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csa

Distributed CSA (Conformational Space Annealing) Command 1. The distributed CSA commands will be based on the recent MSCALE commands in CHARMM. The MSCALE commands allow diverse components of a single hamiltonian to be calculated on additional processors. 2. The CSA module will distribute a repetitive workload of many processors. It will consist of a series of commands, some on the the master and some on the slaves. Slaves can be setup as CHARMM scripts, or run as other separate utility programs. * Syntax / Suggested syntax * Example / Sample CHARMM slave script * Notes / Additional notes
Top [Suggested syntax] --------ON THE MASTER-------- MASTer - ! Use this processor as a master [ NSUBsystems integer ] - ! How many slaves to generate (typ. 50) [ PROGram filename ] - ! What program to run the slaves with (typ. CHARMM) [ NPROC integer ] - ! How many processors each slave will use (def. 1) atom-selection - ! ?? Which atoms will participate (def. all) [ INPUt filename ] - ! Input script for each slave [ OUTPut filename ] ! Output file from each slave CSA - ! The Conformational Space Annealing command [ ] - ! Details to be worked out and implemented [ ] - [ ] ETRAjectory ! Compute the frame by frame energy of a trajectory file. SYSDisplay ! Display the info about the whole setup --------ON THE SLAVES-------- RECEive - ! Receive data and coordinates from the Master [ IFDOne word ] - ! Where to go if exit condition is received [ repeat(flags) ] TRANsmit - ! Send back energies to the Master [ COORdinates ] - ! Send back coordinates too [ FORCes ] - ! Send back forces too [ DATA ] ! ?? Send back other data
Top Sample CHARMM Slave Script ... (setup PSF and stuff) ... LABEL LOOP RECEIVE IFDONE NEXT flag1 flag2 IF @flag1 .eq. 1 THEN MINI SD 50 ... MINI ABNR 200 ... if @flag2 .eq. 1 THEN print energy unit 22 TRANSMIT COORDINATES GOTO LOOP LABEL NEXT ... ...
Top Additional Notes Slaves should send a semaphore when ready to receive. Communication should be non-blocking in general. The master should not assume that all slaves will take the same amount of time. Details for the high level FORTRAN CALLS for master-slave communication need to be worked out (a job for Milan). Suggestion for development: Develop the ETRAJ command first. This will have all of the basic communication calls, and can be used as a base by the CSA developers. The ETRAJ command may proves useful as a stand alone tool... Check syntax above for possible conflicts with other developments