I've written a little script to find the IDs of the processes I'm interested in running kill -9 on. It reads something like this:
ps -A -o pid -o command | egrep 'java' | cut -d' ' -f1
However, I also get the PID for the command that runs the egrep java. I'd like to alter my above command that looks for 'java' to exclude the one that is the egrep java.
I'm fairly new to the command line and I'm not really sure how to do that.
You can try this,
ps -A -o pid -o command | egrep '[f]lash' | cut -d' ' -f1
(OR)
If you have pgrep command,
pgrep 'java'
It will give you the pid.
Related
I wrote a script in R that has several arguments. I want to iterate over 20 directories and execute my script on each while passing in a substring from the file path as my -n argument using sed. I ran the following:
find . -name 'xray_data' -exec sh -c 'Rscript /Users/Caitlin/Desktop/DeMMO_Pubs/DeMMO_NativeRock/DeMMO_NativeRock/R/scipts/dataStitchR.R -f {} -b "{}/SEM_images" -c "{}/../coordinates.txt" -z ".tif" -m ".tif" -a "Unknown|SEM|Os" -d "overview" -y "overview" --overview "overview.*tif" -p FALSE -n "`sed -e 's/.*DeMMO.*[/]\(.*\)_.*[/]xray_data/\1/' "{}"`"' sh {} \;
which results in this error:
ubs/DeMMO_NativeRock/DeMMO_NativeRock/R/scipts/dataStitchR.R -f {} -b "{}/SEM_images" -c "{}/../coordinates.txt" -z ".tif" -m ".tif" -a "Unknown|SEM|Os" -d "overview" -y "overview" --overview "overview.*tif" -p FALSE -n "`sed -e 's/.*DeMMO.*[/]\(.*\)_.*[/]xray_data/\1/' "{}"`"' sh {} \;
sh: command substitution: line 0: syntax error near unexpected token `('
sh: command substitution: line 0: `sed -e s/.*DeMMO.*[/](.*)_.*[/]xray_data/1/ "./DeMMO1/D1T3rep_Dec2019_Ellison/xray_data"'
When I try to use sed with my pattern on an example file path, it works:
echo "./DeMMO1/D1T1exp_Dec2019_Poorman/xray_data" | sed -e 's/.*DeMMO.*[/]\(.*\)_.*[/]xray_data/\1/'
which produces the correct substring:
D1T1exp_Dec2019
I think there's an issue with trying to use single quotes inside the interpreted string but I don't know how to deal with this. I have tried replacing the single quotes around the sed pattern with double quotes as well as removing the single quotes, both result in this error:
sed: RE error: illegal byte sequence
How should I extract the substring from the file path dynamically in this case?
To loop through the output of find.
while IFS= read -ru "$fd" -d '' files; do
echo "$files" ##: do whatever you want to do with the files here.
done {fd}< <(find . -type f -name 'xray_data' -print0)
No embedded commands in quotes.
It uses a random fd just in case something inside the loop is eating/slurping stdin
Also -print0 delimits the files with null bytes, so it should be safe enough to handle spaces tabs and newlines on the path and file names.
A good start is always put an echo in front of every commands you want to do with the files, so you have an idea what's going to be executed/happen just in case...
This is the solution that ultimately worked for me due to issues with quotes in sed:
for dir in `find . -name 'xray_data'`;
do sampleID="`basename $(dirname $dir) | cut -f1 -d'_'`";
Rscript /Users/Caitlin/Desktop/DeMMO_Pubs/DeMMO_NativeRock/DeMMO_NativeRock/R/scipts/dataStitchR.R -f "$dir" -b "$dir/SEM_images" -c "$dir/../coordinates.txt" -z ".tif" -m ".tif" -a "Unknown|SEM|Os" -d "overview" -y "overview" --overview "overview.*tif" -p FALSE -n "$sampleID";
done
I am trying to fetch the number of threads of a process in a UNIX using command line. After going through the man page of unix command, I learnt that following command:
ps -o nlwp <pid>
returns the number of threads spawned in a process.
Whenever i executed above command in unix, it returned:
NLWP
7
Now, I want to neglect NLWP and a space before 7.
That is I am just interested in a value, as I will be using it in a script, that I am writing for unit testing?
Is it possible to fetch only value, and neglect everything(Title NLWP, space)?
You can always use the --no-headers option in ps to get rid of the headers.
In that case, use awk to just print the first value:
ps --no-headers -o nlwp <pid> | awk '{print $1}'
Or tr to remove the spaces:
ps --no-headers -o nlwp <pid> | tr -d ' '
If --no-headers is not supported in your ps version, either of these make it:
ps -o nlwp <pid> | awk 'END {print $1}'
ps -o nlwp <pid> | tail -1 | tr -d' '
I have a directory that has one file with information (call it masterfile.inc) and several files that are empty (call them file1.inc-file20.inc)
I'm trying to formulate an xargs command that copies the contents of masterfile.inc into all of the empty files.
So far I have
ls -ltr | awk '{print $9}' | grep -v masterfile | xargs -I {} cat masterfile.inc > {}
Unfortunately, all this does is creates a file called {} and prints masterfile.inc into it N times.
Is there something I'm missing with the syntax here?
Thanks in advance
You can use this command to copy file 20 times:
$ tee <masterfile.inc >/dev/null file{1..20}.inc
Note: file{1..20}.inc will expand to file1, file2, ... , file20
If you disternation filenames are random:
$ shopt -s extglob
$ tee <masterfile.inc >/dev/null $(ls !(masterfile.inc))
Note: $(ls !(masterfile.inc)) will expand to all file in current directory except masterfile.inc (please don't use spaces in filename)
While the tee trick is really brilliant you might be interested in a solution that is easier to adapt for other situations. Here using GNU Parallel:
ls -ltr | awk '{print $9}' | grep -v masterfile | parallel "cat masterfile.inc > {}"
It takes literally 10 seconds to install GNU Parallel:
wget pi.dk/3 -qO - | sh -x
Watch the intro videos to learn more: https://www.youtube.com/playlist?list=PL284C9FF2488BC6D1
I'm using tcsh, and I'm trying to grep a path from a file with several ID, I'm doing:
grep I241149 $ENV_CASTRO/ALL_CMD_LINES.BAK | grep -o \$"ENV_CASTRO.*.asm"
that gets me:
$ENV_CASTRO/central/WS678/test_do_all.asm
but if I try
cp `grep I241149 $ENV_CASTRO/ALL_CMD_LINES.BAK | grep -o \$"ENV_CASTRO.*.asm"` .
it prompts
cp: cannot stat `$ENV_CASTRO/central/WS678/test_do_all.asm': No such file or directory
How do I tell tcsh that the output of grep contains a $ that means it is an environment variable and is not plain text?
Thanks in advance.
eval is your friend ....
eval cp `grep I241149 $ENV_CASTRO/ALL_CMD_LINES.BAK | grep -o \$"ENV_CASTRO.*.asm"` .
I don't have the time to create files to test this.
I hope this helps.
The problem is that the output of the grep command is not being evaluated by the shell, and so variable substitution is not happening.
One way to solve this would be to execute the desired command within another shell, for example,
sh -c "cp `grep I241149 $ENV_CASTRO/ALL_CMD_LINES.BAK | grep -o '$ENV_CASTRO.*.asm'` ."
i am trying the following command on the command line
ps -u `id | cut -f2 -d"=" | cut -f1 -d"("` -f | grep ppLSN | awk '{print $9}' | awk '{FS="=";print $2}' | grep KLMN | wc -l
the value of teh command is returned as 7.
but when i am putting the same command inside a script abc_sh like below
ps -u `id | cut -f2 -d"=" | cut -f1 -d"("` -f | grep ppLSN | awk '{print $9}' | awk '{FS="=";print $2}' | grep $XYZ | wc -l
and i am calling the script on the command line as abc_sh XYZ=KLMN and it does not work and returns 0
the problem is with the grep in the command grep $XYZ
could anybody please tell why this is not working?
Because your $1 variable (first argument to the script) is set to XYZ=KLMN.
Just use abc_sh KLMN and grep $1 instead of grep $XYZ.
(Assuming we are talking about bash here)
The other alternative is defining a temporary environment variable in which case you would have to call it like this: XYZ=KLMN abc_sh
EDIT:
Found what you were using, you have to use set -k (see SHELL BUILTIN COMMANDS in the BASH manual)
-k All arguments in the form of assignment statements are
placed in the environment for a command, not just those
that precede the command name.
So
vinko#parrot:~$ more abc
#!/bin/bash
echo $XYZ
vinko#parrot:~$ set -k
vinko#parrot:~$ ./abc XYZ=KLMN
KLMN
vinko#parrot:~$ set +k
vinko#parrot:~$ ./abc XYZ=KLMN
vinko#parrot:~$
So, the place where this was working probably has set -k in one of the startup scripts (bashrc or profile.)
Try any of these to set a temporary environment variable:
XYZ=KLMN abc_sh
env XYZ=KLMN abc_sh
(export XYZ=KLMN; abc_sh)
you are using so many commands chained together....
ps -u `id -u` -f | awk -v x="$XYZ" -v p="ppLSN" '$0~p{
m=split($9,a,"=")
if(a[2]~x){count++}
}
END{print count}'
Call this script:
#!/bin/ksh
ps -u $(id -u) -o args | grep $XYZ | cut -f2- -d " "
Like this:
XYZ=KLMN abc_sh