Re: [netcdfgroup] netcdf fortran error - HDF5: infinite loop closing library


Roy, thanks for your response. I tried adding the call to nf90_redef after the open, as you suggest, and then re-write the attributes, but I still get the same error.
Alison

On 3/7/2016 9:36 PM, Roy Mendelssohn - NOAA Federal wrote:
Hi Alison:

I am not certain of this,  but nc_create and nc_open behave differently.  nc_create 
creates the file and puts you in define mode, nc_open does not put you in define 
mode.  I donât know what is magic about 30 attributes, perhaps that is what it 
takes to exceed the global attributes space because the history changes, but I 
wonder what happens if after the nc_open you call NF90_REDEF and then rewrite the 
global attributes.

As I said, I could be wrong, but it would be easy enough to test.

-Roy




On Mar 7, 2016, at 7:01 PM, Alison Walker <postings@xxxxxxxxxxxxxxxxxxxxxx> 
wrote:

Hi netcdf folks,
I'm getting this error when changing the values of global attributes in a 
netcdf4 file using the fortran interface:

HDF5: infinite loop closing library
D,G,A,S,T,F,FD,P,FD,P,FD,P,E,E,SL,FL,FL,FL,FL,FL,FL,FL,FL,FL,FL,FL,FL,FL,FL,FL,FL,FL,FL,FL,FL,FL,FL,FL,FL,FL,FL,FL,FL,FL,FL,FL,FL,FL,FL,FL,FL,FL,FL,FL,FL,FL,FL,FL,FL,FL,FL,FL,FL,FL,FL,FL,FL,FL,FL,FL,FL,FL,FL,FL,FL,FL,FL,FL,FL,FL,FL,FL,FL,FL,FL,FL,FL,FL,FL,FL,FL,FL,FL,FL,FL,FL,FL,FL,FL,FL,FL,FL,FL,FL,FL,FL,FL,FL

Here is a little test program that illustrates the problem. It first creates a 
netcdf file and writes some global attributes, then tries to write them again 
after closing and re-opening the file. Interestingly, if the number of 
attributes is less than 30, there is no error. If the number is 30, the error 
occurs. I'm using netcdf 4.3.0, netcdf fortran 4.2 and hdf5 1.8.16 on Linux 
x86_64.

program tester

  use netcdf
  implicit none

  integer, parameter :: n_attrs = 30

  integer :: iok, ncid, varid, i
  character*10 :: myattr

  ! Create the file and write global attrs

  iok = nf90_create('tester.nc',NF90_HDF5,ncid)
  print *,'create iok=',iok
  do i=1,n_attrs
     write(unit=myattr,fmt='(a6,i4.4)') 'myattr',i
     iok = nf90_put_att(ncid,NF90_GLOBAL,myattr,i)
     print *,i,' put iok=',iok
  enddo
  iok = nf90_close(ncid)
  print *,'close iok=',iok

  ! Open the file again and re-write global attrs

  iok = nf90_open('tester.nc',NF90_WRITE,ncid)
  print *,'open iok=',iok
  do i=1,n_attrs
     write(unit=myattr,fmt='(a6,i4.4)') 'myattr',i
     iok = nf90_put_att(ncid,NF90_GLOBAL,myattr,i)
     print *,i,' put iok=',iok
  enddo
  iok = nf90_close(ncid)
  print *,'close iok=',iok

end program tester

When I run this test program with 30 attributes I get this error result:

create iok=           0
           1  put iok=           0
           2  put iok=           0
           3  put iok=           0
           4  put iok=           0
           5  put iok=           0
           6  put iok=           0
           7  put iok=           0
           8  put iok=           0
           9  put iok=           0
          10  put iok=           0
          11  put iok=           0
          12  put iok=           0
          13  put iok=           0
          14  put iok=           0
          15  put iok=           0
          16  put iok=           0
          17  put iok=           0
          18  put iok=           0
          19  put iok=           0
          20  put iok=           0
          21  put iok=           0
          22  put iok=           0
          23  put iok=           0
          24  put iok=           0
          25  put iok=           0
          26  put iok=           0
          27  put iok=           0
          28  put iok=           0
          29  put iok=           0
          30  put iok=           0
close iok=           0
open iok=           0
           1  put iok=           0
           2  put iok=           0
           3  put iok=           0
           4  put iok=           0
           5  put iok=           0
           6  put iok=           0
           7  put iok=           0
           8  put iok=           0
           9  put iok=           0
          10  put iok=           0
          11  put iok=           0
          12  put iok=           0
          13  put iok=           0
          14  put iok=           0
          15  put iok=           0
          16  put iok=           0
          17  put iok=           0
          18  put iok=           0
          19  put iok=           0
          20  put iok=           0
          21  put iok=           0
          22  put iok=           0
          23  put iok=           0
          24  put iok=           0
          25  put iok=           0
          26  put iok=           0
          27  put iok=           0
          28  put iok=           0
          29  put iok=           0
          30  put iok=           0
close iok=           0
HDF5: infinite loop closing library
D,G,A,S,T,F,FD,P,FD,P,FD,P,E,E,SL,FL,FL,FL,FL,FL,FL,FL,FL,FL,FL,FL,FL,FL,FL,FL,FL,FL,FL,FL,FL,FL,FL,FL,FL,FL,FL,FL,FL,FL,FL,FL,FL,FL,FL,FL,FL,FL,FL,FL,FL,FL,FL,FL,FL,FL,FL,FL,FL,FL,FL,FL,FL,FL,FL,FL,FL,FL,FL,FL,FL,FL,FL,FL,FL,FL,FL,FL,FL,FL,FL,FL,FL,FL,FL,FL,FL,FL,FL,FL,FL,FL,FL,FL,FL,FL,FL,FL,FL,FL,FL,FL,FL,FL

Can anyone help me to understand why this error is occurring when re-writing 
the attributes?is it a bug with netcdf/hdf or am I doing something wrong?
Thanks,
Alison

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Roy Mendelssohn
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NOAA/NMFS
Environmental Research Division
Southwest Fisheries Science Center
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