[yt-users] install failure
Mordecai-Mark Mac Low
mordecai at amnh.org
Sun Sep 28 17:00:34 PDT 2014
Nathan,
I’ve posted the full install log to
https://dl.dropboxusercontent.com/u/31830722/yt_install.log
It does look like ipython is trying to compile readline.
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.
Best,
Mordecai
On Sep 28, 2014, at 19:33, yt-users-request at lists.spacepope.org wrote:
> Message: 1
> Date: Sun, 28 Sep 2014 13:57:47 -0700
> From: Nathan Goldbaum <nathan12343 at gmail.com>
> To: Discussion of the yt analysis package
> <yt-users at lists.spacepope.org>
> Subject: Re: [yt-users] install failure
> Message-ID:
> <CAJXewO=G9M7V0deBGtU46s68kdKPVTqsmhEBxV+yG7-K=8HcgQ at mail.gmail.com>
> Content-Type: text/plain; charset="utf-8"
>
> Hi Mordecai,
>
> We've had some reports about incompatibilities with the install script on
> OS X Mavericks recently, but I don't think this error has been reported
> before. Unfortunately getting the install script to work portably in all
> cases is a labor of love and sometimes errors like these crop up.
>
> Googling for your error returns this discussion on the readline mailing
> list: https://lists.gnu.org/archive/html/bug-readline/2013-12/msg00002.html.
> Apparently the version you're compiling needs to be patched to compile
> cleanly on mavericks. I haven't checked whether the patch has made its way
> into a readline release.
>
> I'm not sure what exactly is compiling readline (IPython maybe?), but
> earlier in the install script we should have installed a pure-python
> version of the readline library from pypi if we were unable to import it.
> It would help to figure out what went wrong if you could upload the full
> install log somewhere.
>
> Do you have a python environment setup on your laptop already? It's very
> straightforward to install yt using anaconda, canopy, or a manually
> configured python environment, bypassing all the bootstrapping that the
> install script must do. Take a look at the following page in the
> documentation:
>
> http://yt-project.org/doc/installing.html#installing-yt-using-anaconda
> http://yt-project.org/doc/installing.html#installing-yt-using-pip-or-from-source
>
> Hope that's helpful.
>
> -Nathan
>
>
> On Sun, Sep 28, 2014 at 12:36 PM, Mordecai-Mark Mac Low <mordecai at amnh.org>
> wrote:
>
>> 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:
>>
>>
>> # Here's where you put the HDF5 path if you like; otherwise it'll download
>> it
>> # and install it on its own
>> #HDF5_DIR=/opt/local/lib
>>
>> # If you need to supply arguments to the NumPy or SciPy build, supply them
>> here
>> # This one turns on gfortran manually:
>> #NUMPY_ARGS="--fcompiler=gnu95"
>> # If you absolutely can't get the fortran to work, try this:
>> #NUMPY_ARGS="--fcompiler=fake"
>>
>> INST_HG=0 # Install Mercurial or not? If hg is not already
>> # installed, yt cannot be installed.
>> INST_ZLIB=1 # On some systems (Kraken) matplotlib has issues with
>> # the system zlib, which is compiled statically.
>> # If need be, you can turn this off.
>> INST_BZLIB=1 # On some systems, libbzip2 is missing. This can
>> # lead to broken mercurial installations.
>> INST_PNG=1 # Install a local libpng? Same things apply as with zlib.
>> INST_FTYPE=1 # Install FreeType2 locally?
>> INST_ENZO=0 # Clone a copy of Enzo?
>> INST_SQLITE3=1 # Install a local version of SQLite3?
>> INST_PYX=1 # Install PyX? Sometimes PyX can be problematic without a
>> # working TeX installation.
>> INST_0MQ=1 # Install 0mq (for IPython) and affiliated bindings?
>> INST_ROCKSTAR=1 # Install the Rockstar halo finder?
>> INST_SCIPY=0 # Install scipy?
>>
>>
>> After downloading and activating Xcode command line tools, I got the
>> script to complete successfully. I activated it using the activate.csh
>> script.
>>
>> 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.
>>
>> 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:
>>
>> 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
>> Apple LLVM version 6.0 (clang-600.0.51) (based on LLVM 3.5svn)
>> Target: x86_64-apple-darwin13.3.0
>> Thread model: posix
>> clang: error: invalid argument '-compatibility_version 6' only allowed
>> with '-dynamiclib'
>> clang: error: invalid argument '-compatibility_version 6' only allowed
>> with '-dynamiclib'
>> make[1]: *** [libreadline.6.2.dylib] Error 1
>> make: [shared] Error 2 (ignored)
>>
>> Any insight on how to proceed?
>>
>> Best,
>>
>> Mordecai
>>
>>
>> --
>> Mordecai-Mark Mac Low Curator & Professor
>> +1-212-496-3443 Department of Astrophysics
>> +1-212-769-5007 (fax) American Museum of Natural History
>> mmaclow (Skype, Hangout) 79th St at CPW, NY, NY, 10024-5192, USA
>>
>>
>>
>>
>>
>> _______________________________________________
>> yt-users mailing list
>> yt-users at lists.spacepope.org
>> http://lists.spacepope.org/listinfo.cgi/yt-users-spacepope.org
>>
>>
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> Message: 2
> Date: Sun, 28 Sep 2014 19:33:51 -0400
> From: Professor Maller <amaller at citytech.cuny.edu>
> To: yt-users at lists.spacepope.org
> Subject: Re: [yt-users] install failure
> Message-ID:
> <CACCSjdNPC0QVrxDooBEQ2W7Mp6KaBJxNJZ9eLvH6TG8WyD7m0Q at mail.gmail.com>
> Content-Type: text/plain; charset="utf-8"
>
> Hi Mordecai,
>
> 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. https://store.continuum.io/cshop/anaconda/.
>
>
> Ari
>
>
>
> On Sun, Sep 28, 2014 at 4:30 PM, <yt-users-request at lists.spacepope.org>
> wrote:
>
>> Send yt-users mailing list submissions to
>> yt-users at lists.spacepope.org
>>
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>>
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>>
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>>
>>
>> Today's Topics:
>>
>> 1. Re: ProfilePlot in YT-3.0 (Nathan Goldbaum)
>> 2. install failure (Mordecai-Mark Mac Low)
>> 3. Re: install failure (Peter Teuben)
>>
>>
>> ----------------------------------------------------------------------
>>
>> Message: 1
>> Date: Sun, 28 Sep 2014 12:14:04 -0700
>> From: Nathan Goldbaum <nathan12343 at gmail.com>
>> To: Discussion of the yt analysis package
>> <yt-users at lists.spacepope.org>
>> Subject: Re: [yt-users] ProfilePlot in YT-3.0
>> Message-ID:
>> <
>> CAJXewOkKaMPBE02RH_VY4rNTXgOobeJ02qOOZY5PRk332GGveg at mail.gmail.com>
>> Content-Type: text/plain; charset="utf-8"
>>
>> On Sunday, September 28, 2014, John Regan <johnanthonyregan at gmail.com>
>> wrote:
>>
>>> Hi Nathan,
>>>
>>> Thanks for that. I'll have a look at what helper functions would be
>> useful
>>> as I use the ProfilePlot routine and I can issue a PR then. I think it
>>> would be worth updating the docs with info like you just sent me.
>>>
>>
>> Again, please feel free to open a pull request.
>>
>>
>>>
>>> Cheers,
>>> John
>>>
>>> On Sun, Sep 28, 2014 at 11:17 AM, Nathan Goldbaum <nathan12343 at gmail.com
>>> <javascript:_e(%7B%7D,'cvml','nathan12343 at gmail.com');>> wrote:
>>>
>>>> Hi John,
>>>>
>>>> ProfilePlot is a wrapper around the Profile1D class, which calculates
>> and
>>>> stores the histograms. To access the underlying data you need to access
>>>> the profile object via the profiles attribute of the ProfilePlot:
>>>>
>>>> import yt
>>>> ds = yt.load('IsolatedGalaxy/galaxy0030/galaxy0030')
>>>> plot = yt.ProfilePlot(ds.all_data(), 'radius', 'density')
>>>> profile = plot.profiles[0]
>>>> print profile.x_field, profile.x
>>>> print profile.field_data.keys(), profile['density']
>>>>
>>>> There are probably a number of ways that the current API can be improved
>>>> to make it more straightforward to access this data. PRs along this
>> front
>>>> would be very welcome, I think.
>>>>
>>>> -Nathan
>>>>
>>>> On Sun, Sep 28, 2014 at 1:05 AM, John Regan <johnanthonyregan at gmail.com
>>>> <javascript:_e(%7B%7D,'cvml','johnanthonyregan at gmail.com');>> wrote:
>>>>
>>>>> HI All,
>>>>>
>>>>> Is there an easy way to access the x_field and the y_fields in the
>>>>> ProfilePlot function?
>>>>>
>>>>> So for example
>>>>>
>>>>> prof = ProfilePlot(sphere, "radius", "density")
>>>>>
>>>>>
>>>>> print prof.x_field
>>>>> print prof.y_field[0]
>>>>>
>>>>> I inserted a couple of hack functions into the ProfilePlot class to
>>>>> return the x_field and the .items() tuple but there is probably a
>> better
>>>>> way?
>>>>>
>>>>> John
>>>>>
>>>>> _______________________________________________
>>>>> yt-users mailing list
>>>>> yt-users at lists.spacepope.org
>>>>> <javascript:_e(%7B%7D,'cvml','yt-users at lists.spacepope.org');>
>>>>> http://lists.spacepope.org/listinfo.cgi/yt-users-spacepope.org
>>>>>
>>>>>
>>>>
>>>> _______________________________________________
>>>> yt-users mailing list
>>>> yt-users at lists.spacepope.org
>>>> <javascript:_e(%7B%7D,'cvml','yt-users at lists.spacepope.org');>
>>>> http://lists.spacepope.org/listinfo.cgi/yt-users-spacepope.org
>>>>
>>>>
>>>
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>> ------------------------------
>>
>> Message: 2
>> Date: Sun, 28 Sep 2014 15:36:55 -0400
>> From: Mordecai-Mark Mac Low <mordecai at amnh.org>
>> To: <yt-users at lists.spacepope.org>
>> Subject: [yt-users] install failure
>> Message-ID: <C2FC80DA-9E95-476E-BB68-E5944D4597F3 at amnh.org>
>> Content-Type: text/plain; charset="windows-1252"
>>
>> 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:
>>
>>
>> # Here's where you put the HDF5 path if you like; otherwise it'll download
>> it
>> # and install it on its own
>> #HDF5_DIR=/opt/local/lib
>>
>> # If you need to supply arguments to the NumPy or SciPy build, supply them
>> here
>> # This one turns on gfortran manually:
>> #NUMPY_ARGS="--fcompiler=gnu95"
>> # If you absolutely can't get the fortran to work, try this:
>> #NUMPY_ARGS="--fcompiler=fake"
>>
>> INST_HG=0 # Install Mercurial or not? If hg is not already
>> # installed, yt cannot be installed.
>> INST_ZLIB=1 # On some systems (Kraken) matplotlib has issues with
>> # the system zlib, which is compiled statically.
>> # If need be, you can turn this off.
>> INST_BZLIB=1 # On some systems, libbzip2 is missing. This can
>> # lead to broken mercurial installations.
>> INST_PNG=1 # Install a local libpng? Same things apply as with zlib.
>> INST_FTYPE=1 # Install FreeType2 locally?
>> INST_ENZO=0 # Clone a copy of Enzo?
>> INST_SQLITE3=1 # Install a local version of SQLite3?
>> INST_PYX=1 # Install PyX? Sometimes PyX can be problematic without a
>> # working TeX installation.
>> INST_0MQ=1 # Install 0mq (for IPython) and affiliated bindings?
>> INST_ROCKSTAR=1 # Install the Rockstar halo finder?
>> INST_SCIPY=0 # Install scipy?
>>
>>
>> After downloading and activating Xcode command line tools, I got the
>> script to complete successfully. I activated it using the activate.csh
>> script.
>>
>> 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.
>>
>> 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:
>>
>> 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
>> Apple LLVM version 6.0 (clang-600.0.51) (based on LLVM 3.5svn)
>> Target: x86_64-apple-darwin13.3.0
>> Thread model: posix
>> clang: error: invalid argument '-compatibility_version 6' only allowed
>> with '-dynamiclib'
>> clang: error: invalid argument '-compatibility_version 6' only allowed
>> with '-dynamiclib'
>> make[1]: *** [libreadline.6.2.dylib] Error 1
>> make: [shared] Error 2 (ignored)
>>
>> Any insight on how to proceed?
>>
>> Best,
>>
>> Mordecai
>>
>>
>> --
>> Mordecai-Mark Mac Low Curator & Professor
>> +1-212-496-3443 Department of Astrophysics
>> +1-212-769-5007 (fax) American Museum of Natural History
>> mmaclow (Skype, Hangout) 79th St at CPW, NY, NY, 10024-5192, USA
>>
>>
>>
>>
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>> ------------------------------
>>
>> Message: 3
>> Date: Sun, 28 Sep 2014 16:30:01 -0400
>> From: Peter Teuben <teuben at astro.umd.edu>
>> To: yt-users at lists.spacepope.org
>> Subject: Re: [yt-users] install failure
>> Message-ID: <54286FC9.1010003 at astro.umd.edu>
>> Content-Type: text/plain; charset="windows-1252"
>>
>>
>> just "abort" usually tells me it can't find enough memory while loading
>> the executable.
>> I assume you got plenty of that.
>>
>> On linux I would then use 'strace' to see if the kernel tells me more.
>> And the ldd
>> command to see what shared libs it might need.
>>
>> On a mac, there appears to be the dtruss command for strace. Me and Mac
>> appear
>> to be in a continues state of dislike, all I got was
>> dtrace: failed to initialize dtrace: DTrace requires additional
>> privileges
>> so I'm sure somebody can tell me what that means (I don't have admin on
>> that mac)
>>
>> peter
>>
>>
>> On 09/28/2014 03:36 PM, Mordecai-Mark Mac Low wrote:
>>> 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:
>>>
>>>
>>> # Here's where you put the HDF5 path if you like; otherwise it'll
>>> download it
>>> # and install it on its own
>>> #HDF5_DIR=/opt/local/lib
>>>
>>> # If you need to supply arguments to the NumPy or SciPy build, supply
>>> them here
>>> # This one turns on gfortran manually:
>>> #NUMPY_ARGS="--fcompiler=gnu95"
>>> # If you absolutely can't get the fortran to work, try this:
>>> #NUMPY_ARGS="--fcompiler=fake"
>>>
>>> INST_HG=0 # Install Mercurial or not? If hg is not already
>>> # installed, yt cannot be installed.
>>> INST_ZLIB=1 # On some systems (Kraken) matplotlib has issues with
>>> # the system zlib, which is compiled statically.
>>> # If need be, you can turn this off.
>>> INST_BZLIB=1 # On some systems, libbzip2 is missing. This can
>>> # lead to broken mercurial installations.
>>> INST_PNG=1 # Install a local libpng? Same things apply as with
>> zlib.
>>> INST_FTYPE=1 # Install FreeType2 locally?
>>> INST_ENZO=0 # Clone a copy of Enzo?
>>> INST_SQLITE3=1 # Install a local version of SQLite3?
>>> INST_PYX=1 # Install PyX? Sometimes PyX can be problematic without
>> a
>>> # working TeX installation.
>>> INST_0MQ=1 # Install 0mq (for IPython) and affiliated bindings?
>>> INST_ROCKSTAR=1 # Install the Rockstar halo finder?
>>> INST_SCIPY=0 # Install scipy?
>>>
>>>
>>> After downloading and activating Xcode command line tools, I got the
>>> script to complete successfully. I activated it using the activate.csh
>>> script.
>>>
>>> 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.
>>>
>>> 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:
>>>
>>> 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
>>> Apple LLVM version 6.0 (clang-600.0.51) (based on LLVM 3.5svn)
>>> Target: x86_64-apple-darwin13.3.0
>>> Thread model: posix
>>> clang: error: invalid argument '-compatibility_version 6' only
>>> allowed with '-dynamiclib'
>>> clang: error: invalid argument '-compatibility_version 6' only
>>> allowed with '-dynamiclib'
>>> make[1]: *** [libreadline.6.2.dylib] Error 1
>>> make: [shared] Error 2 (ignored)
>>>
>>> Any insight on how to proceed?
>>>
>>> Best,
>>>
>>> Mordecai
>>>
>>>
>>> --
>>> Mordecai-Mark Mac Low Curator & Professor
>>> +1-212-496-3443 Department of Astrophysics
>>> +1-212-769-5007 (fax) American Museum of Natural History
>>> mmaclow (Skype, Hangout) 79th St at CPW, NY, NY, 10024-5192, USA
>>>
>>>
>>>
>>>
>>>
>>>
>>> _______________________________________________
>>> yt-users mailing list
>>> yt-users at lists.spacepope.org
>>> http://lists.spacepope.org/listinfo.cgi/yt-users-spacepope.org
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--
Mordecai-Mark Mac Low Curator & Professor
+1-212-496-3443 Department of Astrophysics
+1-212-769-5007 (fax) American Museum of Natural History
mmaclow (Skype, Hangout) 79th St at CPW, NY, NY, 10024-5192, USA
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