How to submit an pool application?

From UGP-Wiki

How to submit a pool application job from the grid portal (eg:- http://grid.ucla.edu)?

Location: Job Services -> Applications -> Pool Applications

Aim:

Submit an application job to a compute resource where users don't have an actual account. Because users' don't have their own account they have to upload all the inputs and any other data that are required for the computation at the target cluster.

Three scenarios:

Please remember to select the appropriate Stagein Hostname for all three options below:

• You only have one input file: Please use the "Staged Input File" text field area to fill in your file name.

• You have a directory that contains many files: Please use the "Staged Input Directory" text field area to fill in your directory name.

• You have a compressed file which may contains many files: Please use the "Stage Compressed File" text field area to fill in your .Z or .gz file name.

We support only one of the above three kinds of job submission at present.

When you stage a directory or a compressed file name, you might get confused how to fill in the arguments or stdin.

Usually, if you have a directory that you want to stage, you can fill in the text field "Staged Input Directory". The program will zip the directory, and transfer the data to the target pool cluster, then unzip into a temporary directory which has a unique name. ($HOME/TIMESTAMP_IN_MILLIS)

If you only filled "Staged Input File", The job will run in: $HOME/TIMESTAMP_IN_MILLIS

If you filled in "Staged Input Directory", the job will run in $HOME/TIMESTAMP_IN_MILLIS/STAGE_INPUT_DIR by default.

Examples:

1. Matlab

   Arguments: 
   Directory:  
   Staged Input File:  matrix.m 
   stdin<   : matrix.m 

   Job Command submitted: 
        cd $HOME/TIMESTAMP_IN_MILLIS; /u/local/matlab/matlab.exe < matrix.m

2. Matlab

   Arguments: 
   Directory:  mydata
   Staged Input Directory:  mydata 
   stdin<   : matrix.m 

   Note: matrix.m is in mydata/matrix.m

   Job Command submitted: 
        cd $HOME/TIMESTAMP_IN_MILLIS/mydata; /u/local/matlab/matlab.exe < matlab.m

In this example user already filled Directory text field with 'mydata'. So a 'cd $HOME/TIMESTAMP_IN_MILLIS/mydata' will be executed before the matlab command is called. By default we 'cd' to the 'Staged Input Directory' name if Directory name is left blank. If matrix.m calls any other files or data, the path to them should be relative to the name of the staged directory name (no absolute path). Eg: If you have 'load input.dat', then input.dat is expected in the mydata directory. If there is a subdirectory called data under mydata and the input.dat is in that location, it should be loaded as 'load data/input.dat'.

3. Matlab

   Arguments: 
   Directory:   sample  
   Staged Input Compress File:  sample.zip 
   stdin<   : sample.m 

   the sample directory will be extracted to $HOME/TIMESTAMP_IN_MILLIS/
   sample.zip contains a directory called sample, and have a file in sample/sample.m 
   

   Job submitted: 
        cd $HOME/TIMESTAMP_IN_MILLIS/sample; /u/local/matlab/matlab.exe < sample.m

When compressed files are staged, Directory field needs to be filled because we don't know the name of the subdirectory it will uncompress.

4. Matlab

   Arguments: 
   Directory:   mydata/july01
   Staged Input Directory:  mydata 
   stdin<   : sample.m 

   Job submitted: 
        cd $HOME/TIMESTAMP_IN_MILLIS/mydata/july01; /u/local/matlab/matlab.exe < sample.m

5. Matlab

   Arguments: 
   Directory:   may04
   Staged Input Directory:  mydata/may04 
   stdin<   : sample.m 

   Job submitted: 
        cd $HOME/TIMESTAMP_IN_MILLIS/may04; /u/local/matlab/matlab.exe < sample.m
   Note that sample.m is in directory "may04" 

6. Amber

   Arguments: -i input.txt -o output.txt
   Directory:   sample
   Staged Input Directory: sample   
   stdin<   : /dev/null

   Job submitted: 
        cd $HOME/TIMESTAMP_IN_MILLIS/sample; /u/local/amber/amber.exe -i input.txt -o output.txt
   Note that input.txt is in directory "sample" 

7. Amber

   Arguments: -i input.txt -o output.txt
   Directory:   
   Staged Input File: input.xt   
   stdin<   : /dev/null

   Job submitted: 
        cd $HOME/TIMESTAMP_IN_MILLIS/; /u/local/amber/amber.exe -i input.txt -o output.txt
   Note that input.txt will be staged in $HOME/TIMESTAMP_IN_MILLIS

For Admin only:

It will submit job as the pool user defined in configuration file: pool.xml