Earthdata Forum

Hi

I'm using Seadas 7.5.3 on a mac and I'm trying to load six .nc files into the lb3 processor and for some reason, I'm getting a list of 3 errors.
I just starting using this software so any help is more than welcome

thank you

this is the list of files on the .txt file I'm trying to load:

A20163362016366.L3b_MO_KD490.nc
A20170012017031.L3b_MO_KD490.nc
A20170322017059.L3b_MO_KD490.nc
A20173352017365.L3b_MO_KD490.nc
A20180012018031.L3b_MO_KD490.nc
A20180322018059.L3b_MO_KD490.nc

and here below is the list of errors:

execution exception: java.io.IOException: l3bin failed with exit code 139.
Check log for more details.
L3BIN 5.12 (Dec 19 2018 12:40:40)
6 input files
HDF5-DIAG: Error detected in HDF5 (1.8.19) thread 0:
  #000: /Users/seadas/ocssw/opt/src/hdf5/hdf5-1.8.19/src/H5F.c line 437 in H5Fis_hdf5(): unable open file
    major: File accessibilty
    minor: Not an HDF5 file
  #001: /Users/seadas/ocssw/opt/src/hdf5/hdf5-1.8.19/src/H5Fint.c line 552 in H5F_is_hdf5(): unable to open file
    major: Low-level I/O
    minor: Unable to initialize object
  #002: /Users/seadas/ocssw/opt/src/hdf5/hdf5-1.8.19/src/H5FD.c line 991 in H5FD_open(): open failed
0 A20163362016366.L3b_MO_KD490.nc
    minor: Unable to initialize object
  #003: /Users/seadas/ocssw/opt/src/hdf5/hdf5-1.8.19/src/H5FDsec2.c line 337 in H5FD_sec2_open(): unable to open file: name = 'A20163362016366.L3b_MO_KD490.nc
', errno = 2, error message = 'No such file or directory', flags = 0, o_flags = 0
    major: File accessibilty
    minor: Unable to open file
/Applications/seadas-7.5.3/ocssw/scripts/ocssw_runner: line 23: 10545 Segmentation fault: 11  $*

Try using the full path of each file in the list.   Directories that have spaces or non-ASCII characters may cause problems.   Sometimes downloads produce some
html page to tell you about some problem or give you a corrupt file (I always request the shasums for bulk downloads, and is not unusual to encounter corrupt downloads).  You can use the "file" command to check the type of the files and "ncdump -h" on each file to make sure they are valid netcdf files,
but the shasums are your best way to verify that downloads are correct.

The error message indicates that it cannot find the first file in your list (and probably wouldn't find the rest as well).  If you are running from the command line then you either need the text file to contain the full directory path to each file or you need to run l3bin from within the directory which contains your input files.  If you are running from the GUI then you either need the text file to contain the full directory path to each file or the text file needs to be in the same directory as the input files because the GUI will run l3bin from within the directory which contains your input file (which in this case is your text file).

Danny

Hello, I have been learning SeaDas, and ran into the same error. I am running SeaDas in Linux, but I believe the solution is the same.

The issue is the text file with the list of filenames, more specifically it is how new lines are defined in the text file.

For SeaDas to read the text file properly, I found that the new lines must be in unix/linux format. Different operating systems have different (and hidden) ways of defining new lines. In Windows, new lines are defined with "Carriage Return Line Feed (CRLF)", in mac, "Carriage Return (CR)" is used. While for unix/linux, "Line Feed (LF)" is used.

Most likely in your text file, the new line character is not in "Line Feed (LF)" format. I suggest to download an advanced text file editor which has the option to show and edit the new line characters (they are usually hidden). For example, the text editor Notepad++ has an option to show all hidden characters and also has the option to change the new line character to the desired format as shown in this image:


https://1.bp.blogspot.com/-YHR0CADERwk/V0c2VX6XshI/AAAAAAAABbg/mVGeKmQnIlIla2CVYzk1oRbDnR6TwHP3gCLcB/s1600/notepad%252B%252B-linux-end-of-file.jpg

I found that by converting the new line character to the unix/linux format, SeaDas was able to read my text file.