1. Hydrodynamic Galactic Simulations
GADGET
Hydrodynamic Galactic Simulations

2. Team Members Bruce Becker Carla Carrubba Luca Calvagna Primo Furno
Tutors
Students
Bruce Becker
Carla Carrubba
Luca Calvagna
Primo Furno
Valentina Marchese

3. Outline Overview and Plan Application Description and Integration
GOAL – what do we want? What does the user want?
Starting point and considerations
Application Description and Integration
Application Description and Dependencies
Typical Execution Workflow
Integration Strategy
Execution Workflow on Science Gateway
Results:
Activities and Milestones
Portlet > Mock-up & GUI
Remaining problems/Open Issues
Summary and Conclusions

4. Overview and Plan Goal Starting point
for end-users: accessing easily to GADGET, cosmological simulator
for us:
knowledge about platform able to provide to end-user an easy access to scientific software
use of online tools in order to realized shared work
Starting point
for the project: mock-up and user requirements
for us: different background between the team members, low knowledge about the platform and development environment

5. Application Description (1/3)
GAlaxies with Dark matter and Gas intEracT
GADGET is a freely available code for cosmological N-body/SPH simulations on massively parallel computers with distributed memory. 
GADGET computes gravitational forces with a hierarchical tree algorithm and represents fluids by means of smoothed particle hydrodynamics (SPH). The code can be used for studies of isolated systems, or for simulations that include the cosmological expansion of space, both with or without periodic boundary conditions.

6. Application Description (2/3)
GADGET can therefore be used to address a wide array of astrophysically interesting problems, ranging from colliding and merging galaxies, to the formation of large-scale structure in the Universe.
GADGET can also be used to study the dynamics of the gaseous intergalactic medium, or to address star formation and its regulation by feedback processes.
The code can be run on essentially all supercomputer systems presently in use, including clusters of workstations or individual PCs.

7. Application Description (3/3)

8. Dependencies
scikit-learn
python
zlib
OpenMPI
GADGET
GSL
HDF5
FFTW

9. Typical Execution Workflow
Create initial condition file for specific problem MUSIC*
Setup parameter input file
Compile GADGET for specific problem
Run the code and wait
Get output: run analysis on the resulting data
Typical Execution Workflow
MUSIC: MUlti-Scale Initial Conditions for cosmological simulations

10. Integration Strategy
GADGET can be run basically on all supercomputer systems presently in use, including clusters of workstations or individual PCs
Solution adopted: GRID
Having GADGET on Science Gateway portal is useful for these reasons:
Availability of huge amount of resources
Parallel processing
Simulator available for end-users without specific SWs
Easy access to the tool for everybody

11. Execution Workflow on SG
1. Initial conditions input
Three-step portlet:
Three-step portlet: 2. Makefile input
3. Parameters input
Validation & Submit (InputSandBox)
MUSIC execution (Input: ICS file)
On-the-fly GADGET compilation (MK file)
GADGET execution (Input: PARs file)
Output returning (OutputSandBox)
Execution Workflow on SG

12. Results > Activities Carried Out
Requirements Analysis
Mock-up Design
GUI Implementation
Job Submission Code Implementation
Shell Script Implementation
Results > Activities Carried Out

13. Milestones (1/2) Sample jobs submitted First beta of GUI
To reach this goal, we need to be able to make calls from the portlet to the GridEngine, with the correct parameters, simulating a submission to the backend
First beta of GUI
This milestone contains all issues related to the development of the GUI. Included are aspects such as
design
implementation
validation
SQA
Software Quality Assurance

14. Milestones (2/2) Fake Submission Working
This is a milestone to complete the development of JSP and Java code necessary to
Create the input files necessary:
MUSIC config file
GADGET param file
GADGET Makefile file
Create the job submission request, with
Input Sandbox properly defined
Output Sandbox properly defined
Job requirements included

15. Portlet > Mock-up

16. Portlet > GUI (1/3) > Initial Conditions Input (for MUSIC)
No SUBMIT, ma CONTINUE

17. Portlet > GUI (2/3) > Makefile Input (for GADGET)

18. Portlet > GUI (3/3) > Parameters Input (for GADGET)

19. (Web) Tools (1/4)
GitHub repositories are places where writers can share their work with the world and solicit feedback, while others can fork the story and make their own variation

20. (Web) Tools (2/4)
Waffle shows GitHub Issues and Pull Requests in real time

21. (Web) Tools (3/4)
Travis takes care of running tests and deploying applications

22. (Web) Tools (4/4)
Build system of the South African National Grid intended for developers and community contact points for scientific research applications

23. Remaining Problems/Open Issues
Simple ”wizard” to generate IC and param files
Parametric jobs (with certain parameter ranges)
Snooping of output to see state of the job

24. Summary and Conclusions
Science Gateway is a wonderful tool collections for different scientific communities
GADGET is a perfect example of having a simulator deployed on SC (high performance computing)
Making the life easier for the end-user corresponds in making “harder” for the developer
In order to deploy applications on SG, end-user’s skills requirement is high
In reaching the main goal we enriched our knowledge making a little step forward

26. Questions ?