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CITA has a network of roughly three dozen workstations running Linux
(currently, Fedora Core 5). There is a machine on the desk of every
faculty member and post-doc as well as several ``public" machines in
1218. All machines share a comon home directory which
means you can sit at
any workstation or remotely login to any other system and still
transparently access all your files and applications.
You can remotely login to any system, but most workstations are used interactively during the day. The only exception is kodiak, which has no display and is intended to be used remotely. All other remote jobs are subject to the following caveats: don't run on a faculty member's machine without permission and always nice your jobs in order to minimize their impact on the person logged onto the console (e.g. nice +15 <myexecutable>&). Your first job should run at nice level 15, and all subsequent ones at nice level 20.
Jobs which require large amounts of CPU and/or RAM are better suited on our High Performance Computing (HPC) systems which include the dolphins, orca, octopus, lobsters, and McKenzie cluster. See the main HPC page for more information.On a linux
box, you can check the processor speed and memory size by looking at
the appropriate files (e.g. cat /proc/cpuinfo andcat /proc/meminfo). In order to allow
fair access to all users, please nice
all jobs which run for more than 15 minutes (e.g. nice +15 <myexecutable>&. Your first
job should run at nice level 15, and all subsequent ones at nice
level 20.
All
CITA accounts are limited to 1GB of space in their home directories.
This space is regularly backed-up onto both tape and disk but it is
still possible to lose files (e.g. if you created a new file but
deleted it before a backup ran). Email requests ASAP if you need to
restore files (let us know the filename, path to the directory and
approximate date & time of the desired version of the file).
If you go over the limit in your home
directory you will not be able to write any new files; this can cause
problems if, for example, you are automatically (or manually) storing
email in your home directory. You will also not be able to login at a
console when over-limit. You will need to login remotely (borrow a
window from somebody else) and move/delete files until you are under
quota.
Large amounts (hundreds of GBs) of temporary
disk space are available to each account (on a
first-come, first-served basis) and are accessible as /cita/d/scratch-week/<username>,
/cita/d/scratch-month/<username>
and /cita/d/scratch-2month/<username>.
Be aware that scratch space is volatile and will be purged at
the given interval. This space is never backed-up and so it is
possible to lose data at any time. You will be sent an e-mail one day
prior to
your data being erased on scratch-week and a week in advance for
scratch-month and scratch-2month.
There is also local scratch space available on
each workstation (in /scratch). In general, you will get better
I/O speeds to local disk so this space can be useful on occasion.
Create a directory with your username if you wish to use this space.
These disks can be accessed from other machines; e.g. cd
/cita/scratch/kodiak will move you to the kodiak scratch disk
from any CITA workstation. Again, this is scratch space and is never
backed-up.
In addition, many faculty and postdocs have opted to buy large
amounts of permanent space on newer raid arrays. These spaces are
accessed as /cita/d/raid-<username>.
They are backed-up and are also protected against single-disk failures
by virtue of the raid 5.
You can monitor disk usage in several different ways.
quota
-reports the disk space
you are using in your home space
du -sh .
-reports the disk spaced used in the current directory and all lower
subdirectories
df -h .
-reports the total space available and used (by all users) on the
current disk
The full name of your home directory will be /cita/h/home-x/<username>
where x is one of 1,2,3. Typing simply cd will move
you to your home directory and pwd will
show you the full path to wherever you are at the moment.
Although NFS works reasonably well, it's nonetheless true that huge
amounts of disk I/O can bog down the network, so a good rule of thumb
is that if you have a program which does a lot of I/O to/from a disk
file, it's probably better to run it, if possible, on whatever system
the disk is connected to. On the other hand, if the program does a
minimal amount of disk I/O but uses a lot of CPU cycles, it's probably
better to run it on the fastest system to which you have access.
If you're unsure of whether a disk is locally- or NFS-mounted, the df
command will tell you: The first column ("Filesystem'') will be /dev/something
for locally-mounted disks, and hostname:/whatever for
NFS-mounted disks.
Tapes,
CD and DVD Burners
It is good practice to periodically make your own backups of critical
files/data. CDs and DVDs are ideal for this purpose. For larger amounts
of data CITA has DLT and AIT tape drives. The DLT drives are attached
to chinook and dolphin4 while there is a tape
library with two AIT-3 drives and an AIT-4 drive on the main server.
Anybody can use
the chinook drive at any time. Arrangements need to be made (email
requests) for access to the other drives. Free tapes for the chinook
drive (10GB apiece) are available from the system administrator. Tapes
(35GB apiece) for the dolphin4 drive must be purchased. AIT-3 (100GB
raw capacity; roughly $70 apiece) and AIT-4 (200GB, $100) tapes must
also be purchased by users.
DVD / CD Burners:
You can store roughly 700MB on a CD. Buy CD-Rs at a local computer
store for ~50 cents (in bulk). Use k3b to burn. Drives available
on most workstations.
DVD Burners:
Available on most workstations. You can store up to ~4.7GB
on a DVD. Buy DVD-R's (check whether your burner is "plus" or "minus" - I believe most at CITA are "minus") for
about 2$ a pop (less in bulk) at local computer shops.
It's easiest to burn DVDs using k3b. If you'd like to work from the console, read on:
Probably best to copy the files you want to save to /scratch on
groundhog (access this as /cita/scratch/groundhog from any CITA
machine) then remotely login to groundhog and burn them.
To write a directory or file to the DVD (NB - when you read the DVD you will immediately find yourself _in_ this directory):
/usr/local/bin/growisofs -Z /dev/scd0 -R -J directory/file-name
If the above didn't work try just:
growisofs -Z /dev/scd0 -R -J directory/file-name
You can then write more directories or files by using -M in place of
-Z. This multi-session writing may glitch sometimes and it's
possible that the DVD's can't be read on some DVD readers (though we
have not had problems reading them on kodiak).
To write an .iso image to dvd (fedora core distribution image for example):
growisofs -dvd-compat -Z /dev/scd0=/path_to_iso/file_to_burn.iso
Useful options for growisofs (see the man page on groundhog) include
-dry-run (does everything but actually write the DVD).
Takes roughly 12 minutes to burn 2.7GB
See appendix
B for a list of CITA disks, and appendix C
for more information on using the various tape devices.
When your account is first set up, your home directories will have a
default set of dotfiles (files whose names begin with ".''), which are
used to tailor one's computing milieu. Most important are probably .cshrc
(or .tcshrc) and .login for those using the default tcsh
shell. There are also various
files which affect your window system (.Xdefaults,.xinitrc,.xsession,.Xresources,
and possibly lots of others for X11). Not all of these
files are necessarily installed by default, you may want to
download and modify these, possibly by swiping interesting things
from other people's dotfiles.
Most people use tcsh as their default command interpreter. This
is an enhanced, feature-laden version of the Berkeley C-shell, with
goodies like command history recall via the arrow keys, and filename
completion. There are other options such as the Bourne shell.
You'll get tcsh unless you ask for something else.
Beware that altering your .cshrc
(or .tcshrc) file can cause
strange behaviour and problems. Stick with the defaults unless you know
what you are doing. A possible starting point is the slightly
modified version of the .tcshrc
file (as of 1 May 2005) used by the CITA Parallel Programmer which is available here.
In other to check your environment settings, type printenv.
This will show your complete list of settings including your login
shell (SHELL), path, path for load libraries etc.
The default printer is trillium, a Canon ImageRunner 330N,
which lives in the coffee-room (it's also our copier). Anything
printed to trillium is double-sided by default. See below for extra
options like stapling. CITA recovers printing costs from faculty and
postdocs (students will be covered by their advisor) - charges
are currently 1 cent per page.
Lower-quality colour printing can be
done on an inkjet printer (Epson Stylus
CX3200) named violet which is
physically attached to kodiak in rm 1218. You should be able to print
to it from any of our linux machines (lpr -Pviolet
snazzyfigure.ps).
Epson-brand transparencies should be loaded so that the cut corner is
at the top right when you face the printer. Other transparencies
should have the rough edge facing you and the paper-strip at the
bottom. Extra cartridges are in the main office (in the cabinet behind
the door, same shelf as the DVDs and CDs. The print-rite brand
cartridges say "Epson C62" on them. The Epson brand cartridges say
"C62/CX3200". If you experience problems, check the notes that are
written on the printer.
Transparencies have a bad habit of smudging so you do NOT want to print more than one at a
time.
Use lpr <file> to print. lpq will show the print queue and kjob IDs. Use cancel or lprm to remove (your own) print jobs. Use mpage (below) to print more than one page on a side of paper.
lpr -o EFDuplexing=None <filename>
-prints single-sided on trillium
lpr -o EFStapler=PUpperLeft <filename> -prints
double-sided on trillium and staples the upper-left corner
lpr -o "EFDuplexing=None EFStapler=PUpperLeft" <filename> -single-sided and stapled
lpr -Ptulip -o InputSlot=Tray1 <filename> -prints transparency on tulip
A good way to save paper sometime is to print more than 1 page on a
side. The following will print 2 pages on one side of paper. See the
man pages for more options.
mpage -2 -t -Ptrillium junk.ps
Most people use TeX for document preparation. Of the plethora of
DVI-to-PostScript converters available, most people use dvips,
since it permits inclusion of PostScript figures (generated by
various other tools) to be embedded in a TeX document. Each has minor
advantages over the other. There are also a number of TeX previewers,
specifically xdvi for the X11
window system. ggv
and ghostview are used for postscript previewers. Try to use
these previewers whenever possible: It saves on paper and toner costs.
Notify requests if a printer is out of toner. Please remember that
paper and toner are expensive, and we use a lot.
Anything you can do to reduce usage is helpful. For example, use
previewers to look at your output whenever possible, rather than
printing a hardcopy. Don't print out hardcopies of routine mail
messages. Use small fonts for things like program listings (if you
have to print them out at all). Don't print out an entire document if
you need only a few pages; ggv
and xpdf will let you
print specific
pages from a postscript/PDF file.
It is simple to change your password on any of the CITA machines except the gateway (gw/falcon),
just use the passwd command.
Please email all questions to requests@cita.utoronto.ca. For questions requiring interactive support, please schedule a time by-email to the same address.