Update (07/28/2015) -- Marissa

Shape

  • Shape is now installed on all local machines! (Grass, Clover, Bamboo). It is installed in /opt/Shape/. In order for it to work, now all the machines have Java as well.
  • Shape has a difficult time rendering large ASCII files.

Recall how Martin's data looks

https://astrobear.pas.rochester.edu/trac/raw-attachment/blog/madams07282015/Screenshot%20from%202015-07-28%2011%3A54%3A31.png https://astrobear.pas.rochester.edu/trac/raw-attachment/blog/madams06042015/shape22_Image__00000.png
3D Module Render Module

Martin's ASCII file has 4,803 lines. Note that the 3D Module illustrates if you have properly imported the simulation into Shape, where as the Render module is the actual emission map of the simulation. In the latter module, one has to go through a rendering process. This generally took a few seconds for Martin's data.

Baowei & Bruce's Data

Here is how it looks Visit:

https://astrobear.pas.rochester.edu/trac/raw-attachment/blog/madams07282015/2Dslice.png

In the 3D Module in Shape:

https://astrobear.pas.rochester.edu/trac/raw-attachment/blog/madams07282015/Screenshot%20from%202015-07-28%2011%3A49%3A15.png
Screen Shot 1

Now rotated to get another perspective:

https://astrobear.pas.rochester.edu/trac/raw-attachment/blog/madams07282015/Screenshot%20from%202015-07-28%2011%3A50%3A18.png
Screen Shot 2

Notes:

  • The Right view in Screen Shot 1 looks like what might be the face of a box.
  • However from the other views in the 3D Module, we can see that the box is not filled in. Wouldn't we expect to see something that does not look so "flat."
  • For instance, Martin's data in the 3D Module sort of looks like the general shape that we would expect it to look like in emission map form.
  • Perhaps the ambient is too strong?
  • Perhaps Shape has a hard time loading in all of the rows?

The fact that we see *something* in the 3D Module that is not a mesh object that you import the data on is a good sign that I have imported the data correctly into Shape.

So at this point I would go on to the Render module to get the emission map. However when I fix my parameters and I am ready to visualize the simulation, Shape has a hard time rendering such a large ASCII file. So I cannot verify if there is a comparable view of the simulation to how it looks in Visit. If Shape were able to render this simulation, I would rotate it to see if there is a view that yields comparable results. However I cannot do that.

The ASCII file that Baowei gave me is in the format px,py,pz,n,vx,vy,vz,T, i.e. position components, density, velocity components, and temperature. In Martin's simulation I did not use temperature. Although when I import the file with or without the temperature column, it still looks the same. So I do not think there is anything wrong with how I am importing it into Shape.

So now let's take a look at the parameters of the simulation (thanks to Baowei):

nDim     = 3
GmX      = 64,64,64
MaxLevel = 0
LastStaticLevel = -1
GxBounds = -32d0,0d0,-32d0,32d0,64d0,32d0

So we have a 3-dimensional simulation, which is good. MaxLevel=0 will help. However it seems that the GmX and the GxBounds are kind of big. We'd have 643 = 262144, which is close to the number of lines that we have in the file: 254727. Keeping the right proportions with a smaller GmX, say 163 = 4,096. Seems more reasonable.

Wires

  • Visualizing on BH2 for the wire simulations seems to be a roadblock.
    • Jonathan suggested using vnc_start -t 480 --mem 60gb however I wait for my job to start for a long time. I have never successfully gotten it to get me onto the node. Maybe other people are using it?
    • debug queue on BH2 ('interactive -p debug -N 32 -t 60'): Cannot do contour plots of any frames. It'll register the object you want to visualize in red text. However for that same frame, I can take a slice and visualize it fine. However say I want to visualize the next frame as a slice, then that frame also has the dreaded red text of death. However if I submit a new job and visualize that frame from the get-go, it works. However there is a similar story for the next frame, etc.
    • Visit with Clover, Grass, Bamboo: with any of the local machines seems to be no good.
    • The maximum space for an AMR=2 chombo that I am trying to visualize is ~50 GB, for one with AMR=1, it is 13GB. The same story of visualization woes holds for both levels of AMR…
    • I don't think the simulation is corrupt as if it was, then I couldn't visualize any frame after I submit a new visualization job.

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