[yt-users] Building yt on Hopper

[Michael Zingale]

has anyone asked NERSC whether they'd be willing to install it sitewide as
a loadable module on hopper?  I'm sure there are lots of us who would want
to use yt there.


On Sat, Feb 1, 2014 at 6:16 PM, Andrew Myers <atmyers2 at gmail.com> wrote:

> Hi Hilary,
>
> Thanks for the suggestion. Unfortunately, it didn't work for me - if I
> install ipython manually, it still fails with the same error message.
>
> I think I'll try to ask this at StackOverflow as well, as per Nathan's
> suggestion.
>
> Thanks,
> Andrew
>
>
> On Sat, Feb 1, 2014 at 10:09 AM, Hilary Egan <hilaryye at gmail.com> wrote:
>
>> I saw the same problem when I was installing on CU's janus machine. I'm
>> pretty sure that I got around it by building just ipython by hand and
>> making sure I was on the compile node when I tried it- no idea if there is
>> an equivalent for Hopper.
>>
>> -download and untar ipython.tar.gz (http://archive.ipython.org/release/)
>>  -cd ipython
>> -python setup.py install
>> -touch done
>>
>> Caveat: I have no idea why this worked when the install script didn't,
>> and I'm just basing my answer on the note I jotted down a few months ago.
>> There's definitely some sort of discussion out there already about this
>> being a problem in some versions in pyzmq (
>> https://github.com/zeromq/pyzmq/pull/218).  Hope that helps!
>>
>> -Hilary
>>
>>
>> On Sat, Feb 1, 2014 at 10:49 AM, Nathan Goldbaum <nathan12343 at gmail.com>wrote:
>>
>>> Hi Andrew,
>>>
>>> Unfortunately I'm not sure what the issue is.
>>>
>>> You might try asking this question on StackOverflow (tagging it with
>>> IPython and ZMQ) or the IPython-dev mailing list, some of the ZMQ/IPy
>>> devs will be more likely to see it.
>>>
>>> Nathan
>>>
>>>
>>> On Saturday, February 1, 2014, Andrew Myers <atmyers2 at gmail.com> wrote:
>>>
>>>> Hi Folks,
>>>>
>>>> I'm trying to install the development version of yt-2.7 on NERSC's
>>>> Hopper machine using the install script. I get to the part where it tries
>>>> to build IPython, and then the script fails with the following error
>>>> message:
>>>>
>>>>
>>>> ============================================================================
>>>> BUILDING IPYTHON
>>>>                 python: 2.7.6 (default, Jan 31 2014, 21:52:04)  [GCC
>>>> 4.8.1
>>>>                         20130531 (Cray Inc.)]
>>>>               platform: linux2
>>>>
>>>> OPTIONAL DEPENDENCIES
>>>>                 sphinx: Not found (required for docs and nbconvert)
>>>>               pygments: Not found (required for docs and nbconvert)
>>>>                   nose: 1.3.0
>>>>                pexpect: no (required for running standalone doctests)
>>>> Traceback (most recent call last):
>>>>   File "setup.py", line 342, in <module>
>>>>     check_for_dependencies()
>>>>   File "/global/u2/a/atmyers/yt-x86_64/src/ipython-1.1.0/setupbase.py",
>>>> line 376, in check_for_dependencies
>>>>     check_for_pyzmq()
>>>>   File
>>>> "/global/u2/a/atmyers/yt-x86_64/src/ipython-1.1.0/setupext/setupext.py",
>>>> line 118, in check_for_pyzmq
>>>>     import zmq
>>>>   File
>>>> "/global/homes/a/atmyers/yt-x86_64/lib/python2.7/site-packages/zmq/__init__.py",
>>>> line 35, in <module>
>>>>     _libzmq = ctypes.CDLL(bundled[0], mode=ctypes.RTLD_GLOBAL)
>>>>   File
>>>> "/global/homes/a/atmyers/yt-x86_64/lib/python2.7/ctypes/__init__.py", line
>>>> 365, in __init__
>>>>     self._handle = _dlopen(self._name, mode)
>>>> OSError:
>>>> /global/homes/a/atmyers/yt-x86_64/lib/python2.7/site-packages/zmq/libzmq.so:
>>>> undefined symbol: clock_gettime
>>>>
>>>> Both ZeroMQ and pyzmq appear to have been installed without errors, but
>>>> then ZeroMQ can't find some of the definitions it needs. Googling around,
>>>> it looks like clock_gettime is supposed to be found in librt.
>>>>
>>>> Has anyone seen this before? Or, relatedly, has anyone been able to
>>>> build yt on the NERSC machines? I know that ZeroMQ isn't strictly
>>>> necessary, but I'd like to be able to use the notebooks.
>>>>
>>>> My complete yt_install.log is here<https://www.dropbox.com/s/pmdq3a9vfrbtwj9/yt_install.log>
>>>> .
>>>>
>>>> Thanks,
>>>> Andrew
>>>>
>>>
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>>
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-- 
Michael Zingale
Associate Professor

Dept. of Physics & Astronomy * Stony Brook University * Stony Brook, NY
11794-3800
*phone*:  631-632-8225
*e-mail*: Michael.Zingale at stonybrook.edu
*web*: http://www.astro.sunysb.edu/mzingale
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