vivek-bala
commented
6 years ago We don't have kernel def files since 0.6, so you won't need them. The main file can have the entire description of a task (environment, arguments, etc. which was there in the kernel def files).
Looking at https://github.com/radical-collaboration/extasy-bpti/blob/master/gmxcoco-bpti/nwexgmx_v002.py, my suggestion would be to convert each kernel in that file into tasks and stages in the new API, one at a time. Once you are done with one or two stages, you should get a handle of it. I have added some more examples to the EnTK documentation as well, so they should help.
There are several files to convert for the full code conversion but I will at first group files in two categories.
File 1 - extasy-bpti/gmxcoco-bpti/nwexgmx_v002.py
I think I will start from an example script in the Entk0.7 training/documentation then add one kernel in at a time. I will make a ticket for each Kernel so we can test the addition of one kernel at a time individually and document it step by step. I will make a more detailed plan here after conversion on Tues 2018_09_11. Vivek and Andre do you have thoughts on how to best manage this conversion process? I have never done something like this before and could use some tips on best practices.
Below will be a rough psuedo code outline of the new structure of the Workflow
Rough outline of new code structure using Entk0.7 API methods
File 2 - Kernel Defs - extasy-bpti/gmxcoco-bpti/kernel_defs/
I am fairly certain we will need to update these kernel files as well. I will add more detailed information to this section when I have the chance to brush up on the new documentation again.
List / Rough outline - of set of changes needed for each Kernel Def init.py Coco,py Gromp.py mdrun.py trajconv.py