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Document dexplode/dencode usage on different schedulers #147

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jeromekelleher opened this issue Apr 26, 2024 · 2 comments
Open

Document dexplode/dencode usage on different schedulers #147

jeromekelleher opened this issue Apr 26, 2024 · 2 comments

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@jeromekelleher
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Here's how you do it with xargs (for my own reference; in reality you'd use the worker processes option):

 seq 0 (NPARTS -1) |  xargs -t -I % -P NUM_PROCS vcf2zarr dexplode-partition [ICF_DIR] %
@benjeffery
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benjeffery commented Apr 26, 2024

On LSF I have a bash script:

N=$LSB_JOBINDEX
vcf2zarr dexplode-partition [ICF_DIR] $((N-1))

Then submit with bsub -J job_name[1-(NPARTS+1)]

@jeromekelleher
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jeromekelleher commented Apr 26, 2024

Should we add a "--one-based" option to dexplode-partition and dencode-partiton? It's fiddly having to translate to zero-based in the shell for these things that want to go 1...N

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