Import error: Anaconda numpy (numpy and Anaconda already installed, virtualenv)

Question

I have a virtual environment my_env in which I installed Anaconda. When I type

which python

I get:

/user/pkgs/anaconda2/envs/my_env/bin/python

I have no errors importing numpy here:

(my_env) user@hostname:~/my_dir$ python
Python 2.7.12 |Continuum Analytics, Inc.| (default, Jul  2 2016, 17:42:40) 
[GCC 4.4.7 20120313 (Red Hat 4.4.7-1)] on linux2
Type "help", "copyright", "credits" or "license" for more information.
Anaconda is brought to you by Continuum Analytics.
Please check out: http://continuum.io/thanks and https://anaconda.org
>>> import numpy as np
>>>

But when I say 'import numpy as np' in a python program and run that from a shell script, I get:

(my_env) user@hostname:~/mydir$ ./program.sh 
Traceback (most recent call last):
  File "../python_program.py", line 3, in <module>
    import numpy as np
ImportError: No module named numpy

How can I fix this?

EDIT: I was asked what is in program.sh. The short answer is that I'm running different parameters in a loop. The long answer is:

#/bin/bash

i=0
while read a1 b1 c1 d1 e1 f1 g1 h1 i1
    do
    i=$(($i+1))
    mkdir RUN_EXP$i
    cp $a1 RUN_EXP$i
    cd RUN_EXP$i
    ../python_program.py --filename $a1 --reps $b1 --pop $c1 --susc $d1 --exp_trans $e1 --inf_period $f1\ $g1 --eps $h1\ $i1
    cd ..
    done < readparas.txt

The file readparas.txt has lines containing filename, reps, pop, susc, exp_trans, inf_period, and eps like this:

run_1.txt 50 162 0.30 0.1 5 9 0.1 0.25
run_1.txt 50 162 0.30 0.3 5 9 0.1 0.25
...

What is in program.sh?

DYZ
– DYZ

2017-03-05 21:15:28 +00:00
Commented Mar 5, 2017 at 21:15 — DYZ
– DYZ, Commented Mar 5, 2017 at 21:15
@DYZ please see edit above.

StatsSorceress
– StatsSorceress

2017-03-05 21:59:27 +00:00
Commented Mar 5, 2017 at 21:59 — StatsSorceress
– StatsSorceress, Commented Mar 5, 2017 at 21:59

OneCricketeer · Accepted Answer · 2017-03-08 20:52:03Z

2

Your shell script doesn't care about having a virtualenv active (it starts in a clean environment).

Instead of ../python_program.py you need to have the full executable path

 export PYTHON_ENV=/user/pkgs/anaconda2/envs/my_env

 $PYTHON_ENV/bin/python ../python_program.py --filename $a1 ...

Or you can append this to the top of python_program.py

#!/usr/bin/env python

Refer: The importance of env (and how it works with virtualenv)

edited Mar 8, 2017 at 20:52

answered Mar 5, 2017 at 22:03

OneCricketeer

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8 Comments

StatsSorceress Over a year ago

Why is the full executable path necessary? It wasn't with a similar program I ran before.

OneCricketeer Over a year ago

Because you are using a virtualenv where numpy is installed at. Your other program was using your system Python and had all the modules available.

StatsSorceress Over a year ago

Except the problem is also happening outside the virtualenv.

OneCricketeer Over a year ago

Yes, the error happens outside the virtualenv because you don't have numpy there. You need to tell your script which python executable needs to run your code.

user707650 Over a year ago

@StatsSorceress To clarify: your shell script starts up a new, cleaner, shell environment. It does not inherit all PATH settings from the standard shell you issue your python command in, hence you need to specifically use that path to the virtualenv Python

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