From 738d91d1753fdb8d95c9f8f8c37545180ebbb623 Mon Sep 17 00:00:00 2001 From: Cornelius Roemer Date: Sat, 11 May 2024 20:29:02 +0200 Subject: [PATCH] fix(k8s/prepro): reducem pox batch size to 5 to not use more than 1GB of memory Use one processing thread to reduce memory consumption --- kubernetes/loculus/values.yaml | 2 +- preprocessing/nextclade/src/loculus_preprocessing/prepro.py | 1 + 2 files changed, 2 insertions(+), 1 deletion(-) diff --git a/kubernetes/loculus/values.yaml b/kubernetes/loculus/values.yaml index 1de8decb97..2c75b0a54a 100644 --- a/kubernetes/loculus/values.yaml +++ b/kubernetes/loculus/values.yaml @@ -392,7 +392,7 @@ defaultOrganisms: nextclade_dataset_tag: 2024-04-19--07-50-39Z genes: - OPG001 - batch_size: 20 + batch_size: 5 processing_spec: total_snps: function: identity diff --git a/preprocessing/nextclade/src/loculus_preprocessing/prepro.py b/preprocessing/nextclade/src/loculus_preprocessing/prepro.py index 3706e77952..b753662d71 100644 --- a/preprocessing/nextclade/src/loculus_preprocessing/prepro.py +++ b/preprocessing/nextclade/src/loculus_preprocessing/prepro.py @@ -109,6 +109,7 @@ def enrich_with_nextclade( f"--output-all={result_dir}", f"--input-dataset={dataset_dir}", f"--output-translations={result_dir}/nextclade.cds_translation.{{cds}}.fasta", + "--jobs=1", "--", f"{input_file}", ]