<meta http-equiv="Content-Type" content="text/html; charset=utf-8"><div dir="ltr">Hi Sushilkumar,<div><br></div><div>Can you try reinstalling yt from scratch?</div><div><br></div><div>-Nathan</div></div><div class="gmail_extra"><br><div class="gmail_quote">On Sat, Dec 26, 2015 at 10:39 AM, Sushilkumar <span dir="ltr"><<a href="mailto:sushil.sush19us@gmail.com" target="_blank">sushil.sush19us@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"><div>Dear yt:<br><br></div>I am currently running yt version 2.6.1 and want to update to version 3 (to read text files). Could you provide me link to so?<br>
<br>
I tried it using yt update --all as per the link<br>
<br>
<a href="https://urldefense.proofpoint.com/v2/url?u=http-3A__yt-2Dproject.org_doc_yt3differences.html-23updating-2Dto-2Dyt-2D3-2D0-2Dfrom-2Dold-2Dversions-2Dand-2Dgoing-2Dback&d=BQMFaQ&c=8hUWFZcy2Z-Za5rBPlktOQ&r=hgcBC3x6dKFoTrmFmMYYbKNfiHZlGLKliIidd1LwmHI&m=VBow0aP3sTY3J4l3DBSmUtTE3nX9b6fLvRDMj6tbYmY&s=Adai8y9KZSDO8c8-QNRb67Hns78lpWTG4M2Ci6jSeng&e=" rel="noreferrer" target="_blank">http://yt-project.org/doc/yt3differences.html#updating-to-yt-3-0-from-old-versions-and-going-back</a><br>
.<br>
<br>
But it wont update to 3.0 and still shows as 2.6.1<br>
<br>
Kindly help<br>
<br>
Thanks in advance<br>
<br>
sushilkumar <br><div><div><div class="gmail_extra"><br><div class="gmail_quote">On Thu, Dec 24, 2015 at 12:25 PM, <span dir="ltr"><<a href="mailto:yt-users-request@lists.spacepope.org" target="_blank">yt-users-request@lists.spacepope.org</a>></span> wrote:<br><blockquote class="gmail_quote" style="margin:0px 0px 0px 0.8ex;border-left:1px solid rgb(204,204,204);padding-left:1ex">Send yt-users mailing list submissions to<br>
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Today's Topics:<br>
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1. Re: problem with slices in non-unitary volumes (Nathan Goldbaum)<br>
<br>
<br>
----------------------------------------------------------------------<br>
<br>
Message: 1<br>
Date: Wed, 23 Dec 2015 17:17:56 -0600<br>
From: Nathan Goldbaum <<a href="mailto:nathan12343@gmail.com" target="_blank">nathan12343@gmail.com</a>><br>
To: Discussion of the yt analysis package<br>
<<a href="mailto:yt-users@lists.spacepope.org" target="_blank">yt-users@lists.spacepope.org</a>><br>
Subject: Re: [yt-users] problem with slices in non-unitary volumes<br>
Message-ID:<br>
<<a href="mailto:CAJXewOmVEX-qB41doTk%2B7DT1AOLsn53KMb8nvfr8dwyFrKY-4g@mail.gmail.com" target="_blank">CAJXewOmVEX-qB41doTk+7DT1AOLsn53KMb8nvfr8dwyFrKY-4g@mail.gmail.com</a>><br>
Content-Type: text/plain; charset="utf-8"<br>
<br>
I get the same error over here. I think it's unrelated to the other error.<br>
The relevant portion of the C stack trace is here:<br>
<br>
Thread 0 Crashed:: Dispatch queue: com.apple.main-thread<br>
0 libsystem_kernel.dylib 0x00007fff8b615286 __pthread_kill + 10<br>
1 libsystem_c.dylib 0x00007fff8bc2a9ab abort + 129<br>
2 libsystem_malloc.dylib 0x00007fff915d5fe2 szone_error + 625<br>
3 libsystem_malloc.dylib 0x00007fff915cf374<br>
small_free_list_remove_ptr + 154<br>
4 libsystem_malloc.dylib 0x00007fff915cac3f<br>
szone_free_definite_size + 1856<br>
5 multiarray.so 0x00000001044c2d16 npy_free_cache + 70<br>
6 multiarray.so 0x00000001044c6ed6 array_dealloc + 182<br>
7 selection_routines.so 0x00000001063ffe34<br>
__pyx_pw_2yt_8geometry_18selection_routines_13SliceSelector_3fill_mask +<br>
8804 (selection_routines.c:19749)<br>
<br>
Line 19749 of selection_routines.c corresponds to line 1158 in<br>
selection_routines.pyx, which is the place where the fill_mask member<br>
variable of the SliceSelector extension type gets defined.<br>
<br>
Unfortunately, I have no idea how to debug this from here...<br>
<br>
-Nathan<br>
<br>
On Wed, Dec 23, 2015 at 4:57 PM, Brian O'Shea <<a href="mailto:bwoshea@gmail.com" target="_blank">bwoshea@gmail.com</a>> wrote:<br>
<br>
> Actually, interesting followup here - I have to take it back. When I do a<br>
> projection plot:<br>
><br>
> yt.ProjectionPlot(ds,'x',("gas",<br>
> "temperature"),center=[0.0,0.0,0.0],width=(0.2,'Mpc')).save()<br>
><br>
> the behavior is perfectly fine and I get projections that look sensible.<br>
> *however*, when I do a slice plot:<br>
><br>
> yt.SlicePlot(ds,'x',("gas",<br>
> "temperature"),center=[0.0,0.0,0.0],width=(0.2,'Mpc')).save()<br>
><br>
> I get a malloc error:<br>
><br>
> yt : [INFO ] 2015-12-23 17:50:59,082 Gathering a field list (this may<br>
> take a moment.)<br>
> yt : [INFO ] 2015-12-23 17:50:59,155 Loading field plugins.<br>
> yt : [INFO ] 2015-12-23 17:50:59,155 Loaded angular_momentum (8 new<br>
> fields)<br>
> yt : [INFO ] 2015-12-23 17:50:59,156 Loaded astro (16 new fields)<br>
> yt : [INFO ] 2015-12-23 17:50:59,156 Loaded cosmology (23 new fields)<br>
> yt : [INFO ] 2015-12-23 17:50:59,156 Loaded fluid (64 new fields)<br>
> yt : [INFO ] 2015-12-23 17:50:59,157 Loaded fluid_vector (96 new<br>
> fields)<br>
> yt : [INFO ] 2015-12-23 17:50:59,157 Loaded geometric (112 new fields)<br>
> yt : [INFO ] 2015-12-23 17:50:59,157 Loaded local (112 new fields)<br>
> yt : [INFO ] 2015-12-23 17:50:59,157 Loaded magnetic_field (120 new<br>
> fields)<br>
> yt : [INFO ] 2015-12-23 17:50:59,158 Loaded my_plugins (120 new fields)<br>
> yt : [INFO ] 2015-12-23 17:50:59,158 Loaded species (122 new fields)<br>
> python2.7(12254,0x7fff72d19310) malloc: *** error for object 0x103e39008:<br>
> incorrect checksum for freed object - object was probably modified after<br>
> being freed.<br>
> *** set a breakpoint in malloc_error_break to debug<br>
> Abort trap: 6<br>
><br>
> This happens on my Mac (OS X 10.9.5, LLVM v6.0) and also on my Linux<br>
> machine (Ubuntu 13.04, gcc 4.6.3), although on the linux machine I just get<br>
> a seg fault instead of the malloc stuff. Using pdb (python -m pdb<br>
> crashing_script.py) gives me the same error with no additional information.<br>
><br>
><br>
> On Wed, Dec 23, 2015 at 5:40 PM, Brian O'Shea <<a href="mailto:bwoshea@gmail.com" target="_blank">bwoshea@gmail.com</a>> wrote:<br>
><br>
>> Bugfix confirmed; this works for me as well. Thank you very much!<br>
>><br>
>> On Wed, Dec 23, 2015 at 5:18 PM, Nathan Goldbaum <<a href="mailto:nathan12343@gmail.com" target="_blank">nathan12343@gmail.com</a>><br>
>> wrote:<br>
>><br>
>>> I've opened a pull request that allows me to load your dataset:<br>
>>><br>
>>><br>
>>> <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=VBow0aP3sTY3J4l3DBSmUtTE3nX9b6fLvRDMj6tbYmY&s=ic9b1e9z0-zHeraJOZs2zbdCvNnf7kc5GYrM5LV8K1M&e=" rel="noreferrer" target="_blank">https://bitbucket.org/yt_analysis/yt/pull-requests/1915/bugfix-avoid-creating-particle-unions-for/diff</a><br>
>>><br>
>>> On Wed, Dec 23, 2015 at 4:08 PM, Brian O'Shea <<a href="mailto:bwoshea@gmail.com" target="_blank">bwoshea@gmail.com</a>> wrote:<br>
>>><br>
>>>> Oh, interesting. Is there a way to circumvent auto-detection of fields?<br>
>>>><br>
>>>> On Wed, Dec 23, 2015 at 4:35 PM, Nathan Goldbaum <<a href="mailto:nathan12343@gmail.com" target="_blank">nathan12343@gmail.com</a><br>
>>>> > wrote:<br>
>>>><br>
>>>>> It looks like field detection is breaking for this Enzo-3.0 active<br>
>>>>> particle dataset. StoredEnergy is available on-disk as ('AGNParticle,<br>
>>>>> 'StoredEnergy'), but for some reason the field detection system isn't able<br>
>>>>> to guess that.<br>
>>>>><br>
>>>>> On Wed, Dec 23, 2015 at 3:19 PM, Nathan Goldbaum <<br>
>>>>> <a href="mailto:nathan12343@gmail.com" target="_blank">nathan12343@gmail.com</a>> wrote:<br>
>>>>><br>
>>>>>><br>
>>>>>><br>
>>>>>> On Wed, Dec 23, 2015 at 11:20 AM, Brian O'Shea <<a href="mailto:bwoshea@gmail.com" target="_blank">bwoshea@gmail.com</a>><br>
>>>>>> wrote:<br>
>>>>>><br>
>>>>>>> Dear yt-users,<br>
>>>>>>><br>
>>>>>>> I'm having a problem with making slices in non-unitary volumes. I<br>
>>>>>>> have a 3D enzo simulation that has domain bounds of (-1.6...1.6) in every<br>
>>>>>>> dimension (units of megaparsecs), and after I updated to the tip of yt-3<br>
>>>>>>> (changeset d9502d848029) from a fairly old version of the code I suddenly<br>
>>>>>>> have problems with making simple projections. If I run this set of<br>
>>>>>>> commands:<br>
>>>>>>><br>
>>>>>>><br>
>>>>>> Any idea which version you updated from? I tried on yt-3.1 and get<br>
>>>>>> the same error. This is just so we can bisect and find the change that<br>
>>>>>> introduced the regression.<br>
>>>>>><br>
>>>>>><br>
>>>>>>> import yt<br>
>>>>>>> ds = yt.load("DD0400/DD0400")<br>
>>>>>>> proj =<br>
>>>>>>> yt.SlicePlot(ds,'x','temperature',center=[0.0,0.0,0.0],width=(0.2,'Mpc'))<br>
>>>>>>><br>
>>>>>>> I get this error:<br>
>>>>>>><br>
>>>>>>> <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=VBow0aP3sTY3J4l3DBSmUtTE3nX9b6fLvRDMj6tbYmY&s=njnIdr5BnPvG39peJuthjgCqhXvzh_enWhbLzTM_2MM&e=" rel="noreferrer" target="_blank">http://paste.yt-project.org/show/6115/</a><br>
>>>>>>><br>
>>>>>>> This seems to work fine on an Enzo cosmological dataset (domain<br>
>>>>>>> bounds 0-1 in each dimension), and previously worked fine in yt-3 (using a<br>
>>>>>>> version of the code from a couple of months ago).<br>
>>>>>>><br>
>>>>>>> is this a bug, or am I doing something dumb?<br>
>>>>>>><br>
>>>>>>> Thanks!<br>
>>>>>>><br>
>>>>>>> --Brian<br>
>>>>>>><br>
>>>>>>><br>
>>>>>>> _______________________________________________<br>
>>>>>>> yt-users mailing list<br>
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>>>>>>><br>
>>>>>>><br>
>>>>>><br>
>>>>><br>
>>>>> _______________________________________________<br>
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>>>>><br>
>>>><br>
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>>><br>
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