L2 Bin - processing ocean color data

alysiaherr · by **alysiaherr** » Mon Jan 30, 2017 2:21 pm America/New_York

Hello,

So I'm try to process SST and OC L2 files down to 8-day, 1km resolution L3 products. I'm initially using L2bin to create L3 files, then subsequently time-binning and mapping my L3 files. This worked well with my SST files, but when I try to process the OC files, I get an error:

execution exception: java.io.IOException: l2bin failed with exit code 110.

I can't find mention of the exit code meanings. Any ideas?

Here's the log output:

Execution log for
[/Applications/seadas-7.3.2/ocssw/run/scripts/ocssw_runner, --ocsswroot, /Applications/seadas-7.3.2/ocssw, l2bin, par=/Users/alysiaherr/Dropbox/ALYSIA/MATLAB_alysia/Sat_OC/tmpParFile6373508886277439213.par]
L2BIN 4.0.9 (Apr 27 2016 10:22:37)
INTERP parameter disabled.
Single HDF input
Averaging: standard
Resolution: 1
Max Qual Allowed: 2
prod_avg:
flagusemask: 107599675
required: 0
NetCDF4 input file
/Users/alysiaherr/Dropbox/ALYSIA/MATLAB_alysia/Sat_OC/A2016193121000.L2_LAC_OC.nc   brk: 0   2040 193 43809
total number of bins: 380187134
1970001 2038018 270
krow:    0 out of 17280 (-90.00 to -87.19) Mon Jan 30 11:16:58 2017
krow:   270 out of 17280 (-87.19 to -84.38) Mon Jan 30 11:16:58 2017
krow:   540 out of 17280 (-84.38 to -81.56) Mon Jan 30 11:16:58 2017
krow:   810 out of 17280 (-81.56 to -78.75) Mon Jan 30 11:16:58 2017
krow: 1080 out of 17280 (-78.75 to -75.94) Mon Jan 30 11:16:58 2017
krow: 1350 out of 17280 (-75.94 to -73.12) Mon Jan 30 11:16:58 2017
krow: 1620 out of 17280 (-73.12 to -70.31) Mon Jan 30 11:16:58 2017
krow: 1890 out of 17280 (-70.31 to -67.50) Mon Jan 30 11:16:58 2017
krow: 2160 out of 17280 (-67.50 to -64.69) Mon Jan 30 11:16:58 2017
krow: 2430 out of 17280 (-64.69 to -61.88) Mon Jan 30 11:16:58 2017
krow: 2700 out of 17280 (-61.88 to -59.06) Mon Jan 30 11:16:58 2017
krow: 2970 out of 17280 (-59.06 to -56.25) Mon Jan 30 11:16:58 2017
krow: 3240 out of 17280 (-56.25 to -53.44) Mon Jan 30 11:16:58 2017
krow: 3510 out of 17280 (-53.44 to -50.62) Mon Jan 30 11:16:58 2017
krow: 3780 out of 17280 (-50.62 to -47.81) Mon Jan 30 11:16:58 2017
krow: 4050 out of 17280 (-47.81 to -45.00) Mon Jan 30 11:16:58 2017
krow: 4320 out of 17280 (-45.00 to -42.19) Mon Jan 30 11:16:58 2017
krow: 4590 out of 17280 (-42.19 to -39.38) Mon Jan 30 11:16:58 2017
krow: 4860 out of 17280 (-39.38 to -36.56) Mon Jan 30 11:16:58 2017
krow: 5130 out of 17280 (-36.56 to -33.75) Mon Jan 30 11:16:58 2017
krow: 5400 out of 17280 (-33.75 to -30.94) Mon Jan 30 11:16:58 2017
krow: 5670 out of 17280 (-30.94 to -28.12) Mon Jan 30 11:16:58 2017
krow: 5940 out of 17280 (-28.12 to -25.31) Mon Jan 30 11:16:58 2017
krow: 6210 out of 17280 (-25.31 to -22.50) Mon Jan 30 11:16:58 2017
krow: 6480 out of 17280 (-22.50 to -19.69) Mon Jan 30 11:16:58 2017
krow: 6750 out of 17280 (-19.69 to -16.88) Mon Jan 30 11:16:58 2017
krow: 7020 out of 17280 (-16.88 to -14.06) Mon Jan 30 11:16:58 2017
krow: 7290 out of 17280 (-14.06 to -11.25) Mon Jan 30 11:16:58 2017
krow: 7560 out of 17280 (-11.25 to -8.44) Mon Jan 30 11:16:58 2017
krow: 7830 out of 17280 ( -8.44 to -5.62) Mon Jan 30 11:16:58 2017
krow: 8100 out of 17280 ( -5.62 to -2.81) Mon Jan 30 11:16:58 2017
krow: 8370 out of 17280 ( -2.81 to   0.00) Mon Jan 30 11:16:58 2017
krow: 8640 out of 17280 ( 0.00 to   2.81) Mon Jan 30 11:16:58 2017
krow: 8910 out of 17280 ( 2.81 to   5.62) Mon Jan 30 11:16:58 2017
krow: 9180 out of 17280 ( 5.62 to   8.44) Mon Jan 30 11:16:58 2017
krow: 9450 out of 17280 ( 8.44 to 11.25) Mon Jan 30 11:16:58 2017
krow: 9720 out of 17280 ( 11.25 to 14.06) Mon Jan 30 11:16:58 2017
krow: 9990 out of 17280 ( 14.06 to 16.88) Mon Jan 30 11:16:58 2017
krow: 10260 out of 17280 ( 16.88 to 19.69) Mon Jan 30 11:16:58 2017
krow: 10530 out of 17280 ( 19.69 to 22.50) Mon Jan 30 11:16:58 2017
krow: 10800 out of 17280 ( 22.50 to 25.31) Mon Jan 30 11:16:58 2017
krow: 11070 out of 17280 ( 25.31 to 28.12) Mon Jan 30 11:16:58 2017
krow: 11340 out of 17280 ( 28.12 to 30.94) Mon Jan 30 11:16:58 2017
krow: 11610 out of 17280 ( 30.94 to 33.75) Mon Jan 30 11:16:58 2017
krow: 11880 out of 17280 ( 33.75 to 36.56) Mon Jan 30 11:16:58 2017
krow: 12150 out of 17280 ( 36.56 to 39.38) Mon Jan 30 11:16:58 2017
krow: 12420 out of 17280 ( 39.38 to 42.19) Mon Jan 30 11:16:58 2017
krow: 12690 out of 17280 ( 42.19 to 45.00) Mon Jan 30 11:16:58 2017
krow: 12960 out of 17280 ( 45.00 to 47.81) Mon Jan 30 11:16:58 2017
# allocated per bin :    2

ifile:   0 jsrow: 2000 nsamp: 1354
krow:12960 After data_value fill: Mon Jan 30 11:16:58 2017

krow:12960 After bin processing: Mon Jan 30 11:16:58 2017
krow:12960 Befre free dynic mem: Mon Jan 30 11:16:58 2017
krow:12960 After free dynic mem: Mon Jan 30 11:16:58 2017
krow: 13230 out of 17280 ( 47.81 to 50.62) Mon Jan 30 11:16:58 2017
# allocated per bin :    2

ifile:   0 jsrow: 1600 nsamp: 1354
ifile:   0 jsrow: 1700 nsamp: 1354
ifile:   0 jsrow: 1800 nsamp: 1354
ifile:   0 jsrow: 1900 nsamp: 1354
ifile:   0 jsrow: 2000 nsamp: 1354
krow:13230 After data_value fill: Mon Jan 30 11:16:59 2017

krow:13230 After bin processing: Mon Jan 30 11:16:59 2017
krow:13230 Befre free dynic mem: Mon Jan 30 11:16:59 2017
krow:13230 After free dynic mem: Mon Jan 30 11:16:59 2017
krow: 13500 out of 17280 ( 50.62 to 53.44) Mon Jan 30 11:16:59 2017
# allocated per bin :    2

ifile:   0 jsrow: 1300 nsamp: 1354
ifile:   0 jsrow: 1400 nsamp: 1354
ifile:   0 jsrow: 1500 nsamp: 1354
ifile:   0 jsrow: 1600 nsamp: 1354
ifile:   0 jsrow: 1700 nsamp: 1354
ifile:   0 jsrow: 1800 nsamp: 1354
ifile:   0 jsrow: 1900 nsamp: 1354
ifile:   0 jsrow: 2000 nsamp: 1354
krow:13500 After data_value fill: Mon Jan 30 11:16:59 2017

krow:13500 After bin processing: Mon Jan 30 11:16:59 2017
krow:13500 Befre free dynic mem: Mon Jan 30 11:16:59 2017
krow:13500 After free dynic mem: Mon Jan 30 11:16:59 2017
krow: 13770 out of 17280 ( 53.44 to 56.25) Mon Jan 30 11:16:59 2017
# allocated per bin :    2

ifile:   0 jsrow:   900 nsamp: 1354
ifile:   0 jsrow: 1000 nsamp: 1354
ifile:   0 jsrow: 1100 nsamp: 1354
ifile:   0 jsrow: 1200 nsamp: 1354
ifile:   0 jsrow: 1300 nsamp: 1354
ifile:   0 jsrow: 1400 nsamp: 1354
ifile:   0 jsrow: 1500 nsamp: 1354
ifile:   0 jsrow: 1600 nsamp: 1354
ifile:   0 jsrow: 1700 nsamp: 1354
ifile:   0 jsrow: 1800 nsamp: 1354
krow:13770 After data_value fill: Mon Jan 30 11:16:59 2017

krow:13770 After bin processing: Mon Jan 30 11:16:59 2017
krow:13770 Befre free dynic mem: Mon Jan 30 11:17:00 2017
krow:13770 After free dynic mem: Mon Jan 30 11:17:00 2017
krow: 14040 out of 17280 ( 56.25 to 59.06) Mon Jan 30 11:17:00 2017
# allocated per bin :    2

ifile:   0 jsrow:   500 nsamp: 1354
ifile:   0 jsrow:   600 nsamp: 1354
ifile:   0 jsrow:   700 nsamp: 1354
ifile:   0 jsrow:   800 nsamp: 1354
ifile:   0 jsrow:   900 nsamp: 1354
ifile:   0 jsrow: 1000 nsamp: 1354
ifile:   0 jsrow: 1100 nsamp: 1354
ifile:   0 jsrow: 1200 nsamp: 1354
ifile:   0 jsrow: 1300 nsamp: 1354
ifile:   0 jsrow: 1400 nsamp: 1354
ifile:   0 jsrow: 1500 nsamp: 1354
krow:14040 After data_value fill: Mon Jan 30 11:17:00 2017

krow:14040 After bin processing: Mon Jan 30 11:17:00 2017
krow:14040 Befre free dynic mem: Mon Jan 30 11:17:00 2017
krow:14040 After free dynic mem: Mon Jan 30 11:17:00 2017
krow: 14310 out of 17280 ( 59.06 to 61.88) Mon Jan 30 11:17:00 2017
# allocated per bin :    2

ifile:   0 jsrow:   100 nsamp: 1354
ifile:   0 jsrow:   200 nsamp: 1354
ifile:   0 jsrow:   300 nsamp: 1354
ifile:   0 jsrow:   400 nsamp: 1354
ifile:   0 jsrow:   500 nsamp: 1354
ifile:   0 jsrow:   600 nsamp: 1354
ifile:   0 jsrow:   700 nsamp: 1354
ifile:   0 jsrow:   800 nsamp: 1354
ifile:   0 jsrow:   900 nsamp: 1354
ifile:   0 jsrow: 1000 nsamp: 1354
ifile:   0 jsrow: 1100 nsamp: 1354
ifile:   0 jsrow: 1200 nsamp: 1354
krow:14310 After data_value fill: Mon Jan 30 11:17:01 2017

krow:14310 After bin processing: Mon Jan 30 11:17:01 2017
krow:14310 Befre free dynic mem: Mon Jan 30 11:17:01 2017
krow:14310 After free dynic mem: Mon Jan 30 11:17:01 2017
krow: 14580 out of 17280 ( 61.88 to 64.69) Mon Jan 30 11:17:01 2017
# allocated per bin :    2

ifile:   0 jsrow:    0 nsamp: 1354
ifile:   0 jsrow:   100 nsamp: 1354
ifile:   0 jsrow:   200 nsamp: 1354
ifile:   0 jsrow:   300 nsamp: 1354
ifile:   0 jsrow:   400 nsamp: 1354
ifile:   0 jsrow:   500 nsamp: 1354
ifile:   0 jsrow:   600 nsamp: 1354
ifile:   0 jsrow:   700 nsamp: 1354
ifile:   0 jsrow:   800 nsamp: 1354
ifile:   0 jsrow:   900 nsamp: 1354
krow:14580 After data_value fill: Mon Jan 30 11:17:01 2017

krow:14580 After bin processing: Mon Jan 30 11:17:01 2017
krow:14580 Befre free dynic mem: Mon Jan 30 11:17:01 2017
krow:14580 After free dynic mem: Mon Jan 30 11:17:01 2017
krow: 14850 out of 17280 ( 64.69 to 67.50) Mon Jan 30 11:17:01 2017
# allocated per bin :    2

ifile:   0 jsrow:    0 nsamp: 1354
ifile:   0 jsrow:   100 nsamp: 1354
ifile:   0 jsrow:   200 nsamp: 1354
ifile:   0 jsrow:   300 nsamp: 1354
ifile:   0 jsrow:   400 nsamp: 1354
ifile:   0 jsrow:   500 nsamp: 1354
krow:14850 After data_value fill: Mon Jan 30 11:17:02 2017

krow:14850 After bin processing: Mon Jan 30 11:17:02 2017
krow:14850 Befre free dynic mem: Mon Jan 30 11:17:02 2017
krow:14850 After free dynic mem: Mon Jan 30 11:17:02 2017
krow: 15120 out of 17280 ( 67.50 to 70.31) Mon Jan 30 11:17:02 2017
# allocated per bin :    2

ifile:   0 jsrow:    0 nsamp: 1354
ifile:   0 jsrow:   100 nsamp: 1354
ifile:   0 jsrow:   200 nsamp: 1354
krow:15120 After data_value fill: Mon Jan 30 11:17:02 2017

krow:15120 After bin processing: Mon Jan 30 11:17:02 2017
krow:15120 Befre free dynic mem: Mon Jan 30 11:17:02 2017
krow:15120 After free dynic mem: Mon Jan 30 11:17:02 2017
krow: 15390 out of 17280 ( 70.31 to 73.12) Mon Jan 30 11:17:02 2017
krow: 15660 out of 17280 ( 73.12 to 75.94) Mon Jan 30 11:17:02 2017
krow: 15930 out of 17280 ( 75.94 to 78.75) Mon Jan 30 11:17:02 2017
krow: 16200 out of 17280 ( 78.75 to 81.56) Mon Jan 30 11:17:02 2017
krow: 16470 out of 17280 ( 81.56 to 84.38) Mon Jan 30 11:17:02 2017
krow: 16740 out of 17280 ( 84.38 to 87.19) Mon Jan 30 11:17:02 2017
krow: 17010 out of 17280 ( 87.19 to 90.00) Mon Jan 30 11:17:02 2017
krow:17280 Mon Jan 30 11:17:02 2017
total_filled_bins: 0
rm -f /Users/alysiaherr/Dropbox/ALYSIA/MATLAB_alysia/Sat_OC/A2016193.L3b_DAY_OC.nc*
Freeing Dynamic Memory
Freeing L2 arrays

by **OB SeaDAS - dshea** » Mon Jan 30, 2017 3:34 pm America/New_York

Could you post what is in the par file. The problem is that 0 pixels were binned.

Yes, it looks like the help file for l2bin does not list the return codes. Here they are:

return value: 0=OK, 1=error, 110=north,south,east,west does not intersect
file data.

don

alysiaherr · by **alysiaherr** » Mon Jan 30, 2017 6:55 pm America/New_York

Thanks for your response.

Here's the contents of the par file:

infile=/Users/alysiaherr/Dropbox/ALYSIA/MATLAB_alysia/Sat_OC/A2016193121000.L2_LAC_OC.nc
ofile=/Users/alysiaherr/Dropbox/ALYSIA/MATLAB_alysia/Sat_OC/A2016193.L3b_DAY_OC.nc
resolve=1
flaguse=ATMFAIL,LAND,HILT,HISATZEN,STRAYLIGHT,CLDICE,COCCOLITH,LOWLW,CHLWARN,CHLFAIL,NAVWARN,MAXAERITER,ATMWARN,HISOLZEN,NAVFAIL,FILTER,HIGLINT
prodtype=regional
night=
verbose=1

No place to define spatial domain - any ideas?

gnwiii · by **gnwiii** » Tue Jan 31, 2017 7:34 am America/New_York

The real documentation is the source code. In $OCSSWROOT/run/build/src/l2bin/l2bin.c, search for 110 and you will see that when no bins are filled, the output file is removed and ret_status set to 110:

 printf("total_filled_bins: %d\n", total_filled_bins);

    if (total_filled_bins == 0) {
        strcpy(buf, "rm -f ");
        strcat(buf, input.ofile);
        strcat(buf, "*");
        printf("%s\n", buf);
        system(buf);
        ret_status = 110;  
        goto bail;
    }

As you might guess, bail has return ret_status;.

alysiaherr · by **alysiaherr** » Wed Feb 01, 2017 2:36 pm America/New_York

I see -- so these data files just have no data above my specified quality level in the region covered. (Confirmed this by bumping down the quality level - L2bin was successful).