Input to sagecal must be in CASA MS format, make sure to create a column in the MS to write output data as well. The data can be in raw or averaged form, also initial calibration using other software can be also applied.
Use Duchamp to create a mask for the image. Use buildsky to create a sky model. (see the README file on top level directory). Also create a proper cluster file.
Note: Spectral indices use natural logarithm, ```exp(ln(I0) + p1 * ln(f/f0) + p2 * ln(f/f0)^2 + ..)``` so if you have a model with common logarithms like ```10^(log(J0) + q1*log(f/f0) + q2*log(f/f0)^2 + ..)``` then, conversion is
Use your solution interval (-t 60) so that its big enough to get a decent solution and not too big to make the parameters vary too much. (about 20 minutes per solution is reasonable).
With -a 1, only a simulation of the sky model is done.
With -a 1 and -p 'solutions_file', simulation is done with the sky model corrupted with solutions in 'solutions_file'.
With -a 1 and -p 'solutions_file' and -z 'ignore_file', simulation is done with the solutions in the 'solutions_file', but ignoring the cluster ids in the 'ignore_file'.
Eg. If you need to ignore cluster ids '-1', '10', '999', create a text file :
```./machines``` : will list the host names of the 11 (or fewer) nodes used ( 1st name is the master ) : normally the node where you invoke mpirun
```-f 'MS*pattern'``` : Search MS names that match this pattern and calibrate all of them together. The total number of MS being calibrated can be higher than the actual number of slaves (multiplexing).
```-A 30``` : 30 ADMM iterations.
```-P 2``` : polynomial in frequency has 2 terms.
```-Q``` : can change the type of polynomial used (```-Q 2``` gives Bernstein polynomials).
```-r 5``` : regularization factor is 5.0.
```-G textfile```: each cluster can have a different regularization factor, instead of using ```-r``` option when the regularization is the same for all clusters.
MPI specific options:
```/scratch/users/sarod``` : this is where MPI stores temp files (default is probably ```/tmp```).
```--mca*```: various options to tune the networking and scheduling.
Note: the number of slaves (-np option) can be lower than the number of MS calibrated. The program will divide the workload among the number of available slaves.
Each 8 rows of any given column represent the 8 values of a 2x2 Jones matrix. Lets say these are ```S0,S1,S2,S3,S4,S5,S6``` and ```S7```. Then the Jones matrix is ```[S0+j*S1, S4+j*S5; S2+j*S3, S6+j*S7]``` (the ';' denotes the 1st row of the 2x2 matrix).
