<meta http-equiv="Content-Type" content="text/html; charset=utf-8"><div dir="ltr">If you can format your data as numpy arrays, there are examples of how to load your data into yt here:<div><br></div><div><a href="https://urldefense.proofpoint.com/v2/url?u=http-3A__yt-2Dproject.org_docs_2.6_examining_generic-5Farray-5Fdata.html-3Fhighlight-3Dload-5Funiform-5Fgrid&d=BQMFaQ&c=8hUWFZcy2Z-Za5rBPlktOQ&r=hgcBC3x6dKFoTrmFmMYYbKNfiHZlGLKliIidd1LwmHI&m=ENcwzplX0L86smwbSQy5BhMVe67JNwMsQ4B-YWQQK7Q&s=OnG7UHYeMGWenit8xj2C13lCtEYNB6iOtW4eHJlb2Lc&e=">http://yt-project.org/docs/2.6/examining/generic_array_data.html?highlight=load_uniform_grid</a><br></div><div><br></div><div>yt (2.6.1 or newer) does not support i/o from arbitrary text files.</div></div><div class="gmail_extra"><br><div class="gmail_quote">On Sat, Dec 26, 2015 at 12:30 PM, 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"><p dir="ltr">Dear Nathan:</p><p>I will try it and let you know. In the meanwhile, could you let me know if yt supports loading text file for version 2.6.1? If so could you point me to examples for the same.</p><p>Thanks in advance</p><div><div class="h5">
<br><div class="gmail_quote"><div dir="ltr">On Sat, Dec 26, 2015, 11:44 Nathan Goldbaum <<a href="mailto:nathan12343@gmail.com" target="_blank">nathan12343@gmail.com</a>> wrote:<br></div><blockquote class="gmail_quote" style="margin:0 0 0 .8ex;border-left:1px #ccc solid;padding-left:1ex"><div dir="ltr">This is happening because python is unable to link against an openSSL library.<div><br></div><div>Can you try using the get_yt.sh script install of the install_script.sh script:</div><div><br></div><div><a href="https://urldefense.proofpoint.com/v2/url?u=https-3A__bitbucket.org_yt-5Fanalysis_yt_raw_d9502d84802972ba3e644d2d5c47b87f73a6bd08_doc_get-5Fyt.sh&d=BQMFaQ&c=8hUWFZcy2Z-Za5rBPlktOQ&r=hgcBC3x6dKFoTrmFmMYYbKNfiHZlGLKliIidd1LwmHI&m=ENcwzplX0L86smwbSQy5BhMVe67JNwMsQ4B-YWQQK7Q&s=jqa-Sj_j3HezcX458o1ego99l4yeXCWPKCYzbmnVn34&e=" target="_blank">https://bitbucket.org/yt_analysis/yt/raw/d9502d84802972ba3e644d2d5c47b87f73a6bd08/doc/get_yt.sh</a><br></div><div><br></div><div>This script installs yt using the miniconda python distribution, which includes a precompiled python and openSSL library.</div></div><div dir="ltr"><div><br></div><div>-Nathan</div></div><div class="gmail_extra"><br><div class="gmail_quote">On Sat, Dec 26, 2015 at 11:40 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>Hi Nathan:<br><br></div>Thanks for your reply. <br><br>I had done that before installing version 2.X. I used to get errors as below. Even now I keep getting the same error after reinstalling from scratch. The error comes after "installing pip". I tried it on my pc and also on cluster but same issues. <br><br>********************************************<br> FAILURE REPORT:<br>********************************************<br><br> bootstrap(tmpdir=tmpdir)<br> File "get-pip.py", line 82, in bootstrap<br> import pip<br> File "/tmp/tmpxKqAjR/pip.zip/pip/__init__.py", line 15, in <module><br> File "/tmp/tmpxKqAjR/pip.zip/pip/vcs/subversion.py", line 9, in <module><br> File "/tmp/tmpxKqAjR/pip.zip/pip/index.py", line 30, in <module><br> File "/tmp/tmpxKqAjR/pip.zip/pip/wheel.py", line 35, in <module><br> File "/tmp/tmpxKqAjR/pip.zip/pip/_vendor/distlib/scripts.py", line 14, in <module><br> File "/tmp/tmpxKqAjR/pip.zip/pip/_vendor/distlib/compat.py", line 31, in <module><br>ImportError: cannot import name HTTPSHandler<br><br>********************************************<br>********************************************<br>Failure. Check /home/adrith/yt-x86_64/yt_install.log. The last 10 lines are above.<br></div><div><div><div class="gmail_extra"><br><div class="gmail_quote">On Sat, Dec 26, 2015 at 10:41 AM, 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">Hi Sushilkumar,<div><br></div><div>Can you try reinstalling yt from scratch?</div><span><font color="#888888"><div><br></div><div>-Nathan</div></font></span></div><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=ENcwzplX0L86smwbSQy5BhMVe67JNwMsQ4B-YWQQK7Q&s=5HwEKVTyyX6XD2oAWX8cGCAiLDOzMEL16WJ4rxoGUao&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=ENcwzplX0L86smwbSQy5BhMVe67JNwMsQ4B-YWQQK7Q&s=VsOZ1zAfBuE3cn4z59rXQvr2JfnxsAf_x6m6O4SAGG0&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=ENcwzplX0L86smwbSQy5BhMVe67JNwMsQ4B-YWQQK7Q&s=PCTgz8EykSI8hLwMHloUdYc8r31LSBBUF98gDEh-3EA&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>
>>>>> yt-users mailing list<br>
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>>>>><br>
>>>>><br>
>>>><br>
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>>>><br>
>>>><br>
>>><br>
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><br>
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End of yt-users Digest, Vol 94, Issue 24<br>
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</font></span></blockquote></div><span><font color="#888888"><br><br clear="all"><br>-- <br><div><span style="border-collapse:collapse"><div style="color:rgb(80,0,80);font-family:arial,sans-serif;font-size:13px"><span style="font-family:arial,sans-serif;font-size:13px;border-collapse:collapse"><b><i>SK<sup>2</sup></i></b></span></div><div style="color:rgb(80,0,80);font-family:arial,sans-serif;font-size:13px"><span style="font-family:arial,sans-serif;font-size:13px;border-collapse:collapse"><b><i><sup><br></sup></i></b></span></div><div><span style="color:rgb(80,0,80);font-family:arial,sans-serif;border-collapse:collapse"><b><sup>"</sup></b></span><font color="#500050" face="arial, sans-serif"><b>Claiming that something can move faster than light is a good conversation-stopper in physics. People edge away from you in cocktail parties; friends never return phone calls. You just don’t mess with Albert Einstein.</b></font><b style="color:rgb(80,0,80);font-family:arial,sans-serif"><sup>"</sup></b></div><div style="color:rgb(80,0,80);font-family:arial,sans-serif;font-size:13px"><br></div></span></div>
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</div></div></blockquote></div><br><br clear="all"><br>-- <br><div><span style="border-collapse:collapse"><div style="color:rgb(80,0,80);font-family:arial,sans-serif;font-size:13px"><span style="font-family:arial,sans-serif;font-size:13px;border-collapse:collapse"><b><i>SK<sup>2</sup></i></b></span></div><div style="color:rgb(80,0,80);font-family:arial,sans-serif;font-size:13px"><span style="font-family:arial,sans-serif;font-size:13px;border-collapse:collapse"><b><i><sup><br></sup></i></b></span></div><div><span style="color:rgb(80,0,80);font-family:arial,sans-serif;border-collapse:collapse"><b><sup>"</sup></b></span><font color="#500050" face="arial, sans-serif"><b>Claiming that something can move faster than light is a good conversation-stopper in physics. People edge away from you in cocktail parties; friends never return phone calls. You just don’t mess with Albert Einstein.</b></font><b style="color:rgb(80,0,80);font-family:arial,sans-serif"><sup>"</sup></b></div><div style="color:rgb(80,0,80);font-family:arial,sans-serif;font-size:13px"><br></div></span></div>
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