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I'm trying to delete all qdiscs to do "fresh" configuration:

% tc qdisc del dev enp0s25 root
RTNETLINK answers: No such file or directory

But it's there:

% tc qdisc show
qdisc noqueue 0: dev lo root refcnt 2 
qdisc pfifo_fast 0: dev enp0s25 root refcnt 2 bands 3 priomap  1 2 2 2 1 2 0 0 1 1 1 1 1 1 1 1
qdisc noqueue 0: dev br0 root refcnt 2

I have this interface added to a bridge:

% brctl show
bridge name bridge id       STP enabled interfaces
br0     8000.001999bf72bb   no      enp0s25

Why can't I delete pfifo_fast from the root qdisc?

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It might be the default qdisc (there has to be one), you can change it by editing sysctl properties. For example, if you want fq_codel instead : In /etc/sysctl.d/88-qdisc.conf

net.core.default_qdisc=fq_codel

Then apply the configuration :

sysctl --system

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