Changes between Version 1 and Version 2 of FrequentlyAskedQuestions

Timestamp:

Jul 5, 2011, 12:40:43 PM (13 years ago)

Author:

Patrik Söderström

Comment:

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FrequentlyAskedQuestions

@@ -1 @@
-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.
+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 grid?
 To login, open either Terminal (Mac) or Putty (PC) and type in the following command:
 ssh -Y username@my-mgrid.mykopat.slu.se
 Remember your username is the same as your AD account . You will be prompted for your password, just enter your AD password.
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 2: How do I start my job in the queuing system?
 To start your job in the queuing system please refer to the following guide. 
@@ -15 +18 @@
 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.
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 4: 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.
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 5. 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.
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 6. 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.
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 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.
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 7. 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.