Fatal Python error: initfsencoding: Unable to get the locale encoding File "/cm/shared/apps/anaconda2/4.5.12/lib/python2.7/encodings/init.py"

Question

I am writing a job submission script for SLURM workload manager. First, I have loaded anaconda2/4.5.12 (including python 2.7) module. Then, I have created conda environment with Python3.7 version. I try to submit the script using "sbatsh" command, but I get this error:

Fatal Python error: initfsencoding: Unable to get the locale encoding
File "/cm/shared/apps/anaconda2/4.5.12/lib/python2.7/encodings/__init__.py", line 123
raise CodecRegistryError,\
                        ^
SyntaxError: invalid syntax
Current thread 0x00002aaaaaaffc00 (most recent call first):
/cm/local/apps/slurm/var/spool/job04287/slurm_script: line 19: 40032 
Aborted                 python3 taxo.TXT

This is my script file:

#!/bin/bash
#
#SBATCH --job-name=taxjob
#SBATCH --nodes=4

#SBATCH --tasks-per-node=3
#SBATCH --time=0-03:00:00
#SBATCH --partition=shortq 
#SBATCH --mem=24GB 
#SBATCH --output=/home/s.e/tax/Ftest-%j.out
#SBATCH --error=/home/s.e/tax/Ftest-%j.err
module load anaconda2/4.5.12
source activate py37
python3  taxo.TXT

S.m · Accepted Answer · 2019-04-01 13:50:42Z

2

After many tries, the solution was to add the instruction "unset PYTHONPATH" to my script file as follows:

....    
module load anaconda2/4.5.12
source activate py37
unset PYTHONPATH
python3  taxo.TXT

answered Apr 1, 2019 at 13:50

S.m

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Kolay.Ne · Accepted Answer · 2019-03-26 13:01:00Z

0

The problem is that the "/cm/shared/apps/anaconda2/4.5.12/lib/python2.7/encodings/__init__.py" if a python2 file, like you can see at the path, but it is trying to be interpreted as a python3 file. You can either fix this conda problem and run it using python2.7 or edit the encodings/__init__.py file to make it python3-interpretable

To understand the problem you can try to run this line in python2 and python3 manually:

#Python3
>>> raise Exception,\
  File "<stdin>", line 1
    raise Exception,\
                   ^
SyntaxError: invalid syntax

but

#Python2.7
>>> raise Exception,\
...

Python3 analog of raise Exception,\ "str" is raise Exception("str"). So you can change the 123rd line of the file, but it's not a good idea, because other problems may occur, so it's better to fix something in configs/executing commands of anaconda

answered Mar 26, 2019 at 13:01

Kolay.Ne

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7 Comments

Kolay.Ne Over a year ago

If you decide to edit the file, you have to replace lines 123 to 125 with raise CodecRegistryError('module "%s" (%s) failed to register' % (mod.__name__, mod.__file__))

S.m Over a year ago

Thank you for answering, I am not able to modify the file because only the administrator of the HPC can edit shared modules such as anaconda2/4.5.12

S.m Over a year ago

I can't use Python2.7 as well, because I am using some packages which are available only for python version > 3.x

Kolay.Ne Over a year ago

Then, I guess, you have to switch to the encodings library for python3

S.m Over a year ago

How can I do it, please?

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