Opened 5 years ago

Closed 5 years ago

#100 closed defect (wontfix)

XIOS crash with "NetCDF: HDF error"

Reported by: Ehouarn Millour Owned by: Laurent Fairhead
Priority: major Milestone:
Component: I/O Keywords: XIOS
Cc:

Description

With XIOS the model crashes on Ada with XIOS (but not without), with the following error message: 

terminate called after throwing an instance of 'xios::CNetCdfException'
  what():  Error when calling function nc_enddef(ncId)
NetCDF: HDF error
Unable to end define mode of this file, given its id: 65536
forrtl: error (76): Abort trap signal
Image              PC                Routine            Line        Source             
libifcoremt.so.5   00002ADA7C66B3EF  for__signal_handl     Unknown  Unknown
libpthread-2.12.s  00002ADA7A7F27E0  Unknown               Unknown  Unknown
libc-2.12.so       00002ADA7EEED495  gsignal               Unknown  Unknown
libc-2.12.so       00002ADA7EEEEC75  abort                 Unknown  Unknown
libstdc++.so.6.0.  00002ADA7AA90BCD  _ZN9__gnu_cxx27__     Unknown  Unknown
libstdc++.so.6.0.  00002ADA7AA8EB86  Unknown               Unknown  Unknown
libstdc++.so.6.0.  00002ADA7AA8EBD1  Unknown               Unknown  Unknown
libstdc++.so.6.0.  00002ADA7AA8EDE8  Unknown               Unknown  Unknown
...
gcm_48x36x19_phyl  0000000000D33951  iophy_mp_histwrit         974  iophy.f90
gcm_48x36x19_phyl  0000000002EE3365  phys_output_write         458  phys_output_write_mod.f90
gcm_48x36x19_phyl  00000000018A0037  physiq_mod_mp_phy        4581  physiq_mod.f90
gcm_48x36x19_phyl  00000000013D9905  callphysiq_mod_mp          70  callphysiq_mod.f90
gcm_48x36x19_phyl  0000000001397F34  calfis_loc_               718  calfis_loc.f
gcm_48x36x19_phyl  00000000009B2B81  call_calfis_mod_m         205  call_calfis_mod.f90
gcm_48x36x19_phyl  0000000000596751  leapfrog_loc_             796  leapfrog_loc.f
gcm_48x36x19_phyl  000000000042AC4B  MAIN__                    444  gcm.f90

Problem found on Ada using LMDZ r3543 (but also occurs for other recent revisions) and XIO revision 1659.

Change History (1)

comment:1 Changed 5 years ago by Ehouarn Millour

Resolution: → wontfix
Status: new → closed

After some investigations, it turns out the problem is neither in LMDZ nor XIOS; it is a NetCDF/HDF library issue: if too many variables are put in a single file then this error occurs. Hopefully this will someday be fixed in a future release of the HDF library. For now the only workaround is to not output too many variables in a single file (e.g. by using a high enough "ouput_level").

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