What to do AFTER logging in via ssh to a cluster. How do I run a program?

bjb133 · 09-18-2008, 04:57 PM

Please be kind to these dumb questions and answer simply (I am a biologist, sorry, so answer like your talking to a 5 year old).

I have established and successfully logged in to a supercomputer using ssh (Putty). I am on a PC trying to run a program on a HPC/IBM cluster. First of all, am I asking questions on the right website?

Now I want to run a program that is on my computer (MrBayes) on this supercomputer. Does the program need to be installed at their end (on the cluster)? Alternatively, can I call up the program on my computer, but run it via their processors. How do I go about this.

I do not know any commands, but have tried "help" with every possible command option in the command line box but none of these make sense. Even changing directories is impossible for me. It says I am at /share/home? What does this mean. Is this my home on the supercomputer.

I'm really lost and have no linux experience at all. I have asked for help from the IT folks at the cluster but they are truly slow and vague in their responses.

Thanks and Cheers,
BJS

kilgoretrout · 09-18-2008, 05:55 PM

Quote:

Now I want to run a program that is on my computer (MrBayes) on this supercomputer. Does the program need to be installed at their end (on the cluster)?

Yes it does.

Quote:

Alternatively, can I call up the program on my computer, but run it via their processors.

No, and even if that were possible, the network latencies would be so great that it would not work correctly. It would just take too long to transfer data back and forth from your box running the program to the supercomputer crunching the numbers.

Just to expand a bit, ssh is used to securely login to a computer at a remote location and run commands on that computer as if you were there. As such, any command or program you want to run on that remote computer must be installed and available on the remote computer. When you ssh into a remote computer you are running your commands on that remote box and just sending the command from your local box.

Quote:

It says I am at /share/home? What does this mean.

That is the location that you are at on the remote computer when you login there via ssh.

bjb133 · 09-18-2008, 06:06 PM

Thank-you so very much. That was extremely helpful! I truly appreciate your response.
Cheers,
Barb

chrism01 · 09-18-2008, 08:08 PM

Here's a great free tutorial on all things Linux: http://rute.2038bug.com/index.html.gz
See also
http://tldp.org/LDP/Bash-Beginners-G...tml/index.html

One thing to remember is that in Unix/Linux, the dir separator is '/', not '\', so to change dir its like

cd /some/dir/other/dir

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