SAGECAL
=======
Read INSTALL for installation. This file gives a brief guide to use SAGECal.
Warning: this file may be obsolete. use sagecal -h to see up-to-date options.


Step by Step Introduction:
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1)Calibrate data in the standard way using BBS/CASA or anything else. 
Use NDPP to average the data in your MS to a few channels (also average in time to about 10sec). Also flag any spikes in the data.

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2) Sky Model:
3a)Make an image of your MS (using ExCon/casapy). 
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.
Special options to buildsky: -o 1 (NOTE: not -o 2)

Alternatively, create these files by hand according to the following formats.

2b)Cluster file format:
cluster_id chunk_size source1 source2 ...
e.g.

0 1 P0C1 P0C2
2 3 P11C2 P11C1 P13C1

Note: putting -ve values for cluster_id will not subtract them from data.
chunk_size: find hybrid solutions during one solve run. Eg. if -t 120 is used 
to select 120 timeslots, cluster 0 will find a solution using the full 120 timeslots while cluster 2 will solve for every 120/3=40 timeslots.

2c)Sky model format:
#name h m s d m s I Q U V spectral_index RM extent_X(rad) extent_Y(rad) pos_angle(rad) freq0

or

#name h m s d m s I Q U V spectral_index1 spectral_index2 spectral_index3 RM extent_X(rad) extent_Y(rad) pos_angle(rad) freq0

e.g.

P1C1 0 12 42.996 85 43 21.514 0.030498 0 0 0 -5.713060 0 0 0 0 115039062.0
P5C1 1 18 5.864 85 58 39.755 0.041839 0 0 0 -6.672879 0 0 0 0 115039062.0
# A Gaussian mjor,minor 0.1375,0.0917 deg diameter -> radius(rad), PA 43.4772 deg (-> rad)
# PA: N-> angle, clockwise, NOTE BDSM angle is N-> counterclockwise
G0  5 34 31.75 22 00 52.86 100 0 0 0 0.00 0 0.0012  0.0008 -2.329615801 130.0e6
# A Disk radius=0.041 deg
D01 23 23 25.67 58 48 58 80 0 0 0 0 0 0.000715 0.000715 0 130e6
# A Ring radius=0.031 deg
R01 23 23 25.416 58 48 57 70 0 0 0 0 0 0.00052 0.00052 0 130e6
# A shapelet ('S3C61MD.fits.modes' file must be in the current directory)
S3C61MD 2 22 49.796414 86 18 55.913266 0.135 0 0 0 -6.6 0 1 1 0.0 115000000.0


Note: Comments starting with a '#' are allowed for both sky model and cluster files.
Note: 3rd order spectral indices are also supported, use -F 1 option in sagecal.
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

ln(I0)+p1*ln(f/f0)+p2*ln(f/f0)^2+... = ln(10)*(log(J0)+q1*log(f/f0)+q2*log(f/f0))^2)+...)
=ln(10)*(ln(J0)/ln(10)+q1*ln(f/f0)/ln(10)+q2*ln(f/f0)^2/ln(10)^2+...)

so

I0=J0
p1=q1
p2=q2/ln(10)
p3=q3/ln(10)^2
...


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3)Run sagecal
Optionally: Make sure your machine has (1/2 working NVIDIA GPU cards or Intel Xeon Phi MICs) to use sagecal.
Recommended usage: (with GPUs)

sagecal -d my_data.MS -s my_skymodel -c my_clustering -n no.of.threads -t 60 -p my_solutions -e 3 -g 2 -l 10 -m 7 -w 1 -b 1

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).

Note: It is also possible to calibrate more than one MS together. See the -f option.

Simulations:
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 :

-1
10
999

and use it as the 'ignore_file'.


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4)Distributed calibration

Use mpirun to run sagecal-mpi, example:
 mpirun  -np 11 -hostfile ./machines --map-by node --cpus-per-proc 8 
 --mca yield_when_idle 1 -mca orte_tmpdir_base /scratch/users/sarod 
 /full/path/to/sagecal-mpi -f mslist -A 30 -P 2 -r 5 
 -s sky.txt -c cluster.txt -n 16 -t 1 -e 3 -g 2 -l 10 -m 7 -x 10 -F 1 -j 5

Specific options : 
-np 11 : 11 processes : starts 10 slaves + 1 master
./machines : will list the host names of the 11 nodes used ( 1st name is the master ) : normally the node where you invoke mpirun
/scratch/users/sarod : this is where MPI stores temp files (default /tmp)
mslist : text file with 10 MS names that are used by the 10 slaves
-A 30 : 30 C-ADMM iterations
-P 2 : polynomial in frequency has 2 terms
-r 5 : regularization factor is 5.0

The rest of the options are similar to sagecal.