These are chat archives for dereneaton/ipyrad
@dereneaton @isaacovercast yesterday I was trying to follow the tutorial to get STRUCTURE running parallel that I didn't completely manage in the end, which is a pity but that's OK.
However today I am getting issues:
at first after ipyrad -p params-good_samples.txt -s 34567 -c 15
the error returned something about ipcluster so after searching a bit I found this which I tried without success
ipcluster start --n=15 --daemonize --profile=ipyrad
ipyrad -p params-good_samples.txt -s 34567 -c 15 --ipcluster
loading Assembly: good_samples
from saved path: /data/filer-5-2/brassac/Boechera/good_samples.json
Encountered an error (see details in ./ipyrad_log.txt)
Error summary is below -------------------------------
No ipcluster instance found. This may be a problem with your installation
setup. I would recommend that you contact the ipyrad developers.
I think I screwed something up, any idea how to get it working again?
@dereneaton I was running the tutorial outside the jupyter-notebook.
I don't exactly remember where I got stuck, it was pretty late yesterday when I tried it. However today while I was trying to repeat it I got problems with
import pandas as pd ValueError Traceback (most recent call last) <ipython-input-8-af55e7023913> in <module>() ----> 1 import pandas as pd /data/filer-5-2/brassac/miniconda2/lib/python2.7/site-packages/pandas/__init__.py in <module>() 23 24 try: ---> 25 from pandas import hashtable, tslib, lib 26 except ImportError as e: # pragma: no cover 27 module = str(e).lstrip('cannot import name ') # hack but overkill to use re pandas/src/numpy.pxd in init pandas.lib (pandas/lib.c:85430)() ValueError: numpy.dtype has the wrong size, try recompiling. Expected 88, got 96
although numpy loaded without error...
I tried running ipyrad without "--profile=ipyrad", it's running fine.