refactoring to array population and write formats

- array is now populated by in-memory size and the number of rows is calculated automatically;
- array is populated using chunks of data to save some memory;
- parameter to choose between format ZBlk0 (one zodb object) and ZBlk1 (group of zodb objects).

performance_test.py

@@ -19,33 +19,38 @@ def bigger_than_memory(self):
   message_list.extend(bigger_than_memory_read(self))
   return message_list
   
-def bigger_than_memory_write(self, out_of_core_index=False):
+def bigger_than_memory_write(self, out_of_core_index=False, zblk_format='0', **kwargs):
   message_list = []
   message_list.append('Write start: ' + get_process_memory_usage())
 
   _, array_schema = get_field_names_and_schema()
-  float_dtype = dtype(float64)
+  float_dtype = np.dtype(float64)
                 
-  array_memory_size = 1*GB
+  array_memory_size = 251*MB
   array_number_of_items = array_memory_size // array_schema.itemsize
   
   big_array = create_zbigarray(memory_size=array_memory_size, dtype=array_schema)
 
   root = self.getPhysicalRoot()
-  if out_of_core_index:
-    big_index = create_zbigarray(memory_size=array_number_of_items, dtype=float_dtype)
-    big_array, big_index = store_arrays(root, [big_array, 'big_array'], [big_index, 'big_index'])
-  else:
-    big_index = np.arange(array_number_of_items)
-    big_array = store_arrays(root, [big_array, 'big_array'])[0]
+  with timer('Create arrays instances', message_list):
+    if out_of_core_index:
+      big_index = create_zbigarray(array_number_of_items*float_dtype.itemsize, float_dtype)
+      big_array, big_index = store_arrays(root, [big_array, 'big_array'], [big_index, 'big_index'])
+    else:
+      big_index = np.arange(array_number_of_items)
+      big_array = store_arrays(root, [big_array, 'big_array'])[0]
+  
+  message_list.append(set_zblock_format(big_array, zblk_format))
+  check_zblock_format(big_array, zblk_format)
   
+  message_list.append('Populating array with %s rows.' % array_number_of_items)
   response = populate_array(self, big_array, big_index, array_schema)
   message_list.extend(response['messages'])
-  
+
   message_list.append('Write end: ' + get_process_memory_usage())
   return message_list
 
-def bigger_than_memory_read(self, out_of_core_index=False):
+def bigger_than_memory_read(self, out_of_core_index=False, **kwargs):
   message_list = []
   message_list.append('Read start ' + get_process_memory_usage())
   
@@ -78,38 +83,57 @@ def timer(name, message_list):
   start_time = time()
   yield
   elapsed_time = time() - start_time
-  message_list.append('[%s] finished in % seconds' % (name, elapsed_time))
+  message_list.append('[%s] finished in %s seconds' % (name, elapsed_time))
 
 def get_process_memory_usage():
   '''Return the runnign process' memory usage.'''
   process = psutil.Process(os.getpid())
   m = process.memory_info()
   return 'VIRT: %i MB\tRSS: %iMB' % (m.vms//MB, m.rss//MB)
+  
+def get_available_memory():
+  return psutil.virtual_memory().available
 
 def get_field_names_and_schema():
   '''Returns the array's dtype and its field names.'''
   field_names = ['f%s' % number if not number == 13 else 'quantity' for number in range(23)]
-  
-  # TODO: parameterize to get normalize or not normalized schema
   array_schema = np.dtype({
     'names' : field_names,
     'formats': map(
       np.dtype,
       ['i8', 'i8', 'i8', 'i8', 'i8', 'i8', 'i8', 'i8', 'i8', 'i8',
         'i8', 'i8', 'i8', 'f8', 'i8', 'i8', 'f8', 'f8', 'f8',
-        # 'a50', 'a50', 'a50', 'a50']
-        'f8', 'f8', 'f8', 'f8']
+        'a50', 'a50', 'a50', 'a50']
+        #'f8', 'f8', 'f8', 'f8']
     )
   })
   return field_names, array_schema
 
 def create_zbigarray(memory_size=None, dtype=None):
   '''Create a ZBigArray with memory_size bytes with the defined dtype.'''
-  if memory_size and dtype:
-    element_number = memory_size // dtype.itemsize
-    return ZBigArray((element_number,), dtype)
+  # if memory_size  and dtype:
+  element_number = memory_size // dtype.itemsize
+  return ZBigArray((element_number,), dtype)
+  # else:
+    # raise Exception('You need to provide memory_size and dtype, %s - %s' % (memory_size, dtype))
+    
+def set_zblock_format(array, zblk_format):
+  '''Set the array to write with the provide zblock format.
+  Formats are:
+    - 0 (low-overhead access time and high-overhead storage size)
+    - 1 (low overhead storage size and high-overhead access time)
+  '''
+  if zblk_format in ('0', '1'):
+    array._fileh.ZBlk_fmt_write = zblk_format_string = 'ZBlk%s' % zblk_format
+    return 'Writting with format: %s' % zblk_format_string
+  else:
+    raise 'Unknown zblk_format provided. Choose between 0 and 1. See docs strings for more information.'
+
+def check_zblock_format(array, zblk_format):
+  if not array._fileh.ZBlk_fmt_write == 'ZBlk%s' % zblk_format:
+    raise 'Zblk format didnt match'
   else:
-    raise Exception('You need to provide memory_size and dtype')
+    return True
   
 def store_arrays(root, *arrays_filenames):
   '''Store all [array, filename] pair in arrays_filenames in root and return an
@@ -124,13 +148,26 @@ def store_arrays(root, *arrays_filenames):
 def populate_array(root, big_array, big_index, schema):
   '''Fill big_array with copies of a MySQL row until it is completely full'''
   message_list = []
-  data = root.stock_offset(my_offset=0, my_limit=1)
-  columns = data._names
   with timer('Time to prepare data for assignment', message_list):
-    row = tuple([filter_item(item, normalize=True) for item in data.tuples()[0]])
-  with timer('Time to fill ZBigArray', message_list):
-    big_array[:] = row
-  transaction.commit()
+    data = root.stock_offset(my_offset=0, my_limit=1)
+    columns = data._names
+    row = tuple([filter_item(item, normalize=False) for item in data.tuples()[0]])
+  
+  max_memory_usage =  100*MB
+  message_list.append('%s megabytes of memory can be used per chunk.' % (max_memory_usage//MB))
+  message_list.append('Total array size is %s megabytes.' % (big_array.nbytes//MB))
+  # little trick here to do a ceil-division instead of floor-division: ceil(a / b) = -(-a // b)
+  chunks = -(-big_array.nbytes // max_memory_usage)
+  chunk_begin = 0
+  chunksize = len(big_array) // chunks
+  message_list.append('Using %s chunks of %s items.' % (chunks, chunksize))
+      
+  with timer('Complete assign & store ZBigArray', message_list):
+    for i in range(chunks):
+      big_array[chunk_begin:chunksize*(i+1)] = row
+      chunk_begin = chunksize + 1
+      with timer('Commit each ZBigArray chunk', message_list):
+        transaction.commit()
   return {'messages': message_list, 'columns': columns}
 
 # method to cast Zope's DateTime objects, falsy-values and strings to floats
@@ -155,6 +192,9 @@ def process_data(big_array, big_index, columns):
   message_list = []
   result = None
   
+  # When benchmarking, only runs either pandas or numpy, one process creates
+  # a cache for the other and this gives deceiving results.
+  # TODO: add parameter to choose wether numpy or pandas should be used
   try:
     with timer('pandas sum', message_list):
       df = pd.DataFrame.from_records(big_array, index=big_index)