From 3511966f7b1812b0c122ceb2f41673d0ce9b5382 Mon Sep 17 00:00:00 2001 From: Robrecht Cannoodt Date: Fri, 21 Aug 2026 08:30:52 +0200 Subject: [PATCH] point scprint's triton at its own ptxas --- CHANGELOG.md | 2 ++ src/methods/scprint/config.vsh.yaml | 6 +++++- 2 files changed, 7 insertions(+), 1 deletion(-) diff --git a/CHANGELOG.md b/CHANGELOG.md index f172d233..fbd5f1f1 100644 --- a/CHANGELOG.md +++ b/CHANGELOG.md @@ -57,6 +57,8 @@ * Fix `methods/scgpt_zeroshot` and `methods/scgpt_finetuned` failing to build: stop installing `flash-attn`. Both scripts pass `use_fast_transformer=False`, so it was never used. Behind it sat three more pins with no python 3.12 wheels, now `numpy<2`, `torchtext==0.17.2` and `transformers==4.36.2`. +* Fix `methods/scprint` erroring with `Triton only support CUDA 10.0 or higher`: point triton at the ptxas it bundles, + since its version table stops at CUDA 12 and the base image now ships CUDA 13. * Split Scanorama into two methods/scores - Split Scanorama into embedding (integrate) and count-correction (correct) modes, instead of running both together. diff --git a/src/methods/scprint/config.vsh.yaml b/src/methods/scprint/config.vsh.yaml index cd10ef6c..3f30cb07 100644 --- a/src/methods/scprint/config.vsh.yaml +++ b/src/methods/scprint/config.vsh.yaml @@ -73,6 +73,11 @@ engines: - type: docker image: openproblems/base_pytorch_nvidia:1 setup: + # scprint pins torch 2.2 / triton 2.2, whose ptx version table stops at CUDA 12, while the base + # image now ships CUDA 13 at /usr/local/cuda. Point triton at the ptxas it bundles itself. + - type: docker + env: + - TRITON_PTXAS_PATH=/usr/local/lib/python3.12/dist-packages/triton/third_party/cuda/bin/ptxas - type: python pip: - scprint==2.3.5 @@ -86,7 +91,6 @@ engines: script: from scdataloader.utils import populate_my_ontology; populate_my_ontology() runners: - type: executable - # docker_run_args: --gpus all - type: nextflow directives: label: [hightime, highmem, midcpu, gpu, highsharedmem]