path: root/doxygen/dox/IntroParExamples.dox

/** @page IntroParContHyperslab Writing by Contiguous Hyperslab

Navigate back: \ref index "Main" / \ref GettingStarted / \ref IntroParHDF5
<hr>

This example shows how to write a contiguous buffer in memory to a contiguous hyperslab in a file. In this case,
each parallel process writes a contiguous hyperslab to the file.

In the C example (figure a), each hyperslab in memory consists of an equal number of consecutive rows. In the FORTRAN
90 example (figure b), each hyperslab in memory consists of
an equal number of consecutive columns. This reflects the difference in the storage order for C and FORTRAN 90.
<table>
<tr>
<th><strong>Figure a</strong>   C Example</th>
<th><strong>Figure b</strong>   Fortran Example</th>
</tr><tr>
<td>
\image html pcont_hy_figa.gif
</td>
<td>
\image html pcont_hy_figb.gif
</td>
</tr>
</table>

\section secIntroParContHyperslabC Writing a Contiguous Hyperslab in C
In this example, you have a dataset of 8 (rows) x 5 (columns) and each process writes an equal number
of rows to the dataset. The dataset hyperslab is defined as follows:
\code
     count [0] = dimsf [0] / number_processes
     count [1] = dimsf [1]
\endcode
where,
\code
    dimsf [0] is the number of rows in the dataset
    dimsf [1] is the number of columns in the dataset
\endcode
The offset for the hyperslab is different for each process:
\code
     offset [0] = k * count[0]
     offset [1] = 0
\endcode
where,
\code
    "k" is the process id number
    count [0] is the number of rows written in each hyperslab
    offset [1] = 0 indicates to start at the beginning of the row
\endcode

The number of processes that you could use would be 1, 2, 4, or 8. The number of rows that would be written by each slab is as follows:
<table>
<tr>
<th><strong>Processes</strong></th>
<th><strong>Size of count[0](\# of rows) </strong></th>
</tr><tr>
<td>1</td><td>8</td>
</tr><tr>
<td>2</td><td>4</td>
</tr><tr>
<td>4</td><td>2</td>
</tr><tr>
<td>8</td><td>1</td>
</tr>
</table>

If using 4 processes, then process 1 would look like:
<table>
<tr>
<td>
\image html pcont_hy_figc.gif
</td>
</tr>
</table>

The code would look like the following:
\code
    71      /*
    72       * Each process defines dataset in memory and writes it to the hyperslab
    73       * in the file.
    74       */
    75      count[0] = dimsf[0]/mpi_size;
    76      count[1] = dimsf[1];
    77      offset[0] = mpi_rank * count[0];
    78      offset[1] = 0;
    79      memspace = H5Screate_simple(RANK, count, NULL);
    80
    81      /*
    82       * Select hyperslab in the file.
    83       */
    84      filespace = H5Dget_space(dset_id);
    85      H5Sselect_hyperslab(filespace, H5S_SELECT_SET, offset, NULL, count, NULL);
\endcode

Below is the example program:
<table>
<tr>
<td>
<a href="https://github.com/HDFGroup/hdf5-examples/blob/master/C/H5Parallel/ph5_hyperslab_by_row.c">hyperslab_by_row.c</a>
</td>
</tr>
</table>

If using this example with 4 processes, then,
\li    Process 0 writes "10"s to the file.
\li    Process 1 writes "11"s.
\li    Process 2 writes "12"s.
\li    Process 3 writes "13"s.

The following is the output from h5dump for the HDF5 file created by this example using 4 processes:
\code
HDF5 "SDS_row.h5" {
GROUP "/" {
   DATASET "IntArray" {
      DATATYPE  H5T_STD_I32BE  
      DATASPACE  SIMPLE { ( 8, 5 ) / ( 8, 5 ) } 
      DATA {
         10, 10, 10, 10, 10,
         10, 10, 10, 10, 10,
         11, 11, 11, 11, 11,
         11, 11, 11, 11, 11,
         12, 12, 12, 12, 12,
         12, 12, 12, 12, 12,
         13, 13, 13, 13, 13,
         13, 13, 13, 13, 13
      } 
   } 
} 
} 
\endcode


\section secIntroParContHyperslabFort Writing a Contiguous Hyperslab in Fortran
In this example you have a dataset of 5 (rows) x 8 (columns). Since a contiguous hyperslab in Fortran 90
consists of consecutive columns, each process will be writing an equal number of columns to the dataset.

You would define the size of the hyperslab to write to the dataset as follows:
\code
      count(1) = dimsf(1)
      count(2) = dimsf(2) / number_of_processes
\endcode

where,
\code
    dimsf(1) is the number of rows in the dataset
    dimsf(2) is the number of columns
\endcode

The offset for the hyperslab dimension would be different for each process:
\code
      offset (1) = 0
      offset (2) = k * count (2)
\endcode

where,
\code
    offset (1) = 0 indicates to start at the beginning of the column
    "k" is the process id number
    "count(2) is the number of columns to be written by each hyperslab
\endcode

The number of processes that could be used in this example are 1, 2, 4, or 8. The number of
columns that could be written by each slab is as follows:
<table>
<tr>
<th><strong>Processes</strong></th>
<th><strong>Size of count (2)(\# of columns) </strong></th>
</tr><tr>
<td>1</td><td>8</td>
</tr><tr>
<td>2</td><td>4</td>
</tr><tr>
<td>4</td><td>2</td>
</tr><tr>
<td>8</td><td>1</td>
</tr>
</table>

If using 4 processes, the offset and count parameters for Process 1 would look like:
<table>
<tr>
<td>
\image html pcont_hy_figd.gif
</td>
</tr>
</table>

The code would look like the following:
\code
    69       ! Each process defines dataset in memory and writes it to the hyperslab
    70       ! in the file.
    71       !
    72       count(1) = dimsf(1)
    73       count(2) = dimsf(2)/mpi_size
    74       offset(1) = 0
    75       offset(2) = mpi_rank * count(2)
    76       CALL h5screate_simple_f(rank, count, memspace, error)
    77       !
    78       ! Select hyperslab in the file.
    79       !
    80       CALL h5dget_space_f(dset_id, filespace, error)
    81       CALL h5sselect_hyperslab_f (filespace, H5S_SELECT_SET_F, offset, count, error)
\endcode

Below is the F90 example program which illustrates how to write contiguous hyperslabs by column in Parallel HDF5:
<table>
<tr>
<td>
<a href="https://github.com/HDFGroup/hdf5-examples/blob/master/Fortran/H5Parallel/ph5_f90_hyperslab_by_col.F90">hyperslab_by_col.F90</a>
</td>
</tr>
</table>

If you run this program with 4 processes and look at the output with h5dump you will notice that the output is
much like the output shown above for the C example. This is because h5dump is written in C. The data would be
displayed in columns if it was printed using Fortran 90 code.

<hr>
Navigate back: \ref index "Main" / \ref GettingStarted / \ref IntroParHDF5

@page IntroParRegularSpaced Writing by Regularly Spaced Data

Navigate back: \ref index "Main" / \ref GettingStarted / \ref IntroParHDF5
<hr>

In this case, each process writes data from a contiguous buffer into disconnected locations in the file, using a regular pattern.

In C it is done by selecting a hyperslab in a file that consists of regularly spaced columns. In F90, it is done by selecting a
hyperslab in a file that consists of regularly spaced rows.
<table>
<tr>
<th><strong>Figure a</strong>   C Example</th>
<th><strong>Figure b</strong>   Fortran Example</th>
</tr><tr>
<td>
\image html preg_figa.gif
</td>
<td>
\image html preg_figb.gif
</td>
</tr>
</table>

\section secIntroParRegularSpacedC Writing Regularly Spaced Columns in C
In this example, you have two processes that write to the same dataset, each writing to
every other column in the dataset. For each process the hyperslab in the file is set up as follows:
\code
    89      count[0] = 1;
    90      count[1] = dimsm[1];
    91      offset[0] = 0;
    92      offset[1] = mpi_rank;
    93      stride[0] = 1;
    94      stride[1] = 2;
    95      block[0] = dimsf[0];
    96      block[1] = 1;
\endcode

The stride is 2 for dimension 1 to indicate that every other position along this
dimension will be written to. A stride of 1 indicates that every position along a dimension will be written to.

For two processes, the mpi_rank will be either 0 or 1. Therefore:
\li Process 0 writes to even columns (0, 2, 4...)
\li Process 1 writes to odd columns (1, 3, 5...)

The block size allows each process to write a column of data to every other position in the dataset.

<table>
<tr>
<td>
\image html preg_figc.gif
</td>
</tr>
</table>

Below is an example program for writing hyperslabs by column in Parallel HDF5:
<table>
<tr>
<td>
<a href="https://github.com/HDFGroup/hdf5-examples/blob/master/C/H5Parallel/ph5_hyperslab_by_col.c">hyperslab_by_col.c</a>
</td>
</tr>
</table>

The following is the output from h5dump for the HDF5 file created by this example:
\code
HDF5 "SDS_col.h5" {
GROUP "/" {
   DATASET "IntArray" {
      DATATYPE  H5T_STD_I32BE  
      DATASPACE  SIMPLE { ( 8, 6 ) / ( 8, 6 ) } 
      DATA {
         1, 2, 10, 20, 100, 200,
         1, 2, 10, 20, 100, 200,
         1, 2, 10, 20, 100, 200,
         1, 2, 10, 20, 100, 200,
         1, 2, 10, 20, 100, 200,
         1, 2, 10, 20, 100, 200,
         1, 2, 10, 20, 100, 200,
         1, 2, 10, 20, 100, 200
      } 
   } 
} 
} 
\endcode


\section secIntroParRegularSpacedFort Writing Regularly Spaced Rows in Fortran
In this example, you have two processes that write to the same dataset, each writing to every
other row in the dataset. For each process the hyperslab in the file is set up as follows:


You would define the size of the hyperslab to write to the dataset as follows:
\code
    83       ! Each process defines dataset in memory and writes it to 
    84       ! the hyperslab in the file.
    85       !
    86       count(1) = dimsm(1)
    87       count(2) = 1
    88       offset(1) = mpi_rank
    89       offset(2) = 0
    90       stride(1) = 2
    91       stride(2) = 1
    92       block(1) = 1
    93       block(2) = dimsf(2)
\endcode

The stride is 2 for dimension 1 to indicate that every other position along this dimension will
be written to. A stride of 1 indicates that every position along a dimension will be written to.

For two process, the mpi_rank will be either 0 or 1. Therefore:
\li Process 0 writes to even rows (0, 2, 4 ...)
\li Process 1 writes to odd rows (1, 3, 5 ...)

The block size allows each process to write a row of data to every other position in the dataset,
rather than just a point of data.

The following shows the data written by Process 1 to the file:
<table>
<tr>
<td>
\image html preg_figd.gif
</td>
</tr>
</table>

Below is the example program for writing hyperslabs by column in Parallel HDF5:
<table>
<tr>
<td>
<a href="https://github.com/HDFGroup/hdf5-examples/blob/master/Fortran/H5Parallel/ph5_f90_hyperslab_by_row.F90">hyperslab_by_row.F90</a>
</td>
</tr>
</table>

The output for h5dump on the file created by this program will look like the output as shown above for the C example. This is
because h5dump is written in C. The data would be displayed in rows if it were printed using Fortran 90 code.

<hr>
Navigate back: \ref index "Main" / \ref GettingStarted / \ref IntroParHDF5

@page IntroParPattern Writing by Pattern

Navigate back: \ref index "Main" / \ref GettingStarted / \ref IntroParHDF5
<hr>

This is another example of writing data into disconnected locations in a file. Each process writes data from the contiguous
buffer into regularly scattered locations in the file.

Each process defines a hyperslab in the file as described below and writes data to it. The C and Fortran 90 examples below
result in the same data layout in the file.

<table>
<tr>
<th><strong>Figure a</strong>   C Example</th>
<th><strong>Figure b</strong>   Fortran Example</th>
</tr><tr>
<td>
\image html ppatt_figa.gif
</td>
<td>
\image html ppatt_figb.gif
</td>
</tr>
</table>

The C and Fortran 90 examples use four processes to write the pattern shown above. Each process defines a hyperslab by:
\li Specifying a stride of 2 for each dimension, which indicates that you wish to write to every other position along a dimension.
\li Specifying a different offset for each process:
<table>
<tr>
<th rowspan="3"><strong>C</strong></th><th>Process 0</th><th>Process 1</th><th>Process 2</th><th>Process 3</th>
</tr><tr>
<td>offset[0] = 0</td><td>offset[0] = 1</td><td>offset[0] = 0</td><td>offset[0] = 1</td>
</tr><tr>
<td>offset[1] = 0</td><td>offset[1] = 0</td><td>offset[1] = 1</td><td>offset[1] = 1</td>
</tr><tr>
<th rowspan="3"><strong>Fortran</strong></th><th>Process 0</th><th>Process 1</th><th>Process 2</th><th>Process 3</th>
</tr><tr>
<td>offset(1) = 0</td><td>offset(1) = 0</td><td>offset(1) = 1</td><td>offset(1) = 1</td>
</tr><tr>
<td>offset(2) = 0</td><td>offset(2) = 1</td><td>offset(2) = 0</td><td>offset(2) = 1</td>
</tr>
</table>
\li Specifying the size of the slab to write. The count is the number of positions along a dimension to write to. If writing a 4 x 2 slab,
then the count would be:
<table>
<tr>
<th><strong>C</strong></th><th>Fortran</th>
</tr><tr>
<td>count[0] = 4</td><td>count(1) =  2</td>
</tr><tr>
<td>count[1] = 2</td><td>count(2) =  4</td>
</tr>
</table>

For example, the offset, count, and stride parameters for Process 2 would look like:
<table>
<tr>
<th><strong>Figure a</strong>   C Example</th>
<th><strong>Figure b</strong>   Fortran Example</th>
</tr><tr>
<td>
\image html ppatt_figc.gif
</td>
<td>
\image html ppatt_figd.gif
</td>
</tr>
</table>

Below are example programs for writing hyperslabs by pattern in Parallel HDF5:
<table>
<tr>
<td>
<a href="https://github.com/HDFGroup/hdf5-examples/blob/master/C/H5Parallel/ph5_hyperslab_by_pattern.c">hyperslab_by_pattern.c</a>
</td>
</tr>
<tr>
<td>
<a href="https://github.com/HDFGroup/hdf5-examples/blob/master/Fortran/H5Parallel/ph5_f90_hyperslab_by_pattern.F90">hyperslab_by_pattern.F90</a>
</td>
</tr>
</table>

The following is the output from h5dump for the HDF5 file created in this example:
\code
HDF5 "SDS_pat.h5" {
GROUP "/" {
   DATASET "IntArray" {
      DATATYPE  H5T_STD_I32BE  
      DATASPACE  SIMPLE { ( 8, 4 ) / ( 8, 4 ) } 
      DATA {
         1, 3, 1, 3,
         2, 4, 2, 4,
         1, 3, 1, 3,
         2, 4, 2, 4,
         1, 3, 1, 3,
         2, 4, 2, 4,
         1, 3, 1, 3,
         2, 4, 2, 4
      } 
   } 
} 
} 
\endcode
The h5dump utility is written in C so the output is in C order.


<hr>
Navigate back: \ref index "Main" / \ref GettingStarted / \ref IntroParHDF5

@page IntroParChunk Writing by Chunk

Navigate back: \ref index "Main" / \ref GettingStarted / \ref IntroParHDF5
<hr>

In this example each process writes a "chunk" of data to a dataset. The C and Fortran 90
examples result in the same data layout in the file.

<table>
<tr>
<th><strong>Figure a</strong>   C Example</th>
<th><strong>Figure b</strong>   Fortran Example</th>
</tr><tr>
<td>
\image html pchunk_figa.gif
</td>
<td>
\image html pchunk_figb.gif
</td>
</tr>
</table>

For this example, four processes are used, and a 4 x 2 chunk is written to the dataset by each process.

To do this, you would:
\li Use the block parameter to specify a chunk of size 4 x 2 (or 2 x 4 for Fortran).
\li Use a different offset (start) for each process, based on the chunk size:
<table>
<tr>
<th rowspan="3"><strong>C</strong></th><th>Process 0</th><th>Process 1</th><th>Process 2</th><th>Process 3</th>
</tr><tr>
<td>offset[0] = 0</td><td>offset[0] = 0</td><td>offset[0] = 4</td><td>offset[0] = 4</td>
</tr><tr>
<td>offset[1] = 0</td><td>offset[1] = 2</td><td>offset[1] = 0</td><td>offset[1] = 2</td>
</tr><tr>
<th rowspan="3"><strong>Fortran</strong></th><th>Process 0</th><th>Process 1</th><th>Process 2</th><th>Process 3</th>
</tr><tr>
<td>offset(1) = 0</td><td>offset(1) = 2</td><td>offset(1) = 0</td><td>offset(1) = 2</td>
</tr><tr>
<td>offset(2) = 0</td><td>offset(2) = 0</td><td>offset(2) = 4</td><td>offset(2) = 4</td>
</tr>
</table>

For example, the offset and block parameters for Process 2 would look like:
<table>
<tr>
<th><strong>Figure a</strong>   C Example</th>
<th><strong>Figure b</strong>   Fortran Example</th>
</tr><tr>
<td>
\image html pchunk_figc.gif
</td>
<td>
\image html pchunk_figd.gif
</td>
</tr>
</table>

Below are example programs for writing hyperslabs by pattern in Parallel HDF5:
<table>
<tr>
<td>
<a href="https://github.com/HDFGroup/hdf5-examples/blob/master/C/H5Parallel/ph5_hyperslab_by_chunk.c">hyperslab_by_chunk.c</a>
</td>
</tr>
<tr>
<td>
<a href="https://github.com/HDFGroup/hdf5-examples/blob/master/Fortran/H5Parallel/ph5_f90_hyperslab_by_chunk.F90">hyperslab_by_chunk.F90</a>
</td>
</tr>
</table>

The following is the output from h5dump for the HDF5 file created in this example:
\code
HDF5 "SDS_chnk.h5" {
GROUP "/" {
   DATASET "IntArray" {
      DATATYPE  H5T_STD_I32BE  
      DATASPACE  SIMPLE { ( 8, 4 ) / ( 8, 4 ) } 
      DATA {
         1, 1, 2, 2,
         1, 1, 2, 2,
         1, 1, 2, 2,
         1, 1, 2, 2,
         3, 3, 4, 4,
         3, 3, 4, 4,
         3, 3, 4, 4,
         3, 3, 4, 4
      } 
   } 
} 
} 
\endcode
The h5dump utility is written in C so the output is in C order.

<hr>
Navigate back: \ref index "Main" / \ref GettingStarted / \ref IntroParHDF5

*/