This section contains general information on commonly asked questions; how do I...?, where do I....?, etc. There is also an extensive set of CICS documentation, including Windows help and basic command-line Unix help - some of these documents are PDFs, requiring the Acrobat Reader.

Rules

Software Available

Application Software on Unix
Compilers on Unix
Windows software

Using the Scanner/Backup PC in H10a

How do I log on?

How do I use the scanner?

How do I back up data?

Can I add some software to this machine?

Handy Shortcuts

How do I find files by name?
How do I find files by size?
How do I do an operation on files I've found with find?
How do I know if a file is being used by another process?
How do I keep my computer safe from viruses, etc?
What's the best way of destroying my computer?

Email

The recommended email approach for roaming users
How do I read/send email on the AM Unix system?
What's the difference between ap1ips@ and I.Staniforth@?
How do I get my email sent to the AM Unix machines?
I've received a uuencoded message - how can I decode it?
Why should I save my mail in my home directory?
I want to send/receive some large (> 1Mb) files.
How do I create folders/mailboxes in CDE Mailtool?
How do I reduce the amount of junk/spam email I get?

Moving data around

How do I copy files from one machine to another?
Do I really have to keep typing in my password every time I want to connect?
How do I transfer data using FTP?
How do I make my data accessible to an external person with FTP?
How do I let an external person transfer data to/from Sheffield?
What SSH (secure shell) facilities are there here?
How can I move files between machines without ftp?
The British Library document supply service

Shells

What shells are available?
How do I know what shell I'm in?
How do I change shells temporarily on a particular machine?
How do I change shells permanently on a particular machine?
How do I set up shortcut commands, or alias commands?
How do I execute a command automatically every time I log in/start a terminal session?
How do I set up shortcut commands, or alias commands?
What's this PATH thing? a.k.a. where do I find all these applications?

Software

This system's rubbish - you haven't got...
I can't find any of the commands you're talking about.
What libraries are available?
What webbrowers are available and supported on the AM Unix system?
Where can I get a VRML plugin?
What editors are available and supported on the AM Unix system?
What compilers are available and supported on the AM Unix system?
Are there any debuggers?
What is make and how do I use it?
What Windows software is available?
How do I view a file?
Is there a basic drawing package?
Is there a basic image viewer?
How do I install and use TeX/LaTeX/MiKTeX etc?
How do I get bold theta-hat in LaTeX?
Where can I get the SoMaS TeX style files?http://www.shef.ac.uk/appliedmaths/manual/general.html#q71
How do I check for NaN in FORTRAN?
How do I convert between data types in FORTRAN?
How do I include a NAG library routine in a FORTRAN programs?
How do I set up OpenOffice?
What's this Starlink software?
Where can I get WinEdt?
How can I see an array of mugshots of my students?
Can you upgrade Netscape on Solaris?
I need quad precision!

File Formats

What are these image formats anyway?
How do I convert a .doc file or a .rtf file into a PDF?
How do I convert from MS-Word (or anything that loads into MS-Word) to Postscript?
How do I convert a file from Postscript to PDF or vice versa?
How do I convert a file from Postscript or PDF to ASCII?
How do I convert a file from Postscript to Encapsulated Postscript?
How do I convert a file from Encapsulated Postscript to anything?
How do I convert a file from JPEG to Encapsulated Postscript?
How do I rename all .x files to .y?
How do I strip the leading 1,2,3,4,etc characters from filenames?
How do I compress and uncompress files?
How do I prevent Windows from hiding file extensions and automatically renaming over them?

Backing up your data

What is backed up for me?
What do I need to back up myself?
How do I burn CDs on Windows XP?
How do I use the Maxtor disk?
How do I mount a memory stick (flash stick, USB stick) on a Linux machine?

Optimising your programs

Optimisation
Parallelisation
Performance monitoring

Rules

Software Available

• Windows XP Pro (from RLB)
• Microsoft Office XP (from departmental office)
• McAfee Anti-virus software (from CICS Novell network)
• Adobe Acrobat Writer (from Linda Wilkinson)
• Adobe Acrobat Reader (download from web)
  
• Maple (from RLB)
• Exceed (from RLB)
• NFS Maestro (from RLB)
• WinEdt (download from web - see instructions in this manual - and ask RLB or DJR for key)
• MikTeX (download from web - see instructions in this manual)
• Matlab is available on iceberg and on the managed XP service.    It is also available for unmanaged XP machines at UKP 80 (initial cost) + UKP 20/person/year.    Therefore we have not got it for unmanaged XP machines.

General Topics

The Scanner/Backup PC in H10a

How do I log on?

Turn the machine on.  Log on with your Novell username and password.   When you are prompted for a local username and password, select username 'User' (without the quotes) and a null (or empty) password.  DO NOT CHANGE THIS USERNAME OR PASSWORD.  Be aware that this is a "public" (within the department) machine, and therefore should not be used for storing anything (but particularly confidential stuff, exam papers, etc, etc).

How do I use the scanner?

 
Double click on the Irfanview icon on the desktop.   Insert your document face-down onto the glass platen and close the lid.   Select File -> Select Twain Source and make sure that "WIA Hewlett Packard ScanJet 5300C 1.0" is selected.  This should be, unless someone's been messing with it.   Select File -> Acquire and let the scanner warm up and scan a Preview scan. 

 You will see it on screen (of very poor quality - the idea is that you get an idea of where you're scanning).  Make sure you are happy with the amount to be scanned - at this stage you can move the elastic perimeter to exclude unwanted regions of the scan area.  You may also change the resolution (higher resolution = crisper picture = larger file) and whether it is grayscale or color.  When you are happy all is ready, click Scan.   Click on the Save button, and save it to a (local) file.  Save this elsewhere and delete the local file.

When you save, decide what format to save your file in.   BMP is an uncompressed bitmap.  JP(E)G compression is good for photographs.   PNG is good for small compact pictures.   File compression is beyond the scope of this text, but be aware that most compression is lossy, all compressions are optimised for something different, and you will need an image reader that is capable of reading your compressed format.  Please do not leave your pictures on this machine - I will periodically clean it up.  This is not a free file repository! :-)

How do I back up data?

The following procedure is the very basic way of writing once to a single-write CD-R. Insert a blank CD-R into the  CD drive. A dialogue will appear: select "Open a writeable CD folder using Windows Explorer". Click OK. The folder will open in a new window. Drag and drop the files you want to write into this folder (this may take some time). Click "Write these files to CD".

Can I add some software to this machine?

No.  Ask Dave Robson or Richard Balthazor to add it.   Any software found on here will be removed without notice.

Handy Shortcuts

How do I find files by name?

To find all files whose names contain the phrase 'XYZ' in your current, and all daughter, directories:

% find . -name '*XYZ*' -print

How do I find files by size?

To find all files bigger than sizeinbytes in your current, and all daughter, directories:

% find . -size +sizeinbytesc -print

% find . -size +1000000c -print

How do I do an operation on all files found with find?

Use the -exec argument with find (man find).For example, to compress all files bigger than 10Mb;

% find . -size +10000000c -exec compress {} \;

How do I know if a file is being used by another process?

For example, has a file finished downloading with ftp? You can use the fuser or lsof commands.

How do I keep my computer safe from viruses, etc?

Keep on top of virus protection and system updates.

For Virii protection in Windows machines, seehttp://www.shef.ac.uk/cics/services/internet/security/virus

To keep your Windows box updated with recent patches; Control Panel -> Windows Update (This can and should be automated so you don't have to rememberregularly; mine is set to check for updates every hour and prompt me toinstall them)

For useful freebies that clean up spyware (programs that download secretlyinto your PC and report on your actions)http://www.lavasoft.de/software/adaware/andhttp://www.safer-networking.org/

What's the best way of destroying my computer?

Running it with the case open. It picks up gunk on the fans, which slow and eventually stop, which means that the processor, power supply, etc, overheat and die by degrees. Please do not run the computer with the case open. :-)

Email

How do I read/send email on the AM Unix system?

I thoroughly recommend the PINE text-based email front end; type 'pine' and follow the very intuitive instructions. Some people use the CDE mailtool. I do not recommend you use the Unix built-in mailer 'mail'.

What's the difference between ap1ips@ and I.Staniforth@?

When you are given a username on the Unix network it will look something like ap1xxx or st1xxx. Mine is ap1ips. You can send e-mail to other users on the AM network by simply using their name (if you know it), and this is the most efficient way to do it. You may also know that someone has a username on the PC network, but not on the Unix system: in this case you could, for example, send a message to ap1ips@Butterley and this would work. However, this is not the best way. Local usernames and system names (such as Butterley) don't make much sense to people outside the University (and not much sense inside, sometimes). To get round this, ACS have introduced an alias system: each user in the University has a mail alias more in keeping with their real name - mine is I.Staniforth@sheffield.ac.uk. This alias points to the username/machine combination which the user has nominated as their preferred mail location. So even if their username or machine changes, you can still contact them with the long form alias. Note that the .ac.uk can be missed off for Sheffield names, and Sheffield can be shortened to Shef. None of this stuff is case sensitive. A final point - if you don't use the alias form, you may be sending someone mail to a machine that they very rarely use - not a good idea.

How do I get my email sent to the AM Unix machines?

If you want any email sent to your email alias (e.g. joe.bloggs@shef.ac.uk) to be routed to your Unix account (e.g. ap1jb@acms1.shef.ac.uk), telephone/email/call at the CICS Helpdesk (tel 21111) and ask them to set this up (this usually goes into effect the following morning when the campus networks update). The default is for incoming email to your alias to be routed to your Novell PC account (e.g. Wintersett/ap1jb). Acms1 is the AM mail server.

I've received a uuencoded message - how can I decode it?

uuencoding is a method of sending non-text files by mail. A uuencoded mail message consists of the usual mail header, followed by a 'BEGIN' line containing the name of the file and its required access permissions. It ends with an 'END' line. To uudecode such a message first save the mail message in a file. Then, in a command window, type 'uudecode filename'. This will create a decoded file in the current directory with the name, which appeared on the 'BEGIN' line of the message.If you have to do this a lot and use CDE mailtool, here's a nifty short cut: under the 'Edit' menu, bring up the 'Properties...' window; under the 'Category' menu, choose 'Alias'; then type in 'uudecode' on the 'Alias:' line, and '|/usr/bin/uudecode' on the 'Adresses:' line; finally click on 'Apply' and dismiss the window. You've now created an alias called uudecode. To decode a message, all you need to do in future is forward it to 'uudecode' and this will produce the decoded file automatically in your home directory.

Why should I save my mail in my home directory?

When mail arrives for you on the AM Unix system, it goes into your system mailbox (in a file in /var/spool/mail). This is a system area shared between all users, and consequently will get full if everyone leaves their old mail in there. When this happens the mail system will stop processing incoming mail. It follows that it is antisocial to leave your mail festering in the system mailbox, and if you want to keep it, you should move it to your home directory either using pine's 'Save' ('S') or the move button in 'mailtool'. To encourage people to do this, the system mailbox files are NOT BACKED UP, so if you blow it, or the disk crashes, you're in big trouble.

I want to send/receive some large (> 1Mb) files.

Use ftp or sftp, not email.

How do I create folders/mailboxes in CDE Mailtool?

Under the mailbox menu is 'New Mailbox'. In this, enter the new folder/mailbox name in the bottom panel labelled 'Enter file name', not the upper panel labelled 'Enter path or folder name'. Click on 'New Mailbox' (thanks to Chris Wilford for this)

How do I reduce the amount of junk/spam email I get?

Prevention

Spammers, those who send 'spam' or junk email (the name coming from the Monty Python 'Spam' sketch), get your email address from trawling through archived mail lists, from newsgroup postings, from web pages, and from seeing you reply to a 'remove me' link on junk email. Therefore:

• Munge your email address (both From: and Reply-To:, if used) on newsgroup and email list postings, and on your webpage, such that it is human-readable but not machine-readable. For example,

  From: r.balthazoraddress@shef.ac.uk
  Organization: Remove address from email before replying.

  or

  Email me at rDOTbalthazorATshefDOTacDOTuk

  This doesn't apply to private emails, which hopefully will only be read by the intended (and presumably trusted) recipient.

• Select to hide your email address on lists you subscribe to (see the list administration).
• Never reply to the 'unsubscribe me' link on junk emails. Doing this simply tells the spammer that your email address is legitimate, and thus they can send you even more crap.   Update 9/2004: at least one spammer is using the 'unsubscribe me' link to force you to download a virus.
  
• Never complain to the sender, as above (and often the address is forged anyway)
• If you do post a lot to newsgroups and/or mailing lists, it may be profitable to set up a 'disposable' email account on, eg, hotmail or yahoo, and use this as your 'public' email address. When spammers overload it, simply forget about it and create another.

Cure

• Delete it unread.
• Use a mail filtering tool. There are comprehensive instructions for those using Pegasus Mail, Pine,Netscape,Outlook Express and the very powerful Procmail (Caveat: procmail can really mess up your email if you get the filter rules wrong!)
• Always test filters by filtering to a junk email folder before you set them to delete the email - the main weakness of filtering is legitimate emails being filtered by mistake.
• If the content is particularly offensive, contact CICS on advisory@shef.ac.uk who may take the matter further.
• If you believe the content is illegal, contact the Internet Watch Foundation. If you believe the illegal content originated in the UK, contact the police as well.
• Always check your logs regularly to see if any genuine email has been accidentally junked.

How do I copy files from one machine to another?

1. Use scp if both systems permit.

% scp user1@machine1:/path/to/sourcefile user2@machine2:/path/to/destfile

eg

% scp richard@acml1:/home/richard/file.ps ap1rb@acms21:/home11/ap1rb/docs/file2.ps

2. Use ftp or rsh. If you want to copy a whole directory structure from THERE to HERE, try

cd heredirrsh THERE '( cd theredir; tar cf - . )' | tar xf -

cd parentdirtar -cvf tarfile.tar directory

tar -xvf tarfile.tar

localhost% ssh-keygen -t rsa1
Generating public/private rsa1 key pair.
Enter file in which to save the key (/home1/ap/ap1rlb/.ssh/identity):
Enter passphrase (empty for no passphrase):
Enter same passphrase again:
Your identification has been saved in /home1/ap/ap1rlb/.ssh/identity.
Your public key has been saved in /home1/ap/ap1rlb/.ssh/identity.pub.
The key fingerprint is:aa:bf:ce:cb:19:5b:82:b5:00:88:ef:12:cd:84:e3:1f ap1rlb@iceberg

remotehost% cat id_rsa.pub >> ~/.ssh/authorized_keys

remotehost% cat identity.pub >> ~/.ssh/authorized_keys

localhost% eval `ssh-agent`
Agent pid 25525

localhost% ssh-add
Enter passphrase for /home1/ap/ap1rlb/.ssh/id_rsa:
Identity added: /home1/ap/ap1rlb/.ssh/id_rsa (/home1/ap/ap1rlb/.ssh/id_rsa)
Identity added: /home1/ap/ap1rlb/.ssh/identity (ap1rlb@iceberg)

localhost% ssh user@remotehost
remotehost%

How do I transfer data using FTP?

ftp is a file transfer protocol program, enabling you to transfer files between networked computers. To learn more about ftp commands, type 'man ftp' at the prompt.. The following examples use Unix command syntax. To run ftp or telnet from a Windows95/98/2000 box, click on Start, click on Run, and type 'ftp' or 'telnet' into the box.

The basic ftp commands are 'put' and 'get', to transfer files 'away' or 'towards' you. Multiple files can be transferred with 'mput' and 'mget', and it will prompt you before transferring each file. The prompt can be turned off by typing the 'prompt' command.

You must tell the ftp program whether you are transferring a BINary or ASCII file. An ASCII file is plain text such as a LaTeX .tex file; a BINary file is encoded (such as a postscript file or an MS-Word document). You specify the file type by typing 'bin' or 'ascii' before the transfer.

How do I make my data accessible to an external person with FTP?

telnet acms1.shef.ac.ukUsername: your-usernamePassword: your-passwordcd /ftp/pubmkdir yournamecd yourname

Copy your file, eg yourfile into this directory. The external person can then obtain the data via anonymous ftp as follows:

ftp acms1.shef.ac.uk
Username: ftp
Password: their-email-address
cd /pub/yourname (e.g. cd /pub/richard)
bin [only if your file is binary]
ascii [only if your file is ascii]
get yourfile
bye

NB: This data will be publicly available to anyone who chances to look at this directory. Thus, sensitive material should not be left here. In the interests of disk space, please remove any files once your colleagues have downloaded them.

How do I let an external person (possibly yourself when away from Sheffield) to transfer data onto acms1?

They can upload data to acms1 anonymously, or you can use your own username. NEVER DISCLOSE YOUR USERNAME AND PASSWORD TO ANYONE, EVER.To upload data anonymously:

ftp acms1.shef.ac.uk
Username: ftp
Password: their-email-address
cd /pub/incoming
bin or ascii
put theirfile
bye

...and they may upload their data into this directory only using the 'put' and 'mput' commands (type 'help put' within ftp). When you are logged onto acms1, you may then move to that directory and move the data elsewhere:

telnet acms1.shef.ac.uk
Username: your-username
Password your-password
cd /ftp/pub/incoming
cp theirfile your-destination-directory

To upload data using your own username:

ftp acms1.shef.ac.uk
Username: your-username
Password your-password
cd anywhere you like

...and you may upload your data.

This section is specifically for CTCD users. First you'll need an ftp client.If you use Windows, I recommend WS_FTP LE downloadable from e.g. Tucows. If you use Unix, I recommend the default 'ftp' at the command line.

Then you need to connect with your client as below:

WS-FTP

Host name: ctcd-data.shef.ac.uk
Host type: automatic detect
User ID: Your CTCD username: ask Richard for an account
Password:  The password, appropriately
(leave everything else as default)

ftp> open ctcd-data.shef.ac.uk
Username: as above
Password: as above

If you are unfamiliar with the ftp clients, use the Help provided (WS-FTP) or type 'man ftp' at the Unix command line.

A handy tip with MS-Windows ftp

Often you want to start up ftp in MS-Windows (Start -> Run -> type in 'ftp') and upload to somewhere else some file on your machine buried deep in a directory heirarchy, and it is tedious to navigate down with lcd.  (You don't know about lcd?  Read the ftp help).   Here is the easy way of doing it: start up ftp, establish the connection, choose the file type, and type 'put ' (ie, put followed by space, without hitting return).  Then open up Windows <STRIKE>Exploder</STRIKE> Explorer and navigate to the file.  Then, drag and drop the file onto the ftp window. It will insert the full pathname.  

What SSH (Secure SHell) facilities are there here?

acms21.shef.ac.uk is an ssh server with a firewall exemption, so you can connect directly to it from outside the university without going through the insecure telnet/gateway method. Other machines have ssh servers running; if you want your Solaris/Linux box to have one, please let me know.

You can download ssh clients for a number of operating systems from Paul Kerry's ftp server. Note that we already have ssh clients on most Solaris and Linux boxes here - you'll only need to go here if you want one on your Windows box, or are connecting from outside the university.

How can I easily move files between machines which don't have an ftp server?

Use scp (Secure CoPy).

To transfer a file from there to here on a Linux box:

here% scp username@there:/path/to/filename .

e.g.

acml27% scp ap1rlb@acms21:~/docs/paper.pdf .

Shells and Shell Commands

What shells are available?

Bourne shell (sh), C shell (csh), Korn shell (ksh), Tcshell (tcsh). There is also a shell mode in emacs.

The Bourne shell (named after Steve Bourne, who wrote it) is the standard Unix shell. It is available on every Unix system, and is good for shell programming. It is still the preferred shell for writing scripts. The interactive facilities are poor though, so...

The C shell was designed to be a basic shell with a C-like syntax, and reasonable interactive facilities like command and filename completion, and a history mechanism for recalling and editing previous commands. Unfortunately these are all rather obscure and hard to use. Also things like redirection and shell programming are broken or brain-damaged. A lot of software assumes you use it.

The Korn ksh was meant to be the best of both worlds, and fancied itself as the new 'standard' shell. However, it fell by the wayside.

The TC shell is extremely user-friendly, with useful features like up-arrow to recall previous commands, and command-line editing (other shells force you to delete back along the command line.) Recommended for novices.

The emacs shell mode is even better, both preserving your underlying shell, and adding excellent editing facilities on top.

You might want to consider perl for scripts.

How do I know what shell I'm in?

% echo $SHELL

How do I change shells temporarily on a particular machine?

Execute the shell binary, eg

% /path/to/shell

How do I change shells permanently on a particular machine?

Ask Richard or Dave.

How do I set up shortcut commands, or alias commands?

alias alias 'command'

eg

alias ll 'ls -l'

How do I execute a command automatically every time I log in/start a terminal session?

All of the shells read a 'resource file' located in your home directory.  The name of the file is:

On Solaris: .cshrc5
On Linux: .cshrc (for the TCshell and C-shell) or .bashrc (for the Bourne/Bash shell)

What's this PATH thing? a.k.a. where's all the software?

Every shell has an environmental variable called PATH. This is a colon-separated list of directories to be searched sequentially when a command is entered. When a command is found in that list of directories, it stops the search and executes it, and doesn't search for any more commands. In the TC-shell (tcsh), you can see this PATH by typing


% echo $PATH


If a piece of software is located in your PATH, then you just need to type its name to execute it (provided it's executable). Eg,

% ls

If a piece of software isn't in your PATH, then you can't invoke it by typing its name; you have to type the full path to the name, eg

% /software/bin/maple9.5/bin/xmaple

This can soon get tedious.  So you can adjust your PATH.    You can add a directory to the PATH by resetting the environmental variable, eg to add the directory /usr/test to the PATH in the TC-shell,

% setenv PATH ${PATH}":/usr/test"

% cd ~

% nedit .cshrc

setenv PATH ${PATH}:/software/bin

This system's rubbish - you haven't got...

Tell me about it, and I'll try and get it. But please note that duplicating functionality across different platforms is generally of lower priority than installing it in the first place.

Please don't ask unless you really want it.  I spent the better part of a week installing a compiler with some fairly awkward dependencies.  A few months later I asked the user how he was getting on with it.   I was told, "Oh, I didn't use it in the end."   Grrrr.

I can't find any of the commands you're talking about.

Make sure /software/bin and/or /usr/local/bin, and any software-specific path, are on your PATH environmental variable.

What libraries are available?

On acms1 (Solaris server)

• Heirarchical Data Format (HDF) libraries in /usr/local/HDF4.1r3/
• PostgreSQL libraries in /home13/packages/pgsql/lib
• NAG libraries (see separate entry)
  

On applied (Linux server)

• NAG libraries (see separate entry)
  
• Starlink libraries
  

What webbrowers are available and supported on the AM Unix system?

Netscape (although be aware that the Netscape port onto Solaris isn't very stable and falls over at the slightest provocation, like daring to read a webpage that has Javascript).

Where can I get a VRML plugin?

Cortona. Click the button to install, and accept all the default suggestions. This seems to work fine for Win XP; I haven't tried it for other systems.

What editors are available and supported on the AM Unix system?

All these editors (except dtpad) can be accessed by typing editor filename at the command prompt, e.g. % vi test.f. Editor choice is very much a personal affair.

• vi is a very basic text editor found on every *nix system imaginable, even when all other editors are down/uninstalled; and is thus a Very Good Thing To Know. However, it has a steep learning curve and commands are non-intuitive.
• textedit is basic and intuitive, but doesn't deal gracefully with quota problems.
• nedit is a very nice editor with language syntax, but has an uncomfortable search facility.
• dtpad is accessible through the CDE menu, under applications (as 'text editor'. It is perhaps the simplest of the editors to use, but lacks much functionality.
• emacs is a very advanced text editor with the ability to compose, send and receive email and news, language specific syntax, interface with compilers, and do your washing-up. But it can require a lot of hunting through the manual to do more complicated things. xemacs is emacs with an X-based front end.
• jove, pico, xedit are other editors with their own followings.

What compilers are available and supported on the AM Unix system?

The current compilers are the Sun Workshop compilers and gcc:

• f77: WorkShop Compilers 5.0 99/09/16 FORTRAN 77 5.0 patch 107596-03
• f90: WorkShop Compilers 5.0 00/05/17 FORTRAN 90 2.0 Patch 107356-05
• cc: WorkShop Compilers 5.0 98/12/15 C 5.0
• gcc version 2.8.1

Are there any debuggers?

dbx is line oriented, debugger is the OpenWindows version. You might like to try out GNU gdb (/usr/local/bin).

What is make and how do I use it?

If you're developing programs and you're not using make, you are wasting a lot of your own time. Fed up of typing 'cc -o thing -I/whatsit -I. -O -Lhere -lthis -lthat -lother' every time you want to compile something? Keep having to retype it because you forgot about that OTHER library you needed to link in? Can't remember which programs need recompiling because you've changed a source file? THEN YOU NEED MAKE.

How to start? The Sun manual in answerbook is quite good (it's also available in /usr/local/docs). Read the first bit, then have a go. The best way to write a makefile is to pinch somebody else's and diddle with it. To that end, you'll find one or more sample makefiles in /usr/local/docs/Makefile.templates.

If you really want to burn rubber, there's an excellent O'Reilly book on the subject: "Managing Projects with Make" (Oram and Talbott).

WARNING: the only problem with make is that different versions can differ in extremely subtle ways (and some don't work at all). So porting makefiles between Sun, DEC, SGI etc is rather fraught. GNU provide a make utility, and this is probably the answer.

What software is available for Windows machines?

CICS have a range of software listed here.

The departmental office has the following CDs that you can borrow:

• Visual Studio Professional
• Visual J++ Professional
• MS-Developer Network Libraries
• Corel Word Perfect 8
• MS-Office XP

Linda Wilkinson has the Full Acrobat Product on CD.

How do I view a type file?

File type	Typical extension	Recommended viewer
Postscript	.ps	gv, ghostview
Any image	.gif, .jpg, .jpeg, .tiff, etc	xv or Netscape
Adobe	.pdf	Adobe Acrobat Reader (/usr/bin/acroread for Solaris machines, or get the full version for Windows from Linda Wilkinson)
Microsoft files	.doc, .xls	Star Office MS-Windows machine [recommended]

Is there a basic drawing package?

xfig [Unix]

Is there a basic image viewer?

xv [Unix] or Irfanview [Windows]. The latter is extremely versatile and allows you to capture screenshots, do basic manipulation, and convert between a multitude of formats.

How do I convert any standard image format to any other standard image format?

How do I install and use TeX/LaTeX?

LaTeX, LaTeX2e, MiKTeX, TeX, et al are variants of a (mathematically-biased) very powerful typesetting system, which many people have found to be vastly superior to Microsoft Word's Equation Editor. It is NOT a WYSIWYG editor; rather, the user writes the typesetting codes into the text using any standard text editor and then processes the file to obtain an encoded device-independent (.dvi) file. This can then be processed again to produce a printable file (for example, a Postscript file). A manual of how to use *TeX* is beyond the scope of this document; however I thoroughly recommend the blue spiral-bound book by Knuth, which is in the secretary's office. Another good reference is the LaTeX project homepage.   And before you ask any other questions, have you read the UK List of UK List of TeX Frequently Asked Questions ?

TeX on the Unix machines

 Type 'latex filename.tex' and then 'dvips -o filename.ps filename'.

TeX on a Windows PC

The recommended variant is MiKTeX, available from http://www.MikTeX.org. Select 'Download MiKTeX', download the install wizard, and follow the instructions. You should install a private installation. When you have downloaded and installed MiKTeX, it can be run from an MS-DOS command line (Start - Programs - MS-DOS Prompt).

How do I get bold theta-hat in LaTeX?

In Maths formula, sometimes LaTeX will not interpret the obvious

{\bf \hat{\theta} }

\mbox{\boldmath{$\hat{\theta}$}}

Where can I get the SoMaS TeX style files?

Jim Green has packaged them:

I've repackaged the Butterley SoMaS TeX files (styles for examinations, letters, memos etc) in a form suited to the Unix TeX package teTeX. The package can be found in

/acms22_p3/pub/somastex.tar.gz

or contact me by email: j.j.green@shef.ac.uk

How do I check for NaN in FORTRAN?

A numeric variable takes the value NaN (Not a Number) when, for example, a number is divided by zero. This can be tested by the following code fragment:

.NOT.(x.GE.0.OR.x.LE.0)

How do I convert between data types in FORTRAN?

You READ from a variable instead of a logical unit. This sample noddy program shows how.

	PROGRAM char2int		
	IMPLICIT NONE		
	
	CHARACTER*3 chvar
	INTEGER ivar
	chvar='345'		

	WRITE (6,*) chvar, ivar		
	READ (UNIT=chvar,FMT='(I3)') ivar		
	WRITE (6,*) chvar, ivar	

	END

How do I include a NAG library function in a FORTRAN program?

The following only applies to the departmental systems.   Iceberg, iceberg, etc, have their own NAG libraries; see the CICS website.

NAG libraries are available on the Linux and Solaris systems for PPARC astronomy (includes STP, Solar) research only.  Your machine must be set up with the /star directory; if it doesn't have a /star directory, ask Richard to install it.

NAG documentation is available on the NAG website under Support/Documentation; there are good FORTRAN examples for most of the function calls.  The documentation is also local under /star/nagdocs.

First you must set up the appropriate variables.

% source /star/etc/login

% source /star/etc/cshrc

 -L/star/lib `nag_link`

f77 -o a.out yourfile.f -L/star/lib `nag_link`

% make clean

% make build

% make run_test

How do I set up OpenOffice?

OpenOffice is the successor to Star Office, and is a suite of word processing, spreadsheet, and similar documents with much the same functionality as Microsoft Office. However it's open source and free, and runs on a variety of operating systems including Windows, Linux and Solaris. We have it installed on most of the AM Linux boxes and the AM Sun system.

To use it on a Solaris box, you must be running at least Solaris 5.7. You need to do the following procedure once only:

% cd /usr/local/OpenOffice.org1.0/program% ./setup

After once-only installation, you can invoke it all by dropping into yourlocal OpenOffice.org directory (under your home directory) and typing

% ./soffice

% ./spadmin

If you want to install it into the menubar such that you can drag and drop files onto it, expand any desired menu by clicking on the up arrow (eg the old Star Office menu if you used that). Then open up file manager, and drag the ~/OpenOffice.../soffice icon onto the Install Icon button.

What's this Starlink software?

A set of interactive data reduction and analysis tools for use in research. Mostly (as the initiative stemmed from astronomy) these are time-series and 2-D image tools. For more information, see the Starlink website. I have installed the core Starlink software set, and all the libraries, on the applied Linux server. If you want any other packages added, let me know.

Where can I get WinEdt?

Go to the WinEdt website, read all the information about installing and upgrading. When you're happy, select download, and download the latest version from a convenient mirror site. The download is a self-extracting executable. Once it is downloaded, you can register it; email Richard or Dave for the licence code, then select Help -> Register and enter the fields as given in the licence code, click OK, and you're set.

How can I see an array of mugshots of my students in CIES?

Download the form and apply to CICS.

integer, parameter :: prec=selected_real_kind(31)

File Formats

How do I convert a .doc file or a .rft file into a PDF?

On Windows: install Adobe Acrobat (CD from Linda Wilkinson).   You will acquire a PDF button in MS-Word.

On Unix/Linux: OpenOffice already has a document-to-PDF button.

How do I convert from MS-Word (or anything that loads into MS-Word) to Postscript?

• Load the program into MS-Word (on any convenient PC)
• Select a Postscript Printer
• Select 'Print to file'
• The resultant file will have a .PRN extension, but can be renamed to have a .ps extension and viewed with gv on the Unix system. However, some other versions of ghostview, notably some Linux variants and the PC program Ghostgum, will display it oddly or refuse to acknowledge that it is a Postscript file.

How do I convert a file from Postscript to PDF or vice versa?

ps2pdf oldfilename.ps newfilename.pdfpdf2ps oldfilename.pdf newfilename.ps

(This works with postscript files produced with the above method, and is thus a good method of getting a platform-independent file out of Microsoft J

How do I convert a file from Postscript or PDF to ASCII?

ps2ascii oldfilename.ps newfilename

How do I convert a file from Postscript to Encapsulated Postscript?

ps2epsi oldfilename.ps newfilename

How do I convert a file from Encapsulated Postscript to anything?

There are a number of dodges which may or may not work.Try loading the file into a postscript viewer or drawing package that allows you to Save As. Possibilities include gv, gs, ghostview or xfig (on the Unix system), Ghostgum, Corel Draw or Irfanview (on PCs)

How do I convert a file from jpeg to postscript?

There is a useful package called jpeg2ps. This is very useful for including images into LaTeX documents.

How do I rename all .x files to .y?

The obvious 'mv *.x *.y' doesn't work (why?). Use the following shell script instead:

#!/bin/sh
for i in *.x
do j=`basename $i '.x'`
  mv $j.x $j.y
done

'basename' forms the basis for many tricks with filenames containing a suffix.

How do I strip the leading 1,2,3,4,etc characters from filenames?

#!/bin/sh
for i in *.jpg
do j=`echo $i | sed 's/^..//'`
mv $i $j
done

On the third line above, put in as many periods as you have characters needing deletion.

How do I compress and uncompress archive files?

• .gz files have been compressed using the gzip command. Use the gunzip command to uncompress the file.
• .Z files have been compressed using the compress command. Use the uncompress command to uncompress the file.
• .tar files have been archived using the tar command. Use the -x option to expand these files back out.
• .tgz files have been archived using the tar command and then compressed with the gzip command (and thus .tgz is shorthand for .tar.gz). Use the extraction commands in the reverse order. Note that sometimes your browser may automatically gunzip a file when you download it, but it will not change the .tgz extension to .tar. Use the file command (man file) to see what sort of file you have.

No, you can't do multiple compressions with the same algorithm to iteratively reduce the filesize! Also note that some file formats (particularly image formats) are already effectively compressed, so it may not be possible to compress them further.

An oft-encountered file is a .tar.gz file, which is a group of files first archived into a tarball with the tar command, then gzipped to compress it.   To uncompress it, gunzip it, then tar it.

How do I prevent Windows from hiding file extensions and automatically renaming over them?

Start -> Settings -> Folder Options -> View Tag -> unselect 'Hide file extensions for known file types'
(Thanks to Youra and Stuart)

Backing up your data

What is backed up for me?

If your data resides on a disk not listed below, it is NOT BACKED UP!, so you will need to do it yourself. And if it is critical, you should BACK IT UP YOURSELF INDEPENDENTLY!

On the Novell Network:

U: drive is backed up - see CICS. 
Your C: drive is NOT backed up by us (except for Robertus's, which is backed up weekly).

On Iceberg:

Your homespace is backed up - see CICS.

On the Applied Maths Solaris network:

The following file systems containing user data are backed up and kept for 8 weeks before being recycled.  If you have lost data and think that it should be backed up as below, please let myself and Dave Robson know, and we will try to retrieve it. Please note that retrieval will take several hours, so if you can recreate the data quicker through other means, it will be more efficient to do so! 

The following contain the user home directories and are backed up thrice weekly.

• /home11 (Sunday, Tuesday, Friday)
• /home12 (Sunday, Tuesday, Thursday)
• /home13 (Tuesday)

The following are all backed up weekly (on Tuesdays)

• /ACMS16_DATA
• /ACMS12_DATA
• /ACMS5_RvFS
• /ACMS20_DATA
• /JCWP_DATA

• /ACMS21_DATA{1,2,3,4}
• /ACMS25_DATA{1,2,3}
• /ACMS23_DATA{1,2}

On the Applied Linux network:

The following systems are backed to tape with a guaranteed weekly backup and a tape retention of 3 weeks 2 days.  Thus, the most that can be lost is a week's data; the tapes are retained for 3 weeks 2 days before being recycled.

If you find you have lost anything, please email us with the filenames and paths you want recovering, eg "/home/user/docs/really_important_presentation.sxw".  The more precise you are, the easier it is for us.  

applied2: /, /var, /boot, /userdata, /software (nb: contains some Solaris data disks)
ctcd-data: /boot, /, /SOFTWARE

acml4: /home
acml5: /home
acml16: /home
acml21: /home
acml23: /home
acml24: /home
acml26: /home
acml27: /home
acml28: /home
acml31: /home
acml32: /home
acml33: /home
acml34: /home
acml35: /home
acml36: /home
acml39: /home

What do I need to back up myself, and what do I need to know about backups?

• Do you really need to back up all your data? Will it be more productive to back up only the source data and the processing chain?
  
• How permanent do you want your backed up data to be? Do you actually want a permanent archive, or are you simply looking to mitigate the effects of a disk crash? Or both?
• Disks DO crash.
• CD-Rs are fairly good, but they can fail to read on a different reader than the one used to create it.  Check all your copies in several machines.
• Tapes have a lifetime of a few years.
• Floppy disks and zip disks are on the way out - it's probably you won't find any hardware for them in a few years.
• Flash/USB/memory sticks haven't been around long enough to check longevity - beware.
  

How do I use the CD-writer in H10a to back up from Windows XP?

Go to the XP machine in H10a (the one with the scanner attached) and log in to your Novell account, and the local "User" account. Do not change the local account's password.   Copy all the files you want to backup to a local directory on the machine (but delete them afterwards, please).    Insert a blank CD (from Lynda or Maureen) into the drive.  A window will open.  Drag the files you want to backup into this window.   When you are ready, click "Write these files".  At the end, click "Finish".  

% mnt /mnt/flash

mount: can't find /mnt/flash in /etc/fstab or /etc/mtab

% mount /mnt/usb 

% umount /mnt/flash

The SPARG big disk

Optimising your programs

c    This is a very inefficient way of addressing FORTRAN arrays.

        DO i=1,arraysize
          DO j=1,arraysize
            a(i,j)=100.0
          END DO
        END DO

c    This is far better.   The array is accessed in a column-major manner,
c    which matches how it is stored in memory.  

        DO j=1,arraysize
          DO i=1,arraysize
            b(i,j)=200.0
          END DO
        END DO

% f90 -xautopar -xloopinfo parallelprog.for

% f90 -g <-all your other flags> program.for

% collect a.out

% analyzer test.1.er

% f90 program.for
% ./a.out