Can't run with Anaconda environment

Question

Can't run with Anaconda environment

kastnerkyle opened this issue 7 years ago · comments

The story so far (copied from chat)

I am using anaconda and had to additionally symlink coco/common in amodalApi to get maskApi.h for build_ext to work

it builds but is still unhappy... ImportError: pycocotools/_mask.so: undefined symbol: PyFPE_jbuf
investigating now, seems related to numpy versions or somesuch. May be an environment problem.

looks like the cython generated c is referencing system python... /usr/local/lib/python2.7/dist-packages/numpy/core/include . After recreating the cython file, it references the python I expect but it still gives the PyFPE_jbuf error.

Yan Zhu · Answer 1 · Fri Jan 27 2017 05:35:50 GMT+0800 (China Standard Time)

Thanks, I am looking now. I saw a similar issue in the cocoApi yesterday:
cocodataset/cocoapi#35

btw, can you run the original cocoApi in this machine?

Kyle Kastner · Answer 2 · Fri Jan 27 2017 05:37:25 GMT+0800 (China Standard Time)

Yes, all is well in the coco api itself with the ipynb examples

Kyle Kastner · Answer 3 · Fri Jan 27 2017 05:38:48 GMT+0800 (China Standard Time)

When I run in the terminal (not notebook) I get a different error

python -c 'from pycocotools.amodal import Amodal'

Gives

Traceback (most recent call last):
  File "<string>", line 1, in <module>
  File "/home/kkastner/anaconda2/lib/python2.7/site-packages/pycocotools/amodal.py", line 58, in <module>
    import mask
  File "/home/kkastner/anaconda2/lib/python2.7/site-packages/pycocotools/mask.py", line 3, in <module>
    import pycocotools._mask as _mask
ImportError: /home/kkastner/anaconda2/lib/python2.7/site-packages/pycocotools/_mask.so: undefined symbol: rleMinus

Yan Zhu · Answer 4 · Fri Jan 27 2017 05:40:07 GMT+0800 (China Standard Time)

oh my bad, I modified maskApi.c, but didn't include the code here...

Let me add those modified files.

Kyle Kastner · Answer 5 · Fri Jan 27 2017 05:53:51 GMT+0800 (China Standard Time)

It's fixed after your pushed files! Thanks a lot.

Yan Zhu · Answer 6 · Fri Jan 27 2017 05:55:14 GMT+0800 (China Standard Time)

np:)

I am still testing the installation on a brand new aws machine. I will need to add a bunch of dependecies in readme.

Kyle Kastner · Answer 7 · Fri Jan 27 2017 05:57:27 GMT+0800 (China Standard Time)

I still get errors in jupyter notebook but commandline is fine. It might be in my environment, I will keep looking too :)

Yan Zhu · Answer 8 · Fri Jan 27 2017 05:58:47 GMT+0800 (China Standard Time)

can you copy the error log ?

Kyle Kastner · Answer 9 · Fri Jan 27 2017 06:14:00 GMT+0800 (China Standard Time)

Here it is, from the notebook ``` ImportError Traceback (most recent call last) <ipython-input-1-e768b8eb76e4> in <module>() 1 get_ipython().magic(u'matplotlib inline') ----> 2 from pycocotools.amodal import Amodal 3 import numpy as np 4 import skimage.io as io 5 import matplotlib.pyplot as plt /home/kkastner/amodalAPI/PythonAPI/pycocotools/amodal.py in <module>() 56 import copy 57 import itertools ---> 58 import mask 59 import os 60 from pycocotools.coco import COCO /home/kkastner/amodalAPI/PythonAPI/pycocotools/mask.py in <module>() 1 __author__ = 'tsungyi' 2 ----> 3 import pycocotools._mask as _mask 4 5 # Interface for manipulating masks stored in RLE format. ImportError: pycocotools/_mask.so: undefined symbol: PyFPE_jbuf ```

…

On Thu, Jan 26, 2017 at 1:58 PM, Yan Zhu ***@***.***> wrote: can you copy the error log ? — You are receiving this because you modified the open/close state. Reply to this email directly, view it on GitHub <#1 (comment)>, or mute the thread <https://github.com/notifications/unsubscribe-auth/ABfbHfNqhmEwZQ_z3iKbvktl6gMwe_cEks5rWRcXgaJpZM4LvI6J> .

Kyle Kastner · Answer 10 · Fri Jan 27 2017 06:46:29 GMT+0800 (China Standard Time)

I am copy pasting more and more of the notebook into a .py file, and so far it seems fine. So I am unsure what is going on...

Yan Zhu · Answer 11 · Fri Jan 27 2017 06:49:13 GMT+0800 (China Standard Time)

unfortunately I cannot reprod this.

After some googling, I am thinking could it because the "pycocotools/_mask.so" is confilcting with your previous installation of cocoAPI?

Maybe try using virtualenv to create a separate python environment?

Kyle Kastner · Answer 12 · Fri Jan 27 2017 06:51:13 GMT+0800 (China Standard Time)

OK, so with myAmodalDemo.ipynb in the main dir it is working, other than some tiny path issues (due to copying up one dir). So I am unsure what that error was, beyond (my guess) imports getting confused by a pycocotools in "." and also "~/anaconda2/lib/site-packages/python2.7"

Yan Zhu · Answer 13 · Fri Jan 27 2017 06:51:30 GMT+0800 (China Standard Time)

or because your ipython and python are using different environment?

which python
which ipython

are they from same path?

Kyle Kastner · Answer 14 · Fri Jan 27 2017 06:52:03 GMT+0800 (China Standard Time)

Yes, both from ~/anaconda2/bin

Kyle Kastner · Answer 15 · Fri Jan 27 2017 06:52:46 GMT+0800 (China Standard Time)

You can close if you like, I think it is path related due to running jupyter notebook in the PythonAPI dir directly.

Yan Zhu · Answer 16 · Fri Jan 27 2017 06:54:38 GMT+0800 (China Standard Time)

okay, feel free to reopen if new error bothers.

I will cleanup the code and enrich readme/installation probably after cvpr rebuttal.

Kyle Kastner · Answer 17 · Fri Jan 27 2017 06:54:56 GMT+0800 (China Standard Time)

OK sounds good, thanks again for your help!