GPU/CUDA Installation Not Detected

[Hina Bandukwala]

Hello,

I currently have a snakemake script that is using Hiccups on an HPC cluster. To run this script, I load the CUDA  module on the cluster but I still get the following error:

WARNING: sun.reflect.Reflection.getCallerClass is not supported. This will impact performance.

WARN [2021-05-17T08:45:12,200]  [Globals.java:138] [main]  Development mode is enabled

Reading file: Analysis_Results/juicer/20-A477-01.hic

Using the following configurations for HiCCUPS:

Config res: 10000 peak: 2 window: 5 fdr: 10% radius: 20000

Config res: 5000 peak: 4 window: 7 fdr: 10% radius: 20000

Using 16 CPU thread(s)

Running HiCCUPS for resolution 10000

jcuda.CudaException: Failed to initialize the driver: CUDA_ERROR_NO_DEVICE

at jcuda.utils.KernelLauncher.initialize(KernelLauncher.java:606)

at jcuda.utils.KernelLauncher.<init>(KernelLauncher.java:586)

at jcuda.utils.KernelLauncher.create(KernelLauncher.java:393)

at jcuda.utils.KernelLauncher.create(KernelLauncher.java:321)

at jcuda.utils.KernelLauncher.compile(KernelLauncher.java:270)

at juicebox.tools.utils.juicer.hiccups.GPUController.<init>(GPUController.java:72)

at juicebox.tools.clt.juicer.HiCCUPS.buildGPUController(HiCCUPS.java:578)

at juicebox.tools.clt.juicer.HiCCUPS.runCoreCodeForHiCCUPS(HiCCUPS.java:505)

at juicebox.tools.clt.juicer.HiCCUPS.access$200(HiCCUPS.java:158)

at juicebox.tools.clt.juicer.HiCCUPS$1.run(HiCCUPS.java:434)

at java.base/java.util.concurrent.ThreadPoolExecutor.runWorker(ThreadPoolExecutor.java:1128)

at java.base/java.util.concurrent.ThreadPoolExecutor$Worker.run(ThreadPoolExecutor.java:628)

at java.base/java.lang.Thread.run(Thread.java:830)

GPU/CUDA Installation Not Detected

Exiting HiCCUPS

Do you have any clues as to why CUDA isn't being detected? Could it be the way I am configuring my snakemake script or an error with the tool? Please let me know. 

[Neva Durand]

I would test by trying nvcc and perhaps a small script using CUDA.

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Neva Cherniavsky Durand, Ph.D. | she, her, hers

Assistant Professor |  Molecular and Human Genetics

Aiden Lab | Baylor College of Medicine

www.aidenlab.org

[zqzne...@gmail.com]

Hina, try Hiccups CPU version as well. 

https://github.com/aidenlab/juicer/wiki/CPU-HiCCUPS

Johnson

[Hina Bandukwala]

Thanks alot Johnson, I will definitely give this a shot!

[Neva Durand]

Alternatively, you could also upload the hic file to Google colab (free) and run hiccups there with the GPU.

Example notebook here:

https://colab.research.google.com/drive/1XelZowBWxBghSyS11rvs90Zmazsj_HPh?usp=sharing

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[Hina Bandukwala]

Hi Neva,

Thanks alot for the option! I just submitted the Hiccups job with --cpu, hopefully that works but if not, I can try with colab. 

[Neva Durand]

No problem. The CPU mode won't return loops that are not near the diagonal, just something to keep in mind.

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