output files are not netcdf4 as expected

[rkandilarov]

Hello guys!

I'm using Revision: 3321 (nemo_v3_4) and it seems that:

• In contrast to the documentation I can link NEMO to !NetCdf4 libs and produce netcdf classic files without using key_netcdf4
• When I link to !NetCdf4 (4.1.3 or 4.2) and define key_netcdf4 when running opa I get only the restart file as hdf(nc4) type but the U,V,T and W files are still nc3 (classic).

Another problem (wich is probably for separated ticket):

• while running NEMO it doesn't "flush" the written record so unless it finishes and save the file properly the first several bytes of the nc files give number of record to 0 as described here: ​http://www.unidata.ucar.edu/software/netcdf/docs/faq.html#recover

Here is my test configuration:

makenemo -r GYRE -n TEST2_nc4.2_hdf5 -m ifort_nc4.2_debug -j 6 add_key "key_netcdf4"

and my ifort_nc4.2_debug file:

%SZIP /usr/opt/szip/intel/12.1.1.256/2.1       

%ZLIB /usr/opt/zlib/intel/12.1.1.256/1.2.6
%HDF5 /usr/opt/hdf5/intel/12.1.1.256/1.8.8_sz2.1_z1.2.6       %NETCDF_C /usr/opt/netcdf/intel/12.1.1.256/4.2_hdf5-1.8.8_sz2.1_z1.2.6 
%NETCDF_F /usr/opt/netcdf-fortran/intel/12.1.1.256/4.2_netcdf-4.2_hdf5-1.8.8_sz2.1_z1.2.6                                             
%NCDF_INC            -I%SZIP/include -I%ZLIB/include -I%HDF5/include -I%NETCDF_C/include -I%NETCDF_F/include
        
%NCDF_LIB            -L%NETCDF_C/lib -L%NETCDF_F/lib -L%HDF5/lib -L%ZLIB/lib -L%SZIP/lib  -Wl,--start-group -lnetcdff -lnetcdf -lhdf5 -lhdf5_fortran -lhdf5_hl -lz -lsz -Wl,--end-group                                       
%FC                  ifort                                       
%FCFLAGS             -r8 -g -traceback                           
%FFLAGS              %FCFLAGS                                    
%LD                  ifort                                       
%FPPFLAGS            -P -C -traditional                          
%LDFLAGS             -static                                       
%AR                  ar                                          
%ARFLAGS             -r                                          
%MK                  make                                        
%USER_INC            %NCDF_INC
%USER_LIB            %NCDF_LIB 

[rkandilarov]

Some more information.

When removing the key_iomput (which selcelts probably the old iom library) I got netcdf4 files as expected.

I also found that in this ticket ​http://forge.ipsl.jussieu.fr/nemo/ticket/372 there is a solution for the feature that I was using in the previous versions and missing in v3_4:  my "flush" is the call of nf90_sync after each write, will try to add it by myslef.

[acc]

Yes there is an error here. Some changes have gone missing from NEMOGCM/EXTERNAL/XMLIO_SERVER/src/IOSERVER/mod_interface_ioipsl.f90
(probably during last year's merge?). The omission means users of key_iomput will get netcdf-3 mean files with or without key_netcdf4 .Reinstatement on the trunk can be discussed at the next system team meeting on Wednesday.
Meanwhile anyone starting a new run can just change the 4 lines indicated here to get netcdf4 working again
with key_iomput:

Index: mod_interface_ioipsl.f90
===================================================================
--- mod_interface_ioipsl.f90    (revision 3334)
+++ mod_interface_ioipsl.f90    (working copy)
@@ -37,6 +37,7 @@
   SUBROUTINE Create_file_definition(nb_server,server_rank)
   USE ioipsl
   USE xmlio
+  USE mod_ioserver_namelist
   IMPLICIT NONE
     INTEGER,INTENT(IN)  :: nb_server
     INTEGER,INTENT(IN)  :: server_rank
@@ -87,14 +88,14 @@
             CALL histbeg(TRIM(full_name),pt_domain%ni,pt_domain%lon, pt_domain%nj, pt_domain%lat, & 
                        pt_zoom%ibegin_loc, pt_zoom%ni_loc,pt_zoom%jbegin_loc,pt_zoom%nj_loc,         &
                        initial_timestep, initial_date, timestep_value,                               &
-                       ioipsl_hori_id, ioipsl_file_id)
+                       ioipsl_hori_id, ioipsl_file_id, snc4chunks=snc4ioset)
            ELSE                                              
 
             CALL set_ioipsl_domain_id(pt_grid,nb_server,server_rank,ioipsl_domain_id)
             CALL histbeg(TRIM(full_name),pt_domain%ni,pt_domain%lon, pt_domain%nj, pt_domain%lat,  &
                        pt_zoom%ibegin_loc, pt_zoom%ni_loc,pt_zoom%jbegin_loc,pt_zoom%nj_loc,          &
                        initial_timestep, initial_date, timestep_value,                                &
-                       ioipsl_hori_id, ioipsl_file_id,domain_id=ioipsl_domain_id)                                              
+                       ioipsl_hori_id, ioipsl_file_id,domain_id=ioipsl_domain_id, snc4chunks=snc4ioset)                                              
           
            ENDIF
         
@@ -141,7 +142,7 @@
                          & real(pt_file%output_freq) )
             ENDIF
           ENDDO
-          CALL histend(ioipsl_file_id)
+          CALL histend(ioipsl_file_id, snc4chunks=snc4ioset)
         ENDIF
         CALL sorted_list__delete(axis_id)
       ENDIF

[rkandilarov]

Great!

It worked for me:).

[acc]

Fix now committed to the trunk. Please be aware the default behaviour for the reference configurations will be changed when compiled with key_netcdf4. Prior to this fix the
v3.4 reference configurations (which use key_iomput) will have been producing netCDF-3 format mean files even when key_netcdf4 was active.
These changes reactivate the functionality first introduced in v3.3 and allow netCDF-4 mean files to be produced on request.

Fix committed at revision 3345