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Posts tagged with 'cylc'

ImportError when debugging cylc in Eclipse

kinow @ Jul 10, 2018 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, owner@host=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!

A simple cylc suite

kinow @ Jul 08, 2018 18:59:13

I have been writing more suites for cylc lately, and found an example that has proved to be useful for debugging certain parts of the code.

It is an extremely simple suite, similar to what is in cylc’s documentation. It sleeps for N seconds, and prints a message.

What makes it extra simpler, is that it cycles through integers, and has a limit of 1 maximum active points.

It is essentially the same as running the command in your shell session. With the difference that it will run through all cylc’s internal, only once, and allow you to debug and diagnostic parts nor related to cycling and graphs (as for these parts you would probably need a more elaborate example).

    cycling mode = integer
    initial cycle point = 1
    max active cycle points = 1
            graph = "hello"
        script = "sleep 10; echo PING"

I also combine this suite with the following global.rc.

    terminal = vim 
    gui = gvim -f

    base port = 44444
    method = http
    maximum number of ports = 1

With “base port” set to 44444, and the maximum number of ports to 1, I will be able to run only one task. But that way I can configure Wireshark and other tools to default to 44444/HTTP, for ease of debugging.

Then initialize the suite with something like: cylc start --non-daemon --debug /home/kinow/Development/python/workspace/example-suite/

Happy cycling!

Geek Vacation 2016

kinow @ Apr 08, 2016 22:17:03

I just had a two week vacation, and I tried to use my time to rest, play some music, and complete a geek todo-list.

The list included things that I used some time ago but wanted to refresh my memory, things that I already used but never spent time reading the manuals, and other things that I saw somewhere but never actually used in any project.

Here the complete list, with the items that were completed highlighted. Some links with pointers to what I used to study.

Going to have less spare time now for Open Source and learning the rest of the stuff on this list, but there’s always some books to read, and things to learn anyway right ¯\(ツ)