RE: ÂÃÂÂÂÂ RE: [Condor-users] Help:How to change the arguments in the submitfile?

["Philip Crawford" <p.crawford@xxxxxxxxxxx>]

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There are a couple of ways to run shell scripts on Windows 2000.

1. You can use Cygwin, (free Linux emulator available from www.cygwin.com ). The default installation doesn't include C-shell, so you will need to install Shells.

I'm using Cygwin on Windows XP myself.

2. Microsoft have a "Microsoft Services for Unix" installer which is certainly available for English. I don't know if it works on other language installations of Windows. I've had problems with cycling a script through generating large numbers of files on this.

 

Another way to look at this is through DOS .bat files. You can definitely loop in a batch file.  You can also use the redirect ">>" to append to a file. Parameters are %1, %2, etc. You can't use the "\n" in an echo command but I think it automatically finishes with a new line. You also don't use quotation marks "" in an echo statement.

 

 

Cheers,

 

Phil

__________________________________________________

Philip Crawford, B. Comp. Sc., MIEEE

Structural BioInformatics and Drug Design Group

http://www.sbio.med.unsw.edu.au/sbio

School of Medical Sciences

The University of NSW

Phone: +61-2-9385 2564

Mobile: +61-419-294 698

Fax: +61-2-9385 1059

Email: p.crawford@xxxxxxxxxxx

__________________________________________________

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From: condor-users-bounces@xxxxxxxxxxx [mailto:condor-users-bounces@xxxxxxxxxxx] On Behalf Of ??
Sent: Tuesday, 6 September 2005 10:32 AM
To: Condor-Users Mail List
Subject: ååï RE: [Condor-users] Help:How to change the arguments in the submitfile?

Thanks a lot!
My OS is windows 2000 so i cannot write shellscripts.

I wander if there is any good idea to set the line  "argument = ..."  in the submit file to let the program run with different parameters automatically?
The first idea Bruno Goncalves gave is some what feasible, but my arguments are really too many. Could anybody ever resolve this problem? Please help,Thank you very much!

Philip Crawford <p.crawford@xxxxxxxxxxx> åéï

I've been using a pair of shellscripts to generate some jobs. The outer one has 5 parameters, one of which is a list of data files to process.

I use the "foreach" construct which is C-shell specific. This generates a submit file which contains nearly 300 jobs. The inner script is the script "build_input" which builds separate input files for each job. (The executable has many parameters.)

If the list of files is "files.lst" it is passed as a parameter to the script which asigns it to a variable "list_name",

foreach f (`cat ${list_name}`)
 set db = ${f:r}
        ./build_input $db $max_mols $rank_mols
        echo "transfer_input_files = ${db}.in, ${f}, ... etc" >> ${submit_file}
 echo "Arguments = -i ${db}.in -o ${db}.out.txt\n" >> ${submit_file}
 echo "Queue\n\n" >> ${submit_file}
end

Depending on how your parameters vary, you may need some nested for loops to do something similar.

Hope this helps.

 

Cheers,

 

Phil Crawford

__________________________________________________

Philip Crawford, B. Comp. Sc., MIEEE

Structural BioInformatics and Drug Design Group

http://www.sbio.med.unsw.edu.au/sbio

School of Medical Sciences

The University of NSW

Phone: +61-2-9385 2564

Mobile: +61-419-294 698

Fax: +61-2-9385 1059

Email: p.crawford@xxxxxxxxxxx

__________________________________________________

 

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From: condor-users-bounces@xxxxxxxxxxx [mailto:condor-users-bounces@xxxxxxxxxxx] On Behalf Of Bruno Goncalves
Sent: Tuesday, 6 September 2005 4:24 AM
To: Condor-Users Mail List
Subject: Re: [Condor-users] Help:How to change the arguments in the submitfile?

You can do something like this:

Arguments = arg1 arg2 arg3...
Queue 1
Arguments = arg1' arg2' arg3' ...
Queue 1
etc...

Just list all the different input arguments you need to run and queue a different job for each of them.

On 9/5/05, éæ <lumiousy@xxxxxxxxxxxx> wrote:

     I have to run a program with a lot of different arguments, but i don't know how to change them  automatically.

     Could anybody help me please?

     for example: the program test.exe have 5 arguments, the first is constant 5,the second varies from 0 to 100, so does the third and the forth.How can i write the submit file to let the job run with different arguments by themselves .

        I am looking forward to it!!! Thank you!!!

 

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Bruno Miguel Tavares Goncalves, MS
PhD Candiate
Emory University
Department of Physics
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