NIKOLA Computing User Documentation

Nikola User FAQ

Here you will find Frequently Asked Questions

  1. How do I get `rm` to behave as normal?
  2. I cannot write to or remove files from my home/project directory and it gives me a "disk quota exceeded" warning. What do I do?
  3. How do I truncate a file?
  4. How do I do x in Unix or linux?
  5. It looks like a SCSI cable, but what kind of SCSI?
  6. Why does Firefox say I have another Firefox window open when I do not?
  7. Why does my home directory only have a quota of x?
  8. What is project space and how should it be used?
  9. What is scratch space and how should it be used?
  10. What is swamp space and how should it be used?
  11. What is data space and how should it be used?
  12. Why does Flash not work on my machine?
  13. How do I print from Firefox?

Q: Every time I try to remove a file with `rm` it asks me if I am sure I want to remove the file. Why does it do this? How do I make it so that it does not prompt me like this?

A: This is a measure implemented to prevent inexperienced users from accidentally deleting important data. It is a global alias of `rm` to `rm -i`. If you are certain that you want to remove this safeguard, simply re-alias `rm` in your .cshrc.local and/or .bashrc.local.

Add this line to .bashrc.local and/or .cshrc.local:

unalias rm

Q: I am getting a "disk quota exceeded" warning when I try to write to or remove a file from my home/project directory. How do I fix this?

A: This happens when a quota is exceeded in a zfs partition. The current way to fix this is to pick a file to truncate within the full file system. Find a file that is at least 100 KB and truncate it, then you will be able to remove further data.

See "How do I truncate a file?"

Q: How do I truncate a file?

A: Truncation of a file is rather simple. If you are doing this to free up space on a full file system, make sure to find a file to truncate that is at least 100KB.

Assume that the file we want to delete is named 'foo':

$ ls -l foo # check that the file size is at least 100K
$ cp /dev/null foo # truncates file
$ ls -l foo # 'foo's size should be 0 now

You should now be able to remove files using normal means ('rm') in order to free up more disk space on the file system.

Q: I need a command to do x on a Red Hat host or what command can I use do to y.

A: This question has a lot of potential answers. UW Tech has a basic command reference sheet here. For more information about a command try using man, for example, man screen will bring up a manual page for screen; also man -k blah will search a keyword database of names and descriptions of commands for 'blah'. Finally, using google search with some appropriate search terms can turn up a wealth of information.

Q: I am looking at a SCSI cable, what type of SCSI is it?

A: See this userdoc page

Q: Firefox says that I have another instance/window of Firefox open, but I have closed all my windows. This happens from time to time when firefox does not close cleanly.

A: In order to fix this issue, you have to delete a parentlock file that is created when firefox opens using your default profile.

There should be a directory in ~/.mozilla/firefox that is named with random letters and numbers and ends in '.default' (for example, '6sfymzvj.default'). Let's call this '$random.default'. In order to remove the parent lock, simply open a terminal, make sure you are in your home directory and remove the parentlock file:

$ cd
$ rm .mozilla/firefox/$random.default/.parentlock

Q: Why does my home directory have a quota of only x?

A: Home directories are meant to be used for personal files. This includes documents, preference files, configuation files, personal scripts, theses, and small, personal projects. Thus, they do not need to have a lot of space. Project and research data should be kept in Project Space.

Q: What is project space, and how should it be used?

A: Project space is available disk space on the file servers where research projects and data should be stored. You can request project space by emailing your lab's computing help. Submit a name for the project (try to keep it short, but desciptive) and an initial space estimate. Project space must be approved by a professor.

Q: What is scratch space and how should it be used?

A: Scratch space is local disk space on all Nikola workstations and compute nodes. You can find it mounted at /sN, where N is integer greater than or equal to zero. To get your own scratch space, use the space_req command. For example:

$ space_req

will list available scratch spaces and their corresponding % use.

$ space_req /s0

will create a scratch space for you (if there is space available) at /s0/username, where username is your username.

Scratch space is meant to be used as temporary data storage. Oftentimes simulations generate large amounts of temporary data. Your simulations should be configured to output data to scratch space. After they are complete, you should move any important results to the appropriate project directory so that they will be backed up.

Remember that scratch space is common space, so be courteous to others and clean up your space when you are done with the data so that others can use the space.

Q: What is swamp (not present in SSLI/MTML) space, and how should it be used?

A: Swamp space, like scratch space, is temporary disk space. What makes it different from scratch space is that it resides on the file servers. You must request swamp space to be created for you, when it is available. Note, that this is also common space, so you should be sure to clean it up when you are done using data so that others can make use of the space.

The benefit of swamp space over scratch space is that it is NFS mountable, meaning, you can access it on any machine on the network. However, you should not use it as a replacement for scratch space.

Q: What is data space (present in SSLI only), and how should it be used?

A: Data space is for data that itself is minimally processed, and is unchanging. Data space is an area for data or programs that are not specific to any particular experiment and are useful to several people. Data space should not be used as storage for the results of experiments, as such it is only backed up semi-annually.

To get data space you will need to email your lab's help queue with how much space is needed, the project name, and if your faculty has approved the space (the faculty needs to do so before we can create new data space).

Q: Why does Flash not work on my machine?

A: This is a known problem. Until version 10, Adobe Flash did not support 64-bit systems at all. However, Flash 10 is not supported on Red Hat Enterprise Linux 4 due to old versions of main system libraries. For now, we recommend using a 32-bit machine.

It is also known that Flash sound does not work in KDE, even on 32-bit machines. There is no way around this due to the design of KDE; use GNOME instead.

Q: How do I print from Firefox?

A: You need to create a small file called .gtkrc-2.0 in your home directory. It should contain the following line:
include "/etc/gtk-2.0/gtkrc"
You only have to do that once. Once it is done, restart Firefox. The printing dialog will now have a print to LPR function.

Your default printer is set in the PRINTER environment variable. Set this variable in ~/.login.local if you use tcsh or ~/.profile.local if you use Bash:
# .login.local
setenv PRINTER "aeo"

# .profile.local
export PRINTER="aeo"