small changes on fh2: start debugging
This commit is contained in:
Michael Stumpf
parent
589cde04f3
commit
b3748eb210
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@ -7,14 +7,13 @@ import os
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class ibmppp:
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"""Parallel Python Postprocessor for the IBM-DNS code"""
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def __init__(self,comm,dir_base,iseq,flowType,chunksPerProc=(1,1,1),numberOfGhosts=(1,1,1)):
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def __init__(self,comm,dir_base,flowType,chunksPerProc=(1,1,1),numberOfGhosts=(1,1,1)):
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"""Class constructor"""
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# Save method arguments for later use
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self.__comm = comm
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self.__rank = comm.Get_rank()
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self.__nproc = comm.Get_size()
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self.__dir_base = dir_base
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self.__iseq = iseq
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self.__nxppp = chunksPerProc[0]
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self.__nyppp = chunksPerProc[1]
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self.__nzppp = chunksPerProc[2]
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@ -88,7 +87,7 @@ class ibmppp:
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'''Read input processor grid, compute processor grid for workers'''
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if self.__rank==0:
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# Read the processor grid
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file_proc = self.__dir_base+'/proc_{:04d}.bin'.format(self.__iseq)
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file_proc = self.__dir_base+'/proc.bin'
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(self.__procGrid1['u'][0], self.__procGrid1['u'][1], self.__procGrid1['u'][2], self.__procGrid1['u'][3], self.__procGrid1['u'][4], self.__procGrid1['u'][5],
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self.__procGrid1['v'][0], self.__procGrid1['v'][1], self.__procGrid1['v'][2], self.__procGrid1['v'][3], self.__procGrid1['v'][4], self.__procGrid1['v'][5],
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self.__procGrid1['w'][0], self.__procGrid1['w'][1], self.__procGrid1['w'][2], self.__procGrid1['w'][3], self.__procGrid1['w'][4], self.__procGrid1['w'][5],
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@ -153,7 +152,7 @@ class ibmppp:
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buffer = None
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if self.__rank==0:
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# Read the grid
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file_grid = self.__dir_base+'/grid_{:04d}.bin'.format(self.__iseq)
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file_grid = self.__dir_base+'/grid.bin'
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buffer = ucf.readGrid(file_grid)
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# Broadcast the data
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buffer = self.__comm.bcast(buffer,root=0)
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@ -204,7 +203,7 @@ class ibmppp:
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# There is No need to distinguish between master and slave particles here, since we will
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# only use them for masking the fields. Also we do not care about particles in ghost cells.
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if self.__rank==0:
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file_input = self.__dir_base+'particles_{:04d}.bin'.format(self.__iseq)
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file_input = self.__dir_base+'particles.bin'
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pp,col = ucf.readParticles(file_input,step=1)
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# Remove time dimension, because we are dealing with a single time step exclusively
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pp = pp[:,:,0]
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@ -252,13 +251,15 @@ class ibmppp:
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sendbuf = (np.ascontiguousarray(pp[:,li_part]),col)
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self.__mpireq.append(self.__comm.isend(sendbuf,dest=rank_dst))
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# Every rank needs to receive the particles, rank 0 send them to itself
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req = self.__comm.irecv(source=0)
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buffsize = 32*1024*1024
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req = self.__comm.irecv(buffsize,source=0)
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(self.particles,self.col) = req.wait()
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if self.__rank==0:
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# Wait for everyone to finish
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MPI.Request.waitall(self.__mpireq)
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# Communication is done! Clear the list of requests
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self.__mpireq.clear()
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self.__comm.Barrier()
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def loadField(self,key,dtype='float64'):
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'''Reads chunks from files'''
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@ -275,19 +276,19 @@ class ibmppp:
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# Also determine file which contains the desired field as well as the
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# dataset ID
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if key[0]=='u':
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filebase = self.__dir_base+'uvwp_{:04d}.'.format(self.__iseq)
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filebase = self.__dir_base+'uvwp.'
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dset = 1
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elif key[0]=='v':
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filebase = self.__dir_base+'uvwp_{:04d}.'.format(self.__iseq)
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filebase = self.__dir_base+'uvwp.'
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dset = 2
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elif key[0]=='w':
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filebase = self.__dir_base+'uvwp_{:04d}.'.format(self.__iseq)
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filebase = self.__dir_base+'uvwp.'
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dset = 3
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elif key[0]=='p':
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filebase = self.__dir_base+'uvwp_{:04d}.'.format(self.__iseq)
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filebase = self.__dir_base+'uvwp.'
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dset = 4
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elif key[0]=='s':
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filebase = self.__dir_base+'scal_{:04d}.'.format(self.__iseq)
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filebase = self.__dir_base+'scal.'
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dset = int(key[1])
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if dset!=1:
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self.fields[key] = None
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@ -860,7 +861,7 @@ class ibmppp:
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stencil[ii] = 2*int(truncate*sigma[ii]+0.5)+1
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if self.__nghx<stencil[0] or self.__nghx<stencil[1] or self.__nghx<stencil[2]:
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raise ValueError('Too few ghost cells for stencil: ',stencil,(self.__nghx,self.__nghy,self.__nghz))
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print(stencil)
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#print(stencil)
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# Run scipy gaussian filter
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self.field[key] = ndimage.gaussian_filter(self.field[key],sigma,truncate=truncate,mode='constant',cval=0.0)
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# Exchange ghost cells and set boundary conditions
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@ -1083,6 +1084,7 @@ class ibmppp:
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self.__communicateGhostCells(key,(+1,+1,+1)) # right,up,back
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# Wait for communication to finish
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MPI.Request.waitall(self.__mpireq)
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self.__comm.Barrier()
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# Communication is done! Clear the list of requests
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self.__mpireq.clear()
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# Assign buffer to array
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@ -1468,4 +1470,14 @@ class ibmppp:
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symm = np.multiply(symm1,symm2)
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else:
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raise ValueError('Invalid operation: ',operation)
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return symm
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return symm
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# Utility functions
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def gaussianFilterStencilWidth(sigma=(1,1,1),truncate=4.0):
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if len(sigma)!=3:
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raise ValueError('Expected one value of sigma for each direction, but only got {}.'.format(len(sigma)))
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# Compute stencil width
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stencil = [0,0,0]
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for ii in range(0,3):
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stencil[ii] = 2*int(truncate*sigma[ii]+0.5)+1
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return stencil
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