SequenceDataMMAP error
Richard Casey
We're running nvBowtie on a single K80. The first run was OK. The second and subsequent runs give the error message below. See line #8. There is no other log file or info about the runs so it's not clear what is causing this error. Any ideas?
info : nvBowtie... started
verbose : cuda devices : 16
verbose : chosen device 0
verbose : device name : Tesla K80
verbose : compute capability : 3.7
visible : mapping reference index... started
info : file: "hg38"
info : SequenceDataMMAP: error mapping file "/nvbio.hg38.seq_info" (2)!
visible : mapping reference index... failed
visible : loading reference index... started
info : file: "hg38"
visible : loading reference index... done
visible : FMIndexData: loading... started
visible : genome : hg38
info : reading bwt... started
info : reading bwt... done
verbose : length: 3209286105
info : building occurrence table... started
info : building occurrence table... done
info : size: 401160768 words
info : reading rbwt... started
info : reading rbwt... done
verbose : length: 3209286105
info : building occurrence table... started
info : building occurrence table... done
visible : primary : 2760693364
visible : rprimary : 1925961725
info : reading SSA... started
info : reading SSA... done
info : reading SSA... started
info : reading SSA... done
visible : memory : 4590.9 MB
visible : FMIndexData: loading... done
visible : opening read file "genome_watson.fa"
verbose : mode = best
verbose : scoring = sw
verbose : score-min = linear:-0.60:-0.60
verbose : alignment type = end-to-end
verbose : seed length = 22
verbose : seed interval = (S, 1.000, 1.150)
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
error : caught a std::bad_alloc exception:
error : std::bad_alloc
39.78user 4.14system 0:20.04elapsed 219%CPU (0avgtext+0avgdata 5615360maxresident)k
0inputs+432outputs (0major+26563minor)pagefaults 0swaps
Richard Casey
Jacopo Pantaleoni
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Richard Casey
nohup time /home/cirrascale/nvbio/nvbio-master/build/nvBowtie/nvBowtie -v 7 -x mycobacterium_tuberculosis_h37rv_ref_genome -U SRR974841.fq --device 0 -S SRR974841.sam &
We get the same error message with or without nohup, with or without time, background or interactive, on every run. Running this on bacterial and human genome data.