Project Initialization Scripts

All about the project-init.sh file.

While crontab-based management of periodic tasks is not available in CoCalc projects, we offer a flexible mechanism to use regular Bash, Python, or SageMath files for the same sort of capability.

Project Initialization

When a CoCalc project starts this is run:

  • an instance of “local hub”. It is used for managing the project, communication with the outside world, monitoring, etc.
  • sshd: the endpoint for remote SSH access.
  • initialization file: an optional bash script called project_init.sh, located in your home directory. It is only started once!

Example 1: record project start time

A very simple example is to record the project’s start time. Go to your home directory and create a file project_init.sh with that content:

date > project-start

This is a very simple bash script, which pipes the output of the date command into the file project-start.

In order to see its effect, the file needs to be saved and the project restarted. Give it a few seconds to come back online and run the script. After that (maybe click the refresh button in the file listing) you should see this file and its content might look like:

Mon Sep 12 11:14:20 UTC 2017

Other languages besides Bash?

You can run any language via bash’s exec! For example, project_init.sh containing:

exec python3 project_init.py

will run a Python 3 initialization file named project_init.py.

Example 2: a periodic task in Python

Here we write a small Python script, which runs an infinite loop (make sure to use time.sleep!) and evaluates a function running a simple command every 10 minutes. This examples uses the library schedule. Feel free to choose any other solution.

  1. project_init.sh: contains exec python3 project_init.py

  2. The content of project_init.py is:

    import schedule
    import time
    from datetime import datetime
    from subprocess import run, PIPE
    
    i = 0
    CMD = "date"
    
    def task():
        global i
        with open('task_output.log', 'a') as fout:
            ts = str(datetime.utcnow())
            status = run(CMD, stdout=PIPE, stderr=PIPE, shell=True)
            out = f"{status.stdout.decode('utf8')}\n{status.stderr.decode('utf8')}"
            fout.write("Task {}: {} output:\n{}\n".format(i, ts, out))
            i += 1
    
    
    schedule.every(10).minutes.do(task)
    
    while True:
        schedule.run_pending()
        time.sleep(60)
    

Indeed, after restarting the project the output of ps auxf shows this task as a child of the project hub:

USER         PID %CPU %MEM    VSZ   RSS TTY      STAT START   TIME COMMAND
user           1  0.1  0.0   4520   756 ?        Ss   09:18   0:00 /cocalc/bin/tini -- sh -c env -i /cocalc/init/init.sh $COCALC_PROJECT_ID $KUCALC_IMAGE_NAME
user           8  0.0  0.0   4628   832 ?        S    09:18   0:00 sh -c env -i /cocalc/init/init.sh $COCALC_PROJECT_ID $KUCALC_IMAGE_NAME
user           9 10.7  0.4 978240 121400 ?       Sl   09:18   0:03  \_ node /cocalc/src/smc-project/local_hub.js --tcp_port 6000 --raw_port 6001 --kucalc
user          21  0.0  0.0  72296  5728 ?        S    09:18   0:00      \_ /usr/sbin/sshd -D -p 2222 -h /tmp/.cocalc/ssh_host_rsa_key -o PidFile=/tmp/.cocalc/sshd.pid -f /cocalc/init/sshd_config
user          22  0.5  0.0  37836 14332 ?        S    09:18   0:00      \_ python3 project_init.py
 ...

and the output file task_output.log contains entries for each run.

Example 3: Periodic task in SageMath

run.sage is similar to the Python script above.

  1. project_init.sh: exec sage run.sage

  2. This results in Sage running a small task every two minutes and appends outputs to sage_output.log:

    import time
    from random import random
    from datetime import datetime
    
    i = 0
    def task():
        global i
        with open('sage_output.log', 'a') as fout:
            ts = str(datetime.utcnow())
            fout.write("Sage Task {}: {} value = {}\n".format(i, ts, random()))
            i += 1
    
    while True:
        task()
        time.sleep(2 * 60)
    

Debugging

To figure out why a script doesn’t work as it should, there are two ways to debug it:

  1. Run it directly in a terminal (create a *.term file) and run bash project_init.sh or python3 project_init.py.
  2. A common pitfall is to assume ~/.bashrc is run. Since this is a non-interactive session, you need to explicitly source any additional environment information.

Note: much of this page is taken from the CoCalc blog article Project Initialization Scripts.