We were trying to process our data with degnorm_mpi, but degnorm was terminated with message:
= BAD TERMINATION OF ONE OF YOUR APPLICATION PROCESSES
= PID 8751 RUNNING AT risoe-r12-cn540
= EXIT CODE: 9
= CLEANING UP REMAINING PROCESSES
= YOU CAN IGNORE THE BELOW CLEANUP MESSAGES
YOUR APPLICATION TERMINATED WITH THE EXIT STRING: Killed (signal 9)
This typically refers to a problem with your application.
Please see the FAQ page for debugging suggestions
From the log file it seems fine that degnorm can load all files properly, but quits in the middle of processing reads.
The idea is to run 20 degnorm_mpi parallel sessions on our cluster and each session takes one computing node (28 CPUS and 128GB RAM) and run with 27 threads.
Does 'Exit Code 9' normally mean 'Out of RAM'? If so, I am wondering how much 'RAM per CPU' does degnorm usually take? With the specs of our cluster, what is the recommended MPI setting?
Hi,
We were trying to process our data with degnorm_mpi, but degnorm was terminated with message:
= BAD TERMINATION OF ONE OF YOUR APPLICATION PROCESSES = PID 8751 RUNNING AT risoe-r12-cn540 = EXIT CODE: 9 = CLEANING UP REMAINING PROCESSES = YOU CAN IGNORE THE BELOW CLEANUP MESSAGES
YOUR APPLICATION TERMINATED WITH THE EXIT STRING: Killed (signal 9) This typically refers to a problem with your application. Please see the FAQ page for debugging suggestions
From the log file it seems fine that degnorm can load all files properly, but quits in the middle of processing reads.
Our degnorm_mpi CMD is: mpiexec -n 20 degnorm_mpi \ --bam-dir /PATH/TO/BAMS \ -g /PATH/TO/REF/*.gtf \ -o degnorm_out \ -p 27 --nmf-iter 5 -d 100 --minimax-coverage 20 --skip-baseline-selection
The idea is to run 20 degnorm_mpi parallel sessions on our cluster and each session takes one computing node (28 CPUS and 128GB RAM) and run with 27 threads.
Does 'Exit Code 9' normally mean 'Out of RAM'? If so, I am wondering how much 'RAM per CPU' does degnorm usually take? With the specs of our cluster, what is the recommended MPI setting?
Thank you for your time.
Cheers, Sen