problem with netcdf syncing

[momme]

With the code as it is from the repository I end up with corrupted netcdf files that clearly had some data written to them (size >1GB), but are inaccessable (header intact, but no data). The problem is avoided by uncommenting the call to NF90_SYNC in histcom.F90 line 2181.
Platform: Fedora Linux 64-bit, sinlge process
Compiler: ifort
Netcdf: 3.6.3
Configuration: ORCA 2dgr, 1D and 3D global

[smasson]

I don't really understand. Do you mean that the time dimension has a size of 0?

Have a look to ​http://www.unidata.ucar.edu/software/netcdf/docs/netcdf-f90/NF90_005fSYNC.html :

The function NF90_SYNC offers a way to synchronize the disk copy of a netCDF dataset with in-memory buffers. There are two reasons you might want to synchronize after writes:

 - To minimize data loss in case of abnormal termination, or
 - To make data available to other processes for reading immediately after it is written. But note that a process that already had the dataset open for reading would not see the number of records increase when the writing process calls NF90_SYNC; to accomplish this, the reading process must call NF90_SYNC.

i think you are in the first case...

Data is automatically synchronized to disk when a netCDF dataset is closed, or whenever you leave define mode.

=> I think the model stopped before the end of the run and didn't get through the call to NF90_CLOSE.

So I think calling NF90_SYNC is not really solving your problem.

[smasson]

There is some additional information from ​NetCDF FAQ web page.
Unfortunately, it appears that the archived support message has been lost, but Russ Rew from netCDF support sent me the information:

You can use an editor which allows you to change binary files, such as emacs (use for example the ​hexl mode), to correct the 'number of records' in the file. This is a bigendian 4 byte integer which begins at the 4th byte in the file.

This is what the first eight bytes would look like in emacs if you had zero records:

CDF^A^@^@^@^@

and this is what it would like if you had 6 records (^F is ascii 6)

CDF^A^@^@^@^F

See ​Appendix B of the netcdf user's guide for more info.

[anaguiar]

In 9231:

Error: Failed to load processor CommitTicketReference

No macro or processor named 'CommitTicketReference' found

[anaguiar]

In 9233:

Error: Failed to load processor CommitTicketReference

No macro or processor named 'CommitTicketReference' found

[anaguiar]

In 9287:

Error: Failed to load processor CommitTicketReference

No macro or processor named 'CommitTicketReference' found