This question already has answers here:
Argument list too long error for rm, cp, mv commands
(31 answers)
Closed 7 years ago.
I am trying to list all files we received in one month
The filename pattern will be
20110101000000.txt
YYYYMMDDHHIISS.txt
The entire directory is having millions of files.
For one month there can be minimum 50000 files.
Idea of sub directory is still pending.
Is there any way to list huge number of files with file name almost similar.
grep -l 20110101*
Am trying this and returning error.
I try php it took a huge time , thats why i use shell script . I dont understand why shell also not giving a result
Any suggestion please!!
$ find ./ -name '20110101*' -print0 -type f | xargs -0 grep -l "search_pattern"
you can use find and xargs. xargs will run grep for each file found by find. You can use -P to run multiple grep's parallely and -n for multiple files per grep command invocation. The print0 argument in find separates each filename with a null character to avoid confusion caused by any spaces in the file name. If you are sure there will not be any spaces you can remove -print0 and -0 args.
This should be the faster way:
find . -name "20110101*" -exec grep -l "search_pattern" {} +
Should you want to avoid the leading dot:
find . -name "20110101*" -exec grep -l "search_pattern" {} + | sed 's/^.\///'
or better thanks to adl:
find . -name "20110101*" -exec grep -l "search_pattern" {} + | cut -c3-
The 20110101* is getting expanded by your shell before getting passed to the command, so you're getting one argument passed for every file in the dir that starts with 20110101.
If you just want a list of matching files you can use find:
find . -name "20110101*"
(note that this will search every subdirectory also)
Some in depth information available here and also another work-around: for FILE in 20110101*; do grep foo ${FILE}; done. Most people will go with xargs and more seasoned admins with -exec {} + which accomplishes exactly the same, except is shorter to type. One would use the inline shell for construct, when running more processes is less important then seeing the results. With the for construct you may end up running grep thousands of times, but you see each match in real time, while using find and/or xargs you see batched results, however grep is run significantly less.
you need to put in a search term, so
grep -l "search term" 20110101*
if you want to just find the files, use ls 20110101*
Just pipe the output of ls to grep: ls | grep '^20110101'
Related
The problem
Sometimes, when I run the grep tool recursively it gets stuck in some big directories or in some big files, and I would like to see the directory or file name because perhaps I may realise I don't need to scan that specific directory/file the next time I use grep for a similar purpose, therefore excluding it with the corresponding grep options.
Is there a way to tell grep the current path directory/file which is being scanned in such searches?
My attempts
I tried to search here but it's impossible to find something since usually the keywords current directory are used for other reasons, so there is a conflicting terminology.
I have also tried things like:
man grep | grep -i current
man grep | grep -i status
(and many others) without success so far.
EDIT: I have just found a useful answer here which is for a different problem, but I guess that it may work if I modify the following code by adding an echo command somewhere in the for loop, although I have also just realised it requires bash 4 and sadly I have bash 3.
# Requires bash 4 and Gnu grep
shopt -s globstar
files=(**)
total=${#files[#]}
for ((i=0; i<total; i+=100)); do
echo $i/$total >>/dev/stderr
grep -d skip -e "$pattern" "${files[#]:i:100}" >>results.txt
done
find . -type f -exec echo grepping {} \; -exec time grep pattern {} \; 2>&1
find . -type f to find all the files recursively.
-exec echo grepping {} to call out each file
-exec time grep ... {} to report the time each grep takes
2>&1 to get time's stderr onto stdout.
This doesn't report a total time per directory. Doing that this way either requires more advanced find, to find leaf dirs for grep -d, or to add some cumulative time per path, which I'd do with perl -p... but that's nontrivial as well.
I am new to bash and I am trying to understand the use of xargs, which is still not clear for me. For example:
history | grep ls
Here I am searching for the command ls in my history. In this command, I did not use xargs and it worked fine.
find /etc - name "*.txt" | xargs ls -l
I this one, I had to use xargs but I still can not understand the difference and I am not able to decide correctly when to use xargs and when not.
xargs can be used when you need to take the output from one command and use it as an argument to another. In your first example, grep takes the data from standard input, rather than as an argument. So, xargs is not needed.
xargs takes data from standard input and executes a command. By default, the data is appended to the end of the command as an argument. It can be inserted anywhere however, using a placeholder for the input. The traditional placeholder is {}; using that, your example command might then be written as:
find /etc -name "*.txt" | xargs -I {} ls -l {}
If you have 3 text files in /etc you'll get a full directory listing of each. Of course, you could just have easily written ls -l /etc/*.txt and saved the trouble.
Another example lets you rename those files, and requires the placeholder {} to be used twice.
find /etc -name "*.txt" | xargs -I {} mv {} {}.bak
These are both bad examples, and will break as soon as you have a filename containing whitespace. You can work around that by telling find to separate filenames with a null character.
find /etc -print0 -name "*.txt" | xargs -I {} -0 mv {} {}.bak
My personal opinion is that there are almost always alternatives to using xargs (such as the -exec argument to find) and you will be better served by learning those.
When you use piping without xargs, the actual data is fed into the next command. On the other hand, when using piping with xargs, the actual data is viewed as a parameter to the next command. To give a concrete example, say you have a folder with a.txt and b.txt. a.txt contains just a single line 'hello world!', and b.txt is just empty.
If you do
ls | grep txt
you would end up getting the output:
a.txt
b.txt
Yet, if you do
ls | xargs grep txt
you would get nothing since neither file a.txt nor b.txt contains the word txt.
If the command is
ls | xargs grep hello
you would get:
hello world!
That's because with xargs, the two filenames given by ls are passed to grep as arguments, rather than the actual content.
Short answer: Avoid xargs for now. Return to xargs when you have written dozens or hundreds of scripts.
Commands can get their input from parameters (like rm bad_example) or can get the input from stdin (not just the y on the question after rm -i is_this_bad_too, but also read answer). Other commands like grep and sed will look for parameters and when the parameters don't show the input, switch to the input.
Your grep example works fine reading from stdin, nothing special needed.
Your ls needs the output of find as a parameter. xargs is just one way to turn things around. Use man xargs for more about xargs. Alternatives:
find /etc -name "*.txt" -exec ls -l {} \;
find /etc -name "*.txt" -ls
ls -l $(find /etc -name "*.txt" )
ls /etc/*.txt
First try to see which of this commands is best when you have a nasty filename with spaces.txt in /etc.
xargs(1) is dangerous (broken, exploitable, etc.) when reading non-NUL-delimited input.
If you're working with filenames, use find's -exec [command] {} + instead.
If you can get NUL-delimited output, use xargs -0.
GNU Parallel can do the same as xargs, but does not have the broken and exploitable "features".
You can learn GNU Parallel by looking at examples http://www.gnu.org/software/parallel/man.html#EXAMPLE:-Working-as-xargs--n1.-Argument-appending and walking through the tutorial http://www.gnu.org/software/parallel/parallel_tutorial.html
This question already has answers here:
How do I recursively grep all directories and subdirectories?
(26 answers)
Closed 7 years ago.
How do I find a string contained in (possibly multiple) files in a folder including hidden files and subfolders?
I tried this command:
find . -maxdepth 1 -name "tes1t" -print0 | sed 's,\.\/,,g'
But this yielded no results.
grep -Hnr PATTERN . if your grep supports -r (recursive, = -d recurse). Note there would be no limit on recursion depths then.
Or try grep -d skip -Hn PATTERN {,.[!.]}*{,/{,.[!.]}*}; this should work since grep accepts multiple file arguments. Just throw away the -d skip stuff if your version of grep doesn't support it. For shells without the brace expansion, use the manually expanded form * */* */.[!.]* .[!.]* .[!.]*/* .[!.]*/.[!.]*.
First of all, your maxdepth should have been 2 instead of 1, now your find command won't descend in subdirectories. Furthermore you can simply grep for your pattern on the output of find. This can be achieved as follows:
find . -maxdepth 2 -type f -exec grep 'pattern here' '{}' \;
Explanation:
find . execute find in current directory.
-maxdepth 2 descend in subdirectories by no further.
-type f find every file that is not a directory.
-exec grep 'pattern' '{}' execute a grep statement with a certain pattern, the {} contains the filename for each file found.
Add options to grep for color highlighting, outputting line numbers and/or the file name.
For more information see man find and man grep.
I am trying to grep 40k files in the current directory and i am getting this error.
for i in $(cat A01/genes.txt); do grep $i *.kaks; done > A01/A01.result.txt
-bash: /usr/bin/grep: Argument list too long
How do one normally grep thousands of files?
Thanks
Upendra
This makes David sad...
Everyone so far is wrong (except for anubhava).
Shell scripting is not like any other programming language because much of the interpretation of lines comes from the power of the shell interpolating them before the command is actually executed.
Let's take something simple:
$ set -x
$ ls
+ ls
bar.txt foo.txt fubar.log
$ echo The text files are *.txt
echo The text files are *.txt
> echo The text files are bar.txt foo.txt
The text files are bar.txt foo.txt
$ set +x
$
The set -x allows you to see how the shell actually interpolates the glob and then passes that back to the command as input. The > points to the line that is actually being executed by the command.
You can see that the echo command isn't interpreting the *. Instead, the shell grabs the * and replaces it with the names of the matching files. Then and only then does the echo command actually executes the command.
When you have 40K plus files, and you do grep *, you're expanding that * to the names of those 40,000 plus files before grep even has a chance to execute, and that's where the error message /usr/bin/grep: Argument list too long is coming from.
Fortunately, Unix has a way around this dilemma:
$ find . -name "*.kaks" -type f -maxdepth 1 | xargs grep -f A01/genes.txt
The find . -name "*.kaks" -type f -maxdepth 1 will find all of your *.kaks files, and the -depth 1 will only include files in the current directory. The -type f makes sure you only pick up files and not a directory.
The find command pipes the names of the files into xargs and xargs will append the names of the file to the grep -f A01/genes.txtcommand. However, xargs has a trick up it sleeve. It knows how long the command line buffer is, and will execute the grep when the command line buffer is full, then pass in another series of file to the grep. This way, grep gets executed maybe three or ten times (depending upon the size of the command line buffer), and all of our files are used.
Unfortunately, xargs uses whitespace as a separator for the file names. If your files contain spaces or tabs, you'll have trouble with xargs. Fortunately, there's another fix:
$ find . -name "*.kaks" -type f -maxdepth 1 -print0 | xargs -0 grep -f A01/genes.txt
The -print0 will cause find to print out the names of the files not separated by newlines, but by the NUL character. The -0 parameter for xargs tells xargs that the file separator isn't whitespace, but the NUL character. Thus, fixes the issue.
You could also do this too:
$ find . -name "*.kaks" -type f -maxdepth 1 -exec grep -f A01/genes.txt {} \;
This will execute the grep for each and every file found instead of what xargs does and only runs grep for all the files it can stuff on the command line. The advantage of this is that it avoids shell interference entirely. However, it may or may not be less efficient.
What would be interesting is to experiment and see which one is more efficient. You can use time to see:
$ time find . -name "*.kaks" -type f -maxdepth 1 -exec grep -f A01/genes.txt {} \;
This will execute the command and then tell you how long it took. Try it with the -exec and with xargs and see which is faster. Let us know what you find.
You can combine find with grep like this:
find . -maxdepth 1 -name '*.kaks' -exec grep -H -f A01/genes.txt '{}' \; > A01/A01.result.txt
you can use recursive feature of grep:
for i in $(cat A01/genes.txt); do
grep -r $i .
done > A01/A01.result.txt
though if you want to select only kaks files:
for i in $(cat A01/genes.txt); do
find . -iregex '.*\.kaks$' -exec grep $i \;
done > A01/A01.result.txt
Put another for loop inside your outer one:
for f in *.kaks; do
grep -H $i "$f"
done
By the way, are you interested in finding EVERY occurrence in each file, or merely if the search string exists in there one or more times? If it is "good enough" to know the string occurs in there one or more times you can specify "-n 1" to grep and it will not bother reading/searching the rest of the file after finding the first match, which could potentially save lots of time.
The following solution has worked for me:
Problem:
grep -r "example\.com" *
-bash: /bin/grep: Argument list too long
Solution:
grep -r "example\.com" .
["In newer versions of grep you can omit the “.“, as the current directory is implied."]
Source:
Reinlick, J. https://www.saotn.org/bash-grep-through-large-number-files-argument-list-too-long/
This is the command I've been using for finding matches (queryString) in php files, in the current directory, with grep, case insensitive, and showing matching results in line:
find . -iname "*php" -exec grep -iH queryString {} \;
Is there a way to also pipe just the file name of the matches to another script?
I could probably run the -exec command twice, but that seems inefficient.
What I'd love to do on Mac OS X is then actually to "reveal" that file in the finder. I think I can handle that part. If I had to give up the inline matches and just let grep show the files names, and then pipe that to a third script, that would be fine, too - I would settle.
But I'm actually not even sure how to pipe the output (the matched file names) to somewhere else...
Help! :)
Clarification
I'd like to reveal each of the files in a finder window - so I'm probably not going to using the -q flag and stop at the first one.
I'm going to run this in the console, ideally I'd like to see the inline matches printed out there, as well as being able to pipe them to another script, like oascript (applescript, to reveal them in the finder). That's why I have been using -H - because I like to see both the file name and the match.
If I had to settle for just using -l so that the file name could more easily be piped to another script, that would be OK, too. But I think after looking at the reply below from #Charlie Martin, that xargs could be helpful here in doing both at the same time with a single find, and single grep command.
I did say bash but I don't really mind if this needs to be ran as /bin/sh instead - I don't know too much about the differences yet, but I do know there are some important ones.
Thank you all for the responses, I'm going to try some of them at the command line and see if I can get any of them to work and then I think I can choose the best answer. Leave a comment if you want me to clarify anything more.
Thanks again!
You bet. The usual thing is something like
$ find /path -name pattern -print | xargs command
So you might for example do
$ find . -name '*.[ch]' -print | xargs grep -H 'main'
(Quiz: why -H?)
You can carry on with this farther; for example. you might use
$ find . -name '*.[ch]' -print | xargs grep -H 'main' | cut -d ':' -f 1
to get the vector of file names for files that contain 'main', or
$ find . -name '*.[ch]' -print | xargs grep -H 'main' | cut -d ':' -f 1 |
xargs growlnotify -
to have each name become a Growl notification.
You could also do
$ grep pattern `find /path -name pattern`
or
$ grep pattern $(find /path -name pattern)
(in bash(1) at least these are equivalent) but you can run into limits on the length of a command line that way.
Update
To answer your questions:
(1) You can do anything in bash you can do in sh. The one thing I've mentioned that would be any different is the use of $(command) in place of using backticks around command, and that works in the version of sh on Macs. The csh, zsh, ash, and fish are different.
(2) I think merely doing $ open $(dirname arg) will opena finder window on the containing directory.
It sounds like you want to open all *.php files that contain querystring from within a Terminal.app session.
You could do it this way:
find . -name '*.php' -exec grep -li 'querystring' {} \; | xargs open
With my setup, this opens MacVim with each file on a separate tab. YMMV.
Replace -H with -l and you will get a list of those filenames that matched the pattern.
if you have bash4, simply do
grep pattern /path/**/*.php
the ** operator is like
grep pattern `find -name \*.php -print`
find /home/aaronmcdaid/Code/ -name '*.cpp' -exec grep -q -iH boost {} \; -exec echo {} \;
The first change I made is to add -q to your grep command. This is "Exit immediately with zero status if any match is found".
The good news is that this speeds up grep when a file has many matching lines. You don't care how many matches there are. But that means we need another exec on the end to actually print the filenames when grep has been successful
The grep result will be sent to stdout, so another -exec predicate is probably the best solution here.
Pipe to another script:
find . -iname "*.php" | myScript
File names will come into the stdin of myScript 1 line at a time.
You can also use xargs to form/execute commands to act on each file:
find . -iname "*.php" | xargs ls -l
act on files you find that match:
find . -iname "*.php" | xargs grep -l pattern | myScript
act that don't match pattern
find . -iname "*.php" | xargs grep -L pattern | myScript
In general using multiple -exec's and grep -q will be FAR faster than piping, since find has implied short circuits -a's separating each juxtaposed pair of expressions that's not separated with an explicit operator. The main problem here, is that you want something to happen if grep matches something AND for matches to be printed. If the files are reasonably sized then this should be faster (because grep -q exits after finding a single match)
find . -iname "*php" -exec grep -iq queryString {} \; -exec grep -iH queryString {} \; -exec otherprogram {} \;
If the files are particularly big, encapsulating it in a shell script may be faster then running multiple grep commands
find . -iname "*php" -exec bash -c \
'out=$(grep -iH queryString "$1"); [[ -n $out ]] && echo "$out" && exit 0 || exit 1' \
bash {} \; -print
Also note, if the matches are not particularly needed, then
find . -iname "*php" -exec grep -iq queryString {} \; -exec otherprogram {} \;
Will virtually always be faster than then a piped solution like
find . -iname "*php" -print0 | xargs -0 grep -iH | ...
Additionally, you should really have -type f in all cases, unless you want to catch *php directories
Regarding the question of which is faster, and you actually care about the minuscule time difference, which maybe you might if you are trying to see which will save your processor some time... perhaps testing using the command as a suffix to the "time" command, and see which one performs better.