Maria,

thank you for your report and confirming the fix.

Kind regards,
Ben.

On 06/03/18 22:51, Maria Krommyda wrote:
Dear Ben,
My apologies for omitting the list from the recipients.
I had included the netcdf-out plugin but I had not included the jna jar.How I 
did this twice, I have still to figure out.
I added the jar and the warning is gone.
Thank you for your time, my apologies for taking so much of your time for 
something that was only an overlook from my side.
Best regards,Maria.

     Στις 11:54 μ.μ. Σάββατο, 3 Μαρτίου 2018, ο/η Ben Caradoc-Davies 
<b...@transient.nz> έγραψε:
  Maria, replies on-list please so everyone can benefit and assist.

Did you install the netcdf-out plugin? Is the next line after the
"Nc4Iosp: NetCDF-4" warning "java.lang.NoClassDefFoundError:
com/sun/jna/Library"?

The netcdf-out plugin provides the jna jar, required to load the native
libraries. Without this plugin, the plain netcdf plugin will work fine,
but the Unidata netcdf4 jar it includes will still try and fail to load
the native libraries, producing the "Nc4Iosp: NetCDF-4" warning you see
followed by "java.lang.NoClassDefFoundError: com/sun/jna/Library". Once
you install the netcdf-out plugin, together with the libnetdcf11 library
you have already installed, everything should just work with no
"Nc4Iosp: NetCDF-4" warning. I have tested this on Ubuntu 16.04.4.

"Stock" just means standard, with no extra packages like an OSGeoLive or
other rebuilt iso image. It looks like you are using standard packages.

The locate results are as expected. The shorter filename will be a
symbolic link to the longer. This is normal.

Kind regards,
Ben.

On 04/03/18 01:15, Maria Krommyda wrote:
Hello Ben,
The locate command returns:/usr/lib/x86_64-linux-gnu/libnetcdf.so.11
/usr/lib/x86_64-linux-gnu/libnetcdf.so.11.0.0
Is this the expected or should I have gotten only one package?
I am attaching the output of the ldd command. To my understanding it shows that 
all dependencies are resolved. [I get the same for both packages so.11 and 
so.11.0.0]

There is nothing to the system logs about the Java process and nothing added 
when I restarted the GeoServer and got the warning.

My Java version is
openjdk version "1.8.0_151"
OpenJDK Runtime Environment (build 1.8.0_151-8u151-b12-0ubuntu0.16.04.2-b12)
OpenJDK 64-Bit Server VM (build 25.151-b12, mixed mode)

I am not sure what stock means, I apologize for that, but I have downloaded a 
mini.iso from the Ubuntu download page and use that for the installation.

Best regards,
Maria.

       Στις 12:37 π.μ. Σάββατο, 3 Μαρτίου 2018, ο/η Ben Caradoc-Davies 
<b...@transient.nz> έγραψε:
   Maria,

yes, it would be good to discover the cause, when you have time.

I suggest using "locate" to see if there are any other libnetcdf.so on
the system:
sudo updatedb
sudo locate libnetcdf.so

Another thing that might prevent libnetcdf.so from being loaded is a
library dependency that has a duplicate, such as a locally installed
libhdf5 or libz. Check that ldd can resolve all its dependencies:
ldd /usr/lib/x86_64-linux-gnu/libnetcdf.so.11.0.0

Either of these problems would be unexpected on a fresh VM. Are you
using stock Ubuntu 16.04.4 LTS? What openjdk-8 package and version?

Anything in the system logs ("sudo journalctl") for apparmor related to
your java process?

Kind regards,
Ben.

On 03/03/18 01:02, Maria Krommyda wrote:
Dear Ben,
Thank you once more for you time and response.
I verified that they are both amd64.( 
/usr/lib/x86_64-linux-gnu/libnetcdf.so.11.0.0 and OpenJDK 64-bit Server VM)
You are right that I only need to read the NetCDF-4 and not write it, so I 
don't need to solve this warning.
I would like to find the solution though, as i have the feeling that it is 
something very simple/trivial that I simply cannot think of.
I will dedicate some time to that as soon as I have some availability and I 
will let you know if I manage to solve it.
Thank you once more for you time and help.
Best regards,Maria.

         Στις 8:28 μ.μ. Πέμπτη, 1 Μαρτίου 2018, ο/η Ben Caradoc-Davies 
<b...@transient.nz> έγραψε:
     Maria,

all dependencies should be installed automatically by the package
management system.

Are your libnetcdf11 and JVM the same same architecture? For example,
both amd64, and not one amd64 and another i386?

I re-read your original question and note that the native NetCDF-4
library is only required to *write* NetCDF-4. The pure Java
implementation included with GeoServer can read NetCDF-4. If you only
want GeoServer to read NetCDF-4, you can safely ignore the WARN message.

Kind regards,
Ben.


On 01/03/18 20:45, Maria Krommyda wrote:
Dear Ben,
Thank you for your response.Unfortunately this did not solve my problem.
I even tried a clean built, on a fresh VM, with only GeoSerever 2.12.2, 
NetCDF-4 and the library installation as you suggested, fearing that my 
multiple attempts to install the library in the previous VM had resulted in 
some conflicts, but I still get the same error.
Is it possible that I am missing an additional package?
Best regards, Maria.

           Στις 10:48 μ.μ. Τετάρτη, 28 Φεβρουαρίου 2018, ο/η Ben Caradoc-Davies 
<b...@transient.nz> έγραψε:
       Maria,

the easiest way to install the NetCDF-4 native libraries on Ubuntu 16.04
is to install the binary package provided by your distribution with:

sudo update
sudo apt-get install libnetcdf11

Restart Jetty and everything should just work.

The GeoServer documentation should suggest using distribution packages
where available, rather than building from source.

Kind regards,
Ben.

On 01/03/18 01:56, Maria Krommyda via Geoserver-users wrote:
Hello everyone,
Let me start be giving you the current status of my installation progress. I have 
installed on a Ubuntu 16.04 machine with openjdk version 1.8.0_151 the Geoserver 
2.12.2 using the Jetty server.I have successfully installed the WPS, importer and 
geomesa-accumulo extentions.I am currently trying to install the NetCDF extention.I 
have downloaded the correct jar for the GeoServer version, added them to the lib 
folder in the geoserver_path/webapps/geoserver/WEB-INF and I can see the NetCDF 
option under Create new data source->Raster data source-> NetCDF.
I have also tried, but apparently failed, to install the NetCDF-4 native 
libraries as I need to import NetCDF-4 data files. I have followed the 
instruction 
http://docs.geoserver.org/stable/en/user/extensions/netcdf-out/nc4.html but 
upon starting the GeoServer I get the error:
WARN [serverStartup] - Nc4Iosp: NetCDF-4 C library not present 
(jna_path='/usr/local/lib/', libname='netcdf').
Please note that the jna_path is not null, as it is implied in the installation 
instructions, in the error that I get, however it is not set by me and running echo 
$jna_path from the same terminal, before and after starting the GeoServer returns the 
expected null.I think that the error might come from step 5 in the installation 
instructions where it say "Make sure to add the lib folder of the package you have 
extracted, to the PATH environment variable."I am not sure to which extracted 
package is referred, given that none of the zlib, hdf5 and NetCDF-4 downloads include a 
lib folder. What I did instead was add the lib folder of my installation directory, based 
on the example /work/libs/nc4libs/lib, to the PATH environment.I have also tried to 
install the NetCDF-4 library at the /usr/local/lib/ path but that didn't change the 
behavior.
Any help and ideas of what might cause such error are highly appreciated. If 
you need any additional information please let me.
Thank you very much for you time, Maria.



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Ben Caradoc-Davies <b...@transient.nz>
Director
Transient Software Limited <https://transient.nz/>
New Zealand

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Please make sure you read the following two resources before posting to this 
list:
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If you want to request a feature or an improvement, also see this: 
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