<html><head><meta http-equiv="Content-Type" content="text/html charset=utf-8"></head><body style="word-wrap: break-word; -webkit-nbsp-mode: space; -webkit-line-break: after-white-space;" class=""><div class="">Hi Caroline,</div><div class=""><br class=""></div><div class="">I can’t help with the crash, but the huge slowdown in streamlining in 3.x versus 2.x is a known <a href="https://bitbucket.org/yt_analysis/yt/pull-request/1514/speed-up-amrkdtree-if-grids-exist/diff" class="">issue</a>, which is not yet been fixed unfortunately.</div><br class=""><div><blockquote type="cite" class=""><div class="">On Jul 1, 2015, at 8:35 AM, Caroline Van Borm <<a href="mailto:borm@astro.rug.nl" class="">borm@astro.rug.nl</a>> wrote:</div><br class="Apple-interchange-newline"><div class="">
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<div bgcolor="#FFFFFF" text="#000000" class="">
Hi yt users,<br class="">
<br class="">
I'm having a problem generating streamlines. I'm following the
cookbook script and it works fine for the IsolatedGalaxy dataset,
but not for my own data (also Enzo). The error I'm getting is the
following:<br class="">
<br class="">
<meta http-equiv="content-type" content="text/html; charset=utf-8" class="">
<blockquote class="">
<meta http-equiv="content-type" content="text/html; charset=utf-8" class="">
<pre style="padding: 0px; font-family: monospace; font-size: 14.3000001907349px; border-top-left-radius: 0px; border-top-right-radius: 0px; border-bottom-right-radius: 0px; border-bottom-left-radius: 0px; display: block; margin: 0px; line-height: 17.6033000946045px; word-break: break-all; word-wrap: break-word; white-space: pre-wrap; border: 0px; vertical-align: baseline; font-style: normal; font-variant: normal; font-weight: normal; letter-spacing: normal; orphans: auto; text-align: left; text-indent: 0px; text-transform: none; widows: 1; word-spacing: 0px; -webkit-text-stroke-width: 0px; background-color: rgb(255, 255, 255);" class=""><span class="ansired" style="color: rgb(139, 0, 0);">---------------------------------------------------------------------------</span>
<span class="ansired" style="color: rgb(139, 0, 0);">AttributeError</span> Traceback (most recent call last)
<span class="ansigreen" style="color: rgb(0, 100, 0);"><ipython-input-20-d3a0fa7307d4></span> in <span class="ansicyan" style="color: rgb(70, 130, 180);"><module><span class="ansiblue" style="color: rgb(0, 0, 139);">()</span>
<span class="ansigreen" style="color: rgb(0, 100, 0);"> 5</span> </span>pos <span class="ansiyellow" style="color: rgb(165, 42, 42);">=</span> c<span class="ansiyellow" style="color: rgb(165, 42, 42);">+</span>pos_dx<span class="ansiyellow" style="color: rgb(165, 42, 42);"></span>
<span class="ansigreen" style="color: rgb(0, 100, 0);"> 6</span> <span class="ansiyellow" style="color: rgb(165, 42, 42);"></span>
<span class="ansigreen" style="color: rgb(0, 100, 0);">----> 7<span class="ansiyellow" style="color: rgb(165, 42, 42);"> </span>streamlines</span> <span class="ansiyellow" style="color: rgb(165, 42, 42);">=</span> Streamlines<span class="ansiyellow" style="color: rgb(165, 42, 42);">(</span>pf<span class="ansiyellow" style="color: rgb(165, 42, 42);">,</span>pos<span class="ansiyellow" style="color: rgb(165, 42, 42);">,</span><span class="ansiblue" style="color: rgb(0, 0, 139);">'x-velocity'</span><span class="ansiyellow" style="color: rgb(165, 42, 42);">,</span> <span class="ansiblue" style="color: rgb(0, 0, 139);">'y-velocity'</span><span class="ansiyellow" style="color: rgb(165, 42, 42);">,</span> <span class="ansiblue" style="color: rgb(0, 0, 139);">'z-velocity'</span><span class="ansiyellow" style="color: rgb(165, 42, 42);">,</span> length<span class="ansiyellow" style="color: rgb(165, 42, 42);">=</span><span class="ansicyan" style="color: rgb(70, 130, 180);">1.0</span>
<span cla="" ss="ansiyellow" style="color: rgb(165, 42, 42);" class="">)</span><span class="ansiyellow" style="color: rgb(165, 42, 42);"></span>
<span class="ansigreen" style="color: rgb(0, 100, 0);"> 8</span> <span class="ansired" style="color: rgb(139, 0, 0);">#streamlines = Streamlines(pf,pos,'x-velocity', 'y-velocity', 'z-velocity', length=pf.domain_width[0])</span><span class="ansiyellow" style="color: rgb(165, 42, 42);"></span><span class="ansiyellow" style="color: rgb(165, 42, 42);"></span>
<span class="ansigreen" style="color: rgb(0, 100, 0);"> 9</span> streamlines<span class="ansiyellow" style="color: rgb(165, 42, 42);">.</span>integrate_through_volume<span class="ansiyellow" style="color: rgb(165, 42, 42);">(</span><span class="ansiyellow" style="color: rgb(165, 42, 42);">)</span><span class="ansiyellow" style="color: rgb(165, 42, 42);"></span>
<span class="ansigreen" style="color: rgb(0, 100, 0);">/data/users/borm/YT/yt-x86_64/src/yt-hg/yt/visualization/streamlines.pyc</span> in <span class="ansicyan" style="color: rgb(70, 130, 180);">__init__<span class="ansiblue" style="color: rgb(0, 0, 139);">(self, pf, positions, xfield, yfield, zfield, volume, dx, length, direction, get_magnitude)</span>
<span class="ansigreen" style="color: rgb(0, 100, 0);"> 102</span> volume = AMRKDTree(self.pf, fields=[self.xfield,self.yfield,self.zfield],
<span class="ansigreen" style="color: rgb(0, 100, 0);"> 103</span> log_fields=[False,False,False])
<span class="ansigreen" style="color: rgb(0, 100, 0);">--> 104<span class="ansiyellow" style="color: rgb(165, 42, 42);"> </span>volume</span><span class="ansiyellow" style="color: rgb(165, 42, 42);">.</span></span>join_parallel_trees<span class="ansiyellow" style="color: rgb(165, 42, 42);">(</span><span class="ansiyellow" style="color: rgb(165, 42, 42);">)</span><span class="ansiyellow" style="color: rgb(165, 42, 42);"></span>
<span class="ansigreen" style="color: rgb(0, 100, 0);"> 105</span> self<span class="ansiyellow" style="color: rgb(165, 42, 42);">.</span>volume <span class="ansiyellow" style="color: rgb(165, 42, 42);">=</span> volume<span class="ansiyellow" style="color: rgb(165, 42, 42);"></span>
<span class="ansigreen" style="color: rgb(0, 100, 0);"> 106</span> <span class="ansigreen" style="color: rgb(0, 100, 0);">if</span> dx <span class="ansigreen" style="color: rgb(0, 100, 0);">is</span> None<span class="ansiyellow" style="color: rgb(165, 42, 42);">:</span><span class="ansiyellow" style="color: rgb(165, 42, 42);"></span>
<span class="ansigreen" style="color: rgb(0, 100, 0);">/data/users/borm/YT/yt-x86_64/src/yt-hg/yt/utilities/amr_kdtree/amr_kdtree.pyc</span> in <span class="ansicyan" style="color: rgb(70, 130, 180);">join_parallel_trees<span class="ansiblue" style="color: rgb(0, 0, 139);">(self)</span>
<span class="ansigreen" style="color: rgb(0, 100, 0);"> 456</span> </span>nid <span class="ansiyellow" style="color: rgb(165, 42, 42);">=</span> np<span class="ansiyellow" style="color: rgb(165, 42, 42);">.</span>array<span class="ansiyellow" style="color: rgb(165, 42, 42);">(</span>nid<span class="ansiyellow" style="color: rgb(165, 42, 42);">)</span><span class="ansiyellow" style="color: rgb(165, 42, 42);"></span>
<span class="ansigreen" style="color: rgb(0, 100, 0);"> 457</span> new_tree = self.rebuild_tree_from_array(nid, pid, lid,
<span class="ansigreen" style="color: rgb(0, 100, 0);">--> 458<span class="ansiyellow" style="color: rgb(165, 42, 42);"> rid, les, res, gid, splitdims, splitposs)
</span><span class="ansigreen" style="color: rgb(0, 100, 0);"> 459</span> <span class="ansiyellow" style="color: rgb(165, 42, 42);"></span></span>
<span class="ansigreen" style="color: rgb(0, 100, 0);"> 460</span> <span class="ansigreen" style="color: rgb(0, 100, 0);">def</span> get_node_arrays<span class="ansiyellow" style="color: rgb(165, 42, 42);">(</span>self<span class="ansiyellow" style="color: rgb(165, 42, 42);">)</span><span class="ansiyellow" style="color: rgb(165, 42, 42);">:</span><span class="ansiyellow" style="color: rgb(165, 42, 42);"></span>
<span class="ansigreen" style="color: rgb(0, 100, 0);">/data/users/borm/YT/yt-x86_64/src/yt-hg/yt/utilities/amr_kdtree/amr_kdtree.pyc</span> in <span class="ansicyan" style="color: rgb(70, 130, 180);">rebuild_tree_from_array<span class="ansiblue" style="color: rgb(0, 0, 139);">(self, nids, pids, lids, rids, les, res, gids, splitdims, splitposs)</span>
<span class="ansigreen" style="color: rgb(0, 100, 0);"> 505</span> </span>N <span class="ansiyellow" style="color: rgb(165, 42, 42);">=</span> nids<span class="ansiyellow" style="color: rgb(165, 42, 42);">.</span>shape<span class="ansiyellow" style="color: rgb(165, 42, 42);">[</span><span class="ansicyan" style="color: rgb(70, 130, 180);">0</span><span class="ansiyellow" style="color: rgb(165, 42, 42);">]</span><span class="ansiyellow" style="color: rgb(165, 42, 42);"></span>
<span class="ansigreen" style="color: rgb(0, 100, 0);"> 506</span> <span class="ansigreen" style="color: rgb(0, 100, 0);">for</span> i <span class="ansigreen" style="color: rgb(0, 100, 0);">in</span> xrange<span class="ansiyellow" style="color: rgb(165, 42, 42);">(</span>N<span class="ansiyellow" style="color: rgb(165, 42, 42);">)</span><span class="ansiyellow" style="color: rgb(165, 42, 42);">:</span><span class="ansiyellow" style="color: rgb(165, 42, 42);"></span>
<span class="ansigreen" style="color: rgb(0, 100, 0);">--> 507<span class="ansiyellow" style="color: rgb(165, 42, 42);"> </span>n</span> <span class="ansiyellow" style="color: rgb(165, 42, 42);">=</span> self<span class="ansiyellow" style="color: rgb(165, 42, 42);">.</span>get_node<span class="ansiyellow" style="color: rgb(165, 42, 42);">(</span>nids<span class="ansiyellow" style="color: rgb(165, 42, 42);">[</span>i<span class="ansiyellow" style="color: rgb(165, 42, 42);">]</span><span class="ansiyellow" style="color: rgb(165, 42, 42);">)</span><span class="ansiyellow" style="color: rgb(165, 42, 42);"></span>
<span class="ansigreen" style="color: rgb(0, 100, 0);"> 508</span> n<span class="ansiyellow" style="color: rgb(165, 42, 42);">.</span>set_left_edge<span class="ansiyellow" style="color: rgb(165, 42, 42);">(</span>les<span class="ansiyellow" style="color: rgb(165, 42, 42);">[</span>i<span class="ansiyellow" style="color: rgb(165, 42, 42);">]</span><span class="ansiyellow" style="color: rgb(165, 42, 42);">)</span><span class="ansiyellow" style="color: rgb(165, 42, 42);"></span>
<span class="ansigreen" style="color: rgb(0, 100, 0);"> 509</span> n<span class="ansiyellow" style="color: rgb(165, 42, 42);">.</span>set_right_edge<span class="ansiyellow" style="color: rgb(165, 42, 42);">(</span>res<span class="ansiyellow" style="color: rgb(165, 42, 42);">[</span>i<span class="ansiyellow" style="color: rgb(165, 42, 42);">]</span><span class="ansiyellow" style="color: rgb(165, 42, 42);">)</span><span class="ansiyellow" style="color: rgb(165, 42, 42);"></span>
<span class="ansigreen" style="color: rgb(0, 100, 0);">/data/users/borm/YT/yt-x86_64/src/yt-hg/yt/utilities/amr_kdtree/amr_kdtree.pyc</span> in <span class="ansicyan" style="color: rgb(70, 130, 180);">get_node<span class="ansiblue" style="color: rgb(0, 0, 139);">(self, nodeid)</span>
<span class="ansigreen" style="color: rgb(0, 100, 0);"> 212</span> <span class="ansigreen" style="color: rgb(0, 100, 0);">for</span> </span>depth <span class="ansigreen" style="color: rgb(0, 100, 0);">in</span> range<span class="ansiyellow" style="color: rgb(165, 42, 42);">(</span><span class="ansicyan" style="color: rgb(70, 130, 180);">1</span><span class="ansiyellow" style="color: rgb(165, 42, 42);">,</span>len<span class="ansiyellow" style="color: rgb(165, 42, 42);">(</span>path<span class="ansiyellow" style="color: rgb(165, 42, 42);">)</span><span class="ansiyellow" style="color: rgb(165, 42, 42);">)</span><span class="ansiyellow" style="color: rgb(165, 42, 42);">:</span><span class="ansiyellow" style="color: rgb(165, 42, 42);"></span>
<span class="ansigreen" style="color: rgb(0, 100, 0);"> 213</span> <span class="ansigreen" style="color: rgb(0, 100, 0);">if</span> path<span class="ansiyellow" style="color: rgb(165, 42, 42);">[</span>depth<span class="ansiyellow" style="color: rgb(165, 42, 42);">]</span> <span class="ansiyellow" style="color: rgb(165, 42, 42);">==</span> <span class="ansiblue" style="color: rgb(0, 0, 139);">'0'</span><span class="ansiyellow" style="color: rgb(165, 42, 42);">:</span><span class="ansiyellow" style="color: rgb(165, 42, 42);"></span>
<span class="ansigreen" style="color: rgb(0, 100, 0);">--> 214<span class="ansiyellow" style="color: rgb(165, 42, 42);"> </span>temp</span> <span class="ansiyellow" style="color: rgb(165, 42, 42);">=</span> temp<span class="ansiyellow" style="color: rgb(165, 42, 42);">.</span>left<span class="ansiyellow" style="color: rgb(165, 42, 42);"></span>
<span class="ansigreen" style="color: rgb(0, 100, 0);"> 215</span> <span class="ansigreen" style="color: rgb(0, 100, 0);">else</span><span class="ansiyellow" style="color: rgb(165, 42, 42);">:</span><span class="ansiyellow" style="color: rgb(165, 42, 42);"></span>
<span class="ansigreen" style="color: rgb(0, 100, 0);"> 216</span> temp <span class="ansiyellow" style="color: rgb(165, 42, 42);">=</span> temp<span class="ansiyellow" style="color: rgb(165, 42, 42);">.</span>right<span class="ansiyellow" style="color: rgb(165, 42, 42);"></span>
<span class="ansired" style="color: rgb(139, 0, 0);">AttributeError</span>: 'NoneType' object has no attribute 'left'
</pre>
</blockquote>
Though sometimes with a different dataset I also get <br class="">
<blockquote class="">
<meta http-equiv="content-type" content="text/html; charset=utf-8" class="">
<pre style="padding: 0px; font-family: monospace; font-size: 14.3000001907349px; border-top-left-radius: 0px; border-top-right-radius: 0px; border-bottom-right-radius: 0px; border-bottom-left-radius: 0px; display: block; margin: 0px; line-height: 17.6033000946045px; word-break: break-all; word-wrap: break-word; white-space: pre-wrap; border: 0px; vertical-align: baseline; font-style: normal; font-variant: normal; font-weight: normal; letter-spacing: normal; orphans: auto; text-align: left; text-indent: 0px; text-transform: none; widows: 1; word-spacing: 0px; -webkit-text-stroke-width: 0px; background-color: rgb(255, 255, 255);" class=""><span class="ansired" style="color: rgb(139, 0, 0);">AttributeError</span>: 'NoneType' object has no attribute 'right'
</pre>
</blockquote>
I'm using yt 2.6, but I've also tried with yt 3.1 and I get the same
error there (only it takes much, much longer before it crashes?) My
datasets do not have particles, not sure if that may be relevant.<br class="">
<br class="">
Any help is much appreciated!<br class="">
<br class="">
Cheers,<br class="">
Caroline<br class="">
<pre style="padding: 0px; font-family: monospace; font-size: 14.3000001907349px; border-top-left-radius: 0px; border-top-right-radius: 0px; border-bottom-right-radius: 0px; border-bottom-left-radius: 0px; display: block; margin: 0px; line-height: 17.6033000946045px; word-break: break-all; word-wrap: break-word; white-space: pre-wrap; border: 0px; vertical-align: baseline; font-style: normal; font-variant: normal; font-weight: normal; letter-spacing: normal; orphans: auto; text-align: left; text-indent: 0px; text-transform: none; widows: 1; word-spacing: 0px; -webkit-text-stroke-width: 0px; background-color: rgb(255, 255, 255);" class=""></pre>
<br class="">
<br class="">
<br class="Apple-interchange-newline">
</div>
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<div class="">--</div><div class="">Mark Krumholz</div>
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