Docker containers
container defaults
$ podman run --security-opt=no-new-privileges \ --rm \ ...
or even
$ podman run --security-opt=no-new-privileges \ --cap-drop=ALL \ --rm \ ...
run a container with custom entrypoint
| run a container with custom cmd | run a container with custom command | run a container with command
$ podman run --security-opt=no-new-privileges \ --cap-drop=ALL \ --rm \ --entrypoint=bash \ -v (realpath ../qiime2_wrappers/qiime2/):/qiime2 \ -it \ --name planemo-instance \ bgruening/planemo
show namespace information (UTS, IPC, CGROUP, ...)
docker ps --ns
show cpu stats per process/per container
# per second cpu stats per process
$ pidstat 1
Linux 5.18.7-arch1-1 (lima-default) 07/07/2022 _x86_64_ (4 CPU)
08:55:58 AM UID PID %usr %system %guest %wait %CPU CPU Command
08:55:59 AM 0 16 0.00 0.99 0.00 0.00 0.99 0 rcu_preempt
08:55:59 AM 0 1371 0.00 4.95 0.00 0.00 4.95 1 kworker/u8:2-events_freezable_power_
08:55:59 AM 0 1474 0.00 31.68 0.00 0.00 31.68 1 kworker/u8:11-btrfs-delalloc
08:55:59 AM 0 1475 0.00 23.76 0.00 0.00 23.76 2 kworker/u8:12-btrfs-delalloc
08:55:59 AM 501 2685 0.00 0.99 0.00 0.00 0.99 1 podman
08:55:59 AM 501 2706 15.84 54.46 0.00 4.95 70.30 3 bash
08:55:59 AM 501 2826 0.00 0.99 0.00 0.00 0.99 0 pidstat
08:55:59 AM UID PID %usr %system %guest %wait %CPU CPU Command
08:56:00 AM 0 1474 0.00 13.00 0.00 0.00 13.00 1 kworker/u8:11-btrfs-delalloc
08:56:00 AM 0 1475 0.00 49.00 0.00 0.00 49.00 3 kworker/u8:12-btrfs-delalloc
08:56:00 AM 501 2685 0.00 1.00 0.00 0.00 1.00 1 podman
08:56:00 AM 501 2706 13.00 54.00 0.00 6.00 67.00 2 bash
08:56:00 AM 501 2826 0.00 1.00 0.00 0.00 1.00 0 pidsta
$ podman ps --ns
CONTAINER ID NAMES PID CGROUPNS IPC MNT NET PIDNS USERNS UTS
0e07e6b36426 quizzical_elion 1484 4026532378 4026532376 4026532373 4026532305 4026532377 4026532303 4026532375
# per second cpu stats for pid 1484
$ pidstat 1 -p 1484
Linux 5.18.7-arch1-1 (lima-default) 07/07/2022 _x86_64_ (4 CPU)
08:45:32 AM UID PID %usr %system %guest %wait %CPU CPU Command
08:45:33 AM 501 1484 3.96 3.96 0.00 0.00 7.92 1 bash
08:45:34 AM 501 1484 5.00 2.00 0.00 1.00 7.00 0 bash
container I/O | container IO
# per second iostats for processes/containers
$ pidstat -d 1
Linux 5.18.7-arch1-1 (lima-default) 07/07/2022 _x86_64_ (4 CPU)
08:54:44 AM UID PID kB_rd/s kB_wr/s kB_ccwr/s iodelay Command
08:54:45 AM 501 2706 0.00 8498.04 0.00 0 bash
08:54:45 AM UID PID kB_rd/s kB_wr/s kB_ccwr/s iodelay Command
08:54:46 AM 501 2706 0.00 8440.00 0.00 0 bash
# per second iostats for pid
$ pidstat -p 2706 -d 1
Linux 5.18.7-arch1-1 (lima-default) 07/07/2022 _x86_64_ (4 CPU)
08:55:09 AM UID PID kB_rd/s kB_wr/s kB_ccwr/s iodelay Command
08:55:10 AM 501 2706 0.00 8463.37 0.00 0 bash
08:55:11 AM 501 2706 0.00 8684.00 0.00 0 bash
08:55:12 AM 501 2706 0.00 8668.00 0.00 0 bash
08:55:13 AM 501 2706 0.00 8564.00 0.00 0 bash
08:55:14 AM 501 2706 0.00 8768.00 0.00 0 bash
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