求助：如何在LSF模式下使用bsub命令拆分作业？

Got it, let's sort out how to split your LSF jobs properly so both the compilation and token-dependent simulation stages get the right resources. The core issue here is that when you submit a single merged job script, LSF only evaluates resource needs based on the entire script upfront—and it can't recognize the token requirements that kick in later for the simulation. Splitting them into separate, dependent jobs fixes this.

This is straightforward if you don't mind copying the compile job ID after submission:

1. First, submit your compilation job with its specific resource requirements:

   bsub -q your_compile_queue -R "rusage[mem=8G]" "make compile"
   

   Replace your_compile_queue with your actual compilation queue, adjust the resource request (rusage[mem=8G]) to match what your compile step needs, and swap "make compile" with your real compile command. After running this, LSF will return a message like Job <12345> is submitted to queue <your_compile_queue>—note down the job ID (12345 here).

2. Next, submit your simulation job with a dependency on the compile job completing successfully, plus its token resources:

   bsub -w "done(12345)" -q your_sim_queue -R "rusage[special_token=1, mem=16G]" "./run_simulation.sh"
   

   • The -w "done(12345)" flag tells LSF to only start this simulation job once job 12345 finishes successfully.
   • Update your_sim_queue to your simulation queue, adjust rusage to include the exact token resource your simulation needs (e.g., special_token=1), and replace ./run_simulation.sh with your simulation command.

If you want to avoid manually copying job IDs, use a small bash script to auto-submit both jobs and link their dependency:

#!/bin/bash

# Submit compilation job and capture its ID
COMPILE_JOB=$(bsub -q your_compile_queue -R "rusage[mem=8G]" "make compile")
COMPILE_JOB_ID=$(echo "$COMPILE_JOB" | grep -oP 'Job <\K[0-9]+')

# Submit simulation job with dependency on compile job success
bsub -w "done($COMPILE_JOB_ID)" -q your_sim_queue -R "rusage[special_token=1, mem=16G]" "./run_simulation.sh"

echo "Compilation job ID: $COMPILE_JOB_ID"
echo "Simulation job submitted with dependency on above job."

Make the script executable (chmod +x split_jobs.sh) and run it—this will handle the entire process automatically.

• Resource Specificity: Make sure each job's -R resource request matches exactly what that stage needs. For the simulation job, explicitly include the token resource LSF needs to allocate (check your cluster's documentation for the exact resource name if you're unsure).
• Dependency Conditions: If you only want the simulation to run if the compile job succeeds (not just finishes), use -w "exit($COMPILE_JOB_ID,0)" instead of done()—this checks that the compile job exited with code 0.
• Multiple Simulations: If you have multiple simulation jobs that depend on the same compile step, just reuse the same done($COMPILE_JOB_ID) condition for each one.

内容的提问来源于stack exchange，提问作者babunp114525