User's Page

h1. Submit Grid Job

*1. Before you can submit Grid jobs you need to prepare your setup.*

Finish first the steps described here: https://p55cc-redmine.utu.fi/projects/user-s-page/wiki/Prepare_For_Grid_Usage

*2. Other preparation*

You use the Grid resources via the ARC (Advanced Resource Connector) middleware, developed by the Nordugrid community.

There are basically two ways to submit Grid job using ARC:

# From ANY other computer but Pleione or Titan Login frontend

# From Pleione or Titan Login frontend. (i.e. pleione.utu.fi or titan.utu.fi)

h3. 2.1 Using the Grid from other computers

Using the Grid from other computers than Pleione or Titan you need to install ARC client software and configure it. Such tasks

are documented here: https://research.csc.fi/fgci-arc-middleware#1.3.2

h3. 2.2 Using the Grid from Pleione or Titan frontend

The rest of this guide is just short version of this guide: https://research.csc.fi/fgci-using-arc-middleware

So you might want to read the comprehensive guide before running the example.

*3. Running self made binaries and FGCI software via runtime environment*

In principle there are two ways to use the Grid resources:

- running self made binaries

- running FGCI pre-installed software via runtime environment

*4. Example of running a simple self made binary as a Grid job from Titan login node*

To run your self made binary as a Grid job you need the following files:

- compiled program (the binary)

- job description file

- batch file

- possibly input file(s)

The c-source of an example program *gtest.c* :

<pre>

#include <stdio.h>

int main(void) {

char *line = NULL;

size_t size;

  printf("Hello UTU.\n");

  while (getline(&line, &size, stdin) != -1)

    printf("%s", line);

  return(0);

}

</pre>

Compile the source:

<pre>

gcc -Wall -o gtest gtest.c

</pre>

The job description file *gtest.xrsl* :

<pre>

&(executable=gtest.sh)

(jobname=g_test)

(runtimeenvironment>="ENV/FGCI")

(join="yes")

(stdout=std.out)

(cpuTime="1 hours")

(count="1")

(memory="1000")

(inputfiles=

   ("gtest" "" )

   ("gtest.txt" "" )

)

(outputfiles=

   ("gtest.tgz" "" )

)

</pre>

The batch file *gtest.sh* :

<pre>

#!/bin/sh

echo "Running gtest"

module load OpenMPI

chmod u+x gtest

mpirun ./gtest < gtest.txt > gtest.out

tar czf gtest.tgz gtest.out

echo "Done"

exit 0

</pre>

Input file for this test run *gtest.txt* :

<pre>

Hello FGCI.

</pre>

*Now you are ready to run the job.*

Get proxy to run the job:

<pre>

$ arcproxy

Enter pass phrase for private key:

Your identity: /DC=org/DC=terena/DC=tcs/C=FI/O=Turun yliopisto/CN=Timo Eronen tke@utu.fi

Proxy generation succeeded

Your proxy is valid until: 2016-12-08 19:46:02

</pre>

Run the job:

<pre>

$ arcsub gtest.xrsl

Job submitted with jobid: gsiftp://io-grid.fgci.csc.fi:2811/jobs/3dxMDmPc7Ypn9NOVEmGrhjGmABFKDmABFKDmXGKKDmABFKDmWJfHjm

</pre>

Query status of the job:

<pre>

$ arcstat gsiftp://io-grid.fgci.csc.fi:2811/jobs/3dxMDmPc7Ypn9NOVEmGrhjGmABFKDmABFKDmXGKKDmABFKDmWJfHjm

Job: gsiftp://io-grid.fgci.csc.fi:2811/jobs/3dxMDmPc7Ypn9NOVEmGrhjGmABFKDmABFKDmXGKKDmABFKDmWJfHjm

 Name: g_test

 State: Finishing

Status of 1 jobs was queried, 1 jobs returned information

</pre>

Job was not yet finished but after awhile:

<pre>

$ arcstat gsiftp://io-grid.fgci.csc.fi:2811/jobs/3dxMDmPc7Ypn9NOVEmGrhjGmABFKDmABFKDmXGKKDmABFKDmWJfHjm

Job: gsiftp://io-grid.fgci.csc.fi:2811/jobs/3dxMDmPc7Ypn9NOVEmGrhjGmABFKDmABFKDmXGKKDmABFKDmWJfHjm

 Name: g_test

 State: Finished

 Exit Code: 0

Status of 1 jobs was queried, 1 jobs returned information

</pre>

Get the results:

<pre>

$ arcget gsiftp://io-grid.fgci.csc.fi:2811/jobs/3dxMDmPc7Ypn9NOVEmGrhjGmABFKDmABFKDmXGKKDmABFKDmWJfHjm

Results stored at: 3dxMDmPc7Ypn9NOVEmGrhjGmABFKDmABFKDmXGKKDmABFKDmWJfHjm

Jobs processed: 1, successfully retrieved: 1, successfully cleaned: 1

</pre>

And then you are ready to view the results:

<pre>

$ ls -l 3dxMDmPc7Ypn9NOVEmGrhjGmABFKDmABFKDmXGKKDmABFKDmWJfHjm/

total 8

-rw------- 1 tke admin 148 Dec  8 09:14 gtest.tgz

-rw------- 1 tke admin  19 Dec  8 09:14 std.out

$ cd 3dxMDmPc7Ypn9NOVEmGrhjGmABFKDmABFKDmXGKKDmABFKDmWJfHjm/

$ cat std.out

Running gtest

Done

$ tar xf gtest.tgz

$ cat gtest.out

Hello UTU.

Hello FGCI.

</pre>

*5. Example of running a Grid job via FGCI runtime environments from Titan login node*

Comprehensive info:

https://research.csc.fi/fgci-using-software-through-runtime-environments

[an example will be added later]