UNIX recipes

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Armand's unix memo


Disc checks

How to find which partition is which ?

sudo fdisk -l /dev/hda

How to check a disk

sudo fsck /dev/sda1

How to find the bad blocks

sudo badblocks /dev/sda1

How to reformat a disc ignoring bad blocks

sudo mke2fs -c /dev/sda1

R tricks

R locale setting for Mac OS X

To enforce US-english setting regardless of the system setting :

system("defaults write org.R-project.R force.LANG en_US.UTF-8")

Note that you must always use .UTF-8 version of the locale, otherwise R.app will not work properly..

System monitoring

list processes


list logged on users, and what they are doing


shows processes


list open files, by process


info about processors

cat /proc/cpuinfo

nb of processor on system

grep -ic ^processor /proc/cpuinfo

Running scripts

How to execute a given command for many different parameters stored in a file

cat paramList.txt | xargs mycommand


How to generate public key

ssh-keygen -f dsa

How to display variables for sshagent


How to create a passphrase


How to authorize ssh connection to a remote machine using the generated key

cat .ssh/id_dsa.pub | ssh machine_name "cat - >> .ssh/authorized_keys"

File manipulation

How to print a section of a file

awk 'NR >= mystart && NR <= myend' myfile

How to count #of columns per line

awk '{ print NF }' myfile

Print a given column (i.e. 2nd one)

awk '{ print $2 }' myfile
cut -f2 myfile

Pasting 2 files together by their columns

paste file1 file2

Joining 2 files by a common column (ie 1st column of file1 contains some common identifiers than the 3rd column of file2)

join -1 1 -2 3 file1 file2

Sorting numerically a file by its 3rd column

sort -n +2 myfile

Sorting numerically a file by its 2nd column then 1st and then 3rd

sort -n -k 2,1,3 myfile

Splitting a file into smaller files with a fixed number of lines (i.e. 100)

split -l 100 myfile

Remove 10 first line of a file

sed '1,10d' myfile

Checking file type :

file myfile

Converting dos "end-like" file to unix

 perl -p -e 's/\r$//' < myfile > mynewfile

Checking ascii content of a file :

od -c myfile | more

Intersect 2 files

comm -12 a b

Substraction (lines unique to a)

comm -23 a b

Symmetric difference

comm -2 a b