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Hi,<br>
<br>
<br>
Update: found the reason of the mpi-error - maybe a PV-bug:<br>
<br>
If i use this formula in a programmable filter<br>
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<p style=" margin-top:0px; margin-bottom:0px; margin-left:0px; margin-right:0px; -qt-block-indent:0; text-indent:0px;"><span style=" font-family:'Hack';">
</span></p>
<p style=" margin-top:0px; margin-bottom:0px; margin-left:0px; margin-right:0px; -qt-block-indent:0; text-indent:0px;"><span style=" font-family:'Hack';">v_bad </span><span style=" font-family:'Hack'; color:#666666;">=</span><span style=" font-family:'Hack';"> </span><span style=" font-family:'Hack'; color:#008000;">min</span><span style=" font-family:'Hack';">((</span><span style=" font-family:'Hack'; color:#666666;">1.</span><span style=" font-family:'Hack';">, </span><span style=" font-family:'Hack'; color:#008000;">max</span><span style=" font-family:'Hack';">((</span><span style=" font-family:'Hack'; color:#666666;">-1.</span><span style=" font-family:'Hack';">, tmp2)))) </span></p>
<br>
then paraview crashes in parallel. If i use the same but written out
in<br>
<br>
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<p style=" margin-top:0px; margin-bottom:0px; margin-left:0px; margin-right:0px; -qt-block-indent:0; text-indent:0px;"><span style=" font-family:'Hack';"> </span><span style=" font-family:'Hack'; font-weight:600; color:#008000;">if</span><span style=" font-family:'Hack';"> (tmp2 </span><span style=" font-family:'Hack'; color:#666666;">></span><span style=" font-family:'Hack';"> </span><span style=" font-family:'Hack'; color:#666666;">-1.</span><span style=" font-family:'Hack';">):</span></p>
<pre style=" margin-top:0px; margin-bottom:0px; margin-left:0px; margin-right:0px; -qt-block-indent:0; text-indent:0px;"><span style=" font-family:'Hack';"> </span><span style=" font-family:'Hack'; font-weight:600; color:#008000;">if</span><span style=" font-family:'Hack';"> (tmp2 </span><span style=" font-family:'Hack'; color:#666666;">></span><span style=" font-family:'Hack';"> </span><span style=" font-family:'Hack'; color:#666666;">1.</span><span style=" font-family:'Hack';">):</span></pre>
<pre style=" margin-top:0px; margin-bottom:0px; margin-left:0px; margin-right:0px; -qt-block-indent:0; text-indent:0px;"><span style=" font-family:'Hack';"> v </span><span style=" font-family:'Hack'; color:#666666;">=</span><span style=" font-family:'Hack';"> </span><span style=" font-family:'Hack'; color:#666666;">1.</span></pre>
<pre style=" margin-top:0px; margin-bottom:0px; margin-left:0px; margin-right:0px; -qt-block-indent:0; text-indent:0px;"><span style=" font-family:'Hack';"> </span><span style=" font-family:'Hack'; font-weight:600; color:#008000;">else</span><span style=" font-family:'Hack';">:</span></pre>
<pre style=" margin-top:0px; margin-bottom:0px; margin-left:0px; margin-right:0px; -qt-block-indent:0; text-indent:0px;"><span style=" font-family:'Hack';"> v </span><span style=" font-family:'Hack'; color:#666666;">=</span><span style=" font-family:'Hack';"> tmp2</span></pre>
<pre style=" margin-top:0px; margin-bottom:0px; margin-left:0px; margin-right:0px; -qt-block-indent:0; text-indent:0px;"><span style=" font-family:'Hack';"> </span><span style=" font-family:'Hack'; font-weight:600; color:#008000;">else</span><span style=" font-family:'Hack';">:</span></pre>
<pre style=" margin-top:0px; margin-bottom:0px; margin-left:0px; margin-right:0px; -qt-block-indent:0; text-indent:0px;"><span style=" font-family:'Hack';"> v </span><span style=" font-family:'Hack'; color:#666666;">=</span><span style=" font-family:'Hack';"> </span><span style=" font-family:'Hack'; color:#666666;">-1.</span></pre>
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</pre>
the result for v is the same, however paraview does not crash.<br>
<br>
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.<br>
<br>
Stefan<br>
<br>
Hi,<br>
<blockquote type="cite"
cite="mid:666115e6-5e02-b56f-f7e2-76cb3332e2ea@DLR.de"> <br>
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?<br>
<br>
Best regards,<br>
<br>
Stefan<br>
<br>
<br>
<br>
<br>
<tt>Executing with:
0
</tt><tt><br>
</tt><tt>Executing with:
0
</tt><tt><br>
</tt><tt>Executing with:
0
</tt><tt><br>
</tt><tt>Executing with:
0
</tt><tt><br>
</tt><tt>Executing with:
0
</tt><tt><br>
</tt><tt>Executing with:
0
</tt><tt><br>
</tt><tt>Executing with:
0
</tt><tt><br>
</tt><tt>Executing with:
0
</tt><tt><br>
</tt><tt>
</tt><tt><br>
</tt><tt>2385958
</tt><tt><br>
</tt><tt>2406377
</tt><tt><br>
</tt><tt>2220610
</tt><tt><br>
</tt><tt>2292001
</tt><tt><br>
</tt><tt>2144431
</tt><tt><br>
</tt><tt>2331490
</tt><tt><br>
</tt><tt>2061524
</tt><tt><br>
</tt><tt>2344595
</tt><tt><br>
</tt><tt>Traceback (most recent call
last):
</tt><tt><br>
</tt><tt> File "<string>", line 22, in
<module>
</tt><tt><br>
</tt><tt> File "<string>", line 76, in
RequestData
</tt><tt><br>
</tt><tt> File
"/opt/PARAVIEW_5_4_0_OpenGL2/ParaView-v5.4.0.bin/lib/site-packages/vtk/numpy_interface/algorithms.py",
line 358, in
max
</tt><tt><br>
</tt><tt> return _global_func(MaxImpl(), array, axis,
controller)
</tt><tt><br>
</tt><tt> 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
</tt><tt><br>
</tt><tt> max_dims, size = _reduce_dims(res,
comm)
</tt><tt><br>
</tt><tt> 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
</tt><tt><br>
</tt><tt> comm.Allreduce([dims, mpitype], [max_dims, mpitype],
MPI.MAX)
</tt><tt><br>
</tt><tt> 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)</tt><tt><br>
</tt><tt>mpi4py.MPI.Exception: MPI_ERR_OTHER: known error not in
list</tt><tt><br>
</tt><tt>Traceback (most recent call last):</tt><tt><br>
</tt><tt> File "<string>", line 22, in <module></tt><tt><br>
</tt><tt>Traceback (most recent call last):</tt><tt><br>
</tt><tt> File "<string>", line 76, in RequestData</tt><tt><br>
</tt><tt> File "<string>", line 22, in <module></tt><tt><br>
</tt><tt> File "<string>", line 76, in RequestData</tt><tt><br>
</tt><tt> File
"/opt/PARAVIEW_5_4_0_OpenGL2/ParaView-v5.4.0.bin/lib/site-packages/vtk/numpy_interface/algorithms.py",
line 358, in max</tt><tt><br>
</tt><tt> File
"/opt/PARAVIEW_5_4_0_OpenGL2/ParaView-v5.4.0.bin/lib/site-packages/vtk/numpy_interface/algorithms.py",
line 358, in max</tt><tt><br>
</tt><tt> return _global_func(MaxImpl(), array, axis,
controller)</tt><tt><br>
</tt><tt> 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</tt><tt><br>
</tt><tt> max_dims, size = _reduce_dims(res, comm)</tt><tt><br>
</tt><tt> return _global_func(MaxImpl(), array, axis,
controller)</tt><tt><br>
</tt><tt> 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</tt><tt><br>
</tt><tt> 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</tt><tt><br>
</tt><tt>max_dims, size = _reduce_dims(res, comm)</tt><tt><br>
</tt><tt> comm.Allreduce([dims, mpitype], [max_dims, mpitype],
MPI.MAX)</tt><tt><br>
</tt><tt> 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)</tt><tt><br>
</tt><tt> 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</tt><tt><br>
</tt><tt>mpi4py.MPI.Exception: MPI_ERR_OTHER: known error not
in list</tt><tt><br>
</tt><tt>comm.Allreduce([dims, mpitype], [max_dims, mpitype],
MPI.MAX)</tt><tt><br>
</tt><tt> 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)</tt><tt><br>
</tt><tt>mpi4py.MPI.Exception: MPI_ERR_OTHER: known error not in
list</tt><tt><br>
</tt><tt><br>
</tt><tt><br>
<br>
<br>
<br>
<br>
<br>
</tt><tt>
<pre><span>
</span></pre>
</tt><tt>
<pre><span>grad </span><span>=</span><span> inputs[</span><span>0</span><span>]</span><span>.</span><span>PointData[</span><span>"Gradients"</span><span>] </span></pre>
<pre><span>npoints </span><span>=</span><span> </span><span>len</span><span>(grad)</span></pre>
<pre><span>print</span><span> npoints </span></pre>
<pre><span>data </span><span>=</span><span> []</span></pre>
<pre><span>for</span><span> i </span><span>in</span><span> </span><span>range</span><span>(npoints):</span></pre>
<pre><span> </span><span># Gradients</span></pre>
<pre><span> dvx </span><span>=</span><span> grad[i,:][</span><span>0</span><span>]</span></pre>
<pre><span> dvy </span><span>=</span><span> grad[i,:][</span><span>1</span><span>]</span></pre>
<pre><span> dvz </span><span>=</span><span> grad[i,:][</span><span>2</span><span>]</span></pre>
<pre><span> </span><span># Symmetrical part of flow tensor -> S</span></pre>
<pre><span> s0 </span><span>=</span><span> dvx[</span><span>0</span><span>]</span></pre>
<pre><span> s1 </span><span>=</span><span> </span><span>0.5</span><span> </span><span>*</span><span> (dvx[</span><span>1</span><span>] </span><span>+</span><span> dvy[</span><span>0</span><span>])</span></pre>
<pre><span> s2 </span><span>=</span><span> </span><span>0.5</span><span> </span><span>*</span><span> (dvx[</span><span>2</span><span>] </span><span>+</span><span> dvz[</span><span>0</span><span>])</span></pre>
<pre><span> s3 </span><span>=</span><span> </span><span>0.5</span><span> </span><span>*</span><span> (dvy[</span><span>0</span><span>] </span><span>+</span><span> dvx[</span><span>1</span><span>])</span></pre>
<pre><span> s4 </span><span>=</span><span> dvy[</span><span>1</span><span>];</span></pre>
<pre><span> s5 </span><span>=</span><span> </span><span>0.5</span><span> </span><span>*</span><span> (dvy[</span><span>2</span><span>] </span><span>+</span><span> dvz[</span><span>1</span><span>])</span></pre>
<pre><span> s6 </span><span>=</span><span> </span><span>0.5</span><span> </span><span>*</span><span> (dvz[</span><span>0</span><span>] </span><span>+</span><span> dvx[</span><span>2</span><span>])</span></pre>
<pre><span> s7 </span><span>=</span><span> </span><span>0.5</span><span> </span><span>*</span><span> (dvz[</span><span>1</span><span>] </span><span>+</span><span> dvy[</span><span>2</span><span>])</span></pre>
<pre><span> s8 </span><span>=</span><span> dvz[</span><span>2</span><span>]</span></pre>
<pre><span> </span><span># Antisymmetrical part of flow tensor -> Omega</span></pre>
<pre><span> Omega0 </span><span>=</span><span> </span><span>0.0</span></pre>
<pre><span> Omega1 </span><span>=</span><span> </span><span>0.5</span><span> </span><span>*</span><span> (dvx[</span><span>1</span><span>] </span><span>-</span><span> dvy[</span><span>0</span><span>])</span></pre>
<pre><span> Omega2 </span><span>=</span><span> </span><span>0.5</span><span> </span><span>*</span><span> (dvx[</span><span>2</span><span>] </span><span>-</span><span> dvz[</span><span>0</span><span>])</span></pre>
<pre><span> Omega3 </span><span>=</span><span> </span><span>0.5</span><span> </span><span>*</span><span> (dvy[</span><span>0</span><span>] </span><span>-</span><span> dvx[</span><span>1</span><span>])</span></pre>
<pre><span> Omega4 </span><span>=</span><span> </span><span>0.0</span></pre>
<pre><span> Omega5 </span><span>=</span><span> </span><span>0.5</span><span> </span><span>*</span><span> (dvy[</span><span>2</span><span>] </span><span>-</span><span> dvz[</span><span>1</span><span>])</span></pre>
<pre><span> Omega6 </span><span>=</span><span> </span><span>0.5</span><span> </span><span>*</span><span> (dvz[</span><span>0</span><span>] </span><span>-</span><span> dvx[</span><span>2</span><span>])</span></pre>
<pre><span> Omega7 </span><span>=</span><span> </span><span>0.5</span><span> </span><span>*</span><span> (dvz[</span><span>1</span><span>] </span><span>-</span><span> dvy[</span><span>2</span><span>])</span></pre>
<pre><span> Omega8 </span><span>=</span><span> </span><span>0.0</span></pre>
<pre><span> </span><span># Matrix M = (S^2 + Omega^2)</span></pre>
<pre><span> </span><span># M is symmetric</span></pre>
<pre><span> </span><span># | m0 m1 m2 |</span></pre>
<pre><span> </span><span># M = | m1 m3 m4 |</span></pre>
<pre><span> </span><span># | m2 m4 m5 |</span></pre>
<pre><span> m0 </span><span>=</span><span> s0</span><span>*</span><span>s0 </span><span>+</span><span> s1</span><span>*</span><span>s3 </span><span>+</span><span> s2</span><span>*</span><span>s6 </span><span>+</span><span> Omega1</span><span>*</span><span>Omega3 </span><span>+</span><span> Omega2</span><span>*</span><span>Omega6</span></pre>
<pre><span> m1 </span><span>=</span><span> s0</span><span>*</span><span>s1 </span><span>+</span><span> s1</span><span>*</span><span>s4 </span><span>+</span><span> s2</span><span>*</span><span>s7 </span><span>+</span><span> Omega2</span><span>*</span><span>Omega7</span></pre>
<pre><span> m2 </span><span>=</span><span> s0</span><span>*</span><span>s2 </span><span>+</span><span> s1</span><span>*</span><span>s5 </span><span>+</span><span> s2</span><span>*</span><span>s8 </span><span>+</span><span> Omega1</span><span>*</span><span>Omega5</span></pre>
<pre><span> m3 </span><span>=</span><span> s3</span><span>*</span><span>s1 </span><span>+</span><span> s4</span><span>*</span><span>s4 </span><span>+</span><span> s5</span><span>*</span><span>s7 </span><span>+</span><span> Omega3</span><span>*</span><span>Omega1 </span><span>+</span><span> Omega5</span><span>*</span><span>Omega7</span></pre>
<pre><span> m4 </span><span>=</span><span> s3</span><span>*</span><span>s2 </span><span>+</span><span> s4</span><span>*</span><span>s5 </span><span>+</span><span> s5</span><span>*</span><span>s8 </span><span>+</span><span> Omega3</span><span>*</span><span>Omega2</span></pre>
<pre><span> m5 </span><span>=</span><span> s6</span><span>*</span><span>s2 </span><span>+</span><span> s7</span><span>*</span><span>s5 </span><span>+</span><span> s8</span><span>*</span><span>s8 </span><span>+</span><span> Omega6</span><span>*</span><span>Omega2 </span><span>+</span><span> Omega7</span><span>*</span><span>Omega5</span></pre>
<pre><span> </span><span># computing now the eigenvalues of M</span></pre>
<pre><span> </span><span># | M - lambda I | = 0</span></pre>
<pre><span> </span><span># returns the characteristic equation:</span></pre>
<pre><span> </span><span># lambda^3 + p*lambda^2 + q*lambda + r = 0</span></pre>
<pre><span> </span><span># due to symmetric Matrix the following assumption can be made:</span></pre>
<pre><span> </span><span># all three eigenvalues will be real root values ( no imaginary parts )</span></pre>
<pre><span> p </span><span>=</span><span> </span><span>-1*</span><span>( m0 </span><span>+</span><span> m3 </span><span>+</span><span> m5)</span></pre>
<pre><span> q </span><span>=</span><span> </span><span>-1*</span><span>( m1</span><span>*</span><span>m1 </span><span>+</span><span> m2</span><span>*</span><span>m2 </span><span>+</span><span> m4</span><span>*</span><span>m4 </span><span>-</span><span> m0</span><span>*</span><span>m3 </span><span>-</span><span> m0</span><span>*</span><span>m5 </span><span>-</span><span> m3</span><span>*</span><span>m5)</span></pre>
<pre><span> r </span><span>=</span><span> </span><span>-1*</span><span>( m0</span><span>*</span><span>m3</span><span>*</span><span>m5 </span><span>+</span><span> </span><span>2*</span><span>m1</span><span>*</span><span>m2</span><span>*</span><span>m4 </span><span>-</span><span> m2</span><span>*</span><span>m2</span><span>*</span><span>m3 </span><span>-</span><span> m4</span><span>*</span><span>m4</span><span>*</span><span>m0 </span><span>-</span><span> m1</span><span>*</span><span>m1</span><span>*</span><span>m5)</span></pre>
<pre><span> </span><span># computing now the reduced equation</span></pre>
<pre><span> </span><span># lambda^3 + s*lambda + t = 0</span></pre>
<pre><span> sx </span><span>=</span><span> (</span><span>3.0</span><span> </span><span>*</span><span> q </span><span>-</span><span> p</span><span>*</span><span>p) </span><span>/</span><span> </span><span>3.0</span></pre>
<pre><span> t </span><span>=</span><span> (</span><span>2.0</span><span> </span><span>*</span><span> math</span><span>.</span><span>pow(p, </span><span>3.0</span><span>) </span><span>/</span><span> </span><span>27.0</span><span>) </span><span>-</span><span> (p </span><span>*</span><span> q </span><span>/</span><span> </span><span>3.0</span><span>) </span><span>+</span><span> r</span></pre>
<pre><span> </span><span># calculate unordered eigenvalues (Cardano's method)</span></pre>
<pre><span> </span><span># -> at first check if ( 1.0 / sqrtt(-s^3) ) can be computed</span></pre>
<pre><span> l </span><span>=</span><span> [</span><span>0</span><span>,</span><span>0</span><span>,</span><span>0</span><span>]</span></pre>
<pre><span> </span><span>if</span><span> ((sx </span><span>*</span><span> sx </span><span>*</span><span> sx) </span><span><</span><span> </span><span>-1e-16</span><span>):</span></pre>
<pre><span> tmp1 </span><span>=</span><span> math</span><span>.</span><span>sqrt( </span><span>-1*</span><span> sx </span><span>/</span><span> </span><span>3.0</span><span> )</span></pre>
<pre><span> tmp2 </span><span>=</span><span> </span><span>-1*</span><span> t </span><span>/</span><span> (</span><span>2.0</span><span> </span><span>*</span><span> tmp1</span><span>*</span><span>tmp1</span><span>*</span><span>tmp1)</span></pre>
<pre><span> c1 </span><span>=</span><span> </span><span>2.0</span><span> </span><span>*</span><span> tmp1 </span></pre>
<pre><span> c2 </span><span>=</span><span> math</span><span>.</span><span>acos( </span><span>min</span><span>((</span><span>1.</span><span>, </span><span>max</span><span>((</span><span>-1.</span><span>, tmp2))) ) ) </span><span>/</span><span> </span><span>3.0</span></pre>
<pre><span> l[</span><span>0</span><span>] </span><span>=</span><span> c1 </span><span>*</span><span> math</span><span>.</span><span>cos(c2) </span><span>-</span><span> p </span><span>/</span><span> </span><span>3.0</span></pre>
<pre><span> l[</span><span>1</span><span>] </span><span>=</span><span> c1 </span><span>*</span><span> math</span><span>.</span><span>cos(c2 </span><span>+</span><span> </span><span>2.*</span><span>math</span><span>.</span><span>pi</span><span>/3.</span><span>) </span><span>-</span><span> p </span><span>/</span><span> </span><span>3.0</span></pre>
<pre><span> l[</span><span>2</span><span>] </span><span>=</span><span> c1 </span><span>*</span><span> math</span><span>.</span><span>cos(c2 </span><span>+</span><span> </span><span>4.*</span><span>math</span><span>.</span><span>pi</span><span>/3.</span><span>) </span><span>-</span><span> p </span><span>/</span><span> </span><span>3.0</span></pre>
<pre><span> </span><span># sort eigenvalues</span></pre>
<pre><span> </span><span># lambda1 <= lambda2 <= lambda3</span></pre>
<pre><span> l</span><span>.</span><span>sort()</span></pre>
<pre><span> </span><span># save second eigenvalue</span></pre>
<pre><span> data</span><span>.</span><span>append(l[</span><span>1</span><span>])</span></pre>
<pre><span>output</span><span>.</span><span>PointData</span><span>.</span><span>append(data, </span><span>"lambda2"</span><span>) </span></pre>
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