UNIX recipes
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
top
list logged on users, and what they are doing
w
shows processes
ps
list open files, by process
lsof
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
SSH
How to generate public key
ssh-keygen -f dsa
How to display variables for sshagent
ssh-agent
How to create a passphrase
ssh-add
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
