UNIX tutorial

Admin

Informations

• Publié par: Siom
• Nombre de lectures: 23
• Langue: English

Extrait

UNIX tutorial

UNIX is a an operating system, like Windows or MacOS.

The flavors of UNIX we use are IRIX

(by Silicon Graphics, Inc or “SGI”) and Linux.

Our computers

SGI workstations (1 processor each): algonquin, colden, nye, panther, street

Linux workstations (1 processor each): blake, dial, eastdix, emmons, porter

Supercomputers (32 processors each, both SGI):

Marcy (owned by Hamilton College)

Olympus (shared with 6 other schools in MERCURY consortium)

Server computers (all SGI)

(small queue of Marcy, 4 processors each): giant, gothics, haystack, skylight, whiteface

(small queue of Olympus, 8 processors): Vesuvius

Notes on working with SGI computers:

1.

You have to have your mouse inside the window you want to type in.

2.

To call a window to the foreground, click on its title bar.

How to use UNIX:

0.

Log out the previous user (after asking him or her, of course) if necessary

a.

On SGI, in the toolchest, select Desktop>Logout.

b.

On Linux, select Logout from the red hat menu in the bottom left corner.

1.

Log in.

Enter your username and password.

Don’t be alarmed if you can’t see your

password as you type it.

2.

Open a UNIX shell

a.

On SGI, in the toolchest, select Desktop>Open Unix Shell

b.

On Linux, right click-hold and then select Open Terminal from the menu

that appears.

General UNIX/Linux command line entries

whoami

reveals username of current user

hostname

reveals computer you are using

pwd

print working directory

Note that the first three of these are usually redundant, as they appear before every command

line.

cat

file

con

cat

enate: displays the contents of a

file

within the UNIX shell

cd

c

hange

d

irectory: the command cd directory will open a subdirectory of the

current directory; typing “cd ~” will return you to your home directory

(/home/hamilton/pchem); “cd ..” will move you up one directory (from /

home/hamilton/pchem to /home/hamilton).

cp

file1

file2

takes

file1

, which exists, and

c

o

p

ies the contents into a new file called

file2

.

As

written, this command will put file2 in the same directory as file1. [see also mv]

exit

exits a computer or user, depending on context (synonymous with logout)

head –50 file

shows the first 50 lines of file within the UNIX shell

tail –20 file

(you can probably guess what this does; note you get to pick the number of lines

to show, or you can omit the –

n

argument and accept a default amount)

kill 3214

kills the process whose PID number is 3214 [see also top]

ls

l

i

s

ts the contents of a directory

lp

print command

grep

string

file

search a

file

for the specified

string

of characters.

For example, the command

“grep energy gausian.log” will search the file gaussian.log for the word energy,

and then display every line in the file which contains the word energy.

Useful

for finding a needle in a haystack (if you know what the needle looks like).

man

man

ual pages (e.g., to find out more about ls, type “man ls” into a UNIX shell)

mkdir

bruno

m

a

k

es a

dir

ectory called

bruno

(directory and file names aer case sensitive)

more

file

shows contents of

file

one screen at a time

mv

renames files or

m

o

v

es them among directories

e.g., mv file1 file2 renames file1 (which exists) as file2 (which does not exist)

e.g., mv file1 /home/hamilton2/tevans/file1 takes file1 out of wherever it is and

puts it in my home directory.

Note that I could change the name of file1 if I

wanted; by default the name remains the same.

rlogin

host

r

emote

login

to a different

host

(computer), e.g. rlogin olympus

rm

file

r

e

m

oves

file

(USE WITH CAUTION: ONCE IT’S GONE THERE’S NO

GETTING IT BACK).

If you should happen to learn any shortcuts that remove

more than one file at once, MAKE SURE YOU KNOW WHAT YOU’RE

DOING.

rmdir

r

e

m

oves empty

dir

ectories, rmdir will not delete directories which are not

empty

top

gives information about how much of a computer is being used and what it’s

doing

ftp

host

“file transfer protocol” logs into the specified

host

, using an ftp shell, as the

name implies, this is a useful command for transferring files via the command

line

get

file

An ftp command used to copy a

file

from a remote location, and copy it to the

local machine.

The Queuing System

Marcy and Olympus have queuing systems to optimize and organize computer resources.

The queues are…

(for Marcy)

large_queue

These jobs run on Marcy itself

small_queue

These jobs are delegated to Giant, Gothics, Haystack, Skylight,

or Whiteface based on availability (you don’t get to pick).

(for Olympus)

large_queue

These jobs run on Olympus itself

small_queue

These jobs are delegated to Vesuvius.

Hence, you only submit jobs to Marcy or Olympus, but these jobs may be delegated to smaller

computers.

To submit a job to Marcy or Olympus, you need use a

.run

(“dot-run”) file, which

tells the queuing program what computer resources you need, what job you want to run and

which program you want to use on your job.

An example run file is given below.

#PBS -N testjob

#PBS -l ncpus=4

#PBS -l mem=1GB

#PBS -q large_queue

#PBS -M [e-mail]

#PBS -m bea

#PBS -j oe

cd /home/hamilton/pchem/jobs

g03 home/hamilton/pchem/jobs/testjob.com

Here is an explanation of what each line does:

#PBS -N testjob

Name of the job. If omitted, uses filename.

#PBS -l ncpus=4

Number of CPUs to be used for the job.

#PBS -l mem=1GB

Amount of memory, in MB or GB, to be used.

#PBS -q large_queue

Name of the queue to run job under.

#PBS -M [e-mail]

Your email address.

#PBS -m bea

Email you when job

b

egins,

e

nds and

a

borts.

#PBS -j oe

 

Merge PBS output and error files.

Note:

This section is “blank line terminated” – you must have an empty

line between here and the next part.

cd /home/hamilton/pchem/jobs

Opens the directory that the input file is in

g03 home/hamilton/pchem/jobs/testjob.com

Command line option: runs the program g03 on the specified command file (testjob.com).

Note that you will probably have to change the “g03” part if you want to run Amber

instead of Gaussian 03.

Note: That you must have an empty line at the bottom of the

.run

file.

It is usually easier to modify a run file that has already been created than to make one from

scratch.

You may copy a generic run file from me by using the following command (suppose

you’re Kate Schirmer and you want to put this in your directory):

cp /home/hamilton2/tevans/run /home/hamilton/pchem/schirmer/

I’ve also put this file in the pchem home directory, but there it can be adulterated by other pchem

users.

Kate could also get this .run file from anywhere in the pchem directory with

cp ~/run ~/schirmer/

Some people find it useful to keep file names analogous (i.e., the run file for filename.com

would be filename.run).

Since some people are working in groups, if you both want e-mail notification of your jobs, you

can add an extra line, e.g.,

#PBS -N testjob

#PBS -l ncpus=4

#PBS -l mem=1GB

#PBS -q large_queue

#PBS -M 

[e-mail]

#PBS –M [e-mail]

#PBS -m bea

#PBS -j oe

Submitting your job

Say your

.run

file is called run and is in the directory /home/hamilton/pchem/schirmer/

Then the following can be used to submit your job to Marcy:

rlogin marcy

cd schirmer

qsub run

Then you can check on the status of your job by typing

qstat –a

Make sure you are logged into the machine you submitted your job to when typing qstat.

Note: R=running, Q=queued, E=error .

Talk to a Professor if

your job has an ‘E’ next to it.

You may kill jobs by looking at the job id number in the lefthand column of the qstat printout

(say it’s 5544) and then typing

qdel 5544

Note that users normally can only kill their own jobs, however since you all share the same user

account you can all (accidently) delete each others jobs.

Be careful with the qdel command!

Editing files

To edit a text

file

issue the following command:

nedit

file

&

This command will open

file

in a text editor called nedit.

Once you get into nedit you should

feel pretty comfortable.

If you exclude the filename, nedit will open to a blank document.

The

ampersand “&” at the end of the command instructs the computer to execute the command in the

background so that you may use the UNIX shell at the same time.

Force Quit Command:

From anywhere in a UNIX shell, no matter what mess you get yourself into, if you hit <ctrl-c>

the computer will stop what it’s doing and give you a fresh command line (quitting any

processes that are running but not in the background).

Be courteous and logout when you are done.