From CITA Computing

Table of contents

Password Changes

Q. How do I change my password?

A. Login to the server trinity and use the special CITA command:


Q. I changed my password, but I just tried to login to a machine and it only accepts the old password, while other ones only accept the new one.

A. CITA password changes can take 30-60 minutes to take effect on some systems. Please try again later to see if the problem is resolved.

Q. I changed my password on a machine other than trinity but it did not work. What's up?

A. CITA password changes must be done on trinity


Q. I logged in to gw.cita.utoronto.ca and I can't change my password/access raid/run X command.

A. gw.cita.utoronto.ca is only for logging in to other machines from outside CITA's network, and accessing your files/transferring files into CITA remotely. While most of our filesystems are mounted here, you will not be able to run most commands/programs on gw. Please log in to trinity or your desktop to do work.

If you would rather dispense with using the gateway, you should try out our VPN.

Getting Help

Q. How do I get help with anything computing?

A. If you still have email functionality, a quick message to requests (at) cita.utoronto.ca describing your issue will be answered promptly by one of the technical experts at CITA. Please remember to include the HOSTNAME of the workstations/server/printer you are having issues with.

A. If you do not have access to email or the issue is very urgent, you may drop by RM 1410, ask our assistant sysadmin for assistance; if they are absent you can also see our computing manager in RM 1408.

Hours (both for the requests list and in person): approximately 9 AM to 5 PM Monday to Friday, Eastern Time, excluding holidays and dates the University of Toronto is closed i.e. winter break; during those hours we will do our best to get back to you promptly but our response time will vary.

Fedora 20 Desktop Environment

Q. How do I get Fedora 20 on my workstation?

A. Please send an e-mail to requests@cita.utoronto.ca and ask for us to install it for you--we will be happy to do so.

Q. I am using Fedora 20 on my workstation and my desktop looks very strange, I can't figure out how to use it! Why does it look so different from CentOS 6?

A. Fedora 20's default desktop environment is GNOME 3, rather than GNOME 2 which you may be used to from CentOS 6; some users may prefer the new environment but many will find it confusing so we have also installed MATE, a replica of the legacy GNOME 2 environment. To use MATE and get a desktop that looks almost identical to CentOS 6: when you are logging into Fedora, on the password screen there is a small gear icon next to the login button, click the gear then click MATE, and that will become your default desktop.

Q. I was using Thunderbird on Fedora, booted back into CentOS and tried to open it, but my e-mail account was broken i.e. my folders and messages didn't show up. What happened?

A. Please read the dual-booting section of the wiki carefully--Thunderbird has a known issue that we have written a warning about where it works fine going from CentOS to Fedora, but as soon as it is opened in Fedora it breaks your account in Thunderbird on CentOS. The only solution once this has happened is to delete your e-mail account in Thunderbird on CentOS and re-add it using the instructions on the Email page of the wiki. To prevent this from happening, only use Thunderbird on one OS or only use one OS altogether.

Login Problems

Q. I get a distressing error after attempting to ssh to a CITA host and cannot login. What is going wrong?

Someone could be eavesdropping on you right now (man-in-the-middle attack)!  
It is also possible that the RSA host key has just been changed.  
The fingerprint for the RSA key sent by the remote host is  
Please contact your system administrator.  
Add correct host key in /home/citauser/.ssh/known_hosts to get rid of this message.  
Offending key in /home/citauser/.ssh/known_hosts:23  

A. The host might have been upgraded recently and the hostkeys have been regenerated. You can clear the key by running the following, e.g. (fill in gw.cita.utoronto.ca with the hostname of the machine you're trying to reach):

ssh-keygen -R gw.cita.utoronto.ca

Or alternatively, remove the line in your .ssh/known_hosts file.

Accessing Storage

Q. Why can't I access /cita/d/raid-cita or /cita/d/raid-project from certain hosts?

A. Make sure you check filesystem mounts with the command 'df'. Certain hosts have lustre files systems mounted via /mnt/ which provides better performance than /cita/d mounts via nfs. Since the /mnt/ mounts work better we expect users to use them when possible, and will only provide support for the more-tempermental /cita/d/ mounts on workstations that lack the /mnt/ mounts.

Filesystem           1K-blocks      Used Available Use% Mounted on
/dev/sda1             33722028   7418348  24563040  24% /
tmpfs                 16512052         0  16512052   0% /dev/shm
quail:/obj/cita-skel      7936      1088      6784  14% /cita
quail:/obj/adm        51606144   1989792  49092064   4% /cita/adm
quail:/obj/mail       77409312  57520416  19102464  76% /var/spool/mail
quail:/obj/doc        10321216    154240  10062144   2% /cita/doc
quail:/obj/man         5160576    141440   4966720   3% /cita/man
quail:/obj/share       5160576    334752   4773408   7% /cita/share
quail:/obj/src        10321216   5038624   5177728  50% /cita/src
                     103212320  18972896  83190848  19% /cita/local
quail:/obj/home-1    825698752 640064576 177245568  79% /cita/h/home-1
quail:/obj/home-2    619274016 167424512 445558048  28% /cita/h/home-2
quail:/obj/home-3    619274016 127624032 485358528  21% /cita/h/home-3
                     33071118948 10155623700 22915492004  31% /mnt/scratch-3week
                     29660853040 27081010500 2579841408  92% /mnt/raid-cita
                     145853659388 98089196632 47764398520  68% /mnt/raid-project
                     7209180984 4047296584 3161884400  57% /obj/backup1
/dev/sdc             7209183032 3512753380 3696429652  49% /obj/backup2

Languages and Compilers

Q. What compilers are available on CITA machines?

A. For more details see the Modules page, a brief summary of a few important tools is included below.

GNU Compilers

A. For newer versions of the gnu compilers, use modules to supersede the default version e.g.,

module load gcc/4.9.0

You can check for other versions with:

module avail gcc

module commands can be put in your ~/.bashrc or ~/.tcshrc files - but be warned that sometimes modules loaded when shells initialize can break your desktop utilities (especially python modules).

Intel Compilers

A. Intel compilers icc, icpc and ifort are generally available on servers and workstations. The servers are generally much faster than your desktop. You load them with the modules package:

module load intel/intel-14.0.0

For other versions, try:

module avail intel


A. There are many versions of python available on CITA machines again loaded using modules e.g., check with:

module avail python

Please be aware that for Python version 3.x.x, after loading the module, python is launched with python3 not 'python'.

Python Packages e.g. astropy, numpy, scipy

Q. I started python and tried to do 'import scipy' [or similar] and the package isn't installed. Can you please install it for me?

A. We would be happy to, but in the above example that package is actually already installed! When you type 'python' into a terminal that normally opens the OS-provided basic installation of Python, on our CentOS 6.5 desktops this is Python 2.6.6, which we have not installed many packages for as it is not a popular version. Instead, please load one of our python modules e.g. 2.7.3 with 'module load python' (see the Modules page of the wiki for more details). Then when you do 'python' you will see that version is the one which will run, and in the case of 2.7.3 if you do 'import scipy' it will work because scipy is installed in that module.

So, if you are looking for a python package (e.g. scipy, numpy, astropy) and it is not available in the module you are using, try loading a different module, i.e. python/2.7.3 generally has the largest number of these packages installed; python/2.7.6 has a good number installed as well and they are generally more recent versions. If you cannot find a package contact requests and we will either point you to the correct module or install it for you in the event that it actually isn't installed yet--when contacting us regarding python packages make sure to include the python module (i.e. python/2.7.3, 2.7.5, etc) you want to use the package in.

Please also refer to Using_and_Developing_with_Python

Wireless Issues

Q. I've connected to the SSID 'cita' and I still can't connect to any webpages

A. Your DHCP request for a wireless IP has timed out. You can verify that is the case if your IP is 192.168.1.x. In your wireless connection options, there should be a button to 'renew lease'. Click the 'renew lease' button. Your IP should change over to 192.168.10.x. Return to your browser and refresh your webpage. You will be prompted with the CITA hotspot login page unless you already have registered your MAC address.

Shell initialization file issues

Q. When I login to my desktop, many gnome services seem broken and various tools and widgets are not working. What's going on?

A. You may have exceeded your CITA home space disk quota. This can be checked by running 'quota' in the terminal. If you have exceeded your 10GB soft limit or worse, hit the 11GB hard limit, please clean up some files to bring yourself back to about 9GB or less--this may fix your problems.

A. If you are having problems on your desktop machine, or with compiling/executing code or using development tools in general, please try removing any "module load X" or path-setting lines in your .bashrc, .cshrc, or other shell initialization file in your home directory--it has come to our attention that these modifications, when done automatically at login (especially loading the python module) instead of manually in the terminal, can cause a wide range of issues. A quick way to test if this is causing your issue is to rename .bashrc/.cshrc to .bashrc.bak/.cshrc.bak and try logging in again to get rid of the modifications. Note: if Python is one of the modules you are automatically loading, that is most likely the source of any strange issues you are having, and even removing "module load python" from your initialization file will usually remedy this.


Q. When I look at the bobMon (http://doug.cita.utoronto.ca/bobMon), many/most of the sunnyvale nodes are down. Why is this? Can I still run jobs?

A. Most of the time, when you see this nothing is wrong--it is simply the case that the cluster uses a lot of electricity and generates a lot of heat, so when it's not very busy we like to turn off idle nodes to save power and money. If you need to run a job, please feel free to submit it normally, you don't need to ask us to turn on nodes or notify us at all--rest assured we monitor the queues as diligently as possible, and usually within a few minutes (during the day) of a job being submitted we will see it and turn on a corresponding number of nodes for you, and make sure your job sees them and starts running ASAP. Whenever there is an actual issue/emergency that has taken down nodes and would prevent jobs from running, we e-mail all CITA account holders to update them on the situation.