from:	 Zhao, Jun-Hui 
to:	 "Petitpas, Glen" 
cc:	 Patricia Mailhot ,
 Thomas Mac Cooper ,
 Jim Moran 
date:	 Tue, Sep 23, 2014 at 7:48 AM
subject:	 Re: SMA MIRIAD Bug Report

SMA MIRIAD Bug Report
Inbox
	x
gpetitpas@cfa.harvard.edu	
Below is the result of the form submission. It was submitted by (gpetitpas@cf...
	Sep 4
Zhao, Jun-Hui 
	
Sep 5
		
to Jim, Glen, smamiriad, bcc: me, bcc: Jun-hui
Hi Glen,
We will look into the problem. It looks like more than the issue of empty chunks of correlator that should be taken care
of by the high-spectral-resolution mode. We will let you guys know as soon as we find solutions.
Thanks, Jun-Hui
Zhao, Jun-Hui 
	
Sep 5
		
to Patricia
Hi Pat,
     Do you receive these email communications?
     Thanks,
     Jun-Hui
Zhao, Jun-Hui 
	
Sep 19
		
to Thomas, Glen, Patricia
Hi Glen,
     I just finished a patch in smalod for handling dual rx with arbitrary correlator setup for each receiver in the 4GHz/2 GHz mode operation.
I installed the new test version on Hilo computer system. You should see miriad prompt at your login:

MIRIAD version < beta 1.5.0 (test) 2014-09-19 for handling SMA 4GHz and 2GHz mode data >
 [CVS] loaded from MIR=/sma/local/miriad_cvs  Optimized for telescope=sma

    Please test it to see if there are any problems for handling the new correlator setup for dual rx.
    We need to check a few things before making a release of this version.

    Thanks.
Zhao, Jun-Hui 
	
Sep 19
		
to Glen, Patricia, Thomas, Jim
Hi Glen,
     Here is a report on the screen from my test run on obsconh (hilo).
     Thanks.
     Jun-Hui

/sma/data/science/mir_data//140904_07:20:08

SmaLod: version 3.12-beta 17-Sept-2014
Drx version 2.3.2: 2014-09-16
*********************************
*  Observing Date: 2014 Sep 04  *
*********************************
principal investigator...........James Moran

Number of antenna in antennas....10
Warning: Number of 10 antennas in antennas, exceeding that of standard SMA.
Geocentrical coordinates (meter) with refant=10:
ANT x y z = 1     11.7395    -53.6647    -40.7245
ANT x y z = 2      0.0000      0.0000      0.0000
ANT x y z = 3    -42.5984    -71.5514     86.1973
ANT x y z = 4    -51.4352   -136.7590    107.9207
ANT x y z = 5    -11.9414   -178.8132     -0.7213
ANT x y z = 6     -6.4003    -68.0017      3.6382
ANT x y z = 7     26.5169   -133.5965   -104.1749
ANT x y z = 8    -16.5631    -27.0246     30.7700
converting geocentrical coordinates to equatorial system (nanosecs).
ANT x y x = 1     39.1588   -179.0062   -135.8422
ANT x y x = 2      0.0000      0.0000      0.0000
ANT x y x = 3   -142.0930   -238.6696    287.5232
ANT x y x = 4   -171.5692   -456.1789    359.9847
ANT x y x = 5    -39.8323   -596.4567     -2.4060
ANT x y x = 6    -21.3491   -226.8293     12.1357
ANT x y x = 7     88.4510   -445.6298   -347.4900
ANT x y x = 8    -55.2485    -90.1444    102.6376
handling header variables........
number of integrations...........1649
number of polarizations..........1:  XX--non polarization
number of receivers..............2:  rx1->230, rx2->400
number of sidebands..............2:  lsb & usb
number of baselines..............14
number of antennas...............5
number of spectra................10 for rxid = 2
number of channels...............1024
solving for antenna-based Tsys...
Warning: Neptune has the source id ( 2 ) different from that ( 1 ) of 3c454.3
but their coordinates are the same:
 RA=22:32:20.6662  Dec= -9:59:55.5608
Warning: found the next integration for Neptune of id=2 at inhset=247 with coordinates:
 RA=22:32:20.6731  Dec= -9:59:55.5368
Update the coordinates for Neptune of id=2
Warning: Per27 has the source id ( 4 ) different from that ( 3 ) of 3c84
but their coordinates are the same:
 RA=03:28:55.5600  Dec= 31:14:36.5991
Warning: found the next integration for Per27 of id=4 at inhset=278 with coordinates:
 RA=03:28:55.5600  Dec= 31:14:36.5991
Update the coordinates for Per27 of id=4
Warning: Per13 has the source id ( 5 ) different from that ( 3 ) of 3c84
but their coordinates are the same:
 RA=03:29:12.0404  Dec= 31:13:01.4987
Warning: found the next integration for Per13 of id=5 at inhset=312 with coordinates:
 RA=03:29:12.0404  Dec= 31:13:01.4987
Update the coordinates for Per13 of id=5
Warning: 3c111 has the source id ( 6 ) different from that ( 4 ) of Per27
but their coordinates are the same:
 RA=04:18:21.2764  Dec= 38:01:35.8008
Warning: found the next integration for 3c111 of id=6 at inhset=371 with coordinates:
 RA=04:18:21.2764  Dec= 38:01:35.8008
Update the coordinates for 3c111 of id=6
sources found in the file........
3c454.3               id=  1 RA=22:53:57.7464 DEC= 16:08:53.5648
Neptune               id=  2 RA=22:32:20.6731 DEC= -9:59:55.5368
3c84                  id=  3 RA=03:19:48.1602 DEC= 41:30:42.1051
Per27                 id=  4 RA=03:28:55.5600 DEC= 31:14:36.5991
Per13                 id=  5 RA=03:29:12.0404 DEC= 31:13:01.4987
3c111                 id=  6 RA=04:18:21.2764 DEC= 38:01:35.8008
loading 400 GHz rx & lsb data
reading visibilities.............inhid  time(UTC) int(s) percent Gbyt W-status
inhset=..........................00000 0d07:19:59  15.5  000 (%) 0.00  OK
inhset=..........................00100 0d08:09:06  29.7  006 (%) 0.12  OK
inhset=..........................00200 0d08:58:34  29.7  012 (%) 0.23  OK
inhset=..........................00300 0d09:48:02  29.7  018 (%) 0.35  OK
inhset=..........................00400 0d10:37:31  29.7  024 (%) 0.46  OK
inhset=..........................00500 0d11:26:59  29.7  030 (%) 0.58  OK
inhset=..........................00600 0d12:16:27  29.7  036 (%) 0.70  OK
inhset=..........................00700 0d13:05:55  29.7  042 (%) 0.81  OK
inhset=..........................00800 0d13:55:24  29.7  048 (%) 0.93  OK
inhset=..........................00900 0d14:44:52  29.7  054 (%) 1.04  OK
inhset=..........................01000 0d15:34:20  29.7  060 (%) 1.16  OK
inhset=..........................01100 0d16:23:49  29.7  066 (%) 1.28  OK
inhset=..........................01200 0d17:13:17  29.7  072 (%) 1.39  OK
inhset=..........................01300 0d17:35:47  29.7  078 (%) 1.51  OK
inhset=..........................01400 0d18:25:15  29.7  084 (%) 1.62  OK
inhset=..........................01500 0d19:14:43  29.7  091 (%) 1.74  OK
inhset=..........................01600 0d20:04:12  29.7  097 (%) 1.86  OK
inhset=............              01647 0d20:27:27  29.7  099 (%) 1.91  OK
processed 400 GHz rx & Read the data successfully.
the lsb data have been written into Miriad
Real time used =   99 sec.
Output file = 140904_rx2.lsb
Zhao, Jun-Hui 
	
Sep 22
		
to Jun-hui
Zhao, Jun-Hui 
	
Sep 22
		
to Jun-hui
Petitpas, Glen	
Hi Jun-Hui. Sorry about the delay. I finally got around to testing it on the ...
	Sep 22
Zhao, Jun-Hui 
	
Sep 23
		
to Glen, Patricia, Thomas, Jim
Thanks, Glen.
    
     Jun-Hui

On Mon, Sep 22, 2014 at 10:20 PM, Petitpas, Glen  wrote:

    Hi Jun-Hui.

    Sorry about the delay. I finally got around to testing it on the older data and it seems to work fine now.

    It looks like 'smauvspec' also core dumped, but I'll look into that in more detail tomorrow hopefully. It may just be one of the switches I use in my pipeline script.

    Many thanks!
    Glen

    On Fri, Sep 19, 2014 at 10:07 AM, Zhao, Jun-Hui  wrote:

        Hi Glen,
             Here is a report on the screen from my test run on obsconh (hilo).
             Thanks.
             Jun-Hui

        /sma/data/science/mir_data//140904_07:20:08

        SmaLod: version 3.12-beta 17-Sept-2014
        Drx version 2.3.2: 2014-09-16
        *********************************
        *  Observing Date: 2014 Sep 04  *
        *********************************
        principal investigator...........James Moran

        Number of antenna in antennas....10
        Warning: Number of 10 antennas in antennas, exceeding that of standard SMA.
        Geocentrical coordinates (meter) with refant=10:
        ANT x y z = 1     11.7395    -53.6647    -40.7245
        ANT x y z = 2      0.0000      0.0000      0.0000
        ANT x y z = 3    -42.5984    -71.5514     86.1973
        ANT x y z = 4    -51.4352   -136.7590    107.9207
        ANT x y z = 5    -11.9414   -178.8132     -0.7213
        ANT x y z = 6     -6.4003    -68.0017      3.6382
        ANT x y z = 7     26.5169   -133.5965   -104.1749
        ANT x y z = 8    -16.5631    -27.0246     30.7700
        converting geocentrical coordinates to equatorial system (nanosecs).
        ANT x y x = 1     39.1588   -179.0062   -135.8422
        ANT x y x = 2      0.0000      0.0000      0.0000
        ANT x y x = 3   -142.0930   -238.6696    287.5232
        ANT x y x = 4   -171.5692   -456.1789    359.9847
        ANT x y x = 5    -39.8323   -596.4567     -2.4060
        ANT x y x = 6    -21.3491   -226.8293     12.1357
        ANT x y x = 7     88.4510   -445.6298   -347.4900
        ANT x y x = 8    -55.2485    -90.1444    102.6376
        handling header variables........
        number of integrations...........1649
        number of polarizations..........1:  XX--non polarization
        number of receivers..............2:  rx1->230, rx2->400
        number of sidebands..............2:  lsb & usb
        number of baselines..............14
        number of antennas...............5
        number of spectra................10 for rxid = 2
        number of channels...............1024
        solving for antenna-based Tsys...
        Warning: Neptune has the source id ( 2 ) different from that ( 1 ) of 3c454.3
        but their coordinates are the same:
         RA=22:32:20.6662  Dec= -9:59:55.5608
        Warning: found the next integration for Neptune of id=2 at inhset=247 with coordinates:
         RA=22:32:20.6731  Dec= -9:59:55.5368
        Update the coordinates for Neptune of id=2
        Warning: Per27 has the source id ( 4 ) different from that ( 3 ) of 3c84
        but their coordinates are the same:
         RA=03:28:55.5600  Dec= 31:14:36.5991
        Warning: found the next integration for Per27 of id=4 at inhset=278 with coordinates:
         RA=03:28:55.5600  Dec= 31:14:36.5991
        Update the coordinates for Per27 of id=4
        Warning: Per13 has the source id ( 5 ) different from that ( 3 ) of 3c84
        but their coordinates are the same:
         RA=03:29:12.0404  Dec= 31:13:01.4987
        Warning: found the next integration for Per13 of id=5 at inhset=312 with coordinates:
         RA=03:29:12.0404  Dec= 31:13:01.4987
        Update the coordinates for Per13 of id=5
        Warning: 3c111 has the source id ( 6 ) different from that ( 4 ) of Per27
        but their coordinates are the same:
         RA=04:18:21.2764  Dec= 38:01:35.8008
        Warning: found the next integration for 3c111 of id=6 at inhset=371 with coordinates:
         RA=04:18:21.2764  Dec= 38:01:35.8008
        Update the coordinates for 3c111 of id=6
        sources found in the file........
        3c454.3               id=  1 RA=22:53:57.7464 DEC= 16:08:53.5648
        Neptune               id=  2 RA=22:32:20.6731 DEC= -9:59:55.5368
        3c84                  id=  3 RA=03:19:48.1602 DEC= 41:30:42.1051
        Per27                 id=  4 RA=03:28:55.5600 DEC= 31:14:36.5991
        Per13                 id=  5 RA=03:29:12.0404 DEC= 31:13:01.4987
        3c111                 id=  6 RA=04:18:21.2764 DEC= 38:01:35.8008
        loading 400 GHz rx & lsb data
        reading visibilities.............inhid  time(UTC) int(s) percent Gbyt W-status
        inhset=..........................00000 0d07:19:59  15.5  000 (%) 0.00  OK
        inhset=..........................00100 0d08:09:06  29.7  006 (%) 0.12  OK
        inhset=..........................00200 0d08:58:34  29.7  012 (%) 0.23  OK
        inhset=..........................00300 0d09:48:02  29.7  018 (%) 0.35  OK
        inhset=..........................00400 0d10:37:31  29.7  024 (%) 0.46  OK
        inhset=..........................00500 0d11:26:59  29.7  030 (%) 0.58  OK
        inhset=..........................00600 0d12:16:27  29.7  036 (%) 0.70  OK
        inhset=..........................00700 0d13:05:55  29.7  042 (%) 0.81  OK
        inhset=..........................00800 0d13:55:24  29.7  048 (%) 0.93  OK
        inhset=..........................00900 0d14:44:52  29.7  054 (%) 1.04  OK
        inhset=..........................01000 0d15:34:20  29.7  060 (%) 1.16  OK
        inhset=..........................01100 0d16:23:49  29.7  066 (%) 1.28  OK
        inhset=..........................01200 0d17:13:17  29.7  072 (%) 1.39  OK
        inhset=..........................01300 0d17:35:47  29.7  078 (%) 1.51  OK
        inhset=..........................01400 0d18:25:15  29.7  084 (%) 1.62  OK
        inhset=..........................01500 0d19:14:43  29.7  091 (%) 1.74  OK
        inhset=..........................01600 0d20:04:12  29.7  097 (%) 1.86  OK
        inhset=............              01647 0d20:27:27  29.7  099 (%) 1.91  OK
        processed 400 GHz rx & Read the data successfully.
        the lsb data have been written into Miriad
        Real time used =   99 sec.
        Output file = 140904_rx2.lsb


        On Fri, Sep 19, 2014 at 3:55 PM, Zhao, Jun-Hui  wrote:

            Hi Glen,
                 I just finished a patch in smalod for handling dual rx with arbitrary correlator setup for each receiver in the 4GHz/2 GHz mode operation.
            I installed the new test version on Hilo computer system. You should see miriad prompt at your login:

            MIRIAD version < beta 1.5.0 (test) 2014-09-19 for handling SMA 4GHz and 2GHz mode data >
             [CVS] loaded from MIR=/sma/local/miriad_cvs  Optimized for telescope=sma

                Please test it to see if there are any problems for handling the new correlator setup for dual rx.
                We need to check a few things before making a release of this version.

                Thanks.
                Jun-Hui


            On Fri, Sep 5, 2014 at 8:36 AM, Zhao, Jun-Hui  wrote:

                Hi Glen,
                We will look into the problem. It looks like more than the issue of empty chunks of correlator that should be taken care
                of by the high-spectral-resolution mode. We will let you guys know as soon as we find solutions.
                Thanks, Jun-Hui



                On Thu, Sep 4, 2014 at 8:22 PM,  wrote:

                    Below is the result of the form submission.  It was submitted by
                     (gpetitpas@cfa.harvard.edu) on Thursday, September 4, 2014 at 20:22:57
                    ---------------------------------------------------------------------------

                    Logging to SMAMBugRpt

                    Bug Tracking No          44

                    User_Name: Glen Petitpas

                    Report_Type: Bug

                    Severity: Major

                    Priority: High

                    Linux: RedHat

                    Linux_Other:

                    Linux_Ver: Linux hilodr2 2.6.32-431.23.3.el6.x86_64

                    Kernel:

                    Hardware: hilodr2

                    Occured_When: Loading

                    Occured_Notes: SmaLod: version 3.11-beta 10-Jun-2013


                    Description: smalod seg faults on both tracks from last night run with the same dual receiver setting. The correlator setup has a lot of zeros, but this is a legacy project so we will be running LOTS of this setup, so getting miriad working for it is important. Other dual receiver tracks run this weekend loaded successfully but they had simpler correlator setups.

                    Is there a work-around or flag that will fix this

                    The correlator setup is as follows:
                    restartCorrelator -R l -s64 -s01:0 -s02:0 -s03:0 -s04:0 -s13:512 -s14:512 -s15:0 -s16:0 -s17:0 -s18:0 -s19:0 -s20:0 -s21:0 -s22:0 -s23:1024 -s24:0 -R h -s64 -s01:0 -s02:0 -s03:0 -s04:1024 -s13:0 -s14:0 -s15:0 -s16:0 -s17:0 -s18:1024 -s19:0 -s20:0 -s21:0 -s22:0 -s23:0 -s24:0

                    Terminal: hilodr2 smalod in=/sma/rtdata/science/mir_data/140904_07:20:08 rxif=-1 sideband=1 nscans=2 options=flagch0 out=test

                    SmaLod: version 3.11-beta 10-Jun-2013
                    Drx version 2.3.1: 2013-04-15

                      Observing Date: 2014 Sep 04

                    principal investigator...........James Moran

                    Number of antenna in antennas....10
                    Warning: Number of 10 antennas in antennas, exceeding that of standard SMA.
                    Geocentrical coordinates (meter) with refant=10:
                    ANT x y z = 1     11.7395    -53.6647    -40.7245
                    ANT x y z = 2      0.0000      0.0000      0.0000
                    ANT x y z = 3    -42.5984    -71.5514     86.1973
                    ANT x y z = 4    -51.4352   -136.7590    107.9207
                    ANT x y z = 5    -11.9414   -178.8132     -0.7213
                    ANT x y z = 6     -6.4003    -68.0017      3.6382
                    ANT x y z = 7     26.5169   -133.5965   -104.1749
                    ANT x y z = 8    -16.5631    -27.0246     30.7700
                    converting geocentrical coordinates to equatorial system (nanosecs).
                    ANT x y x = 1     39.1588   -179.0062   -135.8422
                    ANT x y x = 2      0.0000      0.0000      0.0000
                    ANT x y x = 3   -142.0930   -238.6696    287.5232
                    ANT x y x = 4   -171.5692   -456.1789    359.9847
                    ANT x y x = 5    -39.8323   -596.4567     -2.4060
                    ANT x y x = 6    -21.3491   -226.8293     12.1357
                    ANT x y x = 7     88.4510   -445.6298   -347.4900
                    ANT x y x = 8    -55.2485    -90.1444    102.6376
                    handling header variables........
                    Warning: inhid=1 has baseline of 111 that differs from 56 (for inhid=0)
                    Warning: inhid=2 has baseline of 111 that differs from 56 (for inhid=0)
                    (... repeat 1600 times...)
                    Warning: inhid=1643 has baseline of 111 that differs from 56 (for inhid=0)
                    Warning: inhid=1644 has baseline of 111 that differs from 56 (for inhid=0)
                    Warning: inhid=1645 has baseline of 111 that differs from 56 (for inhid=0)
                    Warning: inhid=1646 has baseline of 111 that differs from 56 (for inhid=0)
                    number of antennas...............5
                    number of spectra................11
                    number of channels...............2560
                    solving for antenna-based Tsys...
                    Warning: Neptune has the source id ( 2 ) different from that ( 1 ) of 3c454.3
                    but their coordinates are the same:
                     RA=22:53:57.7464  Dec= 16:08:53.5648
                    Warning: found the next integration for Neptune of id=2 at inhset=247 with coordinates:
                     RA=22:32:20.6731  Dec= -9:59:55.5368
                    Update the coordinates for Neptune of id=2
                    Warning: Per13 has the source id ( 5 ) different from that ( 4 ) of Per27
                    but their coordinates are the same:
                     RA=03:19:48.1602  Dec= 41:30:42.1051
                    Warning: found the next integration for Per13 of id=5 at inhset=312 with coordinates:
                     RA=03:29:12.0404  Dec= 31:13:01.4987
                    Update the coordinates for Per13 of id=5
                    sources found in the file........
                    3c454.3               id=  1 RA=22:53:57.7464 DEC= 16:08:53.5648
                    Neptune               id=  2 RA=22:32:20.6731 DEC= -9:59:55.5368
                    3c84                  id=  3 RA=22:32:20.6319 DEC= -9:59:55.7909
                    Per27                 id=  4 RA=03:19:48.1602 DEC= 41:30:42.1051
                    Per13                 id=  5 RA=03:29:12.0404 DEC= 31:13:01.4987
                    3c111                 id=  6 RA=03:28:55.5600 DEC= 31:14:36.5991
                    loading 230 GHz rx  usb data
                    reading visibilities.............inhid  time(UTC) int(s) percent Gbyt W-status
                    inhset=..........................00000 0d07:19:59  15.5  000 (%) 0.00  OK
                    inhset=..........................00100 0d08:09:06  29.7  006 (%) 0.12  OK
                    inhset=..........................00200 0d08:58:34  29.7  012 (%) 0.23  OK
                    inhset=..........................00300 0d09:48:02  29.7  018 (%) 0.35  OK
                    inhset=..........................00400 0d10:37:31  29.7  024 (%) 0.46  OK
                    inhset=..........................00500 0d11:26:59  29.7  030 (%) 0.58  OK
                    inhset=..........................00600 0d12:16:27  29.7  036 (%) 0.70  OK
                    inhset=..........................00700 0d13:05:55  29.7  042 (%) 0.81  OK
                    inhset=..........................00800 0d13:55:24  29.7  048 (%) 0.93  OK
                    inhset=..........................00900 0d14:44:52  29.7  054 (%) 1.04  OK
                    inhset=..........................01000 0d15:34:20  29.7  060 (%) 1.16  OK
                    inhset=..........................01100 0d16:23:49  29.7  066 (%) 1.28  OK
                    inhset=..........................01200 0d17:13:17  29.7  072 (%) 1.39  OK
                    inhset=..........................01300 0d17:35:47  29.7  078 (%) 1.51  OK
                    inhset=..........................01400 0d18:25:15  29.7  084 (%) 1.62  OK
                    inhset=..........................01500 0d19:14:43  29.7  091 (%) 1.74  OK
                    inhset=.................... Warning smalod:  Variable corr has zero or negative size, in UVPUTVR
                     Warning smalod:  Variable corr has zero or negative size, in UVPUTVR
                     Warning smalod:  Variable corr has zero or negative size, in UVPUTVR
                     Warning smalod:  Variable corr has zero or negative size, in UVPUTVR
                     Warning smalod:  Variable corr has zero or negative size, in UVPUTVR
                     Warning smalod:  Variable corr has zero or negative size, in UVPUTVR
                     Warning smalod:  Variable corr has zero or negative size, in UVPUTVR
                     Warning smalod:  Variable corr has zero or negative size, in UVPUTVR
                     Warning smalod:  Variable corr has zero or negative size, in UVPUTVR
                     Warning smalod:  Variable corr has zero or negative size, in UVPUTVR
                     Warning smalod:  Variable corr has zero or negative size, in UVPUTVR
                     Warning smalod:  Variable corr has zero or negative size, in UVPUTVR
                     Warning smalod:  Variable corr has zero or negative size, in UVPUTVR
                     Warning smalod:  Variable corr has zero or negative size, in UVPUTVR
                     Warning smalod:  Variable corr has zero or negative size, in UVPUTVR
                     Warning smalod:  Variable corr has zero or negative size, in UVPUTVR
                     Warning smalod:  Variable corr has zero or negative size, in UVPUTVR
                     Warning smalod:  Variable corr has zero or negative size, in UVPUTVR
                     Warning smalod:  Variable corr has zero or negative size, in UVPUTVR
                     Warning smalod:  Variable corr has zero or negative size, in UVPUTVR
                     Warning smalod:  Variable corr has zero or negative size, in UVPUTVR
                     Warning smalod:  Variable corr has zero or negative size, in UVPUTVR
                    Segmentation fault (core dumped)


                    Supplied_Code:

                    ---------------------------------------------------------------------------