I am trying to pipe a stream of string date values (YY-MM-DD HH:MM:SS) and return their epoch values and then find the largest and smallest value.
For a small file, this works fine. However upon using it on a larger file, the limitations of xargs causes it to break down. is there any quick, good alternative?
The line looks as follows:
awk function on a file ... | xargs -i date -d "{}" +%s | another awk function ...
Tried (and failed) originally to pipe into a perl script and may return to that if there isn't a quick win in bash.
Related
I have a problem with my script, it works fine when I loaded a file with fewer records but displays Memory fault(coredump) with file with many records. I suspected this grep code below:
grep "$(awk '{anum=substr($1,3,13); sub(/^0+/, "", anum); print anum}' file1.txt)" file2.txt > output.txt
My resolution is to do it with awk alone but since I'm new to it, I'm seeking for your help.
This is the sample data: (Please note that I'm using thousands of records for both files)
file1.txt
5000000000009258378
5000000000008523654
file2.txt
9258378, 9258380
8665231, 8665231
8523654, 8523658
output.txt
9258378, 9258380
8523654, 8523658
You are taking the output of this :
awk '{anum=substr($1,3,13); sub(/^0+/, "", anum); print anum}' file1.txt
converting it to a string in the shell, and then passing that string as an argument to grep.
If the output is large, the shell or grep might choke on it.
In any case, I don't think that is what you mean to do--
If the output of the awk script is multiple lines, you probably want to handle that in a loop in the shell, and run grep separately for each line.
I'm using terminal on OS 10.X. I have some data files of the format:
mbh5.0_mrg4.54545454545_period0.000722172513951.params.dat
mbh5.0_mrg4.54545454545_period0.00077271543854.params.dat
mbh5.0_mrg4.59090909091_period-0.000355232058085.params.dat
mbh5.0_mrg4.59090909091_period-0.000402015664015.params.dat
I know that there will be some files with similar numbers after mbh and mrg, but I won't know ahead of time what the numbers will be or how many similarly numbered ones there will be. My goal is to cat all the data from all the files with similar numbers after mbh and mrg into one data file. So from the above I would want to do something like...
cat mbh5.0_mrg4.54545454545*dat > mbh5.0_mrg4.54545454545.dat
cat mbh5.0_mrg4.5909090909*dat > mbh5.0_mrg4.5909090909.dat
I want to automate this process because there will be many such files.
What would be the best way to do this? I've been looking into sed, but I don't have a solution yet.
for file in *.params.dat; do
prefix=${file%_*}
cat "$file" >> "$prefix.dat"
done
This part ${file%_*} remove the last underscore and following text from the end of $file and saves the result in the prefix variable. (Ref: http://www.gnu.org/software/bash/manual/bashref.html#Shell-Parameter-Expansion)
It's not 100% clear to me what you're trying to achieve here but if you want to aggregate files into a file with the same number after "mbh5.0_mrg4." then you can do the following.
ls -l mbh5.0_mrg4* | awk '{print "cat " $9 " > mbh5.0_mrg4." substr($9,12,11) ".dat" }' | /bin/bash
The "ls -s" lists the file and the "awk" takes the 9th column from the result of the ls. With some string concatenation the result is passed to /bin/bash to be executed.
This is a linux bash script, so assuming you have /bind/bash, I'm not 100% famililar with OS X. This script also assumes that the number youre grouping on is always in the same place in the filename. I think you can change /bin/bash to almost any shell you have installed.
I want to find string pattern in file in unix. I use below command:
$grep 2005057488 filename
But file contains millions of lines and i have many such files. What is fastest way to get pattern other than grep.
grep is generally as fast as it gets. It's designed to one thing and one thing only - and it does what it does very well. You can read why here.
However, to speed things up there are a couple of things you could try. Firstly, it looks like the pattern you're looking for is a fixed string. Fortunately, grep has a 'fixed-strings' option:
-F, --fixed-strings
Interpret PATTERN as a list of fixed strings, separated by newlines, any of which is to be matched. (-F is specified by POSIX.)
Secondly, because grep is generally pretty slow on UTF-8, you could try disabling national language support (NLS) by setting the environment LANG=C. Therefore, you could try this concoction:
LANG=C grep -F "2005057488" file
Thirdly, it wasn't clear in your question, but if your only trying to find if something exists once in your file, you could also try adding a maximum number of times to find the pattern. Therefore, when -m 1, grep will quit immediately after the first occurrence is found. Your command could now look like this:
LANG=C grep -m 1 -F "2005057488" file
Finally, if you have a multicore CPU, you could give GNU parallel a go. It even comes with an explanation of how to use it with grep. To run 1.5 jobs per core and give 1000 arguments to grep:
find . -type f | parallel -k -j150% -n 1000 -m grep -H -n STRING {}
To grep a big file in parallel use --pipe:
< bigfile parallel --pipe grep STRING
Depending on your disks and CPUs it may be faster to read larger blocks:
< bigfile parallel --pipe --block 10M grep STRING
grep works faster than sed.
$grep 2005057488 filename
$sed -n '/2005057488/p' filename
Still Both works to get that particular string in a file
sed -n '/2005057488/p' filename
Not sure if this is faster than grep though.
Unfortunately, due to the limitations of our Unix Tru64 environment, I am unable to use the GREP -r switch to perform my search for strings within files across multiple directories and sub directories.
Ideally, I would like to pass two parameters. The first will be the directory I want my search is to start on. The second is a file containing a list of all the strings to be searched. This list will consist of various directory path names and will include special characters:
ie:
/aaa/bbb/ccc
/eee/dddd/ggggggg/
etc..
The purpose of this exercise is to identify all shell scripts that may have specific hard coded path names identified in my list.
There was one example I found during my investigations that perhaps comes close, but I am not sure how to customize this to accept a file of string arguments:
eg: find etb -exec grep test {} \;
where 'etb' is the directory and 'test', a hard coded string to be searched.
This should do it:
find dir -type f -exec grep -F -f strings.txt {} \;
dir is the directory from which searching will commence
strings.txt is the file of strings to match, one per line
-F means treat search strings as literal rather than regular expressions
-f strings.txt means use the strings in strings.txt for matching
You can add -l to the grep switches if you just want filenames that match.
Footnote:
Some people prefer a solution involving xargs, e.g.
find dir -type f -print0 | xargs -0 grep -F -f strings.txt
which is perhaps a little more robust/efficient in some cases.
By reading, I assume we can not use the gnu coreutil, and egrep is not available.
I assume (for some reason) the system is broken, and escapes do not work as expected.
Under normal situations, grep -rf patternfile.txt /some/dir/ is the way to go.
a file containing a list of all the strings to be searched
Assumptions : gnu coreutil not available. grep -r does not work. handling of special character is broken.
Now, you have working awk ? no ?. It makes life so much easier. But lets be on the safe side.
Assume : working sed ,one of od OR hexdump OR xxd (from vim package) is available.
Lets call this patternfile.txt
1. Convert list into a regexp that grep likes
Example patternfile.txt contains
/foo/
/bar/doe/
/root/
(example does not print special char, but it's there.) we must turn it into something like
(/foo/|/bar/doe/|/root/)
Assuming echo -en command is not broken, and xxd , or od, or hexdump is available,
Using hexdump
cat patternfile.txt |hexdump -ve '1/1 "%02x \n"' |tr -d '\n'
Using od
cat patternfile.txt |od -A none -t x1|tr -d '\n'
and pipe it into (common for both hexdump and od)
|sed 's:[ ]*0a[ ]*$::g'|sed 's: 0a:\\|:g' |sed 's:^[ ]*::g'|sed 's:^: :g' |sed 's: :\\x:g'
then pipe result into
|sed 's:^:\\(:g' |sed 's:$:\\):g'
and you have a regexp pattern that is escaped.
2. Feed the escaped pattern into broken regexp
Assuming the bare minimum shell escape is available,
we use grep "$(echo -en "ESCAPED_PATTERN" )" to do our job.
3. To sum it up
Building a escaped regexp pattern (using hexdump as example )
grep "$(echo -en "$( cat patternfile.txt |hexdump -ve '1/1 "%02x \n"' |tr -d '\n' |sed 's:[ ]*0a[ ]*$::g'|sed 's: 0a:\\|:g' |sed 's:^[ ]*::g'|sed 's:^: :g' |sed 's: :\\x:g'|sed 's:^:\\(:g' |sed 's:$:\\):g')")"
will escape all characters and enclose it with (|) brackets so a regexp OR match will be performed.
4. Recrusive directory lookup
Under normal situations, even when grep -r is broken, find /dir/ -exec grep {} \; should work.
Some may prefer xargs instaed (unless you happen to have buggy xargs).
We prefer find /somedir/ -type f -print0 |xargs -0 grep -f 'patternfile.txt' approach, but since
this is not available (for whatever valid reason),
we need to exec grep for each file,and this is normaly the wrong way.
But lets do it.
Assume : find -type f works.
Assume : xargs is broken OR not available.
First, if you have a buggy pipe, it might not handle large number of files.
So we avoid xargs in such systems (i know, i know, just lets pretend it is broken ).
find /whatever/dir/to/start/looking/ -type f > list-of-all-file-to-search-for.txt
IF your shell handles large size lists nicely,
for file in cat list-of-all-file-to-search-for.txt ; do grep REGEXP_PATTERN "$file" ;
done ; is a nice way to get by. Unfortunetly, some systems do not like that,
and in that case, you may require
cat list-of-all-file-to-search-for.txt | split --help -a 4 -d -l 2000 file-smaller-chunk.part.
to turn it into smaller chunks. Now this is for a seriously broken system.
then a for file in file-smaller-chunk.part.* ; do for single_line in cat "$file" ; do grep REGEXP_PATTERN "$single_line" ; done ; done ;
should work.
A
cat filelist.txt |while read file ; do grep REGEXP_PATTERN $file ; done ;
may be used as workaround on some systems.
What if my shell doe not handle quotes ?
You may have to escape the file list beforehand.
It can be done much nicer in awk, perl, whatever, but since we restrict our selves to
sed, lets do it.
We assume 0x27, the ' code will actually work.
cat list-of-all-file-to-search-for.txt |sed 's#['\'']#'\''\\'\'\''#g'|sed 's:^:'\'':g'|sed 's:$:'\'':g'
The only time I had to use this was when feeding output into bash again.
What if my shell does not handle that ?
xargs fails , grep -r fails , shell's for loop fails.
Do we have other things ? YES.
Escape all input suitable for your shell, and make a script.
But you know what, I got board, and writing automated scripts for csh just seems
wrong. So I am going to stop here.
Take home note
Use the tool for the right job. Writing a interpreter on bc is perfectly
capable, but it is just plain wrong. Install coreutils, perl, a better grep
what ever. makes life a better thing.
I would like to generate a random filename in unix shell (say tcshell). The filename should consist of random 32 hex letters, e.g.:
c7fdfc8f409c548a10a0a89a791417c5
(to which I will add whatever is neccesary). The point is being able to do it only in shell without resorting to a program.
Assuming you are on a linux, the following should work:
cat /dev/urandom | tr -cd 'a-f0-9' | head -c 32
This is only pseudo-random if your system runs low on entropy, but is (on linux) guaranteed to terminate. If you require genuinely random data, cat /dev/random instead of /dev/urandom. This change will make your code block until enough entropy is available to produce truly random output, so it might slow down your code. For most uses, the output of /dev/urandom is sufficiently random.
If you on OS X or another BSD, you need to modify it to the following:
cat /dev/urandom | env LC_CTYPE=C tr -cd 'a-f0-9' | head -c 32
why do not use unix mktemp command:
$ TMPFILE=`mktemp tmp.XXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXX` && echo $TMPFILE
tmp.MnxEsPDsNUjrzDIiPhnWZKmlAXAO8983
One command, no pipe, no loop:
hexdump -n 16 -v -e '/1 "%02X"' -e '/16 "\n"' /dev/urandom
If you don't need the newline, for example when you're using it in a variable:
hexdump -n 16 -v -e '/1 "%02X"' /dev/urandom
Using "16" generates 32 hex digits.
uuidgen generates exactly this, except you have to remove hyphens. So I found this to be the most elegant (at least to me) way of achieving this. It should work on linux and OS X out of the box.
uuidgen | tr -d '-'
As you probably noticed from each of the answers, you generally have to "resort to a program".
However, without using any external executables, in Bash and ksh:
string=''; for i in {0..31}; do string+=$(printf "%x" $(($RANDOM%16)) ); done; echo $string
in zsh:
string=''; for i in {0..31}; do string+=$(printf "%x" $(($RANDOM%16)) ); dummy=$RANDOM; done; echo $string
Change the lower case x in the format string to an upper case X to make the alphabetic hex characters upper case.
Here's another way to do it in Bash but without an explicit loop:
printf -v string '%X' $(printf '%.2s ' $((RANDOM%16))' '{00..31})
In the following, "first" and "second" printf refers to the order in which they're executed rather than the order in which they appear in the line.
This technique uses brace expansion to produce a list of 32 random numbers mod 16 each followed by a space and one of the numbers in the range in braces followed by another space (e.g. 11 00). For each element of that list, the first printf strips off all but the first two characters using its format string (%.2) leaving either single digits followed by a space each or two digits. The space in the format string ensures that there is then at least one space between each output number.
The command substitution containing the first printf is not quoted so that word splitting is performed and each number goes to the second printf as a separate argument. There, the numbers are converted to hex by the %X format string and they are appended to each other without spaces (since there aren't any in the format string) and the result is stored in the variable named string.
When printf receives more arguments than its format string accounts for, the format is applied to each argument in turn until they are all consumed. If there are fewer arguments, the unmatched format string (portion) is ignored, but that doesn't apply in this case.
I tested it in Bash 3.2, 4.4 and 5.0-alpha. But it doesn't work in zsh (5.2) or ksh (93u+) because RANDOM only gets evaluated once in the brace expansion in those shells.
Note that because of using the mod operator on a value that ranges from 0 to 32767 the distribution of digits using the snippets could be skewed (not to mention the fact that the numbers are pseudo random in the first place). However, since we're using mod 16 and 32768 is divisible by 16, that won't be a problem here.
In any case, the correct way to do this is using mktemp as in Oleg Razgulyaev's answer.
Tested in zsh, should work with any BASH compatible shell!
#!/bin/zsh
SUM=`md5sum <<EOF
$RANDOM
EOF`
FN=`echo $SUM | awk '// { print $1 }'`
echo "Your new filename: $FN"
Example:
$ zsh ranhash.sh
Your new filename: 2485938240bf200c26bb356bbbb0fa32
$ zsh ranhash.sh
Your new filename: ad25cb21bea35eba879bf3fc12581cc9
Yet another way[tm].
R=$(echo $RANDOM $RANDOM $RANDOM $RANDOM $RANDOM | md5 | cut -c -8)
FILENAME="abcdef-$R"
This answer is very similar to fmarks, so I cannot really take credit for it, but I found the cat and tr command combinations quite slow, and I found this version quite a bit faster. You need hexdump.
hexdump -e '/1 "%02x"' -n32 < /dev/urandom
Another thing you can add is running the date command as follows:
date +%S%N
Reads nonosecond time and the result adds a lot of randomness.
The first answer is good but why fork cat if not required.
tr -dc 'a-f0-9' < /dev/urandom | head -c32
Grab 16 bytes from /dev/random, convert them to hex, take the first line, remove the address, remove the spaces.
head /dev/random -c16 | od -tx1 -w16 | head -n1 | cut -d' ' -f2- | tr -d ' '
Assuming that "without resorting to a program" means "using only programs that are readily available", of course.
If you have openssl in your system you can use it for generating random hex (also it can be -base64) strings with defined length. I found it pretty simple and usable in cron in one line jobs.
openssl rand -hex 32
8c5a7515837d7f0b19e7e6fa4c448400e70ffec88ecd811a3dce3272947cb452
Hope to add a (maybe) better solution to this topic.
Notice: this only works with bash4 and some implement of mktemp(for example, the GNU one)
Try this
fn=$(mktemp -u -t 'XXXXXX')
echo ${fn/\/tmp\//}
This one is twice as faster as head /dev/urandom | tr -cd 'a-f0-9' | head -c 32, and eight times as faster as cat /dev/urandom | tr -cd 'a-f0-9' | head -c 32.
Benchmark:
With mktemp:
#!/bin/bash
# a.sh
for (( i = 0; i < 1000; i++ ))
do
fn=$(mktemp -u -t 'XXXXXX')
echo ${fn/\/tmp\//} > /dev/null
done
time ./a.sh
./a.sh 0.36s user 1.97s system 99% cpu 2.333 total
And the other:
#!/bin/bash
# b.sh
for (( i = 0; i < 1000; i++ ))
do
cat /dev/urandom | tr -dc 'a-zA-Z0-9' | head -c 32 > /dev/null
done
time ./b.sh
./b.sh 0.52s user 20.61s system 113% cpu 18.653 total
If you are on Linux, then Python will come pre-installed. So you can go for something similar to the below:
python -c "import uuid; print str(uuid.uuid1())"
If you don't like the dashes, then use replace function as shown below
python -c "import uuid; print str(uuid.uuid1()).replace('-','')"