def compute(self, override=False, *args, **kwargs):
"""
Creates placeholders for the results, applies the :meth:`~pyUSID.processing.process.Process._unit_computation`
to chunks of the dataset
Parameters
----------
override : bool, optional. default = False
By default, compute will simply return duplicate results to avoid recomputing or resume computation on a
group with partial results. Set to True to force fresh computation.
args : list
arguments to the mapped function in the correct order
kwargs : dict
keyword arguments to the mapped function
Returns
-------
h5_results_grp : :class:`h5py.Group`
Group containing all the results
"""
class SimpleFIFO(object):
"""
Simple class that maintains a moving average of some numbers.
"""
def __init__(self, length=5):
"""
Create a SimpleFIFO object
Parameters
----------
length : unsigned integer
Number of values that need to be maintained for the moving average
"""
self.__queue = list()
if not isinstance(length, int):
raise TypeError('length must be a positive integer')
if length <= 0:
raise ValueError('length must be a positive integer')
self.__max_length = length
self.__count = 0
def put(self, item):
"""
Adds the item to the internal queue. If the size of the queue exceeds its capacity, the oldest
item is removed.
Parameters
----------
item : float or int
Any real valued number
"""
if (not isinstance(item, Number)) or isinstance(item, complex):
raise TypeError('Provided item: {} is not a Number'.format(item))
self.__queue.append(item)
self.__count += 1
if len(self.__queue) > self.__max_length:
_ = self.__queue.pop(0)
def get_mean(self):
"""
Returns the average of the elements within the queue
Returns
-------
avg : number.Number
Mean of all elements within the queue
"""
return np.mean(self.__queue)
def get_cycles(self):
"""
Returns the number of items that have been added to the queue in total
Returns
-------
count : int
number of items that have been added to the queue in total
"""
return self.__count
if not override:
if len(self.duplicate_h5_groups) > 0:
if self.mpi_rank == 0:
print('Returned previously computed results at ' + self.duplicate_h5_groups[-1].name)
return self.duplicate_h5_groups[-1]
elif len(self.partial_h5_groups) > 0:
if self.mpi_rank == 0:
print('Resuming computation in group: ' + self.partial_h5_groups[-1].name)
self.use_partial_computation()
resuming = False
if self.h5_results_grp is None:
# starting fresh
if self.verbose and self.mpi_rank == 0:
print('Creating HDF5 group and datasets to hold results')
self._create_results_datasets()
else:
# resuming from previous checkpoint
resuming = True
self._get_existing_datasets()
self._create_compute_status_dataset()
if resuming and self.mpi_rank == 0:
percent_complete = int(100 * len(np.where(self._h5_status_dset[()] == 0)[0]) /
self._h5_status_dset.shape[0])
print('Resuming computation. {}% completed already'.format(percent_complete))
self.__assign_job_indices()
# Not sure if this is necessary but I don't think it would hurt either
if self.mpi_comm is not None:
self.mpi_comm.barrier()
compute_times = SimpleFIFO(5)
write_times = SimpleFIFO(5)
orig_rank_start = self.__start_pos
if self.mpi_rank == 0 and self.mpi_size == 1:
if self._resume_implemented:
print('\tThis class (likely) supports interruption and resuming of computations!\n'
'\tIf you are operating in a python console, press Ctrl+C or Cmd+C to abort\n'
'\tIf you are in a Jupyter notebook, click on "Kernel">>"Interrupt"\n'
'\tIf you are operating on a cluster and your job gets killed, re-run the job to resume\n')
else:
print('\tThis class does NOT support interruption and resuming of computations.\n'
'\tIn order to enable this feature, simply implement the _get_existing_datasets() function')
if self.verbose and self.mpi_rank == self.__socket_master_rank:
print('Rank: {} - with nothing loaded has {} free memory'
''.format(self.mpi_rank, format_size(get_available_memory())))
self._read_data_chunk()
if self.mpi_comm is not None:
self.mpi_comm.barrier()
if self.verbose and self.mpi_rank == self.__socket_master_rank:
print('Rank: {} - with only raw data loaded has {} free memory'
''.format(self.mpi_rank, format_size(get_available_memory())))
while self.data is not None:
num_jobs_in_batch = self.__end_pos - self.__start_pos
t_start_1 = tm.time()
self._unit_computation(*args, **kwargs)
comp_time = np.round(tm.time() - t_start_1, decimals=2) # in seconds
time_per_pix = comp_time / num_jobs_in_batch
compute_times.put(time_per_pix)
if self.verbose:
print('Rank {} - computed chunk in {} or {} per pixel. Average: {} per pixel'
'.'.format(self.mpi_rank, format_time(comp_time), format_time(time_per_pix),
format_time(compute_times.get_mean())))
# Ranks can become memory starved. Check memory usage - raw data + results in memory at this point
if self.verbose and self.mpi_rank == self.__socket_master_rank:
print('Rank: {} - now holding onto raw data + results has {} free memory'
''.format(self.mpi_rank, format_size(get_available_memory())))
t_start_2 = tm.time()
self._write_results_chunk()
# NOW, update the positions. Users are NOT allowed to touch start and end pos
self.__start_pos = self.__end_pos
# Leaving in this provision that will allow restarting of processes
if self.mpi_size == 1:
self.h5_results_grp.attrs['last_pixel'] = self.__end_pos
# Child classes don't even have to worry about flushing. Process will do it.
self.h5_main.file.flush()
dump_time = np.round(tm.time() - t_start_2, decimals=2)
write_times.put(dump_time / num_jobs_in_batch)
if self.verbose:
print('Rank {} - wrote its {} pixel chunk in {}'.format(self.mpi_rank,
num_jobs_in_batch,
format_time(dump_time)))
time_remaining = (self.__rank_end_pos - self.__end_pos) * \
(compute_times.get_mean() + write_times.get_mean())
if self.verbose or self.mpi_rank == 0:
percent_complete = int(100 * (self.__end_pos - orig_rank_start) /
(self.__rank_end_pos - orig_rank_start))
print('Rank {} - {}% complete. Time remaining: {}'.format(self.mpi_rank, percent_complete,
format_time(time_remaining)))
# All ranks should mark the pixels for this batch as completed. 'last_pixel' attribute will be updated later
# Setting each section to 1 independently
for curr_slice in integers_to_slices(self.__pixels_in_batch):
self._h5_status_dset[curr_slice] = 1
self._read_data_chunk()
if self.verbose:
print('Rank {} - Finished computing all jobs!'.format(self.mpi_rank))
if self.mpi_comm is not None:
self.mpi_comm.barrier()
if self.mpi_rank == 0:
print('Finished processing the entire dataset!')
# Update the legacy 'last_pixel' attribute here:
if self.mpi_rank == 0:
self.h5_results_grp.attrs['last_pixel'] = self.h5_main.shape[0]
return self.h5_results_grp
def test_format_size(self):
ret_val = io_utils.format_size(15.23)
self.assertEqual(ret_val, '15.23 bytes')
ret_val = io_utils.format_size(5830418104.32)
self.assertEqual(ret_val, '5.43 GB')
def _set_memory_and_cores(self, cores=None, mem=None):
"""
Checks hardware limitations such as memory, number of CPU cores and sets the recommended data chunk sizes and
the number of cores to be used by analysis methods. This function can work with clusters with heterogeneous
memory sizes (e.g. CADES SHPC Condo).
Parameters
----------
cores : uint, optional, Default = 1
How many cores to use for the computation.
mem : uint, optional, Default = 1024
The amount a memory in Mb to use in the computation
"""
if self.mpi_comm is None:
min_free_cores = 1 + int(psutil.cpu_count() > 4)
if cores is None:
self._cores = max(1, psutil.cpu_count() - min_free_cores)
else:
if not isinstance(cores, int):
raise TypeError('cores should be an integer but got: {}'.format(cores))
cores = int(abs(cores))
self._cores = max(1, min(psutil.cpu_count(), cores))
self.__socket_master_rank = 0
self.__ranks_on_socket = 1
else:
# user-provided input cores will simply be ignored in an effort to use the entire CPU
ranks_by_socket = group_ranks_by_socket(verbose=False)
self.__socket_master_rank = ranks_by_socket[self.mpi_rank]
# which ranks in this socket?
ranks_on_this_socket = np.where(ranks_by_socket == self.__socket_master_rank)[0]
# how many in this socket?
self.__ranks_on_socket = ranks_on_this_socket.size
# Force usage of all available memory
mem = None
self._cores = 1
# Disabling the following line since mpi4py and joblib didn't play well for Bayesian Inference
# self._cores = self.__cores_per_rank = psutil.cpu_count() // self.__ranks_on_socket
# TODO: Convert all to bytes!
_max_mem_mb = get_available_memory() / 1024 ** 2 # in MB
if mem is None:
mem = _max_mem_mb
else:
if not isinstance(mem, int):
raise TypeError('mem must be a whole number')
mem = abs(mem)
self._max_mem_mb = min(_max_mem_mb, mem)
# Remember that multiple processes (either via MPI or joblib) will share this socket
max_data_chunk = self._max_mem_mb / (self._cores * self.__ranks_on_socket)
# Now calculate the number of positions OF RAW DATA ONLY that can be stored in memory in one go PER RANK
mb_per_position = self.h5_main.dtype.itemsize * self.h5_main.shape[1] / 1024 ** 2
self._max_pos_per_read = int(np.floor(max_data_chunk / mb_per_position))
if self.verbose and self.mpi_rank == self.__socket_master_rank:
# expected to be the same for all ranks so just use this.
print('Rank {} - on socket with {} logical cores and {} avail. RAM shared by {} ranks each given {} cores'
'.'.format(self.__socket_master_rank, psutil.cpu_count(), format_size(_max_mem_mb * 1024 ** 2, 2),
self.__ranks_on_socket, self._cores))
print('Allowed to read {} pixels per chunk'.format(self._max_pos_per_read))