These are chat archives for dereneaton/ipyrad

4th
Jun 2018
Rebecca Tarvin
@frogsicles_twitter
Jun 04 2018 01:35
@isaacovercast I've also had ipyrad fail to restart step 6 when it was killed by my cluster for going over the time limit.
Robin Sleith
@R0cknRobin_twitter
Jun 04 2018 12:58
@isaacovercast I experimented with both instances where the job runs out of time, and a qdel command (not sure how exactly qdel kills the job) and neither seem to allow a restart from a completed checkpoint. Im less concerned with the qdel problem, its the job going over the time limit that really gets me in a bind. [################## ] 92% building database | 3 days, 11:25:40 =>> PBS: job killed: walltime 864035 exceeded limit 864000
Isaac Overcast
@isaacovercast
Jun 04 2018 15:37
@R0cknRobin_twitter aggravating that it gets so close and then dies. Is this on the cuny cluster?
tommydevitt
@tommydevitt
Jun 04 2018 19:53

@isaacovercast @edgardomortiz Hey guys, I just followed Edgardo's instructions for installing conda and ipyrad on TACC's Lonestar 5, but now I can't start jupyter or connect to the jupyter server. My jupyter log file says

Traceback (most recent call last):
  File "/home1/02745/tdevitt/miniconda2/bin/jupyter-notebook", line 4, in <module>
    import notebook.notebookapp
  File "/home1/02745/tdevitt/miniconda2/lib/python2.7/site-packages/notebook/notebookapp.py", line 45, in <module>
    ioloop.install()
  File "/home1/02745/tdevitt/miniconda2/lib/python2.7/site-packages/zmq/eventloop/ioloop.py", line 210, in install
    assert (not ioloop.IOLoop.initialized()) or \
AttributeError: type object 'IOLoop' has no attribute 'initialized'

Any advice? Thanks for your help.

Isaac Overcast
@isaacovercast
Jun 04 2018 20:00
Did you completely remove your miniconda install?
This really feels like a conda install mismatch or incompatibility. Mariana and I figured out that rolling back to pyzmq 16 is not necessary (and causes ipcluster to fail silently). I updated the instructions edgardo outlined on the faq: http://ipyrad.readthedocs.io/faq.html#how-do-i-fix-this-error-oserror-lib64-libpthread-so-0-version-glibc-2-12-not-found
Can't hurt to verify you have the most recent miniconda installer as well: https://conda.io/miniconda.html
tommydevitt
@tommydevitt
Jun 04 2018 20:47
@isaacovercast I think so, I followed the instructions just as they are outlined in the faq.