Rightsize import batches [VS-486] #7925
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| else if (num_samples <= 100) then 1 | ||
| else if (num_samples <= 5000) then 5 | ||
| else if (num_samples <= 20000) then 10 | ||
| else 20 |
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perhaps out of scope for this pr, but two suggestions:
- let's maybe do this as a rounded fraction based on the max # of cromwell vms we feel comfortable running (rather than a step function)
- do we want to throw an error or maybe just a warning if someone is trying to run a callset with > 20k samples and they haven't explicitly set a load_data_batch_size?
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(bwahaha this is why I want to scale test with exomes)
Codecov Report
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## ah_var_store #7925 +/- ##
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Coverage ? 86.288%
Complexity ? 35189
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Files ? 2170
Lines ? 164888
Branches ? 17786
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Hits ? 142278
Misses ? 16288
Partials ? 6322 |
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Successful run of GvsJointVariantCalling for this branch. Note the 10 import shards with 1 sample each that were created by default for this sample set of size 10. |
| Int max_auto_batch_size = 20000 | ||
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| if ((num_samples > max_auto_batch_size) && !(defined(load_data_batch_size))) { | ||
| call Utils.TerminateWorkflow as DieDueToTooManySamplesWithoutExplicitLoadDataBatchSize { |
| # At least 1, per limits above not more than 20. | ||
| Int effective_load_data_batch_size = if (defined(load_data_batch_size)) then select_first([load_data_batch_size]) | ||
| else if num_samples < 1000 then 1 | ||
| else num_samples / 1000 |
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do we need to floor / ceil or round this in some way? Or does the Int type do that for us? Could it get us into trouble?
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This logic should be flooring for us.
| Int effective_load_data_maxretries = if (defined(load_data_maxretries_override)) then select_first([load_data_maxretries_override]) | ||
| else if (effective_load_data_batch_size < 12) then 3 | ||
| else effective_load_data_batch_size / 4 | ||
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nit: if you are already changing things---I would appreciate a little more prose on why this is being done this way
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hmm ok, I'll try to come up with something... 😅
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Automatically choose appropriate import batch, preemptible, and max retry values for sample sets up to 20K. This makes 20K samples our effective threshold for where we feel comfortable with the current stability / performance of our import code.