[yt-users] Building yt on Hopper

[Nathan Goldbaum]

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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