nvBowtie CPU loop

[evan-wehi]

I'm trying to benchmark nvBowtie but it is not working for me. It allocates memory in the GPU and then goes into a CPU loop with 0% GPU utilisation and no data are written.

Here is stdout:

info    : nvBowtie... started
verbose :   cuda devices : 1
verbose :   device 0 has compute capability 5.2
verbose :     SM count          : 16
verbose :     SM clock rate     : 1177 Mhz
verbose :     memory clock rate : 2.5 Ghz
verbose :   chosen device 0
verbose :     device name        : GRID M60-8Q
verbose :     compute capability : 5.2
visible : mapping reference index... started
info    :   file: "ref/hg38_no_alt.fa"
info    : SequenceDataMMAP: error mapping file "/nvbio.ref/hg38_no_alt.fa.seq_info" (2)!
visible : mapping reference index... failed
visible : loading reference index... started
info    :   file: "ref/hg38_no_alt.fa"
visible : loading reference index... done
visible : FMIndexData: loading... started
visible :   genome : ref/hg38_no_alt.fa
info    : reading bwt... started
info    : reading bwt... done
verbose :   length: 3088286401
info    : building occurrence table... started
info    : building occurrence table... done
info    :   size: 386035808 words
info    : reading rbwt... started
info    : reading rbwt... done
verbose :   length: 3088286401
info    : building occurrence table... started
info    : building occurrence table... done
visible :    primary : 2655318798
visible :   rprimary : 1993732142
info    : reading SSA... started
info    : reading SSA... done
info    : reading SSA... started
info    : reading SSA... done
visible :   memory   : 4417.8 MB
visible : FMIndexData: loading... done
visible : opening read file [1] ""
visible : opening read file [2] "/stornext/HPCScratch/PapenfussLab/mirror/ftp-trace.ncbi.nlm.nih.gov/giab/ftp/data/NA12878/Garvan_NA12878_HG001_HiSeq_Exome/NIST7035_TAAGGCGA_L001_R2_001_trimmed.fastq.gz"
verbose :   mode           = best
verbose :   scoring        = sw
verbose :   score-min      = log:0.00:10.00
verbose :   alignment type = local
verbose :   pe-policy      = fr
verbose :   seed length    = 20
verbose :   seed interval  = (S, 1.000, 0.750)
verbose :   seed rounds    = 2
verbose :   max hits       = 100
verbose :   max edit dist  = 15
verbose :   max effort     = 15
verbose :   substitutions  = 0
verbose :   mapq filter    = 0
verbose :   randomized     = yes
visible : [0] nvBowtie cuda driver created on device 0
stats   : [0]   allocated device driver data (2.32 GB - 0.4s)
stats   : [0]   estimated allocation sizes: HOST 0 MB, DEVICE 3548 MB)
visible : [0] nvBowtie cuda driver... started
verbose : starting background paired-end input thread
stats   : [0]   device has 4584 of 8191 MB free
stats   : [0]   processing reads in batches of 1024K
stats   : [0]   allocating alignment buffers... started
stats   : [0]     estimated: HOST 0 MB, DEVICE 3548 MB)
verbose : [0]     allocating 384 MB of string storage
verbose : [0]       CIGARs : 128 MB
verbose : [0]       MDs    : 256 MB
verbose : [0]     allocating 1182 MB of DP storage
stats   : [0]   allocating alignment buffers... done
stats   : [0]     allocated: HOST 0 MB, DEVICE 3548 MB)
stats   : [0]   ready to start processing: device has 1035 MB free

Here are the details of the card

Wed Jul 26 13:02:50 2017       
+-----------------------------------------------------------------------------+
| NVIDIA-SMI 367.43                 Driver Version: 367.43                    |
|-------------------------------+----------------------+----------------------+
| GPU  Name        Persistence-M| Bus-Id        Disp.A | Volatile Uncorr. ECC |
| Fan  Temp  Perf  Pwr:Usage/Cap|         Memory-Usage | GPU-Util  Compute M. |
|===============================+======================+======================|
|   0  GRID M60-8Q         Off  | 0000:02:01.0     Off |                  N/A |
| N/A   N/A    P8    N/A /  N/A |   7155MiB /  8191MiB |      0%      Default |
+-------------------------------+----------------------+----------------------+
                                                                               
+-----------------------------------------------------------------------------+
| Processes:                                                       GPU Memory |
|  GPU       PID  Type  Process name                               Usage      |
|=============================================================================|
|    0     29140    C   nvBowtie                                      6579MiB |
+-----------------------------------------------------------------------------+