Espresso is a suite of scripts designed to take the drudgery out of file-based correlation. The idea is to automate as much of the processing as possible. While providing a rapid way to set up and run correlation jobs, the scripts assume the user is 'intelligent' (that's another way of saying the scripts are dumb) - check their output. All the scripts will give some help if initiated with the
–help switch. Please read those help messages before using. A typical Espresso correlation would look like this:
disk_report.py > ~/disk.json
creates a summary of the disks in $DIFX_MACHINES used for storing baseband data.
Transfer the data to the correlator, e.g.:
ssh email@example.com globus-url-copy <options> -r file://<path>/v255z/ATCA/ sshftp://user@magnus-data/<path>/v255z-At/
Following the naming convention for the directories on the correlator (<expname>-<Telescope>) is important.
This transfer can be automated using the
run_copyfiles.sh scripts on cass-01-per:
ssh firstname.lastname@example.org scp cormac@magnus:disk.json ~ #be sure to get a newly generated version of disk.json cd ~/transfers/v255z dtsum v255z # alias for du -cs -BG > du.txt make_copyfiles.py ~/disk.json ./du.txt run_copyfiles.sh copy_v255z_*.sh
make_copyfiles.py will identify destination nodes with sufficient space and create a bunch of shell scripts with the relevant transfer commands. The
run_copyfiles.sh command can then be used to initiate these transfers under
screen -r to view the running transfers.
Update the disk report once the data have been transferred.
disk_report.py > ~/disk.json
Get the .key file from ATNF and run through our local version of SCHED
important to get the best station positions for Mopra and ATCA). This is no longer generally needed unless the vex file needs modification.
cd $CORR_HOME/2015/September/v255z/sched getatnf v255/v255z/v255z.key # alias for wget ftp://ftp.atnf.csiro.au/pub/people/vlbi/v255/v255z/v255z.key sched < v255z.key cp v255z.vex ../ cd ../
Currently “prestart = 0” can be inserted into .key file to avoid scan start times being 5s different from vex file used for observations (SCHED version issues).
Also may need certain setup files from ATNF if these are not available locally. But should always get station positions from database at Curtin as this ($STADB) should be up-to-date with the latest station positions.
You may also have to edit the TRACKS section in the vex file to add the
S2_recording_mode = <samprate>x<nchan>-<nbits>;
e.g. for 32 Msample/sec recording, 4 channels, 2 bits, this would be:
S2_recording_mode = 32×4-2;
If an ATCA pad other than the default W104 was used, then update the station
position. Similarly update ASKAP position if necessary. (If Tid used a station other than what was specified in the vex file, it is probably best to re-run SCHED. However you could use
updatepos.py to swap between the two 34m antennas, DSS34 and DSS45, as these have the same slewing parameters etc.)
updatepos.py ATCA AT_W102 v255z.vex
Create an input (.datafiles) file for lbafilecheck.py:
disk_exper.py v255z ~/disk.json
Create filelists, machines, threads and run file with lbafilecheck.py:
Note: mk5scans.py can add time ranges to Mark5 file lists after creation, but this is deprecated and not usually necessary.
Edit a .v2d file as required for your experiment. (Note: getEOP.py to download the latest EOPs.)
getEOP.py <date> >> v255z.v2d
where <date> is the start date of the experiment in MJD or VEX format.
Run vex2difx and check that number of jobs, etc. look reasonable and .v2d and .vex files parse correctly.
Start a clock search job (output will go
Choose appropriate mjdStart and mjdStop, scan or source selection in the .v2d
espresso.py -c v255z_1
Set up the pipeline directories if they don't exist yet; can use the bash alias:
Run the LBA AIPS pipeline to get clock estimates (either use
mkpipe or copy a template .inp file
from ~corrtest/progs/Pypeline/lba_template.inp and edit appropriately).
cd $CORR_DATA/v255z/clocks difx2fits v255z_1 V255Z.CLK.FITS LBA.py $PIPE/v255z/in/v255z.inp
The fitted clock residuals will be in
$PIPE/v255z/out/v255z.clocks. Or you can see the raw data graphically in
If you need to inspect the FRING output, e.g. to determine the time of a clock jump, you can use the Pypeline script:
clocks.py -p "1000 V252AZ UVDATA 1 1"
where 1000 is the AIPS user number, and “V252AZ UVDATA 1 1” is the AIPS name, class, disk and sequence number.
Update the clocks in the .v2d file:
cd $CORR_HOME/2015/September/v255z updateclock.py -e 2012y067d04h00m00s -s 'AT,HO,MP' -o '0.5,-.01,0.034' -r '5.1,-3.3,1.2' -f 6642 v255z.v2d
Units for the clock offset (-o) are microsec, the clock rate (-r) mHz, and the observing frequency (-f) MHz.
If this experiment requires multiple correlation passes, then make copies of
the .v2d file for each pass, e.g.:
'v255z-cal.v2d'. The naming convention
'<expname>-<passid>.v2d' must be
Run the production correlation job
espresso.py -a v255z-cal
Go make yourself an espresso. You may have time for more than one.
Occasionally jobs will fail to complete.
chklogs is a bash alias to check which jobs did not appear to complete as expected, based on the messages at the end of the *.difxlog files. Specify the output data directory, or by default
chklogs uses the current working directory.
Run the pipeline on the complete dataset, and transfer the pipeline data and summary to the wiki:
cd $CORR_DATA/v255z difx2fits -d V255Z.FITS LBA.py $PIPE/v255z/v255z.inp cd $PIPE/v255z/out lba_feedback.py v255z-cal.wikilog v255z-line.wikilog > v255z.txt archpipe v255z
difx2fits(run with no options for help). Especially important for generating output from correlation with multiple phase centres (option
Archive the correlator output directory using the
archivec.py script to access the Pawsey data store.
archivec.py $CORR_DATA/v255z/ /projects/VLBI/Archive/LBA/v255
See the archive page for notes on distribution of output data to PIs.
On cortex, link the .FITS files from the archive to the ftp site so the PI can
ln /pbstore/groupfs/astrotmp/as03/VLBI/Archive/Curtin/v255/v255q/*.FITS /pbstore/groupfs/astrotmp/astronomy/anonymous/v255q
cortex.ivec.org has a special “feature” that makes it necessary
to make a soft link in one's home area to the /pbstore partition for transfers to work:
ln -s /pbstore ~/pbstore