TL;DR : Getting started with Fermionic Molecular Dynamics

We’ve recently ported an application from the physical sciences domain used to make nuclear calculations using Fermionic Molecular Dynamics models ¹ . The application was requested ² by Katharine Henninger from iThemba L.A.B.S.

Fermionic Molecuar Dynamics in CODE-RADE

FMD-deploy was added to CODE-RADE on July 4th . After some discussion ³ The application has a pretty simple dependency tree, as seen by the Jenkins config :

The dependencies were all passing, so it was just a matter of a few modifications to the source code, the application was included in the CODE-RADE fastrepo .

Getting started

Great ! so the application is in the repo and available at the sites - now what ? I’ve started work on a few examples to explain how to run the application on the grid. Thes are in the CODE-RADE FMD examples directory . I tested these and they give the expected results from a run at ZA-WITS-CORE:

                  
                    you are using fastrepo.sagrid.ac.za versionBuild 199aChecking whether you have modules installedyou are using CODE-RADE version Build 199aGreat, seems that modules are here, at /usr/share/ModulesAppend CVMFS_DIR to the MODULEPATH environment------------ /cvmfs/fastrepo.sagrid.ac.za/modules/physical-sciences ------------FMD/0.1... reading Interaction from file AV18-UsrgD2000f-v11ls-2.0.int... reading Parameters from file He4.fmdinitial:E 
                    =
                      -25.246 MeVstep:   0E 
                    =
                      -25.246 MeVstep:   1E 
                    =
                      -12.864 MeVstep:   2E 
                    =
                      -25.246 MeV... Ozzz: -0.00000... writing Parameters to file He4.fmd... 0.00 minutes computing 
                    time 
                    used
                  
                

Coming soon we’ll add some more complicated submission examples and some further discussion on how to use gLibrary to manage the output.

What we’d like to do now is take FMD to the next level and make some MPI runs with more demanding scenarios.

References and Footnotes