[CIG-MC] ssh and autocombine.py

[Robert Moucha]

Fixed! I went in and tinkered with batchcombine.py, and after reading
some python stuff, I added the following line to the for loop in the
function batchpaste:

   node = node.rstrip()

That did it, though it probably should be done somewhere else in the script.

Cheers
Rob

On Thu, Nov 5, 2009 at 11:36 AM, Robert Moucha <rmoucha at gmail.com> wrote:
> Hi Eh,
>
> I checked and I do have my path variable set correctly so that is not
> the problem. However I did figure out what is happening, but I don't
> know enough python to figure how to fix it:
>
> If I print the variable cmd in the function batchpaste in
> batchcombine.py I get the following:
>
> ssh c0-0
>  pasteCitcomData.py /state/partition1/moucha2/citcoms cookbook6
> coord,velo,visc 3 10 /home/moucha/convection/citcoms/exa
>
> Note the return character after the node name (not an artifact of
> wrapping)! So, the os.system call only executes the ssh c0-0.  This
> explains why I am successively logged into the nodes whey I run
> autocombine.py, but the command pasteCitcomData.py is not executed.
> And when I type exit, the command pasteCitcomData.py is executed, but
> now the file does not exist on the master node and so I get a file not
> found error. I went back into batchcombine.py and added:
>
> print node
> print 'this is a test'
>
> Now I get:
>
> c0-0
>
> this is a test
>
> So the return character is coming from the variable node (note the
> blank line between the print statements). My mpirun.nodes looks like
> this:
>
> c0-0
> c0-34
> c0-33
> c0-46
>
> Once again, thanks for your help on this.
>
> Rob
>
>
> On Wed, Nov 4, 2009 at 4:39 PM, Eh Tan <tan2 at geodynamics.org> wrote:
>> Hi Rob,
>>
>> You need to add the visual/ directory to your PATH environment variable.
>> If you are using bash, you can add this line in your ~/.bashrc:
>>
>> export PATH=$PATH:$HOME/convection/citcoms/visual
>>
>> Eh
>>
>> Robert Moucha wrote:
>>> Hi Eh,
>>>
>>> Thanks for getting back to me so quickly. Our cluster is set-up with
>>> password-less ssh into the nodes. I went into
>>> batchcombine.py and added the line print cmd, to see what command was
>>> being executed, here is what I get:
>>> ------------------------
>>> $ autocombine.py mpirun.nodes pid23816.cfg 10
>>>
>>> ssh c0-0  pasteCitcomData.py /state/partition1/moucha2/citcoms
>>> cookbook6 coord,velo,visc 0 10
>>> /home/moucha/convection/citcoms/examples/Cookbook6
>>>
>>> Last login: Wed Nov  4 16:04:40 2009 from geograppe.local
>>> Rocks Compute Node
>>> Rocks 5.0 (V)
>>> Profile built 16:38 16-Jul-2008
>>>
>>> Kickstarted 16:50 16-Jul-2008
>>> [moucha at compute-0-0 ~]$
>>> -------------------------
>>>
>>> So I tried from my master node:
>>>
>>> $ ssh c0-0  pasteCitcomData.py /state/partition1/moucha2/citcoms
>>> cookbook6 coord,velo,visc 0 10
>>> /home/moucha/convection/citcoms/examples/Cookbook6
>>>
>>> and I get:
>>>
>>> bash: pasteCitcomData.py: command not found
>>>
>>> Now with the full path:
>>>
>>> $ ssh c0-0  ~/software/cig/bin/pasteCitcomData.py
>>> /state/partition1/moucha2/citcoms cookbook6 coord,velo,visc 0 10
>>> /home/moucha/convection/citcoms/examples/Cookbook6
>>>
>>> It works!  Funny though, because when I log into the node, I can
>>> execute the command directly.  Do you know of a way to solve this
>>> without editing the scripts, or is this just the way ssh works?
>>>
>>> Thanks
>>>
>>> Rob
>>>
>> --
>> Eh Tan
>> Staff Scientist
>> Computational Infrastructure for Geodynamics
>> California Institute of Technology, 158-79
>> Pasadena, CA 91125
>> (626) 395-1693
>> http://www.geodynamics.org
>>
>>
>>
>>
>> --
>> Eh Tan
>> Staff Scientist
>> Computational Infrastructure for Geodynamics
>> California Institute of Technology, 158-79
>> Pasadena, CA 91125
>> (626) 395-1693
>> http://www.geodynamics.org
>>
>> _______________________________________________
>> CIG-MC mailing list
>> CIG-MC at geodynamics.org
>> http://geodynamics.org/cgi-bin/mailman/listinfo/cig-mc
>>
>
>
>
> --
> GEOTOP - Département des Sciences de la Terre et de l'Atmosphère
> Université du Québec à Montréal
> CP 8888, succursale Centre-Ville
> Montréall, Québec
> Canada  H3C 3P8
> Tel:     (1-514) 987-3000, ext 1554#
> FAX:     (1-514) 987-3635
>



-- 
GEOTOP - Département des Sciences de la Terre et de l'Atmosphère
Université du Québec à Montréal
CP 8888, succursale Centre-Ville
Montréall, Québec
Canada  H3C 3P8
Tel:     (1-514) 987-3000, ext 1554#
FAX:     (1-514) 987-3635