Hi,
Update: found the reason of the mpi-error - maybe a PV-bug:
If i use this formula in a programmable filter
v_bad = min((1., max((-1., tmp2))))
then paraview crashes in parallel. If i use the same but written out in
if (tmp2 > -1.):
if (tmp2 > 1.):
v = 1.
else:
v = tmp2
else:
v = -1.
the result for v is the same, however paraview does not crash.
Further more, the results of v_bad and v in parallel differ, in serial mode
they are the same. Find attached a short restart file, which demonstrates
the effect.
Stefan
Hi,
i have used a programmable filter (find it below) to calculate the
lambda2-criterion from gradients of velocity. In serial mode this works fine
- running it in parallel an error message comes up. Any idea what does it
mean and whats wrong with the filter?
Best regards,
Stefan
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Traceback (most recent call last):
File "<string>", line 22, in <module>
File "<string>", line 76, in RequestData
File
"/opt/PARAVIEW_5_4_0_OpenGL2/ParaView-v5.4.0.bin/lib/site-packages/vtk/numpy_interface/algorithms.py",
line 358, in max
return _global_func(MaxImpl(), array, axis, controller)
File
"/opt/PARAVIEW_5_4_0_OpenGL2/ParaView-v5.4.0.bin/lib/site-packages/vtk/numpy_interface/algorithms.py",
line 199, in _global_func
max_dims, size = _reduce_dims(res, comm)
File
"/opt/PARAVIEW_5_4_0_OpenGL2/ParaView-v5.4.0.bin/lib/site-packages/vtk/numpy_interface/algorithms.py",
line 168, in _reduce_dims
comm.Allreduce([dims, mpitype], [max_dims, mpitype], MPI.MAX)
File "MPI/Comm.pyx", line 715, in mpi4py.MPI.Comm.Allreduce
(/opt/PARAVIEW_5_4_0_OpenGL2/ParaView-v5.4.0/VTK/ThirdParty/mpi4py/vtkmpi4py/src/mpi4py.MPI.c:99224)
mpi4py.MPI.Exception: MPI_ERR_OTHER: known error not in list
Traceback (most recent call last):
File "<string>", line 22, in <module>
Traceback (most recent call last):
File "<string>", line 76, in RequestData
File "<string>", line 22, in <module>
File "<string>", line 76, in RequestData
File
"/opt/PARAVIEW_5_4_0_OpenGL2/ParaView-v5.4.0.bin/lib/site-packages/vtk/numpy_interface/algorithms.py",
line 358, in max
File
"/opt/PARAVIEW_5_4_0_OpenGL2/ParaView-v5.4.0.bin/lib/site-packages/vtk/numpy_interface/algorithms.py",
line 358, in max
return _global_func(MaxImpl(), array, axis, controller)
File
"/opt/PARAVIEW_5_4_0_OpenGL2/ParaView-v5.4.0.bin/lib/site-packages/vtk/numpy_interface/algorithms.py",
line 199, in _global_func
max_dims, size = _reduce_dims(res, comm)
return _global_func(MaxImpl(), array, axis, controller)
File
"/opt/PARAVIEW_5_4_0_OpenGL2/ParaView-v5.4.0.bin/lib/site-packages/vtk/numpy_interface/algorithms.py",
line 199, in _global_func
File
"/opt/PARAVIEW_5_4_0_OpenGL2/ParaView-v5.4.0.bin/lib/site-packages/vtk/numpy_interface/algorithms.py",
line 168, in _reduce_dims
max_dims, size = _reduce_dims(res, comm)
comm.Allreduce([dims, mpitype], [max_dims, mpitype], MPI.MAX)
File "MPI/Comm.pyx", line 715, in mpi4py.MPI.Comm.Allreduce
(/opt/PARAVIEW_5_4_0_OpenGL2/ParaView-v5.4.0/VTK/ThirdParty/mpi4py/vtkmpi4py/src/mpi4py.MPI.c:99224)
File
"/opt/PARAVIEW_5_4_0_OpenGL2/ParaView-v5.4.0.bin/lib/site-packages/vtk/numpy_interface/algorithms.py",
line 168, in _reduce_dims
mpi4py.MPI.Exception: MPI_ERR_OTHER: known error not in list
comm.Allreduce([dims, mpitype], [max_dims, mpitype], MPI.MAX)
File "MPI/Comm.pyx", line 715, in mpi4py.MPI.Comm.Allreduce
(/opt/PARAVIEW_5_4_0_OpenGL2/ParaView-v5.4.0/VTK/ThirdParty/mpi4py/vtkmpi4py/src/mpi4py.MPI.c:99224)
mpi4py.MPI.Exception: MPI_ERR_OTHER: known error not in list
grad = inputs[0].PointData["Gradients"]
npoints = len(grad)
print npoints
data = []
for i in range(npoints):
# Gradients
dvx = grad[i,:][0]
dvy = grad[i,:][1]
dvz = grad[i,:][2]
# Symmetrical part of flow tensor -> S
s0 = dvx[0]
s1 = 0.5 * (dvx[1] + dvy[0])
s2 = 0.5 * (dvx[2] + dvz[0])
s3 = 0.5 * (dvy[0] + dvx[1])
s4 = dvy[1];
s5 = 0.5 * (dvy[2] + dvz[1])
s6 = 0.5 * (dvz[0] + dvx[2])
s7 = 0.5 * (dvz[1] + dvy[2])
s8 = dvz[2]
# Antisymmetrical part of flow tensor -> Omega
Omega0 = 0.0
Omega1 = 0.5 * (dvx[1] - dvy[0])
Omega2 = 0.5 * (dvx[2] - dvz[0])
Omega3 = 0.5 * (dvy[0] - dvx[1])
Omega4 = 0.0
Omega5 = 0.5 * (dvy[2] - dvz[1])
Omega6 = 0.5 * (dvz[0] - dvx[2])
Omega7 = 0.5 * (dvz[1] - dvy[2])
Omega8 = 0.0
# Matrix M = (S^2 + Omega^2)
# M is symmetric
# | m0 m1 m2 |
# M = | m1 m3 m4 |
# | m2 m4 m5 |
m0 = s0*s0 + s1*s3 + s2*s6 + Omega1*Omega3 + Omega2*Omega6
m1 = s0*s1 + s1*s4 + s2*s7 + Omega2*Omega7
m2 = s0*s2 + s1*s5 + s2*s8 + Omega1*Omega5
m3 = s3*s1 + s4*s4 + s5*s7 + Omega3*Omega1 + Omega5*Omega7
m4 = s3*s2 + s4*s5 + s5*s8 + Omega3*Omega2
m5 = s6*s2 + s7*s5 + s8*s8 + Omega6*Omega2 + Omega7*Omega5
# computing now the eigenvalues of M
# | M - lambda I | = 0
# returns the characteristic equation:
# lambda^3 + p*lambda^2 + q*lambda + r = 0
# due to symmetric Matrix the following assumption can be made:
# all three eigenvalues will be real root values ( no imaginary parts )
p = -1*( m0 + m3 + m5)
q = -1*( m1*m1 + m2*m2 + m4*m4 - m0*m3 - m0*m5 - m3*m5)
r = -1*( m0*m3*m5 + 2*m1*m2*m4 - m2*m2*m3 - m4*m4*m0 - m1*m1*m5)
# computing now the reduced equation
# lambda^3 + s*lambda + t = 0
sx = (3.0 * q - p*p) / 3.0
t = (2.0 * math.pow(p, 3.0) / 27.0) - (p * q / 3.0) + r
# calculate unordered eigenvalues (Cardano's method)
# -> at first check if ( 1.0 / sqrtt(-s^3) ) can be computed
l = [0,0,0]
if ((sx * sx * sx) < -1e-16):
tmp1 = math.sqrt( -1* sx / 3.0 )
tmp2 = -1* t / (2.0 * tmp1*tmp1*tmp1)
c1 = 2.0 * tmp1
c2 = math.acos( min((1., max((-1., tmp2))) ) ) / 3.0
l[0] = c1 * math.cos(c2) - p / 3.0
l[1] = c1 * math.cos(c2 + 2.*math.pi/3.) - p / 3.0
l[2] = c1 * math.cos(c2 + 4.*math.pi/3.) - p / 3.0
# sort eigenvalues
# lambda1 <= lambda2 <= lambda3
l.sort()
# save second eigenvalue
data.append(l[1])
output.PointData.append(data, "lambda2")
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_______________________________________________
Powered by www.kitware.com
Visit other Kitware open-source projects at
http://www.kitware.com/opensource/opensource.html
Please keep messages on-topic and check the ParaView Wiki at:
http://paraview.org/Wiki/ParaView
Search the list archives at: http://markmail.org/search/?q=ParaView
Follow this link to subscribe/unsubscribe:
http://public.kitware.com/mailman/listinfo/paraview
