A Graphical User Interface for Job Submission and Control at RHIC/STAR using PERL/CGI

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1 A Graphical User Interface for Job Submission and Control at RHIC/STAR using PERL/CGI Crystal Nassouri Wayne State University Brookhaven National Laboratory Upton, NY Physics Department, STAR Summer 2004

2 Abstract Introduction What is STAR? Problems with data at STAR. My role in finding solutions using PERL and SQL. Main How PERL is applied to SQL. Creating an interface to manage data. Implementing the final product. Conclusion Acknowledgments

3 What is STAR? Solenoidal Tracker at RHIC (STAR) is a detector and collaboration at the Brookhaven National Laboratory, Upton, NY, which specializes in tracking the thousands of particles produced by each ion collision at the Relativistic Heavy Icon Collider (RHIC). RHIC was designed to study the quark-gluon plasma, and the massive 1,200-ton STAR detector is used to search for this-as well as investigate the behavior of matter at high energy densities. As experiments progress the data is processed using different libraries as the code matures and is collected. Problems with data at STAR As STAR collects petabytes of data, the need for an efficient method of processing becomes urgent. A data production consists of several 1000 of jobs, and many production may occur in parallel, making the organization and handling of the production tedious and complicated. However, all production series are handled in a similar fashion: for a given data set for a given year and library, jobs are created using a reconstruction chain, then submitted or failed. Successful jobs are tracked and disk space is managed manually. Each job series must be created by hand through the UNIX command line, a very tedious process with a high margin of error and non reproducibility (unless extraneous documentation is kept). My role in finding solutions using PERL and SQL The need for a streamlined, organized, and user-friendly process is essential to make use of the obtained information. One would ideally organize those productions into SQL databases according to different libraries and production, and the manually executed scripts, extracting the needed information from the database rather than created manually and the scripts could then be made automatic. The solution to devising a data-processing method is to eliminate the need to key each entry at the program s command line. I began by creating a Web CGI (Common Gateway Interface) which implements PERL to manage the STAR SQL database. This Web CGI permits a user to add, modify, and delete records containing the necessary information for each production, job generation, and submission. After creating the Database Management Web CGI, the existing PERL scripts are then modified to obtain records from the database and process them. Accomplishing this entire process required that I learn how to program in PERL, understand and manipulate CGI scripts, and refresh my HTML programming skills, including forms. Understanding forms was a crucial part of this process as this is how information is obtained from a user. In a matter of 3 weeks, I learned the PERL language and wrote code to correctly store and analyze the user-inputted data. How PERL is applied to SQL PERL is an excellent tool to create interfaces that allow the accessing and maintaining of information from an SQL database. It is a simple all-purpose and intuitive programming language that, because of its many built-in modules and object-orientated packages, is easy to use and therefore well received for Web and Database applications. It does not need to be compiled, allowing a user to view the result immediately. The use of

4 these modules enables SQL databases to gather and process data without having to create lengthy program subroutines- popularizing PERL over C, and C++. The Database Interface (DBI) module is of particular interest. The DBI module is a database access module and driver interface created specifically for the PERL programming language. It defines a set of methods, variables, and conventions to provide a consistent database interface, no matter what database is being used. The DBI module works with SQL commands to do a variety of processes. A typical PERL script begins in the following manner: #!/usr/bin/perl use DBI; use CGI; The first line tells the program both that the user is programming in PERL and the location of the PERL program on the server. The second and third lines tell the program to load the DBI and CGI modules respectively. The Common Gateway Interface (CGI) module, although used for other functions not directly involving databases, is important. CGI is the core of the handling and interaction between a user, the client, and the server, and provides shortcut functions that can produce simple HTML. This reduces typing and coding errors while providing functionality for advanced features including support for cookies, file uploading, and frames. Here the PERL script will directly use DBI to access the SQL database: # Define database info my $dbdriver = "driver_name"; # db driver my $dbname = "db_name"; # db name my $hostname = "hostname"; # db host my $username = "username"; # db authentication account #connects to database $dbh = DBI->connect("DBI:$dbdriver:$dbname:$hostname","$username") or die "Can't connect to db $dbname at $hostname"; The first block of code defines variables that the script uses to connect to the database. Concentrating the variables at the beginning of the script allows them to be used throughout and a user can easily change them at a later time without having to modify each instance of the variable. The second block uses the variables to connect the database to the script without having to enter the database information, PERL and the DBI module can be used to implement any standard SQL statement. Below is a short list of some SQL statements used in creating the Database Management Web CGI: Collects data from the database Inserts new rows into database Updates existing records SELECT column FROM table WHERE column operator value INSERT INTO table_name VALUES (value1, value2,...) UPDATE table_name

5 SET column_name = new_value WHERE column_name = some_value Deletes records from database DELETE FROM table_name WHERE column_name = some_value The following block of code is an example of PERL directly using the SQL statement INSERT (highlighted in grey) to prepare the database to receive information from the user. #prepares database to be written to my $sth = $dbh->prepare(" INSERT INTO RProdControl (production, library, chainoption, chainname,catalogselect,outputdisk, Queue, Qdrop, State, storagetype, status) values (?,?,?,?,?,?,?,?,?,?,?) "); This prepares a SQL statement for execution by the database engine and returns a statement handle ($sth) which is used to invoke the execute method. The INSERT INTO statement is followed by values denoted by question marks. It prepares the database for incoming information from the user, and without using placeholders, the INSERT statement would have to contain the literal values to be inserted and would have to be re-prepared and re-executed for each row. With placeholders, the insert statement only needs to be prepared once. The bind values for each row (the question marks) can be given to the "execute" method each time the statement is called. Avoiding the need to re-prepare the statement for each row makes the application run many times faster. The action is then executed in the following manner:! 8/22/04 22:56 Formatted: Indent: First line: 0.5" $sth->execute(); After the statement is no longer used in the script, end with the following command: $sth ->finish(); Checking for errors in the code becomes vital, as sometimes the errors are logical. This means that the code itself may be correct, but the desired results will not be achieved. Resolving this issue using the PERL statement print is the simplest method. At crucial steps in the script, such as an if statement, a debug statement is printed, indicating the step was executed. After the coding is completed and the script is deemed free of logical errors, the debug statements can be removed. Creating an interface to manage data It was crucial for the site to be user-friendly, organized, and easy to navigate. Keeping the user in mind, the web interface was designed to have three main options to choose from: Add New Record To Database, Display All Records, and Edit All Records. Subroutines were written for each website function so the code would be organized and-in the event anything needed to be modified- easily edited. The main interface was created and allows the user to simply select the corresponding button of the desired function which executes the appropriate subroutine. The web interface is shown in Figure 1.

6 Figure 1. Database Management Website Interface Figure 2 demonstrates the Add New Record To Database feature of the website. This is the second subroutine created for the website, using the SQL statement INSERT INTO. An interesting and valuable aspect of this feature is that the script will not allow the addition of any blank entries or duplicate entries to the database; preventing a possible error when running job processing scripts that will access it. Figure 2. Add New Record To the Database When adding new records, a user enters Production, Library, Chain, Chain Name, Catalog, and Output Disk into text fields, and has drop down menus for Queue, Drop Queue, State, and Storage. Status is a checkbox indicating whether or not the entry will be active. Active in this case is simply a 1 in the database and the entry is displayed in red when a user views the database in the table. The State and Storage options are both enumerations specified in the SQL database that can change anytime. This means that no modification to the script is required when changing the State or Storage options. Next, the SQL SELECT statement was used in this situation by selecting each row of data. Using PERL to display HTML, the table is filled using with the contents of the database. Figure 3 demonstrates this feature. Note the user options are available above the table allowing access to all options at any time. Jerome LAURET! 8/22/04 22:54 Comment: Jerome, if you can send me a reference of what each one does again I would appreciate it!

7 Figure 3. User Options and Database Display Table The third feature--shown in Figure 4-- enables a user to edit existing records in the database. This is an especially useful function of the webpage as it also includes a delete option for each entry. The options are identical that of the Add New Record To Database option and also prohibit blank fields. Figure 4. Edit Database Records Implementing the final product Having a user-friendly database management system is the first step in streamlining the job submission process. The next step involves having the job processing scripts automatically receive data rather than having a user enter each by hand at the command line. This is where the web interface becomes the core of the system. By having drop-down menus, one can assign specific criteria to each record and have existing job scripts read the database. For example, an existing script was modified to receive records from the database where none of the fields were blank or null, the Status was set to on (checkbox checked) indicating that the specified production is active, and State was set to GENERATE from the drop down menu. This adds the entry to a list of jobs that are ready for submission and changes the State from GENERATE to SUBMIT in the database. When the state is changed to SUBMIT, the job will then be ready for processing. With other programming languages, setting this criterion would be a challenge. Fortunately, the PERL DBI module made this very easy to accomplish. By slightly

8 manipulating the SQL statements, filtering of the included entries was made possible. Using the not operator ( <> ) and AND * IS NOT NULL ( * includes every record), the script would also not include blank or null entries. Theoretically this should never occur as the web interface does not permit blank entries, but this is a safeguard in case the situation did ever arise. The next block of code demonstrates these actions: #prepares to select all production from RProdControl with status=1 (on) my $sth_loop = $dbh->prepare("select production, library, chainoption, chainname, storagetype FROM RProdControl WHERE status=1 AND * IS NOT NULL AND storagetype = 'GENERATE' AND production <> '' AND library <> '' AND chainoption <> '' AND chainname <> '' AND storagetype <> '' "); To change the State from GENERATE to SUBMIT after the script finished the processing, we used the following statement: #Changes the state from "GENERATE" to "SUBMIT" my $sth2 = $dbh->prepare("update RProdControl SET State='SUBMIT' WHERE status=1 AND storagetype = 'GENERATE' AND production <> '' AND library <> '' AND chainoption <> '' AND chainname <> '' AND storagetype <> ''"); A similar concept as before, but the SQL statement UPDATE modified the existing contents of the database. Conclusion As STAR continues experiments and more and more data is collected, efficiently organizing the information becomes necessary. The Database Management Web CGI has many useful features that give a user the ability to add new records, modify existing entries, delete, and display the contents of the database. Simple checkboxes allow users to easily activate or deactivate certain entries. Scripting the code was done in care using subroutines allowing for straightforward reading and drop down menus run by enumerations for uncomplicated addition of options. The CGI made managing records easy for a user as well as provide a method of generating a list of jobs ready for processing. It eradicated the need for a user to key each job series through the UNIX command line which eliminates chance for error and non reproducibility. From the interface, a user could select what jobs to send for processing, and the CGI generates a list. The list can then be sent to other scripts for submission. This greatly reduces time, increases accuracy, and speeds up the process immensely. While the final script given to me for editing has not been entirely completed, the main part of the project (the Database Management Web CGI) was accomplished in full. This website will greatly organize jobs and allow users to manage and maintain records. Acknowledgements I would like to thank the National Science Foundation (NSF) and Wayne State University for providing me with this opportunity and financial support to be a part of the research at Brookhaven National Laboratory. I am also thankful to my mentor, Dr. Jerome Lauret, for his guidance and support in this project and to Lidia Didenko for her help in the last two weeks of the summer. Special thanks go to Prof. Claude Pruneau, Giovanni Bonvicini, Sean Gavin and the rest of the REU staff at Wayne State University for their help, support, and faith in me as a student. This has been one of the best experiences of my life

9 and I am eternally grateful for the friends I have made here, the experiences I have had, and the programming skills I have acquired.

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