ImportError when debugging cylc in Eclipse

kinow @ 2018-07-10 00:47:13 ()

Since I started reading cylc’s source code in Eclipse to create some sequence diagrams, I have not been able to debug it properly without hitting errors in some part of the program execution.

The error message was “ImportError: cannot import name _remove_dead_weakref”, which was a bit enigmatic as I never heard about that function, but it seemed to be something internal, or at least not from the project code base. And searching the Internet did not help much.

Here is the complete console output in Eclipse.

pydev debugger: starting (pid: 15124)
timeout 10 ps -opid,args 13640  # return 1

            | |            The Cylc Suite Engine [7.7.1-37-g09c8a]    
._____._. ._| |_____.           Copyright (C) 2008-2018 NIWA          
| .___| | | | | .___|  _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _
| !___| !_! | | !___.  This program comes with ABSOLUTELY NO WARRANTY;
!_____!___. |_!_____!  see `cylc warranty`.  It is free software, you 
      .___! |           are welcome to redistribute it under certain  
      !_____!                conditions; see `cylc conditions`.       
2018-07-10T01:00:47+12 INFO - Suite starting: server=localhost:44444 pid=15124
2018-07-10T01:00:47+12 INFO - Cylc version: 7.7.1-37-g09c8a
2018-07-10T01:00:47+12 INFO - Run mode: live
2018-07-10T01:00:47+12 INFO - Initial point: 1
2018-07-10T01:00:47+12 INFO - Final point: None
2018-07-10T01:00:47+12 INFO - Cold Start 1
2018-07-10T01:00:47+12 DEBUG - [hello.1] -released to the task pool
2018-07-10T01:00:47+12 DEBUG - BEGIN TASK PROCESSING
2018-07-10T01:00:47+12 DEBUG - [hello.1] -waiting => queued
2018-07-10T01:00:47+12 DEBUG - 1 task(s) de-queued
2018-07-10T01:00:47+12 INFO - [hello.1] -submit-num=1, [email protected]=localhost
2018-07-10T01:00:47+12 DEBUG - [hello.1] -queued => ready
2018-07-10T01:00:47+12 DEBUG - END TASK PROCESSING (took 0.023609161377 seconds)
2018-07-10T01:00:48+12 DEBUG - ['cylc', 'jobs-submit', '--debug', '--', '/home/kinow/Development/python/workspace/example-suite/log/job', '1/hello/01']
2018-07-10T01:00:48+12 ERROR - [jobs-submit cmd] cylc jobs-submit --debug -- /home/kinow/Development/python/workspace/example-suite/log/job 1/hello/01
    [jobs-submit ret_code] 1
    [jobs-submit err]
    Traceback (most recent call last):
      File "/home/kinow/Development/python/workspace/cylc/bin/cylc-jobs-submit", line 52, in <module>
        from cylc.batch_sys_manager import BatchSysManager
      File "/home/kinow/Development/python/workspace/cylc/lib/cylc/", line 114, in <module>
        from cylc.task_message import (
      File "/home/kinow/Development/python/workspace/cylc/lib/cylc/", line 26, in <module>
        from logging import getLevelName, WARNING, ERROR, CRITICAL
      File "/home/kinow/Development/python/anaconda2/lib/python2.7/logging/", line 26, in <module>
        import sys, os, time, cStringIO, traceback, warnings, weakref, collections
      File "/home/kinow/Development/python/anaconda2/lib/python2.7/", line 14, in <module>
        from _weakref import (
    ImportError: cannot import name _remove_dead_weakref
2018-07-10T01:00:48+12 ERROR - [jobs-submit cmd] cylc jobs-submit --debug -- /home/kinow/Development/python/workspace/example-suite/log/job 1/hello/01
    [jobs-submit ret_code] 1
    [jobs-submit out] 2018-07-10T01:00:48+12|1/hello/01|1
2018-07-10T01:00:48+12 INFO - [hello.1] -(current:ready) submission failed at 2018-07-10T01:00:48+12
2018-07-10T01:00:48+12 ERROR - [hello.1] -submission failed
2018-07-10T01:00:48+12 DEBUG - [hello.1] -ready => submit-failed
2018-07-10T01:00:48+12 DEBUG - BEGIN TASK PROCESSING
2018-07-10T01:00:48+12 DEBUG - 0 task(s) de-queued
2018-07-10T01:00:48+12 DEBUG - END TASK PROCESSING (took 0.00175499916077 seconds)
2018-07-10T01:00:49+12 WARNING - suite stalled

As the current diagram I am working on has quite a few if‘s and else‘s, I decided to investigate why this error was occurring. Then, after some elimination I found that it was due to the missing Anaconda 2 entry in my $PATH environment variable.

I had this variable configured in a custom script I load whenever I decide to use Anaconda 2. And reproducing the same behaviour in Eclipse was easy.

A screen shot of Eclipse with source code
Locating the bug

Et voilà! Eclipse was happily debugging again!

A screen shot of Eclipse with source code
Locating the bug

So if you have a similar problem, try comparing your environment variables and check if you have some entries missing, and try adding them in Eclipse Debug configuration.

Happy cycling!