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Contents

List of Figures

Chapter 1
Getting Started

1.1 Welcome

Welcome to the University of Virginia Astronomy Department. This booklet hopefully will help orient you to the computing systems used most often within the department and our classrooms.

We use a variety of computer systems with in the department, most of which are Unix based. We began to realize a few years ago that many of the incoming people were more accustomed to Windows and Macintosh systems, so we developed these notes to answer the questions you may have when using these systems. Most people when arriving will either purchase or be assigned a Unix workstation (with either the Solaris or Linux operating system). The Sun Solaris systems are generally the older and slower machines, but they have proven to be quite stable and very dependable over the last few years. The newer generation of machines are Linux workstations based on PC hardware from Dell. These have faster CPUs and generally more RAM.

The first chapter, “Getting Started” will give you a quick walkthrough of common Unix commands. While we will show a few pictures of the different desktop environments, we will not go into great depth about using those desktops. Its up to you to poke around and see what you find out.

The remaining chapters are go into more detail about those topics which need more explanation, such as email and effective ways to manage your data storage needs.

If you have any questions, please always remember that you can email
astro-help@astro.virginia.edu at any time and the department sysadmin will respond to you as soon as reasonably possible.

1.2 What Isn’t Covered in This Handbook

Well, a lot. We can really only offer the briefest glimpse at the shells (bash, tcsh, csh) and don’t discuss many important Unix commands (perl, awk, sed, grep) or the startup files (.cshrc and your other friendly “dot” files, useful for customizing your desktop, and your entire user experience). Text editors (emacs, vi, vim) are absent for this handbook. We also don’t go cover the specialized reduction and plotting software (IRAF, IDL, Mathematica, sm, gnuplot) or typesetting software (TEXand LATEX). However, many of these will become essential parts of your daily work here. There are numerous resources (other than this handbook), including your colleagues, and some documentation in the “Local” section of the Department’s website (http://www.astro.virginia.edu/local), as well as the ITC’s Research Computing website (http://www.itc.virginia.edu/rescomp). In addition, there is also a small library of computing reference books in my office (Room 103), and Ricky Patterson also has a collection of manuals (Room 214).

1.3 Logging In

The first thing you will do is log into the workstation. The process is similar for both Solaris and Linux workstations. (Remember to make sure that Caps Lock is not pressed if you have trouble logging in).

1.4 Shell Conventions

The Unix command line is one of the most powerful interfaces available between a human and a computer. However, it is possibly the least user friendly interface. Don’t be discouraged, there are no experts at using the Unix shell - everyone learns new tricks all the time.

In this section, I’m going to mention some of the standard Unix commands that you will need to know to navigate and see your data on a Unix or Linux machine. I’m going to make use of a standard format such as this:

$ ssh [user@]hostname [command]

The dollar sign ($) is your prompt - meaning that the system is ready for you to input a command. Typically, you’ll get one of these every time you press enter or when a command completes.

The command name (in this case, ssh) comes directly after the dollar sign.

Optional components (such as user in this case) are shown here between square brackets. When you are using this command, you should exclude the square brackets or exclude this component, depending on whether you need it or not.

The above command, when properly used within a shell, winds up looking like this:

[hbp4c@Realos ~]$ ssh hbp4c@astsun.astro.virginia.edu
 
hbp4c’s password:

You see, I began with my command directly after the dollar sign prompt, and while I did use one optional component (user) I left out the other (command). When done properly, ssh then asked me for more information, in this case my password on the computer I was connecting to.

Note that I am following the same conventions used in the Unix man pages.

1.5 Shell Basics

While the names for many Unix commands can appear cryptic, many of them are formed by dropping vowels (and some consonants) from the English word describing the command. For instance: list becomes ls, move becomes mv, cp becomes copy. Other commands like awk, grep and biff have more colorful etymologies. The most common commands:

ls [-l[-k][-h]][-F][--color][directory]
                                                                                  

                                                                                  

This command lists all of the files within a directory. If you omit the directory, ls will output the names of the files within this directory. The optional -l gives more information. The optional -k and -h options when used with -l puts the file size in kilobytes and human readable (M for Megabytes, K for Kilobytes) formats. The -F option lists all the files, including those that are hidden. The –color option (only in Linux) uses colors to display information about the file type.

cd [directory][..][.]

To change to a directory, type cd. If you omit the directory, you will go to your home directory. Two special directories, .. and ., always exist and mean “go up a directory” and “this directory”.

pwd

The print working directory command tells you where you are currently located.

rm [-r][-f] file
                                                                                  

                                                                                  

rm removes files. Once deleted, they cannot be recovered. BE CAREFUL. The -r option means recursively (delete a directory and all contents) and the -f directory means “don’t ask me if I am sure”.

mv file destination

This moves files from one place to another. You can also rename files by simply moving them from the old name to the new one.

cp file destination

This copies files from one place to another. cp, unlike mv, leaves the original file untouched.

quota [-v][-s]

The quota command shows you how much disk space you’ve been allotted, and how much you have remaining. See the chapter on data management for more information.

mkdir [-p]directory

rmdir directory

the mkdir and rmdir commands create and destroy directories (what PC and Mac users might call “folders”), which in turn hold files. rmdir will not delete a directory which contains files or other directories, you must rm the files first.

ps [-A][-u user]

ps lists all of the processes running on the local computer at a given time. This is useful to see if for some reason your computer is running slowly or if you want to see if you have a program already open.

man command
                                                                                  

                                                                                  

The man pages are an online help system that explain, in great detail, almost all of the Unix commands available on your system. This is one of the places a new user should look before they are told to RTFM.

lpr [-P printer] file
 
lpq [-P printer]
 
lprm job-id
 
enscript [-P printer][-2][-r] file

These commands print files and manipulate print jobs which have been sent to the printer. lpr (meaning line printer) submits a job to the printer. lpq shows the status of the queue (which jobs are waiting to be printed). lprm deletes a job in queue (when deleting a job, you cannot use the name of the file, but rather you must use the job-id, which is listed in the output from lpq). For each of these commands, you can specify the -P option to choose a specific printer to work with. enscript is a more advanced version of lpr which allows you to format your file before it is printed. enscript’s -2 option formats your text into two columns. The -r option rotates your text 90 degrees, and prints your document in landscape format. The -2r options are a good way to save paper.

1.6 Passwords

Passwords are an annoying but very important part of computing. Your password will give you access to your files, to your email, and in general is the only way that keeps your stuff safe from other people’s abusing it.

When you first arrive in the Astronomy Department, you’ll be assigned a temporary password that will no doubt be hard to remember. You’re urged to change it to something that you can remember, but you must follow a few guidelines to ensure it is a safe password that other’s can’t readily guess.

Rules:

• The password must be 6, 7 or 8 characters long.
• The password cannot contain part of your name or username.
• The password cannot be all uppercase, all lowercase, or all numbers. A mix of two or all three of these is required.
• Finally, the password cannot spell a word in any language, forwards or backwards.

These rules help you choose a safe and secure password. Recently, I ran a freely available password checking program against our password database, and in six seconds one account password was found.

Remember, if anyone gets into your account, you can be held responsible for anything they do, including sending emails, deleting files, or causing other problems. Don’t share your password with anyone for any reason! This should be considered a “strong” password, and you shouldn’t use this password for other accounts, especially ones transmitted over insecure web pages, etc.

1.6.1 Changing your password

The website https://www.astro.virginia.edu/accounts/passwd.php will allow you to change your password. If you have any problems, please contact astro-help@astro.virginia.edu.

1.7 Permissions

Unix is a permissions oriented system, meaning every file or directory has a list of users and groups associated who can read, write or execute the file, or read, write or cd into a directory.

Permissions can be displayed by using the ’-l’ option for ls:

[hbp4c@Realos home]$ ls -l /home/hbp4c
 
drwx--x--x 148 hbp4c users 8192 2007-09-18 15:42 /home/hbp4c/

you see that the permissions begins with a “d” meaning this is a directory (a dash means it’s a file). The next triplet defines the read, write and execute permissions for you, the user (usually called the owner) of the files. The 2nd triplet defines the permissions for other people in your group, and the final triplet defines the permissions for all other people. The owner and group ownership of the file or directory is also listed, along with the file size and creation date.

By default, your Unix home directory is only readable by you and no one else. Other people can cd into your home directory, but they receive a permission denied error when they try to list it’s contents. While you may find this an non-optimal if you collaborate and want to allow others to see some of your files, it is set this way by default so that each user has to actively “opt-in” to unprotecting their directories. Hopefully this will make everyone aware of the file permissions of their own files.

You can change the file permissions of your home directory (and/or subdirectories) with the chmod command:

[hbp4c@Realos home]$ chmod o+r /home/hbp4c
 
[hbp4c@Realos home]$ ls -l /home/hbp4c
 
drwx--xr-x 148 hbp4c users 8192 2007-09-18 15:42 /home/hbp4c/

Now people outside of my group can read a list of the files in my home directory. To read the files themselves, the read permission of the file has to be set as well. One can use chmod -R to recursively change the permissions of all files and subdirectories. Use the “-R” option with caution.

To add a permisson, use:

chmod [u,g,o]+[r,w,x] filename

To remove a permission, use:

chmod [u,g,o]-[r,w,x] filename

Note that in order to create a personal website in your public_html direcotry, you must have at least the execute bit set on your Unix home directory, and your public_html directory must be world readable. Otherwise, visitors will receive a permission denied error when visiting your website.

Chapter 2
Data Storage

2.1 Workstations

In the UVa Astronomy Department, there are three main types of computers you will use:

• PCs running Linux (by far the most common type in the Department)
• Sun Workstations running Solaris
• PCs running Windows

On each of these platforms, there will be certain amounts of data storage allocated for your use. Some of these data storage locations are local to the machine, and some are network-based.

2.2 A Note about Data Storage

Please help minimize the amount of data you move across the network, both for your own good and for the sanity of those you work with. If you are doing an I/O intensive operation on a large amount of data, you’d be much wiser to either 1) copy the data to your workstation first (to a local directory) and work on it with your workstation’s CPU+RAM, or 2) copy it to a disk physically attached to a server, and use the server’s CPU+RAM, rather than trying to operate on it via one of the /home directories (or on any disk not physically attached to the CPU you are using). Disk I/O is significantly faster than network I/O, so your work will take less time. More importantly, you won’t be tieing up the network, so everyone in the building will be happier.

2.3 PC Linux Workstations

The Linux Workstations are the newer generation of machines recently introduced to the department. Most workstations are running some version of the Redhat Enterprise or Fedora Core Linux operating system. There is a main Linux server which contains all of the Unix home directories for all departmental machines (a network-based filesystem) located in a secured server room and backed up nightly.. Any Linux or Solaris workstation that you log into should contain the same /home directory.

The Linux workstations have a home directory with a 9.5GB soft quota and a 10GB hard quota. When you exhaust your soft quota you will receive an email reminding you that you have 7 days to get back under quota (before being locked out of your account). When you exceed your hard quota, you will not be able to create or write to any files.

On each individual Linux workstation, there is a /local partition where you can create your own directories and write data. The /local partition is the remainder of the internal disk not used by the operating system. Data on the /local partition is not necessarily backed up, and is only visible from that particular workstation. For computational jobs which require lots of reading and writing to the disk, it is recommended to use /local for this and then copy the results somewhere else as necessary.

2.4 Sun Solaris Workstations

There is also a group of Sun Solaris workstations available for use in the Astronomy Department. Most are on desks, but a for small jobs something can sometimes be arranged. The Sun workstations predate the Linux machines, but a few special software packages only exist on this platform.

The Sun workstations share the same Unix home directories as the Linux machines, so when you log into a Sun machine, you should see the same files. Quota rules still apply as usual.

On each individual Sun Solaris workstation, the admins can create for you a writable directory so that you may save files locally on the internal hard drive of the computer you work on most often. The large research groups also have storage areas which can be accessed either over the network or via logging into specific machines to do your work. There are usually no quotas imposed on these directories.

2.5 PC Windows

The Astronomy Department has a small network of Windows-based PCs for those few programs which do not have functional equivalents in the Linux and Solaris world. Windows PCs are located in the computer lab area.

Currently, none of the files on the Windows computers are being backed up. Files saved to network shares may or may not be backed up - if you have questions please ask.

2.6 Filesystem Hierarchies

The Solaris and Linux workstations both share similar filesystem layouts as well as both systems connect to many of the same servers to retrieve data. See Figure 2.1 for a conceptual idea of how this works.

2.7 Using Quota

The quota system is set up on certain user directories to ensure that no one person hogs all of the space on that machine for themselves. The quotas are only in place on common shared machines, such as the home directory servers.

To check your quota, use the quota command:

[hbp4c@realos hbp4c]$ quota -vs
 
Disk quotas for user hbp4c (uid 66302):
 
     Filesystem  blocks   quota   limit   grace   files   quota   limit   grace
 
blackhole.astro.virginia.edu:/local/home/
 
                   476M   9500M   10000M           12220       0       0
 
[hbp4c@realos hbp4c]$

The -v option enables verbose mode (gives more information) while the -s option turns on summaries (puts the output into human readable format, such as using M for Megabytes or G for Gigabytes). The -s option only works on Linux hosts.

The Filesystem field shows which disk or directory you are checking quota against. Blocks explains how much space you have already used. The next three fields, quota, limit, and grace explains how quotas work for you. The quota is your actual quota (in my case, 9.5GB of space). When you surpass this limit, you have grace number of days to remove some files before you get locked out of your directory. The limit is the hard limit, if you try to write beyond this amount of space, you will be stopped and receive an error message to the effect of quota exceeded.

2.8 Unix Backups

Backups are often overlooked and ignored until data is lost and one regrets not having a backup in place. As a systems admin, I have been known to overlook backups myself and regret it very much.

Note that you should only assume that data in your user home directory is backed up. On Linux workstations, sometimes the /local disk is backed up, please check with your local friendly sysadmin to be certain. For Sun workstations, the data on disks that are listed at http://www.itc.virginia.edu/unixsys/backups/ are backed up. Data stored elsewhere is liable to be deleted for any reason, including computer glitches and power losses.

The data stored in your home directory is located on a Redundant Array of Independent Disks (RAID) array. This array of disks is designed such that if any one disk fails for any reason, the data is still intact in other places. Only in the very improbable case where multiple disks fail simultaneously can data be lost.

To guard against catastrophic failure, or (the more frequent scenario of) a file being inadvertently deleted by a user (or an errant program), the home directories are archived to a disk array located offsite.

The places not routinely backed up in any way include the /local (Linux) and the /{hostname} (Solaris) directories on each individual workstation. These directories are rarely backed up by ITC (but in some special cases can and are backed up for a fee). Usually there is no quota limitation on these drives and will often be where many of you will do your heavy-duty work.

The best way I’ve found to handle backups is the following:

• If you have a current backup readily available (such as on tape or USB drive) then the data should be on /local.
• If the data can be recreated or re-downloaded in a short period, the data should be on /local.
• If there is a paper, code or some data that you are working on and which cannot be easily replaced, you should keep the file in /home or somewhere routinely backed up.

Note again that some of the large research groups have their own dedicated storage arrays and servers, which are backed up. In these cases it often makes sense for large amounts of data and intensive I/O and CPU operations be carried out on these servers and not on your local workstation.

In the end, it is up to you to decide where to place your data with respect to where it will be backed up vs. quota limitations, while always keeping in mind bandwidth limitations (§2.2). While we have made an effort to setup a robust backup system (modulo our fiscal constraints), final responsibility for the safety of a user’s data must lie with the user themselves.

2.8.1 Recovering Data from Backups

Home Directory Data

If the lost file was in your Linux home directory, you can recover it yourself. Look in the /backups/home directory on any Linux machine, and you will find daily backups of the files. If you do an ls -l command, you should see that each backup is time stamped when it is completed, so it should be fairly trivial to go into the correct folder and copy the file you need.

Linux internal disk

If your Linux workstation has an internal backup, the backup will be located at /mnt/Backups/. Within this directly is a set of “snapshots” of your data, usually one each day for a week. To recover a file, browse these directories and once you find a copy of your file, simply cp the file to the original location.

Solaris internal disk

If you have a file on a Solaris workstation that you need to restore from backup, you first need to determine the date it was last known to be “good”. If the last known good copy of the file is more than a few weeks old, we might have to “go fishing” to see what we can find. However, the more accurate you can be about when the file was deleted, lost or corrupted, and the more you know about the file (such as name, size, location) the better. Once you have this information, email it to astro-help@astro.virginia.edu

astro_users and astro_owners network disks

The astro_users and astro_owners directories, which are stored on a Linux server in the Astronomy server room, also has nightly backups. The current backup cycle retains data for 31 days before it’s purged from the backup system.

To recover data from the astro_users directory, please email the filename and the “last good file date” to astro-help@astro.virginia.edu

Website data

The Astronomy website has a nightly backup system in place. Currently, the backup system retains data for 7 days before purging the files.

To recover data from the www directory, please email the filename and the “last good file date” to astro-help@astro.virginia.edu

MySQL data

The Astronomy MySQL database is backed up nightly via the mysqldump command. The output file is in plain ascii and can be restored to any other MySQL installation. Backups of our MySQL database take place nightly and are presently retained for 7 days before the oldest data is purged.

To recover data from the MySQL database, please email the database, any affected tables and the “last good file date” to astro-help@astro.virginia.edu

Email

The State of Virginia requires that we NOT keep personal information such as phone records and electronic data logs. However, in case of a disaster, 31 days of email inboxes are retained. Please contact astro-help@astro.virginia.edu

Contact for more information

If you have any problems with the backups, contact astro-help@astro.virginia.edu

2.9 Data Encryption

Especially important for mobile devices such as laptops, one should consider encrypting any sensitive data that might include personal information (medical history, tax information, banking) or data sensitive to UVA (student grades, personal evaluations, anything containing a Social Security Number).

Any disk, computer or storage device that a person can get physical, unrestricted access to is insecure.

Even if permissions on a disk are used to protect data, if a person can steal or get unrestricted access to the physical device holding the data, it is possible for that person to view, copy and/or delete the data on this device.

2.9.1 Windows XP Encryption

Windows XP has a built-in encryption scheme that can be used if the underlying storage device was formatted with the NT Filesystem (NTFS). You can check the format type of a device by going to “My Computer” and viewing the properties of any connected storage device. (See Figure 2.9.1).

To encrypt a folder or an item (such as a word document) first find the object you wish to encrypt. Right click on the item, and choose “Properties” (Figure 2.9.1). In the properties dialog, choose “Advanced” (Figure 2.9.1). On the next screen, choose the box to “Encrypt contents to secure data” (Figure 2.9.1). When you press OK, a confirmation will appear and ask you if you wish to recursively apply encryption (Figure 2.9.1). This step can take some time if the file is very big. Finally, once the encryption is completed, the file or folder will appear green in the Windows Explorer to alert you that it is encrypted (Figure 2.9.1).

Once encrypted, the file can only be opened by the user account that applied the encryption. If your user password gets lost or forgotten, the files cannot be recovered. Moving the files to a second machine with the same account name will NOT recover the files.

Note that if you move the files to another storage device, Windows will alert you that the file can only be moved if you de-encrypt the contents and move an unsecured copy.

2.9.2 Mac Encryption

Mac users can create an encrypted disk image (dmg file) using the Disk utility found in the /Applications/Utilities folder.

Open the Disk Utility and click on “New Image” (Figure 2.8). Choose a location to save the file, and make sure you choose enough space (this file cannot be enlarged later) and enable the encryption (Figure 2.9). Once you click create, OS X will ask you to type in a password with which to encrypt the file (Figure 2.10). If you feel reasonably safe, you can ask your Mac to remember the password by clicking the box that saves your password to your Mac Keychain. Don’t do this on a machine available to the public or a mobile machine like a laptop that could be stolen. Once the encrypted disk image has been created, a drive icon will appear on your desktop (Figure 2.11). This disk works just like a CD or USB key, once you’re done you can place it in the trash to eject it. When ejected, the image is locked and cannot be unencrypted without the password. To re-attach to the encrypted disk image, simply double click on the dmg file (Figure 2.12) and you’ll be prompted for the password again (Figure 2.13).

2.10 Data Security

Note that the University of Virginia is currently auditing and developing a new plan to deal with Social Security Numbers. Please stay tuned for more details.

In recent years the University and it’s employees have had to become much more involved in thinking about data management and security. Please keep a few rules in mind when you create and store files.

Personal identifying information for students and employees should be protected. Personal reviews, grades, especially Social Security Numbers and any other similar information should not be accessible to the outside world. “Available to the world” also roughly includes on personal and departmentally owned laptops, and mobile data storage devices like USB keys. Please take reasonable measures to encrypt any sensitive information or lock it away in a location not easily accessible to a data thief.

Social Security numbers should NOT be used except when absolutely necessary. Students and employees have been assigned a unique ID number which should be used instead.

Personal information (bank records, taxes, credit card numbers) are your own responsibility. Something to keep in mind regarding “phishing” emails: the IRS knows more about your tax situation than you do, and your bank will also know more about your accounts than you do. Never give out information that would allow someone to assume your identity. I can guarantee that the IRS or your bank will NEVER contact you by email saying “We’re sorry, we’ve lost your information. Please log into our website and set your account and personal information up again”. THINK!!

The University is not responsible for any personal information that might be lost or stolen due to your own negligence. You, however, may be held personally responsible for damages resulting from the loss of any information on a computer in your care, which includes theft of laptops or portable storage devices.

Research information should be protected just like private information. If the loss of any research data could jeopardize a grant or funding, take any and all reasonable measures to back that data up and secure it from theft.

ITC has set up a website http://www.itc.virginia.edu/security to help explain security measures and the situations where you would want to use them.

If a data storage device is lost or stolen, you should alert the University if any data on the device is sensitive. Personal information is not necessarily covered by this. The website http://www.itc.virginia.edu/security/reporting.html is updated with the policies and information on who to contact should anything be lost.

Chapter 3
Email

Email is one of the most useful and versatile tools you will need as new member of the Astronomy Department. Many students find it the easiest way to communicate with faculty and with our students. Most general announcements are now sent out only via email distribution lists; this tool has really become an essential part of our work environment, and as such you will need to know how to use it effectively.

3.1 How Email Works at UVa

When you arrive at UVa, you will receive an email handle which is usually your initials followed by a number, followed by one or two random alphabetic characters (mine is hbp4c). This will also be your login ID on UVa and Astronomy Department computers. This email handle is unique to you and will never ever be re-assigned to anyone else ever. Your email handle cannot be changed, even if you change your name. You may, however, alias your email to another unique identifier (covered in §3.6). Your handle will be generated once you either 1) submit your acceptance letter (if you are a student), or 2) you finalize your documents with the UVa Payroll Department (for all non-students.) The UVa Department of Information, Technology and Communications (ITC) generates these IDs and then makes them available to the Astronomy Department.

There are two types of email addresses at UVa, a full email address and a shorter “registered” version. The long version is your email handle, followed by the name of the server where your mail is stored. An example of this “full” address is hbp4c@mail.astro.virginia.edu, while a “registered” address can be of the form hbp4c@virginia.edu. Mail sent to this registered address is directed by the “virginia.edu” server to the correct server (in this case, mail.astro.virginia.edu) (see Figure 3.1 for a graphic view of this). In simplest terms, ”Virginia.EDU” is a server with a very large table of emails and locations. Anytime the “Virginia.EDU” server receives an email for someone, it references that table, locates the correct server, then forwards the email to proper account on that server. “Virginia.EDU” itself does not store any email.

3.2 For Incoming Graduate Students Only

Incoming grads are assigned two accounts; one via ITC, and the other via the Astronomy Department for use on the local Sun and Linux networks within the Astronomy Department. The two accounts have the same login handle and may or may not have the same passwords, etc. (This part is up to you).

Starting in 2008, incoming grads actually receive email accounts on one of Google’s gmail.com mail system, or Microsoft’s Live! mail system (formerly known as hotmail.com). However, the email address is still of the form handle@virginia.edu. Students still receive blue.unix accounts (also known as “home directory” accounts) which provide (limited) storage space.

Incoming grads are expected to know the rules that govern your email and what is considered acceptable behavior for usage of your account. Keep in mind that this is a UVa policy, governed by ITC and not the Astronomy Department. To make sure you all know the ABCs of the UVa Computer Usage Policy, ITC has set up an online quiz which you must successfully complete before you receive your initial password. The quiz is located here: http://www.itc.virginia.edu/accounts/studentaccounts.html

The quiz is not long or difficult; I was actually quite amused at some of the questions asked. See what you think.

Once you’ve taken the ITC computing quiz, you will be given a randomly generated password for the ITC accounts including mail and web storage. Make sure you take note of this password, you will need it to register your email, accessing any UVa computers outside of the Astronomy network, and for other ITC services such as getting access to the wireless network on campus, and downloading digital security certificates.

The second essential part of the accounts process involves setting up your new Astronomy Department accounts. You may contact me at any time after you have received and accepted your position as an incoming student to get your email and Unix accounts setup and activated within the department. My email is astro-help@astro.virginia.edu. Most people primarily use their astronomy account, partly because it provides considerably more storage space for email and other work. Also, keep in mind that much of the email from other Astronomy Department members that is sent to you will be sent to your Astronomy account, so you need to either check it regularly, or arrange to have it automatically forwarded (§3.5) to an account that you do check regularly.

Skip to the section on mail registration below (§3.4) in this document for more information about setting up accounts.

3.3 For Postdocs, Staff and Faculty

ITC does not by default set up email or web space accounts for postdocs, staff or faculty unless specifically requested by the user or by the department.

Faculty, postdocs and staff are asked to take and complete the responsible computing quiz located at:
http://www.itc.virginia.edu/accounts/facstaffaccounts.html

If you would like more information on the accounts ITC has to offer, this page will answer your questions:
http://www.itc.virginia.edu/helpdesk/accounts/

Once you contact ITC, staff and faculty (including postdocs) are usually given a Microsoft Exchange email account (something like computingid@eservices.virginia.edu). This email account does not work well with the Astronomy Linux network (there is some limited functionality, but only a recent version of Windows Outlook allows full access).

Of course, the Astronomy Department is more than happy to create email and Unix accounts for anyone working with us on our local servers. Most people prefer this account over the ITC accounts since it allows considerably more storage space, and tends to make life simpler. If you don’t plan to use your Astronomy Department email account, please arrange to forward any email (§3.5) that is sent to this account to an account you do check regularly. Otherwise, you may find that you are missing many potentially important emails.

You are welcome to contact the Astronomy Department computer support at
astro-help@astro.virginia.edu if you have further questions.

3.4 Mail registration

Now that your accounts have been created and are active, you should be able to receive mail at your_id@some_server.virginia.edu. You now need to to get your mail address registered so that you can get mail via your_id@virginia.edu.

I will be making the assumption that you will be registering your Astronomy email account, rather than the ITC accounts. If you don’t register your Astronomy email account, please be sure to arrange to forward (§3.5) any mail addresses to your Astronomy email account to an address you do check!

The web page for email registration is located at: https://ams.itc.virginia.edu/

On this page, enter your ITC computer ID and password. First, you’ll want to “Manage a Deliverable Address”. Enter your Astronomy account in the space provided and submit the form. You should receive an email sent to your Astronomy account asking you to confirm this address for your account. Follow the link in the email to confirm the account.

Next, you’ll want to create an alias (this is explained in more detail in §3.4.1). You must create at least one alias, which is that of your user ID (for example hbp4c). Without this, an email sent to your_id@virginia.edu will fail.

Once the email registration is complete (see §3.4.1), within a few minutes you should be able to send an email to your_id@virginia.edu and have it arrive in your Astronomy email account.

3.4.1 Email Aliases

While registering, you’ll probably want to set up an email alias or two for yourself (on this same website). These are of the form alias@virginia.edu. The first alias you want to add is your computing id. In the middle of the form, enter your computing id and check availability (it’s guaranteed to be available). Click add to create the alias. You’re also welcome to add any other email aliases to your account if it’s not already in use by anyone else on campus. Some typical ones are [firstname]@virginia.edu, [first initial, last name]@virginia.edu, or you may choose something meaningful to you [ex. Im2cool@virginia.edu]. The only limitations are no profanity (or forms thereof) and nothing that can be mistaken for another person’s handle (so no initials, or initials/number, etc which look like UVa IDs.). Finally, if the alias has been used before it may or may not be recycled, at the postmaster’s discretion.

What email aliases can do for you:
Email aliases allow you to receive email at a simpler email address.

What email aliases do not do:
Email aliases only work for email. You cannot use them as login ids for ITC or departmental computer accounts or web space accounts. If ITC or the computer admins ask for your account name, please use the original id (your “handle”), not the alias.

The ITC accounts management system https://ams.itc.virginia.edu/ allows you to create or change email aliases.

3.5 Mail Forwarding

Mail forwarding is a useful way to make sure that mail does not get scattered around among multiple accounts. If you decide that you want to receive email at another account (ex. a web-based email account for while you are traveling) you can use mail forwarding to do this. Mail forwarding simply forwards the emails to another location and keeps no records of the message; keep this in mind so that you do not loose messages.

To set up mail forwarding, you will need to create/edit a file. In your home directory (on a Linux/Solaris workstation), create a file in using your favorite editor called “.forward” without the quotes. The preceding dot is essential (it indicates that this is a special “dot” file). In this file, on the first line, simply type the complete email address that you wish to send the emails to. When done, save and close the file. Immediately, any new emails you receive on the mail server linked to this computer will be forwarded to wherever you specified. Because mail.astro.virginia.edu handles all of the mail in the department, any mail sent to any server name.astro.virginia.edu will be forwarded by mail.astro.virginia.edu to the forwarding address you specified) To disable forwarding from this machine, simply delete (rm) or rename (mv) the .forward file.

You may also want to forward any email sent to your ITC accounts to your Astronomy account, just in case someone sends you an email to the long address of one of your ITC accounts. This website should help you set up the forward: http://www.itc.virginia.edu and search for “forward email”.

3.6 Checking email

The final part that you need to know is how to check you new email account on the Astronomy server. This information is only for those who decide to keep mail on mail.astro.virginia.edu; the procedure on other servers will vary.

3.6.1 The Easy Way^TM:

If you will be using the Unix workstations (Solaris or Linux) then the easiest way to simply read your email is the pine program. Since email is stored on the same network that you log into, simply typing the word “pine” at a dollar sign prompt should work for you. You can use the arrow keys and the Enter key to navigate around in the pine program (which has an interface reminiscent of DOS), and the bottom two lines of the screen give you additional commands you can use (for deleting, expunging and forwarding emails). The advantages of pine are that it is lightweight, fast, and works on a variety of platforms. However, the GUI-based IMAP email readers offer far more functionality to the user.

3.6.2 UVa Astronomy Webmail

The UVa Astronomy Department uses a webmail program which allows users to check their mail via any web browser from anywhere in the world. The URL for this service is https://www.astro.virginia.edu/webmail. This can be a very useful alternative if you don’t have access to your native IMAP email reader.

3.6.3 Using an IMAP Email Reader:

Most email programs understand the IMAP protocol. IMAP keeps all the email on the central mail server. Any changes you make, including deletions, are synchronized between any computers and mail clients you use to read your mail. Hence, what you see in Thunderbird is what you’ll see in webmail, etc. I highly recommend using IMAP.

The information you will need to set up an IMAP mail program is

                                                                                  

                                                                                  
IMAP Server: mail.astro.virginia.edu
 
Port: 143 (Default - Unencrypted)
 
Port: 993 (Recommended - Uses SSL for encryption)
 

 
SMTP (Sending) Mail Server: mail.astro.virginia.edu
 
Port: 25 (Default - Recommended to use SSL for encryption)
 

 
Note: If you use email off campus, you will need to login and
 
supply a password to send mail.
 

 
Login: (Your login id)
 
Password: (Your password)

An example of a good multi-platform (Linux/Unix/Windows/Mac OSX) IMAP email program is Mozilla’s Thunderbird, while Microsoft Outlook and Outlook Express run under Windows and Apple Mail runs under OSX. Feel free to use whichever mail program you feel most comfortable with.

3.6.4 Using an POP3 Email Reader:

POP3 is an older email protocol that predates IMAP. POP copies the mail off of the server, deletes it from the server (by default; can be over-ridden), and then your email only exists locally on your own machine. If you visit another machine and check your email, you will only receive the email messages sent to you since you last popped your email elsewhere. As such, you can easily scatter and loose mail. Consider yourself warned that this can be disastrous if you are not careful. I discourage using POP.

POP3 Server: mail.astro.virginia.edu
 
Port: 110 (Default - Unencrypted)
 
Port 995 (Recommended - Uses SSL for encryption)
 

                                                                                  

                                                                                  
 
SMTP (Sending) Mail Server: mail.astro.virginia.edu
 
Port: 25 (Default - Recommended to use SSL for encryption)
 

 
Note: If you use email off campus, you will need to login and
 
supply a password to send mail.
 

 
Login: (Your login id)
 
Password: (Your password)

3.7 Spam

Unfortunately, we often receive high volumes of spam in our email accounts. Our websites at UVa are routinely scanned by spammers outside of UVa who look for email addresses and send tons of crap to them in hopes we’ll do something stupid such as give them credit card information.

We are trying to combat this problem by upgrading our mail server with what we hope is the latest and most effective ways to reduce spam. However, we cannot completely eliminate it.

In the Fall of 2006 ITC purchased a commercial piece of hardware called the IronPort, which is reputed to be a very good way to reduce spam. Currently, this device has been deployed for all ITC email accounts, and actively scans any emails incoming to a virginia.edu email address. Additionally, our departmental email server tries to filter spam further, with varying degrees of success.

Many modern mail programs like Thunderbird have a junk filter built into the program which can be trained to recognize and reduce spam. I highly recommend looking into using these features - if you need any help please contact astro-help@astro.virginia.edu.

Realistically, the best way to reduce spam is to make sure that you’re not a cause of it - don’t give out your university email address except to people you know are going to send you legitimate stuff. Many illicit websites and mailing lists collect email addresses which they later sell to other companies for additional revenue. Once your address is sold, it’s going to be very hard to track it and remove yourself from those lists.

If you must sign up for mailing lists or at websites for some reason, you can create a ”disposeable” email address using the special plus notation. To create a disposeable email, simply take your normal email handle (for example, hbp4c), append a plus sign ”+”, and then make up something to identify that this was used to sign up for a list (the name of the item you’re signing up for works well.) The result is something like this:

hbp4c+apple_news@astro.virginia.edu

Now, within your email program you can filter any messages sent to your disposeable email address and send it to a special folder or to the trash folder so that it’ll be deleted later. Note that you must use astro.virginia.edu, if you send the email to virginia.edu it will be rejected. Note also that some web sites check for the plus sign notation when you’re signing up for a list, and will reject the email as invalid.

For web pages, you may want to include an email contact so people can reach you easily. To keep your email from being collected, you can also post your email address on the web in “raw” form, simply using the html code for the @ symbol (&#64;). This will help defeat simple web bots that scan our web site for email addresses. Something like <mailto:hbp4c&#64;virginia.edu> in your html code should keep basic web crawlers confused, but real users will still be able to click the link and send mail to you as the expect.

Additionally (and this is very important although non-intuitive), make sure that your home computer is always up-to-date and patched with any security fixes and is running the latest software. The average home computer has at least one virus or spyware on them, and when you couple that with some sort of dedicated high-speed internet connection, your computer becomes part of the spam problem by relaying messages or generating spam for those who wrote the virus or spyware.

3.8 Mailing Lists

We use many mailing lists in the department to keep each other informed on current events, interesting topics, or social gatherings. To use any of these lists simply send an email to the list address just like you would a normal person’s email.

3.8.1 Subscribing to Mailing Lists

You can subscribe to any mailing list using the web interface for the mailman mailing system. http://mail.astro.virginia.edu/mailman/listinfo/

Incoming students, staff or faculty are subscribed by default to one of ugrads, grads, postdocs, faculty or staff. You are also by default subscribed to the colloquium mailing list.

If you’re a subscriber to a list, you can change options or unsubscribe yourself at the same location.

3.8.2 Making new Mailing Lists

If you want to create a new mailing list, simply contact the admin, who can set one up for you. astro-help@astro.virginia.edu

3.9 Email while away

When you are away visiting another site, it is not always convenient to configure an email program with your mail settings to check your mail. It is not always possible to find an available mail program to log in to mail.astro.virginia.edu. If you are traveling with your laptop, however, it is usually possible to use Thunderbird if you have it configured properly.

The UVa Astronomy Webmail program is an easy way to check your mail remotely. The website for this is:
https://www.astro.virginia.edu/webmail

We have also set up a website with a java-based ssh application which will allow you to at least run pine to check your email quickly when afar. This page is at:
http://www.astro.virginia.edu/~hbp4c/computing/MindTerm/ssh.html

3.10 LDAP Address Books

There are two distributed address books available to UVa personnel. One is a departmental address book, the second is the UVa global address book. You can configure one or both of these address books depending on your needs.

The Official UVa global address book only includes students, staff and faculty here at UVa. Some long term visitors who have ITC email accounts should be in the global address book, but this is not always true.

The Astronomy Department address book includes all the astronomy visitors plus students staff and faculty within the department.

Setting up an LDAP address book is different in each mail client, so I’m giving the general instructions below.

The following are the settings for accessing the UVa Global Address Book:

LDAP Server: ldap.virginia.edu
 
Port: 389
 
Search Base: o=University of Virginia,c=US
 
Scope: Subtree
 
Authentication: None

The following are the settings for accessing the Astronomy Department LDAP Address Book:

LDAP Server: ldap.astro.virginia.edu
 
Port: 389
                                                                                  

                                                                                  
 
Search Base: ou=People,dc=astro,dc=virginia,dc=edu
 
Scope: Subtree
 
Authentication: Simple
 
Login: uid=(Your Astronomy Computing ID),ou=People,dc=astro,dc=virginia,dc=edu
 
Password: (Your Astronomy Password)

Note that “Login” is known as “Bind DN” in Thunderbird.

Please copy and paste the Search Base listed above into your address book program for best results.

It is not necessary to use authentication for either of the two LDAP address books. However, authenticating to the Astronomy LDAP server allows you to see more detailed information in the address book about other users (such as home addresses and phone numbers) which anonymous connections cannot access.

3.11 winmail.dat Attachments

In some lesser cultures people rely on Microsoft Outlook software to organize their email and life. It’s unfortunate, because in typical Microsoft fashion they’ve decided to create their own proprietary format for sending email messages no no other software (including the free version of Outlook Express) can decode.

When a user using Outlook sends an RTF or HTML formatted email (which allows them to modify the fonts and insert pictures inline with text) and when these people attach any file to that email, the receiving person gets a file attachment named winmail.dat. This file is the Transport Neutral Encapsulation Format (TNEF), which contains the message content as well as any formatting information and finally the attachment. Almost every other email program on the planet uses MIME (Multipurpose Internet Mail Extensions) which is a much-relied-upon industry standard.

You can decode these winmail.dat files on the Astronomy Linux platform by using the tnef executable:

                                                                                  

                                                                                  
$ tnef -f winmail.dat

Another solution (if it’s available to you) would be to forward the email to a gmail web email account.

3.12 Final Notes about Email

There are a couple of final notes about email you should be aware of.

If you are going to be off campus using an external (non-UVa) Internet Service Provider, then you will probably experience problems sending emails from your computer. If this occurs, contact your ISP and find out the correct SMTP server information and use that instead of the above SMTP servers.

If you have any problems with email, feel free to contact the friendly Astronomy Systems Administrator. The email is astro-help@astro.virginia.edu. Of course, if you are having problems with email, it may be difficult to email anyone. If this occurs, the main departmental phone number is 434-924-7494. Ask for a computer admin and the secretary will connect you.

Chapter 4
Resources

This chapter will describe some of the resources we have available to members of our department, such as what kinds of computers, how to get on the wireless network, and what is the names of our computing clusters in the Astronomy Department.

4.1 Computing Resources

The Astronomy Department has a wide variety of computer resources available for students, staff and faculty and those visiting our department. This section of the guide is intended to give you an idea of what is available, and where to go about finding it.

4.2 PC/Macintosh Computing Workstations

The Astronomy Department maintains multiple Windows workstations located in room 213 (the AV Room). There an additional permanent computer located in the teaching classroom (Astronomy 265) as well as one computer for presentations in the Classroom at McCormick Observatory. All of these computers are up to date with the latest patches and software fixes from Microsoft, including the Microsoft Office suite of programs.

To connect to the Unix workstations and share data, one can use the SecureFX and SecureCRT programs (works like secure copy and sftp in Unix) or you can use the z: drive (the astro_users), the y: drive (astro_owners) or the h: drive (which connects to your unix home directory). These special network shares are samba networked drives connected to a Linux server.

Any user can connect their personal laptop to the astro_users and astro_owners directories, or your unix home directory. The network paths are \\ORION\astro_users and \\ORION\astro_owners. For your unix home directory, connect to \\ORION\user_id where your user_id is the name you log in with to a Linux machine. Note that this will only work within the Astronomy Building, McCormick Observatory and/or Clark 107.

The following computer lab areas are subject to change at any time.

4.2.1 AV Room - Room 213

The Audio-Video Room has five Windows XP workstations and three Linux Workstations. The poster plotter davinci is also located here, as well as the black and white laser printer named astro-hp. (Well, perhaps the a reminds you that it is in the AV room?) The departmental collection of slides and videos (VHS and DVD) are also kept here.

4.3 Tapes

We maintain a selection of data tape drives for reading and writing from our Linux and Solaris workstations.

4.3.1 Reading Tapes in Linux

There are no public workstations with tape drives attached. Please email astro-help@astro.virginia.edu and describe which drive you need, and something can be arranged.

To use a tape drive connected to a Linux workstation, find the drive you need, and log in to the computer next to it (you can do this remotely, using ssh, from your own desktop). Tape drives may be re-arranged as needed, so don’t be surprised if the drive is moved to another machine.

First, cd (change directory) to the location where you will load your data (note, you cannot load your data directly to /local on your own workstation, because your /local is not visible to the tape drive host computer). Then, use tar to read (extract) the data from the device (the device name is located on a sticker attached to each drive, but see note below). Finally, rewind and eject the tape with the mt command. Note, to avoid potential data loss, you should read the man pages for tar and mt before reading and writing tapes.

A note about tape drive names. Each tape drive actually has multiple names, of the form /dev/(some letters)(a number). The number is the SCSI chain number; this will be unique to the drive. However, each drive can have different combinations of letters in the name, which contain information about the density to use when reading and writing tapes. They also contain information about positioning the tape. If you add an “n” to the device name immediately after the /dev/, this instructs the drive not to rewind the tape after you finish reading the current tar file (this is known as the “no-rewind” option). Tapes often contain multiple tar files; you will need to use the “n” switch in order to read anything other than the first tar file.

tar, which stands for tape archive, is a single file (on tape or disk) which can contain not only files, but also directory structure, with subdirectories and the files therein. The syntax for tar is special in that you aren’t required to use a “-” before the lists of options.

$ cd /local
                                                                                  

                                                                                  
 
$ tar xvf /dev/nst0 (note the ‘‘n’’ that has been inserted into /dev/st0)
 
$ tar xvf /dev/nst0
 
$ tar xvf /dev/nst0 (...until you have extracted all of the tar files you need)
 
$ mt -f /dev/nst0 rewind
 
$ mt -f /dev/nst0 offline

tar can also read (extract) and write (create) gzip compressed tapes, using the -z option.

$ tar xzvf /dev/nst0
 
$ tar czvf /dev/nst0 ‘‘source’’

If you don’t know if a file is actually located on a tape, the -t (table of contents) option to tar will give a listing of the files in a particalar tar file. Note that tar stands for “tape archive” and can contain many files, and even subdirectories and the files contained therein.

$ tar tvf /dev/nst0

If you want to write a tape, use the -c command (create) in tar. You will not get a warning if you over-write a previously used tape, so be sure to use the mt command to correctly position a previously used tape before writing.

                                                                                  

                                                                                  
$ mt -f /dev/nst0 eom (optional, for a tape already containing data)
 
$ tar cvf /dev/nst0 /local/mytape/

Never try to remove a tape which has not been properly rewound and marked as offline. Doing so can jam the drive and destroy your tape.

4.3.2 Reading Tapes in Solaris

If you need to read a tape on a Sun Solaris machine, please contact
astro-help@astro.virginia.edu.

The commands to read and write tapes in Solaris are the same as in linux, tar can read and write tapes, and mt will rewind and eject tapes. Notice that in Solaris, the device name for the tape drive is usually different - for example the first tape drive is usually named /dev/nrmt/0 (here again, the “n” stands for “no-rewind”). The correct device name is labeled on each tape drive.

4.4 Scanners

The Astronomy Department maintains both a flatbed-style scanner and a slide scanner in the AV Room for public use. Additionally, the xerox copy machine in the main office can scan black and white copies and mail a PDF file to any email address.

4.4.1 AV Room

The Windows XP computer in the Audio-Video room has a Nikon Coolpix slide scanner and an HP flatbed scanner with an automatic document feeder attached to it. You can either use the HP scanner as a simple flatbed scanner (open the top and place your document on the glass) or you can load the document face up in the ADF tray, and press scan. The scanner will automatically detect where your document is located and begin scanning.

When you press the scan button, a dialogue will pop up on the PC asking what program to send the image to. I recommend either Adobe Photoshop, Acrobat or the Gimp software package.

4.4.2 Xerox Scanner

The main office has a Xerox photocopier that can scan very, very quickly in black and white and produce a multipage PDF file (for color scans you will need to use the HP scanner). The PDF file then can be mailed to any email address, or transferred to the astro_users directory. There is no charge to create and mail a PDF from the Xerox machine.

4.5 Wireless Ethernet

Most of the office buildings and classrooms at UVa have a wireless ethernet 802.11b or 802.11g network. ITC provides and requires that you register your wireless enabled laptop with their systems before you will be allowed access, guests included. You can do this at
http://www.itc.virginia.edu/wireless.

There are two wireless networks available in most locations. The first is an unencrypted network named “wahoo”. To use wahoo, you will first have to register your wireless card with ITC via the link above (you will need to know your ITC password to do this), then you will have to add the wahoo network to your preferred networks on your computer. Wahoo is not broadcast, you have to know that it is available to use it.

The preferred wireless network is named “cavalier” and is broadcast in all wireless locations. This networks relies on security certificates to encrypt the communication between your computer and the wireless hub. To use this network, you will first have to register the card with ITC, then you will have to register for and download a security certificate for your computer to be able to generate the correct encryption keys. The instructions for this are included at the ITC wireless website.

Wireless is available (although coverage is spotty) at McCormick and Fan Mountain, but it not provided by ITC. Please check with one of the caretakers for more information on getting on the wireless networks at these two locations.

For visitors and guests, a special wireless network called “Astro_visitors” is available throughout the Astronomy Building. This network does not require registration of the network card, but it does require a wireless password. Please contact
astro-help@astro.virginia.edu for details.

4.6 Astronomy Computing Clusters

The Hyades Computing Cluster is a Beowulf-style computing cluster intended for medium-sized parallel processing jobs. It is based on Dell PowerEdge (Pentium IV) hardware with both InfiniBand and gigabit interconnect networking. The cluster runs the ROCKS Clusters Linux distribution along with the PBS job submission software for parallel job queueing. The typical jobs run here are Fortran and C code written using the MPIch message passing libraries for node communications.

The Pleione Computing cluster is also a Beowulf computing cluster for single-threaded and embarrassingly parallel jobs. It has similar specs to the Hyades cluster, but does not have InfiniBand networking.

Please note that the Hyades cluster is reserved for parallel jobs. Any programs which do not intercommunicate between nodes can easily be run elsewhere on faster machines, such as in the Linux and Solaris Computing Labs or on Pleione. This policy is to protect the students and faculty who need the parallel processing ability to carry out their work.

ITC also maintains multiple clusters for different types of computational problems. Dogwood is ITC’s computer cluster which runs the same operating system and PBS software are Hyades. ITC is also building more clusters for specific purposes, please see http://www.itc.virginia.edu/research/linux-cluster/ for more information.

For more information on the Hyades or Pleione clusters, please see
http://www.astro.virginia.edu/~hbp4c/computing/hyades/hom.pdf.

4.7 Software

As a student, staff or faculty member here at UVa, you are entitled to free and reduced price software licensed by ITC. These software packages include the Symantec Antivirus software package, Spysweeper, and even the IDL programming package can be obtained for use on your own personal computer at home.

4.7.1 ITC Software Central

http://www.itc.virginia.edu/central

ITC’s Software Central website includes the major packages that are useful for the general community. Included in these are the Symantec (Norton) AV package and the SecureCRT/SecureFX tools for ssh-based communications with Unix servers.

4.7.2 ITC Research Computing License Database

https://www.web.virginia.edu/rescomp/ldb/SoftwareInfo.asp

ITC’s Research Computing Center is a wealth of information for anyone doing computational-centered research such as IDL, Fortran and C programming. Additionally, their License Database allows you to check out a software license for many of the major computing packages; eg., IDL, Matlab and Mathematica.

4.7.3 Microsoft Campus Contracts

http://www.itc.virginia.edu/licenses/

The University of Virginia has entered into an agreement to cover the limited usage of certain Microsoft software products for school related work. If the computer is owned by the deparment or the University, then any Microsoft products such as Windows or Office can be purchased or installed cheaply or in some cases for free, depending on the software. If the computer is NOT owned by the University, then the only software that could possibly be used via the contract is Microsoft Office. Visit the link above for more details on how to take advantage of that.

Chapter 5
Computing Services

In the final chapter of this handbook, we’ll go into more depth for a couple of very important and heavily used software tools in our computing network - file sharing between Unix and PC, and printing.

5.1 Samba

Samba is the OSS name for the Microsoft protocol to share network drives and printers between Windows based computers. Here in Astronomy, we have a Linux based machine running the Samba software to help facilitate linking Windows computers and our Unix workstations.

The Samba network shares require a user name and a password, these are the same as the name and password you can use to log into any public PC in the Astronomy Building.

We have multiple shares for different purposes. For a list of Samba shares, please see Table 5.1.

To connect to the Samba server (orion.astro.virginia.edu), follow the directions for your operating system:

5.1.1 Windows 2000, XP, (Vista?)

Open “My Computer” and click on “Tools” then “Map Network Drive...” (See Figure 5.1.)

Enter the location to connect to. (Figure 5.2.)

Enter the user name and password. (Figure 5.3.)

...And you’re now connected. (Figure 5.4.)

Note that you connect multiple drives, you will just have a assign a new letter to each one (Z:, Y:, X:, etc.).

5.1.2 Mac OS X

To connect in Mac OS X, follow these steps:

In the Mac Finder, click on “Go” and then “Connect to Server...” (Figure 5.5.)

Fill in the server information (see Figure 5.6.)

Enter the username and password (Figure 5.7.)

When you are done using it, you can disconnect the drive by dragging it to the Trash.

5.2 Printing

There are three main types of printers available for the computer users in the department (and at the observatories). First; we have a number of black and white laser printers distributed throughout the department (and at the observatories). Second, we have a single color laser printer located in the main office, and finally, we have the special use poster plotter located in the AV room. All of our laser printers can be accessed from any Linux or Solaris workstation, as well as any departmental PC or Mac. People who bring in laptops are welcome to add the printers to their operating system (see §5.2.6). For a list of available printers, please see Table 5.2.

In Table 5.2, there is listed a cost per duplex page. Currently, the department does not charge for printing. This cost category is only listed for reference and only reflects the cost of raw materials (paper and toner) and not maintenance or the cost of the printer hardware. For laser prints (all but the poster printer) we assume a ream of paper (500 pages) costs $3.26 (or $0.0065/page) and 5% coverage of toner/page. For poster prints on Davinci, we have assumed 35% coverage per color for a poster size of 36”x48”.

Please only print docouments that you need (and remember to pay for printing non-work related documents). Remember to pick up your printout from the printer; a significant quantity of paper that is printed is never picked up from the printer - if it isn’t important enough to pickup, then presumably it wasn’t important enough to print. There are trays next to most printers where documents awaiting pickup should be placed (these trays are not for recylcing; there are boxes for that purpose).

5.2.1 Printer Locations

As you can see in Figure 5.8, the black and white laser printers are evenly distributed throughout the building. For information on how to set a default printer, see §5.2.6.

5.2.2 B&W Printing

The HP Laserjets all are black and white printers. All of them are equipped with duplexers and can print at high resolution on both sides of the paper. Duplexing is the default when printing from a Linux or Solaris workstation, but please be sure to select this option when printing from a PC or Mac in order to save paper. The main printers in the computer labs (astro-hp, cosmos-hp and whirl-hp) are very high speed printers.

5.2.3 Printing to the Xerox Copier

The Xerox copier in the Astronomy main office also functions as a high-speed, high capacity printer (called xerox) with lots of useful functions that the other printers cannot offer, such as stapling.

Some features of the Xerox printer may not be available on all operating systems.

5.2.4 Color Printing

The printer named colour is a color laser printer. Colour is able to print in duplex mode just like the black and white printers. Compared to our black and white printers, colour is slow, and very expensive per printed page. Please use this printer only for color prints. Please do not print black and white documents on colour. If you have a large document with only a few pages of color, you should consider printer the bulk of the document on another laser printer, and sending only the color pages to colour.

5.2.5 Poster Printing

The last special printer is designated for printing presentation-quality posters only. The printer davinci is a 42-inch inkjet-based printer. When designing a poster for this printer, use the Arch E format for paper size (this will produce a 36-inch by 48-inch poster which is correct for the AAS meetings.) Please remember that this printer incurs a large cost due to the amount of ink and the cost of the paper. You may be charged a fee for using this printer.

The AVPC in room 213 is the only computer attached to the poster printer. This PC knows how to print PowerPoint documents, PDFs and many other formats. Most people use PowerPoint to build their posters. If you make a PowerPoint document on any platform other than a Windows PC, you should proofread the result after you load it onto the AVPC, before printing to davinci, as many errors and font problems can occur when moving the file from another platform.

Note: If you print a PDF document, please note that there is a known software bug which will cause a clipped poster to be produced if you don’t take a couple of extra steps. A poster prepared with Adobe Acrobat will be clipped at the 27-inch mark if you don’t scale the poster to 100% of it’s normal size when printing from a PC (this is a Adobe Acrobat/HP plotter communication issue). To do this, go into the printer properties and look at the finishing tab. There you’ll have a choice to print the poster at it’s original size, or print it at a percentage value. Choose the percentage value and type in 100%. This simple, and non-intuitive change will produce a normal-sized, problem-free poster.

Also, note that at any time you can lift the hood on the poster printer to see how the poster looks. If something is wrong, press the orange “Cancel” button to stop the printer before wasting anymore ink. You should always examine the poster as it begins plotting to ensure there are no problems. The paper and ink are very expensive.

5.2.6 Printer Setup

Use the following directions to set up printers on your own computer (laptops, etc).

Linux and Solaris

The laser printers are already networked and ready to use from our Unix network. The default printer for new users is usually set to be astro-hp; you can (and should) change this to the black and white printer located closest to your office. This is usually set in your .cshrc (or .bashrc) file; simply change the printer name, save the file, and “source” the .cshrc (or .bashrc) file:

When printing a single file, you can override the default printer with the -P option (for lpr, enscript and dvips, for example). This is useful when you need to print a color document: lpr -Pcolour colorfile.ps

Some programs have settings which might override the defaults you have set; you may have to edit the settings (often in a “dot” file for that task).

Windows XP

You must be logged in as an administrator to install a printer.

Note: If you’ve mapped the Samba network drive as described in section 5.1, you can find up-to-date drivers for the printers in the folder z:\Printers\.

Begin by opening the Control Panel, and going to “Add or Remove Programs”. Here, click on the icon for “Add/Remove Windows Components”. It will take a moment to build a list of programs, but you should soon see a screen that looks like Figure 5.9.

Place a check in the box beside “Other Network File and Print Services”, and then click “Next”. This installs the Line Printer Daemon Protocol for Windows XP.

Next, in the Control Panel, open the “Printers and Faxes” wizard.

This printer will be a “Local” printer (even though it’s attached to a network; this is a Windows terminology problem). You’ll have to create a new port (an LPR Port) before you can add the printer.

The print server name is calisto.astro.virginia.edu, and you can choose whichever printer you want to add to the queue field. You’ll finally be allowed to choose the correct print driver for the printer, and decide if you want to print a test page or not. When you finish the wizard, you’ll be able to print from any program to the newly installed printer. (Please see Figures 5.10 through 5.16 for step-by-step examples of adding a new printer to a Windows XP machine.)

Mac OS X

Note: The GutenPrint project provides high-quality printer drivers for many more than the standard printer drivers that ships with Mac OS X. Find out more at
http://gimp-print.sourceforge.net/MacOSX.php3.

Open the hard disk and look inside the /Applications/Utilities folder. Inside should be a program called “Printer Setup Utility” (see Figure 5.17).

When you open this program (see Figure 5.18), you’ll be able to set up additional printers for your system. To print to astronomy printers, click on “IP Printer”, and then choose the “Line Printer Daemon - LPD” protocol. Fill in the additional blanks as you can see in the figure - Address is calisto.astro.virginia.edu, and choose which printer you want to use and type it into the Queue. The Name field is arbitrary, so call it something that easily distinguishes from other names. The Location field is also arbitrary. Finally, you can either use the generic postscript printer driver or assign a specific driver from the list.

After you close the utility, the printer will automatically be ready for you to use. You can assign preferences at print time (such as setting double-sided settings, etc).

5.3 Xerox Copier

The Xerox Copier in the Astronomy main office functions as a copier, fax machine, printer and scanner. When you use the Xerox machine, it’s usually best to clear the settings with the “clear all” button before beginning a job.

The basic usage and quick start guide for the Xerox machine can be found at
http://www.astro.virginia.edu/~hbp4c/computing/handbook/xerox.pdf.

The information below will fill in the details for the email and network scanning functions.

5.3.1 Xerox Scan-to-Email

The Xerox machine in the Astronomy main office can scan any document and produce a pdf or multi-page tiff image which it will then email to any recipient with a valid email address. Notice that large documents (in excess of 20MB of data) cannot be sent through our mail server. (A typical 50 page PDF file usually is 1MB to 2MB in size.)

To email a document, first “clear all” of the settings on the machine. Next, choose the email function, and enter the recipient address in the “To:” section. If you wish, you can modify the “Subject:” section and add any secondary recipients to the “Cc:” or “Bcc:” sections of the menu.

Keep in mind that the emails will always be sent from the email address
astro-help@astro.virginia.edu. If the email fails to send due to a problem, the failure notice will also be routed to this address. Likewise, if someone replies to an email sent by the Xerox machine, it will go to this address. This address is the default mailing list for the Astronomy Department computer admin(s). You may find it easiest to simply mail the file to yourself, and then send it to any intended recipients from your own email client (so that it shows your return address).

5.3.2 Xerox Network Scanning

Similar to the Scan-to-Email function, the network can scan any document and produce a PDF or multi-page TIFF image which it will save on the astro_users Samba share. Any files scanned and saved will be located in z:\xerox\ (Windows), //orion/astro_users/xerox/ (Mac) or /mnt/astro_users/xerox/ (Unix).

Please remove any files once the scan is completed - new scans by default overwrite the original file. The user scanning the next file can explicitly choose a new filename, but if they don’t decide (or remember) to do this the old files will be overwritten.

5.4 CVS

The Astronomy Department maintains a CVS (Concurrent Versions System) repository at cvs.astro.virginia.edu. This CVS repository requires it’s own username and password that are completely separate from the main Astronomy computing network.

CVS is very useful if you want to maintain multiple versions of something (code, html, latex files, etc.) in case you ever want to revisit an earlier version for any reason. CVS is actually a very old system dating from the mid 80’s, so the commands are kind of clunky, but the technology is stable and reliable.

To connect to CVS, you must first get an account on the CVS server. Contact
astro-help@astro.virginia.edu to request an account.

To set up your environment to use cvs, you can set the following variables:

C shell syntax:

(ba)sh shell syntax:

Replace USER with the user ID that the sysadmin set up for you.

Next, you’ll want to log in:

Enter the password you were given. Then run

Replace PROJECT with the name of the project you’re working on. This creates a directory named PROJECT, containing all of your files. This is created in the current directory (where the cvs command is run), and this is now your personal copy of the files.

Any time someone has made a change in the repository that you want, just run

in your PROJECT directory. This gets you the latest copy of everything in the files, and identifies which files in your own copy that you’ve changed. It will not overwrite your changes; if there is any conflict between your changes and ones that someone has added to the repository, CVS will let you know, and you can reconcile this by hand.

If you want to see how your own file is different from the repository copy, use:

To get a modification history on a file, use:

If you think you know what you are doing, and you are sure your changes are ready to submit to the repository, you can use the following commands:

5.5 Subversion

Like CVS, Subversion (I’ll refer to as svn) is another versioning system where users can checkout and checkin file changes which are tracked with a log.

Subversion is a “modern replacement” for CVS. Among its many features is a much better implemented control over branching and merging projects (which are possible under CVS, but most people find them very difficult to manage).

To connect to svn, you’ll need a repository completely unique to the svn service. Please contact astro-help@astro.virginia.edu to request a repository.

The UVa Astronomy Department svn server is located at
https://svn.astro.virginia.edu/svn/REPOSITORY.

You’ll need to replace “REPOSITORY” with the actual name of a subversion repository to which you have access.

The Subversion guide at http://svnbook.red-bean.com/ is a very good resource on how to use svn.

5.6 Wiki

Note: the functionality of the wiki, plus added features, are now available from an ITC-supported package called Collab (which is also replacing “toolkit”, used for instruction). Please see collab.itc.virginia.edu for more information and please consider setting up any new wikis on Collab.

The Astronomy Department wiki website is located at http://www.astro.virginia.edu/twiki. A wiki is a general whiteboard application where anyone who has access can write anything they want or upload new content at their leisure (twiki is the “brand name” of our particular implementation of wiki). Many people in the department (and outside collaborators) are using the wiki as a collaboration tool to share ideas and talk about subjects.

To login, you must first login as a guest (login as TWikiGuest, no password) and create your own account so you can post content and modify pages that already exist. Once your account is created, you simply type in the name of a page you’d like to create, and then follow the examples the application gives you. Note that after creating your account, you will have to close your browser and reopen your browser to log in with your new account - this is because there is no “logout” feature to end your TWikiGuest session.

5.7 www

The Astronomy Department maintains it’s own web server, http://www.astro.virginia.edu. Here we have information about classes, research, observatories, colloquia, etc., which is all stored directly on this server’s internal disk and distributed to the world.

To access the data stored on the web server from any machine look at the directory /net/www.

Note that normal unix permissions apply, so if you don’t have write access you won’t be able to change any files. For information, please contact the webmaster at
webmaster@astro.virginia.edu.

5.8 MySQL

The Astronomy Department maintains a central MySQL server and database available for use on projects and websites. For information on getting access to MySQL, please contact astro-help@astro.virginia.edu.

5.9 VPN

VPN is a very useful system when working in a remote location such as your home or while traveling. VPN provides you an encrypted network connection directly back to the Astronomy Department, and any traffic that uses that tunnel appears to come from the VPN server located on campus. This means that by using VPN, you will have access to any library resources (including journals), any Astronomy computing services (including Samba) and anything else that you can typically only access while on campus.

If you have changed and synchronized your password on the Accounts Management site, https://www.astro.virginia.edu/accounts/passwd.php then your VPN accounts is already setup and ready.

VPN Server: vpn.astro.virginia.edu
 
VPN Type: PPTP (Point-to-Point Tunnel Protocol)
 
Login: (Your astronomy login id)
 
Password: (Your astronomy password)

5.9.1 VPN Automatic Installers

You can download a VPN installer program for either Mac OS X (10.5) or Windows computers from http://www.astro.virginia.edu/~hbp4c/computing/vpn/.

5.9.2 Manual Windows XP VPN Setup

To set up VPN if you’re using Windows XP, follow the following steps, outlined in Figures 5.19 through 5.27.

Ricky reports the following bug on Windows XP when using Firefox:

After I installed and tested VPN, the connection window kept popping up (whenever I had firefox open). To fix this, it is necessary to go to “about:config” in Firefox, and set the network-autodial-helper.enabled to “false”.

5.9.3 Mac 10.4 (Tiger) VPN Setup

Mac OS X 10.4 (Tiger) uses the Internet Connect utility to create a VPN connection. Figures 5.28 through 5.34 will help guide you through this setup.

5.9.4 Manual Mac OS X 10.5 (Leopard) VPN Setup

Mac OS X 10.5 (Leopard) moved all of the VPN settings to the System Preferences Network icon. Refer to Figures 5.35 through 5.40 to help guide you through this setup.

5.10 VNC

VNC (Virtual Network Client) is a bit of software that allows you to connect to your Gnome or KDE desktop just like you were sitting in front of the machine. From anywhere in the world, you’ll see your full desktop including any icons, backgrounds, etc that you might have customized. This setup is opposed to tunneling an application over ssh (such as running firefox) where the displayed portion of a single program gets sent to your computer.

You’ll need to download a VNC client for your laptop or home computer to connect to your desktop in the Astronomy Building. http://www.tightvnc.com/download.html contains a free client software package for Windows and Unix (including Mac) clients.

The VNC Server is built directly into Gnome and KDE. To access the server in Gnome, simply go to System - Preferences - Remote Desktop. Simply check the box that allows others to view (and the box to allow others to control) your VNC session. Make sure you set a password, so that strangers can’t randomly connect and steal your information.

WARNING: VNC is by default unencrypted. You can set up ssh to tunnel the data, but that is an advanced setup and can’t be done via the Remote Desktop preferences above. Because of this, you’ll need to be in the Astronomy building or you’ll need to first connect to the Astronomy VPN service before you start VNC. It’s highly recommended you consider FreeNX instead.

5.11 FreeNX

FreeNX (http://freenx.berlios.de/) is a VNC-like program which has many additional features over the normal VNC software. Basically, FreeNX allows you to connect to your Linux Desktop just like you were in front of it, but from any location in the world. FreeNX handles all of it’s communication over ssh (so it’s encrypted) and it intelligently caches network traffic to make the responses more ”snappy” even over slow internet links. Also, since it works on top of ssh, you do not need to first connect to the Astronomy VPN (but you can if you want to).

To set up the FreeNX client software on your home computer, visit http://www.nomachine.com/download.php. You will specifically want to download the CLIENT software, not the full package. The client software is free to download and includes everything you will need to connect to an astronomy department linux machine.

Once you have the software installed, you will need a copy of the client.id_dsa.key for the host you’re connecting to. Please contact astro-help@astro.virginia.edu for this file.