[yt-users] Building yt on Hopper

[Hilary Egan]

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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