/usr/share/pyshared/adios/adios.py is in python3-adios 1.13.0-1.
This file is owned by root:root, with mode 0o644.
The actual contents of the file can be viewed below.
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import typeMapper
class adiosConfig:
def __init__ (self, config_file_name):
self.config_file_name = config_file_name
#This would be a good time to parse the file...
doc = xml.dom.minidom.parse (config_file_name)
nodes = doc.childNodes
if (nodes.length != 1):
print 'malformed adios config file, should contain only a single adios-config element'
raise SystemExit
self.config_node = nodes[0]
# for each of the groups, instantiate an adiosGroup object, and store in self.adios_groups
self.adios_groups = []
self.methods = []
self.buffer = None
self.host_language = self.config_node.getAttribute ('host-language')
for node in self.config_node.getElementsByTagName('adios-group'):
self.adios_groups.append (adiosGroup (node) )
for node in self.config_node.getElementsByTagName('method'):
self.methods.append (method (node) )
for node in self.config_node.getElementsByTagName ('buffer'):
# there should be only one of these... this code ignores all but the last one.
self.buffer = buffer (node)
#We are currently ignoring any analysis declarations
def get_filename (self):
return self.config_file_name
def get_groups (self):
#return the group with the specified name
return self.adios_groups
def get_buffer (self):
#return the buffer info
print 'implement get_buffer'
def get_host_language (self):
return self.host_language
class adiosGroup:
def __init__ (self, group_node):
self.group_node = group_node
self.time_index = self.group_node.getAttribute ('time-index')
self.vars = []
self.vardict = {}
for node in self.group_node.childNodes:
if (node.localName == 'var'):
newvar = var (node, self, self.time_index)
self.vars.append (newvar)
self.vardict [newvar.get_name()] = newvar
for node in self.group_node.getElementsByTagName('global-bounds'):
for varnode in node.getElementsByTagName('var'):
newvar = var (varnode, self, self.time_index, node)
self.vars.append (newvar)
self.vardict [newvar.get_name()] = newvar
def get_name (self):
return self.group_node.getAttribute ('name')
def get_vars (self):
return self.vars
def get_var (self, varname):
return self.vardict [varname]
class method:
def __init__ (self, method_node):
self.method_node = method_node
class buffer:
def __init__ (self, buffer_node):
self.buffer_node = buffer_node
class var:
def __init__ (self, var_node, group, time_index=None, global_bounds_node=None):
self.var_node = var_node
self.group = group
self.time_index = time_index
self.global_bounds_node = global_bounds_node
def get_name (self):
name = self.var_node.getAttribute ('name')
name = name.replace ("+", "_plus_")
name = name.replace ("%", "_pct_")
name = name.split ('(')[0]
return name
def get_path (self):
path = self.var_node.getAttribute ('path')
return path
def get_fullpath (self):
path = self.get_path()
name = self.get_name()
if (path == ''):
fullpath = name
elif (path == '/'):
fullpath = '/'+name
else:
fullpath = path + '/' + name
return fullpath
def get_gwrite (self):
gw = self.var_node.getAttribute ('gwrite')
if (gw == ''):
gw = self.get_name()
# Trim the name at the first open paren to deal with gts issue
gw = gw.split('(')[0]
gw = gw.replace ("+", "_plus_")
gw = gw.replace ("%", "_pct_")
return gw
def get_group (self):
return self.group
def get_c_type (self):
return typeMapper.get_c_type (self.var_node.getAttribute ('type') )
def get_fortran_type (self):
return typeMapper.get_fortran_type (self.var_node.getAttribute ('type') )
def get_type (self):
return self.var_node.getAttribute ('type')
def get_dimensions (self):
if (self.var_node.getAttribute ('dimensions') == ''):
return None
else:
# place the dimensions in a list and remove the time-index if it is there.
dims = filter (lambda x : x != self.time_index, self.var_node.getAttribute ('dimensions').split(',') )
cleandims = []
for d in dims:
if d.isdigit():
cleandims.append (d)
continue
# Here we need to translate the variable name for this dimension (if it's a var) into the gwrite
# for that variable
dim_var = self.get_group().get_var (d)
if dim_var != None:
d = dim_var.get_gwrite()
# Now clean up any unsightly parts
cleand = d.replace ("+", "_plus_")
cleand = cleand.split('(')[0]
cleandims.append (cleand)
return cleandims
def is_scalar (self):
return self.get_dimensions() == None
# TODO: Implement this
def find_first_use (self):
# Loop through all of the vars in the group
for var in self.group.get_vars():
dim_num = 0;
if var.get_dimensions() is not None:
for dim in var.get_dimensions():
# if this one uses this variable as a dimension, return the name and dim number
if dim == self.get_name():
return var.get_name(), dim_num
dim_num = dim_num + 1
# None found, return None,None
return None,None
class fortranFormatter:
@staticmethod
def get_write_line (var):
retval = '\n call adios_write (adios_handle, "' + var.get_fullpath() + '", ' + var.get_gwrite() + ', adios_error)'
#print retval
return retval
@staticmethod
def get_declaration (var, group_params):
dims = var.get_dimensions()
if (dims == None):
# I think this should be get_name instead of get_gwrite.
#init_val = group_params.get_scalar (var.get_gwrite() ).get_value()
init_val = group_params.get_scalar (var.get_name() ).get_value()
return '\n ' + var.get_fortran_type() + ' :: ' + var.get_gwrite()
else:
#fill_method = group_params.get_array (var.get_gwrite() ).get_fill_method()
dimspec = ''
for d in dims:
dimspec = dimspec + ':,'
dimspec = dimspec.rstrip (',')
return '\n ' + var.get_fortran_type() + ', ALLOCATABLE, DIMENSION(' + dimspec + ') :: ' + var.get_gwrite()
@staticmethod
def get_initialization (var, group_params):
dims = var.get_dimensions()
if (dims == None):
# I think this should be get_name instead of get_gwrite.
#init_val = group_params.get_scalar (var.get_gwrite() ).get_value()
init_val = group_params.get_scalar (var.get_name() ).get_value()
return '\n ' + var.get_gwrite() + ' = ' + init_val
else:
fill_method = group_params.get_array (var.get_gwrite() ).get_fill_method()
return '\n allocate (' + var.get_gwrite() + '(' + fortranFormatter.get_dim_str (var, ',') + ') )'
#return '\n ' + var.get_gwrite() + ' = (' + var.get_c_type() + '*) malloc (' + cFormatter.get_dim_str (var, '*') + ' * sizeof (' + var.get_c_type() + ') );\n' + cFormatter.get_fill (var, fill_method)
@staticmethod
def get_dim_str (var, sep):
rv = ''
for d in var.get_dimensions():
rv += d
rv += sep
return rv.rstrip (sep)
@staticmethod
def get_groupsize_code (group):
groupsize_code_string = ''
groupsize_code_string += '\n\n! Set the adios group size'
groupsize_code_string += '\n adios_groupsize = &'
for v in group.get_vars():
if (v.is_scalar() ):
groupsize_code_string += ('\n %d +' % typeMapper.get_size (v.get_type() ) + ' &')
else:
groupsize_code_string += ('\n %d * ' % typeMapper.get_size (v.get_type() ) )
for d in v.get_dimensions():
# need to check whether this is the timestep
groupsize_code_string += '(' + d + ') * '
groupsize_code_string = groupsize_code_string.rstrip ('* ')
groupsize_code_string += (' + &')
# remove the final +, and add the ;
groupsize_code_string = groupsize_code_string.rstrip('+ &')
groupsize_code_string += '\n call adios_group_size (adios_handle, adios_groupsize, skel_total_size, adios_error)'
return groupsize_code_string;
class cFormatter:
@staticmethod
def get_write_line (var):
# The tricky bit here is deciding whether we need the & before the variable name.
# We omit it in two cases: 1) the variable type is string, or 2) the variable is not a scalar
if (var.get_c_type() == 'string' or var.get_dimensions() != None):
var_prefix = ''
else:
var_prefix = '&'
retval = '\nadios_write (adios_handle, "' + var.get_fullpath() + '", ' + var_prefix + var.get_gwrite() + ');'
#print retval
return retval
@staticmethod
def get_read_all_line (var):
if (var.get_c_type() == 'string' or var.get_dimensions() != None):
var_prefix = ''
else:
var_prefix = '&'
return '\nadios_write (adios_handle, "' + var.get_name() + '", ' + var_prefix + var.get_gwrite() + ');'
@staticmethod
def get_dim_str (var, sep):
rv = ''
for d in var.get_dimensions():
rv += d
rv += sep
return rv.rstrip (sep)
@staticmethod
def get_fill (var, method):
fill_content = ''
if (method == 'rank'):
dims = var.get_dimensions()
fill_content = ''
fill_content += 'for (skel_i = 0; skel_i < ' + cFormatter.get_dim_str (var, '*') + '; skel_i++) \n'
fill_content += ' ' + var.get_gwrite() + '[skel_i] = (' + var.get_c_type() + ') skel_mpi_rank;'
return fill_content
@staticmethod
def get_declaration (var, group_params):
dims = var.get_dimensions()
if (dims == None):
# I think this should be get_name instead of get_gwrite.
#init_val = group_params.get_scalar (var.get_gwrite() ).get_value()
init_val = group_params.get_scalar (var.get_name() ).get_value()
return '\n' + var.get_c_type() + ' ' + var.get_gwrite() + ';'
else:
fill_method = group_params.get_array (var.get_gwrite() ).get_fill_method()
return '\n' + var.get_c_type() + ' * ' + var.get_gwrite() + ';'
@staticmethod
def get_initialization (var, group_params):
dims = var.get_dimensions()
if (dims == None):
# I think this should be get_name instead of get_gwrite.
#init_val = group_params.get_scalar (var.get_gwrite() ).get_value()
init_val = group_params.get_scalar (var.get_name() ).get_value()
return '\n' + var.get_gwrite() + ' = ' + init_val + ';'
else:
fill_method = group_params.get_array (var.get_gwrite() ).get_fill_method()
return '\n' + var.get_gwrite() + ' = (' + var.get_c_type() + '*) malloc (' + cFormatter.get_dim_str (var, '*') + ' * sizeof (' + var.get_c_type() + ') );\n' + cFormatter.get_fill (var, fill_method)
@staticmethod
def get_groupsize_code (group):
groupsize_code_string = ''
groupsize_code_string += '\n\n// Set the adios group size'
groupsize_code_string += '\nadios_groupsize ='
for v in group.get_vars():
if (v.is_scalar() ):
groupsize_code_string += ('\n %d +' % typeMapper.get_size (v.get_type() ) )
else:
groupsize_code_string += ('\n %d * ' % typeMapper.get_size (v.get_type() ) )
for d in v.get_dimensions():
# need to check whether this is the timestep
groupsize_code_string += '(' + d + ') * '
groupsize_code_string = groupsize_code_string.rstrip ('* ')
groupsize_code_string += (' +')
# remove the final +, and add the ;
groupsize_code_string = groupsize_code_string.rstrip('+') + ';'
groupsize_code_string += '\nadios_group_size (adios_handle, adios_groupsize, &skel_total_size);'
return groupsize_code_string;
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