csa (c49b1)
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
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
[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
...
...
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
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