From 4c0ffcb8143ba437004a0f7f95bbd58486ac1155 Mon Sep 17 00:00:00 2001 From: Frank Baker Date: Thu, 11 Mar 2004 15:18:23 -0500 Subject: [svn-r8254] Purpose: Clean up RM formatting. Modify RM HTML code to facilitate automated generation of PDF version. Minor edits. Description: Reworked format of "Options" and "Parameters" sections. Added HTML tags (and pseudo-HTML tags) used by HTMLdoc to generate PDF files. Other minor copy edits. Platforms tested: IE 5 --- doc/html/Tools.html | 1492 ++++++++++++++++++++++++++++++--------------------- 1 file changed, 874 insertions(+), 618 deletions(-) diff --git a/doc/html/Tools.html b/doc/html/Tools.html index 767eab8..2d2007f 100644 --- a/doc/html/Tools.html +++ b/doc/html/Tools.html @@ -64,6 +64,8 @@ And in this document, the

HDF5 Tools

+ +

HDF5 Tool Interfaces

@@ -172,6 +174,7 @@ installed with HDF5. +

@@ -191,23 +194,19 @@ installed with HDF5. It can display the contents of the entire HDF5 file or selected objects, which can be groups, datasets, a subset of a dataset, links, attributes, or datatypes. -

The --header option displays object header information only. -

Names are the absolute names of the objects. h5dump displays objects in the order same as the command order. If a name does not start with a slash, h5dump begins searching for the specified object starting at the root group. -

If an object is hard linked with multiple names, h5dump displays the content of the object in the first occurrence. Only the link information is displayed in later occurrences. -

h5dump assigns a name for any unnamed datatype in the form of @@ -215,14 +214,12 @@ installed with HDF5. oid1 and oid2 are the object identifiers assigned by the library. The unnamed types are displayed within the root group. -

Datatypes are displayed with standard type names. For example, if a dataset is created with H5T_NATIVE_INT type and the standard type name for integer on that machine is H5T_STD_I32BE, h5dump displays H5T_STD_I32BE as the type of the dataset. -

h5dump can also dump a subset of a dataset. This feature operates in much the same way as hyperslabs in HDF5; @@ -230,12 +227,10 @@ installed with HDF5. function H5Sselect_hyperslab and the resulting selection is displayed. -

The h5dump output is described in detail in the DDL for HDF5, the Data Description Language document. -

Note: It is not permissible to specify multiple attributes, datasets, datatypes, groups, or soft links with one @@ -252,7 +247,6 @@ installed with HDF5. CORRECT:   h5dump -a /attr1 -a /attr2 foo.h5
-

It's possible to select the file driver with which to open the HDF5 file by using the --filedriver (-f) command-line option. @@ -261,7 +255,6 @@ installed with HDF5. isn't specified, then the file will be opened with each driver in turn and in the order specified above until one driver succeeds in opening the file. -

XML Output: @@ -276,115 +269,173 @@ installed with HDF5. HDF5 Java Tools.
Options and Parameters: -
-
-h   or   - --help
-
Print a usage message and exit.
-
-B   or   - --bootblock
-
Print the content of the boot block.
- (This option is not yet implemented.)
-
-H   or   - --header
-
Print the header only; no data is displayed.
-
-A -
Print the header and value of attributes; - data of datasets is not displayed.
-
-i   or   - --object-ids
-
Print the object ids.
-
-r   or   - --string
-
Print 1-bytes integer datasets as ASCII.
-
-V   or   - --version
-
Print version number and exit.
-
-a P   or   - --attribute=P
-
Print the specified attribute.
-
-d P   or   - --dataset=P
-
Print the specified dataset.
-
-f D   or   - --filedriver=D
-
Specify which driver to open the file with.
-
-g P   or   - --group=P
-
Print the specified group and all members.
-
-l P   or   - --soft-link=P
-
Print the value(s) of the specified soft link.
-
-o F   or   - --output=F
-
Output raw data into file F.
-
-t T   or   - --datatype=T
-
Print the specified named datatype.
-
-w N   or   - --width=N
-
Set the number of columns of output.
-
-x   or   - --xml
-
Output XML using XML schema (default) instead of DDL.
-
-u   or   - --use-dtd
-
Output XML using XML DTD instead of DDL.
-
-D U   or   - --xml-dtd=U
-
In XML output, refer to the DTD or schema at U - instead of the default schema/DTD.
-
-X S   or   - --xml-dns=S
-
In XML output, (XML Schema) use qualified names in the XML:
-       - ":": no namespace, default: "hdf5:"
-
-s L   or   - --start=L
-
Offset of start of subsetting selection. -
- Default: the beginning of the dataset.
- -
-S L   or   - --stride=L
-
Hyperslab stride. -
- Default: 1 in all dimensions.
-
-c L   or   - --count=L
-
Number of blocks to include in the selection.
-
-k L   or   - --block=L
-
Size of block in hyperslab. -
- Default: 1 in all dimensions.
-
--
-
Indicate that all following arguments are non-options. - E.g., to dump a file called `-f', use h5dump -- -f.
-
file
-
The file to be examined.
+
    + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + +
    -h   or   --helpPrint a usage message and exit.
    -B   or   --bootblockPrint the content of the boot block.
    (This + option is not yet implemented.)
    -H   or   --headerPrint the header only; no data is displayed.
    -APrint the header and value of attributes; data of datasets + is not displayed.
    -i   or   --object-idsPrint the object ids.
    -r   or   --stringPrint 1-bytes integer datasets as ASCII.
    -V   or   --versionPrint version number and exit.
    -a P  or  --attribute=P    Print the specified attribute.
    -d P   or   + --dataset=PPrint the specified dataset.
    -f D  or  --filedriver=D        Specify which driver to open the file with.
    -g P   or   + --group=PPrint the specified group and all members.
    -l P  or  --soft-link=P    Print the value(s) of the specified soft link.
    -o F   or   + --output=FOutput raw data into file F.
    -t T   or   + --datatype=TPrint the specified named datatype.
    -w N   or   + --width=NSet the number of columns of output.
    -x   or   + --xmlOutput XML using XML schema (default) instead of DDL.
    -u   or   + --use-dtdOutput XML using XML DTD instead of DDL.
    -D U   or   + --xml-dtd=UIn XML output, refer to the DTD or schema at U + instead of the default schema/DTD.
    -X S   or   + --xml-dns=SIn XML output, (XML Schema) use qualified names in + the XML:
          ":": no namespace, default: + "hdf5:"
    -s L   or   + --start=LOffset of start of subsetting selection.
    + Default: the beginning of the dataset.
    -S L   or   + --stride=LHyperslab stride.
    + Default: 1 in all dimensions.
    -c L   or   + --count=LNumber of blocks to include in the selection.
    -k L   or   + --block=LSize of block in hyperslab.
    + Default: 1 in all dimensions.
    --Indicate that all following arguments are non-options. + E.g., to dump a file called `-f', use h5dump -- -f.
    fileThe file to be examined.
    +


-
The option parameters listed above are defined as follows: -
D -- which file driver to use in opening the - file. Acceptable values are "sec2", "family", "split", - "multi", and "stream". Without the file driver flag the - file will be opened with each driver in turn and in the - order specified above until one driver succeeds in - opening the file.
-
P -- The full path from the root group to - the object
-
T -- The name of the datatype
-
F -- A filename
-
N -- An integer greater than 1
-
L -- A list of integers, the number of which is + +
    + The option parameters listed above are defined as follows: + + + + + + + + + + + + + + + + + + + + + + +
    D    which file driver to use in opening the + file. Acceptable values are "sec2", "family", "split", + "multi", and "stream". Without the file driver flag the + file will be opened with each driver in turn and in the + order specified above until one driver succeeds in + opening the file.
    PThe full path from the root group to + the object
    TThe name of the datatype
    FA filename
    NAn integer greater than 1
    LA list of integers, the number of which is equal to the number of dimensions in the dataspace being - queried -
    U -- A URI (as defined in + queried
    UA URI (as defined in [IETF RFC 2396], updated by [IETF RFC 2732]) - that refers to the DTD to be used to validate the XML -

    -
    Subsetting parameters can also be expressed in a convenient + that refers to the DTD to be used to validate the XML
    + +

    Subsetting parameters can also be expressed in a convenient compact form, as follows:
             @@ -393,50 +444,59 @@ installed with HDF5. All of the semicolons (;) are required, even when a parameter value is not specified. When not specified, default parameter values are used. -

-

- +

Examples: -
    -
  1. Dumping the group /GroupFoo/GroupBar in the file - quux.h5: -
    - h5dump -g /GroupFoo/GroupBar quux.h5 -
    + + + +
    +
      +
    1. Dumping the group /GroupFoo/GroupBar in the file + quux.h5:
      +      + h5dump -g /GroupFoo/GroupBar quux.h5 +
      +
    2. Dumping the dataset Fnord in the group - /GroupFoo/GroupBar in the file quux.h5: -
      - h5dump -d /GroupFoo/GroupBar/Fnord quux.h5 -
      + /GroupFoo/GroupBar in the file quux.h5:
      +      + h5dump -d /GroupFoo/GroupBar/Fnord quux.h5 +
      +
    3. Dumping the attribute metadata of the dataset Fnord which is in group - /GroupFoo/GroupBar in the file quux.h5: -
      - h5dump -a /GroupFoo/GroupBar/Fnord/metadata quux.h5 -
      + /GroupFoo/GroupBar in the file quux.h5:
      +      + h5dump -a /GroupFoo/GroupBar/Fnord/metadata quux.h5 +
      +
    4. Dumping the attribute metadata which is an - attribute of the root group in the file quux.h5: -
      - h5dump -a /metadata quux.h5 -
      -
    5. Producing an XML listing of the file bobo.h5: -
      - h5dump --xml bobo.h5 > bobo.h5.xml -
      - + attribute of the root group in the file quux.h5:
      +      + h5dump -a /metadata quux.h5 +
      +
      +
    6. Producing an XML listing of the file bobo.h5:
      +      + h5dump --xml bobo.h5 > bobo.h5.xml +
      +
    7. Dumping a subset of the dataset /GroupFoo/databar/ - in the file quux.h5 -
      - h5dump -d /GroupFoo/databar --start="1,1" --stride="2,3" -
               - --count="3,19" --block="1,1" quux.h5       -
      + in the file quux.h5:
      +      + h5dump -d /GroupFoo/databar --start="1,1" --stride="2,3" +
               + --count="3,19" --block="1,1" quux.h5       +
      +
    8. The same example using the short form to specify the - subsetting parameters: -
      - h5dump -d "/GroupFoo/databar[1,1;2,3;3,19;1,1]" quux.h5 -
      -
    + subsetting parameters:
    +      + h5dump -d "/GroupFoo/databar[1,1;2,3;3,19;1,1]" quux.h5 +
    +
    +
    +
    Current Status:
    The current version of h5dump displays the following information: @@ -497,20 +557,24 @@ installed with HDF5.
    See Also: + + + +
    +
  2. HDF5 Data Description Language syntax at + DDL for HDF5 +
  3. HDF5 XML Schema at + http://hdf.ncsa.uiuc.edu/DTDs/HDF5-File.xsd +
  4. HDF5 XML information at + http://hdf.ncsa.uiuc.edu/HDF5/XML/ +
    5. + +
    Tool Name: h5ls @@ -525,60 +589,74 @@ installed with HDF5.
    h5ls prints selected information about file objects in the specified format.
    Options and Parameters: -
    -
    -h   or   - -?   or   - --help -
    Print a usage message and exit. -
    -a   or   - --address -
    Print addresses for raw data. -
    -d   or   --data -
    Print the values of datasets. -
    -e   or   - --errors -
    Show all HDF5 error reporting. -
    -f   or   - --full -
    Print full path names instead of base names. -
    -g   or   - --group -
    Show information about a group, not its contents. -
    -l   or   - --label -
    Label members of compound datasets. -
    -r   or   - --recursive -
    List all groups recursively, avoiding cycles. -
    -s   or   - --string -
    Print 1-bytes integer datasets as ASCII. -
    -S   or   - --simple -
    Use a machine-readable output format. -
    -wN   or   - --width=N -
    Set the number of columns of output. -
    -v   or   - --verbose -
    Generate more verbose output. -
    -V   or   - --version -
    Print version number and exit. -
    -x   or   - --hexdump -
    Show raw data in hexadecimal format. -
    file -
    The file name may include a printf(3C) integer format - such as %%05d to open a file family. -
    objects -
    Each object consists of an HDF5 file name optionally +
      + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + +
      -h  or  -?  or   + --help    Print a usage message and exit.
      -a   or   + --addressPrint addresses for raw data.
      -d   or   --dataPrint the values of datasets.
      -e   or   + --errorsShow all HDF5 error reporting.
      -f   or   + --fullPrint full path names instead of base names.
      -g   or   + --groupShow information about a group, not its contents.
      -l   or   + --labelLabel members of compound datasets.
      -r   or  --recursive    List all groups recursively, avoiding cycles.
      -s   or   + --stringPrint 1-bytes integer datasets as ASCII.
      -S   or   + --simpleUse a machine-readable output format.
      -wN   or   + --width=N    Set the number of columns of output.
      -v   or   + --verboseGenerate more verbose output.
      -V   or   + --versionPrint version number and exit.
      -x   or   + --hexdumpShow raw data in hexadecimal format.
      fileThe file name may include a printf(3C) integer format + such as %%05d to open a file family.
      objectsEach object consists of an HDF5 file name optionally followed by a slash and an object name within the file (if no object is specified within the file then the contents of the root group are displayed). The file name may include a printf(3C) integer format such - as "%05d" to open a file family. - + as "%05d" to open a file family.
    +
    Tool Name: h5diff    (Beta version) @@ -622,47 +701,52 @@ installed with HDF5. H5diff Examples.
    Options and Parameters: -
    -
    file1 -
    file2 -
    The HDF5 files to be compared. -
    -h -
    Print all differences. -
    -r -
    Print only the names of objects that differ; - do not print the differences. - These objects may be HDF5 datasets, groups, - or named datatypes. -
    -n count -
    Print difference up to count differences, - then stop. - count must be a positive integer. -
    -d delta -
    Print only differences that are greater than the - limit delta. - delta must be a positive number. - The comparison criterion is whether the - absolute value of the difference of - two corresponding values is greater than - delta -
    (e.g., |a–b| > delta, - where a is a value in file1 and - b is a value in file2). -
    -p relative -
    Print only differences that are greater than a - relative error. - relative must be a positive number. - The comparison criterion is whether the - absolute value of the difference 1 - and the ratio of two corresponding values - is greater than relative - (e.g., |1–(b/a)| > relative - where a is a value in file1 and - b is a value in file2). -
    object1 -
    object2 -
    Specific object(s) within the files to be compared. -
    +
      + + + + + + + + + + + + + + + + + + + + + + + + + + + +
      file1 
      file2The HDF5 files to be compared.
      -hPrint all differences.
      -rPrint only the names of objects that differ; + do not print the differences. These objects may be HDF5 + datasets, groups, or named datatypes.
      -n countPrint difference up to count + differences, then stop. count must be a positive integer.
      -d deltaPrint only differences that are greater than the + limit delta. delta must be a positive number. + The comparison criterion is whether the absolute value of the + difference of two corresponding values is greater than + delta +
      (e.g., |a–b| > delta, + where a is a value in file1 and + b is a value in file2).
      -p relative        Print only differences that are greater than a + relative error. relative must be a positive number. + The comparison criterion is whether the absolute value of the + difference 1 and the ratio of two corresponding values + is greater than relative + (e.g., |1–(b/a)| > relative + where a is a value in file1 and + b is a value in file2).
      object1 
      object2Specific object(s) within the files to be compared.
    Examples:
    The following h5diff call compares the object /a/b in file1 @@ -684,6 +768,7 @@ installed with HDF5.
    +
    Tool Name: h5repart @@ -711,20 +796,26 @@ installed with HDF5. format such as %d.
    Options and Parameters: -
    -
    -v -
    Produce verbose output. -
    -V -
    Print a version number and exit. -
    -bN -
    The I/O block size, defaults to 1kB -
    -mN -
    The destination member size or 1GB -
    source_file -
    The name of the source file -
    dest_file -
    The name of the destination files -
    +
      + + + + + + + + + + + + + + + + + + +
      -vProduce verbose output.
      -VPrint a version number and exit.
      -bNThe I/O block size, defaults to 1kB
      -mNThe destination member size or 1GB
      source_file    The name of the source file
      dest_fileThe name of the destination files
    +
    Tool Name: h5import @@ -1288,50 +1380,40 @@ installed with HDF5.
    - + -

    - The help option:
    - The help option, expressed as one of - - - - - -
         - h5import -h
    - or
    - h5import -help
    -
    prints the h5import usage summary
         - - h5import -h[elp], OR
    - h5import <infile> <options> - [<infile> <options>...] - -o[utfile] <outfile>     -
    then exits.
    -

    - +

    Options and Parameters: -
    -
    infile(s) -
    Name of the Input file(s). -
    in_options -
    Input options. Note that while only the -dims argument - is required, arguments must used in the order in which they are listed below. -
    -
    -d dim_list -
    -dims dim_list -
    Input data dimensions. + +
      + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + +
      infile(s)Name of the Input file(s).
      in_optionsInput options. Note that while only the -dims argument + is required, arguments must used in the order in which they are listed below.
        -d dim_list 
        -dims dim_listInput data dimensions. dim_list is a string of comma-separated numbers with no spaces describing the dimensions of the input data. For example, a 50 x 100 2-dimensional array would be specified as -dims 50,100.
      Required argument: if no configuration file is used, - this command-line argument is mandatory. -
      -p pathname -
      -pathname pathname -
      pathname is a string consisting of + this command-line argument is mandatory.
        -p pathname 
        -pathname pathname   +
      +                             		pathname is a string consisting of one or more strings separated by slashes (/) specifying the path of the dataset in the output file. If the groups in the path do no exist, they will be @@ -1347,36 +1429,55 @@ installed with HDF5. When an existing dataset of a conflicting name is encountered, h5import quits with an error; the current input file and any subsequent input files - are not processed. -
      -t input_class -
      -type input_class -
      input_class specifies the class of the + are not processed.
        -t input_class 
        -type input_class  input_class specifies the class of the input data and determines the class of the output data.
      Valid values are as defined in the Keyword/Values table in the section "The configuration file" above.
      Optional argument: if not specified, - the default value is FP. -
      -s input_size -
      -size input_size -
      input_size specifies the size in bits + the default value is FP.
        -s input_size 
        -size input_sizeinput_size specifies the size in bits of the input data and determines the size of the output data.
      Valid values for signed or unsigned integers are 8, 16, 32, and 64.
      Valid values for floating point data are 32 and 64.
      Optional argument: if not specified, - the default value is 32. -
      -c config_file -
      config_file specifies a + the default value is 32.
        -c config_fileconfig_file specifies a configuration file.
      This argument replaces all other arguments except infile and - -o outfile - -
      outfile -
      Name of the HDF5 output file. - + -o outfile
        -h 
        -help + Prints the h5import usage summary:
      + h5import -h[elp], OR
      + h5import <infile> <options> [<infile> <options>...] -o[utfile] <outfile>
      + Then exits. +
      outfileName of the HDF5 output file.
    +
    Examples:
    Using command-line arguments: @@ -1456,6 +1557,7 @@ installed with HDF5. +
    Tool Name: gif2h5 @@ -1469,12 +1571,14 @@ installed with HDF5. and produces the HDF5 file h5_file as output.
    Options and Parameters: -
    -
    gif_file -
    The name of the input GIF file -
    h5_file -
    The name of the output HDF5 file -
    +
      + + + + + + +
      gif_file    The name of the input GIF file
      h5_fileThe name of the output HDF5 file
      +
      Tool Name: h52gif @@ -1511,18 +1616,22 @@ installed with HDF5. up to 50 times, for a maximum of 50 images.
      Options and Parameters: -
      -
      h5_file -
      The name of the input HDF5 file -
      gif_file -
      The name of the output GIF file -
      -i h5_image -
      Image option, specifying the name of an HDF5 image or - dataset containing an image to be converted -
      -p h5_palette -
      Palette option, specifying the name of an HDF5 dataset - containing a palette to be used in an image conversion -
      +
        + + + + + + + + + + + + +
        h5_fileThe name of the input HDF5 file
        gif_fileThe name of the output GIF file
        -i h5_imageImage option, specifying the name of an HDF5 image or + dataset containing an image to be converted
        -p h5_palette    Palette option, specifying the name of an HDF5 dataset + containing a palette to be used in an image conversion
      +
      Tool Name: h5toh4 @@ -1628,16 +1738,20 @@ installed with HDF5.

      Options and Parameters: -
      -
      -h -
      Displays a syntax summary. -
      -m -
      Converts multiple HDF5 files to multiple HDF4 files. -
      h5file -
      The HDF5 file to be converted. -
      h4file -
      The HDF4 file to be created. -
      +
        + + + + + + + + + + + + +
        -hDisplays a syntax summary.
        -mConverts multiple HDF5 files to multiple HDF4 files.
        h5file    The HDF5 file to be converted.
        h4fileThe HDF4 file to be created.
      +
      Tool Name: h4toh5 @@ -1749,18 +1864,22 @@ installed with HDF5. Converting between HDF (4.x) and HDF5.

      Options and Parameters: -
      -
      -h -
      Displays a syntax summary. +
        + + + -
        h4file -
        The HDF4 file to be converted. -
        h5file -
        The HDF5 file to be created. - +
        + + + + + +
        -hDisplays a syntax summary.
        h4file    The HDF4 file to be converted.
        h5fileThe HDF5 file to be created.
      +
      Tool Name: h5perf @@ -1821,171 +1941,273 @@ installed with HDF5. HDF5_PARAPREFIX   Sets the prefix for parallel output data files. -
      Options and Parameters: -
      -
      These terms are used as follows in this section: - - - - -
           - file   - A filename
        - size - A size specifier, expressed as an integer greater than or equal - to 0 (zero) followed by a size indicator:
      -     K for kilobytes (1024 bytes)
      -     M for megabytes (1048576 bytes)
      -     G for gigabytes (1073741824 bytes)
      - Example: 37M specifies 37 megabytes or 38797312 bytes.
        - N - An integer greater than or equal to 0 (zero)
      -

      -

      -h, --help -
      Prints a usage message and exits. -
      -a size, --align=size -
      Specifies the alignment of objects in the HDF5 file. - (Default: 1) -
      -A api_list, --api=api_list -
      Specifies which APIs to test. - api_list is a comma-separated list with the - following valid values: - - - - -
           - phdf5  Parallel HDF5
        - mpiioMPI-I/O
        - posixPOSIX
      - (Default: All APIs)

      - Example, --api=mpiio,phdf5 specifies that the - MPI I/O and parallel HDf5 APIs are to be monitored.

      - + +
      Options and Parameters: + +
        + + + + + + + + + + + + +
        These terms are used as follows in this section:
        file  A filename
        sizeA size specifier, expressed as an integer + greater than or equal to 0 (zero) followed by a size indicator:
        +     K for kilobytes (1024 bytes)
        +     M for megabytes (1048576 bytes)
        +     G for gigabytes (1073741824 bytes)
        + Example: 37M specifies 37 megabytes or 38797312 bytes.
        NAn integer greater than or equal to 0 (zero)

        + + + + + + + + + + + + + + + + + + + + + + + -
        -B size, --block-size=size -
        Specifies the block size within the transfer buffer. - (Default: 128K)

        - Block size versus transfer buffer size: - The transfer buffer size is the size of a - buffer in memory. The data in that buffer is broken - into block size pieces and written to the - file.

        - Transfer block size is set by the - -x (or --min-xfer-size) and - -X (or --max-xfer-size) - options.
        - The pattern in which the blocks - are written to the file is described in the discussion - of the -I (or --interleaved) - option.

        -
        -c, --chunk -
        Creates HDF5 datasets in chunked layout. - (Default: Off) -
        -C, --collective -
        Use collective I/O for the MPI I/O and Parallel HDF5 APIs.
        - (Default: Off, i.e., independent I/O)

        - If this option is set and the MPI-I/O and PHDF5 APIs - are in use, all the blocks in each transfer buffer - will be written at once with an MPI derived type. -

        -
        -d N, --num-dsetsN -
        Sets the number of datasets per file. - (Default: 1) -
        -D debug_flags, --debug=debug_flags -
        Sets the debugging level. - debug_flags is a comma-separated list of - debugging flags with the following valid values: -
        -h, --help
                Prints a usage message and exits.
        -a size, --align=size
                Specifies the alignment of objects in the HDF5 file. + (Default: 1)
        -A api_list, --api=api_list
                Specifies which APIs to test. api_list + is a comma-separated list with the following valid values: + + + + + + + + + + + + + + + + +
             phdf5  Parallel HDF5
          mpiioMPI-I/O
          posixPOSIX
        + (Default: All APIs)

        + Example, --api=mpiio,phdf5 specifies that the MPI I/O + and parallel HDf5 APIs are to be monitored.
        - - - - - - - -
             - 1  Minimal debugging
          - 2Moderate debugging (“not quite everything”)
          - 3Extensive debugging (“everything”)
          - 4All possible debugging (“the kitchen sink”)
          - rRaw data I/O throughput information
          - tTimes, in additions to throughputs
          - vVerify data correctness
        - (Default: No debugging)

        - Example: --debug=2,r,t specifies to - run a moderate level of debugging - while collecting raw data I/O throughput information - and verifying the correctness of the data.

        -
        -e size, --num-bytes=size -
        Specifies the number of bytes per process per dataset. - (Default: 256K) -
        -F N, --num-files=N -
        Specifies the number of files. - (Default: 1) -
        -i N, --num-iterations=N -
        Sets the number of iterations to perform. - (Default: 1) -
        -I, --interleaved -
        Sets interleaved block I/O.
        - (Default: Contiguous block I/O)

        + + -B size, --block-size=size + + +          + Specifies the block size within the transfer + buffer. (Default: 128K)

        + Block size versus transfer buffer size: The transfer buffer size + is the size of a buffer in memory. The data in that buffer is broken + into block size pieces and written to the file.

        + Transfer block size is set by the -x (or --min-xfer-size) + and -X (or --max-xfer-size) options.
        + The pattern in which the blocks are written to the file is described + in the discussion of the -I (or --interleaved) + option.
        + + + -c, --chunk + + +          + Creates HDF5 datasets in chunked layout. (Default: + Off) + + + -C, --collective + + +          + Use collective I/O for the MPI I/O and + Parallel HDF5 APIs.
        + (Default: Off, i.e., independent I/O)

        + If this option is set and the MPI-I/O and PHDF5 APIs are in use, all + the blocks in each transfer buffer will be written at once with an + MPI derived type.
        + + + -d N, --num-dsetsN + + +          + Sets the number of datasets per file. (Default: 1) + + + -D debug_flags, --debug=debug_flags + + +          + Sets the debugging level. debug_flags + is a comma-separated list of debugging flags with the following valid + values: + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + +
             1  Minimal debugging
          2Moderate debugging (“not quite everything”)
          3Extensive debugging (“everything”)
          4All possible debugging (“the kitchen sink”)
          rRaw data I/O throughput information
          tTimes, in additions to throughputs
          vVerify data correctness
        + (Default: No debugging)

        + Example: --debug=2,r,t specifies to run a moderate level + of debugging while collecting raw data I/O throughput information + and verifying the correctness of the data.
        + + + -e size, --num-bytes=size + + +          + Specifies the number of bytes per process per dataset. + (Default: 256K) + + + -F N, --num-files=N + + +          + Specifies the number of files. (Default: 1) + + + -i N, --num-iterations=N + + +          + Sets the number of iterations to perform. (Default: + 1) + + + - Interleaved vs. Contiguous blocks - in a parallel environment:
        - When contiguous blocks are written to a dataset, - the dataset is divided into m regions, - where m is the number of processes writing - separate portions of the dataset. Each process - then writes data to its own region. - When interleaved blocks are written to a dataset, - space for the first block of the first process is - allocated in the dataset, then space is allocated - for the first block of the second process, etc., - until space has been allocated for the first block - of each process. Space is then allocated for - the second block of the first process, - the second block of the second process, etc.

        - For example, in the case of a 4 process run - with 1M bytes-per-process, 256K transfer buffer size, - and 64KB block size, 16 contiguous blocks - per process would be written to the file in the - manner
        -     1111111111111111222222222222222233333333333333334444444444444444
        - while 16 interleaved blocks per process would be - written to the file as -     1234123412341234123412341234123412341234123412341234123412341234
        - If collective I/O is turned on, all of the four - blocks per transfer buffer will be written in - one collective I/O call.

        -
        -m, --mpi-posix -
        Sets use of MPI-posix driver for HDF5 I/O. - (Default: MPI-I/O driver) -
        -n, --no-fill -
        Specifies to not write fill values to HDF5 datasets. - This option is supported only in HDF5 Release v1.6 or later.
        - (Default: Off, i.e., write fill values) -
        -o file, --output=file -
        Sets the output file for raw data to file. - (Default: None) -
        -p N, --min-num-processes=N -
        Sets the minimum number of processes to be used. - (Default: 1) -
        -P N, --max-num-processes=N -
        Sets the maximum number of processes to be used.
        - (Default: All MPI_COMM_WORLDprocesses) -
        -T size, --threshold=size -
        Sets the threshold for alignment of objects in the HDF5 file. - (Default: 1) -
        -w, --write-only -
        Performs only write tests, not read tests. - (Default: Read and write tests) -
        -x size, --min-xfer-size=size -
        Sets the minimum transfer buffer size. - (Default: 128K) -
        -X size, --max-xfer-size=size -
        Sets the maximum transfer buffer size. - (Default: 1M) -
      + + + + + + + + +
      -I, --interleaved
              Sets interleaved block I/O.
      + (Default: Contiguous block I/O)

      + Interleaved vs. Contiguous blocks in a parallel environment:
      + When contiguous blocks are written to a dataset, the dataset is divided + into m regions, where m is the number of processes + writing separate portions of the dataset. Each process then writes + data to its own region. When interleaved blocks are written to a dataset, + space for the first block of the first process is allocated in the + dataset, then space is allocated for the first block of the second + process, etc., until space has been allocated for the first block + of each process. Space is then allocated for the second block of the + first process, the second block of the second process, etc.

      + For example, in the case of a 4 process run with 1M bytes-per-process, + 256K transfer buffer size, and 64KB block size, 16 contiguous + blocks per process would be written to the file in the manner
      +     1111111111111111222222222222222233333333333333334444444444444444
      + while 16 interleaved blocks per process would be written to the file + as     1234123412341234123412341234123412341234123412341234123412341234
      + If collective I/O is turned on, all of the four blocks per transfer + buffer will be written in one collective I/O call.
      + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + +
      -m, --mpi-posixSets use of MPI-posix driver for HDF5 I/O. (Default: + MPI-I/O driver)
      -n, --no-fillSpecifies to not write fill values to HDF5 datasets. + This option is supported only in HDF5 Release v1.6 or later.
      + (Default: Off, i.e., write fill values)
      -o file, --output=fileSets the output file for raw data to file. + (Default: None)
      -p N, --min-num-processes=NSets the minimum number of processes to be used. (Default: + 1)
      -P N, --max-num-processes=N
      +         +          +          +           +       		Sets the maximum number of processes to be used.
      + (Default: All MPI_COMM_WORLDprocesses)
      -T size, --threshold=sizeSets the threshold for alignment of objects in the + HDF5 file. (Default: 1)
      -w, --write-onlyPerforms only write tests, not read tests. (Default: + Read and write tests)
      -x size, --min-xfer-size=sizeSets the minimum transfer buffer size. (Default: 128K)
      -X size, --max-xfer-size=size    Sets the maximum transfer buffer size. (Default: 1M)
      + +
      Tool Name: h5redeploy @@ -2015,28 +2238,32 @@ installed with HDF5. the HDF5 software has been installed in a new location.
      Options and Parameters: -
      -
      help, -help -
      Prints a help message. -
      -echo -
      Shows all the shell commands executed. -
      -force -
      Performs the requested action without offering any prompt - requesting confirmation. -
      -prefix=dir -
      Specifies a new directory in which to find the - HDF5 subdirectories lib/ and - include/.
      - (Default: current working directory) -
      -tool=tool -
      Specifies the tool to update. - tool must be in the current directory - and must be writable.
      - (Default: h5cc) -
      -show -
      Shows all of the shell commands to be executed - without actually executing them. -
      +
        + + + + + + + + + + + + + + + + + + +
        help, -helpPrints a help message.
        -echoShows all the shell commands executed.
        -forcePerforms the requested action without offering any prompt + requesting confirmation.
        -prefix=dir    Specifies a new directory in which to find the + HDF5 subdirectories lib/ and include/. +
        (Default: current working directory)
        -tool=toolSpecifies the tool to update. tool must + be in the current directory and must be writable. +
        (Default: h5cc)
        -showShows all of the shell commands to be executed + without actually executing them.
      +
      Tool Name: h5cc @@ -2071,53 +2299,63 @@ installed with HDF5. HDF5. In fact, since h5cc is only a convenience script, you are still able to compile HDF5 modules in the normal way. In that case, you will have to specify the HDF5 libraries - and include paths yourself. -

      + and include paths yourself.

      + An example of how to use h5cc to compile the program hdf_prog, which consists of modules prog1.c and prog2.c and uses the HDF5 shared library, would be as follows: - 
      +        
+		
               # h5cc -c prog1.c
         # h5cc -c prog2.c
-        # h5cc -shlib -o hdf_prog prog1.o prog2.o
-        
      
+        # h5cc -shlib -o hdf_prog prog1.o prog2.o
      +
      Options and Parameters: -
      -
      -
      -help -
      Prints a help message. -
      -echo -
      Show all the shell commands executed. -
      -prefix=DIR -
      Use the directory DIR to find the HDF5 +
        + + + + + + + + + + + + + + + + + + + + + +
        -helpPrints a help message.
        -echoShow all the shell commands executed.
        -prefix=DIRUse the directory DIR to find the HDF5 lib/ and include/ subdirectories.
        - Default: prefix specified when configuring HDF5. -
        -show -
        Show the commands without executing them. -
        -shlib -
        Compile using shared HDF5 libraries. -
        -noshlib -
        Compile using static HDF5 libraries [default]. -
        <compile line> -
        The normal compile line options for your compiler. + Default: prefix specified when configuring HDF5.
        -showShow the commands without executing them.
        -shlibCompile using shared HDF5 libraries.
        -noshlibCompile using static HDF5 libraries [default].
        <compile line>    The normal compile line options for your compiler. h5cc uses the same compiler you used to compile HDF5. Check your compiler's manual for more information on which - options are needed. - + options are needed.
      Environment Variables:
      When set, these environment variables override some of the built-in defaults of h5cc. -
      -
      HDF5_CC -
      Use a different C compiler. -
      HDF5_CLINKER -
      Use a different linker. -
      HDF5_USE_SHLIB=[yes|no] -
      Use shared version of the HDF5 library [default: no]. -
      +
        + + + + + + + + + +
        HDF5_CCUse a different C compiler.
        HDF5_CLINKERUse a different linker.
        HDF5_USE_SHLIB=[yes|no]    Use shared version of the HDF5 library [default: no].
      - + +
      Tool Name: h5fc @@ -2162,37 +2401,43 @@ installed with HDF5. 
               # h5fc -c prog1.f90
         # h5fc -c prog2.f90
-        # h5fc -o hdf_prog prog1.o prog2.o
-
      + # h5fc -o hdf_prog prog1.o prog2.o
      +
      Options and Parameters: -
      -
      -
      -help -
      Prints a help message. -
      -echo -
      Show all the shell commands executed. -
      -prefix=DIR -
      Use the directory DIR to find HDF5 +
        + + + + + + + + + + + + + + + +
        -helpPrints a help message.
        -echoShow all the shell commands executed.
        -prefix=DIRUse the directory DIR to find HDF5 lib/ and include/ subdirectories
        - Default: prefix specified when configuring HDF5. -
        -show -
        Show the commands without executing them. -
        <compile line> -
        The normal compile line options for your compiler. + Default: prefix specified when configuring HDF5.
        -showShow the commands without executing them.
        <compile line>    The normal compile line options for your compiler. h5fc uses the same compiler you used to compile HDF5. Check your compiler's manual for - more information on which options are needed. - + more information on which options are needed.
      Environment Variables:
      When set, these environment variables override some of the built-in defaults of h5cc. -
      -
      HDF5_FC -
      Use a different Fortran90 compiler. -
      HDF5_FLINKER -
      Use a different linker. -
      +
        + + + + + + +
        HDF5_FCUse a different Fortran90 compiler.
        HDF5_FLINKER    Use a different linker.
      +
      Tool Name: h5c++ @@ -2237,35 +2483,43 @@ installed with HDF5. # h5c++ -c prog1.cpp # h5c++ -c prog2.cpp # h5c++ -o hdf_prog prog1.o prog2.o +
      Options and Parameters: -
      -
      -
      -help -
      Prints a help message. -
      -echo -
      Show all the shell commands executed. -
      -prefix=DIR -
      Use the directory DIR to find HDF5 +
        + + + + + + + + + + + + + + + +
        -helpPrints a help message.
        -echoShow all the shell commands executed.
        -prefix=DIRUse the directory DIR to find HDF5 lib/ and include/ subdirectories
        - Default: prefix specified when configuring HDF5. -
        -show -
        Show the commands without executing them. -
        <compile line> -
        The normal compile line options for your compiler. + Default: prefix specified when configuring HDF5.
        -showShow the commands without executing them.
        <compile line>
        +                         		The normal compile line options for your compiler. h5c++ uses the same compiler you used to compile HDF5. Check your compiler's manual for - more information on which options are needed. - + more information on which options are needed.
      Environment Variables:
      When set, these environment variables override some of the built-in defaults of h5c++. -
      -
      HDF5_CXX -
      Use a different C++ compiler. -
      HDF5_CXXLINKER -
      Use a different linker. -
      +
        + + + + + + +
        HDF5_CXXUse a different C++ compiler.
        HDF5_CXXLINKER    Use a different linker.
      + +
      @@ -2360,7 +2616,7 @@ And in this document, the Describes HDF5 Release 1.7, the unreleased development branch; working toward HDF5 Release 1.8.0
      -- cgit v0.12