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  • explicity list every file/directory in transfer_input_files (it doens't grok regexps).  This would be a large list .  E.g.
    • transfer_input_files = "working/VIP_iter0.gridwt, working/VIP_iter0.pb.tt0, working/VIP_iter0.psf.tt0, working/VIP_iter0.psf.tt1, working/VIP_iter0.psf.tt2, working/VIP_iter0.sumwt.tt0, working/VIP_iter0.sumwt.tt1, working/VIP_iter0.sumwt.tt2, working/VIP_iter0.weight.tt0, working/VIP_iter0.weight.tt1, working/VIP_iter0.weight.tt2"
  • Can transfer_input_fies take a manifest?  E.g a file containing the list of files to transfer.  Sort of using the include syntax
  • Make a temporary director directory on the submit host, and transfer that (possibly tarring it up).  PRE and POST scripts might be useful here.
  • Set the inputs and outputs for both data and working as a variables in the unified DAG file.  The task.sh script uses rsync to merge the various data_inputs together into one data directory and the various working_inputs together into one working directory.  Then at the end, task.sh moves data to data-<dagstep> and working to working-<dagstep> and the appropriate dirs/files from these are transferred back to the submithost.  The result of all this is that the data needed as an input for a step (E.g. Task08) may need to be combined from multiple places (initial data and data output from Task07)

...

  • DONE: write .log, .out and .png files one level up so they are not in the working directory and therefore not copied to execute hosts.
  • DONE: add rm -f *.last to the sh script?
  • DONE: Task24 and Task25 swapped with 8cores so they need to run with fewer cores.  So I may need to make another variable to pass to the sh script for this.
  • Task19 needs to be unwraveled from NRAO filesystems.
  • DONE: re-create my DOT graph after finishing task01-25-parallel-dag4. Also make a PDF instead of a PS.
  • DONE: Craft parallel-dag5 with the concept of running tclean at CHTC and everything else locally.
  • DONE: I don't like using the I don't like using the name Task as that has meaning to CASA.  A better term might be Step as in DAG Step.
  • Look into running Task22 at the same time as another Task.  If it is possible, perhaps this can be done for some other tasks as well.  Note, I specificly avoided using the work parallel here so as not to confuse this idea with using mpicasa.
  • Figure out how to not copy SYSPOWER in the MS.  Presumably we can just cp /dev/null SYSPOWER/table.DONE: Figure out how to not copy SYSPOWER in the MS.  Presumably we can just cp /dev/null SYSPOWER/table.f0 and cp /dev/null SYSPOWER/table.f0i

Task01

Doesn't alter the MS

run_tclean( 'iter0', cfcache=cfcache_nowb, robust=-2.0, uvtaper='3arcsec', calcres=False  )

Task02

This tasks creates VIP_iter0b.* but I don't see those files ever referenced in this script again.  What does this task do that is necessary to other tasks?  Josh Marvil said that this is a leftover task and can be removed.

Doesn't alter the MS

run_tclean( 'iter0b', cfcache=cfcache_nowb, calcres=False  )

Task03

...

  • I am doing this with my dag5 test now.
  • DONE: Setup testpost-serv-1 with Lustre access over IB so we can start submitting to CHTC.
  • DONE: Need to make the MS in my DAG script a variable.  Right now I specify data/VLASS.../table.f23_TSM1
  • Task19 needs to be unwraveled from NRAO filesystems.  Actually maybe not.  This can be a task we always run here.  But it does need to move into a VLASS area instead of Josh's home acocunt.
  • Task06 has parallel=false and I am using 8core mpicasa which is a waste of cores.
  • Update this document to reflect the changes needed for CASA-6.

Possible Improvements

  • Task03 could perhaps be run concurrently with Task01 as long as Task04 is run after both.
  • Task13 could perhaps be run concurrently with Task12.
  • Task13 could perhaps be run concurrently with Taks11 and Task12 as long as Task14 is run after both Task11 and Task13.
  • Task21 could perhaps be run concurrently with Task11 or later as long as Task22 is run after both Task21 and Task12.


Task01 - Step01

Doesn't alter the MS

maskrun_from_catalog(inext=inext,outext="QLcatmask.mask",catalog_search_size=1.5,catalog_fits_file='../VLASS1Q.fits'tclean( 'iter0', cfcache=cfcache_nowb, robust=-2.0, uvtaper='3arcsec', calcres=False  )

  • input: ../data
  • input: ../VLASS1Q.fits, VIP_iter0.psf.tt0
  • output: mask_from_cat.crtf, VIP_QLcatmask.mask

...


Task02

This task doesn't parallelize and only takes tens of seconds to run.  Should this be stuck on the end of task01?

Doesn't alter the MS

runmask_from_tclean( 'iter1', robust=-2.0, uvtaper="3arcsec"  catalog(inext=inext,outext="QLcatmask.mask",catalog_search_size=1.5,catalog_fits_file='../VLASS1Q.fits')

  • input: ../data
  • input: ../VLASS1Q.fits, VIP_iter0.psf.tt0
  • output: mask_from_cat.crtf, VIP_iter1QLcatmask.*mask

...


Task03

Doesn't alter the MS

This task could possibly run at the same time as Task01 except that I have combined this with Task04 which requires both Task01 and Task34.

run_tcleanreplace_psf( 'iter1','iter0'), robust=-2.0, uvtaper="3arcsec"  )

  • input: ../data
  • output: VIP_iter1.*


Task04

Doesn't alter the MS

replace_psf('iter1','iter0')

This is just some python that deletes VIP_iter1.psf.[tt0|tt1|tt2] and copies VIPThis is just some python that deletes VIP_iter1.psf.* and copies VIP_iter0.psf.* [tt0|tt1|tt2] to VIP_iter1.psf.*[tt0|tt1|tt2].  It is would be inefficient to ever make this task be its own DAG .  step because the job would have to transfer iter0 and iter1 to the scratch area just to make the copy.  I suggest it always be in the same DAG step as Task04Task03.  Will It will produce an error because *.workdirectory doesn't exist but that error is ignorable.

  • input: VIP_iter0.psf.*, VIP_iter1.psf.*
  • output: VIP_iter1.psf.*

...


Task05 - Step05

Doesn't alter the MS

run_tclean( 'iter1', robust=-2.0, uvtaper="3arcsec", niter=20000, nsigma=5.0, mask="QLcatmask.mask", calcres=False, calcpsf=False  )

  • input: ../data
  • input: VIP_iter1.*, VIP_QLcatmask.mask
  • output: VIP_iter1.*

...


Task06 - Step06

Alters the MS

Note that this sets parallel=False which means running mpicasa may be a waste of cores.  Hopefully this step will not be necessary with CASA-6.

run_tclean( 'iter1', calcres=False, calcpsf=False, savemodel='modelcolumn', parallel=False  )

...

Task07 - Step07

Alters the MS

Tasks 08, 09, 10 and 11 take only minutes to run so could be combined into one DAG step.

...

...


Task08

Alters the MS

statwt(vis=vis,combine='field,scan,state,corr',chanbin=1,timebin='1yr', datacolumn='residual_data' )

...


Task09

Doesn't alter the MS

gaincal(vis=vis,caltable='g.0',gaintype='T',calmode='p',refant='0',combine='field,spw',minsnr=5)

  • input: ../data
  • output: g.0

...



Task10

Alters the MS

applycal(vis=vis,calwt=False,applymode='calonly',gaintable='g.0',spwmap=18*[2], interp='nearest')

...


Task11

Doesn't alter the MS

run_tclean( 'iter0c', datacolumn='corrected', cfcache=cfcache_nowb, robust=-2.0, uvtaper='3arcsec', calcres=False  )

  • input: ../data
  • output: VIP_iter0c.*

...


Task12

Doesn't alter the MS

Could this run in parallel with one or more previous run_tclean calls like Task11?

run_tclean( 'iter0d', datacolumn='corrected', cfcache=cfcache_nowb, calcres=False  )

  • input: ../data
  • output: VIP_iter0d.*

...


Task13

Doesn't alter the MS

This task could possibly run at the same time as Task11 and/or Task12 except that I have combined this with Task14 which requires both Task13 and Task11.

run_tclean( 'iter1b', datacolumn='corrected', robust=-2.0, uvtaper="3arcsec" )

  • input: ../data
  • output: VIP_iter1b.*

...


Task14

Doesn't alter the MS

replace_psf('iter1b','iter0c')

This is just some python that deletes VIP_iter1b.psf.* and copies VIP_iter0c.psf.* to VIP_iter1b.psf.*.  It is inefficient to ever make this task be its own DAG.  I suggest it always be in the same DAG as Task14.  Will produce an error because *.workdirectory doesn't exist but that error is ignorable.

We could remove iter0c because it is never used again.

  • input: VIPinput: VIP_iter1b.psf.*, VIP_iter0c.psf.*
  • output: VIP_iter1b.psf.*

...


Task15 - Step15

Doesn't alter the MS

run_tclean( 'iter1b', datacolumn='corrected', robust=-2.0, uvtaper="3arcsec", niter=20000, nsigma=5.0, mask="QLcatmask.mask", calcres=False, calcpsf=False  )

  • input: ../data
  • input: VIP_iter1b.*, VIP_QLcatmask.mask
  • output: inter1b

...

  • VIP_iter1b.*


Task16 - Step16

Doesn't alter the MS

imsmooth(imagename=imagename_base+"iter1b.image.tt0", major='5arcsec', minor='5arcsec', pa='0deg', outfile=imagename_base+"iter1b.image.smooth5.tt0")

  • input: ../data
  • input: VIP_iter1b.image.tt0
  • output: VIP_iter1b.image.smooth5.tt0

...


Task17

Doesn't alter the MS

exportfits(imagename=imagename_base+"iter1b.image.smooth5.tt0", fitsimage=imagename_base+"iter1b.image.smooth5.fits")

  • input: ../data
  • input: VIP_iter1b.image.smooth5.tt0
  • output: VIP_iter1b.image.smooth5.fits

...


Task18

This needs some modification. It calls a script from Josh's homedir and runs bdsf out of /lustre. Also, I have been unable to run this task by itself.  I get the following errors.  I am going to combine this with tasks17, 18, 20 and 21 so it isn't an issue right now.

2020-07-29 16:13:07     SEVERE  exportfits::image::tofits (file ../../tools/images/image_cmpt.cc, line 6211)    Exception Reported: Exception: File VIP_iter1b.image.smooth5.fits exists, and the user does not want to remove it..
2020-07-29 16:13:07     SEVERE  exportfits::image::tofits (file ../../tools/images/image_cmpt.cc, line 6211)+   ... thrown by static void casa::ImageFactory::_checkOutfile(const casacore::String&, casacore::Bool) at File: ../../imageanalysis/ImageAnalysis/ImageFactory2.cc, line: 568
2020-07-29 16:13:07     SEVERE  exportfits::::@testpost001:MPIClient    An error occurred running task exportfitsSEVERE  exportfits::::@testpost001:MPIClient    An error occurred running task exportfits.

I de-linked everything in bdsf_1.8.15-py27-rh7-env to make it more portable but then would sometimes get Failed to transfer files errors in the condor.log which seems to be related to the number of files which was about 12,000. I could reproduce the problem by transferring a directory with about 10,008 files in it but not repeatedly reproduce it.  So there is something else going wrong.  Anyway, since these tasks are not planned to run at CHTC I am going to go back to calling this out of Josh's home account.  A longer-term solution might be to move it out of josh's area and into VLASS or tar up the portable directory and copy that instead.


Doesn't alter the MS

subprocess.call(['/users/jmarvil/scripts/run_bdsf.py', imagename_base+'iter1b.image.smooth5.fits'],env={'PYTHONPATH':''})

  • input: ../data
  • input: VIP_iter1b.image.smooth5.fits
  • input: ??
  • output:
    • VIP_iter1b.image.smooth5.cat.ds9.reg
    ,
    • VIP_iter1b.image.smooth5.cat.fits
    ,
    • VIP_iter1b.image.smooth5.fits.island.mask
    ,
    • VIP_iter1b.image.smooth5.fits.pybdsf.log
    ,
    • VIP_iter1b.image.smooth5.fits.rms
    • VIP_iter1b.image.smooth5
    .fits.rms, VIP_iter1b.image.smooth5.fits

...

    • .fits


Task19

This needs iter0.psf.tt0 which is set to the variable inext.  VIP_iter0 was copied to VIP_iter1 back in Task04

Doesn't alter the MS

edit_pybdsf_islands(catalog_fits_file=imagename_base+'iter1b.image.smooth5.cat.fits')

...

  • input: VIP_iter1b.image.smooth5.cat.fits
  • input: VIP_iter1b.image.smooth5.cat.edited.fits, VIP_iter0.psf.tt0
  • output: secondmask.mask

...


Task20

Doesn't alter the MS

immath(imagename=[imagename_base+'secondmask.mask',imagename_base+'QLcatmask.mask'],expr='IM0+IM1',outfile=imagename_base+'sum_of_masks.mask')

im.mask(image=imagename_base+'sum_of_masks.mask',mask=imagename_base+'combined.mask',threshold=0.5)

  • input: secondmask.mask, VIP_QLcatmask.mask
  • output: sum_of_masks.mask
  • input: sum_of_masks.mask
  • output: VIP_combined.mask

...


Task21

Doesn't alter the MS

As far as I can tell at this point, ../data has not changed since Task11 Task10 (applycal).

Could this run in parallel with one or more previous run_tclean calls like Task16Task15?

run_tclean( 'iter2', datacolumn='corrected' )

  • input: ../data
  • output: VIP_iter2.*

...


Task22

Doens't alter the MS

replace_psf('iter2', 'iter0d')

This is just some python that deletes VIP_iter2.psf.* and copies VIP_iter0d.psf.* to VIP_iter2.psf.*.  It is inefficient to ever make this task be its own DAG.  I suggest it always be in the same DAG as Task22Task21.

  • input: VIP_iter2.psf.*, VIP_iter0d.psf.*
  • output: VIP_iter2.psf.*

...


Task23 - Step23

Doesn't alter the MS

At this point I think we are using iter2's image with iter0d's psf.

...

  • input: ../data
  • input: VIP_iter2.*, VIP_QLcatmask.mask
  • output: VIP_iter2.*

...


Task24 - Step24

os.system('rm -rf *.workdirectory')

...

  • input: ../data
  • input: VIP_iter2.*, VIP_combined.mask
  • output: VIP_iter2.*