter = x.filter; + } + + /* Add the new filter to the pipeline */ + idx = pline->nfilters; + pline->filter[idx].id = filter; + pline->filter[idx].flags = flags; + pline->filter[idx].name = NULL; /*we'll pick it up later*/ + pline->filter[idx].cd_nelmts = cd_nelmts; + if (cd_nelmts>0) { + pline->filter[idx].cd_values = H5MM_malloc(cd_nelmts*sizeof(uintn)); + if (NULL==pline->filter[idx].cd_values) { + HRETURN_ERROR(H5E_RESOURCE, H5E_NOSPACE, FAIL, + "memory allocation failed for filter"); + } + for (i=0; ifilter[idx].cd_values[i] = cd_values[i]; + } + } + pline->nfilters++; - FUNC_LEAVE (ret_value); + FUNC_LEAVE(SUCCEED); } /*------------------------------------------------------------------------- - * Function: H5Z_register + * Function: H5Z_find * - * Purpose: Same as the public version except this one allows compression - * methods to be set for predefined method numbers <16. + * Purpose: Given a filter ID return a pointer to a global struct that + * defines the filter. * - * Return: Success: SUCCEED + * Return: Success: Ptr to entry in global filter table. * - * Failure: FAIL + * Failure: NULL * * Programmer: Robb Matzke - * Thursday, April 16, 1998 + * Wednesday, August 5, 1998 * * Modifications: * *------------------------------------------------------------------------- */ -herr_t -H5Z_register (H5Z_method_t method, const char *name, H5Z_func_t cfunc, - H5Z_func_t ufunc) +static H5Z_class_t * +H5Z_find(H5Z_filter_t id) { - FUNC_ENTER (H5Z_register, FAIL); + size_t i; - assert (method>=0 && method<=H5Z_USERDEF_MAX); - H5MM_xfree (H5Z_g[method].name); - H5Z_g[method].name = H5MM_xstrdup (name); - H5Z_g[method].compress = cfunc; - H5Z_g[method].uncompress = ufunc; + FUNC_ENTER(H5Z_find, NULL); - FUNC_LEAVE (SUCCEED); + for (i=0; ifilter[].flags). The filters are processed in + * definition order unless the H5Z_FLAG_REVERSE is set. The + * FILTER_MASK is a bit-mask to indicate which filters to skip + * and on exit will indicate which filters failed. Each + * filter has an index number in the pipeline and that index + * number is the filter's bit in the FILTER_MASK. NBYTES is the + * number of bytes of data to filter and on exit should be the + * number of resulting bytes while BUF_SIZE holds the total + * allocated size of the buffer, which is pointed to BUF. * - * Return: Success: Number of bytes compressed into DST limited - * by DST_NBYTES. + * If the buffer must grow during processing of the pipeline + * then the pipeline function should free the original buffer + * and return a fresh buffer, adjusting BUF_SIZE accordingly. * - * Failure: 0 + * Return: Success: 0 + * + * Failure: -1 * * Programmer: Robb Matzke - * Thursday, April 16, 1998 + * Tuesday, August 4, 1998 * * Modifications: * *------------------------------------------------------------------------- */ -static size_t -H5Z_zlib_c (unsigned int flags, size_t __unused__ cd_size, - const void __unused__ *client_data, size_t src_nbytes, - const void *src, size_t dst_nbytes, void *dst/*out*/) +herr_t +H5Z_pipeline(H5F_t *f, const H5O_pline_t *pline, uintn flags, + uintn *filter_mask/*in,out*/, size_t *nbytes/*in,out*/, + size_t *buf_size/*in,out*/, void **buf/*in,out*/) { - size_t ret_value = 0; -#if defined(HAVE_LIBZ) && defined(HAVE_ZLIB_H) - const Bytef *z_src = (const Bytef*)src; - Bytef *z_dst = (Bytef*)dst; - uLongf z_dst_nbytes = (uLongf)dst_nbytes; - uLong z_src_nbytes = (uLong)src_nbytes; - int level = flags % 10; - int status; + size_t i, idx, new_nbytes; + H5Z_class_t *fclass=NULL; + uintn failed = 0; +#ifdef H5Z_DEBUG + H5_timer_t timer; #endif - FUNC_ENTER (H5Z_zlib_c, 0); - -#if defined(HAVE_LIBZ) && defined (HAVE_ZLIB_H) - status = compress2 (z_dst, &z_dst_nbytes, z_src, z_src_nbytes, level); - if (Z_BUF_ERROR==status) { - ret_value = dst_nbytes; - } else if (Z_MEM_ERROR==status) { - HGOTO_ERROR (H5E_COMP, H5E_CANTINIT, 0, "deflate memory error"); - } else if (Z_OK!=status) { - HGOTO_ERROR (H5E_COMP, H5E_CANTINIT, 0, "deflate error"); - } else { - ret_value = z_dst_nbytes; - } -#else - HGOTO_ERROR (H5E_COMP, H5E_UNSUPPORTED, 0, - "hdf5 was not compiled with zlib-1.0.2 or better"); + FUNC_ENTER(H5Z_pipeline, FAIL); + + assert(f); + assert(0==(flags & ~H5Z_FLAG_INVMASK)); + assert(filter_mask); + assert(nbytes && *nbytes>0); + assert(buf_size && *buf_size>0); + assert(buf && *buf); + assert(!pline || pline->nfilters<32); + + if (pline && (flags & H5Z_FLAG_REVERSE)) { + for (i=pline->nfilters; i>0; --i) { + idx = i-1; + + if (*filter_mask & ((unsigned)1<filter[idx].id))) { + failed |= (unsigned)1 << idx; + HRETURN_ERROR(H5E_PLINE, H5E_READERROR, FAIL, + "required filter is not registered"); + } +#ifdef H5Z_DEBUG + H5_timer_begin(&timer); +#endif + new_nbytes = (fclass->func)(flags|(pline->filter[idx].flags), + pline->filter[idx].cd_nelmts, + pline->filter[idx].cd_values, + *nbytes, buf_size, buf); +#ifdef H5Z_DEBUG + H5_timer_end(&(fclass->stats[1].timer), &timer); + fclass->stats[1].total += MAX(*nbytes, new_nbytes); + if (0==new_nbytes) fclass->stats[1].errors += *nbytes; +#endif + if (0==new_nbytes) { + failed |= (unsigned)1 << idx; + HRETURN_ERROR(H5E_PLINE, H5E_READERROR, FAIL, + "filter returned failure"); + } + *nbytes = new_nbytes; + } + } else if (pline) { + for (idx=0; idxnfilters; idx++) { + if (*filter_mask & ((unsigned)1<filter[idx].id))) { + failed |= (unsigned)1 << idx; + if (pline->filter[idx].flags & H5Z_FLAG_OPTIONAL) { + H5E_clear(); + continue; + } else { + HRETURN_ERROR(H5E_PLINE, H5E_WRITEERROR, FAIL, + "required filter is not registered"); + } + } +#ifdef H5Z_DEBUG + H5_timer_begin(&timer); +#endif + new_nbytes = (fclass->func)(flags|(pline->filter[idx].flags), + pline->filter[idx].cd_nelmts, + pline->filter[idx].cd_values, + *nbytes, buf_size, buf); +#ifdef H5Z_DEBUG + H5_timer_end(&(fclass->stats[0].timer), &timer); + fclass->stats[0].total += MAX(*nbytes, new_nbytes); + if (0==new_nbytes) fclass->stats[0].errors += *nbytes; #endif + if (0==new_nbytes) { + failed |= (unsigned)1 << idx; + if (0==(pline->filter[idx].flags & H5Z_FLAG_OPTIONAL)) { + HRETURN_ERROR(H5E_PLINE, H5E_WRITEERROR, FAIL, + "filter returned failure"); + } else { + H5E_clear(); + } + } else { + *nbytes = new_nbytes; + } + } + } - done: - FUNC_LEAVE (ret_value); + *filter_mask = failed; + FUNC_LEAVE(SUCCEED); } /*------------------------------------------------------------------------- - * Function: H5Z_zlib_u + * Function: H5Z_filter_deflate * - * Purpose: Uncompress SRC_NBYTES from SRC into at most DST_NBYTES of - * DST. + * Purpose: * - * Return: Success: Number of bytes returned in DST. + * Return: Success: * - * Failure: 0 + * Failure: * * Programmer: Robb Matzke * Thursday, April 16, 1998 @@ -466,39 +519,99 @@ H5Z_zlib_c (unsigned int flags, size_t __unused__ cd_size, *------------------------------------------------------------------------- */ static size_t -H5Z_zlib_u (unsigned int __unused__ flags, size_t __unused__ cd_size, - const void __unused__ *client_data, size_t src_nbytes, - const void *src, size_t dst_nbytes, void *dst/*out*/) +H5Z_filter_deflate (uintn flags, size_t cd_nelmts, const uintn cd_values[], + size_t nbytes, size_t *buf_size, void **buf) { size_t ret_value = 0; -#ifdef HAVE_ZLIB_H - const Bytef *z_src = (const Bytef*)src; - Bytef *z_dst = (Bytef*)dst; - uLongf z_dst_nbytes = (uLongf)dst_nbytes; - uLong z_src_nbytes = (uLong)src_nbytes; + int aggression = 6; + void *outbuf = NULL; +#if defined(HAVE_LIBZ) && defined(HAVE_ZLIB_H) int status; #endif - FUNC_ENTER (H5Z_zlib_u, 0); + FUNC_ENTER (H5Z_filter_deflate, 0); + + /* Get aggression level */ + if (cd_nelmts!=1 || cd_values[0]>9) { + HGOTO_ERROR(H5E_ARGS, H5E_BADVALUE, 0, + "invalid deflate aggression level"); + } + aggression = cd_values[0]; #if defined(HAVE_LIBZ) && defined (HAVE_ZLIB_H) - status = uncompress (z_dst, &z_dst_nbytes, z_src, z_src_nbytes); - if (Z_BUF_ERROR==status) { - HGOTO_ERROR (H5E_COMP, H5E_CANTINIT, 0, - "deflate destination buffer was too small"); - } else if (Z_MEM_ERROR==status) { - HGOTO_ERROR (H5E_COMP, H5E_CANTINIT, 0, "deflate memory error"); - } else if (Z_DATA_ERROR==status) { - HGOTO_ERROR (H5E_COMP, H5E_CANTINIT, 0, "deflate corrupted data"); - } else if (Z_OK!=status) { - HGOTO_ERROR (H5E_COMP, H5E_CANTINIT, 0, "deflate error"); + if (flags & H5Z_FLAG_REVERSE) { + /* Input; uncompress */ + z_stream z_strm; + size_t nalloc = *buf_size; + + outbuf = H5MM_malloc(nalloc); + HDmemset(&z_strm, 0, sizeof(z_strm)); + z_strm.next_in = *buf; + z_strm.avail_in = nbytes; + z_strm.next_out = outbuf; + z_strm.avail_out = nalloc; + if (Z_OK!=inflateInit(&z_strm)) { + HGOTO_ERROR(H5E_PLINE, H5E_CANTINIT, 0, "inflateInit() failed"); + } + while (1) { + status = inflate(&z_strm, Z_SYNC_FLUSH); + if (Z_STREAM_END==status) break; /*done*/ + if (Z_OK!=status) { + inflateEnd(&z_strm); + HGOTO_ERROR(H5E_PLINE, H5E_CANTINIT, 0, "inflate() failed"); + } + if (Z_OK==status && 0==z_strm.avail_out) { + nalloc *= 2; + outbuf = H5MM_realloc(outbuf, nalloc); + z_strm.next_out = (char*)outbuf + z_strm.total_out; + z_strm.avail_out = nalloc - z_strm.total_out; + } + } + + H5MM_xfree(*buf); + *buf = outbuf; + outbuf = NULL; + *buf_size = nalloc; + ret_value = z_strm.total_out; + inflateEnd(&z_strm); + + } else { + /* + * Output; compress but fail if the result would be larger than the + * input. The library doesn't provide in-place compression, so we + * must allocate a separate buffer for the result. + */ + const Bytef *z_src = (const Bytef*)(*buf); + Bytef *z_dst; /*destination buffer */ + uLongf z_dst_nbytes = (uLongf)nbytes; + uLong z_src_nbytes = (uLong)nbytes; + + if (NULL==(z_dst=outbuf=H5MM_malloc(nbytes))) { + HGOTO_ERROR(H5E_RESOURCE, H5E_NOSPACE, 0, + "unable to allocate deflate destination buffer"); + } + status = compress2 (z_dst, &z_dst_nbytes, z_src, z_src_nbytes, + aggression); + if (Z_BUF_ERROR==status) { + HGOTO_ERROR(H5E_PLINE, H5E_CANTINIT, 0, "overflow"); + } else if (Z_MEM_ERROR==status) { + HGOTO_ERROR (H5E_PLINE, H5E_CANTINIT, 0, "deflate memory error"); + } else if (Z_OK!=status) { + HGOTO_ERROR (H5E_PLINE, H5E_CANTINIT, 0, "deflate error"); + } else { + H5MM_xfree(*buf); + *buf = outbuf; + outbuf = NULL; + *buf_size = nbytes; + ret_value = z_dst_nbytes; + } } - ret_value = z_dst_nbytes; #else - HGOTO_ERROR (H5E_COMP, H5E_UNSUPPORTED, 0, + HGOTO_ERROR (H5E_PLINE, H5E_UNSUPPORTED, 0, "hdf5 was not compiled with zlib-1.0.2 or better"); #endif done: + H5MM_xfree(outbuf); FUNC_LEAVE (ret_value); } diff --git a/src/H5Zprivate.h b/src/H5Zprivate.h index 288ec07..7330265 100644 --- a/src/H5Zprivate.h +++ b/src/H5Zprivate.h @@ -10,14 +10,13 @@ #include -struct H5O_compress_t; /*forward decl*/ +struct H5O_pline_t; /*forward decl*/ -herr_t H5Z_register (H5Z_method_t method, const char *name, - H5Z_func_t compress, H5Z_func_t uncompress); -size_t H5Z_compress (const struct H5O_compress_t *compress, size_t nbytes, - const void *src, void *dst/*out*/); -size_t H5Z_uncompress (const struct H5O_compress_t *compress, - size_t src_nbytes, const void *src, size_t dst_nbytes, - void *dst/*out*/); +herr_t H5Z_register(H5Z_filter_t id, const char *comment, H5Z_func_t filter); +herr_t H5Z_append(struct H5O_pline_t *pline, H5Z_filter_t filter, uintn flags, + size_t cd_nelmts, const unsigned int cd_values[]); +herr_t H5Z_pipeline(H5F_t *f, const struct H5O_pline_t *pline, uintn flags, + uintn *filter_mask/*in,out*/, size_t *nbytes/*in,out*/, + size_t *buf_size/*in,out*/, void **buf/*in,out*/); #endif diff --git a/src/H5Zpublic.h b/src/H5Zpublic.h index 2ce1326..04b5f3a 100644 --- a/src/H5Zpublic.h +++ b/src/H5Zpublic.h @@ -9,59 +9,50 @@ #define _H5Zpublic_H /* - * Compression methods. Method zero means no compression. Methods 1 through - * 15 are defined by the library. Methods 16-255 are user-defined. + * Filter identifiers. Values 0 through 255 are for filters defined by the + * HDF5 library. Values 256 through 511 are available for testing new + * filters. Subsequent values should be obtained from the HDF5 development + * team at hdf5dev@ncsa.uiuc.edu. These values will never change because they + * appear in the HDF5 files. */ -typedef int H5Z_method_t; -#define H5Z_NONE 0 /*no compression, must be zero */ -#define H5Z_DEFLATE 1 /*deflation like gzip */ -#define H5Z_RES_2 2 /*reserved for internal use */ -#define H5Z_RES_3 3 /*reserved for internal use */ -#define H5Z_RES_4 4 /*reserved for internal use */ -#define H5Z_RES_5 5 /*reserved for internal use */ -#define H5Z_RES_6 6 /*reserved for internal use */ -#define H5Z_RES_7 7 /*reserved for internal use */ -#define H5Z_RES_8 8 /*reserved for internal use */ -#define H5Z_RES_9 9 /*reserved for internal use */ -#define H5Z_RES_10 10 /*reserved for internal use */ -#define H5Z_RES_11 11 /*reserved for internal use */ -#define H5Z_RES_12 12 /*reserved for internal use */ -#define H5Z_RES_13 13 /*reserved for internal use */ -#define H5Z_RES_14 14 /*reserved for internal use */ -#define H5Z_RES_15 15 /*reserved for internal use */ -/* user-defined 16-255 */ -#define H5Z_USERDEF_MIN 16 /*first user-defined method */ -#define H5Z_USERDEF_MAX 255 /*last user-defined method */ +typedef int H5Z_filter_t; +#define H5Z_FILTER_ERROR (-1) /*no filter */ +#define H5Z_FILTER_NONE 0 /*reserved indefinitely */ +#define H5Z_FILTER_DEFLATE 1 /*deflation like gzip */ +#define H5Z_FILTER_MAX 65535 /*maximum filter id */ + +/* Flags for filter definition */ +#define H5Z_FLAG_DEFMASK 0x00ff /*definition flag mask */ +#define H5Z_FLAG_OPTIONAL 0x0001 /*filter is optional */ + +/* Additional flags for filter invocation */ +#define H5Z_FLAG_INVMASK 0xff00 /*invocation flag mask */ +#define H5Z_FLAG_REVERSE 0x0100 /*reverse direction; read */ /* - * A compression function takes some configuration data which comes from the - * compression message, namely FLAGS, CD_SIZE, and CLIENT_DATA. It should - * read SRC_NBYTES from SRC and compress them into at most DST_NBYTES of DST. - * If the compressed data would be larger than DST_NBYTES the function should - * return a value greater than or equal to DST_NBYTES. On failure the - * function may return zero. + * A filter gets definition flags and invocation flags (defined above), the + * client data array and size defined when the filter was added to the + * pipeline, the size in bytes of the data on which to operate, and pointers + * to a buffer and its allocated size. * - * The uncompression function is the inverse of compression and takes the - * same arguments. The SRC_NBYTES argument is the number of compressed bytes - * in SRC. The function should uncompress SRC into DST. For redundancy, - * DST_NBYTES contains the size of the DST buffer although if the algorithm - * is operating properly and the file has not been corrupted the uncompressed - * data will never be larger than DST_NBYTES. The function should return the - * number of bytes in the DST buffer or zero on failure. Failure includes - * the overflow of the DST buffer. + * The filter should store the result in the supplied buffer if possible, + * otherwise it can allocate a new buffer, freeing the original. The + * allocated size of the new buffer should be returned through the BUF_SIZE + * pointer and the new buffer through the BUF pointer. + * + * The return value from the filter is the number of bytes in the output + * buffer. If an error occurs then the function should return zero and leave + * all pointer arguments unchanged. */ -typedef size_t (*H5Z_func_t)(unsigned int flags, size_t cd_size, - const void *client_data, size_t src_nbytes, - const void *src, size_t dst_nbytes, - void *dst/*out*/); - +typedef size_t (*H5Z_func_t)(unsigned int flags, size_t cd_nelmts, + const unsigned int cd_values[], size_t nbytes, + size_t *buf_size, void **buf); #ifdef __cplusplus extern "C" { #endif -herr_t H5Zregister (H5Z_method_t method, const char *name, H5Z_func_t compress, - H5Z_func_t uncompress); +herr_t H5Zregister(H5Z_filter_t id, const char *comment, H5Z_func_t filter); #ifdef __cplusplus } diff --git a/src/H5config.h.in b/src/H5config.h.in index 5978d92..8a7b573 100644 --- a/src/H5config.h.in +++ b/src/H5config.h.in @@ -83,6 +83,9 @@ /* Define if you have the BSDgettimeofday function. */ #undef HAVE_BSDGETTIMEOFDAY +/* Define if you have the difftime function. */ +#undef HAVE_DIFFTIME + /* Define if you have the fork function. */ #undef HAVE_FORK diff --git a/src/H5private.h b/src/H5private.h index 7f26ff3..0b2aba8 100644 --- a/src/H5private.h +++ b/src/H5private.h @@ -215,6 +215,7 @@ typedef struct { void H5_timer_reset (H5_timer_t *timer); void H5_timer_begin (H5_timer_t *timer); void H5_timer_end (H5_timer_t *sum/*in,out*/, H5_timer_t *timer/*in,out*/); +void H5_bandwidth(char *buf/*out*/, double nbytes, double nseconds); /* * Redefine all the POSIX functions. We should never see a POSIX @@ -254,7 +255,11 @@ void H5_timer_end (H5_timer_t *sum/*in,out*/, H5_timer_t *timer/*in,out*/); #define HDctermid(S) ctermid(S) #define HDctime(T) ctime(T) #define HDcuserid(S) cuserid(S) +#ifdef HAVE_DIFFTIME #define HDdifftime(X,Y) difftime(X,Y) +#else +#define HDdifftime(X,Y) ((double)(X)-(double)(Y)) +#endif #define HDdiv(X,Y) div(X,Y) #define HDdup(F) dup(F) #define HDdup2(F,I) dup2(F,I) diff --git a/src/hdf5.h b/src/hdf5.h index a80945b..de1c727 100644 --- a/src/hdf5.h +++ b/src/hdf5.h @@ -35,6 +35,6 @@ #include /* Property lists */ #include /* Dataspaces */ #include /* Datatypes */ -#include /* Data compression */ +#include /* Data filters */ #endif diff --git a/test/.distdep b/test/.distdep index 82aaa44..2b28ca4 100644 --- a/test/.distdep +++ b/test/.distdep @@ -492,4 +492,5 @@ mtime.o: \ ../src/H5Ppublic.h \ ../src/H5Zpublic.h \ ../src/H5Spublic.h \ - ../src/H5Tpublic.h + ../src/H5Tpublic.h \ + ../src/H5private.h diff --git a/test/dsets.c b/test/dsets.c index 6ad7ee0..1a66600 100644 --- a/test/dsets.c +++ b/test/dsets.c @@ -40,7 +40,7 @@ #define DSET_COMPRESS_NAME "compressed" #define DSET_BOGUS_NAME "bogus" -#define H5Z_BOGUS 255 +#define H5Z_BOGUS 305 /*------------------------------------------------------------------------- @@ -354,9 +354,9 @@ test_tconv(hid_t file) /*------------------------------------------------------------------------- * Function: bogus * - * Purpose: A bogus compression method. + * Purpose: A bogus compression method that doesn't do anything. * - * Return: Success: SRC_NBYTES, see compression documentation. + * Return: Success: Data chunk size * * Failure: 0 * @@ -368,12 +368,11 @@ test_tconv(hid_t file) *------------------------------------------------------------------------- */ static size_t -bogus (unsigned int __unused__ flags, size_t __unused__ cd_size, - const void __unused__ *client_data, size_t src_nbytes, const void *src, - size_t __unused__ dst_nbytes, void *dst/*out*/) +bogus(unsigned int __unused__ flags, size_t __unused__ cd_nelmts, + const unsigned int __unused__ cd_values[], size_t nbytes, + size_t __unused__ *buf_size, void __unused__ **buf) { - memcpy (dst, src, src_nbytes); - return src_nbytes; + return nbytes; } @@ -586,7 +585,7 @@ test_compression(hid_t file) points[hs_offset[0]+i][hs_offset[1]+j] = rand (); } } - H5Sselect_hyperslab (space, H5S_SELECT_SET, hs_offset, NULL, hs_size, NULL); + H5Sselect_hyperslab(space, H5S_SELECT_SET, hs_offset, NULL, hs_size, NULL); status = H5Dwrite (dataset, H5T_NATIVE_INT, space, space, xfer, points); if (status<0) goto error; @@ -603,8 +602,10 @@ test_compression(hid_t file) printf(" At index %lu,%lu\n", (unsigned long)(hs_offset[0]+i), (unsigned long)(hs_offset[1]+j)); - printf(" At original: %d\n", (int)points[hs_offset[0]+i][hs_offset[1]+j]); - printf(" At returned: %d\n", (int)check[hs_offset[0]+i][hs_offset[1]+j]); + printf(" At original: %d\n", + (int)points[hs_offset[0]+i][hs_offset[1]+j]); + printf(" At returned: %d\n", + (int)check[hs_offset[0]+i][hs_offset[1]+j]); goto error; } } @@ -619,11 +620,11 @@ test_compression(hid_t file) printf ("%-70s", "Testing compression (app-defined method)"); fflush (stdout); - H5Zregister (H5Z_BOGUS, "bogus", bogus, bogus); - H5Pset_compression (dc, H5Z_BOGUS, 0, 0, NULL); - H5Dclose (dataset); - H5Sclose (space); - space = H5Screate_simple (2, size, NULL); + if (H5Zregister (H5Z_BOGUS, "bogus", bogus)<0) goto error; + if (H5Pset_filter (dc, H5Z_BOGUS, 0, 0, NULL)<0) goto error; + if (H5Dclose (dataset)<0) goto error; + if (H5Sclose (space)<0) goto error; + if ((space = H5Screate_simple (2, size, NULL))<0) goto error; dataset = H5Dcreate (file, DSET_BOGUS_NAME, H5T_NATIVE_INT, space, dc); assert (dataset>=0); diff --git a/test/mtime.c b/test/mtime.c index cd78cc1..019ce26 100644 --- a/test/mtime.c +++ b/test/mtime.c @@ -20,7 +20,7 @@ #define TRUE 1 #define FILE_NAME_1 "mtime.h5" -#include +#include #ifndef HAVE_ATTRIBUTE # undef __attribute__ # define __attribute__(X) /*void*/ @@ -130,7 +130,7 @@ main(void) puts(" Modification times will be mantained in the file bug cannot"); puts(" be queried on this system. See H5O_mtime_decode()."); return 1; - } else if (fabs(difftime(now, sb.mtime))>60.0) { + } else if (fabs(HDdifftime(now, sb.mtime))>60.0) { puts("*FAILED*"); tm = localtime(&(sb.mtime)); strftime(buf1, sizeof buf1, "%Y-%m-%d %H:%M:%S", tm); diff --git a/tools/h5ls.c b/tools/h5ls.c index c79c8d1..52ac9cb 100644 --- a/tools/h5ls.c +++ b/tools/h5ls.c @@ -175,7 +175,7 @@ list (hid_t group, const char *name, void __unused__ *op_data) hid_t obj; hid_t (*func)(void*); void *edata; - int i; + int i, nf; char buf[512], comment[50]; H5G_stat_t statbuf; struct tm *tm; @@ -204,6 +204,30 @@ list (hid_t group, const char *name, void __unused__ *op_data) printf ("}\n"); H5Dclose (space); H5Aiterate (obj, NULL, list_attr, NULL); + + /* Print additional information about datasets */ + if (verbose_g>0) { + hid_t dcpl = H5Dget_create_plist(obj); + if ((nf = H5Pget_nfilters(dcpl))>0) { + for (i=0; i=0) { printf ("Group\n"); @@ -240,7 +264,7 @@ list (hid_t group, const char *name, void __unused__ *op_data) if (comment[0]) printf(" %-10s %s\n", "Comment:", comment); } - if (dump_g && (obj=H5Dopen(group, name))) { + if (dump_g && (obj=H5Dopen(group, name))>=0) { /* Turn on error reporting before dumping the data */ H5Eset_auto(func, edata); dump_dataset_values(obj); diff --git a/tools/h5tools.c b/tools/h5tools.c index fae2251..0472074 100644 --- a/tools/h5tools.c +++ b/tools/h5tools.c @@ -293,8 +293,10 @@ h5dump_simple(FILE *stream, const h5dump_t *info, hid_t dset, hid_t p_type) hs_size, NULL); H5Sselect_hyperslab(sm_space, H5S_SELECT_SET, zero, NULL, &hs_nelmts, NULL); - H5Dread(dset, p_type, sm_space, f_space, H5P_DEFAULT, sm_buf); - + if (H5Dread(dset, p_type, sm_space, f_space, H5P_DEFAULT, sm_buf)<0) { + return -1; + } + /* Print the data */ for (i=0; i