<div dir="ltr">I'm trying to build Paraview 4.1 with mvapich2, gcc, cuda55, and qt 4.8.1. Â I've done the iterative configure process and I generate a make file but make -j 8 gives me this error:<div><br></div><div>
<p class="">/usr/bin/ld: /cm/shared/apps/mvapich2/gcc/64/1.9/lib/libmpich.a(setbotf.o): relocation R_X86_64_32 against `mpifcmb2_' can not be used when making a shared object; recompile with -fPIC</p>
<p class="">/cm/shared/apps/mvapich2/gcc/64/1.9/lib/libmpich.a: could not read symbols: Bad value</p>
<p class="">collect2: ld returned 1 exit status</p>
<p class="">make[2]: *** [lib/libvtkVPIC-pv4.1.so.1] Error 1</p>
<p class="">make[1]: *** [VTK/ThirdParty/VPIC/CMakeFiles/VPIC.dir/all] Error 2</p>
<p class="">make[1]: *** Waiting for unfinished jobs....</p><p class="">The make ends with</p><p class="">[ Â 4%] Building CXX object ThirdParty/protobuf/vtkprotobuf/src/CMakeFiles/protoc_compiler.dir/google/protobuf/compiler/parser.cc.o</p>
<p class="">[ Â 4%] Building C object VTK/ThirdParty/libxml2/vtklibxml2/CMakeFiles/vtklibxml2.dir/xpath.c.o</p><p class="">[ Â 4%] Building C object VTK/ThirdParty/libxml2/vtklibxml2/CMakeFiles/vtklibxml2.dir/xpointer.c.o</p>
<p class="">Linking CXX executable ../../../../bin/protoc</p><p class="">[ Â 4%] Built target protoc_compiler</p><p class="">Linking C shared library ../../../../lib/<a href="http://libvtklibxml2-pv4.1.so">libvtklibxml2-pv4.1.so</a></p>
<p class="">[ Â 4%] Built target vtklibxml2</p><p class="">make: *** [all] Error 2</p></div><div>Can someone translate for me? Â Can I buy a vowel? Â The google has run out of gas.</div></div><div class="gmail_extra"><br><br>
<div class="gmail_quote">On Tue, Apr 22, 2014 at 10:00 AM, <span dir="ltr"><<a href="mailto:paraview-request@paraview.org" target="_blank">paraview-request@paraview.org</a>></span> wrote:<br><blockquote class="gmail_quote" style="margin:0 0 0 .8ex;border-left:1px #ccc solid;padding-left:1ex">
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Today's Topics:<br>
<br>
  1. Re: Fwd: Stream Tracer Scaling (Amir A)<br>
  2. Re: [vtkusers] vtkStripper/TriangleStrips not working on this<br>
   particular data, why? (Dr. Roman Grothausmann)<br>
  3. Re: Fwd: Stream Tracer Scaling (Berk Geveci)<br>
<br>
<br>
----------------------------------------------------------------------<br>
<br>
Message: 1<br>
Date: Mon, 21 Apr 2014 17:20:24 -0500<br>
From: Amir A <<a href="mailto:amiramir12345@outlook.com">amiramir12345@outlook.com</a>><br>
To: Berk Geveci <<a href="mailto:berk.geveci@kitware.com">berk.geveci@kitware.com</a>>, "<a href="mailto:paraview@paraview.org">paraview@paraview.org</a>"<br>
    <<a href="mailto:paraview@paraview.org">paraview@paraview.org</a>><br>
Subject: Re: [Paraview] Fwd: Stream Tracer Scaling<br>
Message-ID: <SNT151-W25522E46C192AC769D4DDFED5E0@phx.gbl><br>
Content-Type: text/plain; charset="iso-8859-1"<br>
<br>
Hi Berk:<br>
Thank you for your reply. I am doing the visualization on a distributed cluster. And the StreamTracer filter is used with a point source of radius 0.1 and 100 seeds.<br>
It is surprising that the streamtracer in parallel takes orders of magnitude more time than when applied in serial. I tried to first apply D3 filter and then the streamtracer. That helps a little bit but still the time is prohibitively long (about an hour compared to ~5min when done in serial). I do not know if I am missing something or this is usual.<br>
Here is the visualization that I want to create in parallel (I had to do it in serial because of this problem):<a href="https://www.dropbox.com/s/r3kkon3khjdpqs6/foam_3.png" target="_blank">https://www.dropbox.com/s/r3kkon3khjdpqs6/foam_3.png</a><br>
The original dataset is about 4GB. Â Here is a smaller one (~1GB) with the state files: <a href="https://www.dropbox.com/s/r6lh3sx2wojfva2/sample.tar.gz" target="_blank">https://www.dropbox.com/s/r6lh3sx2wojfva2/sample.tar.gz</a><br>
I would highly appreciate any suggestions.-Amir<br>
From: <a href="mailto:berk.geveci@kitware.com">berk.geveci@kitware.com</a><br>
Date: Mon, 21 Apr 2014 11:34:25 -0400<br>
To: <a href="mailto:andy.bauer@kitware.com">andy.bauer@kitware.com</a><br>
CC: <a href="mailto:paraview@paraview.org">paraview@paraview.org</a><br>
Subject: Re: [Paraview] Fwd: Stream Tracer Scaling<br>
<br>
Actually, if the integration is fairly load balanced across partitions, the streamline integration can scale OK. It is highly dependent on how the seeds are distributed and if the integration ends up clustering on a few processes. Amir:<br>
<br>
<br>
- How big is your seed source? Does it span multiple partitions? How many seed points?- Do the streamlines stay together or do the move around the domain more independently?<br>
<br>
<br>
Are you running on a single machine by the way? I have been thinking about parallelizing the streamline filter over threads, which should scale better on a single machine.<br>
Best,-berk<br>
<br>
<br>
<br>
<br>
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------------------------------<br>
<br>
Message: 2<br>
Date: Tue, 22 Apr 2014 11:33:46 +0200<br>
From: "Dr. Roman Grothausmann" <<a href="mailto:grothausmann.roman@mh-hannover.de">grothausmann.roman@mh-hannover.de</a>><br>
Cc: VTK Mailing List <<a href="mailto:vtkusers@vtk.org">vtkusers@vtk.org</a>>, "<a href="mailto:paraview@paraview.org">paraview@paraview.org</a>"<br>
    <<a href="mailto:paraview@paraview.org">paraview@paraview.org</a>><br>
Subject: Re: [Paraview] [vtkusers] vtkStripper/TriangleStrips not<br>
    working on this particular data, why?<br>
Message-ID: <<a href="mailto:5356377A.1020809@mh-hannover.de">5356377A.1020809@mh-hannover.de</a>><br>
Content-Type: text/plain; charset=ISO-8859-1; format=flowed<br>
<br>
Thanks Bill, Goodwin and Des for Your answers.<br>
I see, perhaps this should be given as a hint in the docs. The patch seems to be<br>
doing something similar to my new approach. However, since my polylines<br>
originate from a vtkGraph, I decided to reorder the nodes/vertices with BFS.<br>
<br>
Many thanks again for Your help<br>
Roman<br>
<br>
On 11/04/14 17:13, Bill Lorensen wrote:<br>
> If this were a closed contour, I believe you would get one polyline.<br>
> But for a open contour you are not guaranteed to get a single<br>
> polyline. The algorithm starts with a point (looks like it is the<br>
> first point in the first line segment) and collects as many points as<br>
> it can for the first polyline. This completes the first polyline. If<br>
> the first point of the first line is not one of the end points of your<br>
> original data, then it will generate two polylines. At least that is<br>
> what I recall.<br>
><br>
> Bill<br>
><br>
><br>
> On Fri, Apr 11, 2014 at 10:43 AM, Dr. Roman Grothausmann<br>
> <<a href="mailto:grothausmann.roman@mh-hannover.de">grothausmann.roman@mh-hannover.de</a>> wrote:<br>
>> Dear mailing list members,<br>
>><br>
>><br>
>> Attached is a very simple test.vtp (see *_01.png) which for some reason<br>
>> cannot be converted into a single vtkPolyLine with vtkStripper. Even if I<br>
>> use paraview with Clean+Triangulate+TriangleStrip the result still consists<br>
>> of two vtkPolyLine (see extracted cell 0 (thicker line) and green cell<br>
>> labels in *_03.png).<br>
>> Why does vtkStripper not yield a single vtkPolyLine from this particular<br>
>> dataset? Is it the odd order of the points and lines?<br>
>> Is this a bug?<br>
>> If not, how can I achieve what I need, i.e. getting a single vtkPolyLine?<br>
>><br>
>> Any help or hints are very much appreciated<br>
>> Roman<br>
>><br>
>> --<br>
>> Dr. Roman Grothausmann<br>
>><br>
>> Tomographie und Digitale Bildverarbeitung<br>
>> Tomography and Digital Image Analysis<br>
>><br>
>> Institut f?r Funktionelle und Angewandte Anatomie, OE 4120<br>
>> Medizinische Hochschule Hannover<br>
>> Carl-Neuberg-Str. 1<br>
>> D-30625 Hannover<br>
>><br>
>> Tel. <a href="tel:%2B49%20511%20532-9574" value="+495115329574">+49 511 532-9574</a><br>
>><br>
>> _______________________________________________<br>
>> Powered by <a href="http://www.kitware.com" target="_blank">www.kitware.com</a><br>
>><br>
>> Visit other Kitware open-source projects at<br>
>> <a href="http://www.kitware.com/opensource/opensource.html" target="_blank">http://www.kitware.com/opensource/opensource.html</a><br>
>><br>
>> Please keep messages on-topic and check the VTK FAQ at:<br>
>> <a href="http://www.vtk.org/Wiki/VTK_FAQ" target="_blank">http://www.vtk.org/Wiki/VTK_FAQ</a><br>
>><br>
>> Follow this link to subscribe/unsubscribe:<br>
>> <a href="http://www.vtk.org/mailman/listinfo/vtkusers" target="_blank">http://www.vtk.org/mailman/listinfo/vtkusers</a><br>
>><br>
><br>
><br>
><br>
<br>
--<br>
Dr. Roman Grothausmann<br>
<br>
Tomographie und Digitale Bildverarbeitung<br>
Tomography and Digital Image Analysis<br>
<br>
Institut f?r Funktionelle und Angewandte Anatomie, OE 4120<br>
Medizinische Hochschule Hannover<br>
Carl-Neuberg-Str. 1<br>
D-30625 Hannover<br>
<br>
Tel. <a href="tel:%2B49%20511%20532-9574" value="+495115329574">+49 511 532-9574</a><br>
<br>
<br>
------------------------------<br>
<br>
Message: 3<br>
Date: Tue, 22 Apr 2014 09:07:18 -0400<br>
From: Berk Geveci <<a href="mailto:berk.geveci@kitware.com">berk.geveci@kitware.com</a>><br>
To: Amir A <<a href="mailto:amiramir12345@outlook.com">amiramir12345@outlook.com</a>><br>
Cc: "<a href="mailto:paraview@paraview.org">paraview@paraview.org</a>" <<a href="mailto:paraview@paraview.org">paraview@paraview.org</a>><br>
Subject: Re: [Paraview] Fwd: Stream Tracer Scaling<br>
Message-ID:<br>
    <CAE32kpWSP-cvM=Y-crFx4PxaicJaGnxSki3nYa8aTQ=<a href="mailto:USH%2Bgbg@mail.gmail.com">USH+gbg@mail.gmail.com</a>><br>
Content-Type: text/plain; charset="utf-8"<br>
<br>
Hmmm. It certainly should not be much slower. Even in the worst load<br>
balancing case, it should be at most slightly slower. I will take a look.<br>
<br>
-berk<br>
<br>
<br>
On Mon, Apr 21, 2014 at 6:20 PM, Amir A <<a href="mailto:amiramir12345@outlook.com">amiramir12345@outlook.com</a>> wrote:<br>
<br>
> Hi Berk:<br>
><br>
> Thank you for your reply. I am doing the visualization on a distributed<br>
> cluster. And the StreamTracer filter is used with a point source of radius<br>
> 0.1 and 100 seeds.<br>
><br>
> It is surprising that the streamtracer in parallel takes orders of<br>
> magnitude more time than when applied in serial. I tried to first apply D3<br>
> filter and then the streamtracer. That helps a little bit but still the<br>
> time is prohibitively long (about an hour compared to ~5min when done in<br>
> serial). I do not know if I am missing something or this is usual.<br>
><br>
> Here is the visualization that I want to create in parallel (I had to do<br>
> it in serial because of this problem):<br>
> <a href="https://www.dropbox.com/s/r3kkon3khjdpqs6/foam_3.png" target="_blank">https://www.dropbox.com/s/r3kkon3khjdpqs6/foam_3.png</a><br>
><br>
> The original dataset is about 4GB. Â Here is a smaller one (~1GB) with the<br>
> state files:<br>
> <a href="https://www.dropbox.com/s/r6lh3sx2wojfva2/sample.tar.gz" target="_blank">https://www.dropbox.com/s/r6lh3sx2wojfva2/sample.tar.gz</a><br>
><br>
> I would highly appreciate any suggestions.<br>
> -Amir<br>
><br>
> ------------------------------<br>
> From: <a href="mailto:berk.geveci@kitware.com">berk.geveci@kitware.com</a><br>
> Date: Mon, 21 Apr 2014 11:34:25 -0400<br>
> To: <a href="mailto:andy.bauer@kitware.com">andy.bauer@kitware.com</a><br>
> CC: <a href="mailto:paraview@paraview.org">paraview@paraview.org</a><br>
> Subject: Re: [Paraview] Fwd: Stream Tracer Scaling<br>
><br>
><br>
> Actually, if the integration is fairly load balanced across partitions,<br>
> the streamline integration can scale OK. It is highly dependent on how the<br>
> seeds are distributed and if the integration ends up clustering on a few<br>
> processes. Amir:<br>
><br>
> - How big is your seed source? Does it span multiple partitions? How many<br>
> seed points?<br>
> - Do the streamlines stay together or do the move around the domain more<br>
> independently?<br>
><br>
> Â Are you running on a single machine by the way? I have been thinking<br>
> about parallelizing the streamline filter over threads, which should scale<br>
> better on a single machine.<br>
><br>
> Best,<br>
> -berk<br>
><br>
><br>
> _______________________________________________ Powered by www.kitware.comVisit other Kitware open-source projects at<br>
> <a href="http://www.kitware.com/opensource/opensource.html" target="_blank">http://www.kitware.com/opensource/opensource.html</a> Please keep messages<br>
> on-topic and check the ParaView Wiki at: <a href="http://paraview.org/Wiki/ParaViewFollow" target="_blank">http://paraview.org/Wiki/ParaViewFollow</a> this link to subscribe/unsubscribe:<br>
> <a href="http://www.paraview.org/mailman/listinfo/paraview" target="_blank">http://www.paraview.org/mailman/listinfo/paraview</a><br>
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</blockquote></div><br><br clear="all"><div><br></div>-- <br><div dir="ltr">Jack Vant<br>System Engineer - HPC<br>Office of Information Technology<br>Boise State University<br>208-426-4446<br>208-863-0031</div>
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