These are chat archives for dereneaton/ipyrad

Jun 2018
Jun 05 2018 00:55
@isaacovercast I followed the instructions but still get
ImportError: /lib64/ version `GLIBC_2.12' not found (required by 
Isaac Overcast
Jun 05 2018 02:00
@tommydevitt Is it possible that different parts of the UT cluster have different operating system configurations?
You could try rolling back both pyzmq and ipyparallel:
conda install pyzmq=16
conda install ipyparallel=5.2
Jun 05 2018 14:50
@isaacovercast I guess that's possible, I don't really know. I tried rolling back pyzmq and ipyparallel as you suggested. Now when trying to run the pipeline I'm getting time out error messages. Any other suggestions? Thanks Isaac.
Encountered an unexpected error (see ./ipyrad_log.txt)
  Error message is below -------------------------------
Hub connection request timed out
Isaac Overcast
Jun 05 2018 15:46
@tommydevitt Did you try running ipcluster by hand? Try running ipcluster start -n 4. If it returns the console to you rather than blocking then ipcluster is messed up.
Jun 05 2018 17:56
@isaacovercast tried as you suggested via a development node and just received dozens upon dozens of error messages like this one:
ERROR:tornado.application:Exception in callback (7, <function null_wrapper at 0x2aaab47bc9b0>)
Traceback (most recent call last):
  File "/home1/02745/tdevitt/miniconda2/lib/python2.7/site-packages/tornado/", line 1064, in start
    handler_func(fd_obj, events)
  File "/home1/02745/tdevitt/miniconda2/lib/python2.7/site-packages/tornado/", line 276, in null_wrapper
    return fn(*args, **kwargs)
  File "/home1/02745/tdevitt/miniconda2/lib/python2.7/site-packages/ipyparallel/apps/", line 310, in handle_stdout
  File "/home1/02745/tdevitt/miniconda2/lib/python2.7/site-packages/ipyparallel/apps/", line 326, in poll
AttributeError: 'NoneType' object has no attribute 'stop'
2018-06-05 12:52:08.963 [IPClusterStart] Removing pid file: /home1/02745/tdevitt/.ipython/profile_default/pid/
Isaac Overcast
Jun 05 2018 19:15
@tommydevitt Yeah, something is just broken with the conda install. Perhaps you have more than one version of conda installed? One thing I could suggest is to rm -rf your miniconda directory, then do a which python and make sure there is no other miniconda installed. Make sure $PYTHONPATH isn't set. It might be one strategy to contact someone with a known working minconda install and have them tar -czv -f miniconda2.tgz miniconda2 and then copy you the tgz file, then you can unpack it in your home directory and you should be good to go. This is somewhat hackish, but it's better than endlessly troubleshooting your own conda install if we know somebody who has one working (mariana for example).
Jun 05 2018 19:18

@isaacovercast Just spoke with Mariana and I followed her directions to uninstall/reinstall, which seemed essentially the same as Edgardo's but I guess something was different. Everything is working again now. Whew. This is what I did:

rm -rf ~/miniconda2
rm -rf ~/.condarc ~/.conda ~/.continuum
source ~/.bashrc
conda install llvmlite=0.22
conda install -c ipyrad ipyrad

Jun 05 2018 19:30

Still can't import the Python libraries in the Jupyter structure cookbook though.

import ipyrad.analysis as ipa ## ipyrad analysis toolkit
import ipyparallel as ipp ## parallel processing
import toyplot ## plotting library


IPyradErrorTraceback (most recent call last)
<ipython-input-8-11fdbfdcd03d> in <module>()
----> 1 import ipyrad.analysis as ipa      ## ipyrad analysis toolkit
      2 ## import ipyparallel as ipp          ## parallel processing
      3 ## import toyplot                     ## plotting library

/home1/02745/tdevitt/miniconda2/lib/python2.7/site-packages/ipyrad/analysis/ in <module>()
     16 #from toytree import tree
     17 #from .tetrad import Tetrad as tetrad
---> 18 from .structure import Structure as structure
     19 from .treemix import Treemix as treemix
     20 from .tetrad2 import Tetrad as tetrad

/home1/02745/tdevitt/miniconda2/lib/python2.7/site-packages/ipyrad/analysis/ in <module>()
     10 import numpy as np
     11 import pandas as pd
---> 12 from ipyrad.analysis.tetrad import get_spans
     13 from ipyrad.assemble.util import Params, IPyradWarningExit

/home1/02745/tdevitt/miniconda2/lib/python2.7/site-packages/ipyrad/analysis/ in <module>()
     62     conda install toytree -c eaton-lab
---> 63     """)

/home1/02745/tdevitt/miniconda2/lib/python2.7/site-packages/ipyrad/assemble/util.pyc in __init__(self, *args, **kwargs)
     50     def __init__(self, *args, **kwargs):
     51         if ipyrad.__interactive__:
---> 52             raise IPyradError(*args, **kwargs)
     53         else:
     54             SystemExit.__init__(self, *args, **kwargs)

    Error: tetrad requires the dependency 'toytree', which we haven't yet
    included in the ipyrad installation. For now, you can install toytree
    using conda with the following command: 

    conda install toytree -c eaton-lab
Mariana Vasconcellos
Jun 05 2018 20:25
@tommydevitt Try conda install toytree -c eaton-lab. This might do the trick.
Jun 05 2018 20:28
@marypsiboas_twitter I'll try...
Jun 05 2018 20:41
@marypsiboas_twitter Didn't work. Invalid syntax.
conda install toytree -c eaton-lab
File "<ipython-input-4-c4de7fdc2886>", line 5
    conda install toytree -c eaton-lab
SyntaxError: invalid syntax
Isaac Overcast
Jun 05 2018 20:51
You have to run the conda command in a terminal. Or you can run it in a notebook cell if you precede it with a bang:
!conda install toytree -c eaton-lab
Jun 05 2018 20:52
@isaacovercast ah, the bang, right! Forgot.