[yt-users] volume rendering job dies

[Sam Skillman]

Hi Geoffrey,

You also need to modify your script so that all the cores don't try to
write out the image.  Your code should be something like:

# 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))):
    if cam.comm.rank == 0:
        print "starting image %i" % i
        write_bitmap(snapshot, 'Volume/camera_movement_%04i.png' % frame)
    frame += 1


I also just want to note here that the rendering has been used on a 4096^3
Athena dataset in the past, running on somewhere between 128 and 256 cores.
 For the 800^3 you should be fine running on up to the number of cores that
was used to run the simulation. Memory shouldn't be much of an issue, so
just increase core count if you want to go faster.  Also remember to run on
a power of 2 processors -- otherwise there will be idle cores (it should
still work).

Sam

On Tue, Apr 17, 2012 at 3:05 PM, Geoffrey So <gsiisg at gmail.com> wrote:

> 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.
>> !DSPAM:10175,4f8dd938113491945726294!
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