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Reduce memory usage when indexing #347

Merged
merged 1 commit into from
Sep 28, 2023
Merged

Reduce memory usage when indexing #347

merged 1 commit into from
Sep 28, 2023

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marcelm
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@marcelm marcelm commented Sep 27, 2023

A full copy of each reference sequence was inadvertently made in each worker thread.

Reduces memory usage, especially when indexing genomes with large scaffolds in parallel.

When indexing rye with 8 threads, memory usage is reduced from 35.2 GiB to 33.4 GiB.

See #345

A full copy of each reference sequence was inadvertently made in each worker
thread.

Reduces memory usage, especially when indexing in parallel.

For 8 threads and when indexing rye, memory usage is reduced
from 35.2 GiB to 33.4 GiB.
@ksahlin
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ksahlin commented Sep 27, 2023

Perfect, approved!

@marcelm marcelm merged commit 88f5f82 into main Sep 28, 2023
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@marcelm marcelm deleted the fixmem branch September 28, 2023 07:26
@marcelm marcelm mentioned this pull request Nov 14, 2023
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marcelm added a commit that referenced this pull request Nov 23, 2023
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2 participants