Error: No data product writer for the 'HDF5' format available in gpt.sh (v7.5)

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zhigang
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Error: No data product writer for the 'HDF5' format available in gpt.sh (v7.5)

by zhigang » Wed May 30, 2018 3:45 am America/New_York

Greetings,

I would like to export the L2_LAC_OC file to HDF5 file via gpt.sh (v7.5) in command line, but it didn't work. The error is :

[optics@localhost tmp]$ /home/optics/seadas-7.5/bin/gpt.sh /home/optics/tmp/A2017243214000_gpt.xml -t /mnt/da81fa5a-016e-4718-a7ed-b89f4cd59da5/saltonsea/A2017243214000_niglas.h5 -f 'HDF5' /home/optics/tmp/A2017243214000_QKM.L2_LAC_OC
SLF4J: Class path contains multiple SLF4J bindings.
SLF4J: Found binding in [jar:file:/home/optics/seadas-7.5/lib/slf4j-jdk14-1.6.1.jar!/org/slf4j/impl/StaticLoggerBinder.class]
SLF4J: Found binding in [jar:file:/home/optics/seadas-7.5/lib/slf4j-log4j12-1.6.1.jar!/org/slf4j/impl/StaticLoggerBinder.class]
SLF4J: See http://www.slf4j.org/codes.html#multiple_bindings for an explanation.

Error: No data product writer for the 'HDF5' format available


This command works well in the v7.4. According to the previous post, I find the jhdf5.jar and libjhdf5.so in ~/optics/seadas-7.4/modules/lib-hdf-2.7/lib
But the ~/seadas-7.5/modules/lib-hdf-2.7 was a jar file in v7.5, not a directory. In the jar file, jhdf5.jar and libjhdf5.so did be located under lib,
lib/jdf.jar
lib/jhdf5.jar
lib/linux64/libjhdf.so
lib/linux64/libjhdf5.so


However, I can not find these files in my system:
[optics@localhost modules]$ which libjhdf.so
/usr/bin/which: no libjhdf.so in (/home/optics/seadas/lcps:/home/optics/ocssw/run/bin3/linux_64:/home/optics/ocssw/run/scripts:/home/optics/ocssw/run/bin/linux_64:/home/optics/seadas-7.5/bin:/usr/local/bin:/usr/bin:/usr/local/sbin:/usr/sbin:/home/optics/.local/bin:/home/optics/bin)


And, in fact, the exporting as a NetCDF4-CF file works in, only the HDF-5 file can not be exported.
[optics@localhost tmp]$ /home/optics/seadas-7.5/bin/gpt.sh /home/optics/tmp/A2017243214000_gpt.xml -t /mnt/da81fa5a-016e-4718-a7ed-b89f4cd59da5/saltonsea/A2017243214000_niglas.nc -f 'NetCDF4-CF' /home/optics/tmp/A2017243214000_QKM.L2_LAC_OC
SLF4J: Class path contains multiple SLF4J bindings.
SLF4J: Found binding in [jar:file:/home/optics/seadas-7.5/lib/slf4j-jdk14-1.6.1.jar!/org/slf4j/impl/StaticLoggerBinder.class]
SLF4J: Found binding in [jar:file:/home/optics/seadas-7.5/lib/slf4j-log4j12-1.6.1.jar!/org/slf4j/impl/StaticLoggerBinder.class]
SLF4J: See http://www.slf4j.org/codes.html#multiple_bindings for an explanation.
[optics@localhost saltonsea]$ cd /mnt/da81fa5a-016e-4718-a7ed-b89f4cd59da5/saltonsea
[optics@localhost saltonsea]$ ls
A2017243214000_niglas.nc
[optics@localhost saltonsea]$ ls -l
-rw-rw-r--. 1 optics optics 1687760 May  30 15:38 A2017243214000_niglas.nc


I'm not sure if the lost these files caused the problem, or something else? Could someone give me some suggestions?

Regards,
Zhigang

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OB SeaDAS - dshea
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Error: No data product writer for the 'HDF5' format available in gpt.sh (v7.5)

by OB SeaDAS - dshea » Wed May 30, 2018 8:46 am America/New_York

Yes, we have had trouble with the HDF5 libraries not being found.  Which is really strange since NetCDF4 uses the HDF5 libraries to write its file.
We will look into this.  In the interim, you can easily read a NetCDF4 file with an HDF5 program.

don

zhigang
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Error: No data product writer for the 'HDF5' format available in gpt.sh (v7.5)

by zhigang » Wed May 30, 2018 10:34 pm America/New_York

Thanks, Don. So, for now, I have to write a NetCDF4 file.

OB SeaDAS - dshea
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Error: No data product writer for the 'HDF5' format available in gpt.sh (v7.5)

by OB SeaDAS - dshea » Thu May 31, 2018 1:39 pm America/New_York

Yes, until we can resolve the HDF5 lib problem

don

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