CSIL Linux/Unix Known Issues Page


About System Access (login issues)


I could not login to any CSIL Linux workstation. What should I do?

There are number of potential reasons for this.

_ Did you register late?

In this case, your account may simply have not been processed yet.

Accounts are enabled in CSIL within one business day of being processed by the Registrar. If you don't have access after two business days of registering, email helpdesk.

_ Did you exceed the disk quota?

Every user gets a limited amount of disk space to use, and if the limit is reached, the Graphical User Interface (GUI) login session won't work. Some tips on how to fix this can be found here.

_ When was the last time you changed your SFU login password?

Due to technical limitations, the CSIL Linux workstations could only recognize the accounts which have the password changed since January of 2013. You may find more on the next Q&A.

If none of these applies to your encounter, or you'd like more help, please email helpdesk.

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I could login to CSIL Windows workstations but not the Ubuntu Linux. What should I do?

At this moment, all of the CSIL Linux workstations are binding to ADSFU domain for "roaming profile" feature.

If you could not login to the Linux workstation binding to ADSFU, please do the following:

launch a web browser

navigate to URL: https://my.sfu.ca/ChangePassword

change your password

wait for 15 minutes

This process ensures SFU AD can recognize your account from Linux. You may try to login after the wait.

If you still could not login, please checkout this Q&A now.

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I have logged in to CSIL Linux workstations previously, but now I can't login. What's wrong?

This might be a disk quota (of user profile) issue. Please read this Q&A for a solution.

If the answer does not resolve your login issue, please email helpdesk.

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After I use my correct password login and click yes to agree with the CSIL policy, the system kicks me out. What's going on?

The most likely cause is: you've reached the quota of your CSIL home (aka profile folder).

The profile folder is "~", which is "/home/username". If you filled this up with big files, you will not be able to login through GUI. Please note: /home/username/sfuhome is mounted on a different server which is not part of the profile.

To be able to login properly again, please use Virtual Console login to this CSIL host and move the files you stored under /home/username to your SFU Home /home/username/sfuhome. Please check this Q&A for more instructions.

Remember: Always save files under your SFU Home /home/username/sfuhome, never anywhere else!

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About Home Space (SFU Home)


I could not find my sfuhome after I logged in to a CSIL Linux workstation. What should I do?

This is a known issue. We are working to find a solution and we need your help.

There is one possibility: on the login screen, there are spaces in the Login ID box. Please logout and try to login again - please make sure there is no leading nor trailing spaces around your login ID.

Please try to re-mount the sfuhome by running the customized command:

mount.sfuhome

One thing you may try is: reset your account's password, especially when you haven't changed the password for more than a few months.

Logout and login again; if you still could not find "sfuhome", please email helpdesk with the output from the following commands to help us identify the culprit.

klist
mount
ls  -l  ~

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I could not see any files under my sfuhome after I logged in to a CSIL Linux workstation. What should I do?

This is a known issue. We are working to find a solution and we need your help.

Here are some of the steps you may want to try:

1) re-mount the sfuhome by running the customized command:

mount.sfuhome

2) logout and login again

3) switch to another computer, it might work for you.

4) log on to a CSIL Windows and check in your U:/ drive

If you have tried all of these and you still could not see files under "sfuhome", please email helpdesk with the results of your tries and the output from the following commands to help us identify the problem.

klist
mount
ls  -l  ~

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I could not write to my sfuhome. What should I do?

If you can, please logout and reboot your workstation, or try a different workstation.  If you still cannot write to your sfuhome, please email helpdesk with the details.

If the problem persists, there are two main possibilities:

(1) you may have reached your quota on the ITS file server.

Currently (as of 2019), there is a 10GB quota limit for everyone.  You may need to remove some files to free up space.

Login to a CSIL Linux workstation and run the following command to identify which folder/file(s) are especially large:

cd ~/sfuhome
du  -skh  .[!.]*  * | sort -n

After you identify the big file(s) and you are sure they are no longer needed, you may want to delete them.  Note: there could be a huge Trash file you definitely want to delete.

(2) there might be technical issues with the ITS file server.

Logon to a CSIL Windows machine (or leto.csil.sfu.ca remotely) and see if you can write to your home.  Your U: frive there is what is seen as sfuhome in CSIL Linux, so if you can make a file there, that filesystem is ok.

If you are not over quota and still can't make a file in yourCSIL U: drive, the CS helpdesk cannot assist you; please contact the SFU help line. You can find more details on this page.

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I could not see any files under my sfuhome after I use ssh key logged in to a CSIL Linux system. What should I do?

Please logout - and try login without using the "ssh key". Please do not use ssh key to login to any CSIL systems.

The technical details:

When login with user/password paring, multiple resources are authenticated which includes the sfuhome.
When login with ssh keys, only the machine is authenticated, thus the network mounts (including sfuhome) won't work.

So, again: do not use ssh key to login to any CSIL systems.

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About Linux Desktop Environment (User Profile)

The system shows I exceeded my disk quota, but I only have a few MB on my SFU Home space. What's the deal?

The system is likely referring to your "profile" space, not your SFU Home space.

On all CSIL Linux workstations, each user's profile has a disk quota of 1GB (1000MB), this restriction is on /home/username. If this quota has been reached, the Graphical User Interface (GUI) login session won't work thus user could not login any more.

Please see the following Q&A for instructions on claiming back the space and then being able to login.

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I somehow exceeded my space quota. What should I do?

Being over quota on your CSIL home directory prevents you from logging on to CSIL Linux via the GUI (the graphical user interface). You need to log on to CSIL Linux not via the GUI and clear up your space usage.  You can do this from a CSIL windows system, or your own computer if you have an SSH program like MobaXterm or Putty, or from a CSIL Linux box's Virtual Console.


Virtual ConsoleFrom the CSIL Linux workstation login screen, press the key combination Ctrl-Alt-F1, this will make the system switch to a Virtual Console. Be sure to log off from it (use the "exit" command) when you are done.

CSIL WindowsPress the Windows key (near Ctrl, lower left of the keyboard) and type "putty". Choose the PuTTY to connect to a CSIL Linux computer, e.g. csil-cpu3.csil.sfu.ca, on port 24, and log on.


Once logged on to CSIL Linux with a non-GUI session, check your space usage and free up space:

1a. check to see how much space you've used by using the commands:

cd
du -smch

There is a 2GB hard quota limit on your CSIL home directory. If the result you got is close to 2GB, you must free up some space before you can log on with the GUI. If du reports your usage is significantly smaller than 2GB, please contact helpdesk and describe the situation.

1b. Or check if you are over quota with the command

quota -v

Check the first two numbers of the output, if they are very close, it means you've almost used up your quota.

For example, the output may look like this one:

Disk quotas for user username (uid 99999):
     Filesystem  blocks   quota   limit   grace   files   quota   limit   grace
rcg-nfs02.its.sfu.ca:/csilhomes
                    910751  921600 1048576            1270       0       0         

As you can see, this specific user has an upper limit of 921600 blocks of disk space (quota), and the usage is very close. Normally, the usage should be much less than the quota, but this user is out of disk space and GUI login on CSIL Linux fails.

Once you know that you are at or over quota, look for files to delete or to move to your sfuhome, where the quota is 10GB (at the time of writing). Use this command at the Linux prompt:

du -sh ~/* ~/.??* | sort -n

(Explained: list the space used by files and directories (folders) in your CSIL home directory (that's what "~" means in the command above), sorted by the amount of space they occupy.)

You may get something like this:

4K       /home/username/.bash_history
104M     /home/username/.cache
...
20M      /home/username/Desktop
888M     /home/username/sfuhome
974M     /home/username/cmpt000

Space is shown in units like K (kilobytes), M (megabytes) and G (gigabytes).

In this example, the "cmpt000" folder occupies more than 900MB space - it must be checked.

Also, you could use the following 3 commands at the Linux prompt:

cd folder-in-question
find . -size +10M -print

du -sk ./* ./.??* | sort -n

The results of find list larger files or directories. Find out in what location these huge files are, then cd to these big directories and remove files you don't need.

2. Here are some common cleaning steps the CSIL users have tried and succeeded:

1) Often, the quota is filled up by the web browser cache. You may safely remove the files/folder under these cache folders, e.g.

rm -fr ~/.cache/mozilla

rm -fr ~/.cache/chromium

2) There could be a huge Trash file you definitely want to delete; e.g. run the command like:

rm ~/.Trash-????? -fr

3) When a Linux program crashes, it may create a memory image for future troubleshooting called core. Core files are often quite large but it's usually safe to just delete them. To do so:

find ~ -name core | xargs \rm

4) If one of your programs has an infinite loop, it may keep writing to an output file till all the space is filled up. Delete such files - and then debug your code.

If you freed up enough file space by deleting unwanted files (use the "du -smch ~"  command again), you should be able to login to the system normally. Please do so after logging out from the Virtual Console first.

Important!!

Do not go back to the Graphics login screen before you have logged out of the Linux Virtual Console. If you forget to log out of the Virtual Console you will remain logged in to the Virtual Console, regardless of any logging out of any subsequent GUI sessions. If you forget to log out of the Virtual Console, anyone coming along later can then use your Virtual Console session and will have total access to all of your files!

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I customized my desktop environment yesterday, but it is gone today. What should I do?

If you are always using the workstations in CSIL and having this issue, please email helpdesk.

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About Processes


There is a runaway process or an application that seems to have 'frozen' and is not responding. How can I stop it?

Given the complex nature of computers and software, it is inevitable that applications sometimes 'freeze' or 'hang'. There are many reasons why an application stops responding to the user, but often it is because the application programmer has entered defective code into their program. When this happens, often the only thing the user can do is interrupt the program.

Every application on the UNIX system runs as a separate process, and each process is assigned a process id number or pid. To read more on processes and how to terminate them, read the following page on How to kill Unix Processes.

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How to kill runway processes?

This Q&A has been moved to here.

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About Remote Access (the CSIL Linux Terminal Server)


I could not connect to CSIL Linux Terminal Server, what's going on?

We have reports that the following error message shows up and the connection is refused:

"Reached the maximum number of concurrent sessions on this server"

This means the server has reached its limits. If you see this message, please try it again later or come to CSIL to use the physical workstations.

To ensure the responsiveness of each remote session, we have setup a cap - the number of concurrent logins - on this server.

In the good news department: we are working on expanding the capacity of our CSIL Linux Terminal Server.

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I could not connect back to my suspended remote session. What should I do?

We have many reports on the failing to resume suspended/disconnected remote sessions. The symptoms are: the session has disappeared; when the same user tries to start a new remote session, there is this error message:

"The session negotiation failed. Error: Server capacity: reached for user: ????"

If this happens to you, you may try these steps:

1) try to "reset" your remote NX session by ssh into the corresponding NX server then do the following:

remove all files under ~/.nx/

kill all processes (click here for detailed instructions)

2) remote desktop to our CSIL Windows Terminal Servers and run NX Client from this computer.

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I just installed the latest client from NoMachine, but it won't connect to the CSIL Linux Terminal Server, what's going on?

The cause of the issue is the version mismatch between the client and the server.

The NX server on the CSIL Linux Terminal Server is version 3, use default settings of the the latest client (version 4) won't be able to connect to this server.

To resolve this issue, please follow these steps after installing the NX client version 4 on your own computer.

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Miscellaneous


Mozilla Firefox won't start and claims that "Firefox is already running". What should I do?

Firefox stores start up information in its configuration directory, .mozilla/firefox/profilefolder/, located in your home directory. When Firefox terminates abnormally, sometimes it does not clean up the configuration directory properly. It may leave behind a lock and a .parentlock file in your profile sub-directory. Firefox uses these files to tell which profile is the active profile, as you can have more than one profile. If the lock and .parentlock files are present when Firefox is not running, then it will not start up. If you manually delete these files, you will be able to run Firefox.

First:

cd ~/.mozilla/firefox/

Then locate the profile folder. It will have a strange name, followed by a dot, followed by the name of the profile - normally default, for the default profile. For example:

cd gx93dladd0.default
ls -al

should show you the 'lock' and '.parentlock' files. Remove them and attempt to restart Firefox.

For resolving the same issue on a CSIL Windows system, click here.

For more information on Firefox profiles, click here.

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I have trouble using Eclipse. What should I do?

The Eclipse stores configurations under this (hidden) directory:

~/.eclipse

If you have trouble using Eclipse, please close all your Eclipse sessions and delete this folder.

For resolving the same issue on a CSIL Windows system, click here.

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Is your question not on the list? Have you checked the CSIL Linux/UNIX FAQ?

Contact us!

Having comments, suggestions, inquiries and more questions? Contact us!

Please click here and use the best practices to get assistance from helpdesk.

 

Last updated @ 2020.03.03