I have a program that when it runs, outputs hundreds of lines starting with "Info:" and a few lines that have useful output. To make things easier, I have created a simple python and bash combination script to emulate the issue I'm having:
wait_2sec.py:
import time
print("Hello!")
time.sleep(2)
print("Goodbye!")
I am attempting to trim my output by running:
python wait_2sec.py | sed '/Goodbye/d'
However, sed does not output Hello! until after the python script has finished. I don't know whether the pipe waits until after the program is finished to begin running the sed command, or if the sed command is the hangup.
I am open to using another command to trim output if sed does not work for this use-case.
I don't know whether the pipe waits until after the program is finished to begin running the sed command, or if the sed command is the hangup.
It's actually neither of both, it's that python normally buffers its output (if not to a terminal) until the buffer is full, hence Moustapha's suggestion may work provided that unbuffer is installed. But you can simply use python's built-in option -u (Force the stdout and stderr streams to be unbuffered.) instead:
python -u wait_2sec.py | sed '/Goodbye/d'
You can try to run your script using the following command:
unbuffer python wait_2sec.py | sed '/Goodbye/d'
Refrence: https://unix.stackexchange.com/a/200413
Related
Is there a way to run shell commands without output buffering?
For example, hexdump file | ./my_script will only pass input from hexdump to my_script in buffered chunks, not line by line.
Actually I want to know a general solution how to make any command unbuffered?
Try stdbuf, included in GNU coreutils and thus virtually any Linux distro. This sets the buffer length for input, output and error to zero:
stdbuf -i0 -o0 -e0 command
The command unbuffer from the expect package disables the output buffering:
Ubuntu Manpage: unbuffer - unbuffer output
Example usage:
unbuffer hexdump file | ./my_script
AFAIK, you can't do it without ugly hacks. Writing to a pipe (or reading from it) automatically turns on full buffering and there is nothing you can do about it :-(. "Line buffering" (which is what you want) is only used when reading/writing a terminal. The ugly hacks exactly do this: They connect a program to a pseudo-terminal, so that the other tools in the pipe read/write from that terminal in line buffering mode. The whole problem is described here:
http://www.pixelbeat.org/programming/stdio_buffering/
The page has also some suggestions (the aforementioned "ugly hacks") what to do, i.e. using unbuffer or pulling some tricks with LD_PRELOAD.
You could also use the script command to make the output of hexdump line-buffered (hexdump will be run in a pseudo terminal which tricks hexdump into thinking its writing its stdout to a terminal, and not to a pipe).
# cf. http://unix.stackexchange.com/questions/25372/turn-off-buffering-in-pipe/
stty -echo -onlcr
script -q /dev/null hexdump file | ./my_script # FreeBSD, Mac OS X
script -q -c "hexdump file" /dev/null | ./my_script # Linux
stty echo onlcr
One should use grep or egrep "--line-buffered" options to solve this. no other tools needed.
Usually, stdout is line-buffered. In other words, as long as your printf argument ends with a newline, you can expect the line to be printed instantly. This does not appear to hold when using a pipe to redirect to tee.
I have a C++ program, a, that outputs strings, always \n-terminated, to stdout.
When it is run by itself (./a), everything prints correctly and at the right time, as expected. However, if I pipe it to tee (./a | tee output.txt), it doesn't print anything until it quits, which defeats the purpose of using tee.
I know that I could fix it by adding a fflush(stdout) after each printing operation in the C++ program. But is there a cleaner, easier way? Is there a command I can run, for example, that would force stdout to be line-buffered, even when using a pipe?
you can try stdbuf
$ stdbuf --output=L ./a | tee output.txt
(big) part of the man page:
-i, --input=MODE adjust standard input stream buffering
-o, --output=MODE adjust standard output stream buffering
-e, --error=MODE adjust standard error stream buffering
If MODE is 'L' the corresponding stream will be line buffered.
This option is invalid with standard input.
If MODE is '0' the corresponding stream will be unbuffered.
Otherwise MODE is a number which may be followed by one of the following:
KB 1000, K 1024, MB 1000*1000, M 1024*1024, and so on for G, T, P, E, Z, Y.
In this case the corresponding stream will be fully buffered with the buffer
size set to MODE bytes.
keep this in mind, though:
NOTE: If COMMAND adjusts the buffering of its standard streams ('tee' does
for e.g.) then that will override corresponding settings changed by 'stdbuf'.
Also some filters (like 'dd' and 'cat' etc.) dont use streams for I/O,
and are thus unaffected by 'stdbuf' settings.
you are not running stdbuf on tee, you're running it on a, so this shouldn't affect you, unless you set the buffering of a's streams in a's source.
Also, stdbuf is not POSIX, but part of GNU-coreutils.
Try unbuffer (man page) which is part of the expect package. You may already have it on your system.
In your case you would use it like this:
unbuffer ./a | tee output.txt
The -p option is for pipeline mode where unbuffer reads from stdin and passes it to the command in the rest of the arguments.
You can use setlinebuf from stdio.h.
setlinebuf(stdout);
This should change the buffering to "line buffered".
If you need more flexibility you can use setvbuf.
You may also try to execute your command in a pseudo-terminal using the script command (which should enforce line-buffered output to the pipe)!
script -q /dev/null ./a | tee output.txt # Mac OS X, FreeBSD
script -c "./a" /dev/null | tee output.txt # Linux
Be aware the script command does not propagate back the exit status of the wrapped command.
The unbuffer command from the expect package at the #Paused until further notice answer did not worked for me the way it was presented.
Instead of using:
./a | unbuffer -p tee output.txt
I had to use:
unbuffer -p ./a | tee output.txt
(-p is for pipeline mode where unbuffer reads from stdin and passes it to the command in the rest of the arguments)
The expect package can be installed on:
MSYS2 with pacman -S expect
Mac OS with brew install expect
Update
I recently had buffering problems with python inside a shell script (when trying to append timestamp to its output). The fix was to pass -u flag to python this way:
run.sh with python -u script.py
unbuffer -p /bin/bash run.sh 2>&1 | tee /dev/tty | ts '[%Y-%m-%d %H:%M:%S]' >> somefile.txt
This command will put a timestamp on the output and send it to a file and stdout at the same time.
The ts program (timestamp) can be installed with the moreutils package.
Update 2
Recently, also had problems with grep buffering the output, when I used the argument grep --line-buffered on grep to it stop buffering the output.
If you use the C++ stream classes instead, every std::endl is an implicit flush. Using C-style printing, I think the method you suggested (fflush()) is the only way.
The best answer IMO is grep's --line-buffer option as stated here:
https://unix.stackexchange.com/a/53445/40003
I have a few commands i run between brackets which i then redirect to a named pipe and tail the pipe however it looks like the redirection happens only after the block has finished executing as i don't see any output from the tail command for a while and it only shows the last command ouput when i do. Any ideas how view the output of the block in realtime?
Example Script
#!/usr/bin/env bash
mkfifo /tmp/why_you_no_out;
trap "rm /tmp/why_you_no_out" 0;
{
for ((i=1;i<=100;i++)); do
printf "$i";
done
sleep 10s;
printf "\n12356";
} >> /tmp/why_you_no_out &
printf "here";
tail -n 1 -f /tmp/why_you_no_out
Sounds like the issue is buffering. Most shells don't want to write data a byte at a time because it's wasteful. Instead, they wait until they have a sizable chunk of data before committing it unless the output is connected to your terminal.
If you're looking to unbuffer the output of an arbitrary command, you may find the "unbuffer" utility helpful or any of the solutions mentioned in this question: How to make output of any shell command unbuffered?
If you're dealing with specific applications, they may have options to reduce buffering. For example, GNU's grep includes the --line-buffered option.
I have a complex command on my bash script which prints a lot of info on stdout. This command is complex and takes some time to finish but is fully working. At the same time, I'm using a pipe with tee to write it into a file for a post-parsing task.
cmd="myComplexCommand | tee /dev/fd/5"
exec 5>&1
stored_output=$(eval "${cmd}")
Until here everything is working.
Now, I'm trying to implement ccze to colorize screen output. Usually to use it on any command is as simple as:
anyCommand | ccze -A
And everything is printed in a beauty colorized way. The problem is if I try to apply this to my particular case, after using the pipe to ccze on my myComplexCommand, the output on screen is colorized (nice!) but it alters the output stored on the file I want to parse on my post-parse task and it doesn't work.
Is there a Bash way to print a command using ccze in a beauty way on screen and at the same time store it in a file (without ccze modifications) to parse it later?
tee to file at a point in the pipeline before the colorization takes place:
myComplexCommand | tee filename | ccze -A
Incidentally, with bash 4.1 or later, if you want to send a lot of data both to a file and in colorized form to the TTY, you might put both those operations in a single process substitution:
exec {stdout_backup}>&1
exec {store_and_colorize}> >(tee filename | ccze -A | tee /dev/fd/"$stdout_backup")
and then reuse that process substitution as many times as you like:
result=$(something >&$store_and_colorize)
another_result=$(something_else >&$store_and_colorize)
That way you've got exactly one copy of ccze persisting across multiple uses.
I've got a script like:
#!/bin/bash
exec /usr/bin/some_binary > /tmp/my.log 2>&1
Problem is that some_binary sends all of its logging to stdout, and buffering makes it so that I only see output in chunks of a few lines. This is annoying when something gets stuck and I need to see what the last line says.
Is there any way to make stdout unbuffered before I do the exec that will affect some_binary so it has more useful logging?
(The wrapper script is only setting a few environment variables before the exec, so a solution in perl or python would also be feasible.)
GNU coreutils-8.5 also has the stdbuf command to modify I/O stream buffering:
http://www.pixelbeat.org/programming/stdio_buffering/
So, in your example case, simply invoke:
stdbuf -oL /usr/bin/some_binary > /tmp/my.log 2>&1
This will allow text to appear immediately line-by-line (once a line is completed with the end-of-line "\n" character in C). If you really want immediate output, use -o0 instead.
This way could be more desirable if you do not want to introduce dependency to expect via unbuffer command. The unbuffer way, on the other hand, is needed if you have to fool some_binary into thinking that it is facing a real tty standard output.
You might find that the unbuffer script that comes with expect may help.
Some command line programs have an option to modify their stdout stream buffering behaviour. So that's the way to go if the C source is available ...
# two command options ...
man file | less -p '--no-buffer'
man grep | less -p '--line-buffered'
# ... and their respective source code
# from: http://www.opensource.apple.com/source/file/file-6.2.1/file/src/file.c
if(nobuffer)
(void) fflush(stdout);
# from: http://www.opensource.apple.com/source/grep/grep-28/grep/src/grep.c
if (line_buffered)
fflush (stdout);
As an alternative to using expect's unbuffer script or modifying the program's source code, you may also try to use script(1) to avoid stdout hiccups caused by a pipe:
See: Trick an application into thinking its stdin is interactive, not a pipe
# Linux
script -c "[executable string]" /dev/null
# FreeBSD, Mac OS X
script -q /dev/null "[executable string]"
I scoured the internets for an answer, and none of this worked for uniq which is too stubborn to buffer everything except for stdbuf:
{piped_command_here} | stdbuf -oL uniq | {more_piped_command_here}
GNU Coreutils-8 includes a program called stdbuf which essentially does the LD_PRELOAD trick. It works on Linux and reportedly works on BSD systems.
An environment variable can set the terminal IO mode to unbuffered.
export NSUnbufferedIO=YES
This will set the terminal unbuffered for both C and Ojective-C terminal output commands.