Simple script which can be used to monitor and log CPU and RAM usage of submitted cluster jobs
Project description
ClusterMonitor
A very simple python script which monitors and records the CPU and RAM consumption of submitted cluster jobs.
Usage
To start recording use the cpu_ram_log.py
script. This script requires 3 arguments:
-u
which corresponds to your username.-o
which specifies the output file (in tsv format)--interval
which specifies the time (in seconds) over which the CPU and RAM usage gets averaged
Example:
python cpu_ram_log.py -u nickhir -o cpu_ram.log --interval 5
The script can simply be included in your cluster job submittion like this:
#!/bin/bash
#SBATCH --job-name=Example_run
sambamba sort -t 20 some_bam.bam &
MainScript=$!
python cpu_ram_log.py -u nickhir -o cpu_ram.log --interval 5 &
wait $MainScript
pkill -P $$
Afterwards the resulting log file can be plotted (for that matplotlib
is needed).
For that use the visualize_log.py
script which needs 2 arguments:
-i
which specifies the path to the log file which was created withcpu_ram_log.py
-o
which specifies the path to the resulting PDF which contains a plot for the CPU and RAM usage.
Example:
python visualize_log.py -i cpu_ram.log -o cpu_ram_visualization.pdf
The resulting plots will look somewhat like this:
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