Frequently Asked Questions

This page is used to collect Frequently Asked Questions and their answers. Please add questions here if you think the answer is relevant to other users.

1. How do I login to the cluster?

To login, open either Terminal (Mac) or Putty (PC) and type in the following command: ssh -Y username@… Remember your username is the same as your AD account . You will be prompted for your password, just enter your AD password.

Once you have logged in you will see that your in your Home folder - the prompt will look like this: les@my-mgrid:~$ Notice the server name before the prompt.

2. How to get into my project folder?

To get into your project folder each time you login, you must first call that folders name by using the command:

proj (project name) - no brackets

(this enables the project, essentially changing your users group membership to the project and setup environment variables to tell the queue system to access that project)

Your project folder can be found by using:

cd proj/(project name)

Please note: when submitting project names, please keep make sure they are no longer than 7 characters.

3. What are some basic Linux and SGE commands?

Below you will find a list of basic Linux commands.

ls Show files and folder in the current folder cp Copy files from one location to another, ex. cp filename newdir/filename less Opens a textfile in read-only, ex less filename cd .. Changes directory - one level lower. If you use cd /folder name - it will change directory to that folder.

Commonly-Used SGE Commands qsub Submit a Job qstat Determine the Status of a Job qdel Cancel a job qhold Place a hold on a queued job to prevent it from running qrls Release a job held with qhold qhost Display Node Information qmon An X-Windows interface to SGE commands

4. How do I start my job in the queuing system?

To start your job in the queuing system please refer to the following guide. In brief, you will create a script file that will contain the information needed to run your job, including a command to start whatever program you want to run with its parameters. The script also contains information on your email address, what folder to run the program in , how much time the job will need and how much memory the job will need (RAM).

5. How do I start an interactive job using the queue system for programs like: Blast2Go, Tablet and Mothur?

To start these types of programs you must first get a VNC (Virtual Network Computing) session opened in Terminal or Putty. Logon to the grid as you would do normally and once the prompt is up, type in the command vncserver. This will start a vnc session and you will get some feedback on the session number, as follows: New 'my-mgrid:2 (les)' desktop is my-mgrid:2 Note the number at the end of this line, in this case 2 and then open up a VNC connection to the server using either the Go function on Macs or TightVNC viewer on PCs. The address to the server and session you will need to put in will look like the following: my-mgrid.mykopat.slu.se:5902 - notice the session number here is 590 and then the number 2 from the session you opened on the server. A VNC window should open up and you will be in the Debian GUI (Graphical User Interface). You can then go into Applications/Terminal? in the GUI and run Blast2Go, Tablet or Mothur.

6. How do I transfer files between my computer and my grid home folder?

To transfer files, you can use either Terminal/Putty? or a GUI program such as Fugu/WinSCP. To transfer in Terminal/Putty? use the copy command - cp, (for example: cp filename source folder/filename destination). In Fugu/WinSCP you connect to the server and basically drag and drop like in Finder and Explorer.

7. Can I drag and drop files in Fugu and WinSCP?

You can drag and drop files within Fugu and WinSCP but not directly from your desktop to either program. You must have either program setup so that there are two windows so you can select a source on one side and destination on the other.

8. How do I start the program Velvet, or any other program on the grid for that matter?

To start programs on the grid, most of the manuals have commands that are usually used in starting the programs. However, on our grid, we have simplified the process somewhat and most of the time you will only need to type in the program name to get it to start. For example - From the Velvet manual it tells you to type: ./velveth

On our grid you only need to type: velveth This is also the case with running any specific scripts - you will not need to use " ./ " before the script name to get it to run.

9. How do I start Mr. Bayes as an interactive job in the queue?

To start Mr Bayes in the interactive queue, at the prompt you type in the command qrsh. This will start a job in the queue, please note you must ask for a run time and RAM allocation just as you would with a regular job request. Once the session is open in another shell, you would simply run the program Mr Bayes by going into the directory where you have the program and your data files and start the program.

Your command would look like the following:

qrsh -l h_rt=1:0:0 h_vmem=8G - this request would then start a session that would run for 1 hour and have 8GB RAM available. Note: after one hour this session would finish. Also note that the terminal or putty window must be open at all times with this type of job submission.

You can also start a job without having to have your terminal or putty window open the whole session. You have to create a nexxus file for Mr. Bayes - with all the configuration parameters for your job, then create a regular queue script for the queue system with the last line being the command to start Mr. Bayes with the nexxus file.

Please refer to this guide for an example.

10. How do I run the shuffleSequences_fastq.pl script under Velvet?

This script has been replaced in our sytem with the script shuffleSeqs. Simple type in the script name "shuffleSeqs" at the prompt and it will show you the input format to use.