Date: Tue, 12 Jun 2012 14:12:41 -0400 (EDT)
From: Jun-Hui Zhao 
To: Berengere Parise 
Cc: Tyler Bourke , pmailhot@cfa
Subject: Re: Miriad on Ubuntu for SMA data reduction



On Tue, 12 Jun 2012, Berengere Parise wrote:

> Dear Jun-Hui,
>
> The last version you uploaded is much better, thanks a lot! I can now go
> forth with the
> reduction. I however noticed a couple of small details that are not working
> fine:

    Good to hear that; we are converging.
>
> - the result of uvindex for me is very slightly different from the one
> you sent me.
>   It seems that a very small fraction of the data does not get read in
> my case.
>   It claims 12.07 hours of data in my case, when you got 12.48 hours.
>   There is no difference in the table of read scans, except for the very
> last line.
>   A "diff" of the two log files gives:
>
> < 11JUN22:15:29:06.2 Total number of records
> 43680    2911
> ---
> > 11JUN22:15:22:08.0 Total number of records
> 43275    2884
> < Total observing time is 12.18 hours
> ---
> > Total observing time is 12.07 hours

    Do you swicth back to ubuntu 32bit?
    I thought you were on ubuntu 64bit.
    The difference is due to the one that I sent you
was from my RH linux (64bit). I also noticed for 32 bit
software, your data file exceeds the integer limit at the integration
2885. SMALOD detected this problem and dropped the
problematic data. The rest of the data is identical
to those from my RH (64). In other words, the 32bit loading
lost a part of the scans on your calibrator 3C454.3.
I went through the loaded data on 32bit ubuntu. They
worked fine.

    Meanwhile, Pat just got 64bit  ubuntu 12.
She is configuring the dell to 64bit ubuntu.

>
>
> - The keyword "edge" does not work for flagging the edge pixels:
>
>   In SmaMfCal, I get the following error:
>    ### Fatal Error [smamfcal]:  Illegal edge parameter
>
>   In uvflag, when using "edge=5,5" for windows which have obviously more
> than
>     10 spectral channels, I get the following error:
>   uvflag: beta 09-Jan-10
>   ### Fatal Error [uvflag]:  Edge selection would drop all channels
>

      This is because that miriad added two channels on the first two
empty chunks (s1, and s2) in order to keep the original online
correlator configuration, which appear to cause some problems for
other routines (SMAmfcal and uvflag, for example) in Miriad.
      To get rid of the problem, one can use UVAVER
by selecting the data chunks,

uvaver vis=110622_rx0.usb out=data110622_rx0.usb \
select='window(3,4,5,6,7,8,9,10,11,12,13,14,15,16,17,18,19,20,21,22,23,24)'

      The rest of data handling procedure should be straight forward.
      Thanks again for helping us debug Ubuntu OS.

      Jun-Hui



>
> Thanks a lot for your help.
> Cheers,
>
> Berengere
>
>
>
>
>
>
>
>
> On 06/12/2012 04:04 PM, Jun-Hui Zhao wrote:
> > Dear Berengere,
> >     I noticed those problems.
> >     There was a confusion about which online mode
> > (correlator software) took your data. Now it is
> > clear that your data was indeed taken from the old
> > correlator software (2GHz mode) and two chunks of
> > data were skipped.
> >     I have fixed several coding problems for ubundu
> > and just updated 1.4.4 (Binary UB 10_32bit) a few minutes ago. Please
> > download the updated package and re-install it on
> > your ubuntu. After your installation, check "more $MIR/VERSION",
> > the output should read as
> > "beta 1.4.4. 2012-06-12 for handling SMA 4GHz and 2GHz mode data
> > (Ubuntu)".
> >     I quickly went through the file (USB). Your data looks good.
> > Below are the uvindex outputs; please note under the frequency
> > configuration, in the first two chunks, a flagged channel is
> > added, which was required to show the online correlator configuration;
> > otherwise, miriad routines skip the empty spectral chunks. To get rid of
> > them, you can use "uvaver" to select those spectral chunks with actual
> > data,
> >
> > uvaver vis=my.uv out=mynew.uv \
> > select='window(3,4,5,6,7,8,9,10,11,12,13,14,15,16,17,18,19,20,21,22,23,24)'
> >
> >       Please let us know if you have any problems and question in handling
> > your data.
> >
> >       Jun-Hui
> >
> >
> > UVINDEX: version 25-Jan-2012
> >
> > Summary listing for data-set 110622_rx0.usb
> >
> >        Time        Source        Antennas Spectral Wideband  Freq  Record
> > IntId
> >                     Name                  Channels Channels Config   No.
> > No.
> >
> > 11JUN22:03:13:55.0 3c279             8      6146        0      1       1       0
> > 11JUN22:04:49:25.1 titan             8      6146        0      1    5551     370
> > 11JUN22:05:10:19.5 1625-254          8      6146        0      1    6766     451
> > 11JUN22:05:13:25.3 IRAS16293-2422    8      6146        0      1    6946     463
> > 11JUN22:05:21:25.4 1626-298          8      6146        0      1    7411     494
> > 11JUN22:05:24:15.8 IRAS16293-2422    8      6146        0      1    7576     505
> > 11JUN22:05:32:15.9 1625-254          8      6146        0      1    8041     536
> > 11JUN22:05:35:06.2 IRAS16293-2422    8      6146        0      1    8206     547
> > 11JUN22:05:43:06.3 1626-298          8      6146        0      1    8671     578
> > 11JUN22:05:45:56.7 IRAS16293-2422    8      6146        0      1    8836     589
> > 11JUN22:05:53:56.7 1625-254          8      6146        0      1    9301     620
> > 11JUN22:05:56:47.1 IRAS16293-2422    8      6146        0      1    9466     631
> > 11JUN22:06:04:47.2 1626-298          8      6146        0      1    9931     662
> > 11JUN22:06:07:37.5 IRAS16293-2422    8      6146        0      1   10096     673
> > 11JUN22:06:15:37.6 1625-254          8      6146        0      1   10561     704
> > 11JUN22:06:18:28.0 IRAS16293-2422    8      6146        0      1   10726     715
> > 11JUN22:06:26:28.1 1626-298          8      6146        0      1   11191     746
> > 11JUN22:06:29:18.4 IRAS16293-2422    8      6146        0      1   11356     757
> > 11JUN22:06:37:34.0 1625-254          8      6146        0      1   11836     789
> > 11JUN22:06:43:45.7 1751+096          8      6146        0      1   12196     813
> > 11JUN22:06:53:23.8 1625-254          8      6146        0      1   13696     912
> > 11JUN22:06:57:00.6 IRAS16293-2422    8      6146        0      1   13906     926
> > 11JUN22:07:05:16.2 1626-298          8      6146        0      1   14386     958
> > 11JUN22:07:08:06.6 IRAS16293-2422    8      6146        0      1   14551     969
> > 11JUN22:07:16:06.7 1625-254          8      6146        0      1   15016    1000
> > 11JUN22:07:18:57.0 IRAS16293-2422    8      6146        0      1   15181    1011
> > 11JUN22:07:26:57.1 1626-298          8      6146        0      1   15646    1042
> > 11JUN22:07:29:47.5 IRAS16293-2422    8      6146        0      1   15811    1053
> > 11JUN22:07:37:47.5 1625-254          8      6146        0      1   16276    1084
> > 11JUN22:07:40:37.9 IRAS16293-2422    8      6146        0      1   16441    1095
> > 11JUN22:07:48:53.5 1626-298          8      6146        0      1   16921    1127
> > 11JUN22:07:51:43.8 IRAS16293-2422    8      6146        0      1   17086    1138
> > 11JUN22:07:59:43.9 1625-254          8      6146        0      1   17551    1169
> > 11JUN22:08:02:34.3 IRAS16293-2422    8      6146        0      1   17716    1180
> > 11JUN22:08:10:34.3 1626-298          8      6146        0      1   18181    1211
> > 11JUN22:08:13:24.7 IRAS16293-2422    8      6146        0      1   18346    1222
> > 11JUN22:08:21:40.3 1625-254          8      6146        0      1   18826    1254
> > 11JUN22:08:24:30.6 IRAS16293-2422    8      6146        0      1   18991    1265
> > 11JUN22:08:32:46.2 1626-298          8      6146        0      1   19471    1297
> > 11JUN22:08:35:36.5 IRAS16293-2422    8      6146        0      1   19636    1308
> > 11JUN22:08:43:36.6 1625-254          8      6146        0      1   20101    1339
> > 11JUN22:08:46:27.0 IRAS16293-2422    8      6146        0      1   20266    1350
> > 11JUN22:08:54:27.1 1626-298          8      6146        0      1   20731    1381
> > 11JUN22:08:57:17.4 IRAS16293-2422    8      6146        0      1   20896    1392
> > 11JUN22:09:05:33.0 1625-254          8      6146        0      1   21376    1424
> > 11JUN22:09:08:23.4 IRAS16293-2422    8      6146        0      1   21541    1435
> > 11JUN22:09:16:38.9 1626-298          8      6146        0      1   22021    1467
> > 11JUN22:09:19:29.3 IRAS16293-2422    8      6146        0      1   22186    1478
> > 11JUN22:09:27:44.9 1625-254          8      6146        0      1   22666    1510
> > 11JUN22:09:30:35.2 IRAS16293-2422    8      6146        0      1   22831    1521
> > 11JUN22:09:38:35.3 1626-298          8      6146        0      1   23296    1552
> > 11JUN22:09:41:41.1 IRAS16293-2422    8      6146        0      1   23476    1564
> > 11JUN22:09:49:41.2 1625-254          8      6146        0      1   23941    1595
> > 11JUN22:09:52:31.6 IRAS16293-2422    8      6146        0      1   24106    1606
> > 11JUN22:10:00:47.1 1626-298          8      6146        0      1   24586    1638
> > 11JUN22:10:03:37.5 IRAS16293-2422    8      6146        0      1   24751    1649
> > 11JUN22:10:11:37.6 1625-254          8      6146        0      1   25216    1680
> > 11JUN22:10:14:27.9 IRAS16293-2422    8      6146        0      1   25381    1691
> > 11JUN22:10:22:43.5 1626-298          8      6146        0      1   25861    1723
> > 11JUN22:10:25:33.9 IRAS16293-2422    8      6146        0      1   26026    1734
> > 11JUN22:10:33:49.4 1625-254          8      6146        0      1   26506    1766
> > 11JUN22:10:36:39.8 IRAS16293-2422    8      6146        0      1   26671    1777
> > 11JUN22:10:44:39.9 1626-298          8      6146        0      1   27136    1808
> > 11JUN22:10:47:30.2 IRAS16293-2422    8      6146        0      1   27301    1819
> > 11JUN22:10:55:30.3 1625-254          8      6146        0      1   27766    1850
> > 11JUN22:10:58:20.7 IRAS16293-2422    8      6146        0      1   27931    1861
> > 11JUN22:11:06:36.2 1626-298          8      6146        0      1   28411    1893
> > 11JUN22:11:09:26.6 IRAS16293-2422    8      6146        0      1   28576    1904
> > 11JUN22:11:17:42.2 1625-254          8      6146        0      1   29056    1936
> > 11JUN22:11:20:32.5 IRAS16293-2422    8      6146        0      1   29221    1947
> > 11JUN22:11:28:32.6 1626-298          8      6146        0      1   29686    1978
> > 11JUN22:11:31:23.0 IRAS16293-2422    8      6146        0      1   29851    1989
> > 11JUN22:11:39:23.1 1625-254          8      6146        0      1   30316    2020
> > 11JUN22:11:42:13.4 IRAS16293-2422    8      6146        0      1   30481    2031
> > 11JUN22:11:50:13.5 1626-298          8      6146        0      1   30946    2062
> > 11JUN22:11:53:03.8 IRAS16293-2422    8      6146        0      1   31111    2073
> > 11JUN22:12:01:19.4 1625-254          8      6146        0      1   31591    2105
> > 11JUN22:12:04:25.3 IRAS16293-2422    8      6146        0      1   31771    2117
> > 11JUN22:12:12:40.8 1626-298          8      6146        0      1   32251    2149
> > 11JUN22:12:15:31.2 IRAS16293-2422    8      6146        0      1   32416    2160
> > 11JUN22:12:23:46.8 1625-254          8      6146        0      1   32896    2192
> > 11JUN22:12:26:37.1 IRAS16293-2422    8      6146        0      1   33061    2203
> > 11JUN22:12:34:52.7 1625-254          8      6146        0      1   33541    2235
> > 11JUN22:12:37:43.0 uranus            8      6146        0      1   33706    2246
> > 11JUN22:13:24:57.1 3c454.3           8      6146        0      1   36451    2429
> > 11JUN22:15:29:06.2 Total number of records                         43680    2911
> >
> > ------------------------------------------------
> >
> > Total observing time is 12.18 hours
> >
> > The input data-set contains the following frequency configurations:
> >
> > Frequency Configuration 1
> >   Spectral Channels  Freq(chan=1)  Increment
> >                 1     239.93509     0.104000 GHz
> >                 1     240.01909     0.104000 GHz
> >               512     240.10936     0.000203 GHz
> >               512     240.19136     0.000203 GHz
> >               128     240.28017     0.000812 GHz
> >               128     240.36217     0.000812 GHz
> >               512     240.43736     0.000203 GHz
> >               256     240.51936     0.000406 GHz
> >               512     240.60756     0.000203 GHz
> >               256     240.68977     0.000406 GHz
> >               128     240.76536     0.000812 GHz
> >               128     240.84736     0.000812 GHz
> >               256     240.93577     0.000406 GHz
> >               256     241.01777     0.000406 GHz
> >               256     241.09336     0.000406 GHz
> >               256     241.17536     0.000406 GHz
> >               128     241.26417     0.000812 GHz
> >               128     241.34617     0.000812 GHz
> >               256     241.42136     0.000406 GHz
> >               512     241.50336     0.000203 GHz
> >               128     241.59217     0.000812 GHz
> >               128     241.67417     0.000812 GHz
> >               512     241.74936     0.000203 GHz
> >               256     241.83136     0.000406 GHz
> >
> > ------------------------------------------------
> >
> > The input data-set contains the following polarizations:
> > There were 43680 records of polarization I
> >
> > ------------------------------------------------
> >
> > The input data-set contains the following pointings:
> >  Source                   RA            DEC             dra(arcsec)
> > ddec(arcsec)
> > 1625-254               16:25:46.89   -25:27:38.32           0.00         0.00
> > 1626-298               16:26:06.02   -29:51:26.97           0.00         0.00
> > 1751+096               17:51:32.82   9:39:00.73             0.00         0.00
> > 3c279                  12:56:11.17   -5:47:21.52            0.00         0.00
> > 3c454.3                22:53:57.75   16:08:53.56            0.00         0.00
> > IRAS16293-2422         16:32:22.80   -24:28:34.00           0.00         0.00
> > titan                  12:42:29.21   -1:50:33.25            0.00         0.00
> > uranus                 0:17:28.20    1:05:23.89             0.00         0.00
> >