Command line inconsistency

Posted by Simon Walker on Wed 09 March 2016

RTFM!

Today I brought down our head node at work, because of a misunderstanding of command line arguments for a linux program.

In fairness, I should have read the man page more carefully for the entry in question!

I was using xargs for some nice command line parallelism and process running. The command I ran was:

ls | grep action119 | grep exposureCycle | xargs -n 1 -I {} find {} -name 'IMAGE*.fits' | xargs -n 1 -P 0 bzip2 -k

In summary this finds the directories containing "action119" and "exposureCycle" in the current directory, finds all of the files called IMAGE*.fits in each directory and then in parallel compresses them while keeping the original file (-k).

xargs is used twice in this invocation, and is one of my new favourite tools. It takes a multi-line input on stdin, and passes each line to whatever command that follows, e.g.:

ls | xargs echo

is the same as

ls | while read filename; do echo $filename; done
# or
# for file in $(ls); do echo $filename; done

It just dumps the input on the end of the command that follows xargs. The argument -n says run the following command for each line on the input, otherwise it dumps them all[1] on the end of the command. -I {} replaces all occurrences of {} in the command with the input argument.

The first xargs invocation runs find for each directory, which then prints a long list of files. The second xargs invocation bzips the files in parallel, whilst keeping the original.

The key error was the -P argument. From the man page:

--max-procs=max-procs
-P max-procs
    Run up to max-procs processes at a time; the default is 1.  If
    max-procs is 0, xargs will run as many processes as possible at a
    time.  Use the -n option with -P; otherwise chances are that only
    one exec will be done.

In other linux programs I've used (e.g. GNU parallel) specifying 0 for the number of processes means run the same as the number of processors on the machine. For xargs, importantly it says "run as many processes as possible", pretty much meaning one per input file.

I expected 16 processes to be spawned, one for each (virtual) core. It spawned ~5k processes one per input file.

It brought the system down for about an hour, but it did seem to recover ok.

In conclusion: RTFM!

[1] actually because of linux command length restrictions, it splits the lines up to follow this limitation, and runs the command multiple times in groups if need be

tags: linux