[netCDFJava #YCN-767203]: Using native NetCDF 4 library with assertions enabled

ok, can you give me a small test program that reproduces the problem?

John

> FYI I also tried updating to Java HDF version 2.11 to and got a similar error 
> from my test program, though more informative:
> 
> > Writing version netcdf3
> > Jan 22, 2015 12:27:49 PM ncsa.hdf.hdf5lib.H5 loadH5Lib
> > INFO: HDF5 library: jhdf5
> > Jan 22, 2015 12:27:49 PM ncsa.hdf.hdf5lib.H5 loadH5Lib
> > INFO:  successfully loaded from java.library.path
> > Found HDF 5 version = false
> > file.exists() = true
> > file.length() = 65612
> > file.delete() = true
> > Writing version netcdf4
> >  Netcdf nc_inq_libvers='4.3.2 of Oct 20 2014 09:49:08 $' isProtected=false
> >  Exception in thread "main" java.io.IOException: -101: NetCDF: HDF error
> >     at ucar.nc2.jni.netcdf.Nc4Iosp.create(Nc4Iosp.java:2253)
> >     at ucar.nc2.NetcdfFileWriter.create(NetcdfFileWriter.java:794)
> >     at NetCDFTest.main(NetCDFTest.java:39)
> 
> 
> Peter
> --
> Peter Hollemans <address@hidden>, Terrenus Earth Sciences
> Web: http://www.terrenus.ca  Phone: +1 (778) 533-2896
> 
> > On Jan 22, 2015, at 11:35 AM, Peter Hollemans <address@hidden> wrote:
> >
> > I'm using the latest version available here:
> >
> > ftp://ftp.unidata.ucar.edu/pub/netcdf-java/v4.5/toolsUI-4.5.jar
> >
> > Peter
> > --
> > Peter Hollemans <address@hidden>, Terrenus Earth Sciences
> > Web: http://www.terrenus.ca  Phone: +1 (778) 533-2896
> >
> >> On Jan 22, 2015, at 9:33 AM, Unidata netCDF Java Support <address@hidden> 
> >> wrote:
> >>
> >> Hi Peter: what version netcdf-java? if no using latest 4.5, can you try 
> >> with that and report? thanks
> >>
> >>> Hi John,
> >>>
> >>> I've tracked the problem down a little further, and found the the string 
> >>> "not a valid cdfid" comes from the HDF JNI library and the error is _not_ 
> >>> related to assertions:
> >>>
> >>>> Beanlet-Pro:test_case_1 phollema$ strings libjhdf.jnilib | grep "not a 
> >>>> valid cdfid"
> >>>> %d is not a valid cdfid
> >>>>
> >>>
> >>> which is from my Mac, or similarly in Linux:
> >>>
> >>>> Beanlet-Pro:test_case_1 phollema$ strings libjhdf.so | grep "not a valid 
> >>>> cdfid"
> >>>> %d is not a valid cdfid
> >>>>
> >>>
> >>> I've been able to reduce the code to just the essentials needed to 
> >>> recreate the error on Mac, but on Linux I've not been able to reproduce 
> >>> using the same code.  Essentially, I do these steps in the attached code:
> >>>
> >>> Step 1) Use the Java NetCDF library to create and write a NetCDF 3 file
> >>> Step 2) Use the Java HDF object interface to check if the file created is 
> >>> HDF 5
> >>> Step 3) Use the Java NetCDF library to create and write a NetCDF 4 file
> >>> Step 4) Use the Java HDF object interface to check if the file created is 
> >>> HDF 5
> >>>
> >>> When I run on Mac, Step 3 never completes and my program exits with 
> >>> "netcdf: 65536 is not a valid cdfid" just when I perform the create() 
> >>> call.
> >>>
> >>> Peter
> >>> --
> >>> Peter Hollemans <address@hidden>, Terrenus Earth Sciences
> >>> Web: http://www.terrenus.ca  Phone: +1 (778) 533-2896
> >>>
> >>>> On Jan 9, 2015, at 12:39 PM, Unidata netCDF Java Support 
> >>>> <address@hidden> wrote:
> >>>>
> >>>> hi peter:
> >>>>
> >>>> can you try it with 4.5.4 version of java-netcdf?
> >>>> if still persists, send me the file so i can try to reproduce.
> >>>> thanks
> >>>> John
> >>>>
> >>>>> Full Name: Peter Hollemans
> >>>>> Email Address: address@hidden
> >>>>> Organization: NOAA
> >>>>> Package Version: 4.5.3
> >>>>> Operating System: Mac OS X 10.10.1
> >>>>> Hardware: MacBook Pro 13" 2011
> >>>>> Description of problem: Hello!
> >>>>>
> >>>>> I have an interesting problem which I think I've tracked down to
> >>>>> assertions.  If I run my Java code with assertions enabled just for my
> >>>>> package (-ea:noaa.coastwatch...), I seem to have assertions enabled for
> >>>>> the NetCDF 4 library that's JNA mapped via Nc4Iosp as well.  If I turn 
> >>>>> off
> >>>>> assertions (ie: I just run as normal), then my code runs to completion
> >>>>> (no errors thrown, but no assertions checked either).  The message I'm
> >>>>> getting with assertions enabled looks like this (running from ant):
> >>>>>
> >>>>> [java]
> >>>>> [java] ***** class noaa.coastwatch.io.CFNCWriter *****
> >>>>> [java] Testing writing of NetCDF version 3 format ... OK
> >>>>> [java] Testing writing of NetCDF version 4 format ...  Netcdf 
> >>>>> nc_inq_libvers='4.3.2 of Oct 20 2014 09:49:08 $' isProtected=false
> >>>>> [java] netcdf: 65536 is not a valid cdfid
> >>>>> [java]
> >>>>> [java] Java Result: 3
> >>>>>
> >>>>> I can see the nc_inq_libvers message is coming from the Nc4Iosp class
> >>>>> after it runs the Native.loadLibrary() call, but I can't see anywhere in
> >>>>> the Java code that the "not a valid cdfid" is coming from, so I assume
> >>>>> it must be from the NetCDF 4 native layer.
> >>>>>
> >>>>> Any ideas on how to fix this aside from going into the NetCDF 4 source
> >>>>> and trying to determine why the assertion (if that's what it is) is
> >>>>> being tripped?  I thought, maybe there's a way to tell the loadLibrary
> >>>>> call to not propagate the JVM assertion mode into the native layer,
> >>>>> but couldn't find any documentation on if that's possible.
> >>>>>
> >>>>> Peter
> >>>>>
> >>>>>
> >>>>
> >>>>
> >>>> Ticket Details
> >>>> ===================
> >>>> Ticket ID: YCN-767203
> >>>> Department: Support netCDF Java
> >>>> Priority: Normal
> >>>> Status: Open
> >>>>
> >>>
> >>>
> >>>
> >>>
> >>>
> >>>
> >>
> >>
> >> Ticket Details
> >> ===================
> >> Ticket ID: YCN-767203
> >> Department: Support netCDF Java
> >> Priority: Normal
> >> Status: Open
> >>
> >
> 
> 


Ticket Details
===================
Ticket ID: YCN-767203
Department: Support netCDF Java
Priority: High
Status: Open