<html><head><meta http-equiv="Content-Type" content="text/html charset=windows-1252"></head><body style="word-wrap: break-word; -webkit-nbsp-mode: space; -webkit-line-break: after-white-space;"><div style="margin: 0px; font-size: 10px; font-family: Monaco;">Here’s are examples of the problem. yt fails immediately with any usage. As you can see, I don’t have a lot of information here!</div><div style="margin: 0px; font-size: 10px; font-family: Monaco;"><br></div><div style="margin: 0px; font-size: 10px; font-family: Monaco;"><br></div><div style="margin: 0px; font-size: 10px; font-family: Monaco;">[yt-x86_64] sagittariusb 1 % yt</div><div style="margin: 0px; font-size: 10px; font-family: Monaco;">Abort</div><div style="margin: 0px; font-size: 10px; font-family: Monaco;">[yt-x86_64] sagittariusb 2 % yt --help</div><div style="margin: 0px; font-size: 10px; font-family: Monaco;">Abort</div><div style="margin: 0px; font-size: 10px; font-family: Monaco;">[yt-x86_64] sagittariusb 3 % python</div><div style="margin: 0px; font-size: 10px; font-family: Monaco;">Python 2.7.8 (default, Sep 28 2014, 20:55:56) </div><div style="margin: 0px; font-size: 10px; font-family: Monaco;">[GCC 4.2.1 Compatible Apple LLVM 6.0 (clang-600.0.51)] on darwin</div><div style="margin: 0px; font-size: 10px; font-family: Monaco;">Type "help", "copyright", "credits" or "license" for more information.</div><div style="margin: 0px; font-size: 10px; font-family: Monaco;">>>> import yt</div><div style="margin: 0px; font-size: 10px; font-family: Monaco;">Abort</div><div style="margin: 0px; font-size: 10px; font-family: Monaco;">[yt-x86_64] sagittariusb 4 % </div><div><br></div><div>I tried your suggestion of using the bash activate script:</div><div><br></div><div><div style="margin: 0px; font-size: 13px; font-family: Monaco;">[yt-x86_64] sagittariusB 40 % bash yt-x86_64/bin/activate</div><div style="margin: 0px; font-size: 13px; font-family: Monaco;">[yt-x86_64] sagittariusB 41 % yt</div><div style="margin: 0px; font-size: 13px; font-family: Monaco;">Abort</div><div style="margin: 0px; font-size: 13px; font-family: Monaco;">[yt-x86_64] sagittariusB 42 % </div><div><br></div><div><br></div><div>FWIW, I do note that the “Abort” appears to be appearing a lot faster with the readline problem corrected.</div><div><br></div><div>- Mordecai</div><div><br></div><div><br></div><div>Begin forwarded message:</div><br class="Apple-interchange-newline"><blockquote type="cite"><div style="margin-top: 0px; margin-right: 0px; margin-bottom: 0px; margin-left: 0px;"><span style="font-family:'Helvetica'; color:rgba(0, 0, 0, 1.0);"><b>From: </b></span><span style="font-family:'Helvetica';">Nathan Goldbaum <<a href="mailto:nathan12343@gmail.com">nathan12343@gmail.com</a>><br></span></div><div style="margin-top: 0px; margin-right: 0px; margin-bottom: 0px; margin-left: 0px;"><span style="font-family:'Helvetica'; color:rgba(0, 0, 0, 1.0);"><b>Subject: </b></span><span style="font-family:'Helvetica';"><b>Re: [yt-users] install failure</b><br></span></div><div style="margin-top: 0px; margin-right: 0px; margin-bottom: 0px; margin-left: 0px;"><span style="font-family:'Helvetica'; color:rgba(0, 0, 0, 1.0);"><b>Date: </b></span><span style="font-family:'Helvetica';">September 28, 2014 at 21:38:36 EDT<br></span></div><div style="margin-top: 0px; margin-right: 0px; margin-bottom: 0px; margin-left: 0px;"><span style="font-family:'Helvetica'; color:rgba(0, 0, 0, 1.0);"><b>To: </b></span><span style="font-family:'Helvetica';">Mordecai-Mark Mac Low <<a href="mailto:mordecai@amnh.org">mordecai@amnh.org</a>><br></span></div><div style="margin-top: 0px; margin-right: 0px; margin-bottom: 0px; margin-left: 0px;"><span style="font-family:'Helvetica'; color:rgba(0, 0, 0, 1.0);"><b>Cc: </b></span><span style="font-family:'Helvetica';"><<a href="mailto:teuben@astro.umd.edu">teuben@astro.umd.edu</a>><br></span></div><br><div><meta http-equiv="Content-Type" content="text/html; charset=utf-8"><div dir="ltr"><div><br></div><div>In your original message you said that you were using activate.csh - can you under bash with the bash activate script?</div><div><br></div><div>When you say "on startup", can you copy/paste a session where the error happens? Are you saying that python is failing to start or do you get the abort error when you import yt?<br><div><div class="gmail_extra"><br><div class="gmail_quote">On Sun, Sep 28, 2014 at 6:35 PM, Mordecai-Mark Mac Low <span dir="ltr"><<a href="mailto:mordecai@amnh.org" target="_blank">mordecai@amnh.org</a>></span> wrote:<br><blockquote class="gmail_quote" style="margin:0 0 0 .8ex;border-left:1px #ccc solid;padding-left:1ex"><div style="word-wrap:break-word">I’m taking this off the general list for the moment…<div><br></div><div>I have replaced readline with gnureadline as you suggested, and that does eliminate the error during installation (see <a href="https://dl.dropboxusercontent.com/u/31830722/yt_install-v2.log" target="_blank">https://dl.dropboxusercontent.com/u/31830722/yt_install-v2.log</a>). Unfortunately, it doesn’t change the behavior on startup: Abort, with no further errors.</div></div></blockquote><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; position: static; z-index: auto;"><div style="word-wrap:break-word"><div><br></div><div>At Peter Teuben’s suggestion, I also ran dtruss on this, but he saw nothing obviously wrong — just a whole lot of files being opened (around 900 at his estimate).</div><span class="HOEnZb"><font color="#888888"><div><br></div><div>- Mordecai</div><div><br></div></font></span><div> <br><div><span class=""><div>On Sep 28, 2014, at 20:45, Nathan Goldbaum <<a href="mailto:nathan12343@gmail.com" target="_blank">nathan12343@gmail.com</a>> wrote:</div><br></span><div><div class="h5"><blockquote type="cite"><div dir="ltr"><div><br></div><div><div class="gmail_quote">---------- Forwarded message ----------<br>From: <b class="gmail_sendername">Nathan Goldbaum</b> <span dir="ltr"><<a href="mailto:nathan12343@gmail.com" target="_blank">nathan12343@gmail.com</a>></span><br>Date: Sun, Sep 28, 2014 at 5:29 PM<br>Subject: Re: [yt-users] install failure<br>To: Discussion of the yt analysis package <<a href="mailto:yt-users@lists.spacepope.org" target="_blank">yt-users@lists.spacepope.org</a>><br><br><br><div dir="ltr">So looking at the install log, it's actually the install script that's trying to build readline, right here: <a href="https://bitbucket.org/yt_analysis/yt/src/4cf5c5369df9b012759ab979330d8e356d1b0e00/doc/install_script.sh?at=yt#cl-987" target="_blank">https://bitbucket.org/yt_analysis/yt/src/4cf5c5369df9b012759ab979330d8e356d1b0e00/doc/install_script.sh?at=yt#cl-987</a><div><br></div><div>I'm actually able to reproduce this on my OSX Mavericks laptop when I do "pip install readline". It seems that the readline package on pypi hasn't been updated since 2012: <a href="https://pypi.python.org/pypi/readline" target="_blank">https://pypi.python.org/pypi/readline</a>. </div><div><br></div><div>I never noticed this issue because I use homebrew's python, and homebrew links against the gnu readline library when they build python.</div><div><br></div><div>It seems the gnureadline package has supplanted the old readline package: <a href="https://pypi.python.org/pypi/gnureadline" target="_blank">https://pypi.python.org/pypi/gnureadline</a></div><div><br></div><div>I've gone ahead and created a pull request to make the install script install gnureadline instead of readline: <a href="https://bitbucket.org/yt_analysis/yt/pull-request/1225/install-gnureadline-package-since-readline/diff" target="_blank">https://bitbucket.org/yt_analysis/yt/pull-request/1225/install-gnureadline-package-since-readline/diff</a></div><div><br></div><div>You can probably just modify your local copy of the install script to use "pip install gnureadline" instead of "pip install readline".</div><div><br></div><div>Hope that fixes your issue, thanks very much for the report.</div><span><font color="#888888"><div><br></div><div>-Nathan</div></font></span></div><div><div class="gmail_extra"><br><div class="gmail_quote">On Sun, Sep 28, 2014 at 5:00 PM, Mordecai-Mark Mac Low <span dir="ltr"><<a href="mailto:mordecai@amnh.org" target="_blank">mordecai@amnh.org</a>></span> wrote:<br><blockquote class="gmail_quote" style="margin:0 0 0 .8ex;border-left:1px #ccc solid;padding-left:1ex">Nathan,<br>
<br>
I’ve posted the full install log to<br>
<br>
<a href="https://dl.dropboxusercontent.com/u/31830722/yt_install.log" target="_blank">https://dl.dropboxusercontent.com/u/31830722/yt_install.log</a><br>
<br>
It does look like ipython is trying to compile readline.<br>
<br>
I have the regular Mac Python installation, but would have to learn anaconda or canopy before using them for an installation, which I was hoping to avoid for the moment by using the install script.<br>
<br>
Best,<br>
<br>
Mordecai<br>
<span><br>
<br>
On Sep 28, 2014, at 19:33, <a href="mailto:yt-users-request@lists.spacepope.org" target="_blank">yt-users-request@lists.spacepope.org</a> wrote:<br>
> Message: 1<br>
</span>> Date: Sun, 28 Sep 2014 13:57:47 -0700<br>
<span>> 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>
</span>> Subject: Re: [yt-users] install failure<br>
> Message-ID:<br>
> <CAJXewO=G9M7V0deBGtU46s68kdKPVTqsmhEBxV+yG7-K=<a href="mailto:8HcgQ@mail.gmail.com" target="_blank">8HcgQ@mail.gmail.com</a>><br>
> Content-Type: text/plain; charset="utf-8"<br>
<span>><br>
> Hi Mordecai,<br>
><br>
> We've had some reports about incompatibilities with the install script on<br>
> OS X Mavericks recently, but I don't think this error has been reported<br>
> before. Unfortunately getting the install script to work portably in all<br>
> cases is a labor of love and sometimes errors like these crop up.<br>
><br>
> Googling for your error returns this discussion on the readline mailing<br>
> list: <a href="https://lists.gnu.org/archive/html/bug-readline/2013-12/msg00002.html" target="_blank">https://lists.gnu.org/archive/html/bug-readline/2013-12/msg00002.html</a>.<br>
> Apparently the version you're compiling needs to be patched to compile<br>
> cleanly on mavericks. I haven't checked whether the patch has made its way<br>
> into a readline release.<br>
><br>
> I'm not sure what exactly is compiling readline (IPython maybe?), but<br>
> earlier in the install script we should have installed a pure-python<br>
> version of the readline library from pypi if we were unable to import it.<br>
> It would help to figure out what went wrong if you could upload the full<br>
> install log somewhere.<br>
><br>
> Do you have a python environment setup on your laptop already? It's very<br>
> straightforward to install yt using anaconda, canopy, or a manually<br>
> configured python environment, bypassing all the bootstrapping that the<br>
> install script must do. Take a look at the following page in the<br>
> documentation:<br>
><br>
> <a href="http://yt-project.org/doc/installing.html#installing-yt-using-anaconda" target="_blank">http://yt-project.org/doc/installing.html#installing-yt-using-anaconda</a><br>
> <a href="http://yt-project.org/doc/installing.html#installing-yt-using-pip-or-from-source" target="_blank">http://yt-project.org/doc/installing.html#installing-yt-using-pip-or-from-source</a><br>
><br>
> Hope that's helpful.<br>
><br>
</span>> -Nathan<br>
><br>
><br>
> On Sun, Sep 28, 2014 at 12:36 PM, Mordecai-Mark Mac Low <<a href="mailto:mordecai@amnh.org" target="_blank">mordecai@amnh.org</a>><br>
<div>> wrote:<br>
><br>
>> Hi, I am having a fatal problem installing yt on my MacBook Pro running OS<br>
>> X v10.9.4. I am using the install script, with the options set as follows:<br>
>><br>
>><br>
>> # Here's where you put the HDF5 path if you like; otherwise it'll download<br>
>> it<br>
>> # and install it on its own<br>
>> #HDF5_DIR=/opt/local/lib<br>
>><br>
>> # If you need to supply arguments to the NumPy or SciPy build, supply them<br>
>> here<br>
>> # This one turns on gfortran manually:<br>
>> #NUMPY_ARGS="--fcompiler=gnu95"<br>
>> # If you absolutely can't get the fortran to work, try this:<br>
>> #NUMPY_ARGS="--fcompiler=fake"<br>
>><br>
>> INST_HG=0 # Install Mercurial or not? If hg is not already<br>
>> # installed, yt cannot be installed.<br>
>> INST_ZLIB=1 # On some systems (Kraken) matplotlib has issues with<br>
>> # the system zlib, which is compiled statically.<br>
>> # If need be, you can turn this off.<br>
>> INST_BZLIB=1 # On some systems, libbzip2 is missing. This can<br>
>> # lead to broken mercurial installations.<br>
>> INST_PNG=1 # Install a local libpng? Same things apply as with zlib.<br>
>> INST_FTYPE=1 # Install FreeType2 locally?<br>
>> INST_ENZO=0 # Clone a copy of Enzo?<br>
>> INST_SQLITE3=1 # Install a local version of SQLite3?<br>
>> INST_PYX=1 # Install PyX? Sometimes PyX can be problematic without a<br>
>> # working TeX installation.<br>
>> INST_0MQ=1 # Install 0mq (for IPython) and affiliated bindings?<br>
>> INST_ROCKSTAR=1 # Install the Rockstar halo finder?<br>
>> INST_SCIPY=0 # Install scipy?<br>
>><br>
>><br>
>> After downloading and activating Xcode command line tools, I got the<br>
>> script to complete successfully. I activated it using the activate.csh<br>
>> script.<br>
>><br>
>> However, when I then try to start yt, it pauses for 30 seconds or so, and<br>
>> then issues the response ?Abort?, with no further errors. I get the same<br>
>> response if I try to import yt into the python (running in the yt<br>
>> environment). Abort, and return to the command line.<br>
>><br>
>> I have tried erasing the yt-x86_64 directory and reinstalling from<br>
>> scratch, with no change in behavior. I also examined the yt_install.log.<br>
>> I found a number of, presumably irrelevant, errors in the configuration<br>
>> tests, but also an error at the end of the long section on building Ipython<br>
>> (almost at the end of the script, just before readline assembly that looks<br>
>> possibly relevant:<br>
>><br>
>> gcc -dynamic -arch i386 -arch x86_64 -arch_only `/usr/bin/arch`<br>
>> -install_name /usr/local/lib/libreadline.6.2.dylib -current_version 6.2<br>
>> -compatibility_version 6 -v -o libreadline.6.2.dylib readline.so vi_mode.so<br>
>> funmap.so keymaps.so parens.so search.so rltty.so complete.so bind.so<br>
>> isearch.so display.so signals.so util.so kill.so undo.so macro.so input.so<br>
>> callback.so terminal.so text.so nls.so misc.so xmalloc.so xfree.so<br>
>> history.so histexpand.so histfile.so histsearch.so shell.so mbutil.so<br>
>> tilde.so compat.so -lncurses<br>
>> Apple LLVM version 6.0 (clang-600.0.51) (based on LLVM 3.5svn)<br>
>> Target: x86_64-apple-darwin13.3.0<br>
>> Thread model: posix<br>
>> clang: error: invalid argument '-compatibility_version 6' only allowed<br>
>> with '-dynamiclib'<br>
>> clang: error: invalid argument '-compatibility_version 6' only allowed<br>
>> with '-dynamiclib'<br>
>> make[1]: *** [libreadline.6.2.dylib] Error 1<br>
>> make: [shared] Error 2 (ignored)<br>
>><br>
>> Any insight on how to proceed?<br>
>><br>
>> Best,<br>
>><br>
>> Mordecai<br>
>><br>
>><br>
>> --<br>
>> Mordecai-Mark Mac Low Curator & Professor<br>
>> <a href="tel:%2B1-212-496-3443" value="+12124963443" target="_blank">+1-212-496-3443</a> Department of Astrophysics<br>
>> <a href="tel:%2B1-212-769-5007" value="+12127695007" target="_blank">+1-212-769-5007</a> (fax) American Museum of Natural History<br>
>> mmaclow (Skype, Hangout) 79th St at CPW, NY, NY, 10024-5192, USA<br>
>><br>
>><br>
>><br>
>><br>
>><br>
>> _______________________________________________<br>
>> yt-users mailing list<br>
>> <a href="mailto:yt-users@lists.spacepope.org" target="_blank">yt-users@lists.spacepope.org</a><br>
>> <a href="http://lists.spacepope.org/listinfo.cgi/yt-users-spacepope.org" target="_blank">http://lists.spacepope.org/listinfo.cgi/yt-users-spacepope.org</a><br>
>><br>
>><br>
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><br>
> ------------------------------<br>
><br>
> Message: 2<br>
> Date: Sun, 28 Sep 2014 19:33:51 -0400<br>
> From: Professor Maller <<a href="mailto:amaller@citytech.cuny.edu" target="_blank">amaller@citytech.cuny.edu</a>><br>
<span>> To: <a href="mailto:yt-users@lists.spacepope.org" target="_blank">yt-users@lists.spacepope.org</a><br>
> Subject: Re: [yt-users] install failure<br>
> Message-ID:<br>
</span>> <<a href="mailto:CACCSjdNPC0QVrxDooBEQ2W7Mp6KaBJxNJZ9eLvH6TG8WyD7m0Q@mail.gmail.com" target="_blank">CACCSjdNPC0QVrxDooBEQ2W7Mp6KaBJxNJZ9eLvH6TG8WyD7m0Q@mail.gmail.com</a>><br>
> Content-Type: text/plain; charset="utf-8"<br>
<div>><br>
> Hi Mordecai,<br>
><br>
> Depending on what you want to do with yt, if you need the latest build or<br>
> not, but I've had success on Mac with the anaconda distribution of python<br>
> which includes yt-3.0. <a href="https://store.continuum.io/cshop/anaconda/" target="_blank">https://store.continuum.io/cshop/anaconda/</a>.<br>
><br>
><br>
> Ari<br>
><br>
><br>
><br>
> On Sun, Sep 28, 2014 at 4:30 PM, <<a href="mailto:yt-users-request@lists.spacepope.org" target="_blank">yt-users-request@lists.spacepope.org</a>><br>
> wrote:<br>
><br>
>> Send yt-users mailing list submissions to<br>
>> <a href="mailto:yt-users@lists.spacepope.org" target="_blank">yt-users@lists.spacepope.org</a><br>
>><br>
>> To subscribe or unsubscribe via the World Wide Web, visit<br>
>> <a href="http://lists.spacepope.org/listinfo.cgi/yt-users-spacepope.org" target="_blank">http://lists.spacepope.org/listinfo.cgi/yt-users-spacepope.org</a><br>
>> or, via email, send a message with subject or body 'help' to<br>
>> <a href="mailto:yt-users-request@lists.spacepope.org" target="_blank">yt-users-request@lists.spacepope.org</a><br>
>><br>
>> You can reach the person managing the list at<br>
>> <a href="mailto:yt-users-owner@lists.spacepope.org" target="_blank">yt-users-owner@lists.spacepope.org</a><br>
>><br>
>> When replying, please edit your Subject line so it is more specific<br>
>> than "Re: Contents of yt-users digest..."<br>
>><br>
>><br>
>> Today's Topics:<br>
>><br>
>> 1. Re: ProfilePlot in YT-3.0 (Nathan Goldbaum)<br>
>> 2. install failure (Mordecai-Mark Mac Low)<br>
>> 3. Re: install failure (Peter Teuben)<br>
>><br>
>><br>
>> ----------------------------------------------------------------------<br>
>><br>
>> Message: 1<br>
>> Date: Sun, 28 Sep 2014 12:14:04 -0700<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] ProfilePlot in YT-3.0<br>
>> Message-ID:<br>
>> <<br>
>> <a href="mailto:CAJXewOkKaMPBE02RH_VY4rNTXgOobeJ02qOOZY5PRk332GGveg@mail.gmail.com" target="_blank">CAJXewOkKaMPBE02RH_VY4rNTXgOobeJ02qOOZY5PRk332GGveg@mail.gmail.com</a>><br>
>> Content-Type: text/plain; charset="utf-8"<br>
>><br>
>> On Sunday, September 28, 2014, John Regan <<a href="mailto:johnanthonyregan@gmail.com" target="_blank">johnanthonyregan@gmail.com</a>><br>
>> wrote:<br>
>><br>
>>> Hi Nathan,<br>
>>><br>
>>> Thanks for that. I'll have a look at what helper functions would be<br>
>> useful<br>
>>> as I use the ProfilePlot routine and I can issue a PR then. I think it<br>
>>> would be worth updating the docs with info like you just sent me.<br>
>>><br>
>><br>
>> Again, please feel free to open a pull request.<br>
>><br>
>><br>
>>><br>
>>> Cheers,<br>
>>> John<br>
>>><br>
>>> On Sun, Sep 28, 2014 at 11:17 AM, Nathan Goldbaum <<a href="mailto:nathan12343@gmail.com" target="_blank">nathan12343@gmail.com</a><br>
>>> <javascript:_e(%7B%7D,'cvml','<a href="mailto:nathan12343@gmail.com" target="_blank">nathan12343@gmail.com</a>');>> wrote:<br>
>>><br>
>>>> Hi John,<br>
>>>><br>
>>>> ProfilePlot is a wrapper around the Profile1D class, which calculates<br>
>> and<br>
>>>> stores the histograms. To access the underlying data you need to access<br>
>>>> the profile object via the profiles attribute of the ProfilePlot:<br>
>>>><br>
>>>> import yt<br>
>>>> ds = yt.load('IsolatedGalaxy/galaxy0030/galaxy0030')<br>
>>>> plot = yt.ProfilePlot(ds.all_data(), 'radius', 'density')<br>
>>>> profile = plot.profiles[0]<br>
>>>> print profile.x_field, profile.x<br>
>>>> print profile.field_data.keys(), profile['density']<br>
>>>><br>
>>>> There are probably a number of ways that the current API can be improved<br>
>>>> to make it more straightforward to access this data. PRs along this<br>
>> front<br>
>>>> would be very welcome, I think.<br>
>>>><br>
>>>> -Nathan<br>
>>>><br>
>>>> On Sun, Sep 28, 2014 at 1:05 AM, John Regan <<a href="mailto:johnanthonyregan@gmail.com" target="_blank">johnanthonyregan@gmail.com</a><br>
>>>> <javascript:_e(%7B%7D,'cvml','<a href="mailto:johnanthonyregan@gmail.com" target="_blank">johnanthonyregan@gmail.com</a>');>> wrote:<br>
>>>><br>
>>>>> HI All,<br>
>>>>><br>
>>>>> Is there an easy way to access the x_field and the y_fields in the<br>
>>>>> ProfilePlot function?<br>
>>>>><br>
>>>>> So for example<br>
>>>>><br>
>>>>> prof = ProfilePlot(sphere, "radius", "density")<br>
>>>>><br>
>>>>><br>
>>>>> print prof.x_field<br>
>>>>> print prof.y_field[0]<br>
>>>>><br>
>>>>> I inserted a couple of hack functions into the ProfilePlot class to<br>
>>>>> return the x_field and the .items() tuple but there is probably a<br>
>> better<br>
>>>>> way?<br>
>>>>><br>
>>>>> John<br>
>>>>><br>
>>>>> _______________________________________________<br>
>>>>> yt-users mailing list<br>
>>>>> <a href="mailto:yt-users@lists.spacepope.org" target="_blank">yt-users@lists.spacepope.org</a><br>
>>>>> <javascript:_e(%7B%7D,'cvml','<a href="mailto:yt-users@lists.spacepope.org" target="_blank">yt-users@lists.spacepope.org</a>');><br>
>>>>> <a href="http://lists.spacepope.org/listinfo.cgi/yt-users-spacepope.org" target="_blank">http://lists.spacepope.org/listinfo.cgi/yt-users-spacepope.org</a><br>
>>>>><br>
>>>>><br>
>>>><br>
>>>> _______________________________________________<br>
>>>> yt-users mailing list<br>
>>>> <a href="mailto:yt-users@lists.spacepope.org" target="_blank">yt-users@lists.spacepope.org</a><br>
>>>> <javascript:_e(%7B%7D,'cvml','<a href="mailto:yt-users@lists.spacepope.org" target="_blank">yt-users@lists.spacepope.org</a>');><br>
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>>>><br>
>>>><br>
>>><br>
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>>><br>
>><br>
>> ------------------------------<br>
>><br>
>> Message: 2<br>
>> Date: Sun, 28 Sep 2014 15:36:55 -0400<br>
>> From: Mordecai-Mark Mac Low <<a href="mailto:mordecai@amnh.org" target="_blank">mordecai@amnh.org</a>><br>
>> To: <<a href="mailto:yt-users@lists.spacepope.org" target="_blank">yt-users@lists.spacepope.org</a>><br>
>> Subject: [yt-users] install failure<br>
>> Message-ID: <<a href="mailto:C2FC80DA-9E95-476E-BB68-E5944D4597F3@amnh.org" target="_blank">C2FC80DA-9E95-476E-BB68-E5944D4597F3@amnh.org</a>><br>
>> Content-Type: text/plain; charset="windows-1252"<br>
>><br>
>> Hi, I am having a fatal problem installing yt on my MacBook Pro running OS<br>
>> X v10.9.4. I am using the install script, with the options set as follows:<br>
>><br>
>><br>
>> # Here's where you put the HDF5 path if you like; otherwise it'll download<br>
>> it<br>
>> # and install it on its own<br>
>> #HDF5_DIR=/opt/local/lib<br>
>><br>
>> # If you need to supply arguments to the NumPy or SciPy build, supply them<br>
>> here<br>
>> # This one turns on gfortran manually:<br>
>> #NUMPY_ARGS="--fcompiler=gnu95"<br>
>> # If you absolutely can't get the fortran to work, try this:<br>
>> #NUMPY_ARGS="--fcompiler=fake"<br>
>><br>
>> INST_HG=0 # Install Mercurial or not? If hg is not already<br>
>> # installed, yt cannot be installed.<br>
>> INST_ZLIB=1 # On some systems (Kraken) matplotlib has issues with<br>
>> # the system zlib, which is compiled statically.<br>
>> # If need be, you can turn this off.<br>
>> INST_BZLIB=1 # On some systems, libbzip2 is missing. This can<br>
>> # lead to broken mercurial installations.<br>
>> INST_PNG=1 # Install a local libpng? Same things apply as with zlib.<br>
>> INST_FTYPE=1 # Install FreeType2 locally?<br>
>> INST_ENZO=0 # Clone a copy of Enzo?<br>
>> INST_SQLITE3=1 # Install a local version of SQLite3?<br>
>> INST_PYX=1 # Install PyX? Sometimes PyX can be problematic without a<br>
>> # working TeX installation.<br>
>> INST_0MQ=1 # Install 0mq (for IPython) and affiliated bindings?<br>
>> INST_ROCKSTAR=1 # Install the Rockstar halo finder?<br>
>> INST_SCIPY=0 # Install scipy?<br>
>><br>
>><br>
>> After downloading and activating Xcode command line tools, I got the<br>
>> script to complete successfully. I activated it using the activate.csh<br>
>> script.<br>
>><br>
>> However, when I then try to start yt, it pauses for 30 seconds or so, and<br>
>> then issues the response ?Abort?, with no further errors. I get the same<br>
>> response if I try to import yt into the python (running in the yt<br>
>> environment). Abort, and return to the command line.<br>
>><br>
>> I have tried erasing the yt-x86_64 directory and reinstalling from<br>
>> scratch, with no change in behavior. I also examined the yt_install.log.<br>
>> I found a number of, presumably irrelevant, errors in the configuration<br>
>> tests, but also an error at the end of the long section on building Ipython<br>
>> (almost at the end of the script, just before readline assembly that looks<br>
>> possibly relevant:<br>
>><br>
>> gcc -dynamic -arch i386 -arch x86_64 -arch_only `/usr/bin/arch`<br>
>> -install_name /usr/local/lib/libreadline.6.2.dylib -current_version 6.2<br>
>> -compatibility_version 6 -v -o libreadline.6.2.dylib readline.so vi_mode.so<br>
>> funmap.so keymaps.so parens.so search.so rltty.so complete.so bind.so<br>
>> isearch.so display.so signals.so util.so kill.so undo.so macro.so input.so<br>
>> callback.so terminal.so text.so nls.so misc.so xmalloc.so xfree.so<br>
>> history.so histexpand.so histfile.so histsearch.so shell.so mbutil.so<br>
>> tilde.so compat.so -lncurses<br>
>> Apple LLVM version 6.0 (clang-600.0.51) (based on LLVM 3.5svn)<br>
>> Target: x86_64-apple-darwin13.3.0<br>
>> Thread model: posix<br>
>> clang: error: invalid argument '-compatibility_version 6' only allowed<br>
>> with '-dynamiclib'<br>
>> clang: error: invalid argument '-compatibility_version 6' only allowed<br>
>> with '-dynamiclib'<br>
>> make[1]: *** [libreadline.6.2.dylib] Error 1<br>
>> make: [shared] Error 2 (ignored)<br>
>><br>
>> Any insight on how to proceed?<br>
>><br>
>> Best,<br>
>><br>
>> Mordecai<br>
>><br>
>><br>
>> --<br>
>> Mordecai-Mark Mac Low Curator & Professor<br>
>> <a href="tel:%2B1-212-496-3443" value="+12124963443" target="_blank">+1-212-496-3443</a> Department of Astrophysics<br>
>> <a href="tel:%2B1-212-769-5007" value="+12127695007" target="_blank">+1-212-769-5007</a> (fax) American Museum of Natural History<br>
>> mmaclow (Skype, Hangout) 79th St at CPW, NY, NY, 10024-5192, USA<br>
>><br>
>><br>
>><br>
>><br>
>> -------------- next part --------------<br>
>> An HTML attachment was scrubbed...<br>
>> URL: <<br>
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>>><br>
>><br>
>> ------------------------------<br>
>><br>
>> Message: 3<br>
>> Date: Sun, 28 Sep 2014 16:30:01 -0400<br>
>> From: Peter Teuben <<a href="mailto:teuben@astro.umd.edu" target="_blank">teuben@astro.umd.edu</a>><br>
>> To: <a href="mailto:yt-users@lists.spacepope.org" target="_blank">yt-users@lists.spacepope.org</a><br>
>> Subject: Re: [yt-users] install failure<br>
>> Message-ID: <<a href="mailto:54286FC9.1010003@astro.umd.edu" target="_blank">54286FC9.1010003@astro.umd.edu</a>><br>
>> Content-Type: text/plain; charset="windows-1252"<br>
>><br>
>><br>
>> just "abort" usually tells me it can't find enough memory while loading<br>
>> the executable.<br>
>> I assume you got plenty of that.<br>
>><br>
>> On linux I would then use 'strace' to see if the kernel tells me more.<br>
>> And the ldd<br>
>> command to see what shared libs it might need.<br>
>><br>
>> On a mac, there appears to be the dtruss command for strace. Me and Mac<br>
>> appear<br>
>> to be in a continues state of dislike, all I got was<br>
>> dtrace: failed to initialize dtrace: DTrace requires additional<br>
>> privileges<br>
>> so I'm sure somebody can tell me what that means (I don't have admin on<br>
>> that mac)<br>
>><br>
>> peter<br>
>><br>
>><br>
>> On 09/28/2014 03:36 PM, Mordecai-Mark Mac Low wrote:<br>
>>> Hi, I am having a fatal problem installing yt on my MacBook Pro<br>
>>> running OS X v10.9.4. I am using the install script, with the options<br>
>>> set as follows:<br>
>>><br>
>>><br>
>>> # Here's where you put the HDF5 path if you like; otherwise it'll<br>
>>> download it<br>
>>> # and install it on its own<br>
>>> #HDF5_DIR=/opt/local/lib<br>
>>><br>
>>> # If you need to supply arguments to the NumPy or SciPy build, supply<br>
>>> them here<br>
>>> # This one turns on gfortran manually:<br>
>>> #NUMPY_ARGS="--fcompiler=gnu95"<br>
>>> # If you absolutely can't get the fortran to work, try this:<br>
>>> #NUMPY_ARGS="--fcompiler=fake"<br>
>>><br>
>>> INST_HG=0 # Install Mercurial or not? If hg is not already<br>
>>> # installed, yt cannot be installed.<br>
>>> INST_ZLIB=1 # On some systems (Kraken) matplotlib has issues with<br>
>>> # the system zlib, which is compiled statically.<br>
>>> # If need be, you can turn this off.<br>
>>> INST_BZLIB=1 # On some systems, libbzip2 is missing. This can<br>
>>> # lead to broken mercurial installations.<br>
>>> INST_PNG=1 # Install a local libpng? Same things apply as with<br>
>> zlib.<br>
>>> INST_FTYPE=1 # Install FreeType2 locally?<br>
>>> INST_ENZO=0 # Clone a copy of Enzo?<br>
>>> INST_SQLITE3=1 # Install a local version of SQLite3?<br>
>>> INST_PYX=1 # Install PyX? Sometimes PyX can be problematic without<br>
>> a<br>
>>> # working TeX installation.<br>
>>> INST_0MQ=1 # Install 0mq (for IPython) and affiliated bindings?<br>
>>> INST_ROCKSTAR=1 # Install the Rockstar halo finder?<br>
>>> INST_SCIPY=0 # Install scipy?<br>
>>><br>
>>><br>
>>> After downloading and activating Xcode command line tools, I got the<br>
>>> script to complete successfully. I activated it using the activate.csh<br>
>>> script.<br>
>>><br>
>>> However, when I then try to start yt, it pauses for 30 seconds or so,<br>
>>> and then issues the response ?Abort?, with no further errors. I get<br>
>>> the same response if I try to import yt into the python (running in<br>
>>> the yt environment). Abort, and return to the command line.<br>
>>><br>
>>> I have tried erasing the yt-x86_64 directory and reinstalling from<br>
>>> scratch, with no change in behavior. I also examined the<br>
>>> yt_install.log. I found a number of, presumably irrelevant, errors in<br>
>>> the configuration tests, but also an error at the end of the long<br>
>>> section on building Ipython (almost at the end of the script, just<br>
>>> before readline assembly that looks possibly relevant:<br>
>>><br>
>>> gcc -dynamic -arch i386 -arch x86_64 -arch_only `/usr/bin/arch`<br>
>>> -install_name /usr/local/lib/libreadline.6.2.dylib -current_version<br>
>>> 6.2 -compatibility_version 6 -v -o libreadline.6.2.dylib readline.so<br>
>>> vi_mode.so funmap.so keymaps.so parens.so search.so rltty.so<br>
>>> complete.so bind.so isearch.so display.so signals.so util.so kill.so<br>
>>> undo.so macro.so input.so callback.so terminal.so text.so nls.so<br>
>>> misc.so xmalloc.so xfree.so history.so histexpand.so histfile.so<br>
>>> histsearch.so shell.so mbutil.so tilde.so compat.so -lncurses<br>
>>> Apple LLVM version 6.0 (clang-600.0.51) (based on LLVM 3.5svn)<br>
>>> Target: x86_64-apple-darwin13.3.0<br>
>>> Thread model: posix<br>
>>> clang: error: invalid argument '-compatibility_version 6' only<br>
>>> allowed with '-dynamiclib'<br>
>>> clang: error: invalid argument '-compatibility_version 6' only<br>
>>> allowed with '-dynamiclib'<br>
>>> make[1]: *** [libreadline.6.2.dylib] Error 1<br>
>>> make: [shared] Error 2 (ignored)<br>
>>><br>
>>> Any insight on how to proceed?<br>
>>><br>
>>> Best,<br>
>>><br>
>>> Mordecai<br>
>>><br>
>>><br>
>>> --<br>
>>> Mordecai-Mark Mac Low Curator & Professor<br>
>>> <a href="tel:%2B1-212-496-3443" value="+12124963443" target="_blank">+1-212-496-3443</a> Department of Astrophysics<br>
>>> <a href="tel:%2B1-212-769-5007" value="+12127695007" target="_blank">+1-212-769-5007</a> (fax) American Museum of Natural History<br>
>>> mmaclow (Skype, Hangout) 79th St at CPW, NY, NY, 10024-5192, USA<br>
>>><br>
>>><br>
>>><br>
>>><br>
>>><br>
>>><br>
>>> _______________________________________________<br>
>>> yt-users mailing list<br>
>>> <a href="mailto:yt-users@lists.spacepope.org" target="_blank">yt-users@lists.spacepope.org</a><br>
>>> <a href="http://lists.spacepope.org/listinfo.cgi/yt-users-spacepope.org" target="_blank">http://lists.spacepope.org/listinfo.cgi/yt-users-spacepope.org</a><br>
>><br>
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>>><br>
>><br>
>> ------------------------------<br>
>><br>
>> Subject: Digest Footer<br>
>><br>
>> _______________________________________________<br>
>> yt-users mailing list<br>
>> <a href="mailto:yt-users@lists.spacepope.org" target="_blank">yt-users@lists.spacepope.org</a><br>
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>><br>
>><br>
>> ------------------------------<br>
>><br>
>> End of yt-users Digest, Vol 79, Issue 40<br>
>> ****************************************<br>
>><br>
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> An HTML attachment was scrubbed...<br>
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<span>><br>
> ------------------------------<br>
><br>
> Subject: Digest Footer<br>
><br>
> _______________________________________________<br>
> yt-users mailing list<br>
> <a href="mailto:yt-users@lists.spacepope.org" target="_blank">yt-users@lists.spacepope.org</a><br>
> <a href="http://lists.spacepope.org/listinfo.cgi/yt-users-spacepope.org" target="_blank">http://lists.spacepope.org/listinfo.cgi/yt-users-spacepope.org</a><br>
><br>
><br>
> ------------------------------<br>
><br>
</span>> End of yt-users Digest, Vol 79, Issue 41<br>
> ****************************************<br>
<div><br>
--<br>
Mordecai-Mark Mac Low Curator & Professor<br>
<a href="tel:%2B1-212-496-3443" value="+12124963443" target="_blank">+1-212-496-3443</a> Department of Astrophysics<br>
<a href="tel:%2B1-212-769-5007" value="+12127695007" target="_blank">+1-212-769-5007</a> (fax) American Museum of Natural History<br>
mmaclow (Skype, Hangout) 79th St at CPW, NY, NY, 10024-5192, USA<br>
<br>
<br>
<br>
<br>
_______________________________________________<br>
yt-users mailing list<br>
<a href="mailto:yt-users@lists.spacepope.org" target="_blank">yt-users@lists.spacepope.org</a><br>
<a href="http://lists.spacepope.org/listinfo.cgi/yt-users-spacepope.org" target="_blank">http://lists.spacepope.org/listinfo.cgi/yt-users-spacepope.org</a><br>
</div></blockquote></div><br></div>
</div></div><br></div></div>
</blockquote></div></div></div><div><div class="h5"><br><div>
--<br>Mordecai-Mark Mac Low <span style="white-space:pre-wrap"> </span>Curator & Professor<br><a href="tel:%2B1-212-496-3443" value="+12124963443" target="_blank">+1-212-496-3443</a> <span style="white-space:pre-wrap"> </span>Department of Astrophysics<br><a href="tel:%2B1-212-769-5007" value="+12127695007" target="_blank">+1-212-769-5007</a> (fax) <span style="white-space:pre-wrap"> </span>American Museum of Natural History<br>mmaclow (Skype, Hangout) <span style="white-space:pre-wrap"> </span>79th St at CPW, NY, NY, 10024-5192, USA<br><br><br><br>
</div>
<br></div></div></div></div></blockquote></div><br></div></div></div></div>
</div></blockquote></div><br><div>
--<br>Mordecai-Mark Mac Low <span class="Apple-tab-span" style="white-space: pre;"> </span>Curator & Professor<br>+1-212-496-3443 <span class="Apple-tab-span" style="white-space: pre;"> </span>Department of Astrophysics<br>+1-212-769-5007 (fax) <span class="Apple-tab-span" style="white-space: pre;"> </span>American Museum of Natural History<br>mmaclow (Skype, Hangout) <span class="Apple-tab-span" style="white-space: pre;"> </span>79th St at CPW, NY, NY, 10024-5192, USA<br><br><br><br>
</div>
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