transition to rappture

[jadhao]

I have created a new branch called rappture. Based on @smarru feedback, we need to work with the current master (that is openMP parallelized) and translate that to rappture friendly version. This will be the subject of this issue. I identify some key steps required here:

1. OpenMP version is fairly well optimized. However we can get in principle a factor of 2 speedup by going from N^2 to N^2 / 2 in force calculations. @kadupitiya will take rappture branch and adapt this optimization.
2. We will take the latest job script from branch accelerate and merge it in rappture. Need to edit to reflect 1 node and n procs within. This is our default set of parameters.
3. We need to simplify input and output; organize input into physical and algorithm/computing parameters. @softmaterialslab/jadhaolab will lead this with @kadupitiya and @smarru joining

• we move the current boost input and output into a new function

• there is a dependency of some parameters on the user-input

• 2 output files stored in datafiles folder: last density profiles for + and - ions

• std output + progress bar

• we have implemented the above features

  4. @smarru will tell us what changes we need to do in Makefile for rappture to read our code

• we have done this with continuous feedback from ncn purdue

5. @smarru will tell us what directories we need to create for rappture and any changes in main.cpp or a metascript generation that is necessary for transition

• we went with the metascript approach using python; we split the material in different folders, we have the rappture friendly dirs

6. @kadupitiya @smarru @softmaterialslab/jadhaolab lead the modification in the metascript or main.cpp that reflects what resources get selected based on user values; what computing parameters get ON based on physical parameters; what range of parameters we want to give in our initial UI; any output requirements we need to communicate to nanoHUB team. @foxsden shares his insights and help on this.

• most features on the input side are in. output is under exploration, waiting on updates from @smarru and nanohub
• this is done.

7. @kadupitiya @smarru benchmark tool performance for the selected parameter ranges using our XSEDE nano allocation and IU big red2. Make sure we identify and remove any "bad" parameter choices.

• in progress by @kadupitiya
• initial benchmarking by @kadupitiya done which produced a tested version of the code. all clear. future benchmarking will be done on nanohub and bigred2.

8. @softmaterialslab/jadhaolab makes the code public on Dec. 8th.

• @softmaterialslab/jadhaolab made this public before target to facilitate nanohub integration

9. @kadupitiya has requested workspace for on nanoHUB; he takes the git and sends it to nanoHUB requesting for gui development etc.

• this ended up being concurrently developed; gui is built with basic functionalities sans output plot, waiting on a testable app run
• we all got workspaces; gui is now built, we have output, app test runs done. code for app is portable to local and cluster computing.

[smarru]

ACK, i will start on this branch.

[jadhao]

this is resolved