Difference between revisions of "INF-BIOX121 H14 RStudio IPython"

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*launch iPython notebook
 
*launch iPython notebook
 
<pre>ipython notebook</pre>
 
<pre>ipython notebook</pre>
−
*check where it says "The IPython Notebook is running at: http://127.0.0.1:8888/" and note the last four digits ('8888' in this case)
+
*check where it says "The IPython Notebook is running at: [http://127.0.0.1:8888/ http://127.0.0.1:8888/]" and note the last four digits ('8888' in this case)
−
*Mac/Linux
+
 
−
*start another terminal session and you create a so-called SSH tunnel, make sure to use the same four digits in the middle
+
*'''Mac/Linux'''
 +
**start another terminal session and you create a so-called SSH tunnel, make sure to use the same four digits in the middle
 
<pre>ssh -L 30000:127.0.0.1:8888 username@bioinfcourse.hpc.uio.no</pre>
 
<pre>ssh -L 30000:127.0.0.1:8888 username@bioinfcourse.hpc.uio.no</pre>
−
*leave both terminal windows open
+
*'''<span style="font-size: 12px;">​Windows</span>'''
−
*<span style="font-size: 12px;">​Windows</span>
+
**see [http://howto.ccs.neu.edu/howto/windows/ssh-port-tunneling-with-putty/ http://howto.ccs.neu.edu/howto/windows/ssh-port-tunneling-with-putty/] on how to set up your tunnel
−
*see http://howto.ccs.neu.edu/howto/windows/ssh-port-tunneling-with-putty/ on how to set up your tunnel
+
**source port: 30000
−
*source port: 30000
+
**destination: 127.0.0.1:8888 (use those same four digits as you noted down above)
−
*destination: 127.0.0.1:8888 (use those same four digits as you noted down above)
+
 
−
*on the classroom PC, open a webbrowser (e.g. firefox)
+
*'''All'''
−
*point the browser to 127.0.0.1:30000
+
**on the classroom PC, open a webbrowser (e.g. firefox)
−
<div><br/></div><div>Using Rstudio</div><div><br/></div><div>Linux or Mac</div><div>open a terminal an write</div><div>ssh -L 20000:localhost:8787 username@bioinfcourse.hpc.uio.no</div><div>the port number on the left (20000) is an example. Choose any large port number > 20000</div><div>the one on the right should *always* be 8787</div><div>Once you type the above command, login with your SSH username and password, like you normally do. &nbsp;</div><div>​Windows</div><div><br/></div><div>see http://howto.ccs.neu.edu/howto/windows/ssh-port-tunneling-with-putty/ on how to set up your tunnel</div><div><br/></div><div>source port: 20000 (choose any large port number > 20000)</div><div><br/></div><div>destination: localhost:8787 (dont change this number)</div><div><br/></div><div>on the classroom PC, open a webbrowser (e.g. firefox)</div><div><br/></div><div>point the browser to localhost:20000 to access the RStudio server login screen. You can then type your username and password to login and access your R environment from your web browser.</div><div><br/></div>
+
**point the browser to 127.0.0.1:30000
 +
<div><br/></div><div>Using Rstudio</div><div><br/></div>
 +
*Linux or Mac
 +
**open a terminal and write
 +
<div>ssh -L 20000:localhost:8787 username@bioinfcourse.hpc.uio.no</div>
 +
**the port number on the left (20000) is an example. Choose any large port number > 20000
 +
**the one on the right should *always* be 8787
 +
**Once you type the above command, login with your SSH username and password, like you normally do. &nbsp;
 +
 
 +
*​Windows
 +
**<span style="font-size: 12px;">see </span>[http://howto.ccs.neu.edu/howto/windows/ssh-port-tunneling-with-putty/ http://howto.ccs.neu.edu/howto/windows/ssh-port-tunneling-with-putty/]<span style="font-size: 12px;">on how to set up your tunnel</span>
 +
**<span style="font-size: 12px;"></span><span style="font-size: 12px;">source port: 20000 (choose any large port number > 20000)</span>
 +
**<span style="font-size: 12px;"></span><span style="font-size: 12px;">destination: localhost:8787 (dont change this number)</span>
 +
*All
 +
**on the classroom PC, open a webbrowser (e.g. firefox)
 +
**<span style="font-size: 12px;">point the browser to localhost:20000 to access the RStudio server login screen. You can then type your username and password to login and access your R environment from your web browser.</span>
 +
<div><br/></div>

Revision as of 10:50, 8 October 2014

Using the IPython Notebook

  • login as usual, with X forwarding on tjhe course server
  • start a so-called virtual Python environment (virtualenv):
source /opt/ipytest/bin/activate
  • this changes your promt, don't worry.
  • move (cd) to a folder if needed, for example where the data is you want to analyse
  • launch iPython notebook
ipython notebook
  • check where it says "The IPython Notebook is running at: http://127.0.0.1:8888/" and note the last four digits ('8888' in this case)
  • Mac/Linux
    • start another terminal session and you create a so-called SSH tunnel, make sure to use the same four digits in the middle
ssh -L 30000:127.0.0.1:8888 username@bioinfcourse.hpc.uio.no
  • All
    • on the classroom PC, open a webbrowser (e.g. firefox)
    • point the browser to 127.0.0.1:30000

Using Rstudio

  • Linux or Mac
    • open a terminal and write
ssh -L 20000:localhost:8787 username@bioinfcourse.hpc.uio.no
    • the port number on the left (20000) is an example. Choose any large port number > 20000
    • the one on the right should *always* be 8787
    • Once you type the above command, login with your SSH username and password, like you normally do.  
  • ​Windows
  • All
    • on the classroom PC, open a webbrowser (e.g. firefox)
    • point the browser to localhost:20000 to access the RStudio server login screen. You can then type your username and password to login and access your R environment from your web browser.

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