CellProfilerHPC-Performance-Check.md

Monitoring CellProfiler on Hydra-HPC (Core Status and Parallel Processing)

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1. While the Job is Running: Use sstat or htop

Option A: Monitor Live Job Stats with sstat

sstat -j <jobid> --format=AveCPU,AveRSS,MaxRSS,Elapsed

• <jobid> is the numeric SLURM job ID (you get this after sbatch submission).
• AveCPU shows average CPU usage
• AveRSS and MaxRSS show average and peak memory usage
• Elapsed shows how long the job has been running

Example:

sstat -j 12345678 --format=AveCPU,AveRSS,MaxRSS,Elapsed

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Option B: Use htop on the Node (if you have SSH access to the compute node)

1. Find the node your job is running on:

squeue -u $USER

2. SSH into that node (if allowed):

ssh <nodename>

3. Run:

htop

Then press:

• F2 to configure
• F6 to sort by CPU usage
• Look for your job’s Python processes using up the cores

If you don’t have direct access to compute nodes, stick to sstat.

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2. Inside Your Python Script: Print or Log CPU Info

Add this at the top of nf1_analysis.py:

import os
import multiprocessing

print(f"Total CPUs visible to job: {os.cpu_count()}")
print(f"MAX_WORKERS from env: {os.environ.get('MAX_WORKERS')}")
print(f"Number of plates to process: {len(plate_info_dictionary)}")

And right before launching ProcessPoolExecutor, log:

from datetime import datetime
print(f"Launching ProcessPoolExecutor with {num_processes} workers at {datetime.now()}")

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3. Log CPU Allocation to Your SLURM Output

Everything printed with print() in Python will go into your SLURM log file:

#SBATCH --output=logs/%x_%j.out

Check it with:

less logs/plate3_<jobid>.out

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4. After the Job Finishes: Use sacct

sacct -j <jobid> --format=JobID,JobName%20,Elapsed,TotalCPU,MaxRSS,AveRSS

Example:

sacct -j 12345678 --format=JobID,JobName%20,Elapsed,TotalCPU,MaxRSS,AveRSS

This gives:

• Total CPU time used
• Max and average memory
• Wall-clock time

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Summary Table

Tool	Use	Command Example
sstat	Live job stats	sstat -j <jobid>
squeue	See node used	squeue -u $USER
htop	Live CPU usage (if on node)	htop
sacct	After job finishes	sacct -j <jobid>
print()	From within script	View in log file

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Command for checking SLURM job output:

To watch the real-time output of a Slurm job .out file (like plate3_10792107.out), you can use the tail command with the -f (follow) flag:

tail -f plate3_10792107.out

Explanation:

• tail -f continuously displays new lines as they are added to the file.
• Press Ctrl+C to stop watching the file.

Optional enhancements:

If you want to see the last 50 lines first, and then follow new output:

tail -n 50 -f plate3_10792107.out