I want to diff output from 2 commands
diff output from
cat file1 and cat file2
And I found that the solution is
diff <(cat file1) <(cat file2)
However
If I put this in a shell script
The parentheses cannot be recognized since it means calling sub-shell in shell script.. (I wonder if what I know is correct)
#!bin/bash
diff <(cat $1) <(cat $2)
syntax error near unexpected token `('
Is there any solution to use commands requiring parentheses in shell script ?
I've tried
diff `<(cat $1) <(cat $2)`
diff `<(cat $1)` `<(cat $2)`
diff "<(cat $1) <(cat $2)"
diff <`(`cat $1`)` <`(`cat $2`)`
but none of the above works
I used to dump output to other files and compare those files
cat $1 > out1.txt
cat $2 > out2.txt
diff -b out1.txt out2.txt
I know this could work, but I just want to know if there's any way without dumping the output to files beforehand
If you write a script containing bash commands, you need to run it with bash, not sh. (Consider: Would you expect rm scriptfile to run the bash commands contained in the file?)
If you want something more portable, you can use FIFOs explicitly (in particular, the mkfifo command):
#!/bin/sh
mkfifo fifo1 fifo2
cat "$1" >>fifo1 &
cat "$2" >>fifo2 &
diff -b fifo1 fifo2
rm fifo1 fifo2
i tried this test.sh and get the right output.
#! /bin/bash
diff <(cat $1) <(cat $2)
I have a bash function that i call in parallel using xargs -P like so
echo ${list} | xargs -n 1 -P 24 -I# bash -l -c 'myAwesomeShellFunction #'
Everything works fine but output is messed up for obvious reasons (no buffering)
Trying to figure out a way to buffer output effectively. I was thinking I could use awk, but I'm not good enough to write such a script and I can't find anything worthwhile on google? Can someone help me write this "output buffer" in sed or awk? Nothing fancy, just accumulate output and spit it out after process terminates. I don't care the order that shell functions execute, just need their output buffered... Something like:
echo ${list} | xargs -n 1 -P 24 -I# bash -l -c 'myAwesomeShellFunction # | sed -u ""'
P.s. I tried to use stdbuf as per
https://unix.stackexchange.com/questions/25372/turn-off-buffering-in-pipe but did not work, i specified buffering on o and e but output still unbuffered:
echo ${list} | xargs -n 1 -P 24 -I# stdbuf -i0 -oL -eL bash -l -c 'myAwesomeShellFunction #'
Here's my first attempt, this only captures first line of output:
$ bash -c "echo stuff;sleep 3; echo more stuff" | awk '{while (( getline line) > 0 )print "got ",$line;}'
$ got stuff
This isn't quite atomic if your output is longer than a page (4kb typically), but for most cases it'll do:
xargs -P 24 bash -c 'for arg; do printf "%s\n" "$(myAwesomeShellFunction "$arg")"; done' _
The magic here is the command substitution: $(...) creates a subshell (a fork()ed-off copy of your shell), runs the code ... in it, and then reads that in to be substituted into the relevant position in the outer script.
Note that we don't need -n 1 (if you're dealing with a large number of arguments -- for a small number it may improve parallelization), since we're iterating over as many arguments as each of your 24 parallel bash instances is passed.
If you want to make it truly atomic, you can do that with a lockfile:
# generate a lockfile, arrange for it to be deleted when this shell exits
lockfile=$(mktemp -t lock.XXXXXX); export lockfile
trap 'rm -f "$lockfile"' 0
xargs -P 24 bash -c '
for arg; do
{
output=$(myAwesomeShellFunction "$arg")
flock -x 99
printf "%s\n" "$output"
} 99>"$lockfile"
done
' _
cat a.txt | xargs -I % echo %
In the example above, xargs takes echo % as the command argument. But in some cases, I need multiple commands to process the argument instead of one. For example:
cat a.txt | xargs -I % {command1; command2; ... }
But xargs doesn't accept this form. One solution I know is that I can define a function to wrap the commands, but I want to avoid that because it is complex. Is there a better solution?
cat a.txt | xargs -d $'\n' sh -c 'for arg do command1 "$arg"; command2 "$arg"; ...; done' _
...or, without a Useless Use Of cat:
<a.txt xargs -d $'\n' sh -c 'for arg do command1 "$arg"; command2 "$arg"; ...; done' _
To explain some of the finer points:
The use of "$arg" instead of % (and the absence of -I in the xargs command line) is for security reasons: Passing data on sh's command-line argument list instead of substituting it into code prevents content that data might contain (such as $(rm -rf ~), to take a particularly malicious example) from being executed as code.
Similarly, the use of -d $'\n' is a GNU extension which causes xargs to treat each line of the input file as a separate data item. Either this or -0 (which expects NULs instead of newlines) is necessary to prevent xargs from trying to apply shell-like (but not quite shell-compatible) parsing to the stream it reads. (If you don't have GNU xargs, you can use tr '\n' '\0' <a.txt | xargs -0 ... to get line-oriented reading without -d).
The _ is a placeholder for $0, such that other data values added by xargs become $1 and onward, which happens to be the default set of values a for loop iterates over.
You can use
cat file.txt | xargs -i sh -c 'command {} | command2 {} && command3 {}'
{} = variable for each line on the text file
With GNU Parallel you can do:
cat a.txt | parallel 'command1 {}; command2 {}; ...; '
For security reasons it is recommended you use your package manager to
install. But if you cannot do that then you can use this 10 seconds
installation.
The 10 seconds installation will try to do a full installation; if
that fails, a personal installation; if that fails, a minimal
installation.
$ (wget -O - pi.dk/3 || lynx -source pi.dk/3 || curl pi.dk/3/ || \
fetch -o - http://pi.dk/3 ) > install.sh
$ sha1sum install.sh | grep 883c667e01eed62f975ad28b6d50e22a
12345678 883c667e 01eed62f 975ad28b 6d50e22a
$ md5sum install.sh | grep cc21b4c943fd03e93ae1ae49e28573c0
cc21b4c9 43fd03e9 3ae1ae49 e28573c0
$ sha512sum install.sh | grep da012ec113b49a54e705f86d51e784ebced224fdf
79945d9d 250b42a4 2067bb00 99da012e c113b49a 54e705f8 6d51e784 ebced224
fdff3f52 ca588d64 e75f6033 61bd543f d631f592 2f87ceb2 ab034149 6df84a35
$ bash install.sh
I prefer style which allows dry run mode (without | sh) :
cat a.txt | xargs -I % echo "command1; command2; ... " | sh
Works with pipes too:
cat a.txt | xargs -I % echo "echo % | cat " | sh
This is just another approach without xargs nor cat:
while read stuff; do
command1 "$stuff"
command2 "$stuff"
...
done < a.txt
This seems to be the safest version.
tr '[\n]' '[\0]' < a.txt | xargs -r0 /bin/bash -c 'command1 "$#"; command2 "$#";' ''
(-0 can be removed and the tr replaced with a redirect (or the file can be replaced with a null separated file instead). It is mainly in there since I mainly use xargs with find with -print0 output) (This might also be relevant on xargs versions without the -0 extension)
It is safe, since args will pass the parameters to the shell as an array when executing it. The shell (at least bash) would then pass them as an unaltered array to the other processes when all are obtained using ["$#"][1]
If you use ...| xargs -r0 -I{} bash -c 'f="{}"; command "$f";' '', the assignment will fail if the string contains double quotes. This is true for every variant using -i or -I. (Due to it being replaced into a string, you can always inject commands by inserting unexpected characters (like quotes, backticks or dollar signs) into the input data)
If the commands can only take one parameter at a time:
tr '[\n]' '[\0]' < a.txt | xargs -r0 -n1 /bin/bash -c 'command1 "$#"; command2 "$#";' ''
Or with somewhat less processes:
tr '[\n]' '[\0]' < a.txt | xargs -r0 /bin/bash -c 'for f in "$#"; do command1 "$f"; command2 "$f"; done;' ''
If you have GNU xargs or another with the -P extension and you want to run 32 processes in parallel, each with not more than 10 parameters for each command:
tr '[\n]' '[\0]' < a.txt | xargs -r0 -n10 -P32 /bin/bash -c 'command1 "$#"; command2 "$#";' ''
This should be robust against any special characters in the input. (If the input is null separated.) The tr version will get some invalid input if some of the lines contain newlines, but that is unavoidable with a newline separated file.
The blank first parameter for bash -c is due to this: (From the bash man page) (Thanks #clacke)
-c If the -c option is present, then commands are read from the first non-option argument com‐
mand_string. If there are arguments after the command_string, the first argument is assigned to $0
and any remaining arguments are assigned to the positional parameters. The assignment to $0 sets
the name of the shell, which is used in warning and error messages.
One thing I do is to add to .bashrc/.profile this function:
function each() {
while read line; do
for f in "$#"; do
$f $line
done
done
}
then you can do things like
... | each command1 command2 "command3 has spaces"
which is less verbose than xargs or -exec. You could also modify the function to insert the value from the read at an arbitrary location in the commands to each, if you needed that behavior also.
Another possible solution that works for me is something like -
cat a.txt | xargs bash -c 'command1 $#; command2 $#' bash
Note the 'bash' at the end - I assume it is passed as argv[0] to bash. Without it in this syntax the first parameter to each command is lost. It may be any word.
Example:
cat a.txt | xargs -n 5 bash -c 'echo -n `date +%Y%m%d-%H%M%S:` ; echo " data: " $#; echo "data again: " $#' bash
My current BKM for this is
... | xargs -n1 -I % perl -e 'system("echo 1 %"); system("echo 2 %");'
It is unfortunate that this uses perl, which is less likely to be installed than bash; but it handles more input that the accepted answer. (I welcome a ubiquitous version that does not rely on perl.)
#KeithThompson's suggestion of
... | xargs -I % sh -c 'command1; command2; ...'
is great - unless you have the shell comment character # in your input, in which case part of the first command and all of the second command will be truncated.
Hashes # can be quite common, if the input is derived from a filesystem listing, such as ls or find, and your editor creates temporary files with # in their name.
Example of the problem:
$ bash 1366 $> /bin/ls | cat
#Makefile#
#README#
Makefile
README
Oops, here is the problem:
$ bash 1367 $> ls | xargs -n1 -I % sh -i -c 'echo 1 %; echo 2 %'
1
1
1
1 Makefile
2 Makefile
1 README
2 README
Ahh, that's better:
$ bash 1368 $> ls | xargs -n1 -I % perl -e 'system("echo 1 %"); system("echo 2 %");'
1 #Makefile#
2 #Makefile#
1 #README#
2 #README#
1 Makefile
2 Makefile
1 README
2 README
$ bash 1369 $>
Try this:
git config --global alias.all '!f() { find . -d -name ".git" | sed s/\\/\.git//g | xargs -P10 -I{} git --git-dir={}/.git --work-tree={} $1; }; f'
It runs ten threads in parallel and does what ever git command you want to all repos in the folder structure. No matter if the repo is one or n levels deep.
E.g: git all pull
I have good idea to solve the problem.
Only write a comman mcmd, then you can do
find . -type f | xargs -i mcmd echo {} ## cat {} #pipe sed -n '1,3p'
The mcmd content as follows:
echo $* | sed -e 's/##/\n/g' -e 's/#pipe/|/g' | csh
I need to run more than one command in bash without waiting to finishing first one and starting other command. The commands can be like this inside bash file.
#!/bin/bash
perl test.pl -i file1 -o out1
perl test.pl -i file2 -o out2
and so on
All should run at the same time in different cores instead of running one after another.
Background them with &:
#!/bin/bash
perl test.pl -i file1 -o out1 &
perl test.pl -i file2 -o out2 &
Or better yet, use GNU parallel. This will allow you to use multiple CPUs and lots more.
I want to submit several "cat jobs" on the fly to a cluster using qsub. Currently I'm concatenating several files with cat to a single one at the end (using > output_file) at the end of the command.
The problem is that qsub takes the > output_file from the command as part of the qsub, putting there the log of the job instead of the cat output.
qsub -b y -cwd -q bigmem cmd1
where cmd1 looks like:
cat file1 file2 filen > output_file
Alternatively to dbeer's answer, if your code is disposable, you can use echo:
echo "cat file1 file2 ... filen > outfile" | qsub -cwd <options>
When a job is running via pbs, stdout is redirected to the output file of the job, so the way to do this is to write a script:
#!/bin/bash
cat file1 file2 ... filen
You don't need to redirect the output to a file because the mom daemon will do that for you in setting up the job, you just need to specify the output file you desire using -o. For example, if you named the above script script.sh (make sure it is executable) you'd submit:
qsub script.sh -b y -q bigmem -o output_file