Try setting suggested env var in scprint

openproblems-bio · Jan 17, 2025 · 232e4fc · 232e4fc
1 parent 6e63cf9
commit 232e4fc
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diff --git 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
@@ -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":