[Paraview] Paraview and Multicore
Guido Staub
gstaub at udec.cl
Thu May 20 08:31:50 EDT 2010
Andy,
thanks for your suggestion, however it does not work, I guess what
you have mentioned about that Paraview was not designed as a
parallel grid generation tool is the crucial point here. I will try to
find a solution for my problem without falling back to serial
processing.
Guido
Am Thu, 20 May 2010 10:55:21 -0400 schrieb Andy Bauer
<andy.bauer at kitware.com>:
> If I remember correctly, after you partition your points, you try to
> create a grid with the Delaunay2D filter. It looks like the
> Delaunay2D filter isn't a "true" parallel filter meaning that each
> process does the triangulation on all of the points that are assigned
> to it but doesn't take into account creating cells between close
> points that are on different processes. The best suggestion I have
> is to try the following: 1) use D3 to partition your points
> 2) triangulate on each process using Delaunay2D
> 3) extract the edges on each process using Extract Edges
> 4) try the Delaunay2D to stitch these edges together (this may not
> work as desired)
> 5) append the datasets/polydatas together using the Append Datasets
> filter
>
> I have no idea whether or not this will work for you. The main
> problem is that VTK/ParaView wasn't designed to be used as a parallel
> grid generation tool.
>
> Andy
>
> On Wed, May 19, 2010 at 5:49 AM, Guido Staub <gstaub at udec.cl> wrote:
>
> > So, with D3 things run faster now. Solved as well the mentioned
> > problem, it was due to not scaling the z values. However, maybe a
> > logical behaviour, the result of the triangulation now consists of
> > four tiles. Anybody knows how to for example connect them? I have
> > attached a screenshot showing the separation (vertical lines) of the
> > tiles.
> >
> > Guido
> >
> > Am Tue, 18 May 2010 17:17:06 +0000 schrieb Guido Staub
> > <gstaub at udec.cl>:
> >
> > > Using Process ID Scalars results in an Data Array ProcessId which
> > > in case of np 3 ranges from 0 to 2 (and from 0 to 3 in case of np
> > > 4). I have selected colorBy ProcessID to see if the input is well
> > > balanced or not, unfortunately all the points have the same
> > > color. So I conclude that the data is not well balanced, right?
> > >
> > > If I apply the D3 filter I almost see the same results. The only
> > > difference I have noticed is that there is no new Data Array.
> > >
> > > Delaunay 2D is now about three times faster after I applied D3
> > > filter. However I do not like the resulting triangulation, seems
> > > like some isosurfaces have been calculted.
> > >
> > > Guido
> > >
> > > Am Thu, 13
> > > May 2010 20:48:11 -0400 schrieb Andy Bauer
> > > <andy.bauer at kitware.com>:
> > >
> > > > Process Id Scalars doesn't do any load balancing, it just shows
> > > > what cells are assigned to what process. You can try the D3
> > > > filter to do actual load-balancing (your reader may already be
> > > > doing this though in which case you would see the same results
> > > > from a Process Id Scalars filter used after the D3 filter).
> > > > I'm not that familiar with the internals of Delauney2D for
> > > > distributed points but it's quite possible that for the set of
> > > > points you have that the partitioning is not appropriate. As
> > > > Ken said, using the Process Id Scalars to see if the input is
> > > > fairly well balanced.
> > > >
> > > > Andy
> > > >
> > > > On Thu, May 13, 2010 at 3:33 PM, Guido Staub <gstaub at udec.cl>
> > > > wrote:
> > > >
> > > > > Process Id Scalars didn't do the trick, still no performance
> > > > > gain with Delaunay 2D.
> > > > > My data is stored in a h5 file which gets loaded through a
> > > > > xdmf file. After running the Process Id Scalars filter I do
> > > > > not see any changes in the distribution of the data. However
> > > > > I guess that they are already "evenly distributed" by default.
> > > > >
> > > > > So maybe exporting the file to an other format will do it or
> > > > > is there a problem with the Delaunay implementation in
> > > > > general when running in parallel?
> > > > >
> > > > > Guido
> > > > >
> > > > > Am Thu, 13 May 2010 15:08:04
> > > > > -0600 schrieb "Moreland, Kenneth" <kmorel at sandia.gov>:
> > > > >
> > > > > > Ah, I see. It sounds like your data is not balanced. Many
> > > > > > of the "non parallel" file formats will do something stupid
> > > > > > when loading data in parallel. For example, they might load
> > > > > > everything on process 0 or load everything everywhere. (And
> > > > > > now that I think about it, the Delaunay filter may have
> > > > > > trouble in parallel.)
> > > > > >
> > > > > > Try running the "Process Id Scalars" filter on your data.
> > > > > > Do the points look evenly distributed?
> > > > > >
> > > > > > -Ken
> > > > > >
> > > > > >
> > > > > > On 5/13/10 10:17 AM, "Guido Staub" <gstaub at udec.cl> wrote:
> > > > > >
> > > > > > Well if I start pvserver by mpirun -np 4 pvserver I have 3
> > > > > > cores running at almost 100%. Now I connect to the server
> > > > > > and start a Delaunay 2D calculation on one of my datasets.
> > > > > > As a result all of the 4 cores are showing 100%. However I
> > > > > > assume that there is only one core doing the job, because
> > > > > > on the one hand calculation is really slow. I have done
> > > > > > similar processing on an other PC (an outdated one) and
> > > > > > there is no significant performance advantage as one would
> > > > > > expect. And on the other hand, running pvserver with e.g.
> > > > > > -np 2 results in 100% for 2 CPUs when starting the Delaunay
> > > > > > 2D calc (1 core at 100% when cpu is idle).
> > > > > >
> > > > > > Guido
> > > > > >
> > > > > >
> > > > > > Am Thu, 13 May 2010
> > > > > > 12:39:43 -0600 schrieb "Moreland, Kenneth"
> > > > > > <kmorel at sandia.gov>:
> > > > > >
> > > > > > > I am afraid I simply don't understand the question. You
> > > > > > > said in (1) that you have three cores running at 100%.
> > > > > > > Then in (2) you said that you only have one core
> > > > > > > running. Is it happening when you start the client,
> > > > > > > connect the client to the server, launch the server from
> > > > > > > the client, or something else? Is something running or
> > > > > > > is the client sitting idle waiting for the user?
> > > > > > >
> > > > > > > -Ken
> > > > > > >
> > > > > > >
> > > > > > > On 5/13/10 8:15 AM, "Guido Staub" <gstaub at udec.cl> wrote:
> > > > > > >
> > > > > > > Thanks Ken, but I have already read this thread,
> > > > > > > therefore I started the client process anyway without
> > > > > > > taking care of cpu usage for now.
> > > > > > >
> > > > > > > However my second question still keeps me busy. Isn't it
> > > > > > > possible to use all 4 cores?
> > > > > > >
> > > > > > > Guido
> > > > > > >
> > > > > > > Am Thu, 13 May 2010
> > > > > > > 10:29:13 -0600 schrieb "Moreland, Kenneth"
> > > > > > > <kmorel at sandia.gov>:
> > > > > > >
> > > > > > > > The question about why the pvserver processes are
> > > > > > > > always at 100% CPU comes up frequently on the mailing
> > > > > > > > list (such as
> > > > > > > >
> > http://www.paraview.org/pipermail/paraview/2008-December/010338.html
> > > > > ).
> > > > > > > > I've added some information to the Wiki about it to
> > > > > > > > provide an explanation:
> > > > > > > >
> > > > >
> > http://www.paraview.org/Wiki/Setting_up_a_ParaView_Server#Server_processes_always_have_100.25_CPU_usage
> > > > > > > >
> > > > > > > > -Ken
> > > > > > > >
> > > > > > > >
> > > > > > > > On 5/13/10 5:06 AM, "Guido Staub" <gstaub at udec.cl>
> > > > > > > > wrote:
> > > > > > > >
> > > > > > > > Hi all,
> > > > > > > >
> > > > > > > > I have succesfully compiled Paraview with MPI support
> > > > > > > > on my Workstation (Quad Core). I have read that
> > > > > > > > paraview runs serial, pvserver parallel, so I started
> > > > > > > > the server by mpirun -np 4 pvserver and connected
> > > > > > > > through X. Everything seems to work fine.
> > > > > > > >
> > > > > > > > But there are two strange behaviours I have noticed:
> > > > > > > >
> > > > > > > > 1. CPU usage on workstation is almost 100% on three of
> > > > > > > > the four cores although no client is connected (when I
> > > > > > > > type mpirun -np 3 pvserver there are 2 out of 4 running
> > > > > > > > at 100%; with -np 2 only 1). I have noticed this using
> > > > > > > > MPICH2 and OpenMPI.
> > > > > > > >
> > > > > > > > 2. When I now start a client process the server uses
> > > > > > > > only one core (-np 4/3/2/1). Why?
> > > > > > > >
> > > > > > > > Does MPI not work on multicore systems as on
> > > > > > > > multiprocessor systems or is this a Paraview issue?
> > > > > > > >
> > > > > > > > Thanks,
> > > > > > > > Guido
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> > > > > > > >
> > > > > > > >
> > > > > > > > **** Kenneth Moreland
> > > > > > > > *** Sandia National Laboratories
> > > > > > > > ***********
> > > > > > > > *** *** *** email: kmorel at sandia.gov
> > > > > > > > ** *** ** phone: (505) 844-8919
> > > > > > > > *** web:
> > > > > > > > http://www.cs.unm.edu/~kmorel<http://www.cs.unm.edu/%7Ekmorel>
> > <http://www.cs.unm.edu/%7Ekmorel>
> > > > > > > >
> > > > > > >
> > > > > > >
> > > > > > >
> > > > > > >
> > > > > > > **** Kenneth Moreland
> > > > > > > *** Sandia National Laboratories
> > > > > > > ***********
> > > > > > > *** *** *** email: kmorel at sandia.gov
> > > > > > > ** *** ** phone: (505) 844-8919
> > > > > > > *** web:
> > > > > > > http://www.cs.unm.edu/~kmorel
> > > > > > > <http://www.cs.unm.edu/%7Ekmorel><
> > http://www.cs.unm.edu/%7Ekmorel>
> > > > > > >
> > > > > >
> > > > > >
> > > > > >
> > > > > >
> > > > > > **** Kenneth Moreland
> > > > > > *** Sandia National Laboratories
> > > > > > ***********
> > > > > > *** *** *** email: kmorel at sandia.gov
> > > > > > ** *** ** phone: (505) 844-8919
> > > > > > *** web:
> > > > > > http://www.cs.unm.edu/~kmorel
> > > > > > <http://www.cs.unm.edu/%7Ekmorel><
> > http://www.cs.unm.edu/%7Ekmorel>
> > > > > >
> > > > > _______________________________________________
> > > > > 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
> > > > >
> > > > > Follow this link to subscribe/unsubscribe:
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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
> > >
> > > Follow this link to subscribe/unsubscribe:
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