From 232e4fc25bf41d8958a7aad01d5aa73b81c36cb4 Mon Sep 17 00:00:00 2001 From: Luke Zappia Date: Fri, 17 Jan 2025 10:52:44 +0100 Subject: [PATCH] Try setting suggested env var in scprint --- src/methods/scprint/config.vsh.yaml | 2 +- src/methods/scprint/script.py | 3 +++ 2 files changed, 4 insertions(+), 1 deletion(-) diff --git a/src/methods/scprint/config.vsh.yaml b/src/methods/scprint/config.vsh.yaml index 3451fce0..5e57819c 100644 --- a/src/methods/scprint/config.vsh.yaml +++ b/src/methods/scprint/config.vsh.yaml @@ -79,4 +79,4 @@ runners: - type: executable - type: nextflow directives: - label: [midtime, midmem, midcpu, highgpu] + label: [midtime, midmem, midcpu, gpu] diff --git a/src/methods/scprint/script.py b/src/methods/scprint/script.py index 555776b1..deb0bd00 100644 --- a/src/methods/scprint/script.py +++ b/src/methods/scprint/script.py @@ -24,6 +24,9 @@ print(f"====== scPRINT version {scprint.__version__} ======", flush=True) +# Set suggested PyTorch environment variable +os.environ["PYTORCH_CUDA_ALLOC_CONF"] = "expandable_segments:True" + print("\n>>> Reading input data...", flush=True) input = read_anndata(par["input"], X="layers/counts", obs="obs", var="var", uns="uns") if input.uns["dataset_organism"] == "homo_sapiens":