<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="">In the current development version of yt there is also yt.loadtxt, which is essentially a wrapper for numpy.loadtxt which also accepts unit information.<div class=""><br class=""></div><div class="">See <a href="https://urldefense.proofpoint.com/v2/url?u=http-3A__yt-2Dproject.org_docs_dev_analyzing_units_symbolic-5Funits.html-23Saving-2Dand-2DLoading-2DYTArrays-2Dto_from-2Ddisk&d=BQMFaQ&c=8hUWFZcy2Z-Za5rBPlktOQ&r=hgcBC3x6dKFoTrmFmMYYbKNfiHZlGLKliIidd1LwmHI&m=BOYrYD1LYgs8DNlrh2pgGZtwTy0-mi7gr4RfFFVNEyc&s=5-tFlavphHBDlrHmLvy8bvARGTiiSBu0dl3Y8REHTg0&e=" class="">http://yt-project.org/docs/dev/analyzing/units/symbolic_units.html#Saving-and-Loading-YTArrays-to/from-disk</a></div><div class=""><br class=""><div><blockquote type="cite" class=""><div class="">On Dec 30, 2015, at 12:01 PM, Sushilkumar <<a href="mailto:sushil.sush19us@gmail.com" class="">sushil.sush19us@gmail.com</a>> wrote:</div><br class="Apple-interchange-newline"><div class=""><div dir="ltr" style="font-family: Helvetica; font-size: 12px; font-style: normal; font-variant: normal; font-weight: normal; letter-spacing: normal; orphans: auto; text-align: start; text-indent: 0px; text-transform: none; white-space: normal; widows: auto; word-spacing: 0px; -webkit-text-stroke-width: 0px;" class=""><div class=""><div class="">Dear Nathan:<br class=""><br class=""></div>As per your advice I am trying to load my text file to numpy array. But there are two ways to so using numpy.loadtxt and numpy.fromfile. Could you suggest which of them is more efficient for large files and more suitable for yt (if any)?<span class="Apple-converted-space"> </span><br class=""><br class=""></div>Thanks in advance<br class=""></div><div class="gmail_extra" style="font-family: Helvetica; font-size: 12px; font-style: normal; font-variant: normal; font-weight: normal; letter-spacing: normal; orphans: auto; text-align: start; text-indent: 0px; text-transform: none; white-space: normal; widows: auto; word-spacing: 0px; -webkit-text-stroke-width: 0px;"><br class=""><div class="gmail_quote">On Sat, Dec 26, 2015 at 6:43 PM, Sushilkumar Sreekumar<span class="Apple-converted-space"> </span><span dir="ltr" class=""><<a href="mailto:sushil.sush19us@gmail.com" target="_blank" class="">sushil.sush19us@gmail.com</a>></span><span class="Apple-converted-space"> </span>wrote:<br class=""><blockquote class="gmail_quote" style="margin: 0px 0px 0px 0.8ex; border-left-width: 1px; border-left-color: rgb(204, 204, 204); border-left-style: solid; padding-left: 1ex;"><div link="blue" vlink="#954F72" lang="EN-US" class=""><div class=""><p class="MsoNormal">Dear Nathan:</p><p class="MsoNormal"><u class=""></u> <u class=""></u></p><p class="MsoNormal">Thank you for your help<u class=""></u><u class=""></u></p><span class=""><p class="MsoNormal"><u class=""></u> <u class=""></u></p><p class="MsoNormal">--<span class="Apple-converted-space"> </span><br class="">SK2<br class=""><br class="">"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."</p><p class="MsoNormal"><span style="font-size: 12pt; font-family: 'Times New Roman', serif;" class=""><u class=""></u> <u class=""></u></span></p></span><div style="border-style: solid none none; border-top-color: rgb(225, 225, 225); border-top-width: 1pt; padding: 3pt 0in 0in;" class=""><p class="MsoNormal" style="border: none; padding: 0in;"><br class=""><b class="">From:<span class="Apple-converted-space"> </span></b><a href="mailto:nathan12343@gmail.com" target="_blank" class="">Nathan Goldbaum</a><br class=""><b class="">Sent:<span class="Apple-converted-space"> </span></b>Saturday, December 26, 2015 12:34 PM<br class=""><b class="">To:<span class="Apple-converted-space"> </span></b><a href="mailto:sushil.sush19us@gmail.com" target="_blank" class="">Sushilkumar</a><br class=""><b class="">Cc:<span class="Apple-converted-space"> </span></b><a href="mailto:yt-users@lists.spacepope.org" target="_blank" class="">Discussion of the yt analysis package</a><br class=""><b class="">Subject:<span class="Apple-converted-space"> </span></b>Re: [yt-users] problem with yt update to 3.0</p></div><div class=""><div class="h5"><p class="MsoNormal"><span style="font-size: 12pt; font-family: 'Times New Roman', serif;" class=""><u class=""></u> <u class=""></u></span></p><div class=""><p class="MsoNormal"><span style="font-size: 12pt; font-family: 'Times New Roman', serif;" class="">If you can format your data as numpy arrays, there are examples of how to load your data into yt here:</span><span style="font-size: 12pt; font-family: 'Times New Roman', serif;" class=""><u class=""></u><u class=""></u></span></p><div class=""><p class="MsoNormal"><span style="font-size: 12pt; font-family: 'Times New Roman', serif;" class=""><u class=""></u> <u class=""></u></span></p></div><div class=""><p class="MsoNormal"><span style="font-size: 12pt; font-family: 'Times New Roman', serif;" class=""><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=BOYrYD1LYgs8DNlrh2pgGZtwTy0-mi7gr4RfFFVNEyc&s=YbrEEiiLAT3oZYIsSVKflng7q_ZNLDpNOSKyblNctlw&e=" target="_blank" class="">http://yt-project.org/docs/2.6/examining/generic_array_data.html?highlight=load_uniform_grid</a><u class=""></u><u class=""></u></span></p></div><div class=""><p class="MsoNormal"><span style="font-size: 12pt; font-family: 'Times New Roman', serif;" class=""><u class=""></u> <u class=""></u></span></p></div><div class=""><p class="MsoNormal"><span style="font-size: 12pt; font-family: 'Times New Roman', serif;" class="">yt (2.6.1 or newer) does not support i/o from arbitrary text files.<u class=""></u><u class=""></u></span></p></div></div><div class=""><p class="MsoNormal"><span style="font-size: 12pt; font-family: 'Times New Roman', serif;" class=""><u class=""></u> <u class=""></u></span></p><div class=""><p class="MsoNormal"><span style="font-size: 12pt; font-family: 'Times New Roman', serif;" class="">On Sat, Dec 26, 2015 at 12:30 PM, Sushilkumar <<a href="mailto:sushil.sush19us@gmail.com" target="_blank" class="">sushil.sush19us@gmail.com</a>> wrote:<u class=""></u><u class=""></u></span></p><blockquote style="border-style: none none none solid; border-left-color: rgb(204, 204, 204); border-left-width: 1pt; padding: 0in 0in 0in 6pt; margin-left: 4.8pt; margin-right: 0in;" class=""><div class=""><p class="">Dear Nathan:</p><p class="">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 class="">Thanks in advance</p><div class=""><div class=""><p class="MsoNormal"><span style="font-size: 12pt; font-family: 'Times New Roman', serif;" class=""><u class=""></u> <u class=""></u></span></p><div class=""><div class=""><p class="MsoNormal"><span style="font-size: 12pt; font-family: 'Times New Roman', serif;" class="">On Sat, Dec 26, 2015, 11:44 Nathan Goldbaum <<a href="mailto:nathan12343@gmail.com" target="_blank" class="">nathan12343@gmail.com</a>> wrote:<u class=""></u><u class=""></u></span></p></div><blockquote style="border-style: none none none solid; border-left-color: rgb(204, 204, 204); border-left-width: 1pt; padding: 0in 0in 0in 6pt; margin-left: 4.8pt; margin-right: 0in;" class=""><div class=""><p class="MsoNormal"><span style="font-size: 12pt; font-family: 'Times New Roman', serif;" class="">This is happening because python is unable to link against an openSSL library.<u class=""></u><u class=""></u></span></p><div class=""><p class="MsoNormal"><span style="font-size: 12pt; font-family: 'Times New Roman', serif;" class=""><u class=""></u> <u class=""></u></span></p></div><div class=""><p class="MsoNormal"><span style="font-size: 12pt; font-family: 'Times New Roman', serif;" class="">Can you try using the get_yt.sh script install of the install_script.sh script:<u class=""></u><u class=""></u></span></p></div><div class=""><p class="MsoNormal"><span style="font-size: 12pt; font-family: 'Times New Roman', serif;" class=""><u class=""></u> <u class=""></u></span></p></div><div class=""><p class="MsoNormal"><span style="font-size: 12pt; font-family: 'Times New Roman', serif;" class=""><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=BOYrYD1LYgs8DNlrh2pgGZtwTy0-mi7gr4RfFFVNEyc&s=odPzoLKTLk1tnrCYkJLtm-H74c0vxxTyWII_FRXApoA&e=" target="_blank" class="">https://bitbucket.org/yt_analysis/yt/raw/d9502d84802972ba3e644d2d5c47b87f73a6bd08/doc/get_yt.sh</a><u class=""></u><u class=""></u></span></p></div><div class=""><p class="MsoNormal"><span style="font-size: 12pt; font-family: 'Times New Roman', serif;" class=""><u class=""></u> <u class=""></u></span></p></div><div class=""><p class="MsoNormal"><span style="font-size: 12pt; font-family: 'Times New Roman', serif;" class="">This script installs yt using the miniconda python distribution, which includes a precompiled python and openSSL library.<u class=""></u><u class=""></u></span></p></div></div><div class=""><div class=""><p class="MsoNormal"><span style="font-size: 12pt; font-family: 'Times New Roman', serif;" class=""><u class=""></u> <u class=""></u></span></p></div><div class=""><p class="MsoNormal"><span style="font-size: 12pt; font-family: 'Times New Roman', serif;" class="">-Nathan<u class=""></u><u class=""></u></span></p></div></div><div class=""><p class="MsoNormal"><span style="font-size: 12pt; font-family: 'Times New Roman', serif;" class=""><u class=""></u> <u class=""></u></span></p><div class=""><p class="MsoNormal"><span style="font-size: 12pt; font-family: 'Times New Roman', serif;" class="">On Sat, Dec 26, 2015 at 11:40 AM, Sushilkumar <<a href="mailto:sushil.sush19us@gmail.com" target="_blank" class="">sushil.sush19us@gmail.com</a>> wrote:<u class=""></u><u class=""></u></span></p><blockquote style="border-style: none none none solid; border-left-color: rgb(204, 204, 204); border-left-width: 1pt; padding: 0in 0in 0in 6pt; margin-left: 4.8pt; margin-right: 0in;" class=""><div class=""><div class=""><p class="MsoNormal" style="margin-bottom: 12pt;"><span style="font-size: 12pt; font-family: 'Times New Roman', serif;" class="">Hi Nathan:<u class=""></u><u class=""></u></span></p></div><p class="MsoNormal"><span style="font-size: 12pt; font-family: 'Times New Roman', serif;" class="">Thanks for your reply.<span class="Apple-converted-space"> </span><br class=""><br class="">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.<span class="Apple-converted-space"> </span><br class=""><br class="">********************************************<br class=""> <span class="Apple-converted-space"> </span>FAILURE REPORT:<br class="">********************************************<br class=""><br class=""> <span class="Apple-converted-space"> </span>bootstrap(tmpdir=tmpdir)<br class=""> <span class="Apple-converted-space"> </span>File "get-pip.py", line 82, in bootstrap<br class=""> <span class="Apple-converted-space"> </span>import pip<br class=""> <span class="Apple-converted-space"> </span>File "/tmp/tmpxKqAjR/pip.zip/pip/__init__.py", line 15, in <module><br class=""> <span class="Apple-converted-space"> </span>File "/tmp/tmpxKqAjR/pip.zip/pip/vcs/subversion.py", line 9, in <module><br class=""> <span class="Apple-converted-space"> </span>File "/tmp/tmpxKqAjR/pip.zip/pip/index.py", line 30, in <module><br class=""> <span class="Apple-converted-space"> </span>File "/tmp/tmpxKqAjR/pip.zip/pip/wheel.py", line 35, in <module><br class=""> <span class="Apple-converted-space"> </span>File "/tmp/tmpxKqAjR/pip.zip/pip/_vendor/distlib/scripts.py", line 14, in <module><br class=""> <span class="Apple-converted-space"> </span>File "/tmp/tmpxKqAjR/pip.zip/pip/_vendor/distlib/compat.py", line 31, in <module><br class="">ImportError: cannot import name HTTPSHandler<br class=""><br class="">********************************************<br class="">********************************************<br class="">Failure. Check /home/adrith/yt-x86_64/yt_install.log. The last 10 lines are above.<u class=""></u><u class=""></u></span></p></div><div class=""><div class=""><div class=""><p class="MsoNormal"><span style="font-size: 12pt; font-family: 'Times New Roman', serif;" class=""><u class=""></u> <u class=""></u></span></p><div class=""><p class="MsoNormal"><span style="font-size: 12pt; font-family: 'Times New Roman', serif;" class="">On Sat, Dec 26, 2015 at 10:41 AM, Nathan Goldbaum <<a href="mailto:nathan12343@gmail.com" target="_blank" class="">nathan12343@gmail.com</a>> wrote:<u class=""></u><u class=""></u></span></p><blockquote style="border-style: none none none solid; border-left-color: rgb(204, 204, 204); border-left-width: 1pt; padding: 0in 0in 0in 6pt; margin-left: 4.8pt; margin-right: 0in;" class=""><div class=""><p class="MsoNormal"><span style="font-size: 12pt; font-family: 'Times New Roman', serif;" class="">Hi Sushilkumar,<u class=""></u><u class=""></u></span></p><div class=""><p class="MsoNormal"><span style="font-size: 12pt; font-family: 'Times New Roman', serif;" class=""><u class=""></u> <u class=""></u></span></p></div><div class=""><p class="MsoNormal"><span style="font-size: 12pt; font-family: 'Times New Roman', serif;" class="">Can you try reinstalling yt from scratch?<u class=""></u><u class=""></u></span></p></div><div class=""><p class="MsoNormal"><span style="font-size: 12pt; font-family: 'Times New Roman', serif; color: rgb(136, 136, 136);" class=""><u class=""></u> <u class=""></u></span></p></div><div class=""><p class="MsoNormal"><span style="font-size: 12pt; font-family: 'Times New Roman', serif; color: rgb(136, 136, 136);" class="">-Nathan<u class=""></u><u class=""></u></span></p></div></div><div class=""><div class=""><div class=""><p class="MsoNormal"><span style="font-size: 12pt; font-family: 'Times New Roman', serif;" class=""><u class=""></u> <u class=""></u></span></p><div class=""><p class="MsoNormal"><span style="font-size: 12pt; font-family: 'Times New Roman', serif;" class="">On Sat, Dec 26, 2015 at 10:39 AM, Sushilkumar <<a href="mailto:sushil.sush19us@gmail.com" target="_blank" class="">sushil.sush19us@gmail.com</a>> wrote:<u class=""></u><u class=""></u></span></p><blockquote style="border-style: none none none solid; border-left-color: rgb(204, 204, 204); border-left-width: 1pt; padding: 0in 0in 0in 6pt; margin-left: 4.8pt; margin-right: 0in;" class=""><div class=""><div class=""><p class="MsoNormal" style="margin-bottom: 12pt;"><span style="font-size: 12pt; font-family: 'Times New Roman', serif;" class="">Dear yt:<u class=""></u><u class=""></u></span></p></div><p class="MsoNormal"><span style="font-size: 12pt; font-family: 'Times New Roman', serif;" class="">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 class=""><br class="">I tried it using yt update --all as per the link<br class=""><br class=""><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=BOYrYD1LYgs8DNlrh2pgGZtwTy0-mi7gr4RfFFVNEyc&s=gAWnE9vkY54-4SKWVuLsJ31WR4sFuf-fdLmR-0DjwCg&e=" target="_blank" class="">http://yt-project.org/doc/yt3differences.html#updating-to-yt-3-0-from-old-versions-and-going-back</a><br class="">.<br class=""><br class="">But it wont update to 3.0 and still shows as 2.6.1<br class=""><br class="">Kindly help<br class=""><br class="">Thanks in advance<br class=""><br class="">sushilkumar<span class="Apple-converted-space"> </span><u class=""></u><u class=""></u></span></p><div class=""><div class=""><div class=""><p class="MsoNormal"><span style="font-size: 12pt; font-family: 'Times New Roman', serif;" class=""><u class=""></u> <u class=""></u></span></p><div class=""><p class="MsoNormal"><span style="font-size: 12pt; font-family: 'Times New Roman', serif;" class="">On Thu, Dec 24, 2015 at 12:25 PM, <<a href="mailto:yt-users-request@lists.spacepope.org" target="_blank" class="">yt-users-request@lists.spacepope.org</a>> wrote:<u class=""></u><u class=""></u></span></p><blockquote style="border-style: none none none solid; border-left-color: rgb(204, 204, 204); border-left-width: 1pt; padding: 0in 0in 0in 6pt; margin-left: 4.8pt; margin-right: 0in;" class=""><p class="MsoNormal"><span style="font-size: 12pt; font-family: 'Times New Roman', serif;" class="">Send yt-users mailing list submissions to<br class=""> <span class="Apple-converted-space"> </span><a href="mailto:yt-users@lists.spacepope.org" target="_blank" class="">yt-users@lists.spacepope.org</a><br class=""><br class="">To subscribe or unsubscribe via the World Wide Web, visit<br class=""> <span class="Apple-converted-space"> </span><a href="https://urldefense.proofpoint.com/v2/url?u=http-3A__lists.spacepope.org_listinfo.cgi_yt-2Dusers-2Dspacepope.org&d=BQMFaQ&c=8hUWFZcy2Z-Za5rBPlktOQ&r=hgcBC3x6dKFoTrmFmMYYbKNfiHZlGLKliIidd1LwmHI&m=BOYrYD1LYgs8DNlrh2pgGZtwTy0-mi7gr4RfFFVNEyc&s=CcoB_oBJNykL4N2K9L8QfEx1xXUaJFkUCtiF6-6At5Y&e=" target="_blank" class="">http://lists.spacepope.org/listinfo.cgi/yt-users-spacepope.org</a><br class="">or, via email, send a message with subject or body 'help' to<br class=""> <span class="Apple-converted-space"> </span><a href="mailto:yt-users-request@lists.spacepope.org" target="_blank" class="">yt-users-request@lists.spacepope.org</a><br class=""><br class="">You can reach the person managing the list at<br class=""> <span class="Apple-converted-space"> </span><a href="mailto:yt-users-owner@lists.spacepope.org" target="_blank" class="">yt-users-owner@lists.spacepope.org</a><br class=""><br class="">When replying, please edit your Subject line so it is more specific<br class="">than "Re: Contents of yt-users digest..."<br class=""><br class=""><br class="">Today's Topics:<br class=""><br class=""> 1. Re: problem with slices in non-unitary volumes (Nathan Goldbaum)<br class=""><br class=""><br class="">----------------------------------------------------------------------<br class=""><br class="">Message: 1<br class="">Date: Wed, 23 Dec 2015 17:17:56 -0600<br class="">From: Nathan Goldbaum <<a href="mailto:nathan12343@gmail.com" target="_blank" class="">nathan12343@gmail.com</a>><br class="">To: Discussion of the yt analysis package<br class=""> <span class="Apple-converted-space"> </span><<a href="mailto:yt-users@lists.spacepope.org" target="_blank" class="">yt-users@lists.spacepope.org</a>><br class="">Subject: Re: [yt-users] problem with slices in non-unitary volumes<br class="">Message-ID:<br class=""> <span class="Apple-converted-space"> </span><<a href="mailto:CAJXewOmVEX-qB41doTk%2B7DT1AOLsn53KMb8nvfr8dwyFrKY-4g@mail.gmail.com" target="_blank" class="">CAJXewOmVEX-qB41doTk+7DT1AOLsn53KMb8nvfr8dwyFrKY-4g@mail.gmail.com</a>><br class="">Content-Type: text/plain; charset="utf-8"<br class=""><br class="">I get the same error over here. I think it's unrelated to the other error.<br class="">The relevant portion of the C stack trace is here:<br class=""><br class="">Thread 0 Crashed:: Dispatch queue: com.apple.main-thread<br class="">0 libsystem_kernel.dylib 0x00007fff8b615286 __pthread_kill + 10<br class="">1 libsystem_c.dylib 0x00007fff8bc2a9ab abort + 129<br class="">2 libsystem_malloc.dylib 0x00007fff915d5fe2 szone_error + 625<br class="">3 libsystem_malloc.dylib 0x00007fff915cf374<br class="">small_free_list_remove_ptr + 154<br class="">4 libsystem_malloc.dylib 0x00007fff915cac3f<br class="">szone_free_definite_size + 1856<br class="">5 multiarray.so 0x00000001044c2d16 npy_free_cache + 70<br class="">6 multiarray.so 0x00000001044c6ed6 array_dealloc + 182<br class="">7 selection_routines.so 0x00000001063ffe34<br class="">__pyx_pw_2yt_8geometry_18selection_routines_13SliceSelector_3fill_mask +<br class="">8804 (selection_routines.c:19749)<br class=""><br class="">Line 19749 of selection_routines.c corresponds to line 1158 in<br class="">selection_routines.pyx, which is the place where the fill_mask member<br class="">variable of the SliceSelector extension type gets defined.<br class=""><br class="">Unfortunately, I have no idea how to debug this from here...<br class=""><br class="">-Nathan<br class=""><br class="">On Wed, Dec 23, 2015 at 4:57 PM, Brian O'Shea <<a href="mailto:bwoshea@gmail.com" target="_blank" class="">bwoshea@gmail.com</a>> wrote:<br class=""><br class="">> Actually, interesting followup here - I have to take it back. When I do a<br class="">> projection plot:<br class="">><br class="">> yt.ProjectionPlot(ds,'x',("gas",<br class="">> "temperature"),center=[0.0,0.0,0.0],width=(0.2,'Mpc')).save()<br class="">><br class="">> the behavior is perfectly fine and I get projections that look sensible.<br class="">> *however*, when I do a slice plot:<br class="">><br class="">> yt.SlicePlot(ds,'x',("gas",<br class="">> "temperature"),center=[0.0,0.0,0.0],width=(0.2,'Mpc')).save()<br class="">><br class="">> I get a malloc error:<br class="">><br class="">> yt : [INFO ] 2015-12-23 17:50:59,082 Gathering a field list (this may<br class="">> take a moment.)<br class="">> yt : [INFO ] 2015-12-23 17:50:59,155 Loading field plugins.<br class="">> yt : [INFO ] 2015-12-23 17:50:59,155 Loaded angular_momentum (8 new<br class="">> fields)<br class="">> yt : [INFO ] 2015-12-23 17:50:59,156 Loaded astro (16 new fields)<br class="">> yt : [INFO ] 2015-12-23 17:50:59,156 Loaded cosmology (23 new fields)<br class="">> yt : [INFO ] 2015-12-23 17:50:59,156 Loaded fluid (64 new fields)<br class="">> yt : [INFO ] 2015-12-23 17:50:59,157 Loaded fluid_vector (96 new<br class="">> fields)<br class="">> yt : [INFO ] 2015-12-23 17:50:59,157 Loaded geometric (112 new fields)<br class="">> yt : [INFO ] 2015-12-23 17:50:59,157 Loaded local (112 new fields)<br class="">> yt : [INFO ] 2015-12-23 17:50:59,157 Loaded magnetic_field (120 new<br class="">> fields)<br class="">> yt : [INFO ] 2015-12-23 17:50:59,158 Loaded my_plugins (120 new fields)<br class="">> yt : [INFO ] 2015-12-23 17:50:59,158 Loaded species (122 new fields)<br class="">> python2.7(12254,0x7fff72d19310) malloc: *** error for object 0x103e39008:<br class="">> incorrect checksum for freed object - object was probably modified after<br class="">> being freed.<br class="">> *** set a breakpoint in malloc_error_break to debug<br class="">> Abort trap: 6<br class="">><br class="">> This happens on my Mac (OS X 10.9.5, LLVM v6.0) and also on my Linux<br class="">> machine (Ubuntu 13.04, gcc 4.6.3), although on the linux machine I just get<br class="">> a seg fault instead of the malloc stuff. Using pdb (python -m pdb<br class="">> crashing_script.py) gives me the same error with no additional information.<br class="">><br class="">><br class="">> On Wed, Dec 23, 2015 at 5:40 PM, Brian O'Shea <<a href="mailto:bwoshea@gmail.com" target="_blank" class="">bwoshea@gmail.com</a>> wrote:<br class="">><br class="">>> Bugfix confirmed; this works for me as well. Thank you very much!<br class="">>><br class="">>> On Wed, Dec 23, 2015 at 5:18 PM, Nathan Goldbaum <<a href="mailto:nathan12343@gmail.com" target="_blank" class="">nathan12343@gmail.com</a>><br class="">>> wrote:<br class="">>><br class="">>>> I've opened a pull request that allows me to load your dataset:<br class="">>>><br class="">>>><br class="">>>><span class="Apple-converted-space"> </span><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=BOYrYD1LYgs8DNlrh2pgGZtwTy0-mi7gr4RfFFVNEyc&s=C10HPEKVKo2n1N6WxH9Z_M9a9BiUk52wJpaCyMe-e9U&e=" target="_blank" class="">https://bitbucket.org/yt_analysis/yt/pull-requests/1915/bugfix-avoid-creating-particle-unions-for/diff</a><br class="">>>><br class="">>>> On Wed, Dec 23, 2015 at 4:08 PM, Brian O'Shea <<a href="mailto:bwoshea@gmail.com" target="_blank" class="">bwoshea@gmail.com</a>> wrote:<br class="">>>><br class="">>>>> Oh, interesting. Is there a way to circumvent auto-detection of fields?<br class="">>>>><br class="">>>>> On Wed, Dec 23, 2015 at 4:35 PM, Nathan Goldbaum <<a href="mailto:nathan12343@gmail.com" target="_blank" class="">nathan12343@gmail.com</a><br class="">>>>> > wrote:<br class="">>>>><br class="">>>>>> It looks like field detection is breaking for this Enzo-3.0 active<br class="">>>>>> particle dataset. StoredEnergy is available on-disk as ('AGNParticle,<br class="">>>>>> 'StoredEnergy'), but for some reason the field detection system isn't able<br class="">>>>>> to guess that.<br class="">>>>>><br class="">>>>>> On Wed, Dec 23, 2015 at 3:19 PM, Nathan Goldbaum <<br class="">>>>>><span class="Apple-converted-space"> </span><a href="mailto:nathan12343@gmail.com" target="_blank" class="">nathan12343@gmail.com</a>> wrote:<br class="">>>>>><br class="">>>>>>><br class="">>>>>>><br class="">>>>>>> On Wed, Dec 23, 2015 at 11:20 AM, Brian O'Shea <<a href="mailto:bwoshea@gmail.com" target="_blank" class="">bwoshea@gmail.com</a>><br class="">>>>>>> wrote:<br class="">>>>>>><br class="">>>>>>>> Dear yt-users,<br class="">>>>>>>><br class="">>>>>>>> I'm having a problem with making slices in non-unitary volumes. I<br class="">>>>>>>> have a 3D enzo simulation that has domain bounds of (-1.6...1.6) in every<br class="">>>>>>>> dimension (units of megaparsecs), and after I updated to the tip of yt-3<br class="">>>>>>>> (changeset d9502d848029) from a fairly old version of the code I suddenly<br class="">>>>>>>> have problems with making simple projections. If I run this set of<br class="">>>>>>>> commands:<br class="">>>>>>>><br class="">>>>>>>><br class="">>>>>>> Any idea which version you updated from? I tried on yt-3.1 and get<br class="">>>>>>> the same error. This is just so we can bisect and find the change that<br class="">>>>>>> introduced the regression.<br class="">>>>>>><br class="">>>>>>><br class="">>>>>>>> import yt<br class="">>>>>>>> ds = yt.load("DD0400/DD0400")<br class="">>>>>>>> proj =<br class="">>>>>>>> yt.SlicePlot(ds,'x','temperature',center=[0.0,0.0,0.0],width=(0.2,'Mpc'))<br class="">>>>>>>><br class="">>>>>>>> I get this error:<br class="">>>>>>>><br class="">>>>>>>><span class="Apple-converted-space"> </span><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=BOYrYD1LYgs8DNlrh2pgGZtwTy0-mi7gr4RfFFVNEyc&s=AMTPRC44biA-nsZoO5-88a3DK1J9eOarfnsWv51RN2o&e=" target="_blank" class="">http://paste.yt-project.org/show/6115/</a><br class="">>>>>>>><br class="">>>>>>>> This seems to work fine on an Enzo cosmological dataset (domain<br class="">>>>>>>> bounds 0-1 in each dimension), and previously worked fine in yt-3 (using a<br class="">>>>>>>> version of the code from a couple of months ago).<br class="">>>>>>>><br class="">>>>>>>> is this a bug, or am I doing something dumb?<br class="">>>>>>>><br class="">>>>>>>> Thanks!<br class="">>>>>>>><br class="">>>>>>>> --Brian<br class="">>>>>>>><br class="">>>>>>>><br class="">>>>>>>> _______________________________________________<br class="">>>>>>>> yt-users mailing list<br class="">>>>>>>><span class="Apple-converted-space"> </span><a href="mailto:yt-users@lists.spacepope.org" target="_blank" class="">yt-users@lists.spacepope.org</a><br class="">>>>>>>><span class="Apple-converted-space"> </span><a href="https://urldefense.proofpoint.com/v2/url?u=http-3A__lists.spacepope.org_listinfo.cgi_yt-2Dusers-2Dspacepope.org&d=BQMFaQ&c=8hUWFZcy2Z-Za5rBPlktOQ&r=hgcBC3x6dKFoTrmFmMYYbKNfiHZlGLKliIidd1LwmHI&m=BOYrYD1LYgs8DNlrh2pgGZtwTy0-mi7gr4RfFFVNEyc&s=CcoB_oBJNykL4N2K9L8QfEx1xXUaJFkUCtiF6-6At5Y&e=" target="_blank" class="">http://lists.spacepope.org/listinfo.cgi/yt-users-spacepope.org</a><br class="">>>>>>>><br class="">>>>>>>><br class="">>>>>>><br class="">>>>>><br class="">>>>>> _______________________________________________<br class="">>>>>> yt-users mailing list<br class="">>>>>><span class="Apple-converted-space"> </span><a href="mailto:yt-users@lists.spacepope.org" target="_blank" class="">yt-users@lists.spacepope.org</a><br class="">>>>>><span class="Apple-converted-space"> </span><a href="https://urldefense.proofpoint.com/v2/url?u=http-3A__lists.spacepope.org_listinfo.cgi_yt-2Dusers-2Dspacepope.org&d=BQMFaQ&c=8hUWFZcy2Z-Za5rBPlktOQ&r=hgcBC3x6dKFoTrmFmMYYbKNfiHZlGLKliIidd1LwmHI&m=BOYrYD1LYgs8DNlrh2pgGZtwTy0-mi7gr4RfFFVNEyc&s=CcoB_oBJNykL4N2K9L8QfEx1xXUaJFkUCtiF6-6At5Y&e=" target="_blank" class="">http://lists.spacepope.org/listinfo.cgi/yt-users-spacepope.org</a><br class="">>>>>><br class="">>>>>><br class="">>>>><br class="">>>>> _______________________________________________<br class="">>>>> yt-users mailing list<br class="">>>>><span class="Apple-converted-space"> </span><a href="mailto:yt-users@lists.spacepope.org" target="_blank" class="">yt-users@lists.spacepope.org</a><br class="">>>>><span class="Apple-converted-space"> </span><a href="https://urldefense.proofpoint.com/v2/url?u=http-3A__lists.spacepope.org_listinfo.cgi_yt-2Dusers-2Dspacepope.org&d=BQMFaQ&c=8hUWFZcy2Z-Za5rBPlktOQ&r=hgcBC3x6dKFoTrmFmMYYbKNfiHZlGLKliIidd1LwmHI&m=BOYrYD1LYgs8DNlrh2pgGZtwTy0-mi7gr4RfFFVNEyc&s=CcoB_oBJNykL4N2K9L8QfEx1xXUaJFkUCtiF6-6At5Y&e=" target="_blank" class="">http://lists.spacepope.org/listinfo.cgi/yt-users-spacepope.org</a><br class="">>>>><br class="">>>>><br class="">>>><br class="">>>> _______________________________________________<br class="">>>> yt-users mailing list<br class="">>>><span class="Apple-converted-space"> </span><a href="mailto:yt-users@lists.spacepope.org" target="_blank" class="">yt-users@lists.spacepope.org</a><br class="">>>><span class="Apple-converted-space"> </span><a href="https://urldefense.proofpoint.com/v2/url?u=http-3A__lists.spacepope.org_listinfo.cgi_yt-2Dusers-2Dspacepope.org&d=BQMFaQ&c=8hUWFZcy2Z-Za5rBPlktOQ&r=hgcBC3x6dKFoTrmFmMYYbKNfiHZlGLKliIidd1LwmHI&m=BOYrYD1LYgs8DNlrh2pgGZtwTy0-mi7gr4RfFFVNEyc&s=CcoB_oBJNykL4N2K9L8QfEx1xXUaJFkUCtiF6-6At5Y&e=" target="_blank" class="">http://lists.spacepope.org/listinfo.cgi/yt-users-spacepope.org</a><br class="">>>><br class="">>>><br class="">>><br class="">><br class="">> _______________________________________________<br class="">> yt-users mailing list<br class="">><span class="Apple-converted-space"> </span><a href="mailto:yt-users@lists.spacepope.org" target="_blank" class="">yt-users@lists.spacepope.org</a><br class="">><span class="Apple-converted-space"> </span><a 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class="">****************************************<u class=""></u><u class=""></u></span></p></blockquote></div><p class="MsoNormal"><span style="font-size: 12pt; font-family: 'Times New Roman', serif; color: rgb(136, 136, 136);" class=""><br class=""><br clear="all" class=""><br class="">--<span class="Apple-converted-space"> </span><u class=""></u><u class=""></u></span></p><div class=""><div class=""><p class="MsoNormal"><b class=""><i class=""><span style="font-size: 10pt; font-family: Arial, sans-serif; color: rgb(80, 0, 80);" class="">SK<sup class="">2</sup></span></i></b><span style="font-size: 10pt; font-family: Arial, sans-serif; color: rgb(80, 0, 80);" class=""><u class=""></u><u class=""></u></span></p></div><div class=""><p class="MsoNormal"><span style="font-size: 10pt; font-family: Arial, sans-serif; color: rgb(80, 0, 80);" class=""><u class=""></u> <u class=""></u></span></p></div><div class=""><p class="MsoNormal"><b class=""><sup class=""><span style="font-size: 12pt; font-family: Arial, sans-serif; color: rgb(80, 0, 80);" class="">"</span></sup></b><b class=""><span style="font-size: 12pt; font-family: Arial, sans-serif; color: rgb(80, 0, 80);" class="">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.<sup class="">"</sup></span></b><span style="font-size: 12pt; font-family: 'Times New Roman', serif; color: rgb(136, 136, 136);" class=""><u class=""></u><u class=""></u></span></p></div><div class=""><p class="MsoNormal"><span style="font-size: 10pt; font-family: Arial, sans-serif; color: rgb(80, 0, 80);" class=""><u class=""></u> <u class=""></u></span></p></div></div></div></div></div></div><p class="MsoNormal" style="margin-bottom: 12pt;"><span style="font-size: 12pt; font-family: 'Times New Roman', serif;" class=""><br class="">_______________________________________________<br class="">yt-users mailing list<br class=""><a href="mailto:yt-users@lists.spacepope.org" target="_blank" class="">yt-users@lists.spacepope.org</a><br class=""><a href="https://urldefense.proofpoint.com/v2/url?u=http-3A__lists.spacepope.org_listinfo.cgi_yt-2Dusers-2Dspacepope.org&d=BQMFaQ&c=8hUWFZcy2Z-Za5rBPlktOQ&r=hgcBC3x6dKFoTrmFmMYYbKNfiHZlGLKliIidd1LwmHI&m=BOYrYD1LYgs8DNlrh2pgGZtwTy0-mi7gr4RfFFVNEyc&s=CcoB_oBJNykL4N2K9L8QfEx1xXUaJFkUCtiF6-6At5Y&e=" target="_blank" class="">http://lists.spacepope.org/listinfo.cgi/yt-users-spacepope.org</a></span><span style="font-size: 12pt; font-family: 'Times New Roman', serif;" class=""><u class=""></u><u class=""></u></span></p></blockquote></div><p class="MsoNormal"><span style="font-size: 12pt; font-family: 'Times New Roman', serif;" class=""><u class=""></u> <u class=""></u></span></p></div></div></div></blockquote></div><p class="MsoNormal"><span style="font-size: 12pt; font-family: 'Times New Roman', serif;" class=""><br class=""><br clear="all" class=""><br class="">--<span class="Apple-converted-space"> </span><u class=""></u><u class=""></u></span></p><div class=""><div class=""><p class="MsoNormal"><b class=""><i class=""><span style="font-size: 10pt; font-family: Arial, sans-serif; color: rgb(80, 0, 80);" class="">SK<sup class="">2</sup></span></i></b><span style="font-size: 10pt; font-family: Arial, sans-serif; color: rgb(80, 0, 80);" class=""><u class=""></u><u class=""></u></span></p></div><div class=""><p class="MsoNormal"><span style="font-size: 10pt; font-family: Arial, sans-serif; color: rgb(80, 0, 80);" class=""><u class=""></u> <u class=""></u></span></p></div><div class=""><p class="MsoNormal"><b class=""><sup class=""><span style="font-size: 12pt; font-family: Arial, sans-serif; color: rgb(80, 0, 80);" class="">"</span></sup></b><b class=""><span style="font-size: 12pt; font-family: Arial, sans-serif; color: rgb(80, 0, 80);" class="">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.<sup class="">"</sup></span></b><span style="font-size: 12pt; font-family: 'Times New Roman', serif;" class=""><u class=""></u><u class=""></u></span></p></div><div class=""><p class="MsoNormal"><span style="font-size: 10pt; font-family: Arial, sans-serif; color: rgb(80, 0, 80);" class=""><u class=""></u> <u class=""></u></span></p></div></div></div></div></div></blockquote></div><p class="MsoNormal"><span style="font-size: 12pt; font-family: 'Times New Roman', serif;" class=""><u class=""></u> <u class=""></u></span></p></div></blockquote></div></div></div></div></blockquote></div></div><p class="MsoNormal"><span style="font-size: 12pt; font-family: 'Times New Roman', serif;" class=""><u class=""></u> <u class=""></u></span></p><p class="MsoNormal"><u class=""></u> <u class=""></u></p></div></div></div></div></blockquote></div><br class=""><br clear="all" class=""><br class="">--<span class="Apple-converted-space"> </span><br class=""><div class="gmail_signature"><span style="border-collapse: collapse;" class=""><div style="color: rgb(80, 0, 80); font-family: arial, sans-serif; font-size: 13px;" class=""><span style="font-family: arial, sans-serif; font-size: 13px; border-collapse: collapse;" class=""><b class=""><i class="">SK<sup class="">2</sup></i></b></span></div><div style="color: rgb(80, 0, 80); font-family: arial, sans-serif; font-size: 13px;" class=""><span style="font-family: arial, sans-serif; font-size: 13px; border-collapse: collapse;" class=""><b class=""><i class=""><sup class=""><br class=""></sup></i></b></span></div><div class=""><span style="color: rgb(80, 0, 80); font-family: arial, sans-serif; border-collapse: collapse;" class=""><b class=""><sup class="">"</sup></b></span><font color="#500050" face="arial, sans-serif" class=""><b class="">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;" class=""><sup class="">"</sup></b></div><div style="color: rgb(80, 0, 80); font-family: arial, sans-serif; font-size: 13px;" class=""><br class=""></div></span></div></div><span style="font-family: Helvetica; font-size: 12px; font-style: normal; font-variant: normal; font-weight: normal; letter-spacing: normal; orphans: auto; text-align: start; text-indent: 0px; text-transform: none; white-space: normal; widows: auto; word-spacing: 0px; -webkit-text-stroke-width: 0px; float: none; display: inline !important;" class="">_______________________________________________</span><br style="font-family: Helvetica; font-size: 12px; font-style: normal; font-variant: normal; font-weight: normal; letter-spacing: normal; orphans: auto; text-align: start; text-indent: 0px; text-transform: none; white-space: normal; widows: auto; word-spacing: 0px; -webkit-text-stroke-width: 0px;" class=""><span style="font-family: Helvetica; font-size: 12px; font-style: normal; font-variant: normal; font-weight: normal; letter-spacing: normal; orphans: auto; text-align: start; text-indent: 0px; text-transform: none; white-space: normal; widows: auto; word-spacing: 0px; -webkit-text-stroke-width: 0px; float: none; display: inline !important;" class="">yt-users mailing list</span><br style="font-family: Helvetica; font-size: 12px; font-style: normal; font-variant: normal; font-weight: normal; letter-spacing: normal; orphans: auto; text-align: start; text-indent: 0px; text-transform: none; white-space: normal; widows: auto; word-spacing: 0px; -webkit-text-stroke-width: 0px;" class=""><a href="mailto:yt-users@lists.spacepope.org" style="font-family: Helvetica; font-size: 12px; font-style: normal; font-variant: normal; font-weight: normal; letter-spacing: normal; orphans: auto; text-align: start; text-indent: 0px; text-transform: none; white-space: normal; widows: auto; word-spacing: 0px; -webkit-text-stroke-width: 0px;" class="">yt-users@lists.spacepope.org</a><br style="font-family: Helvetica; font-size: 12px; font-style: normal; font-variant: normal; font-weight: normal; letter-spacing: normal; orphans: auto; text-align: start; text-indent: 0px; text-transform: none; white-space: normal; widows: auto; word-spacing: 0px; -webkit-text-stroke-width: 0px;" class=""><a href="https://urldefense.proofpoint.com/v2/url?u=http-3A__lists.spacepope.org_listinfo.cgi_yt-2Dusers-2Dspacepope.org&d=BQMFaQ&c=8hUWFZcy2Z-Za5rBPlktOQ&r=hgcBC3x6dKFoTrmFmMYYbKNfiHZlGLKliIidd1LwmHI&m=BOYrYD1LYgs8DNlrh2pgGZtwTy0-mi7gr4RfFFVNEyc&s=CcoB_oBJNykL4N2K9L8QfEx1xXUaJFkUCtiF6-6At5Y&e=" style="font-family: Helvetica; font-size: 12px; font-style: normal; font-variant: normal; font-weight: normal; letter-spacing: normal; orphans: auto; text-align: start; text-indent: 0px; text-transform: none; white-space: normal; widows: auto; word-spacing: 0px; -webkit-text-stroke-width: 0px;" class="">http://lists.spacepope.org/listinfo.cgi/yt-users-spacepope.org</a></div></blockquote></div><br class=""></div></body></html>