Getting Started


Users must sign up for time first before use. If you do not have an account on a machine, please contact the Facility Manger.

Do not lock the workstation with a password. In such instances the machine will be rebooted by the facility manager, resulting the loss of current data. If the user needs to be away from the console while running jobs interactively, please leave a note close to the workstation.

Crystallography Software

In general, the users could type the program name at the Unix command prompt in order to run the crystallography software. The brief document can be found in the X-Ray Lab Guides. The manual for each programs can be found in the Software List.


Log in SGI Altix, Octane, and O2 and transfer data from PC to SGI computers

1, XCOLLECT computer

a), The Xprocess computer can be accessible from F dive in the folder of ¡°My Computer").

b), The shortcut ¡°putty¡± on Desktop can be used to login in SGI Altix 350, Octane and O2.

Login in SGI Altix 350 (IP address:

Click the shortcut ¡°putty¡± on Desktop, type in Host Name (or IP address), then select ¡°SSH¡± in Protocol. The username and password will be needed to be typed.

Login in SGI Octane (IP address:

Click the shortcut ¡°putty¡± on Desktop, type in Host Name (or IP address), then select ¡°telnet¡± in Protocol. The username and password will be needed to be typed.

Login in SGI O2 (IP address:

Click the shortcut ¡°putty¡± on Desktop, type in Host Name (or IP address), then select ¡°telnet¡± in Protocol. The username and password will be needed to be typed.

c), The shortcut ¡°Core FTP Lite¡± can be used to transfer files from Xcollect computer to SGI Altix 350, Octane and O2.

 Type the IP address, the username, and the password. For SGI Altix, select SSH/SFTP. For SGI Octane and O2, unselect SSH/SFTP.

2, XPROCESS computer

a), The Xcollect computer can be accessible from Y drive in the folder of ¡°My Computer")

b), See the above in order to log in SGI Altix 350, Octane and O2 using the shortcut ¡°putty¡±, to Transfer the files from Xprocess computer to SGI Altix 350, Octane and O2 using the shortcut ¡°Core FTP Lite¡±.

c), The shortcut ¡°altix¡± on Desktop can be used to log in SGI Altix and open an X-window.  

3, SGI Altix

SGI octane has been cross-mounted with two directories (/zerg and /ork)

SGI O2 has also cross-mounted with the directory ( /biochem)

Also telnet to access SGI Octane; telnet to access SGI O2.

4, SGI Octane

SGI Altix has been cross-mounted with the directory (/modeling)

5, SGI O2

SGI Altix has been cross-mounted with the directory (/modeling).

SGI octane has been cross-mounted with two directories (/zerg and /ork).

The '.cshrc' file has already been set up with default options. One of the functions of the `.cshrc' file is to set your Unix environment variables to default values. These variables are used by lots of programs on the system to define certain default operations.

The setup file for all the crystallographic packages is xtal.setup. In SGI Octane, it is located in /ork/crys/xtal.setp. In SGI Altix 350, it is in the /opt/xtal.setup. In your .cshrc file, type "source /ork/crys/xtal/xtal.setup" or "source /opt/xtal.setup". After you login, all the crystallographic program will be set up correctly.

#: The ``#'' character at the beginning of a line tells the C shell to ignore the rest of the line.

Alias: define your own time-saving shortcuts. In order to create an alias which will run a program not in your path, you need to know the full absolute path name of that command. Add a line saying: alias commandname  /full/absolute/path/of/program

Set: set local variables.

Set path shell variable: set path=(directory1 directory2 ...)

This tells the shell to look in the directories directory1, directory2, ... when trying to execute a command. A common path may look like `set path=(/usr/bin /usr/local/bin )'.

Setenv: set environmental variables -- "global" variables that are passed on to any programs you run.

Source: Execute the recommended site specific startup file
source /path/to/cns_1.1/cns_solve_env
source .cshrc. ( activating the new .cshrc changes)

limit coredumpsize 0: Don't create core dump files when a program blows up.

umask xxx

This sets your file creation mask to xxx where xxx is a 3 digit hex number specifying which permissions are to be turned off when you create files and directories. Here are some typical settings:

umask 077:
Doesn't allow anyone but yourself to read, write and execute files that you create.

umask 022:
Allows people in your current group and others to read and executes files that you create.

umask 027:
Allows people in your current group to read and executes files that you create, but people not in your group can not read or execute them.


Move to the directory


"cp -r" copies a directory and follows symbolic links. If there is a link to a file in the source directory, an actual copy of the file is placed in the target directory.


df tells you how much disk space is free and used on a disk, in 512-byte blocks. Usually we use "df -k" which gives free space in kilobytes.   


du gives the space used by files and/or directories. The most useful form of this command is probably: du -sk *. The option "k" gives the sizes in kilobytes instead of half-kilobytes. The "s" option tells du to give, for directories, the total size of all the files inside the directory. The asterisk, as usual, matches all files and directories, so if you run this command in your home directory you'll get the sizes of all files and directories in your home directory.   


A typical useful example of this command is to save disk space by compressing all stray uncompressed diffraction images in the current directory and all its subdirectories:                           find . -name "*.img" -exec bzip {} \


Grep searches for lines containing a particular string. For example, to print all lines in the file "minimize.pdb" that contains the word "Rfree": grep Rfree minimize.pdb


Create the directory

man command

Use this to find out what the different command options are.


Remove your temporary directory.


This command prints something on the screen and writes it to a file. It overwrites the file unless you use the "-a" (append) option: echo "This is a message for the log file but it should also be printed on screen." | tee -a log file". If you use the -v option, grep prints lines which do NOT contain the specified text. You can also do very complicated pattern matching; see the man page for information.

 2. Vi command

vi name                 edit file

vi +n name            edit file at line n

vi + name             edit file at the end

File manipulation

:w                         write back changes

:wq                       write and quit

:q                         quit

:q!                        quit and discard changes

:e!                        reedit, discard changes

:w name                write file name

:w! name              overwrite file name


u                         undo last change

<esc>                   abandon incomplete command


i                           before cursor

a                          after cursor

A                         after line

o                          open line below

O                         open line above


x                          delete character under cursor

X                         delete character before cursor

dw                       word

dd                       line

#dd                      # lines

Emacs is a very powerful text editor. Run the emacs at your Unix prompt.

Getting in and out

  • Start emacs: emacs or emacs file
  • Visit/find a file: ^X^V or ^X^F
  • Insert another file: ^X i
  • Write a file: ^X^W
  • Save a file: ^X^S
  • Suspend emacs: ^Z
  • Exit emacs: ^X^C

Moving around

  • forward 1 character: ^F
  • back 1 character: ^B
  • forward 1 word: ESC F
  • back 1 word: ESC B
  • previous line: ^P
  • next line: ^N
  • beginning of line: ^A
  • end of line: ^E
  • beginning of sentence: ESC A
  • end of sentence: ESC E
  • forward 1 screen: ^V
  • back one screen: ESC V
  • beginning of document: ESC <
  • end of document: ESC >


  • Search (incrementally, forward): ^S
  • Reverse-search (back): ^R
  • to stop searching: ESC


  • Delete previous char.: Delete-key
  • Delete next char.: ^-D
  • Delete previous word: ESC Delete-key
  • Delete next word: ESC D
  • Kill to end of line: ^K
  • Kill to end of sent.: ESC K
  • Transpose 2 chars.: ^T
  • Transpose 2 words: ESC T
  • Set mark: ^-spacebar or: ^-@
  • Exchange point and mark: ^X^X
  • Kill region (cut): ^W
  • Copy region (copy): ESC W
  • Yank (paste): ^Y
  • Capitalize word: ESC C
  • Uppercase word: ESC U
  • Lowercase word: ESC L


  • Enterfoo mode: ESC xfoo
  • Set fill column: ^X f
  • Fill paragraph: ESC Q
  • Fill region: ESC G


Run batch jobs on SGI Altix 350

A batch queuing system called TORQUE is available to run the batch jobs. To submit a job a user creates a batch script, which contains the job¡¯s requirements, and then submits the job to the queue. The user can then monitor the job as it progresses.

1, Command:

qsub              Submitting jobs (qsub test.pbs)

qdel               Canceling jobs (qdel job_id), job_id can be obtained from the queue listing using   qstat

qstat              Monitoring and checking the status of jobs. "qstat -u userID" (login name) qstat -s (displays status and elapsed time of job)

2, How to submit jobs

The qsub command is used to submit a job to the queuing system. qsub takes a job  submission script that contains the commands necessary to run your job.

Use qsub to submit a PBS job: qsub script

3, Example (-l )

-l mem=50mb,ncpus=2,walltime=3:00:00

The job will use at most 50 megabytes of memory (mem), 2 processors (ncpus) and will take at most 3 hours (walltime) to execute.

To ask for 4 processors on one node: -l ncpus=4

> qsub -l mem=200mb /home/user/

This job requests a node with 200 MB of available memory.

> qsub -l ncpus=2,walltime=12:00:00

This job will use two processors and request 12 hours to run.