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The BIMCORE Molecular Modelling computers are Silcon Graphics workstations that have UNIX as the operating system. Though many of the programs you might are graphic in nature, it is still quite necessary for you to know some UNIX commands. This page will provide you with the answers to many of the basic questions which you have.
Accounts are available to those Emory affiliates with an interest in Molecular Modelling. Please contact Kim Gernert about getting an id on these systems.
Here is a table with the most frequently used UNIX commands. It is by no means comprehensive or exhaustive. Still it provides you with the basic navigational commands required to get around. Other questions in this FAQ deal with some of these commands in finer detail. For a more in depth on line tutorial, refer to UNIX Intro. This is a very detailed document and will provide you with complete background on how to navigate the UNIX filesystem.
| Command | Purpose | Example |
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| cp | Copy a File | % cp test.dat new.dat (Creates a file
ca lled "new.dat") % cp test.dat /var/tmp (Copies "test.dat" to the directory "/var/tmp") |
| cd | Change Directories | % cd group (Changes to the directory "group") % cd ~ (Changes to your home/default directory) % cd /var/tmp (Changes working directory to /var/tmp/) |
| pwd | Prints The Current Directory | % pwd (Shows your current directory) |
| man | Get Info On A UNIX Commmand | % man ls (Shows the manual page for "ls") |
| ls | List The Directory Contents | % ls (Lists all files in dire
ctory "group") % ls *.dat (Lists all files ending with "dat") % ls f* (Lists all files beginning with "f" % ls -l file.dat (Lists detailed attributes of the file "file.dat" ) |
| lp | Print A File | % lp -d file.out pick (prints the file "file.out" to the printer "pick") |
| ftp | Initiate A File Transfer | % ftp bimcore.emory.edu (connects to the host "bimcore.emory.edu" for file transfers) |
| telnet | Login To Another Host | % telnet bimcore.emory.edu (connects to the host "bimcore.emory.edu" for remote logins) |
| pico | Invoke The Editor | % pico test.input (invokes the editor on the file "test.input") |
| more | Inspect The Contents Of A File | % more test.input (lists the contents of the file "test.input" a page at a time) |
| head | Shows First 10 Lines Of A File | % head test.input (lists first 10 lines of the file "test.input") |
| passwd | Change UNIX Password | % passwd (prompts you for a new password) |
You have been given an account on the Molecular Modelling Silicon Graphics computers located in G239. (You may also be given an account on the BIMCORE system at some point in the near future). These accounts are to be used in conjunction with lab assignments. As mentioned, these are UNIX accounts. See other areas of this document to learn some basics of getting around.
One important aspect of your account is the existence group directory contained in your account. This is where your instructor(s) would place important information relevant to lab assignments. So for example, once you log in to your account:
login: mwind Password: IRIX Release 6.2 IP28 doc Copyright 1987-1996 Silicon Graphics, Inc. All Rights Reserved. Last login: Tue Jan 19 13:44:41 EST 1999 on :0 doc 1% pwd /snowwhite/disk2/people/mwind doc 2% ls -l total 2 drwxr-xr-x 3 mwind gmb790 512 Jan 19 13:44 dumpster lrwxr-xr-x 1 root sys 18 Jan 19 12:54 group -> /sw3/groups/gmb790 drwxr-xr-x 2 mwind gmb790 512 Jan 19 12:52 xtal_info doc 3% doc 3% pwd /snowwhite/disk3/groups/gmb790 doc 4% cd rhmap doc 5% ls readme.doc rh2pt.out rhmax1.dat rhmax2.out rhmaxlik rh2pt rhdoc.ps rhmax1.out rhmax3.dat rhminbrk rh2pt.dat rhdoc.txt rhmax2.dat rhmax3.out rhminbrk.dat doc 6% cd ~ (The "~" charcter returns you to your home directory) doc 7% pwd /snowwhite/disk2/people/mwind doc 8%
So from this example you can see there is some information relating to the RHMAP program. Also, you can see the cd command (change directories) in use. Additionally the pwd command tells you what directory you are currently in and the ls command gives you a listing of the directory contents.
Log in to your account (see next question). Prepare your input data file using an editor such as "pico" (see question editing). Then, depending on which of the programs you wish to use :
rhmap , rhmaxlik, rhminbrk
proceed accordingly. For example,doc % rh2pt rhmap.input ********************************************* ************* PROGRAM RH2PT ************* ********************************************* ************** VERSION 3.00 ************** ********************************************* ************* SEPTEMBER 1996 ************* ********************************************* * BY ELIZABETH HAUSER AND MICHAEL BOEHNKE * ********************************************* INPUT FILE NAME: rhmap.input ( you type this ) OUTPUT FILE NAME: rhmap.out ( you type this )
If you are physically present in the MM lab, you can simply type your userid
and password at the login panel on any of the SGIs. This would be necessary
,in most cases, if you are wishing to use graphics software such as Sybyl.
Another alternative is to login remotely using a program like "NCSA telnet"
on the Macinstosh or "telnet" on a Windows machine. The following hostnames
can be used when telnetting to the MM machines:
grumpy.bimcore.emory.edu bashful.bimcore.emory.edu sleepy.bimcore.emory.edu dopey.bimcore.emory.edu doc.bimcore.emory.edu
For example if you wish to telnet in from a Macintosh using the program NCSA
telnet
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You should then see a screen resembling the folowing:
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Now here is an exmaple showing a telnet example from the dooley/eagle cluster
/home/wsp $ telnet doc.bimcore.emory.edu Trying 170.140.48.204... Connected to doc.bimcore.emory.edu. Escape character is '^]'. IRIX (doc) login: wsp Password: IRIX Release 6.2 IP28 doc Copyright 1987-1996 Silicon Graphics, Inc. All Rights Reserved. Last login: Mon Jan 18 20:59:42 EST 1999 by wsp@catalina.bimcore.emory.edu doc%
There is an SGI program called "jot" which will allow you to create and edit files for use with any of the Molecular modelling programs. To invoke this program, simply enter the word "jot" at your command prompt. You will then see an editing window wherein you may enter text. The jot program is SGI specific so if you are not able to use an SGI workstation the you will have to use another editor such as pico or vi.
If you need to login remotely, then you can use the program "pico"
to create and edit existing files. To invoke "pico", simply type "pico" at
your command prompt. If you wish to edit an existing file, then specify the
filename on the command line. For example,
doc% pico file.dat
In general, pico is one of the simplest UNIX editors to learn. All functions are accessible using control keys in combination with other keys. These functions are documented at the bottom of the pico screen:
From the graphic you can see that to write out the contents of the file you can press the control key along with the "o" key and you will be prompted to enter a filename. Check the PICO guide for a printable PICO cheat sheet. Important key sequences include:
CTRL-X (Exit the pico editor)
CTRL-G (Displays the pico HELP menu)
CTRL-W (Searches for a particular string of text within the file)
CTRL-K (Deletes a line of text)
CTRL-T (Does a spell check on the file)
The UNIX command that you need to learn about is "cp". So, for example,
you can issue a command such as:
doc% cp file.dat newfile.dat
to copy the file "file.dat" to "newfile.dat". In general this all you need to know though part of your work may involve copying files from a another "directory" in which case you need to specify a "pathname". For example:
doc% cp /sw3/groups/gmb790/file.dat file.dat
Will copy the file "file.dat" from the directory /sw3/groups/gmb790/file.dat to your currect working directory (sometimes known as "path")
Printing to shovel is not free ! If you need to print to this printer then please discuss this with Kim Gernert
The lp command is used to print documents to the MM printer pick.
doc% lp -d pick file.datIt is also possible to transfer (see the question on ftp) the files you want to print over to your dooley or learnlink account or even to a Mac or PC in your area. From there you can print to whatever printers are available.
If you are using a Macintosh, you can use a program called "Fetch" to transfer files to and from the MM SGIS as well as the BIMCORE server. Here is an example:
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You will then see a screen resembling the following:
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You will then see a screen like:
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Here is an example of using FTP between the dooley/eagle cluster and the BIMCORE hosts
The command you need to learn about is ftp. So, for example, let's
assume that you want to transfer a file called "test.dat" from your
SGI account to your dooley account. While logged into your SGI account, here
is how the process might look:
dopey% ftp dooley.cc.emory.edu
Connected to timeshare.service.emory.edu.
220 curly FTP server (SunOS 5.6) ready.
Name (dooley.cc.emory.edu:wsp): wsp
331 Password required for wsp.
Password:
230 User wsp logged in.
Remote system type is UNIX.
Using binary mode to transfer files.
ftp> put test.dat
local: test.dat remote: test.dat
200 PORT command successful.
150 Binary data connection for test.dat (170.140.48.209,8450).
226 Transfer complete.
26 bytes sent in 0.00 seconds (60.74 Kbytes/s)
ftp> quit
dooley account. After the transfer , you type "quit" to terminate the ftp program. If you had wanted to transfer a file from the dooley account over to your SGI account you would have used the "get" command while in ftp. This retrieves the file you specified.
It is also possible to transfer files from your SGI account to a Macintosh computer using the fetch program. You can use fetch to connect with any other machine names indicated above. You will log in with your account information and then specify the name of the file you wish to "fetch" from the SGI.
The short answer is no. Basically, these systems are setup for special purposes and while we do have e-mail capability and in some cases use it, we won't guarantee e-mail delivery to and from these machines. The Dooley/Eagle cluster and Learnlink systems provide 24 X 7 e-mail support. All Emory affiliates are eligible for free accounts on one or both of these systems. Please call (404) 727-7777 for more information. If you have a BIMCORE id then you may use that for reliable e-mail also.
Issue the following command: du -sk .
You will see results resembling the following:
156723 /sw5/people/testid
The number is a the total number of kilobytes in use within the current directory. Divide this number by 1,000 to get a measurement in megabytes. So in this example the directory "testid" is using 156 Megabytes of data.
It depends. You have two choices. 4mm tape and ZIP disks. The capacity of the 4mm tapes is 4 Gigbabytes which is much more than the capacity of ZIP drives which is 100 MB. However the ZIP drive is more universal that 4mm drives. If you are simply interested in backing up several data files then you can FTP your SGI files over to a machine which has a ZIP drive. Thats it. You are done. But if you have a large directory structure that you are trying to preserve and you will be using it on another UNIX machine at some point then you should consider the 4mm option. To sum it all up:
Use a ZIP disk if:
Use a 4mm tape if:
A. You may back up your files to 4mm tape. In general , you should employ this option if you have over several hundred megabytes of data as anything less is a waste of tape media since a 4mm tape can hold up to 4 gigabytes of data. For smaller amounts of data you can FTP files down to a ZIP drive on a PC or Mac. Also keep in mind that the backup format is in tar format which is a well known UNIX format. Here is an example. Lets say that you userid is testid and you want to backup your entire home directory.
You will see something similar to the following:
a ./testid/.zmailrc 1 block a ./testid/Logos/blade1.ps 61 blocks a ./testid/Logos/blade2.ps 56 blocks a ./testid/Logos/blade3.ps 57 blocks a ./testid/Logos/blade4.ps 60 blocks a ./testid/Logos/blade5.ps 66 blocks a ./testid/Logos/blade6.ps 57 blocks a ./testid/Modeller/IC140/GLE/1gp2.pdb 295 blocks a ./testid/Modeller/IC140/GLE/5homol.log01 451 blocks a ./testid/Modeller/IC140/GLE/5homol.top 2 blocks a ./testid/Modeller/IC140/GLE/Solution1/1gp2.pdb 295 blocks a ./testid/Modeller/IC140/GLE/Solution1/1gp2_2.pdb 295 blocks a ./testid/Modeller/IC140/GLE/Solution1/1gp3.pdb 308 blockssneezey
It is possible to backup more than one directory onto tape. That is one can place several sets of files onto the tape. For example , lets say that you wanted to place three directories onto tape. They are called Sybyl_Dir, Modeller_Dir, and Dock_Dir (this example assumes that these directories are contained within your home directory). Follow the steps indicated above though you will be entering a variation of the tar command.
The program will behave in the same way as indicated in the previous example. It is also possible to stack individual tar files onto the tape one after another. So one can place , for example, related user directoies onto the tape one after another in different sessions. This would address the case where you have made a tar file of a single userid to tape and then maybe three weeks later you want to add another userid to the tape without overwriting the existing contents of the tape. This requires some knowledge of UNIX tape positioning commands (like mt). See Steve if you need to do this. Right now this case is a bit beyond the scope of this FAQ.
You can use the tar command to inspect the contents of a tape Lets say that your userid is testid. Go to either doc or bashful and insert the tape into the 4mm drive.
You should see something resembling:
rw-r--r-- 1127/1101 632 Jun 2 15:00 1998 ./testid/.login rw-r--r-- 1127/1101 660 Sep 27 22:54 1998 ./testid/.mailcap rw-r--r-- 1127/1101 766 Aug 5 17:48 1998 ./testid/.mailcap.bak rw-r--r-- 1127/1101 291 Aug 4 16:51 1998 ./testid/.mime.types rw-r--r-- 1127/1101 6396 Jun 18 16:15 1998 ./testid/.pine-debug1 rw-r--r-- 1127/1101 10326 Jun 18 16:15 1998 ./testid/.pinerc rw-r--r-- 1127/1101 767 Jun 2 15:00 1998 ./testid/.profile rw-r--r-- 1127/1101 319 Jul 29 12:31 1998 ./testid/.zmailrc rw-r--r-- 1127/1101 30756 Aug 3 11:31 1998 ./testid/Logos/blade1.ps rw-r--r-- 1127/1101 28396 Aug 3 11:25 1998 ./testid/Logos/blade2.ps rw-r--r-- 1127/1101 29148 Aug 3 11:37 1998 ./testid/Logos/blade3.ps rw-r--r-- 1127/1101 30604 Aug 3 11:41 1998 ./testid/Logos/blade4.ps
This is a variation on the previous question. Go to doc or bashful and insert the tape into the 4mm drive.
For example , if you want to restore the contents of the tape as a sub directory of your home directory then make sure you are in your home directory. Another common approach is to change directories to the /var/tmp directory. This is a standard directory on every UNIX machine where you can create and manipulate files on a temporary basis.
You should see something resembling the following:
x ./wtmp.solaris, 1939 bytes, 4 tape blocks x ./wtmp_dis.c, 1337 bytes, 3 tape blocks x ./S94., 360 bytes, 1 tape blocks x ./pac_dis.c, 1471 bytes, 3 tape blocks x ./wtmp.sunos, 2049 bytes, 5 tape blocks x ./summary.console, 622 bytes, 2 tape blocks x ./summary.vn, 636 bytes, 2 tape blocks x ./summary_b.console, 617 bytes, 2 tape blocks x ./summary_b.vn, 657 bytes, 2 tape blocks x ./fixvn.nis, 818 bytes, 2 tape blocks x ./fixvn.flat, 342 bytes, 1 tape blocks
The typical 4mm tape holds about 4 Gigabytes worth of data which is considerable. However if you determine (e.g. using the du -sk command) that you have close to 4 Gigabytes of data or even more then you can specify the compressed tape device when using the tar command to backup data. The format and usage of the tar command is the same regardless though you specify the compressed device which is /dev/rmt/tps0d2c. Please note that this device specification is unique to the SGI systems. So using tar to backup your home directory to the compressed device:
tar -cvf /dev/rmt/tps0d2c ./homedir
Insert the 4mm tape into the drive. Now you will use the mt command to forward the position of the tape right after the end of the existing tar archive on the tape.
% mt -f /dev/nrtape fsf 1
It is essential that you specify the device /dev/nrtape. This will forward the tape to the end of the first TAR archive. At this point you can use the tar command to archive more data to tape. Keep in mind that if you do use the tar command and you specify the "rewindable" device /dev/tape then the tape will rewind after you have completed the tar. This isn't necessarily bad but should you wish to append yet more data then you would have to use the mt command once again to forward past the end of the second archive:
% mt -f /dev/nrtape fsf 2
First insert the tape into the drive and then use the mt command to position the tape after the first two tar archives. Make sure to use the non-rewinding device.
% mt -f /dev/nrtape fsf 2 % tar -xvf /dev/tape (to read the tape)
There are two C compilers available for use. The first is the GNU C compiler named gcc. The second is the Silicon Graphics compiler called cc. In general you should use gcc to compile your programs as it is the simplest to use. Currently gcc is available only on snowwhite.
To use gcc simply type
% gcc file.c
If you are using a Makefile to compile a set of programs then edit
the Makefile to reflect the correct compliler. For example it is
typical for a Makefile to contain a line like:
CC=/bin/ccChange the line to read:
CC=/usr/local/bin/gcc
If you have started a process that you didn't mean to or you determine that one of your processes has been running for too long then you have the ability to terminate this job using the UNIX command kill. Please note that you can only terminate jobs that you have initiated. That is you cannot terminate jobs started by others. First use the ps command to see what jobs you have running on the system:
% ps -fu userid (Note: where "userid" is your userid)
UID PID PPID C STIME TTY TIME CMD
userid 33371 33418 0 15:43:40 pts/0 0:01 -csh
userid 20683 1 0 May 31 ? 5709:47 /sw5/SYBYL6.5/bin/sybyl.exe
userid 18208 1 0 May 30 ? 6389:46 /sw5/SYBYL6.5/bin/sybyl.exe
Find the PID associated with the process you would like to terminate. So for example in the above example assume that you wish to terminate the first instance of sybyl.exe which corresponds to PID number 20683. So issue the kill command as follows:
% kill 20684
Re-issue the "ps" command again to make sure the process has ended.
% ps -fu userid
UID PID PPID C STIME TTY TIME CMD
userid 33371 33418 0 15:43:40 pts/0 0:01 -csh
userid 18208 1 0 May 30 ? 6389:46 /sw5/SYBYL6.5/bin/sybyl.exe
If the job persists (i.e. it still shows up in the process list) then re-issue the kill
command using the "-9" option.
% kill -9 20684
From time to time the monitor on an SGI will go blank leaving one with the impression that the monitor or the SGI itself is dead. As of the writing of this (6/00) it seems to be happening with greater frequency on grumpy and bashful. Should you encounter this situation inform Steve Pittard, Kim Gernet, or Bill Thiel and they should be able to execute the following procedure to revive the SGI
From another SGI telnet into the ailing machine (e.g. grumpy). Login as your normal id (e.g. gernert). Then use the "ps" command to determine the PID of the SGI X Window Manager (aka "XSgi")
% ps -ef | grep -i Xsgi
root 54104 54135 0 17:07:46 pts/7 0:00 grep -i Xsgi
root 683 677 0 May 19 ? 19:58 /usr/bin/X11/Xsgi -bs -n
obitscale -c -pseudomap 4sight -solidroot sgilightblue
In this case the PID is 683. Make sure you select the number form the leftmost
column. Okay. now you can do this:
grumpy % sudo kill -HUP 683
(and you will see something like)
We trust you have received the usual lecture from the local System
Administrator. It usually boils down to these two things:
#1) Respect the privacy of others.
#2) Think before you type.
Password:
Upon entry of your password the kill command which would normally
have required root privileges will now be executed courtesy of the
sudo program. If the window manager was the culrpit then in about
10 seconds the Window manager on the afflicted machine (in this case grumpy)
will restart.
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