[yt-users] volume rendering job dies

[Geoffrey So]

Matt's right on the spot went and checked the script, it's missing the
"--parallel", must have copied an old line of the submission script and ran
it serial.  Going to try this with less nodes!

From
G.S.

On Tue, Apr 17, 2012 at 2:03 PM, Nathan Goldbaum <goldbaum at ucolick.org>wrote:

> Hi Geoffrey,
>
> I'm not sure why your run is crashing but I've solved similar problems in
> the past by directly calling the garbage collector at the end of the loop.
>  Your loop should look like:
> import gc
>
> … doing stuff …
>
> # Do a rotation over 30 frames
> for i, snapshot in enumerate(cam.rotation(2*na.pi, 36,
> rot_vector=(0.0,0.0,1.0))):
>     print "starting image %i" % i
>     write_bitmap(snapshot, 'Volume/camera_movement_%04i.png' % frame)
>     frame += 1
>     gc.collect()
>
> Hope that helps!
>
> Nathan Goldbaum
> Graduate Student
> Astronomy & Astrophysics, UCSC
> goldbaum at ucolick.org
> http://www.ucolick.org/~goldbaum
>
> On Apr 17, 2012, at 1:57 PM, Geoffrey So wrote:
>
> Hi all,
>
> I'm starting to do some volume rendering of my 800 cube simulation, but
> the job in the super computer just dies without any kind of error in the
> logs.  The last few lines are:
>
> yt : [INFO     ] 2012-04-15 16:15:22,264 Warning: no_ghost is currently
> True (default). This may lead to artifacts at grid boundaries.
> yt : [INFO     ] 2012-04-15 16:15:33,307 Max Value is 2.46548e-24 at
> 0.9743750000000000 0.0193750000000000 0.1781250000000000 in grid
> EnzoGrid_0442 at level 0 (79, 15, 42)
> yt : [INFO     ] 2012-04-15 16:15:33,309 Warning: no_ghost is currently
> True (default). This may lead to artifacts at grid boundaries.
> yt : [INFO     ] 2012-04-15 16:15:47,133 Max Value is 2.46548e-24 at
> 0.9743750000000000 0.0193750000000000 0.1781250000000000 in grid
> EnzoGrid_0442 at level 0 (79, 15, 42)
> yt : [INFO     ] 2012-04-15 16:15:47,135 Warning: no_ghost is currently
> True (default). This may lead to artifacts at grid boundaries.
> yt : [INFO     ] 2012-04-15 16:15:49,839 Max Value is 2.46548e-24 at
> 0.9743750000000000 0.0193750000000000 0.1781250000000000 in grid
> EnzoGrid_0442 at level 0 (79, 15, 42)
> yt : [INFO     ] 2012-04-15 16:15:49,841 Warning: no_ghost is currently
> True (default). This may lead to artifacts at grid boundaries.
>
> I'm wondering if it is again an memory issue.  I ran this job with 16
> nodes with 16 cores per node and 4GB per core.  This setup is enough memory
> to do the halo finding, I'm wondering what the memory requirements is for
> volume rendering, and what's the biggest volume people have done up to date?
>
> The script works on my tiny test problem of 64 cube:
> http://paste.yt-project.org/show/2289/
>
> If this isn't a problem people have with rendering larger volumes than
> mine, then it might be a machine issue.  I haven't moved the data to
> another super computer, but will try that next if others have done larger
> volume rendering with no problems at all.
>
> From
> G.S.
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