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# ubuntu
sudo apt install -y build-essential unzip parallel curl git zlib1g-dev libbz2-dev liblzma-dev libncurses5-dev libperl-dev libgsl-dev
sudo cpan DBI Try::Tiny LWP::Simple Set::IntervalTree PerlIO::gzip

# windows ActivePerl 5.24 https://downloads.activestate.com/ActivePerl/releases/5.24.3.2404/ActivePerl-5.24.3.2404-MSWin32-x64-404865.exe
# ppm install Set-IntervalTree 
# https://www.activestate.com/blog/goodbye-ppm-hello-state-tool

# http://strawberryperl.com/download/5.32.0.1/strawberry-perl-5.32.0.1-64bit.msi
cpan Set::IntervalTree

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# CrystalDiskMark 8 NVMe
fio --loops=5 --size=1g --runtime=5 --time_based=1 --stonewall --direct=1 --group_reporting \
    --name=SeqQ8T1read --bs=1048576 --iodepth=8 --rw=read \
    --name=SeqQ8T1write --bs=1048576 --iodepth=8 --rw=write \
    --name=Seq128kQ32T1read --bs=131072 --iodepth=32 --rw=read \
    --name=Seq128kQ32T1write --bs=131072 --iodepth=32 --rw=write \
    --name=4kQ32T16read --bs=4096 --iodepth=32 --numjobs=16 --rw=randread \
    --name=4kQ32T16write --bs=4096 --iodepth=32 --numjobs=16 --rw=randwrite \
    --name=4kQ1T1read --bs=4096 --iodepth=1 --rw=randread \
    --name=4kQ1T1write --bs=4096 --iodepth=1 --rw=randwrite

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900p 480GB
SeqQ32T1read: (groupid=0, jobs=1): err= 0: pid=29758: Tue Jan  8 06:12:55 2019
  read: IOPS=15.1k, BW=1884MiB/s (1976MB/s)(5120MiB/2717msec)
    clat (usec): min=62, max=348, avg=65.73, stdev= 5.52
     lat (usec): min=62, max=348, avg=65.81, stdev= 5.52
    clat percentiles (usec):
     |  1.00th=[   63],  5.00th=[   63], 10.00th=[   63], 20.00th=[   64],
     | 30.00th=[   64], 40.00th=[   64], 50.00th=[   65], 60.00th=[   65],
     | 70.00th=[   65], 80.00th=[   65], 90.00th=[   75], 95.00th=[   76],
     | 99.00th=[   93], 99.50th=[   95], 99.90th=[  105], 99.95th=[  109],

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8x 970pro 1tb
SeqQ32T1read: (groupid=0, jobs=1): err= 0: pid=69405: Sat Mar  2 10:16:09 2019
  read: IOPS=17.5k, BW=2186MiB/s (2292MB/s)(5120MiB/2342msec)
    clat (usec): min=53, max=2750, avg=56.51, stdev=37.14
     lat (usec): min=53, max=2750, avg=56.60, stdev=37.14
    clat percentiles (usec):
     |  1.00th=[   55],  5.00th=[   55], 10.00th=[   55], 20.00th=[   55],
     | 30.00th=[   55], 40.00th=[   55], 50.00th=[   55], 60.00th=[   55],
     | 70.00th=[   56], 80.00th=[   57], 90.00th=[   59], 95.00th=[   60],
     | 99.00th=[  109], 99.50th=[  127], 99.90th=[  161], 99.95th=[  180],

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4x P1 1TB
SeqQ32T1read: (groupid=0, jobs=1): err= 0: pid=29929: Tue Jan  8 06:20:35 2019
  read: IOPS=10.5k, BW=1313MiB/s (1377MB/s)(5120MiB/3900msec)
    clat (usec): min=58, max=2411, avg=94.64, stdev=52.07
     lat (usec): min=58, max=2411, avg=94.70, stdev=52.07
    clat percentiles (usec):
     |  1.00th=[   60],  5.00th=[   60], 10.00th=[   60], 20.00th=[   60],
     | 30.00th=[   61], 40.00th=[   63], 50.00th=[   77], 60.00th=[   93],
     | 70.00th=[  110], 80.00th=[  120], 90.00th=[  139], 95.00th=[  182],
     | 99.00th=[  310], 99.50th=[  343], 99.90th=[  351], 99.95th=[  351],

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lustre
SeqQ32T1read: (groupid=0, jobs=1): err= 0: pid=262: Wed Jan  9 22:44:57 2019
  read: IOPS=1044, BW=131MiB/s (137MB/s)(5120MiB/39232msec)
    clat (usec): min=413, max=326768, avg=955.13, stdev=4388.08
     lat (usec): min=413, max=326768, avg=955.40, stdev=4388.09
    clat percentiles (usec):
     |  1.00th=[   482],  5.00th=[   506], 10.00th=[   519], 20.00th=[   537],
     | 30.00th=[   553], 40.00th=[   578], 50.00th=[   611], 60.00th=[   652],
     | 70.00th=[   717], 80.00th=[   889], 90.00th=[  1139], 95.00th=[  1336],
     | 99.00th=[  9110], 99.50th=[ 14091], 99.90th=[ 31065], 99.95th=[ 41157],

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#!/bin/sh
sudo swapoff -a
sudo swapon -a

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sudo mdadm --create --raid-devices=8 --level=0 /dev/md127 /dev/nvme{1,2,3,4,5,6,7,8}n1

sudo mkfs.ext4 -E lazy_itable_init=1,lazy_journal_init=1,nodiscard /dev/md127
sudo mkdir /raid
sudo mount /dev/md127 /raid
sudo chmod 777 /raid

# new disk
sudo parted
select /dev/nvme0n1

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#!/bin/sh
sudo timedatectl set-timezone Asia/Taipei
sudo timedatectl set-local-rtc 1 --adjust-system-clock

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git clone https://github.com/lh3/bwa.git -b v0.7.17
cd bwa
make -j $(nproc)

wget ftp://[email protected]/bundle/b37/human_g1k_v37_decoy.*
ls *.gz | parallel gzip -dk
bwa index human_g1k_v37_decoy.fasta
bwa mem -t $(nproc) human_g1k_v37_decoy.fasta sample_R1.fastq sample_R2.fastq > sample.sam