My initial response went to Alison only, by accident; my apologies. I’ve
been able to observe the issue in a C program provided by Alison, so that
rules out a Fortran-specific cause.
I’ve opened a ticket on GitHub for this issue, viewable at
https://github.com/Unidata/netcdf-c/issues/233 . Searching the web for |HDF5:
infinite loop closing library| turns up a number of other instances of this
happening. Interestingly enough, when building a version of hdf5 1.8.16 for
debugging, the issue itself disappeared. I’m going to try to narrow down which
of the configure options (|--enable-codestack|, |--enable-debug=all|,
|--enable-using-memchecker|) resulted in the issue resolving itself.
I’ll be posting my findings at the GitHub issue linked above as well as
following up here once there’s a resolution, but the short answer (as has
already been pointed out) is that Alison isn’t doing anything wrong in the test
(although using |redef| isn’t a bad idea).
-Ward
On Tue, Mar 8, 2016 at 9:57 PM, rweed <rweed@xxxxxxxxxxxxxxxx
<mailto:rweed@xxxxxxxxxxxxxxxx>> wrote:
Alison
If you change
write(unit=myattr,fmt='(a6,i4.4)') 'myattr',i
to
write(unit=myattr,fmt='(a6,i4)') 'myattr',i
the error disappears
after the write with your format, myattr
looks something like myattr0001 etc
If you replace i4.4 with i4 myattr looks
like myattr 1 (spaces instead of 0's
I'm not sure why this would make a difference but it does.
RW
On 03/08/2016 02:19 PM, Alison Walker wrote:
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 don’t 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
<mailto: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
<http://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
<http://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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**********************
"The contents of this message do not reflect any position of the
U.S.
Government or NOAA."
**********************
Roy Mendelssohn
Supervisory Operations Research Analyst
NOAA/NMFS
Environmental Research Division
Southwest Fisheries Science Center
***Note new address and phone***
110 Shaffer Road
Santa Cruz, CA 95060
Phone: (831)-420-3666 <tel:%28831%29-420-3666>
Fax: (831) 420-3980 <tel:%28831%29%20420-3980>
e-mail: Roy.Mendelssohn@xxxxxxxx <mailto:Roy.Mendelssohn@xxxxxxxx>
www: http://www.pfeg.noaa.gov/
"Old age and treachery will overcome youth and skill."
"From those who have been given much, much will be expected"
"the arc of the moral universe is long, but it bends toward justice"
-MLK Jr.
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--
--
---
Richard Weed, Ph.D.
Associate Research Professor
Center for Advanced Vehicular Systems (CAVS)
Mississippi State University
Email: rweed@xxxxxxxxxxxxxxxx <mailto:rweed@xxxxxxxxxxxxxxxx>
Ph: (662) 325-5450 <tel:%28662%29%20325-5450>
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