<div dir="ltr">Hi Mordecai,<div><br></div><div>Depending on what you want to do with yt, if you need the latest build or not, but I've had success on Mac with the anaconda distribution of python which includes yt-3.0. <a href="https://store.continuum.io/cshop/anaconda/">https://store.continuum.io/cshop/anaconda/</a>.</div><div><br></div><div><br></div><div>Ari<br><div><br></div><div><br><div class="gmail_extra"><br><div class="gmail_quote">On Sun, Sep 28, 2014 at 4:30 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-width:1px;border-left-color:rgb(204,204,204);border-left-style:solid;padding-left:1ex">Send yt-users mailing list submissions to<br>
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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">nathan12343@gmail.com</a>><br>
To: Discussion of the yt analysis package<br>
<<a href="mailto:yt-users@lists.spacepope.org">yt-users@lists.spacepope.org</a>><br>
Subject: Re: [yt-users] ProfilePlot in YT-3.0<br>
Message-ID:<br>
<<a href="mailto:CAJXewOkKaMPBE02RH_VY4rNTXgOobeJ02qOOZY5PRk332GGveg@mail.gmail.com">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">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 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">nathan12343@gmail.com</a><br>
> <javascript:_e(%7B%7D,'cvml','<a href="mailto:nathan12343@gmail.com">nathan12343@gmail.com</a>');>> wrote:<br>
><br>
>> Hi John,<br>
>><br>
>> ProfilePlot is a wrapper around the Profile1D class, which calculates 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 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">johnanthonyregan@gmail.com</a><br>
>> <javascript:_e(%7B%7D,'cvml','<a href="mailto:johnanthonyregan@gmail.com">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 better<br>
>>> way?<br>
>>><br>
>>> John<br>
>>><br>
>>> _______________________________________________<br>
>>> yt-users mailing list<br>
>>> <a href="mailto:yt-users@lists.spacepope.org">yt-users@lists.spacepope.org</a><br>
>>> <javascript:_e(%7B%7D,'cvml','<a href="mailto:yt-users@lists.spacepope.org">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">yt-users@lists.spacepope.org</a><br>
>> <javascript:_e(%7B%7D,'cvml','<a href="mailto:yt-users@lists.spacepope.org">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>
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<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">mordecai@amnh.org</a>><br>
To: <<a href="mailto:yt-users@lists.spacepope.org">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">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 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 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 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 script to complete successfully. I activated it using the activate.csh script.<br>
<br>
However, when I then try to start yt, it pauses for 30 seconds or so, and then issues the response ?Abort?, with no further errors. I get the same response if I try to import yt into the python (running in the yt environment). Abort, and return to the command line.<br>
<br>
I have tried erasing the yt-x86_64 directory and reinstalling from scratch, with no change in behavior. I also examined the yt_install.log. I found a number of, presumably irrelevant, errors in the configuration tests, but also an error at the end of the long section on building Ipython (almost at the end of the script, just before readline assembly that looks possibly relevant:<br>
<br>
gcc -dynamic -arch i386 -arch x86_64 -arch_only `/usr/bin/arch` -install_name /usr/local/lib/libreadline.6.2.dylib -current_version 6.2 -compatibility_version 6 -v -o libreadline.6.2.dylib readline.so vi_mode.so funmap.so keymaps.so parens.so search.so rltty.so complete.so bind.so isearch.so display.so signals.so util.so kill.so undo.so macro.so input.so callback.so terminal.so text.so nls.so misc.so xmalloc.so xfree.so history.so histexpand.so histfile.so 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 allowed with '-dynamiclib'<br>
clang: error: invalid argument '-compatibility_version 6' only 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>
+1-212-496-3443 Department of Astrophysics<br>
+1-212-769-5007 (fax) American Museum of Natural History<br>
mmaclow (Skype, Hangout) 79th St at CPW, NY, NY, 10024-5192, USA<br>
<br>
<br>
<br>
<br>
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<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">teuben@astro.umd.edu</a>><br>
To: <a href="mailto:yt-users@lists.spacepope.org">yt-users@lists.spacepope.org</a><br>
Subject: Re: [yt-users] install failure<br>
Message-ID: <<a href="mailto:54286FC9.1010003@astro.umd.edu">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 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,<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>
> +1-212-496-3443 Department of Astrophysics<br>
> +1-212-769-5007 (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">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>
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</blockquote></div><br></div></div></div></div>