Re: [Condor-users] Using shell script to invoke executable instandard universe

["Jones, Torrin A \(US SSA\)" <torrin.jones@xxxxxxxxxxxxxx>]

Here is an example of a typical usage of scp.

scp user@xxxxxxxxxxx:/home/user/image.jpg /tmp/image.jpg

This copies /home/user/image.jpg from example.com using username user to
/tmp/image.jpg on the current host using a secure session.  You can
probably get better information from the man page.

http://www.openbsd.org/cgi-bin/man.cgi?query=scp

You will get a password prompt if ssh isn't setup to use a key.  I don't
remember how to set it up hopefully somebody else will be able to help
you.  Or you can use look at the ssh-keygen man page.

http://www.openbsd.org/cgi-bin/man.cgi?query=ssh-keygen


-----Original Message-----
From: condor-users-bounces@xxxxxxxxxxx
[mailto:condor-users-bounces@xxxxxxxxxxx] On Behalf Of Brian Dandurand
Sent: Friday, September 28, 2007 14:31
To: Daniel Forrest
Cc: bdandur@xxxxxxxxxxx; Condor-Users Mail List
Subject: Re: [Condor-users] Using shell script to invoke executable
instandard universe


Thank you for your help.

I have another question because I don't think that I'm setting up the
scp
line correctly. I know everything else works.

For
/usr/bin/scp myhost:myprogram

is 'myhost' the station where the job was submitted from? If I
understand
this right, this line transfers the executable from the submitting
machine
to the remote machine assigned to run the job.

When I run this through Condor, I get no error nor output message, but
the
log file indicates return code of 1.

Also, when I run the shell script on my computer, when it gets to the
scp
part, I get a prompt for my unix account password. I don't know if that
would happen on the remote machine as well when it is run through
Condor.

On the Condor website they have

# grab a standard universe executable designed specifically
# for this host
scp elsewhere@xxxxxxxxxxx:${host} executable

for that line in the shell script. I do not understand the scp command
thoroughly, so maybe I'm mistaken, but that doesn't look syntactically
correct. Again, the name 'elsewhere@...' brings up the question of
whether
this is the submitting machine or the remote machine.


> Brian,
>
>> I have a C program which has been successfully compiled and linked
using
>> the condor_compile command with cc. I ran it first through a shell
script,
>> and I got an error in my log file stating that the job was not
properly
linked for Condor. Then I ran it directly by specifying the executable
directly on the 'executable=' line of the class ad and it worked. Is
there a way to call an executable compiled for the standard universe
from a shell script, or does it have to be called directly?
>
> In your job file include:
>
> Allow_Startup_Script = True
>
>
> Then your script needs to include something like:
>
> #!/bin/sh
> ...
> ... other stuff...
> ...
> /usr/bin/scp myhost:myprogram .
> exec ./myprogram ${1+"$@"}
>
>
> This is described in the condor_submit manual page.
>
> --
> Daniel K. Forrest	Laboratory for Molecular and
> forrest@xxxxxxxxxxxxx	Computational Genomics
> (608) 262 - 9479	University of Wisconsin, Madison
>


----------------------------------------
Brian C. Dandurand
Clemson University
Department of Mathematical Sciences
Ph.D. Student
Office: Martin Hall E-6
Office Phone: (864)656-4749
----------------------------------------



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