Questions regarding multithreading
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- Dominant language
- C
- Stars
- 207
- Forks
- 61
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Description
Hello,
I am currently running smartpca on a HPC using slurm.
smartpca version is 18140, and I use the following parameter file.
altnormstype: NO
numoutevec: 20
numoutlieriter: 0
numoutlierevec: 0
outliersigmathresh: 6.0
numthreads: 8
qtmode: 0
lsqproject: YES
I am not used to multithreading and running jobs in parallel.
I wanted to run threads in parallel, so I tried assigning 8 cpu per job, however when I login the computing nodes, only one processor is working per job, even though the log files say the job will work on 8 threads.
Is there another option to assign each thread to a cpu, or is it blocked somehow by my options?
Thank you in advance.
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Research direction
Start with the smartpca entry point and the supplied parameter file, especially numthreads: 8, then compare its threading behavior with the eight CPUs requested through Slurm. The issue names no source file or test; done would require a clear explanation of the single-processor behavior or a reproducible fix for multithreading allocation.
Written by the indexing model from the issue text.
Assessment
- Tech stack
- c
- Domain
- bioinformatics, hpc, performance
- Issue type
- Bug
- Difficulty
- 4/5
- Estimated time
- 3-5 days
- Activity status
- Stale
- Clarity
- Needs clarification
- Newbie friendliness
- 20/100