disulfidebond/ont_guppy_setup.md

## ont_guppy_setup.md

      
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              ont_guppy_setup.md
            
          
    Overview

This markdown file contains the steps involved in configuring a new computer, runnning Ubuntu 16.04, to run ONT Guppy GPU basecalling.
Prerequisites


CUDA must be installed, which can be simple or extremely difficult,
depending on if the CUDA gods smile on you.
The computer must be running Ubuntu 16.04 'xenial', with all updates installed.

Steps


The steps in the installation manual were followed as directed.


For the graphics card that was installed, a RTX 2080ti, no additional configuration was necessary, similar to the recommendations for the GTX 1080ti.


guppy_basecaller was tested with the following parameters and a simple bash for loop:
  # directory contains 0.tar.gz, 1.tar.gz, ...
  for i in *.tar.gz ; do
    V=$(echo "$i" | cut -d. -f1)
    OUTDIRPATH=/output/path
    INPUTDIRPATH=/input/path
    mkdir $OUTDIRPATH/${V}
    guppy_basecaller -x "cuda:0" --input_path $INPUTDIRPATH --output_path $OUTDIRPATH --flowcell $FLOWCELL --kit $KIT --records_per_fastq 0
    echo "basecalling for $i done"
  done
  # the option "-x" specifies a CUDA graphics card at slot 0
  # if you have only 1 card, or the card you want is at slot 0, this is not necessary
  # to get info on graphics cards, use this command:
  nvidia-smi


Stats/Benchmark


The graphics card at cuda:0 was used:
  bash$ nvidia-smi 
  Fri May 24 18:31:05 2019       
  +-----------------------------------------------------------------------------+
  | NVIDIA-SMI 418.67       Driver Version: 418.67       CUDA Version: 10.1     |
  |-------------------------------+----------------------+----------------------+
  | GPU  Name        Persistence-M| Bus-Id        Disp.A | Volatile Uncorr. ECC |
  | Fan  Temp  Perf  Pwr:Usage/Cap|         Memory-Usage | GPU-Util  Compute M. |
  |===============================+======================+======================|
  |   0  GeForce RTX 208...  Off  | 00000000:17:00.0 Off |                  N/A |
  | 52%   82C    P2   252W / 250W |   4218MiB / 10989MiB |     78%      Default |
  +-------------------------------+----------------------+----------------------+
  |   1  Quadro P400         Off  | 00000000:65:00.0  On |                  N/A |
  | 34%   43C    P8    N/A /  N/A |    233MiB /  1992MiB |      0%      Default |
  +-------------------------------+----------------------+----------------------+
                                                                                 
  +-----------------------------------------------------------------------------+
  | Processes:                                                       GPU Memory |
  |  GPU       PID   Type   Process name                             Usage      |
  |=============================================================================|
  |    0      7762      C   guppy_basecaller                            4207MiB |
  |    1      1309      G   /usr/lib/xorg/Xorg                           133MiB |
  |    1      2481      G   compiz                                        87MiB |
  +-----------------------------------------------------------------------------+


Here is the output from a test basecalling run:
  ONT Guppy basecalling software version 3.1.5+781ed57
  config file:        /opt/ont/guppy/data/dna_r9.4.1_450bps_hac.cfg
  model file:         /opt/ont/guppy/data/template_r9.4.1_450bps_hac.jsn
  input path:         /media/drive2/ONTdata/50
  save path:          /media/databk1/ONTdata_05242019-output/50
  chunk size:         1000
  chunks per runner:  1000
  records per file:   0
  num basecallers:    4
  gpu device:         cuda:0
  kernel path:
  runners per device: 2

  Found 4000 fast5 files to process.
  Init time: 1547 ms

  0%   10   20   30   40   50   60   70   80   90   100%
  |----|----|----|----|----|----|----|----|----|----|
  ***************************************************
  Caller time: 56515 ms, Samples called: 558584255, samples/s: 9.88382e+06
  Finishing up any open output files.
  Basecalling completed successfully.