lytools-HPC 0.0.1

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HPC Functions

Monitoring you jobs with a progress bar.

This requires a Redis server to store the progress information. The following steps will guide you through setting up the Redis server and using submitit with a progress bar.

Python packages required:

pip install submitit redis pathos rich 

Step 1: Deploy a Redis service

DO NOT deploy it on a HPC nodes. You can use your local machine or a server with a public IP address.

Deploy redis via Docker

Compose file for Redis server:

services:
  redis-progress:
    image: redis:7
    container_name: redis-progress
    restart: unless-stopped

    ports:
      - "6379:6379"

    volumes:
      - ./redis_data:/data

    command: >
      redis-server
      --appendonly yes
      --requirepass yourpassword
      --maxmemory 2gb
      --maxmemory-policy allkeys-lru
      
    deploy:
      resources:
        limits:
          memory: 3g

docker compose up -d # Start the Redis server

Test Redis connection

import redis
r = redis.Redis(host='your_redis_host', port=6379, password='yourpassword')
r.set('test_key', 'test_value')
print(r.get('test_key').decode())

Create redis connection configuration file

Location: ~/.config/redis/redis.conf

your_redis_host
6379
yourpassword

Step 2: Submit your jobs

from HPC_func import *

def my_function(x):
    return x * x

job_name = 'Your_job_name'
params_list = [1,2,3,4,5,6,7,8,9,10]
log_folder = 'Your_log_folder'
init_job(job_name, params_list)
sumbit_jobs_array(my_function, params_list, log_folder,
                  job_name=job_name,
                  job_number_limit=1,
                  parallel_process_per_task=2,
                  slurm_array_parallelism=1,
                  parallel_process_p_or_t='p',
                  cpus_per_task=10,
                  mem_gb=2,
                  timeout_min=10,
                  slurm_partition="general",
                  exclude_nodes=None,
                  pbar_update_freq=1,
                  )

Step 3: Monitor the progress bar

from HPC_func import *
job_name = 'Your_job_name'
progress_bar_monitoring(job_name)

Step 4: Check the log files

from HPC_func import *
log_folder = 'Your_log_folder'
Check_logs(log_folder).read_err_files() # Read error files
Check_logs(log_folder).read_out_files() # Read output files