[yt-users] Building yt on Hopper

[Andrew Myers]

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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