My python script cuts off strings when run via cron.
I have a python script that captures the output from the unix "top" command, iterates through to find the metrics I require and prints these to an output file. I want to capture these metrics every 15 minutes so I have added the script to the user crontab.
However, the script executed via cron produces different output.
Command line output (Desired):
User %CPU %MEM Time_Running Command
-------------------------------------------------------------------------------------------------------
hpc 977.8 12.1 19689:06 ./mix99s
3tb 94.4 0.1 0:06.67 python -c import sys;
3tb 94.4 2.2 50:57.58 /apps/anaconda3/bin/python3 Cross_Platform_Validation.py
fhpc 16.7 0.0 0:00.05 top -b -c -n1
---------------------------------------------------------------------------------------------------------
Cron job output:
User %CPU %MEM Time_Running Command
-------------------------------------------------------------------------------------------------------
hpc 977.8 12.1 19689:06 ./mix99s
3tb 94.4 0.1 0:06.67 python -c+
3tb 94.4 2.2 50:57.58 /apps/ana+
fhpc 16.7 0.0 0:00.05 top -b -c+
---------------------------------------------------------------------------------------------------------
The cron job always cuts off any field greater than 10 characters long (see "Command" above)
I thought this may be due to buffersize in the subprocess Popen but changing the bufsize=-1 had no impact.
The important parts of my script are:
# Get Top command output
top_out = subprocess.Popen(['top', '-b', '-c', '-n1'], bufsize=-1, stdout=subprocess.PIPE).stdout
...
# Task output always starts on line 7
elif i > 6:
# sep=None ie. split by whitespace. Max 11 splits
cols = line.split(None, 11)
user = cols[1]
cpu = cols[8]
mem = cols[9]
time_run = cols[10]
command = cols[11]
outfile.write('{}'.format(user))
outfile.write('{}'.format(cpu))
outfile.write('{}'.format(mem))
outfile.write('{}'.format(time_run))
outfile.write('{}'.format(command))
The problem was to do with the top command output being truncated to 80 characters when run via cron as answered here: https://unix.stackexchange.com/questions/95877/output-of-top-gets-truncated-to-80-columns-when-run-by-cron
Changing my cron job to include the COLUMNS option fixed the problem
Original
# Run monitor script every 15 minutes
*/15 * * * * /mnt/active/monitor_cluster/monitor.py
Working
# Run monitor script every 15 minutes
*/15 * * * * COLUMNS=200 /mnt/active/monitor_cluster/monitor.py