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Old 09-09-2017, 11:30 PM   #1
tirohia
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Location: Auckland, NZ

Join Date: Nov 2011
Posts: 45
Default Hisat2 multithreading not working.

As best I can see, this should be working. I've got 16 cores:

Code:
$ grep -c ^processor /proc/cpuinfo     
16
I then attempt to use hisat2 with multiple threads. I've tried using both --threads -p
Code:
hisat2 --threads 15 -x ../genome/genome -1 fq1.fq -2 fq2.fq -S aligned.sam
Neither works. If I flick to another screen and run top, it looks like:
Code:
top - 07:29:52 up  4:17,  2 users,  load average: 0.61, 0.34, 0.44
Tasks: 164 total,   2 running, 162 sleeping,   0 stopped,   0 zombie
%Cpu(s):  2.3 us,  4.0 sy,  0.0 ni, 93.7 id,  0.0 wa,  0.0 hi,  0.0 si,  0.0 st
KiB Mem:  61976884 total, 61398192 used,   578692 free,    35588 buffers
KiB Swap:        0 total,        0 used,        0 free. 59440624 cached Mem

  PID USER      PR  NI    VIRT    RES    SHR S  %CPU %MEM     TIME+ COMMAND         
10666 tirohia   20   0  982432   3984   3700 R 100.0  0.0   3:28.93 hisat2-align-s  
10667 tirohia   20   0   25740   2948   2440 R   0.3  0.0   0:00.28 top             
    1 root      20   0   28564   4744   3120 S   0.0  0.0   0:01.46 systemd
    2 root      20   0       0      0      0 S   0.0  0.0   0:00.00 kthreadd
hisat2 isn't getting past 100% - my understanding of top is that it's percentage is based of the usage of a single cpu - so it should be showing 1500%.

What am I missing?

Cheers
Ben.
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Old 09-10-2017, 07:59 AM   #2
mastal
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Default

I haven't used hisat2, but with tophat, not all of the stages of the analysis were multi-threaded. So unless you look at top while hisat2 is running one of the multi-threaded stages, you might only see it using 100% CPU.
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Old 09-10-2017, 06:24 PM   #3
tirohia
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Location: Auckland, NZ

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Default

So when I run an alignment with bowtie2, it takes maybe an hour or. When I do it with Hisat2, it'll run for days.

I've been logging the CPU usage with:
Code:
while true; do (echo "%CPU %MEM ARGS $(date)" && ps -e -o pcpu,pmem,args --sort=pcpu | cut -d" " -f1-5 | tail) >> ps.log; sleep 5; done
When I run hisat2, the cpu usage stays at about 100%. When I run bowtie2, it shoots up to ~1500%, as I would expect. Which suggests to me that the hisat2 multiple threading section isn't kicking off at all.

Which, I have to say, leaves me contemplating just returning to bowtie2.
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Old 09-11-2017, 12:20 AM   #4
dpryan
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Default

Please report this as a bug to the developers. I should note that it runs multithreaded for us, so there's some odd interaction between the binary and your system.
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Old 09-11-2017, 01:07 PM   #5
tirohia
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Is there a formal bug submission process (if so I can't find it), or does one just submit a new issues via github?
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Old 09-11-2017, 11:10 PM   #6
dpryan
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Github is usually as formal as things get, so yes, post it there.
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