<meta http-equiv="Content-Type" content="text/html; charset=utf-8"><div dir="ltr">I get the same error over here. I think it's unrelated to the other error. The relevant portion of the C stack trace is here:<div><br></div><div><div>Thread 0 Crashed:: Dispatch queue: com.apple.main-thread</div><div>0 libsystem_kernel.dylib <span style="white-space:pre-wrap"> </span>0x00007fff8b615286 __pthread_kill + 10</div><div>1 libsystem_c.dylib <span style="white-space:pre-wrap"> </span>0x00007fff8bc2a9ab abort + 129</div><div>2 libsystem_malloc.dylib <span style="white-space:pre-wrap"> </span>0x00007fff915d5fe2 szone_error + 625</div><div>3 libsystem_malloc.dylib <span style="white-space:pre-wrap"> </span>0x00007fff915cf374 small_free_list_remove_ptr + 154</div><div>4 libsystem_malloc.dylib <span style="white-space:pre-wrap"> </span>0x00007fff915cac3f szone_free_definite_size + 1856</div><div>5 multiarray.so <span style="white-space:pre-wrap"> </span>0x00000001044c2d16 npy_free_cache + 70</div><div>6 multiarray.so <span style="white-space:pre-wrap"> </span>0x00000001044c6ed6 array_dealloc + 182</div><div>7 selection_routines.so <span style="white-space:pre-wrap"> </span>0x00000001063ffe34 __pyx_pw_2yt_8geometry_18selection_routines_13SliceSelector_3fill_mask + 8804 (selection_routines.c:19749)</div><div><br></div><div>Line 19749 of selection_routines.c corresponds to line 1158 in selection_routines.pyx, which is the place where the fill_mask member variable of the SliceSelector extension type gets defined.</div></div><div><br></div><div>Unfortunately, I have no idea how to debug this from here...</div><div><br></div><div>-Nathan</div><div class="gmail_extra"><br><div class="gmail_quote">On Wed, Dec 23, 2015 at 4:57 PM, Brian O'Shea <span dir="ltr"><<a href="mailto:bwoshea@gmail.com" target="_blank">bwoshea@gmail.com</a>></span> wrote:<br><blockquote class="gmail_quote" style="margin:0 0 0 .8ex;border-left:1px #ccc solid;padding-left:1ex"><div dir="ltr">Actually, interesting followup here - I have to take it back. When I do a projection plot:<div><br></div><div> yt.ProjectionPlot(ds,'x',("gas", "temperature"),center=[0.0,0.0,0.0],width=(0.2,'Mpc')).save()<br></div><div><br></div><div>the behavior is perfectly fine and I get projections that look sensible. *however*, when I do a slice plot:</div><div><br></div><div> yt.SlicePlot(ds,'x',("gas", "temperature"),center=[0.0,0.0,0.0],width=(0.2,'Mpc')).save()</div><div><br></div><div><div style="font-size:12.8px">I get a malloc error:</div></div><div style="font-size:12.8px"><br></div><div style="font-size:12.8px"><div style="font-size:12.8px">yt : [INFO ] 2015-12-23 17:50:59,082 Gathering a field list (this may take a moment.)</div><div style="font-size:12.8px">yt : [INFO ] 2015-12-23 17:50:59,155 Loading field plugins.</div><div style="font-size:12.8px">yt : [INFO ] 2015-12-23 17:50:59,155 Loaded angular_momentum (8 new fields)</div><div style="font-size:12.8px">yt : [INFO ] 2015-12-23 17:50:59,156 Loaded astro (16 new fields)</div><div style="font-size:12.8px">yt : [INFO ] 2015-12-23 17:50:59,156 Loaded cosmology (23 new fields)</div><div style="font-size:12.8px">yt : [INFO ] 2015-12-23 17:50:59,156 Loaded fluid (64 new fields)</div><div style="font-size:12.8px">yt : [INFO ] 2015-12-23 17:50:59,157 Loaded fluid_vector (96 new fields)</div><div style="font-size:12.8px">yt : [INFO ] 2015-12-23 17:50:59,157 Loaded geometric (112 new fields)</div><div style="font-size:12.8px">yt : [INFO ] 2015-12-23 17:50:59,157 Loaded local (112 new fields)</div><div style="font-size:12.8px">yt : [INFO ] 2015-12-23 17:50:59,157 Loaded magnetic_field (120 new fields)</div><div style="font-size:12.8px">yt : [INFO ] 2015-12-23 17:50:59,158 Loaded my_plugins (120 new fields)</div><div style="font-size:12.8px">yt : [INFO ] 2015-12-23 17:50:59,158 Loaded species (122 new fields)</div><div style="font-size:12.8px">python2.7(12254,0x7fff72d19310) malloc: *** error for object 0x103e39008: incorrect checksum for freed object - object was probably modified after being freed.</div><div style="font-size:12.8px">*** set a breakpoint in malloc_error_break to debug</div><div style="font-size:12.8px">Abort trap: 6</div><div style="font-size:12.8px"><br></div><div style="font-size:12.8px">This happens on my Mac (OS X 10.9.5, LLVM v6.0) and also on my Linux machine (Ubuntu 13.04, gcc 4.6.3), although on the linux machine I just get a seg fault instead of the malloc stuff. Using pdb (python -m pdb crashing_script.py) gives me the same error with no additional information.</div></div><div style="font-size:12.8px"><br></div></div><div><div><div class="gmail_extra"><br><div class="gmail_quote">On Wed, Dec 23, 2015 at 5:40 PM, Brian O'Shea <span dir="ltr"><<a href="mailto:bwoshea@gmail.com" target="_blank">bwoshea@gmail.com</a>></span> wrote:<br><blockquote class="gmail_quote" style="margin:0 0 0 .8ex;border-left:1px #ccc solid;padding-left:1ex"><div dir="ltr">Bugfix confirmed; this works for me as well. Thank you very much!</div><div><div><div class="gmail_extra"><br><div class="gmail_quote">On Wed, Dec 23, 2015 at 5:18 PM, Nathan Goldbaum <span dir="ltr"><<a href="mailto:nathan12343@gmail.com" target="_blank">nathan12343@gmail.com</a>></span> wrote:<br><blockquote class="gmail_quote" style="margin:0 0 0 .8ex;border-left:1px #ccc solid;padding-left:1ex"><div dir="ltr">I've opened a pull request that allows me to load your dataset:<div><br></div><div><a href="https://urldefense.proofpoint.com/v2/url?u=https-3A__bitbucket.org_yt-5Fanalysis_yt_pull-2Drequests_1915_bugfix-2Davoid-2Dcreating-2Dparticle-2Dunions-2Dfor_diff&d=BQMFaQ&c=8hUWFZcy2Z-Za5rBPlktOQ&r=hgcBC3x6dKFoTrmFmMYYbKNfiHZlGLKliIidd1LwmHI&m=wQlxydkJvQzNn2hCxGaoS-scytL6xCbt3ldmYqtwpv0&s=mJiE6Y-j_ZpLv8PpuHDkXHoqYYK07rh3zcCF0UV5_Pg&e=" target="_blank">https://bitbucket.org/yt_analysis/yt/pull-requests/1915/bugfix-avoid-creating-particle-unions-for/diff</a><br></div></div><div><div><div class="gmail_extra"><br><div class="gmail_quote">On Wed, Dec 23, 2015 at 4:08 PM, Brian O'Shea <span dir="ltr"><<a href="mailto:bwoshea@gmail.com" target="_blank">bwoshea@gmail.com</a>></span> wrote:<br><blockquote class="gmail_quote" style="margin:0 0 0 .8ex;border-left:1px #ccc solid;padding-left:1ex"><div dir="ltr">Oh, interesting. Is there a way to circumvent auto-detection of fields?</div><div><div><div class="gmail_extra"><br><div class="gmail_quote">On Wed, Dec 23, 2015 at 4:35 PM, Nathan Goldbaum <span dir="ltr"><<a href="mailto:nathan12343@gmail.com" target="_blank">nathan12343@gmail.com</a>></span> wrote:<br><blockquote class="gmail_quote" style="margin:0 0 0 .8ex;border-left:1px #ccc solid;padding-left:1ex"><div dir="ltr">It looks like field detection is breaking for this Enzo-3.0 active particle dataset. StoredEnergy is available on-disk as ('AGNParticle, 'StoredEnergy'), but for some reason the field detection system isn't able to guess that.</div><div><div><div class="gmail_extra"><br><div class="gmail_quote">On Wed, Dec 23, 2015 at 3:19 PM, Nathan Goldbaum <span dir="ltr"><<a href="mailto:nathan12343@gmail.com" target="_blank">nathan12343@gmail.com</a>></span> wrote:<br><blockquote class="gmail_quote" style="margin:0 0 0 .8ex;border-left:1px #ccc solid;padding-left:1ex"><div dir="ltr"><br><div class="gmail_extra"><br><div class="gmail_quote"><span>On Wed, Dec 23, 2015 at 11:20 AM, Brian O'Shea <span dir="ltr"><<a href="mailto:bwoshea@gmail.com" target="_blank">bwoshea@gmail.com</a>></span> wrote:<br></span><span><blockquote class="gmail_quote" style="margin:0 0 0 .8ex;border-left:1px #ccc solid;padding-left:1ex"><div dir="ltr">Dear yt-users,<div><br></div><div>I'm having a problem with making slices in non-unitary volumes. I have a 3D enzo simulation that has domain bounds of (-1.6...1.6) in every dimension (units of megaparsecs), and after I updated to the tip of yt-3 (changeset d9502d848029) from a fairly old version of the code I suddenly have problems with making simple projections. If I run this set of commands:</div><div><br></div></div></blockquote><div><br></div></span><div>Any idea which version you updated from? I tried on yt-3.1 and get the same error. This is just so we can bisect and find the change that introduced the regression.</div><div> </div><blockquote class="gmail_quote" style="margin:0 0 0 .8ex;border-left:1px #ccc solid;padding-left:1ex"><span><div dir="ltr"><div></div><div><div>import yt</div><div>ds = yt.load("DD0400/DD0400")<br></div><div>proj = yt.SlicePlot(ds,'x','temperature',center=[0.0,0.0,0.0],width=(0.2,'Mpc'))<br></div></div><div><br></div><div>I get this error:</div><div><br></div><div><a href="https://urldefense.proofpoint.com/v2/url?u=http-3A__paste.yt-2Dproject.org_show_6115_&d=BQMFaQ&c=8hUWFZcy2Z-Za5rBPlktOQ&r=hgcBC3x6dKFoTrmFmMYYbKNfiHZlGLKliIidd1LwmHI&m=wQlxydkJvQzNn2hCxGaoS-scytL6xCbt3ldmYqtwpv0&s=tDjkgTYOl5MJgJC2j-F6PORHf_nGKcXLv5gA1iBCXKI&e=" target="_blank">http://paste.yt-project.org/show/6115/</a><br></div><div><br></div><div>This seems to work fine on an Enzo cosmological dataset (domain bounds 0-1 in each dimension), and previously worked fine in yt-3 (using a version of the code from a couple of months ago).</div><div><br></div><div>is this a bug, or am I doing something dumb?</div><div><br></div><div>Thanks!<span><font color="#888888"><br><br></font></span></div><span><font color="#888888"><div>--Brian</div><div><br></div></font></span></div>
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