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!<div><br></div>
<div>From</div><div>G.S.<br><br><div class="gmail_quote">On Tue, Apr 17, 2012 at 2:03 PM, Nathan Goldbaum <span dir="ltr"><<a href="mailto:goldbaum@ucolick.org">goldbaum@ucolick.org</a>></span> wrote:<br><blockquote class="gmail_quote" style="margin:0 0 0 .8ex;border-left:1px #ccc solid;padding-left:1ex">
<div style="word-wrap:break-word"><div>Hi Geoffrey,</div><div><br></div><div>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:</div>
<div><div><span style="white-space:pre-wrap"> </span></div></div><div><div style="margin-top:0px;margin-right:0px;margin-bottom:0px;margin-left:0px;font:normal normal normal 12px/normal Courier">import gc</div><div style="margin-top:0px;margin-right:0px;margin-bottom:0px;margin-left:0px;font:normal normal normal 12px/normal Courier;min-height:14px">
<br></div><div style="margin-top:0px;margin-right:0px;margin-bottom:0px;margin-left:0px;font:normal normal normal 12px/normal Courier">… doing stuff … </div><div style="margin-top:0px;margin-right:0px;margin-bottom:0px;margin-left:0px;font:normal normal normal 12px/normal Courier;min-height:14px">
<br></div><div style="margin-top:0px;margin-right:0px;margin-bottom:0px;margin-left:0px;font:normal normal normal 12px/normal Courier"># Do a rotation over 30 frames</div><div style="margin-top:0px;margin-right:0px;margin-bottom:0px;margin-left:0px;font:normal normal normal 12px/normal Courier">
for i, snapshot in enumerate(cam.rotation(2*na.pi, 36, rot_vector=(0.0,0.0,1.0))):</div><div style="margin-top:0px;margin-right:0px;margin-bottom:0px;margin-left:0px;font:normal normal normal 12px/normal Courier"> print "starting image %i" % i</div>
<div style="margin-top:0px;margin-right:0px;margin-bottom:0px;margin-left:0px;font:normal normal normal 12px/normal Courier"> write_bitmap(snapshot, 'Volume/camera_movement_%04i.png' % frame)</div><div style="margin-top:0px;margin-right:0px;margin-bottom:0px;margin-left:0px;font:normal normal normal 12px/normal Courier">
frame += 1</div><div style="margin-top:0px;margin-right:0px;margin-bottom:0px;margin-left:0px;font:normal normal normal 12px/normal Courier"> gc.collect()</div></div><div style="margin-top:0px;margin-right:0px;margin-bottom:0px;margin-left:0px;font:normal normal normal 12px/normal Courier">
<br></div><div style="margin-top:0px;margin-right:0px;margin-bottom:0px;margin-left:0px;font:normal normal normal 12px/normal Courier"><span style="font-family:Helvetica;font-size:medium">Hope that helps!</span></div><div style="margin-top:0px;margin-right:0px;margin-bottom:0px;margin-left:0px;font:normal normal normal 12px/normal Courier">
<span style="font-family:Helvetica;font-size:medium"><br></span></div><div style="margin-top:0px;margin-right:0px;margin-bottom:0px;margin-left:0px;font:normal normal normal 12px/normal Courier"><span style="font-family:Helvetica;font-size:medium">Nathan Goldbaum</span></div>
<div><div style="word-wrap:break-word"><div style="word-wrap:break-word"><span style="text-indent:0px;letter-spacing:normal;font-variant:normal;font-style:normal;font-weight:normal;line-height:normal;border-collapse:separate;text-transform:none;font-size:medium;white-space:normal;font-family:Helvetica;word-spacing:0px"><div style="word-wrap:break-word">
Graduate Student<br>Astronomy & Astrophysics, UCSC<br><a href="mailto:goldbaum@ucolick.org" target="_blank">goldbaum@ucolick.org</a><br><a href="http://www.ucolick.org/~goldbaum" target="_blank">http://www.ucolick.org/~goldbaum</a></div>
</span></div></div>
</div>
<br><div><div><div class="h5"><div>On Apr 17, 2012, at 1:57 PM, Geoffrey So wrote:</div><br></div></div><blockquote type="cite"><div><div class="h5">Hi all,<div><br></div><div>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:</div>
<div><br></div>
<div><div>yt : [INFO ] 2012-04-15 16:15:22,264 Warning: no_ghost is currently True (default). This may lead to artifacts at grid boundaries.</div><div>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)</div>
<div>yt : [INFO ] 2012-04-15 16:15:33,309 Warning: no_ghost is currently True (default). This may lead to artifacts at grid boundaries.</div><div>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)</div>
<div>yt : [INFO ] 2012-04-15 16:15:47,135 Warning: no_ghost is currently True (default). This may lead to artifacts at grid boundaries.</div><div>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)</div>
<div>yt : [INFO ] 2012-04-15 16:15:49,841 Warning: no_ghost is currently True (default). This may lead to artifacts at grid boundaries.</div></div><div><br></div><div>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?</div>
<div><br></div><div>The script works on my tiny test problem of 64 cube:</div><div><div><a href="http://paste.yt-project.org/show/2289/" target="_blank">http://paste.yt-project.org/show/2289/</a></div></div><div><br></div>
<div>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.</div>
<div><br></div><div>From</div><div>G.S.</div></div></div>
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