[Paraview] MPI-Error during using "Programmable Filter"...

Stefan Melber Stefan.Melber at DLR.de
Mon Jun 19 08:34:17 EDT 2017


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
>
>
>
>
> Executing with: 0
> Executing with: 0
> Executing with: 0
> Executing with: 0
> Executing with: 0
> Executing with: 0
> Executing with: 0
> Executing with: 0
>
> 2385958
> 2406377
> 2220610
> 2292001
> 2144431
> 2331490
> 2061524
> 2344595
> 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)
> printnpoints
> data =[]
> fori inrange(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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