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Topic SeaDAS / SeaDAS 6.x Virtual Appliance for Windows / L3binning program does not work (locked)

By egido Date 2012-12-05 16:58

Hi:
I am trying to binning some images with L3 binnig program of SeaDAS Virtual Appliance, which seems to do something, telling me "Running seadas l3 binning program" but, nothing happens!
Could you help me plesae? I have been dealing with it for months! I did downloaded all the processing programs included into SeaDAS virtual appliance page but nothing goes better.

Thank you very much in advance for your kindest help.

Janitzio

By gnwiii Date 2012-12-06 16:15

There isn't much information in your message. Do you have the most recent SeaDAS 6.4 VA? What files are you using? The seadas benchmark script includes l3 binning. It is a useful check on the all the processing programs using a small image. If the benchmarks work that helps narrow down the possibilities. Please run the benchmark and report any problems (after you post a message you can add the log file to it). Assuming the benchmark works, some things that might cause your problem include:

too little memory allocated to the virtual machine
files stored on a non-linux filesystem (e.g., external FAT32 USB drive)
filenames with long paths
permission problems (e.g., no write access to the directory where the output should go)
anti-virus software
disk problems

If none of these apply then you need to construct the simplest possible example that demonstrates the problem and post enough detail so others can reproduce it.

By egido Date 2013-02-08 19:34

Dear WhiteG:

Thank you very much for your answer. Yes, I am working on SeaDAS 6.4 VA, in a PC. I am newbie on this but I did run benchmark script, and the results whee the follow:

===============================================================
Creating L1B file (modis_L1B.py)...
===============================================================

modis_L1B.py A2006167181000.L1A A2006167181000.GEO -o A2006167181000.L1B \
   --lutver=6.1.15.5\
   --lutdir=./ancillary \
   --del-hkm --del-qkm
ERROR: File A2006167181000.GEO does not exist.
Command exited with non-zero status 1
real 0.07
user 0.03
sys 0.01

===============================================================
Creating L2 file (l2gen)...
===============================================================

l2gen par="A2006167181000.par"

-E- /home/swdev/seadas/build/src/l2gen/getformat.c: Input file 'A2006167181000.L1B' does not exist or cannot open.
-E- /home/swdev/seadas/build/src/l2gen/msl12_input.c Line 1195: Could not find type for file A2006167181000.L1B.
-E- /home/swdev/seadas/build/src/l2gen/msl12_input.c: Error reading program options.
-E- l2gen: Error parsing input parameters.
Command exited with non-zero status 1
real 0.15
user 0.01
sys 0.00

===============================================================
Creating 2km spatially binned file (l2bin)...
===============================================================

l2bin infile=A2006167181000.L2 \
ofile=A2006167181000.L3b_space.hdf l3bprod="chlor_a" resolve=2

L2BIN 2.4.5 (Jun 1 2012 12:34:18)
Input listing file: "A2006167181000.L2" not found.
This is version 2.4.5 of l2bin (compiled on Jun 1 2012 12:34:18)

Usage: l2bin parfile=parfile or
infile=infile ofile=ofile [sday=sday] [eday=eday]
resolve=resolve [flaguse=flaguse] [l3bprod=l3bprod]
[prodtype=prodtype] [noext=noext] [verbose=verbose
[rowgroup=rowgroup] [night=night] [pversion=pversion]

   parfile   = parameter filename
   infile = input filename/filelist
   ofile    = output bin filename
   sday = start datadate (YYYYDDD) [ignored for "regional" prodtype]
   eday = end datadate   (YYYYDDD) [ignored for "regional" prodtype]
   resolve   = bin resolution (H,1,2,4,9,36)
   flaguse   = flags masked [see /SENSOR/l2bin_defaults.par]
   l3bprod   = bin products [default=all products]
   Set to "ALL" or "all" for all L2 products in 1st input file.
   Use ':' or ',' or ' ' as delimiters.
   Use ';' or '=' to delineate minimum values.
   prodtype = product type (Set to "regional" to bin all scans.) [default=day]
   pversion = production version [default=Unspecified]
   noext    = set to 1 to suppress generation of external files
   [default=0, (1 for "regional" prodtype)]
   rowgroup = # of bin rows to process at once.
   night    = set to 1 for SST night processing [default=0]
   qual_prod = quality product field name
   qual_max = maximum acceptable quality [default=2]
   verbose   = Allow more verbose screen messages [default=0]
real 0.05
user 0.00
sys 0.00

===============================================================
Creating time binned file (l3bin)...
===============================================================

l3bin in=A2006167181000.L3b_space.hdf \
out=A2006167181000.L3b_time.hdf noext=1

(sending l3bin output to /dev/null)

HDF5-DIAG: Error detected in HDF5 (1.8.7) thread 0:
#000: H5F.c line 794 in H5Fis_hdf5(): unable to open file
major: Low-level I/O
minor: Unable to initialize object
#001: H5FD.c line 1086 in H5FD_open(): open failed
major: Virtual File Layer
minor: Unable to initialize object
#002: H5FDsec2.c line 348 in H5FD_sec2_open(): unable to open file: name = 'A2006167181000.L3b_space.hdf', errno = 2, error message = 'No such file or directory', flags = 0, o_flags = 0
major: File accessability
minor: Unable to open file
Command exited with non-zero status 255
real 0.13
user 0.00
sys 0.01

===============================================================
Creating standard mapped image (smigen)...
===============================================================

smigen ifile=A2006167181000.L3b_time.hdf \
   ofile=A2006167181000.smi_chlor_a_mn.hdf \
   prod="chlor_a" resolution=2km \
   loneast=-62 lonwest=-78 latsouth=30 latnorth=46

smigen 4.27 (Jun 1 2012 12:34:23)
HDF5-DIAG: Error detected in HDF5 (1.8.7) thread 0:
#000: H5F.c line 794 in H5Fis_hdf5(): unable to open file
major: Low-level I/O
minor: Unable to initialize object
#001: H5FD.c line 1086 in H5FD_open(): open failed
major: Virtual File Layer
minor: Unable to initialize object
#002: H5FDsec2.c line 348 in H5FD_sec2_open(): unable to open file: name = 'A2006167181000.L3b_time.hdf', errno = 2, error message = 'No such file or directory', flags = 0, o_flags = 0
major: File accessability
minor: Unable to open file
Error: Cannot open input HDF file on Hopen - A2006167181000.L3b_time.hdf
Command exited with non-zero status 1
real 0.27
user 0.00
sys 0.01

===============================================================
SeaDAS v6.4 MODIS PROCESSING TIMES
===============================================================
CPU TIMES (user + sys):
========================
L0 to L1A    : 15.80s
L1A to GEO : .79s
L1A to L1B : .04s
L1B to L2    : .01s
space binning   : 0s
time binning : .01s
L3bin to SMI : .01s
========================
TOTAL CPU TIME : 16.66s
===============================================================
WALL CLOCK TIMES (real):
========================
L0 to L1A    : 101.65s
L1A to GEO : 191.85s
L1A to L1B : 0.07s
L1B to L2    : 0.15s
space binning   : 0.05s
time binning : 0.13s
L3bin to SMI : 0.27s
========================
TOTAL REAL TIME : 294.17s
===============================================================

seadas@seadas-vm:/disk01/seadas/seadas/benchmarks$

Thanks a lot

By gnwiii Date 2013-02-09 17:36

You are missing the first few steps of the benchmark processing. Maybe you pasted the terminal output, as there should be a complete record in the L0_seadas_benchmark.log file.

You can edit your message to attach this file as the problem seems to have occurred in one of the very early stages. At this stage all we know is that the
A2006167181000.GEO file wasn't created. There may be some other log files with useful details.

By egido Date 2013-02-11 18:22

Hello again: Yes, I realized I trimed the message. Here it is the complete text of L0_seadas_bemchmark.log file:

===============================================================
SeaDAS Benchmarking Script - MODIS processing
===============================================================

Fri Feb 8 14:08:53 EST 2013
SeaDAS v6.4 running on Linux 2.6.32-26-generic i686 unknown
OS Release: Ubuntu 10.04.1 LTS

===============================================================
Creating L1A file (modis_L1A.py)...
===============================================================

modis_L1A.py A2006167181000.L0 \
-o A2006167181000.L1A

L1A version: 5.0.5 built on Jun 1 2012 (12:34:35)
Scan Number: 0 Fri Feb 8 14:09:00 2013
Scan Number: 10 Fri Feb 8 14:09:33 2013
Scan Number: 20 Fri Feb 8 14:09:35 2013
Scan Number: 30 Fri Feb 8 14:09:39 2013
Scan Number: 40 Fri Feb 8 14:09:41 2013
Scan Number: 50 Fri Feb 8 14:09:45 2013
Scan Number: 60 Fri Feb 8 14:09:48 2013
Scan Number: 70 Fri Feb 8 14:09:50 2013
Scan Number: 80 Fri Feb 8 14:09:54 2013
Scan Number: 90 Fri Feb 8 14:09:56 2013
Scan Number: 100 Fri Feb 8 14:09:59 2013
Scan Number: 110 Fri Feb 8 14:10:03 2013
Scan Number: 120 Fri Feb 8 14:10:06 2013
Scan Number: 130 Fri Feb 8 14:10:10 2013
Scan Number: 140 Fri Feb 8 14:10:13 2013
Scan Number: 150 Fri Feb 8 14:10:16 2013
Scan Number: 160 Fri Feb 8 14:10:19 2013
Scan Number: 170 Fri Feb 8 14:10:21 2013
Scan Number: 180 Fri Feb 8 14:10:25 2013
Scan Number: 190 Fri Feb 8 14:10:28 2013
Scan Number: 200 Fri Feb 8 14:10:32 2013
real 101.65
user 4.42
sys 11.38

===============================================================
Creating GEO file (modis_GEO.py)...
===============================================================

modis_GEO.py A2006167181000.L1A \
-o A2006167181000.GEO \
-a ./ancillary/PM1ATTNR.P2006167.1800.002 \
-e ./ancillary/PM1EPHND.P2006167.1200.001

Searching for first requested record .........
10 EPHEMERIS RECORDS WRITTEN. LAST JED =    2436496.50
20 EPHEMERIS RECORDS WRITTEN. LAST JED =    2436816.50
30 EPHEMERIS RECORDS WRITTEN. LAST JED =    2437136.50
40 EPHEMERIS RECORDS WRITTEN. LAST JED =    2437456.50
50 EPHEMERIS RECORDS WRITTEN. LAST JED =    2437776.50
60 EPHEMERIS RECORDS WRITTEN. LAST JED =    2438096.50
70 EPHEMERIS RECORDS WRITTEN. LAST JED =    2438416.50
80 EPHEMERIS RECORDS WRITTEN. LAST JED =    2438736.50
90 EPHEMERIS RECORDS WRITTEN. LAST JED =    2439056.50
100 EPHEMERIS RECORDS WRITTEN. LAST JED =    2439376.50
110 EPHEMERIS RECORDS WRITTEN. LAST JED =    2439696.50
120 EPHEMERIS RECORDS WRITTEN. LAST JED =    2440016.50
130 EPHEMERIS RECORDS WRITTEN. LAST JED =    2440336.50
140 EPHEMERIS RECORDS WRITTEN. LAST JED =    2440656.50
150 EPHEMERIS RECORDS WRITTEN. LAST JED =    2440976.50
160 EPHEMERIS RECORDS WRITTEN. LAST JED =    2441296.50
170 EPHEMERIS RECORDS WRITTEN. LAST JED =    2441616.50
180 EPHEMERIS RECORDS WRITTEN. LAST JED =    2441936.50
190 EPHEMERIS RECORDS WRITTEN. LAST JED =    2442256.50
200 EPHEMERIS RECORDS WRITTEN. LAST JED =    2442576.50
210 EPHEMERIS RECORDS WRITTEN. LAST JED =    2442896.50
220 EPHEMERIS RECORDS WRITTEN. LAST JED =    2443216.50
230 EPHEMERIS RECORDS WRITTEN. LAST JED =    2443536.50
240 EPHEMERIS RECORDS WRITTEN. LAST JED =    2443856.50
250 EPHEMERIS RECORDS WRITTEN. LAST JED =    2444176.50
260 EPHEMERIS RECORDS WRITTEN. LAST JED =    2444496.50
270 EPHEMERIS RECORDS WRITTEN. LAST JED =    2444816.50
280 EPHEMERIS RECORDS WRITTEN. LAST JED =    2445136.50
290 EPHEMERIS RECORDS WRITTEN. LAST JED =    2445456.50
300 EPHEMERIS RECORDS WRITTEN. LAST JED =    2445776.50
310 EPHEMERIS RECORDS WRITTEN. LAST JED =    2446096.50
320 EPHEMERIS RECORDS WRITTEN. LAST JED =    2446416.50
330 EPHEMERIS RECORDS WRITTEN. LAST JED =    2446736.50
340 EPHEMERIS RECORDS WRITTEN. LAST JED =    2447056.50
350 EPHEMERIS RECORDS WRITTEN. LAST JED =    2447376.50
360 EPHEMERIS RECORDS WRITTEN. LAST JED =    2447696.50
370 EPHEMERIS RECORDS WRITTEN. LAST JED =    2448016.50
380 EPHEMERIS RECORDS WRITTEN. LAST JED =    2448336.50
390 EPHEMERIS RECORDS WRITTEN. LAST JED =    2448656.50
400 EPHEMERIS RECORDS WRITTEN. LAST JED =    2448976.50
410 EPHEMERIS RECORDS WRITTEN. LAST JED =    2449296.50
420 EPHEMERIS RECORDS WRITTEN. LAST JED =    2449616.50
430 EPHEMERIS RECORDS WRITTEN. LAST JED =    2449936.50
440 EPHEMERIS RECORDS WRITTEN. LAST JED =    2450256.50
450 EPHEMERIS RECORDS WRITTEN. LAST JED =    2450576.50
460 EPHEMERIS RECORDS WRITTEN. LAST JED =    2450896.50
470 EPHEMERIS RECORDS WRITTEN. LAST JED =    2451216.50
480 EPHEMERIS RECORDS WRITTEN. LAST JED =    2451536.50
490 EPHEMERIS RECORDS WRITTEN. LAST JED =    2451856.50
500 EPHEMERIS RECORDS WRITTEN. LAST JED =    2452176.50
510 EPHEMERIS RECORDS WRITTEN. LAST JED =    2452496.50
520 EPHEMERIS RECORDS WRITTEN. LAST JED =    2452816.50
530 EPHEMERIS RECORDS WRITTEN. LAST JED =    2453136.50
540 EPHEMERIS RECORDS WRITTEN. LAST JED =    2453456.50
550 EPHEMERIS RECORDS WRITTEN. LAST JED =    2453776.50
560 EPHEMERIS RECORDS WRITTEN. LAST JED =    2454096.50
570 EPHEMERIS RECORDS WRITTEN. LAST JED =    2454416.50
580 EPHEMERIS RECORDS WRITTEN. LAST JED =    2454736.50
590 EPHEMERIS RECORDS WRITTEN. LAST JED =    2455056.50
600 EPHEMERIS RECORDS WRITTEN. LAST JED =    2455376.50
610 EPHEMERIS RECORDS WRITTEN. LAST JED =    2455696.50
620 EPHEMERIS RECORDS WRITTEN. LAST JED =    2456016.50
630 EPHEMERIS RECORDS WRITTEN. LAST JED =    2456336.50
640 EPHEMERIS RECORDS WRITTEN. LAST JED =    2456656.50
650 EPHEMERIS RECORDS WRITTEN. LAST JED =    2456976.50
660 EPHEMERIS RECORDS WRITTEN. LAST JED =    2457296.50
670 EPHEMERIS RECORDS WRITTEN. LAST JED =    2457616.50
680 EPHEMERIS RECORDS WRITTEN. LAST JED =    2457936.50
690 EPHEMERIS RECORDS WRITTEN. LAST JED =    2458256.50
700 EPHEMERIS RECORDS WRITTEN. LAST JED =    2458576.50
710 EPHEMERIS RECORDS WRITTEN. LAST JED =    2458896.50
720 EPHEMERIS RECORDS WRITTEN. LAST JED =    2459216.50
Connection error, retrying up to 5 more time(s)
Connection error, retrying up to 4 more time(s)
Connection error, retrying up to 3 more time(s)
Connection error, retrying up to 2 more time(s)
Connection error, retrying up to 1 more time(s)
Traceback (most recent call last):
File "/disk01/seadas/seadas/run/scripts/modis_GEO.py", line 124, in <module>
m.utcleap()
File "/disk01/seadas/seadas/run/scripts/modules/modis_GEO_utils.py", line 130, in utcleap
l.update_modis()
File "/disk01/seadas/seadas/run/scripts/modules/lut_utils.py", line 137, in update_modis
status = ProcUtils.httpdl(self.data_site + "/Ancillary/LUTs/"+msn[self.mission] +"/cal/OPER/" + f,localpath=outputdir)
File "/disk01/seadas/seadas/run/scripts/modules/ProcUtils.py", line 62, in httpdl
httpdl(url, localpath=localpath, ntries=ntries - 1, uncompress=uncompress)
File "/disk01/seadas/seadas/run/scripts/modules/ProcUtils.py", line 62, in httpdl
httpdl(url, localpath=localpath, ntries=ntries - 1, uncompress=uncompress)
File "/disk01/seadas/seadas/run/scripts/modules/ProcUtils.py", line 62, in httpdl
httpdl(url, localpath=localpath, ntries=ntries - 1, uncompress=uncompress)
File "/disk01/seadas/seadas/run/scripts/modules/ProcUtils.py", line 62, in httpdl
httpdl(url, localpath=localpath, ntries=ntries - 1, uncompress=uncompress)
File "/disk01/seadas/seadas/run/scripts/modules/ProcUtils.py", line 62, in httpdl
httpdl(url, localpath=localpath, ntries=ntries - 1, uncompress=uncompress)
File "/disk01/seadas/seadas/run/scripts/modules/ProcUtils.py", line 73, in httpdl
return URLError.code
AttributeError: type object 'URLError' has no attribute 'code'
Command exited with non-zero status 1
real 191.85
user 0.53
sys 0.26

===============================================================
Creating L1B file (modis_L1B.py)...
===============================================================

modis_L1B.py A2006167181000.L1A A2006167181000.GEO -o A2006167181000.L1B \
   --lutver=6.1.15.5\
   --lutdir=./ancillary \
   --del-hkm --del-qkm
ERROR: File A2006167181000.GEO does not exist.
Command exited with non-zero status 1
real 0.07
user 0.03
sys 0.01

===============================================================
Creating L2 file (l2gen)...
===============================================================

l2gen par="A2006167181000.par"

-E- /home/swdev/seadas/build/src/l2gen/getformat.c: Input file 'A2006167181000.L1B' does not exist or cannot open.
-E- /home/swdev/seadas/build/src/l2gen/msl12_input.c Line 1195: Could not find type for file A2006167181000.L1B.
-E- /home/swdev/seadas/build/src/l2gen/msl12_input.c: Error reading program options.
-E- l2gen: Error parsing input parameters.
Command exited with non-zero status 1
real 0.15
user 0.01
sys 0.00

===============================================================
Creating 2km spatially binned file (l2bin)...
===============================================================

l2bin infile=A2006167181000.L2 \
ofile=A2006167181000.L3b_space.hdf l3bprod="chlor_a" resolve=2

L2BIN 2.4.5 (Jun 1 2012 12:34:18)
Input listing file: "A2006167181000.L2" not found.
This is version 2.4.5 of l2bin (compiled on Jun 1 2012 12:34:18)

Usage: l2bin parfile=parfile or
infile=infile ofile=ofile [sday=sday] [eday=eday]
resolve=resolve [flaguse=flaguse] [l3bprod=l3bprod]
[prodtype=prodtype] [noext=noext] [verbose=verbose
[rowgroup=rowgroup] [night=night] [pversion=pversion]

   parfile   = parameter filename
   infile = input filename/filelist
   ofile    = output bin filename
   sday = start datadate (YYYYDDD) [ignored for "regional" prodtype]
   eday = end datadate   (YYYYDDD) [ignored for "regional" prodtype]
   resolve   = bin resolution (H,1,2,4,9,36)
   flaguse   = flags masked [see /SENSOR/l2bin_defaults.par]
   l3bprod   = bin products [default=all products]
   Set to "ALL" or "all" for all L2 products in 1st input file.
   Use ':' or ',' or ' ' as delimiters.
   Use ';' or '=' to delineate minimum values.
   prodtype = product type (Set to "regional" to bin all scans.) [default=day]
   pversion = production version [default=Unspecified]
   noext    = set to 1 to suppress generation of external files
   [default=0, (1 for "regional" prodtype)]
   rowgroup = # of bin rows to process at once.
   night    = set to 1 for SST night processing [default=0]
   qual_prod = quality product field name
   qual_max = maximum acceptable quality [default=2]
   verbose   = Allow more verbose screen messages [default=0]
real 0.05
user 0.00
sys 0.00

===============================================================
Creating time binned file (l3bin)...
===============================================================

l3bin in=A2006167181000.L3b_space.hdf \
out=A2006167181000.L3b_time.hdf noext=1

(sending l3bin output to /dev/null)

HDF5-DIAG: Error detected in HDF5 (1.8.7) thread 0:
#000: H5F.c line 794 in H5Fis_hdf5(): unable to open file
major: Low-level I/O
minor: Unable to initialize object
#001: H5FD.c line 1086 in H5FD_open(): open failed
major: Virtual File Layer
minor: Unable to initialize object
#002: H5FDsec2.c line 348 in H5FD_sec2_open(): unable to open file: name = 'A2006167181000.L3b_space.hdf', errno = 2, error message = 'No such file or directory', flags = 0, o_flags = 0
major: File accessability
minor: Unable to open file
Command exited with non-zero status 255
real 0.13
user 0.00
sys 0.01

===============================================================
Creating standard mapped image (smigen)...
===============================================================

smigen ifile=A2006167181000.L3b_time.hdf \
   ofile=A2006167181000.smi_chlor_a_mn.hdf \
   prod="chlor_a" resolution=2km \
   loneast=-62 lonwest=-78 latsouth=30 latnorth=46

smigen 4.27 (Jun 1 2012 12:34:23)
HDF5-DIAG: Error detected in HDF5 (1.8.7) thread 0:
#000: H5F.c line 794 in H5Fis_hdf5(): unable to open file
major: Low-level I/O
minor: Unable to initialize object
#001: H5FD.c line 1086 in H5FD_open(): open failed
major: Virtual File Layer
minor: Unable to initialize object
#002: H5FDsec2.c line 348 in H5FD_sec2_open(): unable to open file: name = 'A2006167181000.L3b_time.hdf', errno = 2, error message = 'No such file or directory', flags = 0, o_flags = 0
major: File accessability
minor: Unable to open file
Error: Cannot open input HDF file on Hopen - A2006167181000.L3b_time.hdf
Command exited with non-zero status 1
real 0.27
user 0.00
sys 0.01

===============================================================
SeaDAS v6.4 MODIS PROCESSING TIMES
===============================================================
CPU TIMES (user + sys):
========================
L0 to L1A    : 15.80s
L1A to GEO : .79s
L1A to L1B : .04s
L1B to L2    : .01s
space binning   : 0s
time binning : .01s
L3bin to SMI : .01s
========================
TOTAL CPU TIME : 16.66s
===============================================================
WALL CLOCK TIMES (real):
========================
L0 to L1A    : 101.65s
L1A to GEO : 191.85s
L1A to L1B : 0.07s
L1B to L2    : 0.15s
space binning   : 0.05s
time binning : 0.13s
L3bin to SMI : 0.27s
========================
TOTAL REAL TIME : 294.17s
===============================================================

I hope it could help.

Thank a lot

Janitzio

By gnwiii Date 2013-02-11 23:16

The problem is with modis_GEO.py:


Connection error, retrying up to 5 more time(s)
Connection error, retrying up to 4 more time(s)
Connection error, retrying up to 3 more time(s)
Connection error, retrying up to 2 more time(s)
Connection error, retrying up to 1 more time(s)
Traceback (most recent call last):
  File "/disk01/seadas/seadas/run/scripts/modis_GEO.py", line 124, in <module>
    m.utcleap()
  File "/disk01/seadas/seadas/run/scripts/modules/modis_GEO_utils.py", line 130, in utcleap
    l.update_modis()
  File "/disk01/seadas/seadas/run/scripts/modules/lut_utils.py", line 137, in update_modis
    status = ProcUtils.httpdl(self.data_site + "/Ancillary/LUTs/"+msn[self.mission] +"/cal/OPER/" + f,localpath=outputdir)
  File "/disk01/seadas/seadas/run/scripts/modules/ProcUtils.py", line 62, in httpdl
    httpdl(url, localpath=localpath, ntries=ntries - 1, uncompress=uncompress)
  File "/disk01/seadas/seadas/run/scripts/modules/ProcUtils.py", line 62, in httpdl
    httpdl(url, localpath=localpath, ntries=ntries - 1, uncompress=uncompress)
  File "/disk01/seadas/seadas/run/scripts/modules/ProcUtils.py", line 62, in httpdl
    httpdl(url, localpath=localpath, ntries=ntries - 1, uncompress=uncompress)
  File "/disk01/seadas/seadas/run/scripts/modules/ProcUtils.py", line 62, in httpdl
    httpdl(url, localpath=localpath, ntries=ntries - 1, uncompress=uncompress)
  File "/disk01/seadas/seadas/run/scripts/modules/ProcUtils.py", line 62, in httpdl
    httpdl(url, localpath=localpath, ntries=ntries - 1, uncompress=uncompress)
  File "/disk01/seadas/seadas/run/scripts/modules/ProcUtils.py", line 73, in httpdl
    return URLError.code
AttributeError: type object 'URLError' has no attribute 'code'
Command exited with non-zero status 1

Do you have an internet connection? What happens when you run "update_luts.py -v aqua" in
a terminal? If you search the forums you will see that others have had similar problems. If you are
using a system (laptop) that only has intermittent internet access, it may work to run
the "update_luts.py -v aqua" while online and then run the benchmark script while offline.

By egido Date 2013-02-12 20:36

Hi: Yes, I have an internet connection, I did run update_luts.py and results were the follow:

seadas@seadas-vm:/disk01/seadas/seadas$ update_luts.py -v aqua
[ MODIS ]
+ leapsec.dat
Connection error, retrying up to 5 more time(s)
Connection error, retrying up to 4 more time(s)
Connection error, retrying up to 3 more time(s)
Connection error, retrying up to 2 more time(s)
Connection error, retrying up to 1 more time(s)
Traceback (most recent call last):
File "/disk01/seadas/seadas/run/scripts/update_luts.py", line 60, in <module>
l.update_modis()
File "/disk01/seadas/seadas/run/scripts/modules/lut_utils.py", line 98, in update_modis
status = ProcUtils.httpdl(url, localpath=outputdir)
File "/disk01/seadas/seadas/run/scripts/modules/ProcUtils.py", line 62, in httpdl
httpdl(url, localpath=localpath, ntries=ntries - 1, uncompress=uncompress)
File "/disk01/seadas/seadas/run/scripts/modules/ProcUtils.py", line 62, in httpdl
httpdl(url, localpath=localpath, ntries=ntries - 1, uncompress=uncompress)
File "/disk01/seadas/seadas/run/scripts/modules/ProcUtils.py", line 62, in httpdl
httpdl(url, localpath=localpath, ntries=ntries - 1, uncompress=uncompress)
File "/disk01/seadas/seadas/run/scripts/modules/ProcUtils.py", line 62, in httpdl
httpdl(url, localpath=localpath, ntries=ntries - 1, uncompress=uncompress)
File "/disk01/seadas/seadas/run/scripts/modules/ProcUtils.py", line 62, in httpdl
httpdl(url, localpath=localpath, ntries=ntries - 1, uncompress=uncompress)
File "/disk01/seadas/seadas/run/scripts/modules/ProcUtils.py", line 73, in httpdl
return URLError.code
AttributeError: type object 'URLError' has no attribute 'code'
seadas@seadas-vm:/disk01/seadas/seadas$

best regards

Janitzio

By seanbailey Date 2013-02-12 21:18

Janitzio,

The issues you're seeing with the benchmark script are not related to l3bin.
However, you may want to apply the recent update (which may resolve the
LUT retrieval problem - at the very least should resolve the error)
You'll want to choose the 32bit Linux version for the VM.

Since the L1A process within the benchmark script was successful, it is highly likely that the problem does not reside with the processing code.

You can run the l2bin and l3bin programs from the command line in a terminal window. Run them without arguments to see the calling parameters.

Regards,
Sean

By egido Date 2013-02-13 18:33

Hello Sean: Do you mean I should download the version named "VMware Player for Linux 32-bit"?

By seanbailey Date 2013-02-13 18:48

No. The update is applied to the existing installed version.

By egido Date 2013-02-15 17:44

Hi Sean:
OK, I did choose 32bit Linux version for the VM, and ran the process into a terminal window. The results are into the file attached to this message. I would like to ask you if there is an inconsistency about the path, in the left frame is clear that the file is in Home/seadas/Desktop/, but in the left frame (terminal) the file is looked for into /disk01/seadas/Desktop/
Thank you

Janitzio

Attachment: inconsistency.png (160k)

By gnwiii Date 2013-02-15 18:04 Edited 2013-02-15 18:41

You need to provide more details, in part because it will be useful to others if the forum record errs on the side of including too much information. SeaDAS is "research" quality code, so can have some rough edges ("pioneering work is crude").

1. are you able to run the benchmark script and generate good level-3 files?

Once you have a good A2006167181000.L3b_space.hdf file, you can try the simplest possible listfile:

 
$ echo A2006167181000.L3b_space.hdf > listfile
$ l3bin in=listfile out=outfile
L3BIN 3.41 (Jan  2 2013 14:43:46)
1 input files
0 A2006167181000.L3b_space.hdf
chlor_a
irow:     0 of     8640 Fri Feb 15 14:16:46 2013
[...]
irow:  8500 of     8640 Fri Feb 15 14:16:47 2013
$ ls -l outfile*
-rw-r--r-- 1 gwhite bod 2603868 Feb 15 14:21 outfile.main
-rw-r--r-- 1 gwhite bod  961952 Feb 15 14:21 outfile.x00
$ ncdump_hdf -h outfile.main
netcdf outfile {

variables:

// global attributes:
                :Product Name = "outfile" ;
                :Title = "HMODISA Level-3 Binned Data" ;
                :Sensor Name = "HMODISA" ;
                :Mission = "" ;
                :Mission Characteristics = "" ;
                :Sensor = "" ;
                :Sensor Characteristics = "" ;
                :Product Type = "other" ;
                :Processing Version = "Unspecified" ;
                :Software Name = "L3BIN" ;
                :Software Version = "3.41" ;
                :Orbit = 21910 ;
                :Start Orbit = 21910 ;
                :End Orbit = 21910 ;
                :Processing Time = "2013046182123000" ;
                :Processing Control = "l3bin in=listfile verbose=0 out=outfile" ;
                :Input Parameters = "INFILE = listfile|OFILE = outfile|PFILE = outfile|SYEAR = 9999|EYEAR = 9999|SDAY = 999|EDAY = 999|SORBIT = -1|EORBIT = -1|OUT_PARM = DEFAULT|TFLAG = O|PROCESSING VERSION = Unspecified|REDUCE_FAC = 1|MERGED = |LONEAST = 180.000000|LONWEST = -180.000000|LATNORTH = 90.000000|LATSOUTH = -90.000000|VERBOSE = 0|UNIT_WGT = 0|MEDIAN = 0|" ;
                :Input Files = "A2006167181000.L3b_space.hdf" ;
                :L2 Flag Names = "ATMFAIL,LAND,HILT,HISATZEN,STRAYLIGHT,CLDICE,COCCOLITH,LOWLW,CHLWARN,CHLFAIL,NAVWARN,MAXAERITER,ATMWARN,HISOLZEN,NAVFAIL,FILTER,HIGLINT" ;
                :Period Start Year = 0s ;
                :Period Start Day = 0s ;
                :Period End Year = 9999s ;
                :Period End Day = 999s ;
                :Start Time = "2006167181007870" ;
                :End Time = "2006167181504770" ;
                :Start Year = 2006s ;
                :Start Day = 167s ;
                :Start Millisec = 65407870 ;
                :End Year = 2006s ;
                :End Day = 167s ;
                :End Millisec = 65704770 ;
                :Latitude Units = "degrees North" ;
                :Longitude Units = "degrees East" ;
                :Northernmost Latitude = 50.052082f ;
                :Southernmost Latitude = 30.03125f ;
                :Easternmost Longitude = -64.76754f ;
                :Westernmost Longitude = -83.267113f ;
                :Data Bins = 120180 ;
                :Percent Data Bins = 0.12644289f ;
                :Units = "chlor_a:mg m^-3" ;
                :Bin Resolution = "2 km" ;
}

2. exactly what commands did you enter leading up to the error? Your image indicates the error came from the HDF5 library, which should not be needed for level-3 binning as the images are HDF4 format, so there is probably some problem with your command line or in the format of the listfile. I recall seeing something similar for a too large "listfile", due to some fixed buffer allocation in the l3bin program. As you can guess from the above listing, the contents of the listfile gets added to the header of the output file, so it is helpful to people who use the files if the avoids long complicated paths like "/net/our_really_big_server.domain.organization.org/our_really_big_mass_storage_facility/data_from-NASA_Ocean_Biology.../Year_2013/January/Day_001/....".

By egido Date 2013-03-04 18:56

Hi WhiteG:
Thank for your answer, the commands I did enter that lead to the error was the follow:

seadas@seadas-vm:/disk01/seadas/seadas$ l3bin in="./listadisc01.txt", out="/disk01/seadas/Desktop/M20061702006174.L3b_GAC", out_parm="chlor_a", noext=1, latsouth=27.28, latnorth=28.12, lonwest=-111.60, loneast=-110.68

If I enter /home/ directory as it appears in the left side of the image, the system indicates me that Home directory does not exist.

best regards

Janitzio

By gnwiii Date 2013-03-04 19:30

You used the IDL format with commas separating entries for a bash command line. The error message in your image refers to "/disk01/seadas/Desktop/M20061702006174.L3b_GAC," where the comma now appears after the "C" in "GAC" du to the way the bash shell handles quotes. The command cd home fails because the leading "/" was omitted. You may find it helpful to look a some linux command-line tutorials to become more familiar with bash.

Topic SeaDAS / SeaDAS 6.x Virtual Appliance for Windows / L3binning program does not work (locked)