WEEKLY STATUS REPORT
Sean Leslie
July 14, 2008

 

ACTIVITIES:
This past week was a frustrating one. We would go to campus believing our remote access was working only to find it was not. We don’t like bouncing back and forth between school and home since it eats up a lot of time so we were staying on campus and typing things up in the mean time. Last week we were writing code to add sessions for login and file uploading. Testing things has been a pain with no access or various tools being down.

 

Despite all of this some progress was made in understanding work we need to do in order to read met files. Additionally we feel more confident about what variables we are using in the namelist file. We also met with Seychelles and Elias online and shared knowledge about what we have been doing and gained knowledge of what they have been doing.

ACCOMPLISHMENTS:
No big accomplishments this week.

 
ISSUES/PROBLEMS:

• VPN access is still sketchy at the campus although we are told the issue is resolved.
• Tomcat server was down when we had code to test, but this was fixed as well.
• Although the problems were resolved waiting for resolutions has stalled our work.

 

PLANS:
Short Term:

• Keep working on the database. Lack of VPN access meant we weren’t doing much of anything with it last week.
• Look into the met file access scripting language that Javier mentioned.
• Actually put the code we had made on the site and test it.
• Look into what the JFM interface requires.

Long term:

• JFM interfacing.
• Run a test case.

 

 

 

 

WEEKLY STATUS REPORT
Sean Leslie
June 30, 2008

 

ACTIVITIES:
This past week we have been practicing using YUI and have been slowing creating a mockup page. We are creating a series of sample WRF portal pages with limited functionality in the hopes of sharing the design we have with the group. We are trying to establish the proper procedure the user will take in order to submit a job to the grid. Making a mockup portal is part of this as it gives all of us a visual guide to work with. Once we realize the limitations of the UI as well as the expectations of the user, as well as the system then I feel we will be well on our way to making some real progress in the portals creation.

 

Our meeting with Dr. Duran was fruitful as always and he has been great at providing feedback as well as making suggestions. He has suggested the use of servlets, beans, and JSP.

ACCOMPLISHMENTS:
A mockup GUI was created using yahoo UI. Limited functionality is present but this gives us a good visual idea of how the flow of user input will go from uploading files to submission of the job.

 
ISSUES/PROBLEMS:
No new problems this week.

 

PLANS:
Short Term:

• Database planning
• Add more functionality to the mockup

Long term:

• Upload a sample input file via the portal
• Expose variables from the sample input file
• Save changes to variables

 

SUMMARIES/CRITIQUES OF PAPERS:

 

I’ve only been going over the sample code sites for YUI recently which I have already outlined. No new papers, websites, or literature this week.

 

 

WEEKLY STATUS REPORT
Sean Leslie
June 23, 2008

 

ACTIVITIES:
The past week has been spent getting familiar with some of the tools we are going to be using. Primarily I have been looking over YAHOO!UI. I have been looking over many examples and getting more familiar with what YUI can do. We are designing a mock-up for our variable entry page. Allison and I have been discussing plans for different parts of the system. One thing we were not very certain about was the way we were going to have our database set up. We have been going over the advantages and disadvantages to entering all variables as fields in a database, as opposed to only storing the complete pathname of a file which contains the variable values. In the end I think we are going to go with storing the namelist variables in the database as fields.

 

Dr. Duran has provided us with some feedback on our SRS that I hope will help us make a clearer and complete definition of the system.

ACCOMPLISHMENTS:
No major accomplishments this week.

 
ISSUES/PROBLEMS:
This past week has been spent finding sufficient online examples to grasp the functionality YUI can find. Additionally we were still waiting for SRS feedback from our Clients. Dr. Sadjadi gave us the go ahead to start making decisions based solely on our judgment if people are not getting back to us in time. Hopefully with this in mind our waiting problems will be solved as long as our initial concept of the system was generally correct.

 

PLANS:
Short Term:

• More examples of YUI
• Look into getting some database planning done
• Work out details regarding the API of JFM

Long term:

• Upload a sample input file via the portal
• Expose variables from the sample input file
• Save changes to variables

 

SUMMARIES/CRITIQUES OF PAPERS:

 

This week has been spent looking over web samples on YUI. I found two websites that have a lot of good information.

 

Website 1: http://developer.yahoo.com/yui/ (The Yahoo! User Interface Library)

 

This website is the official development page for the ongoing Yahoo UI project. It contains a lot of information on what YUI is as well as tons of examples. The sample code is nicely organized by “component” which seems to resemble class or library. The site itself seems to focus largely on samples and tutorials on how to get the most out of YUI. The primary focus of the site is obviously towards being a one stop shop for learning how to use YUI.

The examples are presented in a nice way in that they are sparse on additional functions that are not what the sample is trying to showcase. An example is the grid sample pages they provide contain dummy text formatted into columns. No other YUI components are used in the example so when viewing the sample code it is easy to determine what code is providing the additional functionality of that component. This make for very clear and concise examples. There are not needlessly complex samples where the component the sample is supposed to showcase is hidden amongst much more complex components. I feel the overall organization of the site is done well and I have found the sample code useful.

This site is providing me with the direct help and support I need in order to start learning a YUI which I am completely unfamiliar with. A vast majority of the projects visual aspects will be done using this tool, so a good website with sample code is crucial.

 

 

Website 2: http://blog.davglass.com/2006/06/yui-code-samples/ (Dav Glass YUI Blog)

 

           Dav Glass was an independent developer who was creating additional functionality for YUI. He generated some very good code samples and has roughly 130 samples of YUI code available on his website. He was hired by the YUI team and has been working on components for them for the past year. The bulk of my time on his site has been spent in his sample code section.

           The examples Glass provides are very nice and numerous. I have been going over a few of his simpler examples as well as reviewing a presentation he had made. The examples are of good quality and showcase the features they are supposed to in a concise and clear manner. It would be nice if he had the samples organized in a better fashion. Presently there is a long alphabetized list, and the only other organization is the naming scheme of the examples. Some things are somewhat out of place and going through a specific set of related examples can have you scrolling up and down the list looking for them all.

           Once again this site is providing me with the essential samples I need to get more familiar with YUI. Multiple sources of samples help me get a more diverse understanding of the various functionalities that YUI can provide.

 

 

WEEKLY STATUS REPORT
Sean Leslie
June 16, 2008

 

ACTIVITIES:
This week was mainly about meetings, preparation, getting sick, and getting better. Last week we met with Dr. Sadjadi as well as Eric Johnson, Khalid, Seychelles, and Elias via EVO. Solutions too many of our virtual job space problems were discussed and as of this morning a server has been provided for the WRF portal team to use. Early last week I caught a bit of a stomach bug which slowed me down quite a bit. I was however able to get some discussion in with Allison about some of the other aspects of the portal. Allison located the “namelist” file which contains the various variables which we will need to expose to our users and allow them to change.

 

While I was sick Allison managed to find some code samples in JSP. Dr. Sadjadi also provided us with access to a site containing a lot of the information done by prior students on the WRF portal. Additionally Dr. Sadjadi had a meeting with Salim, who is in charge of the JFM portion of the site. As a result of this meeting they agreed that our input will be a BPEL template which resembles an XML scheme.

ACCOMPLISHMENTS:
No major accomplishments this week.

 
ISSUES/PROBLEMS:
This week’s primary problem was fighting a stomach virus for 4 days. Besides that there was a lot of communication and problem solving going on that made this past week an opportune time to get ill, if there is such a time, since nothing required large quantities of my undivided attention.

 

The only thing we were hoping for but haven’t gotten back yet is feedback on the WRF Portal SRS. I am sure we will hear some feedback this week though.

 

PLANS:
Short Term:

• Analyze some of the tools we now have access to
• Find out more information on some of the other aspects of the system such as the API between WRF Portal and JFM.
• Choose a design model for our system
• Catch up on readings I missed while sick!

Long term:

• Upload a sample input file via the portal
• Expose variables from the sample input file
• Save changes to variables

 

SUMMARIES/CRITIQUES OF PAPERS:

 

I didn’t do any extra reading of research papers this week.

 

 

WEEKLY STATUS REPORT
Sean Leslie
June 9, 2008

 

ACTIVITIES:
This first week has been a lot of introductions and settling in. We are working on one of the Universidad de Guadalajara campuses called CUCEA. We met with Isabel in the Department of Study Abroad as well as some of her staff. We were given a tour of the campus as well as some of its facilities. We met with Dr. Duran, and discussed expectations of our work here and how close of a collaboration is desired. He showed us where we will be working as well. Allison and I spent our work time discussing the portal design as well as creating the Software Requirements Specification.

ACCOMPLISHMENTS:
The first draft of the SRS for the Turbulence Experiment portion of the portal is complete.

 
ISSUES/PROBLEMS:
We have had a few technical issues that are going to be sorted out soon we hope.

• Lack of a designated digital work space
• Lack of remote access to FIU resources
• Lack of access to sample input files (due to size of files)

 

PLANS:
Short Term:

• Determine tools necessary to complete or at least begin work on the portal
• Analyze these tools
• Determine if it’s worth using any of the prototype WRF Portal that was already created
• Choose a design model for our system (MVC perhaps, thanks Dr. Duran)

Long term:

• Upload a sample input file via the portal
• Expose variables from the sample input file
• Save changes to variables

 

SUMMARIES/CRITIQUES OF PAPERS:

Papers Read:

 

“A Workflow Management System for Automating Weather

and Climate Simulations”

Christopher W Harrop, Ligia Bernardet, Mark Govett, Jeff S Smith, Stephen

Weygandt

 

 

“A Workflow Management System for Automating Weather and Climate Simulations” is about a system used to ease the burden of complex workflow creation off of meteorologists. In order for scientists to perform an end-to-end weather simulation many tools and processes are involved. In order to obtain results useable in a real world forecast hundreds of runs are required. Some of these runs depend on the results of prior runs before they can begin. This results in a complex web of dependencies. Creating a formal specification for such an ensemble demands a lot of a scientist’s time. WFMS is designed with the scientist in mind, and works to automate as much of this process as possible. It does this by exposing only a simple “English like” informal specification method to the scientist. The WFMS system will then take this English like form, or workflow document, and generate an XML workflow. Then this is taken and run through different layers of abstraction. These layers allow for job creation, and the ability to check the status.

This paper was written very well. The overall language was not overly technical and was quite easy to understand. The motivation was very well defined. I would like to have been given more explanation as to what the scope of the system was. The authors state several times that the smaller scope of the system contributed to its success, but I was left without a clear understanding of what that scope was. The explanation of the system was good enough for me. Enough detail was presented in order to understand the overall functionality of the system without going into so much technical detail that I became lost. In the end I feel it was an informative and well written paper.

This paper is not directly related to my research. This paper is more closely related to the Job Flow Manager layer of the grid enablement project. I did find some relevance in the overall motivation of the paper, and the details of how and why an ensemble forecast is created. I now have a better understanding of why we want to lessen the computer science burden on the meteorologist.

Well it was an exciting transition from Miami to Guadalajara. Funny enough the culture differences haven’t been jarring at all. Miami had such a diverse Latin culture that no Mexican cultural nuances seem out of place. Guadalajara at first glance seems unwelcoming with its walls, gates, and barbed wire, but this is quickly diffused by its friendly and helpful people. Our housing seems Spartan but adequate. We have our own bathroom which is a huge plus, but unfortunately we have no AC. The lack of AC wouldn’t be a huge issue if the unseasonal heat wave wasn’t currently throwing Guadalajara into a drought. As it is I find myself consuming at least 1.5 - 2 liters of water per day and I am sweating most of it out. Needless to say I am taking more showers than one might consider usual.

Food is quite affordable depending on the kind of food your willing to eat. Relatively cheap local fair from stands, local vendors, and fast-food style chains will run us about $2-$6 US. The food tastes great and I am experimenting with new foods I never thought of attempting while at home in Miami. The downside to this is that the cheaper food is quite unhealthy, and more health conscious options will run a little bit more. The cheapest option seems to be buying groceries and making meals yourself. This would be an option if we found ourselves in the housing more than we do. Majority of our time is likely going to be spent on campus working or out in the city seeing the sites.

The Universidad de Guadalajara has a campus called CUCEA which is where we are working. The campus is very nice, and I must say that I like many aspects of the CUCEA campus better than FIU. CUCEA features friendly staff and faculty, wonderful landscaping, well thought out facilities, and a diverse eating area. We met with Dr. Duran and some of his staff yesterday, and everyone was very friendly. The staff for the study abroad program here in Guadalajara has been very kind to us and forthcoming with information about the campus, the area, and our housing. The campus itself is quite pretty with lush greenery, butterfly gardens, and shady areas. The shady trees and well maintained lawns make for an inviting atmosphere which students take advantage of by lounging in the shady trees for a siesta (a nap). The Universities facilities are also something to take note of. Most notable are the Cyber Garden and Foreign Language Studies building. The Cyber Garden is an outdoor wireless hotspot centered on a fountain and pond. Students sit on shaded benches which have electrical outlets and Ethernet outlets. It is a very social area and there is even a cart where students can take advantage of a printing, copying, and cd-burning service. The lab we are working in is quite nice. We have a spacious work area with outlets for our laptops and Ethernet connections. We have a white board as well as AC controls and a water cooler. As of right now it is the most comfortable place in Guadalajara in my opinion. We can sit in comfort as we are lulled into a state of bliss by the hum of an AC unit working at full blast.

A local student, Luis, has offered to help us get to and from the University which was very nice of him. We turned him down in favor of taking the local public transit to and from the campus. The bus costs us only 50 cents US and runs quite frequently once you know which bus goes where. The busses themselves are kind of run down, but they get the job done. The bus driver goes through 4 gears just to get over 10 mph. When the busses get busy being a passenger becomes quite a workout. When forced to stand for half an hour while the bus lurches to a stop and sudden start again works more muscle groups than most of the workout gimmicks on TV. Keeping your balance becomes something of a game where you are pitted against the bus driver to see how long you can keep your balance.

The language has proved an interesting but not unconquerable challenge. Having Camilo with us has made the trip an absolute joy not only because he’s a great guy but he is social and willing to translate for us when we miss things. I am learning things slowly but need to make more of an effort in learning the language.

In the end the heat is absolutely the number one most difficult challenge on this trip. I am consuming more water than I normally would, getting bit by more bugs, and willing to walk to fewer places. The heat makes me sweat nearly all the time, and makes me uncomfortable in many situations where I find yourself in close contact with people (like the bus). Hopefully the heat will ease off and we can look forward to the cool climate we were promised!

I’ll report on some of our more touristy activities later.

Student Name:  Sean Leslie

Supervisor’s Name and Title at FIU/FAU:

Dr. Masoud Sadjadi

Assistant Professor

Name of the PIRE International Partner’s Institution: Universidad de Guadalajara

 

Supervisor’s Name and Title at the PIRE International Partner’s Institution:

Dr. Hector Alejandro Durán Limón

Research professor Titular A

Project Title:

Grid WRF Portal

Problem Statement:

The purpose of this project is to facilitate remote access to the grid enabled WRF (Weather Research and Forecasting) system, via a web based portal. The task is to provide a service that will give meteorologists the ability to input WRF configurations, run simulation ensembles, and views the results in a visual manner. The Portal should alleviate the need for meteorologists to set up WRF on a local system, and simultaneously provide remote access to a grid enabled WRF which will facilitate the use of greater computational power needed to obtain more accurate forecasting data.

Motivation and Impact:

The creation of a web based portal that provides meteorologists with the necessary tools needed to run hurricane forecasting models on a grid enabled system has many benefits. The portal will be designed to facilitate the use of WRF without the previously necessary Computer Science knowledge. In other words meteorologists should be able to use WRF without being computer scientists as well. With the portal a meteorologist could remotely run a weather simulation with an increase in resolution, and obtain more accurate forecasting data in a reasonable amount of time. This data can then be used to create forecasting models, and provided to other users via the portal as well. The portal has the potential to then provide businesses and Emergency Operations personnel with a model which contains additional information relevant to them.

Current Status:

The Grid WRF Portal is currently being planned and designed. Some planning has been created and an overall WRF Portal project roadmap created. Grid enabling WRF is also a project that is presently being undertaken by several other research teams at FIU with each focusing on different aspects including, profiling WRF, job-flow management, and Meta-Scheduling. NOAA has recently created a WRF portal for their non-grid enabled WRF system.

Research Roadmap:

The goal of the research is to enable as much as WRF Portal 0.5 as possible. This will be done by completing the following:

• Provide a simple website that facilitates configuration of WRF simulations
• Add functionality to portal that enables the sending of a job
• Visualization of job output
• Add sessions and logon capability to website
• Begin work on ensemble enablement (WRF Portal 1.0)
• Write on research findings

Relation to PIRE Core Research Projects:

The WRF Portal fits into cyberinfastructure because it will enable meteorologists to make faster and more accurate hurricane forecasts. This places the WRF portal firmly in the “Hurricane mitigation apps.” section in the CI application layer of Cyberinfastructure Application Enablement.