pycompact - performance improvement, buffer reuse and x-dir tiling
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ignis
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1 changed files with 60 additions and 43 deletions
103
pycompact.py
103
pycompact.py
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@ -7,6 +7,8 @@ class CompactScheme:
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pi8 = np.arccos(-1., dtype=np.float64)
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self.nb = 32
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self.shape = (nz, ny, nx)
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self.px = px
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@ -195,34 +197,36 @@ class CompactScheme:
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return coef
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def ddx (self, src):
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def ddx (self, src, dst=None):
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if src.shape != self.shape:
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print ("error")
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if src.shape != self.shape: print ("error: src.shape wrong!")
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nz, ny, nx = self.shape
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nb = self.nb
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dst = np.zeros((nz, ny, nx,), dtype=np.float64,)
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if dst is None or dst.shape != self.shape :
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dst = np.zeros((nz, ny, nx,), dtype=np.float64,)
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if self.px: # Periodic BC
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for i in range(nz):
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dst[i] = compact.dfp(self.hx, src[i], 1)
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for j in range(0, ny, nb):
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dst[i,j:j+nb] = compact.dfp(self.hx, src[i,j:j+nb], 1)
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else:
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for i in range(nz):
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dst[i] = compact.dfnonp(self.hx, src[i], 1)
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for j in range(0, ny, nb):
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dst[i,j:j+nb] = compact.dfnonp(self.hx, src[i,j:j+nb], 1)
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# return np.swapaxes(dst, 1, 2)
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return dst
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def ddy (self, src):
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def ddy (self, src, dst=None):
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if src.shape != self.shape:
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print ("error")
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if src.shape != self.shape: print ("error: src.shape wrong!")
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nz, ny, nx = self.shape
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dst = np.zeros((nz, ny, nx,), dtype=np.float64,)
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if dst is None or dst.shape != self.shape :
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dst = np.zeros((nz, ny, nx,), dtype=np.float64,)
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if self.py: # Periodic BC
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for i in range(nz):
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@ -232,53 +236,60 @@ class CompactScheme:
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for i in range(nz):
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dst[i] = compact.dfnonp(self.hx, src[i].T, 2).T
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# return np.swapaxes(dst, 1, 2)
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return dst
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def ddz (self, src):
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def ddz (self, src, dst=None):
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if src.shape != self.shape:
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print ("error")
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if src.shape != self.shape: print ("error: src.shape wrong!")
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nz, ny, nx = self.shape
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# dst = np.zeros((nx, ny, nz,), order="F")
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dst = np.zeros((nz, ny, nx,), dtype=np.float64,)
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if dst is None or dst.shape != self.shape :
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dst = np.zeros((nz, ny, nx,), dtype=np.float64,)
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zxsrc = np.zeros((nz, nx))
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if self.pz: # Periodic BC
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for i in range(ny):
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dst[:,i,:] = compact.dfp(self.hx, src[:,i,:].T, 3).T
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zxsrc[:,:] = src[:,i,:]
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dst[:,i,:] = compact.dfp(self.hx, zxsrc.T, 3).T
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else:
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for i in range(ny):
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dst[:,i,:] = compact.dfnonp(self.hx, src[:,i,:].T, 3).T
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zxsrc[:,:] = src[:,i,:]
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dst[:,i,:] = compact.dfnonp(self.hx, zxsrc.T, 3).T
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# return np.swapaxes(dst, 1, 2)
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return dst
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def d2dx (self, src):
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def d2dx (self, src, dst=None):
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if src.shape != self.shape: print ("error")
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if src.shape != self.shape: print ("error: src.shape wrong!")
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nz, ny, nx = self.shape
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nb = self.nb
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dst = np.zeros((nz, ny, nx,), dtype=np.float64,)
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if dst is None or dst.shape != self.shape :
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dst = np.zeros((nz, ny, nx,), dtype=np.float64,)
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if self.px: # Periodic BC
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for i in range(nz):
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dst[i] = compact.d2fp(self.hx, src[i], 1)
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for j in range(0, ny, nb):
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dst[i,j:j+nb] = compact.d2fp(self.hx, src[i,j:j+nb], 1)
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else:
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for i in range(nz):
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dst[i] = compact.d2fnonp(self.hx, src[i], 1)
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for j in range(0, ny, nb):
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dst[i,j:j+nb] = compact.d2fnonp(self.hx, src[i,j:j+nb], 1)
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return dst
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def d2dy (self, src):
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def d2dy (self, src, dst=None):
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if src.shape != self.shape: print ("error")
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if src.shape != self.shape: print ("error: src.shape wrong!")
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nz, ny, nx = self.shape
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dst = np.zeros((nz, ny, nx,), dtype=np.float64,)
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if dst is None or dst.shape != self.shape :
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dst = np.zeros((nz, ny, nx,), dtype=np.float64,)
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if self.py: # Periodic BC
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for i in range(nz):
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@ -289,20 +300,25 @@ class CompactScheme:
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return dst
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def d2dz (self, src):
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def d2dz (self, src, dst=None):
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if src.shape != self.shape: print ("error")
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if src.shape != self.shape: print ("error: src.shape wrong!")
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nz, ny, nx = self.shape
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dst = np.zeros((nz, ny, nx,), dtype=np.float64,)
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if dst is None or dst.shape != self.shape :
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dst = np.zeros((nz, ny, nx,), dtype=np.float64,)
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zxsrc = np.zeros((nz, nx))
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if self.pz: # Periodic BC
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for i in range(ny):
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dst[:,i,:] = compact.d2fp(self.hx, src[:,i,:].T, 3).T
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zxsrc[:,:] = src[:,i,:]
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dst[:,i,:] = compact.d2fp(self.hx, zxsrc.T, 3).T
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else:
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for i in range(ny):
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dst[:,i,:] = compact.d2fnonp(self.hx, src[:,i,:].T, 3).T
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zxsrc[:,:] = src[:,i,:]
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dst[:,i,:] = compact.d2fnonp(self.hx, zxsrc.T, 3).T
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return dst
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@ -513,7 +529,7 @@ def validate_trigonometric():
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print(" DDX Test ")
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Y1[:] = np.sin(1.1 * xx) * np.sin(3.0 * yy) * np.sin(2.0 * zz)[:]
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true[:] = (1.1 * np.cos(1.1 * xx) * np.sin(3.0 * yy) * np.sin(2.0 * zz))[:]
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dY1 = cs.ddx(Y1)[:]
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dY1 = cs.ddx(Y1, dY1)[:]
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compare_3d_result(true, dY1)
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@ -521,7 +537,7 @@ def validate_trigonometric():
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print("D2DX Test ")
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Y1[:] = np.sin(1.1 * xx) * np.sin(3.0 * yy) * np.sin(2.0 * zz)[:]
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true[:] = (- 1.1 * 1.1 * np.sin(1.1 * xx) * np.sin(3.0 * yy) * np.sin(2.0 * zz))[:]
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dY1 = cs.d2dx(Y1)[:]
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dY1 = cs.d2dx(Y1, dY1)[:]
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compare_3d_result(true, dY1)
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@ -529,7 +545,7 @@ def validate_trigonometric():
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print(" DDY Test ")
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Y1[:] = np.sin(1.1 * xx) * np.sin(3.0 * yy) * np.sin(2.0 * zz)[:]
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true[:] = (3.0 * np.sin(1.1 * xx) * np.cos(3.0 * yy) * np.sin(2.0 * zz))[:]
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dY1 = cs.ddy(Y1)[:]
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dY1 = cs.ddy(Y1, dY1)[:]
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compare_3d_result(true, dY1)
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@ -537,7 +553,7 @@ def validate_trigonometric():
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print(" DDZ Test ")
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Y1[:] = np.sin(1.1 * xx) * np.sin(3.0 * yy) * np.sin(2.0 * zz)[:]
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true[:] = (2.0 * np.sin(1.1 * xx) * np.sin(3.0 * yy) * np.cos(2.0 * zz))[:]
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dY1 = cs.ddz(Y1)[:]
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dY1 = cs.ddz(Y1, dY1)[:]
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compare_3d_result(true, dY1)
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@ -576,6 +592,7 @@ def performance_benchmark():
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print ("Test ddx")
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Y1 = np.zeros(shape)
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dY1 = np.zeros(shape)
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true = np.zeros(shape)
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@ -605,7 +622,7 @@ def performance_benchmark():
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true[:] = (1.1 * np.cos(1.1 * xx) * np.sin(3.0 * yy) * np.sin(2.0 * zz))[:]
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t0 = time.perf_counter()
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for i in range(100):
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dY1 = cs.ddx(Y1)[:]
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cs.ddx(Y1, dY1)
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t1 = time.perf_counter()
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print ("Elapsed time in sec for 100 repetition: ", t1-t0)
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compare_3d_result(true, dY1)
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@ -614,7 +631,7 @@ def performance_benchmark():
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true[:] = (- 1.1 * 1.1 * np.sin(1.1 * xx) * np.sin(3.0 * yy) * np.sin(2.0 * zz))[:]
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t0 = time.perf_counter()
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for i in range(100):
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dY1 = cs.d2dx(Y1)[:]
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cs.d2dx(Y1, dY1)
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t1 = time.perf_counter()
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print ("Elapsed time in sec for 100 repetition: ", t1-t0)
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compare_3d_result(true, dY1)
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@ -623,7 +640,7 @@ def performance_benchmark():
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true[:] = (3.0 * np.sin(1.1 * xx) * np.cos(3.0 * yy) * np.sin(2.0 * zz))[:]
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t0 = time.perf_counter()
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for i in range(100):
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dY1 = cs.ddy(Y1)[:]
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cs.ddy(Y1, dY1)
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t1 = time.perf_counter()
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print ("Elapsed time in sec for 100 repetition: ", t1-t0)
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compare_3d_result(true, dY1)
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@ -632,7 +649,7 @@ def performance_benchmark():
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true[:] = (-3. * 3.0 * np.sin(1.1 * xx) * np.sin(3.0 * yy) * np.sin(2.0 * zz))[:]
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t0 = time.perf_counter()
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for i in range(100):
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dY1 = cs.d2dy(Y1)[:]
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cs.d2dy(Y1, dY1)
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t1 = time.perf_counter()
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print ("Elapsed time in sec for 100 repetition: ", t1-t0)
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compare_3d_result(true, dY1)
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@ -641,7 +658,7 @@ def performance_benchmark():
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true[:] = (2.0 * np.sin(1.1 * xx) * np.sin(3.0 * yy) * np.cos(2.0 * zz))[:]
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t0 = time.perf_counter()
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for i in range(100):
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dY1 = cs.ddz(Y1)[:]
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cs.ddz(Y1, dY1)
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t1 = time.perf_counter()
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print ("Elapsed time in sec for 100 repetition: ", t1-t0)
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compare_3d_result(true, dY1)
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@ -651,7 +668,7 @@ def performance_benchmark():
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true[:] = (-2. * 2.0 * np.sin(1.1 * xx) * np.sin(3.0 * yy) * np.sin(2.0 * zz))[:]
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t0 = time.perf_counter()
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for i in range(100):
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dY1 = cs.d2dz(Y1)[:]
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cs.d2dz(Y1, dY1)
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t1 = time.perf_counter()
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print ("Elapsed time in sec for 100 repetition: ", t1-t0)
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compare_3d_result(true, dY1)
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