Sangmi Lee Pallickara

Advanced debugging of submitting jobs to Swarm-Grid

2009-12-14T14:37:00.005-05:00

This instruction is for the advanced users of Swarm-Grid to track their submitted jobs.
(1) Checking the remote cluster
[Step 1] login to a machine which has Globus installed.
[Step 2] get your proxy certificate
myproxy-logon -s myproxy.teragrid.org -l your_user_name
[Step 3] submit a request to remote cluster
globusrun -o -r grid-co.ncsa.teragrid.org/jobmanager '&(executable=/bin/ls)'

* If this step works fine, your remote cluster and the jobmanager on the cluster works fine.
* If your myproxy-logon cannot be located, check your globus user environment is set up correctly.
source $GLOBUS_LOCATION/etc/globus-user-env.sh

(2) Checking the mySQL table directly
[Step 1] login to the mySQL with username and password for the swarm.
mysql -u jobsub -p
[Step 2] select the database
use jobsubmission;
[Step 3] check the debugging log for your job
select * from SubmitRecord where TicketID="213655869" AND InternalID=200;
* As soon as the job reaches the stage, swarm records the time to the field. Therefore if the value of the field is NULL, the job has not been reached to that stage.

(3) Globus Temporary Files and Locations
your_home
--.globus
----g1
------h6.bigred.teragrid.iu.edu
-------- directories with the actual globus job numbers
-----------remote_io_url
-----------scheduler_loadleveler_job_script:
-----------stdout
-----------x509_up
-- Globus*** : temporary directory: keeps input,output etc.. files. This is the directory your script will process as current directory.

* Temporary directory is mostly deleted after the job is processed. This is for the bigred. Other teragrid machines have similar structures for the temporary files and unstaged files.

Adding EC2 computing nodes to your Hadoop Cluster

2009-05-12T16:43:00.006-04:00

If you want to add EC2 nodes as your slave nodes of existing Hadoop cluster:

Step1] Create a EC2 instance which has hadoop installed.
ec2-describe-images -x all | grep hadoop

Step2] Make sure that the version of hadoop MUST be identical on all the machines in your cluster.

Step3] Generate public key on your master machine:

ssh-keygen -t rsa

Then your publickey is stored in,

.ssh/id_rsa.pub

Step4] Copy your public key (id_rsa.pub) to .ssh/authorized_keys on your EC2 instance. Now you can ssh to your instance without your keypair.

Step5] Add your new slave node to your hadoop_loc/conf/slaves
Mine looks like:

localhost
ec2-111-222-333-444.compute-1.amazonaws.com

Step6] Synchronize or copy your configufation files to the slave nodes:
-hadoop-site.xml
-slaves
-master

Step7] format your namenode (if you need)

Step8] start your cluster!!

Additional Teragrid resources for Bioinformatics Software(CAP3)

2009-03-18T10:29:00.002-04:00

Last week, I found three additional teragrid sites working with Swarm. Please note that I have experinece some problem with ANL while I was stage out files before. And Marlon informed me that Pople doesn't support community certificate.

NCSA-Abe
(1) grid_resource: gt2 grid-abe.ncsa.teragrid.org:2119/jobmanager-pbs
(2) globusrsl: (jobtype=single)(count=1)
(3) Test cap3: success

Pople
(1) grid_resource: gt2 gram.pople.psc.teragrid.org:2119/jobmanager-pbs
(2) globusrsl: (jobtype=single)(count=1)
(3) Test cap3: success

ANL
(1) grid_resource: gt2 tg-grid.uc.teragrid.org:2119/jobmanager-pbs
(2) globusrsl: (jobtype=single)(count=1)
(3) Test cap3: success

Being a nice client of Inca service: monitoring Grid Resource

2009-03-06T10:33:00.010-05:00

If you consider a monitoring mechanism for the TeraGrid resources, the Inca project from SDSC provides very useful information. (http://inca.sdsc.edu/) With access to Inca service, you can easily utilize monitoring information with light-weight software component. Thank you for hosting the service and very helpful supports from the Inca team! It was very pleasant experience.

If you are using the TeraGrid resources, you might be interested in the Inca's real time monitoring testbed (http://www.teragridforum.org/mediawiki/index.php?title=Inca_Real-Time_Monitoring_Testbed). Inca server runs the testing described in above document. Those information is available through RESTful URLs for the clients. The information is encoded either XML or HTML.

However, to use access the result, you have to create a query. There are pre-created query available for the particular projects including the TeraGrid Resource Monitoring page in the TeraGrid user portal. This query includes result of monitoring status of remote login to the TeraGrid cluster, pre-ws gatekeeper, and ws gatekeeper server. If you want to see the most recent result of the testing encoded in XML:
http://inca.teragrid.org/inca/XML/kit-status-v1/portal
Or, as a HTML page,
http://inca.teragrid.org/inca/HTML/kit-status-v1/portal

For more detail information,
http://inca.teragrid.org/inca/XML/kit-status-v1/portal/[clusterID]/prews-gram-batch
For example,
http://inca.teragrid.org/inca/XML/kit-status-v1/portal/sdsc-ia64/prews-gram-batch
You will see the more detail information about the SDSC IA64 clusters such as testing intervals.

To create a query for your own purpose, you have to contact the administrator of the Inca service. Inca provides nice user interface for the administrator to create new query. After you create new query, you can access your result through:
http://inca.teragrid.org/inca/[XML|HTML]/kit-status-v1//

This output can be easily integrated to your software though light-weight way such as HTTP client. After downloding the information, we used conventional Java DOM implementation. With customized query, the response size seems to be reasonable to run with DOM implementation.

Please note that if you access Inca service hosted by SDSC, the testing interval is not changable.

Here is my test code:

import java.net.*;
import java.io.*;
import javax.xml.parsers.*;
import org.w3c.dom.*;

public class Test{
public static void main(String[] args){
try {
DocumentBuilderFactory dbf = DocumentBuilderFactory.newInstance();
DocumentBuilder db = dbf.newDocumentBuilder();
Document dom = db.parse("http://inca.teragrid.org/inca/XML/kit-status-v1/portal_summary");
Element docEle = dom.getDocumentElement();
NodeList nl = docEle.getElementsByTagName("row");

System.out.println("There are "+ nl.getLength()+ " elements.");
if(nl != null && nl.getLength() > 0) {
for(int i = 0 ; i < nl.getLength();i++) {

//get the employee element
Element el = (Element)nl.item(i);
NodeList sub1 = el.getElementsByTagName("reportSummary");
NodeList sub2 = ((Element)sub1.item(0)).getElementsByTagName("hostname");
String hostname = ((Element)sub2.item(0)).getFirstChild().getNodeValue();
System.out.println("HostName "+i+":"+hostname);
}
}
} catch (Exception e) {
e.printStackTrace();
}
}
}

Store and Register your EC2 machine image

2009-02-20T16:57:00.003-05:00

To retrieve your machine image later, your machine image should be stored in S3. To do that, there are multiple steps required.

Step 1) Copy your X.509 certificate and private key to your instance.
scp -i id_rsa-gsg-keypair pk-HKZYKTAIG2ECMXYIBH3HXV4ZBZQ55CLO.pem cert-HKZYKTAIG2ECMXYIBH3HXV4ZBZQ55CLO.pem root@domU-12-34-31-00-00-05.compute-1.amazonaws.com:/mnt

This is done on your local desktop. Than, your security files will be stored in /mnt directory of your instance.

Step 2) Now you have to bundle your instance with the commmand:
ec2-bundle-vol -d /mnt -k /mnt/pk-HKZYKTAIG2ECMXYIBH3HXV4ZBZQ55CLO.pem -c /mnt/cert-HKZYKTAIG2ECMXYIBH3HXV4ZBZQ55CLO.pem -u 495219933132 -r i386 -p sampleimage

This takes some time. (several minutes) If it was successful, you can see the bundled files under your /mnt directory. They are bunch of files with names of smapleimage*.

Step 3) Upload bundled files to S3 from your instance
ec2-upload-bundle -b -m /mnt/sampleimage.manifest.xml -a -s

I had some problem with this process. Although I have S3 access, this command complained that I don't have S3 access. Interestingly, I created a bucket in S3 manually, and it worked.
I use the firefox extension that recommanded in a EC2 forum.
http://www.s3fox.net/
It is quite useful. If I want to sync part of my disk, it would be a great tool.

Step 4) Then, logout your instance, and on your desktop,
ec2-register /sampleimage.manifest.xml

Now you can see your machine image from,
ec2-describe-images -o self

Step 5) That's it! whenever you want to reload your machine image,
ec2-run-instances ami-5bae4b32

for the longer version of tutorial,
http://docs.amazonwebservices.com/AWSEC2/latest/GettingStartedGuide/

Getting started with EC2

2009-02-17T15:00:00.004-05:00

To get start with EC2, you have to create an account in EC2 site.
After you successfully create your EC2 account from the amazon site, there are several steps to actually use EC2 instances.

Step1) Create X.509 certificate
Login to you Amazon account and AWS access identifiers page. In the X.509 certificate section, click Create New. Also Download your Certificate and store ot into your desktop safely.
mkdir .ec2
cd .ec2
mv ~/Desktop/*.pem .

Step2) Download EC2 command line tools. http://developer.amazonwebservices.com/connect/entry.jspa?externalID=351&categoryID=88
And unzip files under the ec2 directory.
mv ~/Desktop/ec2-api-tools.zip .
unzip ec2-api-tools.zip

Step3) Modify your shell script file. In my .bashrc file, I added,
export EC2_HOME=~/.ec2
export PATH=$PATH:$EC2_HOME/bin
export EC2_PRIVATE_KEY=pk-YOURKEYNAME.pem
export EC2_CERT=cert-YOURKEYNAME.pem

Step 4) Generate key pair to ssh to your instance
cd .ec2
ec2-add-keypair pstam-keypair > id_rsa-pstam-keypair

Step 5) Now select your new instance
ec2-describe-images -o amazon

Step 6) Create an instance
ec2-run-instances ami-6138dd08 -k pstam-keypair

Step 7) Check the description of the instance
Loading an instance takes some time. If you see the valid URL for the instance in the description of the instance, it's ready to access.
To check the description,
ec2-describe-instances

Step 8) Open the ports for ssh and http connection
You have to open some of the port you will allow to outside of the instances.
ec2-authorize default -p 22
ec2-authorize default -p 80

After this you can ssh to your instance.

Step 9) SSH to your instance
ssh -i id_rsa-pstam-keypair root@ec2-XXX-XXX-XXX-XXX.z-2.compute-1.amazonaws.com

Step 10) Getting a static IP address
For your application, sometimes you need a static IP address for your instance.
First you have to assign a static IP and tie the address to your instance.
ec2-allocate-address
ec2-associate-address -i i-yourinstance XXX.XXX.XXX.XXX

Step 11) Now you can SSH to your instance like to other remote machine.
ssh root@XXX.XXX.XXX.XXX

Step 12) Terminate Instance
ec2-terminate-instances i-yourinstance

Recent Change in TG

2009-02-11T16:42:00.002-05:00

cobalt requires (queue=) in rsl string. It was optional previously. Now if you don't put either
standard or industrial, globus will through exception,
Globus error 37

Also condor will through exception,
Exec format error Code 6 Subcode 8

Submitting job to Ranger

2009-02-11T13:17:00.003-05:00

Gatekeeper : gatekeeper.ranger.tacc.teragrid.org:2119/jobmanager-sge
Batch queue system: SGE
Check the queue status:showq -u

(Test 0) try locally installed executables with datafiles stored in scratch directory
./cap3 /scratch/00891/tg459282/2mil/cluster1807.fsa -p 95 -o 49 -t 100

(Test 1) try simple job submission through globus toolkit.
globusrun -o -r gatekeeper.ranger.tacc.teragrid.org:2119/jobmanager-sge '&(executable=/bin/ls)'

It works with swarm!

Submit and Manage Vanilla Condor Job to Swarm

2009-02-09T13:16:00.002-05:00

To submit Vanilla condor job(s) to Swarm, first you have to install swarm and configure the service to process vanilla condor jobs. the source code is available from
svn co https://ogce.svn.sourceforge.net/svnroot/ogce/ogce-services-incubator

For the general information to install swarm, please refer,
http://decemberstorm.blogspot.com/2008/11/swarm-sever-installation-guide.html

Now, configure your swarm for the Vanilla condor pool.
Step 1. modify swarm/TGResource.properties, to process only vanilla condor pool. This is my properties:
matchmaking=FirstAvailableResource
taskQueueMaxSize = 100
taskQueueScanningInterval = 3000
condorCluster=true
teragridHPC=false
eucalyptus=false
condorCluster_numberOfToken=10
condorRefreshInterval = 2000

Step 2. start swarm server.
Upload swarm/build/jobsub.aar to your axis2 installation.

Step 3. Client example of vanilla condor job is stored at,
swarm/src/core/org/ogce/jobsub/clients/SubmitVanillaJob.java

There are three example methods:
submitJobWithStandardOutput(): job with standard output wihout input files
submitJobWithOutputTransfer(): job with standard output and output files
submitJobWithInputOutputTransfer(): job with standard output, output files, and local input files

Step 4. Compile example file
[swarm]ant clean
[swarm]ant

Step 5. Run example file
[swarm]./run.sh submit_vanilla_job

Step 6. Check the status
[swarm]cd ClientKit
[ClientKit]./swarm status http://serverIP:8080/axis2/services/Swarm your_ticket_ID

Step 7. Get the location of output file
[ClientKit]./swarm outputURL http://serverIP:8080/axis2/services/Swarm your_ticket_ID
This will return the URL of the output file.

renewing proxy

2008-12-09T23:28:00.000-05:00

more /usr/local/gateway/RenewCred/renewCred.sh
#!/bin/bash
export GLOBUS_LOCATION=$HOME/globus-condor/globus
source $GLOBUS_LOCATION/etc/globus-user-env.sh
myproxy-logon -s myproxy.teragrid.org -l quakesim -t 5000 -S << EOF
PUT_PASSWORD_HERE
EOF

Writing simple Java application with HBase APIs[0]

2008-12-01T16:45:00.004-05:00

To write a simple Java application with HBase APIs, you surely need hadoop and hbase installation on your machine. For this example, I used hadoop installation with pseudo distributed setup on the localhost.
The code is mainly downloaded from the hbase site,
http://hadoop.apache.org/hbase/docs/r0.2.1/api/index.html


import java.io.IOException;
import org.apache.hadoop.hbase.client.HTable;
import org.apache.hadoop.hbase.client.Scanner;
import org.apache.hadoop.hbase.io.BatchUpdate;
import org.apache.hadoop.hbase.io.Cell;
import org.apache.hadoop.hbase.io.RowResult;
import org.apache.hadoop.hbase.HBaseConfiguration;

public class MySimpleTest {

 public static void main(String args[]) throws IOException {
   // You need a configuration object to tell the client where to connect.
   // But don't worry, the defaults are pulled from the local config file.
   HBaseConfiguration config = new HBaseConfiguration();

   // This instantiates an HTable object that connects you to the "myTable"
   // table.
   HTable table = new HTable(config, "myTable");

   // To do any sort of update on a row, you use an instance of the BatchUpdate
   // class. A BatchUpdate takes a row and optionally a timestamp which your
   // updates will affect.
   BatchUpdate batchUpdate = new BatchUpdate("myRow");

   // The BatchUpdate#put method takes a Text that describes what cell you want
   // to put a value into, and a byte array that is the value you want to
   // store. Note that if you want to store strings, you have to getBytes()
   // from the string for HBase to understand how to store it. (The same goes
   // for primitives like ints and longs and user-defined classes - you must
   // find a way to reduce it to bytes.)
   batchUpdate.put("myColumnFamily:columnQualifier1",
     "columnQualifier1 value!".getBytes());

   // Deletes are batch operations in HBase as well.
   batchUpdate.delete("myColumnFamily:cellIWantDeleted");

   // Once you've done all the puts you want, you need to commit the results.
   // The HTable#commit method takes the BatchUpdate instance you've been
   // building and pushes the batch of changes you made into HBase.
   table.commit(batchUpdate);

   // Now, to retrieve the data we just wrote. The values that come back are
   // Cell instances. A Cell is a combination of the value as a byte array and
   // the timestamp the value was stored with. If you happen to know that the
   // value contained is a string and want an actual string, then you must
   // convert it yourself.
   Cell cell = table.get("myRow", "myColumnFamily:columnQualifier1");
   String valueStr = new String(cell.getValue());
 
   // Sometimes, you won't know the row you're looking for. In this case, you
   // use a Scanner. This will give you cursor-like interface to the contents
   // of the table.
   Scanner scanner =
     // we want to get back only "myColumnFamily:columnQualifier1" when we iterate
     table.getScanner(new String[]{"myColumnFamily:columnQualifier1"});
 
 
   // Scanners in HBase 0.2 return RowResult instances. A RowResult is like the
   // row key and the columns all wrapped up in a single interface.
   // RowResult#getRow gives you the row key. RowResult also implements
   // Map, so you can get to your column results easily.
 
   // Now, for the actual iteration. One way is to use a while loop like so:
   RowResult rowResult = scanner.next();
 
   while(rowResult != null) {
     // print out the row we found and the columns we were looking for
     System.out.println("Found row: " + new String(rowResult.getRow()) + " with value: " +
      rowResult.get("myColumnFamily:columnQualifier1".getBytes()));
   
     rowResult = scanner.next();
   }
 
   // The other approach is to use a foreach loop. Scanners are iterable!
   for (RowResult result : scanner) {
     // print out the row we found and the columns we were looking for
     System.out.println("Found row: " + new String(result.getRow()) + " with value: " +
      result.get("myColumnFamily:columnQualifier1".getBytes()));
   }
 
   // Make sure you close your scanners when you are done!
   scanner.close();
 }
}

Hadoop: java.io.IOException: Incompatible namespaceIDs

2008-12-01T16:41:00.001-05:00

The error java.io.IOException: Incompatible namespaceIDs in the logs of a datanode (/logs/hadoop-hadoop-datanode-.log) might be caused by bug HADOOP-1212. Here is a site which provides how to get around this bug,
http://www.michael-noll.com/wiki/Running_Hadoop_On_Ubuntu_Linux_(Multi-Node_Cluster)

The complete error message was,

 ... ERROR org.apache.hadoop.dfs.DataNode: java.io.IOException: Incompatible namespaceIDs in /usr/local/hadoop-datastore/hadoop-hadoop/dfs/data: namenode namespaceID = 308967713; datanode namespaceID = 113030094
      at org.apache.hadoop.dfs.DataStorage.doTransition(DataStorage.java:281)
      at org.apache.hadoop.dfs.DataStorage.recoverTransitionRead(DataStorage.java:121)
      at org.apache.hadoop.dfs.DataNode.startDataNode(DataNode.java:230)
      at org.apache.hadoop.dfs.DataNode.(DataNode.java:199)
      at org.apache.hadoop.dfs.DataNode.makeInstance(DataNode.java:1202)
      at org.apache.hadoop.dfs.DataNode.run(DataNode.java:1146)
      at org.apache.hadoop.dfs.DataNode.createDataNode(DataNode.java:1167)
      at org.apache.hadoop.dfs.DataNode.main(DataNode.java:1326)

Test #4(2mil): Nov.21.2008

2008-11-21T14:55:00.009-05:00

Full sequence test for 2million sequences.

(1) Resource setup: BigRed(150), Ornl(80), Cobalt(80)
(2) Service setup: Status check interval: 60 secs
Job queue scan interval: 60 secs
Job queue size: 100
(3) Input files : 2mil.tar copied to each of cluster in the $TG_CLUSTER_SCRATCH directory.
Referred by arguments with full path to the input files
(4) Output files: staged out to swarm host

(5) Client side setup: input files are located in my desktop(same machine with swarm host).
Scan the directory and find files which contain more than 1 sequence(with grep unix command through Java Runtime). Send the request to swarm with 10 batch per rpc call.

Total duration of the Submission: 170364307 milliseconds(around 47.3 hours).
Total number of jobs submitted: 75533
Total number of files scanned: 536825

(6) Completed Jobs : To be added
(7) Held Jobs: To be added
(8) Open Issues:
Submission time requires to be improved.
Reason:

Loading 536825 objects which represent the filename takes too much of memory.[Approach]: Use filefilter and load partial list at a time
Using Java Runtime: Java Runtime requires extra memory to execute system fork. [Approach]: Try checking the number of sequences by means of Java FileInputStream
Running client and host in the same machine.[Approach]: Try the client in different machine.

Java Runtime Class with VM memory

2008-11-14T12:35:00.003-05:00

For swarm service, I worte a client kit to crawl a directory and find cluster files which need to be assembled. To access the files and count the number of gene sequences, I used Java Runtime Process class. With the 2 million sequences, I could get around 600000 clustered files. Those clustered files were visited by the crawler program. Especially when I tried to create DOM object to interact with Web service, this crawler started to throw IO exception-memory allocation error. My Java option was -Xmn 512M -Xmx 1024M.

On linux, Runtime.exec does a fork and execute. That means that you will need double what your current java process is using in virtual memory(real + swap). Therefore, if I specify initial heap as 512M then my total heap must be bigger than 1024M.

I tried to set my java option to -Xmn 256M -Xmx 1024M. Crawler was slowed down quite a bit, but it did not throw IO exception anymore.

Test #3(2mil): Nov.07.2008

2008-11-07T15:21:00.002-05:00

(1) Starting time: 04:00 pm

(2) Server Setup:

-BigRed : max 5

-Cobalt : max5

(3) Client Setup:

-Total job max: 20

-Input source: EST Human 2mil

* Note

New Setup:(1) Increased timeout from 20 secs to 6 mins. (axis2.xml)(2) Decreased resource pool size(3) Decreased client jobs

Test #2(2mil) : Nov.07.2008

2008-11-07T14:19:00.003-05:00

(1) Starting time: 02:05 pm

(2) Server Setup:
-BigRed : max 20
-Cobalt : max20

(3) Client Setup:
-Total job max: 1000
-Input source: EST Human 2mil

* Note
New Setup:
(1) Increased timeout from 20 secs to 6 mins. (axis2.xml)
(2) Decreased resource pool size
(3) Decreased client jobs

Result:
(1) Job submission successfully done. (total 1000 jobs)

References:
First condorjob clusterID: 50537

Test #1(2mil): Nov.07.2008

2008-11-07T14:10:00.006-05:00

(1) Starting time: 12:54 pm

(2) Server Setup:
-BigRed max 400
-Cobalt max 200

(3) Client Setup:
-Max job submission: 2000000
-Input files source: EST Human 2mil

Note:
(1) Reading directory with 2mil sequence takes less than 20 secs.
(2) Client hung with http timeout
(3)Cobalt started to hold jobs with globus err code 17.

[ABSTRACT] Scheduling Large-scale Jobs over the Loosely-Coupled HPC Clusters

2008-10-15T09:27:00.003-04:00

Compute-intensive scientific applications are heavily reliant on the available quantity of computing resources. The Grid paradigm provides a large scale computing environment for scientific users. However, conventional Grid job submission tools do not provide a high-level job scheduling environment for these users across multiple institutions. For extremely large number of jobs, a more scalable job scheduling framework that can leverage highly distributed clusters and supercomputers is required. In this presentation, we propose a high-level job scheduling Web service framework, Swarm. Swarm is developed for scientific applications that must submit massive number of high-throughput jobs or workflows to highly distributed computing clusters. The Swarm service itself is designed to be extensible, lightweight, and easily installable on a desktop or small server. As a Web service, derivative services based on Swarm can be straightforwardly integrated with Web portals and science gateways. In this talk, we present the motivation for this research, the architecture of the Swarm framework, and a performance evaluation of the system prototype.

Installing Hadoop

2008-09-09T14:45:00.006-04:00

This is my note written while I was following the installation documentation from hadoop's webpage.
http://hadoop.apache.org/core/docs/current/quickstart.html
I installed as a root, but I'm not sure if it is necessary.

Step 0. You have to have ssh, rsync, and java VM on your machine. I used,
1)ssh OpenSSH_4.3p2, OpenSSL 0.9.8b 04
2)rsync version 2.6.8
3)java 1.5.0_12

Step 1. Download software from a Hadoop distribution site.
http://hadoop.apache.org/core/releases.html

Step 2. Untar file

Step 3. reset the JAVA_HOME under your_hadoop_dir/conf/hadoop-env.sh
*note: I had JAVA_HOME defined in my .bashrc file. But I had to specify it again in the hadoop-env.sh.

Step 4. now you can just run your standalone operation as it is.
$ mkdir input
$ cp conf/*.xml input
$ bin/hadoop jar hadoop-*-examples.jar grep input output 'dfs[a-z.]+'
$ cat output/*

Step 5. For the Pseudo-Distributed Operation, which runs multiple virtual machines in single node so that it imitates real distributed file systems you have to set up the configuration in conf/hadoop-site.xml
The 'name' element is defined by hadoop system. Therefore, you can just use the names in the example from the hadoop page. I change the value of fs.default.name to hdfs://localhost:54310, and the one of mapred.job.tracker to localhost:54311.

Step 6. Check ssh localhost
In my case, I could not connect to localhost, but I could access to my numerical ip address. I changed my /etc/hosts.allow to have ALL:127.0.0.1 and it started to recognize localhost.
If it requires your passphrase:

$ ssh-keygen -t dsa -P '' -f ~/.ssh/id_dsa
$ cat ~/.ssh/id_dsa.pub >> ~/.ssh/authorized_keys

If you still prefer use the passphrase, it will cause problem during the starting the daemons.

Step 7. Formatting namenode and starting the daemon

$ bin/hadoop namenode -format

$ bin/start-all.sh

Now you can check your namenode at http://localhost:50070/

Also your job tracker is available at http://localhost:50030/

Step 8. Test functions

Copy the input files into the distributed filesystem:
$ bin/hadoop fs -put conf input

Run some of the examples provided:
$ bin/hadoop jar hadoop-*-examples.jar grep input output 'dfs[a-z.]+'

Copy the output files from the distributed filesystem to the local filesytem and examine them:
$ bin/hadoop fs -get output output
$ cat output/*

View the output files on the distributed filesystem:
$ bin/hadoop fs -cat output/*

Step 9. Stop the daemon

$ bin/stop-all.sh

Update OGCE:file-manager portlet with new tacc classes

2008-09-08T15:40:00.004-04:00

This update adds sorted view to the directory. JSP files and two java classes are modified: FileManagerConstants.java and FileManagerPortlet.java
The list of file updated is following.
portlets/comp-file-management/src/main/webapp/jsp/fileBrowser.jsp
portlets/comp-file-management/src/main/webapp/jsp/view.jsp
portlets/comp-file-management/src/main/webapp/css/fileManagement.css
portlets/comp-file-management/src/main/java/edu/tacc/gridport/portlets/interactive/FileManagementConstants.java
portlets/comp-file-management/src/main/java/edu/tacc/gridport/portlets/interactive/FileManagementPortlet.java
portlets/gp-common/src/main/webapp/jsp/fileBrowser.jsp - identical tofileBrowser.jsp above
portlets/gp-common/src/main/webapp/javascript/fileBrowser.js

* editted part is noted as "lukas edit"

Teragrid access end-to-end test

2008-08-21T17:11:00.008-04:00

Teragrid sistes end-to-end test
- condorG (grid universe)
- cap3 apps
- stage output file
(08/22/2008 current)
==============================================================
[bigred] gatekeeper.iu.teragrid.org:2119/jobmanager-loadleveler yes
[steele] tg-steele.purdue.teragrid.org:2119/jobmanager-pbs yes
[sdsc(ds)] dslogin.sdsc.teragrid.org:2119/jobmanager-loadleveler job state write error
[mercury] https://grid-hg.ncsa.teragrid.org:2119/jobmanager-pbs yes
[ornl] tg-login.ornl.teragrid.org:2119/jobmanager-pbs yes
[lonestar] gatekeeper.lonestar.tacc.teragrid.org:2119/jobmanager-lsf job state read error
[cobalt] grid-co.ncsa.teragrid.org:2119/jobmanager-pbs yes
[pople] gram.pople.psc.teragrid.org:2119/jobmanager-pbs cannot login
[sdsc(dtf)]tg-login1.sdsc.teragrid.org:2119/jobmanager-pbs disk quota error

Limit of job submissiont?

2008-08-15T14:13:00.004-04:00

I'm gathering the information about the limit of job submissions.
http://kb.iu.edu/data/awyt.html
http://kb.iu.edu/data/axal.html
NCSA(cobalt)
http://www.ncsa.uiuc.edu/UserInfo/Resources/Hardware/SGIAltix/Doc/Jobs.html
qstat -Q
BigRed
llclass

Java memory setup

2008-08-13T10:33:00.002-04:00

To run Job submitssion service or Swarm service, please note that your environment variable should be set up as,
export JAVA_OPTS="-server -Xms512m -Xmx1024m -XX:MaxPermSize=256m"

Otherwise, your java virtual machine will provide 8M of memory which might be too small for running the server.

Access to the Job Submission Service with PHP using NuSOAP

2008-07-02T11:27:00.006-04:00

If you are new to the PHP and NuSOAP, my previous posting would be helpful too.
Here is the simple example for the getStatus operation,
// Pull in the NuSOAP code
require_once('../lib/nusoap.php');
$client = new soapclient("http://your.service.location:8080/axis2/services/JobSubmissionService?wsdl",true);
$TaskId = array('clusterID' => "403", 'jobID' =>"0");
$taskId = array('TaskId' => $TaskId);
$getStatus = array('taskId'=>$TaskId);
$result = $client->call('getStatus',array('parameters'=> $getStatus),
'http://jobsubmissionservice.ogce.org/xsd','',false,null,'rpc','encoded');
if ($client->fault){
echo 'Fault';
}
print_r($result);

Creating a PHP client of the Web Service(Axis2) using NuSOAP

2008-07-02T11:07:00.007-04:00

You can download NuSOAP library from the NuSOAP project is hosted by SourceForge. It is a package of php files you can keep in your php document directory or in a separate directory. In my case, I copied /lib directory from the NuSOAP project under /usr/local/apache2/htdocs/ which is default location of documents for the apache2 server. Then, copied /sample directory of the NuSOAP project under the same directory, /usr/local/apache2/htdocs/. You can download document from the same site. It contains nusoap method summary. Now, it's time to build a WS client..

Step1. pull in the NuSOAP code into your php source code
require_once('../lib/nusoap.php');

Step2. Create now client and set the WSDL as "true".
soapclient("http://service.location.url:8080/axis2/services/YourTargetService?wsdl",true);

Step3. Send the request using call() method
mixed call (string $operation, [mixed $params = array()], [string $namespace = 'http://tempuri.org'], [string $soapAction = ''], [mixed $headers = false], [boolean $rpcParams = null], [string $style = 'rpc'], [string $use = 'encoded'])
Please note that if you don't specify the namespace, your outgoing SOAP message will include SOAP Body with namespace of 'http://tempuri.org'. This will cause fault from the server.
Here my test request,
$result = $client->call('yourMethod',array('parameters'=> $yourType),
'http://yourservice.namespace.org/xsd','',false,null,'rpc','encoded');
Also, the $params which is arguments passed to the service is the element defined in the wsdl:message . If your service has hierarchical data type structure, you need to track down your WSDL carefully.

Step4. see the result..
I just used print_r($result)...

Running PaCE via Teragrid Job submission service

2008-04-30T10:04:00.006-04:00

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 ={
"http://validURLS:8080/tmp/PaCEexample/Brassica_rapa.mRNA.EST.fasta.PaCE",
"http://validURLS:8080/tmp/PaCEexample/Phase.cfg"
};
String rslString =
"(jobtype=mpi)"+
"(count=4)"+
"(hostCount=2)"+
"(maxWallTime=00:15)"+
"(queue=DEBUG)"+
"(arguments= Brassica_rapa.mRNA.EST.fasta.PaCE 33316 Phase.cfg)";

String [] outputFileString = {
"estClust.33316.3.PaCE",
"ContainedESTs.33316.PaCE",
"estClustSize.33316.3.PaCE",
"large_merges.33316.9.PaCE"};

try{
CondorJob cj = new CondorJob();
cj.setExecutable("/N/u/leesangm/BigRed/bin/PaCE_v9");
cj.setTransfer_input_files(inputFileString);
cj.setGrid_resource("gt2 gatekeeper.bigred.iu.teragrid.org/jobmanager-loadleveler");
cj.setTransfer_output_files(outputFileString);
cj.setGlobusrsl(rslString);
cj.setMyProxyHost("myproxy.teragrid.org:7512");
cj.setMyProxyNewProxyLifetime("7200");
cj.setMyProxyCredentialName(myproxy_username);
cj.setMyProxyPassword(myproxy_passwd);
cj.setMyProxyRefreshThreshold("3600");

System.out.println(cj.toString());

RPCServiceClient serviceClient = new RPCServiceClient();

Options options = serviceClient.getOptions();

EndpointReference targetEPR = new EndpointReference(serviceLoc);

options.setTo(targetEPR);

QName query = new QName("http://jobsubmissionservice.ogce.org/xsd", serviceMethod);
Class [] returnTypes = new Class []{JobMessage[].class};
Object[] queryArgs = new Object[] {cj};
Object [] response = serviceClient.invokeBlocking(query,queryArgs,returnTypes);
JobMessage[] result = (JobMessage[])response[0];

System.out.println(result[0].toString());
}catch (Exception e){
e.printStackTrace();
}
}

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

Running PaCE on BigRed

2008-04-29T15:44:00.004-04:00

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 gatekeeper.bigred.iu.teragrid.org/jobmanager-loadleveler
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)\
(maxWallTime=00:15)\
(arguments= 'Brassica_rapa.mRNA.EST.fasta.PaCE' '33316' 'Phase.cfg')

queue

Sample code: Access Job Submission Service from PHP page

2008-04-23T15:12:00.021-04:00

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

2008-04-23T15:07:00.007-04:00

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
./configure
make
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:

extension=wsf.so
extension=xsl.so
extension_dir="/usr/local/lib/php/extensions/no-debug-non-zts-***".
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/

Running AMBER-pbsa on BigRed:[4] Parallel pmemd through condorG

2008-03-11T13:54:00.007-04:00

There were few obstacles to submit amber jobs through condorG system.

(1) loadleveler specific commands
BigRed uses loadleveler as it's batch system. Compared to PBS or LSF, loadlever has some distinguished keyword, such as class instead of queue, and using machine list file. But we didn't have any problem with those during submitting job through condorG. machine list file is generated and used automatically by the job script file created by job manager.

(2) passing arguments
Amber uses arguments for its input/output/refer... files. You have to include those arguments in the globusrsl string. The condor keyword, "arguments" is related to the arguments for mpirun. However, it didn't really work for mpirun arguments too.

(3) specifying number of process and machine
loadleveler requires commands for setting the number of node and process, such as node, tasks_per_node. Also mpirun provides argument -np to specify the number of total processes being used for this job. To passing right value to loadleveler and mpirun, you have to specify those valued in the globusrsl. "count" in globusrsl string will be mapped to the value of -np in mpirun. And "hostCount" in the globusrsl string will be mapped to the value of "node" in the job script generated by job manager. I could not find how to specify the task_per_node. However, somehow based on the values of node and -np, job manager generated task_per_node.

(4) script
This is the condorG script for this job submission.
========================================================================
executable = /N/soft/linux-sles9-ppc64/amber9-ibm-64/exe/pmemd.MPI
transfer_executable = false
should_transfer_files = yes
when_to_transfer_output = ON_EXIT
transfer_input_files = /home/leesangm/bio/mm_pbsa/amber_min.in, /home/leesangm/bio/mm_pbsa/ZINC04273785_ini.crd, /home/leesangm/bio/mm_pbsa/ZINC04273785_com.top, /home/leesangm/bio/mm_pbsa/ZINC04273785.crd, /home/leesangm/bio/mm_pbsa/ZINC04273785_ini.crd

universe = grid
grid_resource = gt2 gatekeeper.bigred.iu.teragrid.org/jobmanager-loadleveler
transfer_output_files = min.out.$(Cluster), ZINC04273785.crd
error = amber.err.$(Cluster)
log = amber.log.$(Cluster)
x509userproxy = /tmp/x509up_u500

globusrsl = (jobtype=mpi)\
(count=16)\
(hostCount=4)\
(maxWallTime=00:15)\
(queue=DEBUG)\
(arguments= -O -i amber_min.in -o min.out.$(Cluster) -c ZINC04273785_ini.crd -p ZINC04273785_com.top -r ZINC04273785.crd -ref ZINC04273785_ini.crd )

queue
=========================================================================

Running AMBER-pbsa on SDSC machines:[1] Serial Job interactively

2008-03-07T16:10:00.002-05:00

Good News! There were AMBER installations in three of SDSC machines: DataStar, BlueGene and Teragrid. For the serial example, I could not run on BlueGene, because there was no "sander" executable under amber9 installation. However, here are some guidelines about running amber on SDSC machines.
All of the machines keep the amber installation under the directory with same name structure.
/usr/local/apps/amber9
Therefore, just set the environment and run the same command on each of the account.

leesangm/amber> setenv AMBERHOME /usr/local/apps/amber9
leesangm/amber> set path = ( $path $AMBERHOME/exe )
leesangm/amber> $AMBERHOME/exe/sander -O -i amber_min.in -o min.out -c ZINC04273785_ini.crd -p ZINC04273785_com.top -r ZINC04273785.crd -ref ZINC04273785_ini.crd

Running AMBER-pbsa on NCSA machines:[1] Serial Job interactively

2008-03-07T15:46:00.005-05:00

Running on tungsten and cobalt takes much longer time(tungsten:55 mins, cobalt:32 mins) than I expected. It takes longer time than BigRed.

1. tungsten
Set environment variables,
[leesangm@tund mm_pbsa]$ setenv AMBERHOME /usr/apps/chemistry/AMBER/Amber9/amber9
[leesangm@tund mm_pbsa]$ set path = ( $path $AMBERHOME/exe )
And get the same test package of amber test and run the command,
$AMBERHOME/exe/sander -O -i amber_min.in -o min.out -c ZINC04273785_ini.crd -p ZINC04273785_com.top -r ZINC04273785.crd -ref ZINC04273785_ini.crd

2. cobalt
Set environment variables,
[leesangm@tund mm_pbsa]$ setenv AMBERHOME /usr/apps/chemistry/amber/amber9/amber9
[leesangm@tund mm_pbsa]$ set path = ( $path $AMBERHOME/exe )
And get the same test package of amber test and run the command,
$AMBERHOME/exe/sander -O -i amber_min.in -o min.out -c ZINC04273785_ini.crd -p ZINC04273785_com.top -r ZINC04273785.crd -ref ZINC04273785_ini.crd

Running AMBER-pbsa on BigRed:[3] Serial Job submit through CondorG

2008-03-07T14:42:00.001-05:00

[Step 1] First check if you have required environment setup in your .soft file. My .soft file looks like,
#
# This is the .soft file.
# It is used to customize your environment by setting up environment
# variables such as PATH and MANPATH.
# To learn what can be in this file, use 'man softenv'.
#
#
@bigred
@amber9
@teragrid-basic
@globus-4.0
@teragrid-dev
+mpich-mx-ibm-64

[Step 2] Create condor script including relevant arguments. I put all the required arguments in the "argument" command line of the script. I could get the result with using both batch system and system fork. Don't forget to transfer back the output file. My test script file is the following:
executable = /N/soft/linux-sles9-ppc64/amber9-ibm-64/exe/sander
arguments = -O -i amber_min.in -o min.out.$(Cluster) -c ZINC04273785_ini.crd
-p ZINC04273785_com.top -r ZINC04273785.crd
-ref ZINC04273785_ini.crd
transfer_executable = false
should_transfer_files = yes
when_to_transfer_output = ON_EXIT
transfer_input_files = /home/leesangm/bio/mm_pbsa/amber_min.in,
/home/leesangm/bio/mm_pbsa/ZINC04273785_ini.crd,
/home/leesangm/bio/mm_pbsa/ZINC04273785_com.top,
/home/leesangm/bio/mm_pbsa/ZINC04273785.crd,
/home/leesangm/bio/mm_pbsa/ZINC04273785_ini.crd

universe = grid
grid_resource = gt2 gatekeeper.bigred.iu.teragrid.org/jobmanager-loadleveler
transfer_output_files = min.out.$(Cluster)
error = condorG.err.$(Cluster)
log = condorG.log.$(Cluster)
x509userproxy = /tmp/x509up_u500
queue

Running AMBER-pbsa on BigRed:[2] Serial-LoadLeveler

2008-03-06T10:22:00.004-05:00

IU BigRed loadleveler provides several queues such as DEBUG, LONG, and NORMAL, etc. DEBUG queue(class) has limit of 4hours maximum job cpu time and 15 minutes of maximum processor cpu time. I could run my serial job with DEBUG queue and it took 14 minutes. llclass shows the complete list of queues and description.

Step 1. setup the environment in .soft file
@amber9
+mpich-mx-ibm-64

Step 2. go to the work directory

Step 3. llsubmit serial.job

Running AMBER-pbsa on BigRed:[1] Serial-Interactive

2008-03-06T09:45:00.005-05:00

Step 1. Setup the environment in .soft file
@amber9
+mpich-mx-ibm-64

Step 2. Go to the work directory and run the following command

$AMBERHOME/exe/sander -O -i amber_min.in -o min.out -c ZINC04273785_ini.crd -p ZINC04273785_com.top -r ZINC04273785.crd -ref ZINC04273785_ini.crd

Step 3. Output file is updated every 2 minutes and it took 20 minutes for me to finish the job completely.

Draft of PolarGrid database table design

2008-02-18T16:39:00.009-05:00

CREATE DATABASE PolarGrid;
use PolarGrid

# possible entry unit of dataset
# CREATE TABLE Expedition{
# ExpeditionID bigint,
# }
# possible entry unit of dataset
# CREATE TABLE Radar{
# RadarID bigint,
# }

#
# DataChunk
#
# DataChunk is a unit of dataset which is identified by
# (1) spatial information
# (2) temporal information
# (3) triplet of radar information (waveform, transmit antenna, receive antenna)
#
CREATE TABLE DataChunk(
DataChunkID BIGINT NOT NULL AUTO_INCREMENT,
UUID VARCHAR(255),
Desctiption VARCHAR(255),
SamplingFrequency int,
SampleAverage int,
NumberOfWaveform int,
DSPMode VARCHAR(255),
SystemDelay int,
StartPoint point,
StopPoint point,
StartUTC double,
StopUTC double,
Microformat MEDIUMBLOB,
CreationTimestamp timestamp,
RevisionTimestamp timestamp,
PGContactID bigint,
PRIMARY KEY(DataChunkID),
INDEX(StartPoint),
INDEX(StopPoint),
INDEX(StartUTC),
INDEX(StopUTC)

);

#
# FileObject:
#
# FileObject represents minimum unit of dataset. In general
# we assume that this object can be instrumental data or
# output visualization file, or revised data file.
# Please note that WaveformName,TXAntennaName, and RXAntennaName
# are from the file name. There is no validation about this name
# based on the antenna/waveform tables.
#
CREATE TABLE FileObject(
FileObjectID bigint NOT NULL AUTO_INCREMENT,
DataChunkID bigint,
UUID VARCHAR(255),
FileName VARCHAR(255),
RecordTimestamp timestamp,
RadarType VARCHAR(255),
DistributionFormat VARCHAR(255),
WaveformName VARCHAR(255),
TXAntennaName VARCHAR(255),
RXAntennaName VARCHAR(255),
OnlineResource VARCHAR(255),
CreationTimestamp timestamp,
RevisionTimestamp timestamp,
PRIMARY KEY (FileObjectID),
INDEX(DataChunkID),
INDEX(WaveformName),
INDEX(TXAntennaName),
INDEX(RXAntennaName),
INDEX(RecordTimestamp),
);

#
# Waveform
#
# This table defines waveform that transmited between antennas. Each
# radar system can have several different waveforms that it
# can transmit. And that transmitted waveform on that transmit antenna
# can be received on any combinations of antenna. Individual waveform
# describes single waveform that is used by datachunk.
#

CREATE TABLE Waveform(
WaveformID bigint NOT NULL AUTO_INCREMENT,
DataChunkID bigint,
WaveformName VARCHAR(255),
StartFrequency int,
StopFrequence int,
PulseWidth double,
ZeroPiMode int,
PRIMARY KEY (WaveformID),
INDEX(DataChunkID),
);

#
# DataAquisition
#
# This table defines how we describe the setup of antenna.
# This information is included for the waveform and data chunk
# AssociationType field specifies either this setup information is
# used for waveform or data chunk. Similarly, AssociationId field
# specified ID which is exact identity of the item.
#

CREATE TABLE DataAcquisition(
DataAcquisitionID bigint NOT NULL AUTO_INCREMENT,
NumberOfSamples int,
SampleDelay int,
BlankingTime int,
AssociationType VARCHAR(255),
AssociationID bigint,
PRIMARY KEY (DataAcquisitionID),
INDEX(AssociationType),
INDEX(AssociationID)
);

#
# Antenna
#
# This table specifies how we describe the antenna.
#

CREATE TABLE Antenna(
AntennaID bigint NOT NULL AUTO_INCREMENT,
AntennaName VARCHAR(255),
AntennaType VARCHAR(255),
Antennuation int,
AssociationType VARCHAR(255),
AssociationID bigint,
PRIMARY KEY (AntennaID),
INDEX(AssociationType),
INDEX(AssociationID)
);

#
# PGContact
#
# This table specifies contact information.
#
#

CREATE TABLE PGContact(
PGContactID bigint NOT NULL AUTO_INCREMENT,
IndividualName VARCHAR(255),
UNIXLoginName VARCHAR(255),
Email VARCHAR(255),
OrganizationName VARCHAR(255),
PositionName VARCHAR(255),
Voice VARCHAR(255),
Facsimile VARCHAR(255),
Address VARCHAR(255),
OnlineResource VARCHAR(255),
HoursOfService VARCHAR(255),
ContactInstruction VARCHAR(255),
PRIMARY KEY (PGContactID),
INDEX(UNIXLoginName),
INDEX(Email)
);

PolarGrid database table (initial draft)

2008-02-15T15:44:00.003-05:00

This is the basic database table that will directly related to the RSS feeding microformat. Marie and I went through the workflow for generating jpg image and finally agreed on this table design. Thank you so much, Marie!! Still there are some parts which are not that clear to us. As things are clerified, I'll incorperate them to this table.

#CREATE TABLE Expedition{
# ExpeditionID bigint,
#}

CREATE TABLE DataChunk{
DataChunkID bigint NOT NULL,
UUID VARCHAR(255),
Description VARCHAR(255),
SamplingFrequency int,
SampleAverage int,
NumberOfWaveform int,
DSPMode VARCHAR(255),
StartPoint point,
StopPoint point,
StartUTC double,
StopUTC double,
PRIMARY KEY ('DataChunkID')
}

CREATE TABLE FileObject{
FileObjectID bigint NOT NULL,
DataChunkID bigint,
UUID VARCHAR(255),
FileName VARCHAR(255),
RadarType VARCHAR(255),
Timestamp timestamp,
FileType VARCHAR(255),
WaveformName VARCHAR(255),
TXAntennaName VARCHAR(255),
RXAntennaName VARCHAR255).
OnLink VARCHAR(255)
PRIMARY KEY ('FileObjectID')
}

CREATE TABLE Waveform{
WaveformID bigint NOT NULL,
DataChunkID bigint,
WaveformName VARCHAR(255),
StartFrequency int,
StopFrequence int,
PulseWidth double,
ZeroPiMode int,
PRIMARY KEY ('WaveformID')
}

CREATE TABLE DataAcquisition{
DataAcquisitionID bingint NOT NULL,
NumberOfSamples int,
SampleDelay int,
BlankingTime int,
AssociationType VARCHAR(255),
AssociationID bigint
PRIMARY KEY ('DataAcquisitionID')
}

CREATE TABLE Antenna{
AntennaID bigint NOT NULL,
AntennaName VARCHAR(255),
AntennaType VARCHAR(255),
Antennuation int,
AssociationType VARCHAR(255),
AssociationID bigint
PRIMARY KEY ('AntennaID')
}

[PG] 80 TB of mobile data

2008-02-13T16:44:00.007-05:00

40 x 2TB drives... These little guys don't have any idea about being in the -40F for months.. Good luck, boxes!
For more pictures,
http://www.ussg.indiana.edu/~mrlink/gallery/PolarGrid

[PG]mysql GIS [1] Creating Spatial data and using functions

2008-02-06T15:55:00.001-05:00

With MySQL version 5 or higher, you can store GIS data and issue query over it . MySQL provides data types supporting openGIS requirements. Although MySQL does not support full spatial analysis, MBR-based support is very useful, if you want simple bounding box style query. To use this, you don't need any of additional package.

I found useful manual which covers almost everything I was looking for.
http://www.browardphp.com/mysql_manual_en/manual_Spatial_extensions_in_MySQL.html

Running parallel pw.x on the LoneStar of TACC: on site/condorG/condor-birdbath APIs

2008-01-17T10:40:00.002-05:00

(1) submit to the LSF queue on Lonestar
bsub -I -n 4 -W 0:05 -q development -o pwscf.out ibrun /home/teragrid/tg459247/vlab/espresso/bin/pw.x < /home/teragrid/tg459247/vlab/__CC5f_7/Pwscf_Input (2) submit through condorG script file Globus RSL parameter is available at http://www.globus.org/toolkit/docs/2.4/gram/gram_rsl_parameters.html
Actual script file is following,
=============================================
executable = /home/teragrid/tg459247/vlab/bin/pw_mpi.x
transfer_executable = false
should_transfer_files = yes
when_to_transfer_output = ON_EXIT
transfer_input_files = /home/leesangm/catalina/VLAB_Codes/__CC5f_7/008-O-ca--bm3.vdb,/home/leesangm/catalina/VLAB_Codes/__CC5f_7/__cc5_7,/home/leesangm/catalina/VLAB_Codes/__CC5f_7/Mg.vbc3
universe = grid
grid_resource = gt2 tg-login.tacc.teragrid.org/jobmanager-lsf
output = tmpfile.out.$(Cluster)
error = condorG.err.$(Cluster)
log = condorG.log.$(Cluster)
input = /home/leesangm/catalina/VLAB_Codes/__CC5f_7/Pwscf_Input
x509userproxy = /tmp/x509up_u500
globusrsl = (environment=(PATH /usr/bin))\
(jobtype=mpi)\
(count=4)\
(queue=development)\
(maxWallTime=5)

queue

(3) submit through condor birdbath APIs
Almost the same with serial job submission except for setting up the wall clock time. When you generate globusrsl, add

(maxWallTime=yourWallMaxTime)

Job submission to TG machines

2008-01-11T17:16:00.000-05:00

Color code
Blue: Serial pw.x is ready to run and accessible by Task Executor
Red: pw.x installation failed.
Green: Serial + MPI pw.x is ready to run and accessed from Task Executor
==================================================
machine hostname architecture job sub job manager
-----------------------------------------------------------------------------------------
BigRed login.bigred.iu.teragrid.org ppc64 GT4 loadleveler
*QueenBeelogin-qb.lsu-loni.teragrid.org GT4
NCAR tg-login.frost.ncar.teragrid.org i686 GT4
*Abe login-abe.ncsa.teragrid.org Intel64 GT4 pbs
Cobalt login-co.ncsa.teragrid.org ia64 GT4/GT2 pbs/fork
Mercury login-hg.ncsa.teragrid.org ia64 GT4/GT2 pbs/fork
Tungsten login-w.ncsa.teragrid.org ia32 GT4/GT2 LSF/fork
ORNL tg-login.ornl.teragrid.org i686 GT4/GT2 pbs/fork
*BigBen tg-login.bigben.psc.teragrid.org AMD Opteron GT4/GT2 pbs
*Rachel tg-login.rachel.psc.teragrid.org GT4/GT2 pbs
Purdue tg-login.purdue.teragrid.org GT4/GT2 pbs
*sdsc BG bglogin.sdsc.edu ppc64 GT4/GT2 no job manager??
*sdsc DS dslogin.sdsc.edu 002628DA4C00 GT4/GT2 loadleveler/fork
sdsc IBM tg-login.sdsc.teragrid.org ia64 GT4/GT2 pbs/fork
lonestar tg-login.lonestar.tacc.teragrid.org ia64 GT4/GT2 LSF/fork
maverik tg-viz-login.tacc.teragrid.org sun4u GT4/GT2 sge/fork
*ranger tg-login.ranger.tacc.teragrid.org GT4 sge/fork
IA-VIS tg-viz-login.uc.teragrid.org i686 GT4/GT2 pbs
IS-64 tg-login.uc.teragrid.org ia64 GT4/GT2 pbs/fork
=================================================

*QueenBee : could not login
*Abe doesn't support single-sign-on
*BigBen: could not login
*Abe: could not login
*Rachel: could not login
*Purdue: could not login
*sdsc BlueGene: unknown job manager?
*sdsc DataStar: unusual architecture?
*ranger: could not login

Compiling espresso in the TG machines

2008-01-11T15:22:00.000-05:00

To run the executables on the TG machines, first you have to get ready your executables on the site.
Here is the instruction of installation serial run espresso. README.install was very useful.

* Cobalt, Mercury, and Tungsten NCSA

step 1. copy espressoXXX.tar

step 2. On the espresso directory, set the environment variable to select architecture.
setenv BIN_DIR /home/ac/quakesim/vlab/espresso/bin
setenv PSEUDO_DIR /home/ac/quakesim/vlab/espresso/pseudo
setenv TMP_DIR /home/ac/quakesim/vlab/espresso/tmp
setenv ARCH linux64
setenv PARA_PREFIX
setenv PARA_POSTFIX

note: for serial process, PARA_PREFIX MUST be left empty. For parallel process,

setenv PARA_PREFIX "mpirun -np 2"
setenv PARA_POSTFIX

step 2.5 make sure you have tmp, pseudo, bin directory under your espresso directory

step 3. ./configure

step 4. make all

* Lonestar parallel pw.x, ph.x
step 1. setenv PARA_PREFIX "mpirun"
step 2. setenv ARCH linux64
step 3. ./configure
step 4. make all

Submit job to pbs[1]: on site with command line

2008-01-11T11:36:00.000-05:00

(0) create script file which displays hostname of the machine. Name the file as "test"
#!/bin/sh
/bin/hostname
(1) submit job test to the pbs queue.
qsub -o test.out -e test.err test
(2) check result file

*Useful guide
http://www.teragrid.org/userinfo/jobs/pbs.php

Submitting a job to LSF job queue [3]: through CondorG with birdbath APIs

2008-01-04T15:35:00.000-05:00

To submit a job to the LSF thourgh the condor G with birdbath APIs, your ClassAdStructAttr should contains required attributes. I retrieved the list of keywords from my previous example: Submitting a job to LSF job queue [2]. After submitting condor job with example[2], run condor_q -l, than you can get a list of valid keywords. Please note that even though you use wrong keyword, condor WON'T throw any exception, and your job WON'T go through. (now I'm pulling my hair.) Therefore, make something runs correctly even though it's not with birdbath APIs, and start from the valid keywords generated from that example.

* Attributes In, Out, and Err are used for specifying Standard Input, output, and error redirections. Therefore if your executables uses standard input/output and redirects them to files, those should be specified with these attributes.

* In this case, pw.x generates multiple files besides stdout output files. Attribute
TransferOutput specifies files that should be transfered after the process is done.

* Attribute GlobusRSL is equivalant to the keyword globusrsl in the script file for the command line submission by condor_submit.

* Many many thanks to Marlon for helping me out!!

Actual ClassAdStructAttr[] is following:
------------------------------------------------------------------------------------------------------------------------------
ClassAdStructAttr[] extraAttributes =
{
new ClassAdStructAttr("GridResource", ClassAdAttrType.value3, gridResourceVal),
new ClassAdStructAttr("TransferExecutable",ClassAdAttrType.value4,"FALSE"),
new ClassAdStructAttr("Out", ClassAdAttrType.value3, tmpDir+"/"+"pwscf-"+clusterId+".out"),
new ClassAdStructAttr("UserLog",ClassAdAttrType.value3, tmpDir+"/"+"pwscf-"+clusterId+".log"),
new ClassAdStructAttr("Err",ClassAdAttrType.value3, tmpDir+"/"+"pwscf-"+clusterId+".err"),
new ClassAdStructAttr("In",ClassAdAttrType.value3, workDir+"/"+"Pwscf_Input"),
new ClassAdStructAttr("ShouldTransferFiles", ClassAdAttrType.value2,"\"YES\""),
new ClassAdStructAttr("WhenToTransferOutput", ClassAdAttrType.value2,"\"ON_EXIT\""),
new ClassAdStructAttr("StreamOut", ClassAdAttrType.value4, "TRUE"),
new ClassAdStructAttr("StreamErr",ClassAdAttrType.value4,"TRUE"),

new ClassAdStructAttr("TransferOutput",ClassAdAttrType.value2,
"\"pwscf.pot, pwscf.rho, pwscf.wfc, pwscf.md, pwscf.oldrho, pwscf.save, pwscf.update\""),

new ClassAdStructAttr("TransferOutputRemaps",ClassAdAttrType.value2,
"\"pwscf.pot="+tmpDir+"/"+"pwscf-"+clusterId+
".pot; pwscf.rho="+tmpDir+"/"+"pwscf-"+clusterId+
".rho;pwscf.wfc="+tmpDir+"/"+"pwscf-"+clusterId+
".wfc; pwscf.md="+tmpDir+"/"+"pwscf-"+clusterId+
".md; pwscf.oldrho="+tmpDir+"/"+"pwscf-"+clusterId+
".oldrho; pwscf.save="+tmpDir+"/"+"pwscf-"+clusterId+
".save; pwscf.update="+tmpDir+"/"+"pwscf-"+clusterId+".update\""),

new ClassAdStructAttr("GlobusRSL", ClassAdAttrType.value2,
"\"(queue=development)(environment=(PATH /usr/bin))(jobtype=single)(count=1)\""),

new ClassAdStructAttr("x509userproxy",ClassAdAttrType.value3,proxyLocation),

};
------------------------------------------------------------------------------------------------------------------------------

Pwscf output files?

2008-01-04T15:23:00.000-05:00

In my local machine, pw.x generates output files besides the standard output:
pwscf.pot, pwscf.rho, pwscf.wfc
unless I reuse the tmp directory.

However, in lonestar, it genrates,
pwscf.md pwscf.oldrho pwscf.pot pwscf.rho pwscf.save pwscf.update pwscf.wfc

For sure, I transfer all of the possible files from the remote machine.

Submitting a job to LSF job queue [2]: through CondorG with condor_submit

2008-01-04T14:22:00.000-05:00

Now, I tried to submit the same job, pw.x with the remote input files through the CondorG command line which is condor_submit. In this example, I use inputfiles stored in my local machine. Therefore, my script file should specify input files like following lines.

---------------------------------------------------------------------------------------------------------------------------------
executable = /home/teragrid/tg459282/vlab/pw.x
transfer_executable = false
should_transfer_files = yes
when_to_transfer_output = ON_EXIT
transfer_input_files = /home/leesangm/catalina/VLAB_Codes/__CC5f_7/008-O-ca--bm3.vdb,/home/leesangm/catalina/VLAB_Codes/__CC5f_7/__cc5_7,/home/leesangm/catalina/VLAB_Codes/__CC5f_7/Mg.vbc3

universe = grid
grid_resource = gt2 tg-login.tacc.teragrid.org/jobmanager-lsf
output = tmpfile.out.$(Cluster)
error = condorG.err.$(Cluster)
log = condorG.log.$(Cluster)
input = /home/leesangm/catalina/VLAB_Codes/__CC5f_7/Pwscf_Input

globusrsl = (queue=development)\
(environment=(PATH /usr/bin))\
(jobtype=single)\
(count=1)

queue
---------------------------------------------------------------------------------------------------------------------------------

This script file is almost the same with normal condor submit script except for the globusrsl keyword. This is a simple case for the serial job. For the parallel jobs, this should be modified.

Then submit condor job,
condor_submit script_file_name

Submitting a job to LSF job queue [1] : On the Cluster

2008-01-04T11:44:00.000-05:00

* Usefule LSF commands :
bsub: submission jobs
bjobs: display information about the jobs
bkills: send signal to kill
For more commands,
http://its.unc.edu/dci/dci_components/lsf/lsf_commands.htm

* Useful options of bsub command
-q : name of the queue
-n: desired number of processors
-W: Walltime limit in batch jobs -W[hours]:[minutes]
-i : input file
-o : output file
-e: error file

Example lsf submit of pw.x in lonestar
bsub -q development -n 1 -W 15 -i "Pwscf_Input" -o "myout.out" ../pw.x

Building a Client of the Task Executor

2008-01-03T13:33:00.000-05:00

To generate client of the vlab Task Executor service, first we have to create stub code and compile them.
If the service is running on localhost, WSDL file is located at,
http://localhost:8080/task-executor/services/TaskExecutor?wsdl
With this WSDL file, we can generate java classes with WSDL2Java included in the axis package.
java org.apache.axis.wsdl.WSDL2Java http://localhost:8080/task-executor/services/TaskExecutor?wsdl
Then compile/jar the java code.
Required jar files to run WSDL2Java are following:

axis-1.4.jar
activation-1.1.jar
commons-discovery-0.2.jar
saaj.jar
jaxrpc.jar
mail-1.4.jar
wsdl4j-1.5.1.jar

Globus environment

2007-12-14T11:33:00.000-05:00

Step. 0 source $GLOBUS_LOCATION/etc/globus-user-env.sh

Step. 00 export X509_CERT_DIR=/home/leesangm/.globus/certificates

Step. 000 Check if this works,
globusrun -o -r grid-co.ncsa.teragrid.org/jobmanager '&(executable=/bin/ls)'

condor_rm -forcex -all : force the immediate local removal of jobs in the X state

Condor/Birdbath documentations

2007-12-05T16:21:00.000-05:00

Birdbath section in the condor manual:
http://www.cs.wisc.edu/condor/manual/v6.8/4_4Application_Program.html
Marlon's Blog
Condor Installation: http://communitygrids.blogspot.com/2007/07/beating-condor-like-rented-buzzard.html
Submitting Globus job through condor: http://communitygrids.blogspot.com/2006/09/submitting-globus-job-through-condor.html

Condor: Birdbath APIs javadoc

2007-12-05T16:01:00.000-05:00

After few days of suffering, I generated this javadoc from condor birdbath related source codes. I got the source code from,
(1) birdbath jar file: download from http://www.cs.wisc.edu/condor/birdbath/birdbath.jar
(2) type classes generated from WSDL (birdbath1.jar): included in the condor6.8.6 release (/lib/webservice)
http://www.cs.indiana.edu/~leesangm/ogce/condor/docs/

VLAB

2007-11-28T09:17:00.000-05:00

mvn clean install cargo:deploy -Dmaven.test.skip=true -f with_condor/task-executor/pom.xml

FAS Script file for the SC07 Demo

2007-10-29T14:05:00.000-04:00

Script file generateDB.sh is designed especially for the demo at SC07. This script manages three accounts, leesangm, mpierce, and yuma. First, all of the information about these users will be removed.Then new information will be registered. If you want to modify information, open generateDB.sh modify it, and run it.

To run this script,
Step 1. You should download this .
All of the library jar files, and script files are included.
Step 2. Run the command.
./generateDB.sh

That's it.

Command Line Access to the FAS0.7

2007-10-29T13:46:00.000-04:00

Command line tool provides immediate access to the FAS server. This is very useful for the test runs.
To user this command line tool, you don't need to run the service on your site. You will need only client of the service.

Step 1. You should download this .
All of the example, script files are included.

Step 2. Run the command.
(1)To create new user space
./run.sh AddNewUserSpace -f [FAS service location] -l [username] -h [host name] -p [port number] -dn [DN of the community cert for this host] -pr [protocol] -us [logical space for this user]
e.g.) ./run.sh AddNewUserSpace -l leesangm -h "gridfarm001.ucs.indiana.edu" -p "2811" -pr "gridftp" -us "/home/quakesim/"

(2)To query user space
./run.sh QueryUserSpace -f [FAS service location] -l [username] -h [host name] -p [port number] -dn [DN of the community cert for this host] -pr [protocol] -us [logical space for this user]
e.g.) ./run.sh QueryUserSpace -l leesangm

(3)To remove user space
./run.sh RemoveUserSpace -f [FAS service location] -l [username] -h [host name] -p [port number] -dn [DN of the community cert for this host] -pr [protocol] -us [logical space for this user]
e.g.) ./run.sh RemoveUserSpace -l leesangm

[NOTE]
Default value of FAS service location is

http://gridfarm002.ucs.indiana.edu:8080/axis2/services/FileAgentService

Default value of DN of the Community Certificate is Teragrid Quakesim cert.
/C=US/O=National Center for Supercomputing Applications/CN=QuakeSim Community User

File Agent Service V0.7

2007-10-29T11:06:00.001-04:00

1. Introduction
File Agent Serivce is a web service providing access to the information about community user space. This user space is accessed with Teragrid community certificate. This version provides 7 operations including 3 operations from the previous version.

queryDataSpaceInfo
registerDataSpaceInfo
removeDataSpaceInfo
createDataSpace
queryUserSpaceConvention
registerUserSpaceConvention
removeUserSpaceConvention

Section 2 will discribe how to access the service, and each of the operations are described in the section 3.

2. Access to the service
Required jar file:
-FileAgentService.aar and basic jar file for axis2.
Download tarball [48MB contains all the lib and source code].
Service is now up and running on,
http://gridfarm002.ucs.indiana.edu:8080/axis2/services/FileAgentService
The WSDL file is available at,
http://gridfarm002.ucs.indiana.edu:8080/axis2/services/FileAgentService?wsdl
For detail code example, please refer the sample code.

3. Operations
3.1 queryDataSpaceInfo
This operation provides query interface to the data space information. Input parameter is query statement described in WSDL and output parameter is the query result.
Here is how to build an input query for this operation. First, dataspace information includes following items,

username : user's portal id
host: remote location of the data resource
port: port number of the data resource
commCertDN: DN of the community certificate that used for this resource
protocol: protocol to access this resource
LogicalUserSpace: logical user space assigned for the user

Above items are accessible through getter/setter methods of the FASBean object that is included in the FileAgentService.aar file.

For example,
FASBean fb = new FASBean();
fb.setUsername("fiona");
fb.setHost("gridfarm002");
fb.setPort("123");
fb.setCommCertDN("nydb");
fb.setProtocol("gridftp");
fb.setLogicalUserSpace("/home/communityspace/fiona");

For the queryDataSpaceInfo operation, you can build very simple query without knowing any of complicated query language. Specify items that you know exactly. Leave items as null if you are not sure. This operation will process the null item as a wildcard in the query.

For example, if you want to get all the dataspace information about user A in the host GGG, then set the username and host and leave everything else as null. (Just don't set the value).

3.2 registerDataSpaceInfo
This operation registers new data space information. Define FASBean and use it as parameter of this operation. Please refer the sample code.

3.3 removeDataSpaceInfo
This operation removes data space inforamtion. This works very similar to the queryDataSpaceInfo operation. Therefore, if you want to remove all of the information about user A, you should specify username only, and leave all of other itesm null. Please note if you set complete null input parameter to thie operation, it will completely reset your database.

3.4 createDataSpace
[TODO] This operation is almost same with thte registerDataSpaceInfo operation. On top of creating data space information, this operation will access the remote resource and create your's logical space as well.

3.5 queryUserSpaceConvention
This is a utility operation for the advanced users. If the administor wants to organize ther user's logical space with more standard convention, 3.5 ~ 3.7 operations should be very useful.
This operation provides following informations,

host: host name of the remote resource
port: port number of the remote resource
attr: attribution of this convention
defaultLoc : convention of the user space

For example, let's assume that an administrator should organize users' data under the community space which is /g/d/commUser. This space is hosted by host A and port 1234. Also this host has multiple mounted resources such as /tg/h/j/hpss for the HPSS server, and /sc/datacatacitor for the High performance data capacitor. The user's space can be organized following way.

host: A
port: 1234
attr: High performance data capacitor
defaultLoc: /sc/datacapacitor/userspace/username

host: A
port: 1234
attr: Network File System
defaultLoc: /g/d/commUser/userspace/username

host: A
port: 1234
attr: HPSS
defaultLoc: /tg/h/j/hpss/userspace/username

Based on these informations, when a new user tries to create a data space, the system can query the convention of the defaultLoc and create the user space accordingly. Also the application can show the attribute of the location so that it can provide more precise information instead encrypted directory path.

You can use this operation in very similar way to the queryDataSpaceInfo. Specify all of the items you know exactly and send the request. The operation will process your query as predicates combined as AND predicates and process non-specified items as wildcard items.

3.6 registerUserSpaceConvention
This operation registers new User space convention. Section 3.5 explains how to organize the community user space using this operation. For more information, please refer the sample code.

3.7 removeUserSpaceConvention
This operation removes user's space convention. For more information, please refer the sample code.

Appendix. Sample Code
Download tarball [48MB contains all the lib and source code]
Sample Code Directory: src/org/ogce/fileagentservice/client
AddNewUserSpace.java
QueryUserSpace.java
RemoveUserSpace.java
ConventionExample.java

Community Proxy Single sign-on

2007-10-15T15:26:00.000-04:00

This is about the sigle sign-on process with the community proxy certificate for the OGCE porttal (Gridsphere version). As soon as the user's login name and password are verified the portal service accesses teragrid proxy server, gets the community proxy certificate and stores it with user's login name in the proxy manager.

Step 0. prepare the account
-- get community account
-- http://grid.ncsa.uiuc.edu/myproxy/tgsso.html

Step 1. change the code
org.gridlab.gridsphere.impl.service.core.user.LoginServiceImpl
-- access the proxy server (teragrid proxy server)
-- get a proxy cert
-- register to the proxy manager with the currrent login name

Step 2. compile and generate jar
On gridsphere directory,

ant gridsphere-jar

*make sure that the detendent jar files are located in the lib directory.
proxymanager-api-4.2.jar
cog-jglobus-1.2-050621.jar
jgss-1.0.jar

*make sure that the classpath is pointing the lib directory in the compile task.

Step 3. copy jar to current OGCE deployment under,
/shared/lib/

File Agent service access from portlet: compile

2007-10-04T16:29:00.000-04:00

STEP 0: Shut down tomcat

STEP 1: add 3rd party jar for axis2,
axis2-adb-1.3.jar
axis2-kernel-1.3.jar
axiom-api-1.2.5.jar
annogen-0.1.0.jar
axiom-api-1.2.5.jar
axiom-dom-1.2.5.jar
axiom-impl-1.2.5.jar
commons-codec-1.3.jar
commons-httpclient-3.0.1.jar
stax-api-1.0.1.jar
wsdl4j-1.6.2.jar
wstx-asl-3.2.1.jar
XmlSchema-1.3.2.jar
FileAgentService-0.5.aar
command:
ogce-portal-only/maven-2.0.7/bin/mvn install:install-file -DgroupId=axis2 -DartifactId=axis2-adb -Dversion=1.3 -Dfile="axis2-adb-1.3.jar" -Dpackaging=jar
ogce-portal-only/maven-2.0.7/bin/mvn install:install-file -DgroupId=axis2 -DartifactId=axis2-kernel -Dversion=1.3 -Dfile="axis2-kernel-1.3.jar" -Dpackaging=jar
ogce-portal-only/maven-2.0.7/bin/mvn install:install-file -DgroupId=FileAgentService -DartifactId=FileAgentService -Dversion=0.5 -Dfile="FileAgentService-0.5.aar" -Dpackaging=jar
ogce-portal-only/maven-2.0.7/bin/mvn install:install-file -DgroupId=axis2 -DartifactId=axiom-api -Dversion=1.2.5 -Dfile="axiom-api-1.2.5.jar" -Dpackaging=jar

Step 2. Add s to the project.pom file

axis2
axiom-api
1.2.5
compile

axis2
axiom-dom
1.2.5
compile

axis2
axiom-impl
1.2.5
compile

axis2
axis2-adb
1.3
compile

axis2
annogen
0.1.0
compile

axis2
axis2-kernel
1.3
compile

axis2
commons-codec
1.3
compile

axis2
commons-httpclient
3.0.1
compile

axis2
stax-api
1.0.1
compile

axis2
wsdl4j
1.6.2
compile

axis2
wstx-asl
3.2.1
compile

axis2
XmlSchema
1.3.2
compile

FileAgentService
FileAgentService
0.5
compile

STEP 3: compile and install
On the directory of ogce-portal-only,
maven-2.0.7/bin/mvn clean install -f portlets/comp-file-management/pom.xml

STEP 4: try it.
./tomcat-startup.sh

Organizing information about Community proxy

2007-09-14T14:28:00.001-04:00

Well..if a person wants to transfer a file from her community data repository to her personal/remote data file system through the file-comp-management portlet, what do we need to provide? That person will need to access the community proxy to access her community data repository. At a same time, she should access her personal proxy which is relevant to the remote resource. Do we have to ask her every time which proxy she is gonna use? What if it's non-interactive task such as job processing with mix-and-match proxies?

Since remote access to the resource requires the location of the resource, I think about simple but nice organizing of the information about community proxies and personal proxies based on the location. For each of the users, if {Username, Host, Port} is provided after the user issues proxies, ProxyManager will let me find the proxy for the host with the username.

Also if the virtulization of the user space for the community repository is considered, I may have to add the pointer to the user space specified by the system. If it is the community repository based on the Unix file system and the system relocates each of the user's space as /CommunityRepository/[username], than userspace will set as /CommunityRepository/myusername. If it is not a community repository then "~" can simply lead the user to the user's home directory that is specified by the Unix file system. Therefore, now I have, {Username, Host, Port, Userspace}.

Hang on... on top of this, I have to consider about the users who have both of the community acess and personal access to the same resource. For the huge data repository, this can happen quite often. I might have to add some identifier of the proxy, so that Userspace is not confusing. This doesn't have to be universally unique but it should be unique enough within the set of proxies for the same host and user. User's DN which is available from the GSSCredential object can be a good candidate. Now triplet is grown as {Username, Host, Port, Userspace, ProxyIdentifier}.

What else can be added....?

Test note for the ProxyManager Portlet

2007-09-14T14:21:00.000-04:00

1. Test Items

Create a personal proxy
Create a community proxy
Set default proxy
Get a new personal proxy but not create a copy of existing community proxy
Romove proxy
Test with 3rd party user

2. FixMe list
3. Possible addition
display whether it's a community proxy.

Test note for the Comp-file-management portlet.

2007-09-14T14:10:00.000-04:00

1. Test list

File list
GoTo Directory
Go UpperDirectory
Upload
Transfer
Home
Rename

2. FixMe List
(1) After transfer or upload file, file list displays home directory. - Fixed.
(2) After the transfer the file, the size of the file is listed as 0.
(3) Last Modified of the destination File Listing is not human-friendly.

Commands for using maven2

2007-09-12T14:08:00.000-04:00

Installing 3rd party jar
maven-2.0.7/bin/mvn install:install-file -DgroupId=proxymanager-api-4.2.1 -DartifactId=proxymanager-api-4.2.1 -Dversion=4.2.1 -Dfile="/home/leesangm/ogce-portal-only/proxymanager-api-4.2.1.jar" -Dpackaging=jar

Modify comp-file-management portlet to use Cog Abstraction APIs

2007-09-07T09:45:00.000-04:00

Comp-file-management portlet is implemented using the JSR0168 specification, and allows a user to list/browse files on a source and/or destination resource. Also it provides features to upload, and download user's files. User can transfer files between remote resources. Users upload local file to the remote resource as well.
Currently, major gridFTP functionality is implemented by access to the gridFTP APIs. To modify the classes to use COG Abstraction APIs, some of the classes from the grid port package and comp-file-management portlet are re-written.
*All of the added classes are packaged under .utils because of the confliction between the package names.

Added/Modified Classes

1. edu.tacc.gridport.portlets.interactive.utils.FileListingManager

Origin: GridPort

New Package: edu.tacc.gridport.portlets.interactive.utils
Modified Methods:

FileListingBean executeFileListing(ActionRequest req, ActionResponse res, FileListingBean currentListing)
ArrayList constructFileBeans(Collection files, String currentDir)
ArrayList constructFileBeans(FileInfo[] files, String currentDir)

Added Methods:

FileResource getConnect(GSSCredential proxy, String host, String port,String purpose, boolean remotePassive,String provider)

FileResource getConnect(PortalRequest request, String host, String port,String purpose, boolean remotePassive, String provider)
String getUpperDirectory(String currentDirectory)
String getPortalUsername(PortletRequest request)
void putIntoSession(PortletRequest request, String name, Object obj)
String constructPermissionString(Permissions user, Permissions group, Permissions all, boolean dir)

2. edu.tacc.gridport.portlets.interactive.utils.FileUploadManager
Origin: Grid Port
New Package: edu.tacc.gridport.portlets.interactive.utils
Modified Methods:
void uploadFileToRemote(ActionRequest req)

3.edu.tacc.gridport.portlets.interactive.helpers.FileTransfer
Origin: edu.tacc.gridport.portlets.interactive.helpers (comp-file-management portlet)
New Package: no change
Added Methods:
void fileUploadFromUserMachine(String toHost, String localFileFullName, String remoteFileFullName, GSSCredential credential)

Modified Methods:

void thirdPartyTransfer(String fromHost, String fromFileFullName,String toHost, String toFileFullName, GSSCredential credential)

Compile and deploy single portlet

2007-09-05T09:55:00.000-04:00

New version (Sep. 07, 2007)
mvn clean install -f portlets/filetransfer/pom.xml

Old version

Goto /ogce/ogce-portal/ogce-portal
../third_party_tools/maven-1.0.2/bin/maven gp:deploy-portlet -Dportlet.name=filetransfer -Denv.CATALINA_HOME=../portal_deploy/apache-tomcat-5.5.12

Note: use maven V.1.xx
source: http://collab-ogce.blogspot.com/2007/07/re-compiling-individual-portlets.html

setup the globus credential

2007-08-24T11:44:00.000-04:00

setup the globus credential info:(http://manacar.blogspot.com/2006/12/myproxy-guidelines-for-community-grids.html)