The Decl'HDF5 plugin enables one to read and write data from HDF5 files in a declarative way. Decl'HDF5 does not support the full HDF5 feature set but offers a simple declarative interface to access a large subset of it.
metadata: # small values for which PDI keeps a copy
width: int # per proc. width including ghost
height: int # per proc. height including ghost
pwidth: int # nb proc. in the x dim
pheight: int # nb proc. in the y dim
iter: int # curent iteration id
coord: { type: array, subtype: int, size: 2 } # coordinate of the process as [x, y]
data: # values that are not copied by PDI
main_field:
type: array
subtype: double
size: [$width, $height]
plugins:
mpi: # loading MPI_Comm predefines (e.g. $MPI_COMM_WORLD)
decl_hdf5: # a list of file to write to (can be a single element)
file: data${coord[0]}x${coord[1]}.h5 # the file in which to write the data (required)
collision_policy: write_into_and_warn # print a warning if file or any of dataset already exist
on_event: newiter # the event that triggers these actions (default: trigger on data expose)
when: "$iter>0 & $iter<11" # a condition when to actually trigger the actions (default: always true)
communicator: $MPI_COMM_SELF # the MPI communicator used for HDF5 parallel synchronized write (default: $MPI_COMM_SELF, sequential write)
datasets: # a list of datasets inside the file created on first access
data/array: # a dataset name, datasets referenced but not defined are created just big enough to fit the data
type: array
subtype: double # type of the data in the dataset
size: [10, $width-2, $width-2] # size of the dataset
data_iter.*/array: # a dataset name which is a regex. This name allows to write datasets that match this regex in the h5 file
type: array
subtype: double # type of the data in the dataset
size: [$width-2, $width-2] # size of the dataset
write: # a list or map of data to write (default: empty)
main_field: # name of the data, it contains either a list or a single write to execute
- dataset: data/array # a dataset name (default: the data name)
when: "$iter>0&$iter<11" # an additional condition when to actually trigger the actions (default: always true)
communicator: $MPI_COMM_SELF # the MPI communicator used for HDF5 parallel synchronized write (default: that of the file)
mpio: INDEPENDENT # the type of MPI-I/O parallel pointer (default: COLLECTIVE)
memory_selection:
size: [$width-2, $height-2] # number of elements to transfer in each dimension (default: size of the full data)
start: [1, 1] # coordinate of the start point in memory relative to the shared data (default: 0 in each dimensions)
dataset_selection:
size: [1, $width-2, $width-2] # number of elements to transfer in each dimension, must amount to the same number as the memory selection (default: size of memory slab)
start: [$iter, 0, 0] # coordinate of the start point in the file relative to the dataset (default: 0 in each dimensions)
attributes:
size: ($width-2)*($width-2)
width: $width-2
height: $width-2
- dataset: data_iter${iter}/array # a dataset name with an implicit name
memory_selection:
size: [$width-2, $height-2] # number of elements to transfer in each dimension (default: size of the full data)
start: [1, 1] # coordinate of the start point in memory relative to the shared data (default: 0 in each dimensions)
dataset_selection:
size: [ $width-2, $width-2] # number of elements to transfer in each dimension, must amount to the same number as the memory selection (default: size of memory slab)
start: [ 0, 0] # coordinate of the start point in the file relative to the dataset (default: 0 in each dimensions)
read: # a list or map of data to read, similar to write (default: empty)
- another_value
