Wednesday, April 30, 2008

Running PaCE via Teragrid Job submission service

To submit PaCE job through the Teragrid Job submission service, you need,

-- input files (fasta format file(s) and .cfs file) with valid URL(s)
-- number of clusters

Here is the sample java code to access TJSS.
import javax.xml.namespace.QName;

import org.apache.axis2.AxisFault;
import org.apache.axis2.addressing.EndpointReference;
import org.apache.axis2.client.Options;
import org.apache.axis2.rpc.client.RPCServiceClient;
import org.ogce.jobsubmissionservice.databean.*;

public class SubmitPaCEJob{
public static void main(String[] args) throws AxisFault {
int option = 0;
String serviceLoc = "http://localhost:8080/axis2/services/JobSubmissionService";
String serviceMethod = "submitJob";
String myproxy_username = null;
String myproxy_passwd = null;
for (int j = 0; j < argval =" args[j];" option ="1;" option =" 2;" option =" 3;"> 0){
if (option ==1)
serviceLoc = argVal;
else if (option ==2)
myproxy_username = argVal;

else if (option ==3)
myproxy_passwd = argVal;

String [] inputFileString ={
String rslString =
"(arguments= Brassica_rapa.mRNA.EST.fasta.PaCE 33316 Phase.cfg)";

String [] outputFileString = {

CondorJob cj = new CondorJob();


RPCServiceClient serviceClient = new RPCServiceClient();

Options options = serviceClient.getOptions();

EndpointReference targetEPR = new EndpointReference(serviceLoc);


QName query = new QName("", serviceMethod);
Class [] returnTypes = new Class []{JobMessage[].class};
Object[] queryArgs = new Object[] {cj};
Object [] response = serviceClient.invokeBlocking(query,queryArgs,returnTypes);
JobMessage[] result = (JobMessage[])response[0];

}catch (Exception e){

private static void usage(){
System.out.println("Usage: submit_job -s \n"+
"-l \n"+
"-p \n"+
"submit_job "+
"-s http://localhost:8080/axis2/services/JobSubmissionService "+
"-l yourusername "+
"-p yourpassword ");

Tuesday, April 29, 2008

Running PaCE on BigRed

PaCE is software to cluster large collections of Expressed Sequence Tags(EST). BigRed provides PaCE package only for the internal use. Here are examples of job submission for the condorG to the BigRed for the PaCE package. Note: I set the "OutputFolder" parameter in the Phase.cfg as ".". This will let the gram job manager put all of the output files into the globus scratch directory.

executable = /N/u/leesangm/BigRed/bin/PaCE_v9
transfer_executable = false
should_transfer_files = true
when_to_transfer_output = ON_EXIT
transfer_input_files = /home/leesangm/EST/data/Brassica_rapa.mRNA.EST.fasta.PaCE, /home/leesangm/EST/data/Phase.cfg
universe = grid
grid_resource = gt2
transfer_output_files = estClust.33316.3.PaCE
error = PaCE.err.$(Cluster)
err = PaCE.standardErr.$(Cluster)
log = PaCE.log.$(Cluster)
x509userproxy = /tmp/x509up_u500

globusrsl = (jobtype=mpi)(queue=DEBUG)(maxWallTime=00:15)\
(count = 4)\
(hostCount = 2)\
(arguments= 'Brassica_rapa.mRNA.EST.fasta.PaCE' '33316' 'Phase.cfg')


Wednesday, April 23, 2008

Sample code: Access Job Submission Service from PHP page

If you installed WSF/PHP with your php server, you can try simple test php pages to access job submission service. Please make sure the SOAP body part should follow the style defined in the WSDL file. In my case, I could get the XML string from my SOAP monitor easily. However, you can simply download my example and use it as your template.

(1)Example of the SubmitJob operation
source code(mpi job)
source code(perl job)
Please note that you have to replace the username and password with your valid teragrid account.

(2)Example of the job management operations
source code(GetStatus)
source code(GetError)
source code(GetLog)

(3)Example of the retrieving output operation
source code(GetOutput)

Access to a Web Service from your PHP page

If you want to access Axis2 based Web Service such as OGCE local services(Job Submission service, and File Agent service) from your PHP page, there are several ways to do it. NuSOAP and Pear SOAP provide APIs into WebService. Also IMHO PHP has PHP's built-in SOAP libraries.

Since I'm a complete beginner of PHP, I'm not that familliar with the advanced design issues regarding the PHP based application. However, WSO2's WSF/PHP was a good starting point to me. Especially, it could provide us a proof of concept of our service which interacts with PHP pages through the standard WSDL interface.

You can use WSF/PHP both to build a Web Service and to build a client of a Web Service. In my case, I wanted to create a PHP client accessing a Web Service running in the Axis2 container. First, WSF/PHP provides quite simple interface to the PHP clients. For the examples, please refer to the next blog message. Basically, I needed to provide EPR of the service and XML string which are supposed to be in the SOAP body. Besides the ease-to-use feature, I was happy with that WSF/PHP allows the users to control over the SOAP message when it is needed(such as version of SOAP).

I've tried WSF/PHP with PHP5.1.1 on Linux box. Here is the step-by-step guide to the installation.

Step 1.Apache HTTP server install (if you don't have one already)
download PHP5.1.1 and install
download WSO2 WSF/PHP source from the project web site

Step 2. go to the directory of WSF/PHP source code
make install

Step 3. in php.ini (it will be in /usr/local/lib/php.ini if you didn't change the location)
add following lines:
include_path = "/home/username/php/wso2-wsf-php-src-1.2.1/script"

Step 4. copy sample code included in the code distribution to the Web server's document root. Test http://localhost/samples/