As best I can see, this should be working. I've got 16 cores:
I then attempt to use hisat2 with multiple threads. I've tried using both --threads -p
Neither works. If I flick to another screen and run top, it looks like:
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.
Code:
$ grep -c ^processor /proc/cpuinfo 16
Code:
hisat2 --threads 15 -x ../genome/genome -1 fq1.fq -2 fq2.fq -S aligned.sam
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
What am I missing?
Cheers
Ben.
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