User Tools

Site Tools


huibintemaspamfaq

This is an old revision of the document!


SPAM frequently asked questions

This ever-expanding section is based on user feedback. For questions on installing SPAM, see this page. If you encounter a problem not listed below, please feel free to contact me.


SPAM pipeline failure

Q: Why does my SPAM pipeline run fail?

A: Although in general the SPAM pipeline is able to process many different data sets, there will be cases in which it fails. The output of the main pipeline (process_target()) is captured in a log file, located in the datfil directory. This will often provide guidance on the nature of the problem, but is a bit bulky. In your SPAM session, you can get a summary of the log file through

summarize_spam_log( './datfil/spam_<your_target_name>_*.log' )

Look for sudden increases in the noise, or decreases in the number of visibilities or the total cleaned flux. Something will have likely gone wrong between those two steps.


Too many open files

Q: SPAM crashes with a message about “too many open files”. What do I do?

A: Typical Linux installs have a limit on the number of files (or file descriptors) that a user can have open at any given time. The default is usually set to 1024 to prevent runaway programs from doing harm. As a user you can check that number: in (ba)sh, type

ulimit -n

or in (t)csh, type

limit descriptors

Often it is possible as a user to increase the limit on file descriptors. In (ba)sh, type

ulimit -n 4096

or in (t)csh, type

limit descriptors 4096

If this operation is not permitted, go talk to your sysadmin.

UPDATE: The latest ParselTongue distributed with SPAM has an improvement in place to reduce the occurence of this error.


Imaging in CASA

Q: Can I take the calibrated visibilities (.CAL.UVFITS) into CASA for imaging?

A: Yes you can. One limitation is that CASA from version 4.2 onwards doesn't allow stokes I visibilities to be imported. To overcome this, you can re-label the visibilities as being RR, and then image the RR visibilities in CASA. Converting the calibrated visibilities from stokes I to RR can be done in SPAM as follows:

uv = get_aips_file( 1, 'CALIBRATED', 'UVDATA', -1, 'UV' )
read_fits_uv( './fits/<target_visibilities>.CAL.UVFITS', uv )
convert_stokes_I_to_RR( uv )
write_fits_uv( uv, './fits/<target_visibilities>.RR.UVFITS' )
uv.zap()

Next, start CASA and run the importgmrt() task to convert the UVFITS data to a measurement set:

importgmrt( fitsfile = '<target_visibilities>.RR.UVFITS', vis = '<target_visibilities>.RR.ms' )

Then run the clean() task with at least the following options:

clean( vis = '<target_visibilities>.RR.ms', imagename = '<target>', gridmode = 'widefield', 
    wprojplanes = <some number, e.g. 128>, stokes = 'RR', weighting = 'briggs', usescratch = True ... )

Problems running SPAM on new Intel CPUs, possibly after Linux update

Q: Why doesn't the SPAM pipeline work (anymore), with AIPS generating NaNs in certain tasks?

A: Updates of the Linux operating system in 2017 has triggered floating point problems when running AIPS tasks on a new line of Intel Xeon E5-xxx CPUs. This is likely caused by an outdated Intel compiler used to build the AIPS binary install. A GNU compiled version of AIPS 31DEC13 fixes the problem and is available here. It may run a bit slower than the Intel compiled version.


huibintemaspamfaq.1505362347.txt.gz · Last modified: 2017/09/14 06:12 by huibintema