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@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@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.

Thanks,

Andrew 

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