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[netCDFJava #LYK-546339]: Problem with netCDF-Java when also using libjhdf5



Some other thoughs:
1. It is possible also that just loading netcdf library is not
   sufficient to get HDF5 library loaded. You might need to do some
   explicit create/close or open/close thru the netcdf-c library to
   cause libhdf5 to be actually loaded.
2. Having two copies of the hdf5 library might also cause problems.
   you might need to modify the javahdf5 code to explicitly
   use the exact same library (not a copy or symbolic link)
   as netcdf library is using


> Another problem may be that netcdf uses JNA, while apparently javaHDF5
> uses JNI directly. But there is no way to fix that.
> 
> > Order of loading: I have tried both orders. At first I thought netCDF first 
> > was the problem, so I forced jarhdf5 to load first. However, in the last 24 
> > hours I've started seeing the problem when jarhdf5 is loaded first as well.
> >
> > HDF5 version: to my knowledge they are both 1.8.19, but this cannot be 
> > determined with certainty. The version used with netCDF is definitely 
> > 1.8.19, but I cannot find any version information for the files that are 
> > part of the jhdf5 package other than that the online documentation claims 
> > that it is 1.8.19.
> >
> > -PT
> >
> > ?On 4/10/19, 11:56 AM, "Unidata netCDF Java Support" <address@hidden> wrote:
> >
> > Unfortunately, we (Unidata) have not seen this issue either.
> > At the Java level, having two different JNI APIs to the same
> > library should probably be ok. However I might speculate
> > about some possible issues:
> > 1. order of loading - do you know if the netcdf-c library is being
> > loaded before or after  jarhdf5-3.3.2.jar?
> > 2. do you know if the HDF5 versions being used are the same?
> >
> > >
> > > My project, the TESS Science Processing Operations Center (SPOC) at NASA 
> > > Ames, is using the netCDF Java API to run our datastore: we use 
> > > netcdf4-4-6.10.jar and netcdfAll-4-6.8.jar . As I understand it, the Java 
> > > API then uses libnetcdf.so, which in turn makes use of libhdf5.so, both 
> > > through JNA. We are using libhdf5.so.10.3.0 and libnetcdf.so.13.0 .
> > >
> > > So far so good, this has worked well for us for a couple of years. 
> > > However:
> > >
> > > Recently we decided that we wanted to also use straight HDF5 in our Java 
> > > code for another purpose (very long story). For this we are using the 
> > > HDF5-Java implementation available from the HDF5 group: 
> > > jarhdf5-3.3.2.jar, which in turn uses libjhdf5.so.3.3.2 . This library is 
> > > accessed via JNI.
> > >
> > > Unfortunately, we observe problems when we use both of these libraries in 
> > > a single executable on linux:
> > >
> > > What we observe is that there appear to be confusion problems when both 
> > > libraries are loaded. So for example, the netCDF library loads and writes 
> > > an array to disk; after that, we are unable to read HDF5 arrays and get 
> > > errors when attempting to read attributes. As far as we can tell the HDF5 
> > > array in question is valid.
> > >
> > > I realize that this may be kind of vague. Iâm writing in hopes that 
> > > somebody at netCDF has heard about this kind of problem before and knows 
> > > what to do! AFAICT the folks at HDF5 are not familiar with this issue.
> > >
> > > Thanks,
> > > -PT
> > >
> >
> > =Dennis Heimbigner
> > Unidata
> >
> >
> > Ticket Details
> > ===================
> > Ticket ID: LYK-546339
> > Department: Support netCDF Java
> > Priority: Normal
> > Status: Open
> > ===================
> > NOTE: All email exchanges with Unidata User Support are recorded in the 
> > Unidata inquiry tracking system and then made publicly available through 
> > the web.  If you do not want to have your interactions made available in 
> > this way, you must let us know in each email you send to us.
> >
> >
> >
> >
> >
> 
> =Dennis Heimbigner
> Unidata
> 

=Dennis Heimbigner
  Unidata


Ticket Details
===================
Ticket ID: LYK-546339
Department: Support netCDF Java
Priority: Normal
Status: Open
===================
NOTE: All email exchanges with Unidata User Support are recorded in the Unidata 
inquiry tracking system and then made publicly available through the web.  If 
you do not want to have your interactions made available in this way, you must 
let us know in each email you send to us.



NOTE: All email exchanges with Unidata User Support are recorded in the Unidata inquiry tracking system and then made publicly available through the web. If you do not want to have your interactions made available in this way, you must let us know in each email you send to us.