These are chat archives for dereneaton/ipyrad

Jun 2018
Rebecca Tarvin
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
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
Jun 04 2018 15:37
@R0cknRobin_twitter aggravating that it gets so close and then dies. Is this on the cuny cluster?
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/", line 45, in <module>
  File "/home1/02745/tdevitt/miniconda2/lib/python2.7/site-packages/zmq/eventloop/", 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
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:
Can't hurt to verify you have the most recent miniconda installer as well:
Jun 04 2018 20:47
@isaacovercast I think so, I followed the instructions just as they are outlined in the faq.