netCDF library for NEMO on HECToR

[iwi]

I had a job on HECToR fall down with errors saying:

model.exe: posixio.c:213: px_pgout: Assertion `*posp == ((off_t)(-1)) || *posp == lseek(nciop->fd, 0, 1)' failed.
(...above line repeated a few times, and then...)
_pmii_daemon(SIGCHLD): [NID 01761] PE 4 exit signal Aborted
[NID 01761] 2011-01-24 16:21:06 Apid 329716: initiated application termination

Searching for the error, I found this thread:

​http://www.unidata.ucar.edu/mailing_lists/archives/netcdfgroup/2009/msg00462.html

note followup message from Russ Rew in that thread stating: "You are absolutely right about this, and we have already tested the fix, which will be in the upcoming 4.1 release."

I don't know what netCDF version NEMO on HECToR is currently linked to, but in view of the above, could it be linked to the latest available stable version please?

Many thanks,
Alan

[iwi]

P.S. I see (from the "module" command) that netcdf/4.1.1.0 is available on the system and is the default, although earlier versions are available. When compiling NEMO for my run, I certainly didn't do anything deliberate to select an earlier version, but wouldn't really know whether this is configured somewhere in my own UM job or in the shared NEMO installation. (The executable was compiled in job xerae, although that job is now set to run only rather than compile.)

[ros]

Hi Alan,

NEMO on HECToR is not tied to any particular version of netcdf. It uses the default version.

In your xerae000.xerae.d11016.t191016.comp.leave file near the top of the file you can see a list of the currently loaded modules that are being used. It's using netcdf/4.1.1.0

Currently Loaded Modulefiles:
  1) modules
  2) nodestat/2.2-1.0301.23969.4.3.gem
  3) sdb/1.0-1.0301.23089.4.2.gem

<snip> 
 
 23) xtpe-mc12
 24) hdf5/1.8.5.0
 25) netcdf/4.1.1.0

I see from the link you posted, this error is connected with disk full and that in your other ticket #566 you say you have exceeded your quota. Hopefully once your HECToR quota is resolved, this error will go away too.

Regards,
Ros.

[iwi]

Ros,

Thanks, yes - I was coming to the same conclusion. Please close this ticket for now, and it can be reopened later if the problem recurs for other reasons. It's helpful to know that the netCDF version isn't hard-coded in the NEMO build, thanks.

Alan