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sigProfilerExtractor gpu solution can't work

See original GitHub issue


I follow example to execute sigProfilerExtractor with gpu = True. But program interrupted after matrix generation and output folder only job_metadata.txt and SBS96/All_solutions_stat.csv exist.

Below is command and result. sig.sigProfilerExtractor("vcf",testgpu_output",data,startProcess=1,endProcess=3,totalIterations=1000,gpu = True).

************** Reported Current Memory Use: 0.15 GB *****************

Starting matrix generation for SNVs and DINUCs…Completed! Elapsed time: 7.81 seconds. Matrices generated for 15 samples with 0 errors. Total of 93001 SNVs, 505 DINUCs, and 0 INDELs were successfully analyzed. Extracting signature 1 for mutation type 96

What should i do to resolve this issue?

System information is below.

OS: Centos 7 PyTorch Version: 1.2 Python Version: 3.6.8 CUDA/cuDNN Version: 9.2/7.6 GPU Model: NVIDIA Tesla K80

Thanks, Bruce

Issue Analytics

  • State:closed
  • Created 4 years ago
  • Comments:11 (3 by maintainers)

github_iconTop GitHub Comments

mishugebcommented, Feb 29, 2020

Hi Bruce, Could you please install the most recent tool “pip3 install SigProfilerExtractor” and check if you get the error?


mishugebcommented, Nov 22, 2019

Hi Bruce, All the required packages should be installed automatically when you install this package. If there is any error, that will be detected by Travis CI and the build will not pass eventually. I will check that more, but it difficult to replicate an issue if Travis CI cannot detect that. Sorry for the inconvenience. I will check that more thoroughly.

Regards, Mishu

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