Coverage for pySDC/projects/AllenCahn_Bayreuth/AllenCahn_dump.py: 0%

1import numpy as np 

2import json 

3from mpi4py import MPI 

4from mpi4py_fft import newDistArray 

5from pySDC.core.Hooks import hooks 

6 

7 

8class dump(hooks): 

9 def __init__(self): 

10 """ 

11 Initialization of Allen-Cahn monitoring 

12 """ 

13 super(dump, self).__init__() 

14 

15 self.comm = None 

16 self.rank = None 

17 self.size = None 

18 self.amode = MPI.MODE_WRONLY | MPI.MODE_CREATE 

19 self.time_step = None 

20 

21 def pre_run(self, step, level_number): 

22 """ 

23 Overwrite standard pre run hook 

24 

25 Args: 

26 step (pySDC.Step.step): the current step 

27 level_number (int): the current level number 

28 """ 

29 super(dump, self).pre_run(step, level_number) 

30 L = step.levels[0] 

31 

32 # get space-communicator and data 

33 self.comm = L.prob.params.comm 

34 if self.comm is not None: 

35 self.rank = self.comm.Get_rank() 

36 self.size = self.comm.Get_size() 

37 else: 

38 self.rank = 0 

39 self.size = 1 

40 

41 # get real space values 

42 if L.prob.params.spectral: 

43 if hasattr(L.prob, 'ncomp'): 

44 tmp1 = newDistArray(L.prob.fft, False) 

45 tmp = np.zeros(tmp1.shape + (L.prob.ncomp,)) 

46 for i in range(L.prob.ncomp): 

47 tmp[..., i] = L.prob.fft.backward(L.u[0][..., i]) 

48 else: 

49 tmp = L.prob.fft.backward(L.u[0]) 

50 else: 

51 tmp = L.u[0][:] 

52 

53 # compute local offset for I/O 

54 nbytes_local = tmp.nbytes 

55 if self.comm is not None: 

56 nbytes_global = self.comm.allgather(nbytes_local) 

57 else: 

58 nbytes_global = [nbytes_local] 

59 local_offset = sum(nbytes_global[: self.rank]) 

60 

61 # dump initial data 

62 fname = f"./data/{L.prob.params.name}_{0:08d}" 

63 fh = MPI.File.Open(self.comm, fname + ".dat", self.amode) 

64 fh.Write_at_all(local_offset, tmp) 

65 fh.Close() 

66 

67 sizes = list(L.prob.params.nvars) 

68 if hasattr(L.prob, 'ncomp'): 

69 sizes.append(L.prob.ncomp) 

70 

71 # write json description 

72 if self.rank == 0 and step.status.slot == 0: 

73 json_obj = dict() 

74 json_obj['type'] = 'dataset' 

75 json_obj['datatype'] = str(tmp.dtype) 

76 json_obj['endian'] = str(tmp.dtype.byteorder) 

77 json_obj['time'] = L.time 

78 json_obj['space_comm_size'] = self.size 

79 json_obj['time_comm_size'] = step.status.time_size 

80 json_obj['shape'] = sizes 

81 json_obj['elementsize'] = tmp.dtype.itemsize 

82 

83 with open(fname + '.json', 'w') as fp: 

84 json.dump(json_obj, fp) 

85 

86 # set step count 

87 self.time_step = 1 

88 

89 def post_step(self, step, level_number): 

90 """ 

91 Overwrite standard post step hook 

92 

93 Args: 

94 step (pySDC.Step.step): the current step 

95 level_number (int): the current level number 

96 """ 

97 super(dump, self).post_step(step, level_number) 

98 

99 # some abbreviations 

100 L = step.levels[0] 

101 

102 # get real space values 

103 if L.prob.params.spectral: 

104 if hasattr(L.prob, 'ncomp'): 

105 tmp1 = newDistArray(L.prob.fft, False) 

106 tmp = np.zeros(tmp1.shape + (L.prob.ncomp,)) 

107 for i in range(L.prob.ncomp): 

108 tmp[..., i] = L.prob.fft.backward(L.uend[..., i]) 

109 else: 

110 tmp = L.prob.fft.backward(L.uend) 

111 else: 

112 tmp = L.uend[:] 

113 

114 # compute local offset for I/O 

115 nbytes_local = tmp.nbytes 

116 if self.comm is not None: 

117 nbytes_global = self.comm.allgather(nbytes_local) 

118 else: 

119 nbytes_global = [nbytes_local] 

120 local_offset = sum(nbytes_global[: self.rank]) 

121 

122 # dump data 

123 fname = f"./data/{L.prob.params.name}_{self.time_step + step.status.slot:08d}" 

124 fh = MPI.File.Open(self.comm, fname + ".dat", self.amode) 

125 fh.Write_at_all(local_offset, tmp) 

126 fh.Close() 

127 

128 sizes = list(L.prob.params.nvars) 

129 if hasattr(L.prob, 'ncomp'): 

130 sizes.append(L.prob.ncomp) 

131 

132 # write json description 

133 if self.rank == 0: 

134 json_obj = dict() 

135 json_obj['type'] = 'dataset' 

136 json_obj['datatype'] = str(tmp.dtype) 

137 json_obj['endian'] = str(tmp.dtype.byteorder) 

138 json_obj['time'] = L.time + L.dt 

139 json_obj['space_comm_size'] = self.size 

140 json_obj['time_comm_size'] = step.status.time_size 

141 json_obj['shape'] = sizes 

142 json_obj['elementsize'] = tmp.dtype.itemsize 

143 

144 with open(fname + '.json', 'w') as fp: 

145 json.dump(json_obj, fp) 

146 

147 # update step count 

148 self.time_step += step.status.time_size