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gglyptodon / helixer-docker

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FATAL: container creation failed: exec: "/usr/bin/nvidia-container-cli": stat /usr/bin/nvidia-container-cli: no such file or directory #5

Open JWJ13164328557 opened 8 months ago

JWJ13164328557 commented 8 months ago

singularity run --nv /home/liux/miniconda3/envs/braker3/helixer-docker_helixer_v0.3.2_cuda_11.8.0-cudnn8.sif Helixer.py --fasta-path /home/liux/DATA/genomic/RepeatMasker/AT/TAIR10_chr_all.fa --lineage land_plant --gff-output-path /data/liux/zhushi/Arabidopsis_lyrata_chromosome8_helixer.gff3

INFO: Setting 'NVIDIA_VISIBLE_DEVICES=all' to emulate legacy GPU binding. INFO: Setting --writable-tmpfs (required by nvidia-container-cli) FATAL: container creation failed: exec: "/usr/bin/nvidia-container-cli": stat /usr/bin/nvidia-container-cli: no such file or directory

alisandra commented 7 months ago

Hi, I'm not sure what's happening based on this information. A few questions / ideas for debugging.

What version of Singularity are you using?

Can you run other Nvidia-using singularity containers, e.g. https://github.com/sylabs/singularity-userdocs/blob/main/gpu.rst ?

JWJ13164328557 commented 7 months ago

This is singularity version (braker3) [liux@cln01 braker3]$ singularity --version singularity-ce version 3.11.1-1.el7