Hi Nathan and all,

Here's a little more info on that error you asked about regarding glibc. It came up again for me on Pleiades, this time with yt itself.

Traceback (most recent call last):
  File "/u/jzuhone/anaconda/bin/yt", line 4, in <module>
    from yt.utilities.command_line import run_main
  File "/u/jzuhone/anaconda/lib/python2.7/site-packages/yt/utilities/command_line.py", line 29, in <module>
    from yt.mods import *
  File "/u/jzuhone/anaconda/lib/python2.7/site-packages/yt/mods.py", line 60, in <module>
    from yt.data_objects.api import \
  File "/u/jzuhone/anaconda/lib/python2.7/site-packages/yt/data_objects/api.py", line 31, in <module>
    from grid_patch import \
  File "/u/jzuhone/anaconda/lib/python2.7/site-packages/yt/data_objects/grid_patch.py", line 35, in <module>
    from yt.data_objects.data_containers import YTFieldData
  File "/u/jzuhone/anaconda/lib/python2.7/site-packages/yt/data_objects/data_containers.py", line 45, in <module>
    from yt.data_objects.derived_quantities import GridChildMaskWrapper
  File "/u/jzuhone/anaconda/lib/python2.7/site-packages/yt/data_objects/derived_quantities.py", line 36, in <module>
    from yt.utilities.parallel_tools.parallel_analysis_interface import \
  File "/u/jzuhone/anaconda/lib/python2.7/site-packages/yt/utilities/parallel_tools/parallel_analysis_interface.py", line 39, in <module>
    from yt.utilities.lib import \
  File "/u/jzuhone/anaconda/lib/python2.7/site-packages/yt/utilities/lib/__init__.py", line 35, in <module>
    from .png_writer import *
ImportError: /lib64/libc.so.6: version `GLIBC_2.14' not found (required by /u/jzuhone/anaconda/lib/python2.7/site-packages/yt/utilities/lib/png_writer.so)

Best,

John

On Sep 3, 2013, at 3:10 PM, Nathan Goldbaum <nathan12343@gmail.com> wrote:

John, can you give a little more info on that error?  I'm a little concerned that there are binary incompatibilities that conda can't resolve.  Perhaps this is something we should report on the conda issue tracker.

Matt, can't we get the recipes in the same way we get the latest dev install script?  Something like:

wget https://bitbucket.org/yt_analysis/yt_conda/raw/yt/meta.yaml

This doesn't currently work, although it does work for the yt repo, I think because we use named branches in that repository.


On Tue, Sep 3, 2013 at 12:00 PM, John ZuHone <jzuhone@gmail.com> wrote:
Works fine for me on OS X x86_64.

On my Goddard-controlled Linux x86_64 server, everything worked fine except Mercurial, which I "conda install"-ed using the yt link, but the binary had an incompatibility which the glibc that was installed on the machine. Using pip to install Mercurial (which did it from source) was the workaround.

On Sep 3, 2013, at 2:54 PM, Matthew Turk <matthewturk@gmail.com> wrote:

> Hi all,
>
> Thanks to everybody who has reported back on testing.  After some
> talking both offline and on IRC, as well as here, I think we would
> need to do the following things:
>
> * Make a single script that grabs the appropriate distribution of
> miniconda and installs it.  Right now I have a mechanism for doing
> this, but it's currently tied to an architecture.
> * Create a mechanism for installing all the packages we need.  Nearly
> all are available inside the Continuum repos.  What we're hung up on
> is that source installs require a "recipe", and transmitting the
> recipe is where I don't have an idea of what to do.
> * Test this out lots of places
> * Clean up the edges in the (new) install script
> * Move the old install script to maintenance mode
> * Update all documentation to describe this and mothball other
> methods of installation
>
> What would be nice:
>
> * Make available nightly builds of yt on several architectures using binstar
> * Utilize more of the packages included in conda elsewhere in yt, now
> that we can!
>
> Here's my current recipe for get_yt.sh:
>
> http://paste.yt-project.org/show/3843/
>
> (The config thing may get switched to include the --system argument,
> to modify the "yt-conda" condarc.)  The step that I'm most stuck on is
> getting the yt recipe to people.  If we want to make it possible and
> easy to build from source, we need to get the contents of a "conda
> recipe" to people.  They can then run "conda build ." in the
> directory.  Here are the recipes that we've been playing with:
>
> https://bitbucket.org/yt_analysis/yt_conda/src
>
> Basically, in get_yt.sh, to do from source instead of from binary we
> need to insert a step at the end that downloads the recipes somehow
> and then cd's into the right directory and builds them.  The reason
> this is tricky is that we often need to bootstrap ourselves; we can't
> assume anything exists.  We can download the .tar.bz2 of the current
> tip of the repo, but it includes the hash in the directory name that
> it extracts to.
>
> So I think what we need is a mechanism for getting the current state
> of the repo, figuring out the name of the repo's directory, moves into
> it, and then builds.  I believe that all/most of this becomes much,
> much easier if hg gets included in Anaconda, which Nathan has
> submitted a PR for.  So hopefully that will be taken care of, but
> until that time we can possibly figure something out.  I'm not sure
> that we have the resources to continually support binary nightly
> builds in perpetuity for all the architectures that people run on, so
> having source would be awesome.  Plus, one of the biggest appeals of
> how we distribute yt is that the source is included; I would very much
> not like to give this up.
>
> Thoughts?  Has anyone else tested any of this out?
>
> -Matt
>
> On Tue, Sep 3, 2013 at 1:04 PM, Britton Smith <brittonsmith@gmail.com> wrote:
>> Hi everyone,
>>
>> Sorry for chiming in late.  I just moved when this thread began and do not
>> have regular internet access.
>>
>> I really like this idea of conda, especially as a package manager that only
>> optionally makes its own edits to your .bashrc.  I have always really liked
>> that the install script creates a clean python stack with basically
>> everything a python user needs.  I have on occasion suggested it to people
>> just looking to use numpy and matploblib.  It looks like conda will continue
>> to provide this nice by-product, so I'm all for it.
>>
>> I won't be in a position to help with testing and such for another week or
>> so when I get regular internet access, but I would be glad to do so then.
>>
>> Britton
>>
>>
>> On Fri, Aug 30, 2013 at 9:29 PM, Nathan Goldbaum <nathan12343@gmail.com>
>> wrote:
>>>
>>> Everything should be available now for 64 bit linux and OS X.
>>>
>>>
>>> On Fri, Aug 30, 2013 at 10:52 AM, Chris Malone <chris.m.malone@gmail.com>
>>> wrote:
>>>>
>>>> Hi Nathan,
>>>>
>>>> That appears to work as it built the environment and `conda install ...`
>>>> added packages to my environment.
>>>>
>>>> One mistake I made was that I originally downloaded the "latest" OS X
>>>> build of Miniconda, but that happened to be Miniconda3, which is python 3
>>>> based.  Trying to build the environment with that yields an error regarding
>>>> incompatibility of yt and python3.3, as it should.
>>>>
>>>> Chris
>>>>
>>>>
>>>> On Fri, Aug 30, 2013 at 10:42 AM, Nathan Goldbaum <nathan12343@gmail.com>
>>>> wrote:
>>>>>
>>>>> Hey Chris,
>>>>>
>>>>> I don't think mercurial is strictly necessary, can you try again without
>>>>> it?  I think if Matt uploads a mercurial package for OS X this won't be an
>>>>> issue. I'll send him an updated tarball.
>>>>>
>>>>> I submitted a mercurial recipe to conda-recipes yesterday
>>>>> (https://github.com/ContinuumIO/conda-recipes/pull/14) so hopefully a
>>>>> mercurial build will be included in future anaconda releases.
>>>>>
>>>>>
>>>>> On Fri, Aug 30, 2013 at 10:39 AM, Chris Malone
>>>>> <chris.m.malone@gmail.com> wrote:
>>>>>>
>>>>>> I just tried setting this up on OS X 10.7.5 and failed when attempting
>>>>>> to create the conda environment due to a missing mercurial package:
>>>>>>
>>>>>> $ conda create -n ytenv -c http://conda.binstar.org/yt_project yt
>>>>>> mercurial ipython tornado pyzmq pygments jinja2 sphinx
>>>>>> Error: No packages found matching: mercurial
>>>>>>
>>>>>>
>>>>>> On Thu, Aug 29, 2013 at 9:01 PM, Nathan Goldbaum
>>>>>> <nathan12343@gmail.com> wrote:
>>>>>>>
>>>>>>> Yup, please try on OSX as well.  If you make sure Matt's binstar is in
>>>>>>> your .condarc, you should be able to get yt by doing 'conda install yt'.
>>>>>>>
>>>>>>> I built the OSX binary on my laptop so I'd appreciate hearing about
>>>>>>> issues, particularly if there are issues on older OS X releases.
>>>>>>>
>>>>>>> On Thursday, August 29, 2013, Matthew Turk wrote:
>>>>>>>>
>>>>>>>> Hi all,
>>>>>>>>
>>>>>>>> Thank you for the feedback -- I am glad there is some agreement about
>>>>>>>> possible ways forward, and so I'm happy to try to use this as an
>>>>>>>> opportunity to explore simpler, more reliable methods than the
>>>>>>>> install
>>>>>>>> script.
>>>>>>>>
>>>>>>>> This afternoon, I spent a bit of time with Conda, and I think it's
>>>>>>>> quite nice.  There are a few rough corners, particularly related to
>>>>>>>> the binstar service, but it's so far pretty great.  With Nathan's
>>>>>>>> help, I was able to upload a yt-2.5.5 package for linux x86_64 and
>>>>>>>> then install it.
>>>>>>>>
>>>>>>>> The workflow that seems to work:
>>>>>>>>
>>>>>>>> * Get miniconda: http://repo.continuum.io/miniconda/index.html
>>>>>>>> * Run the installer for miniconda
>>>>>>>> * Enter the conda environment and then install yt by doing "conda
>>>>>>>> install yt -c http://conda.binstar.org/yt_project/ ".
>>>>>>>>
>>>>>>>> I think that this can likely all be stuck into a bash script.  A
>>>>>>>> simple, first pass at this is here:
>>>>>>>>
>>>>>>>> http://paste.yt-project.org/show/3833/
>>>>>>>>
>>>>>>>> This right now only works on Linux x86_64, but getting it to work for
>>>>>>>> other machines won't be too hard.  I suspect we will be able to do
>>>>>>>> nightlies very easily as well.  If anyone out there has an x86_64
>>>>>>>> machine they wouldn't mind trying it on, that would be very helpful!
>>>>>>>> I did find that once I ran this script, I had to actually prepend the
>>>>>>>> PATH afterwards as well.  This means doing:
>>>>>>>>
>>>>>>>> export LD_LIBRARY_PATH=$HOME/yt-conda:$LD_LIBRARY_PATH
>>>>>>>> export PATH=$HOME/yt-conda:$PATH
>>>>>>>> source activate ytenv
>>>>>>>>
>>>>>>>> At that point, everything was set up and working for me.  The
>>>>>>>> miniconda install offers to add paths to .bashrc, but I don't think
>>>>>>>> we
>>>>>>>> should go down that route.  That being said, this is also a possible
>>>>>>>> point of friction.
>>>>>>>>
>>>>>>>> One nice thing is that this also completely works with the full
>>>>>>>> anaconda; if someone wants everything that is in the anaconda
>>>>>>>> install,
>>>>>>>> they can even simply do "conda install anaconda" from the command
>>>>>>>> line
>>>>>>>> to get it.  But the stripped down subset is the default.
>>>>>>>>
>>>>>>>> If anyone has a chance to try this out and has feedback, I'd greatly
>>>>>>>> appreciate it!  I think Nathan has done something very similar for
>>>>>>>> OSX.  I've also put a couple simple conda recipes here:
>>>>>>>> https://bitbucket.org/yt_analysis/yt_conda which we can use as a
>>>>>>>> basis
>>>>>>>> for distributing builds and setting them up on buildbots and the
>>>>>>>> like.
>>>>>>>> I'm pretty optimistic about this.
>>>>>>>>
>>>>>>>> -Matt
>>>>>>>>
>>>>>>>> On Thu, Aug 29, 2013 at 5:50 PM, Nathan Goldbaum
>>>>>>>> <nathan12343@gmail.com> wrote:
>>>>>>>>> I think to get everything working in a sustainable fashion, we
>>>>>>>>> would need
>>>>>>>>> buildbots for all platform combinations that we want to support, so
>>>>>>>>> all
>>>>>>>>> permutations of the (32/64 bit,  linux / OS X / windows,
>>>>>>>>> py27/py3.3) tuple.
>>>>>>>>> At the moment anaconda seems to support 32 and 64 bit linux, 64 bit
>>>>>>>>> OS X
>>>>>>>>> (not totally clear if OS X version matters), and 32 and 64 bit
>>>>>>>>> windows.
>>>>>>>>>
>>>>>>>>> Another option is to rely on conda build, which compiles everything
>>>>>>>>> from
>>>>>>>>> source.
>>>>>>>>>
>>>>>>>>>
>>>>>>>>> On Thu, Aug 29, 2013 at 2:45 PM, Stephen Skory <s@skory.us> wrote:
>>>>>>>>>>
>>>>>>>>>> Hi all,
>>>>>>>>>>
>>>>>>>>>> I have less of a skin in this than I used to, but I'd like to
>>>>>>>>>> raise
>>>>>>>>>> the issue of Windows & package managers. For example, Anaconda is
>>>>>>>>>> available for Windows - would that mean that yt might "just work"
>>>>>>>>>> on
>>>>>>>>>> Windows? Or the opposite, and it would require a great deal of
>>>>>>>>>> effort
>>>>>>>>>> to get all the various things we expect to be .so's to work as
>>>>>>>>>> .dll's
>>>>>>>>>> (such as the Cython helpers or halo-finding stuff)?
>>>>>>>>>>
>>>>>>>>>> I don't know the answers to these questions, but I think it's
>>>>>>>>>> worth
>>>>>>>>>> thinking about.
>>>>>>>>>>
>>>>>>>>>> --
>>>>>>>>>> Stephen Skory
>>>>>>>>>> s@skory.us
>>>>>>>>>> http://stephenskory.com/
>>>>>>>>>> 510.621.3687 (google voice)
>>>>>>>>>> _______________________________________________
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>>>>>>>>>
>>>>>>>>>
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