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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> 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> 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 >>>> >>>> _______________________________________________ >>>> netcdfgroup mailing list >>>> netcdfgroup@xxxxxxxxxxxxxxxx >>>> For list information or to unsubscribe, visit: >>>> http://www.unidata.ucar.edu/mailing_lists/ >>>> >>> ********************** >>> "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 >>> Fax: (831) 420-3980 >>> e-mail: 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. >>> >>> >>> >> _______________________________________________ >> netcdfgroup mailing list >> netcdfgroup@xxxxxxxxxxxxxxxx >> For list information or to unsubscribe, visit: >> http://www.unidata.ucar.edu/mailing_lists/ >> > > -- > -- > --- > > Richard Weed, Ph.D. > Associate Research Professor > Center for Advanced Vehicular Systems (CAVS) > Mississippi State University > > Email: rweed@xxxxxxxxxxxxxxxx > Ph: (662) 325-5450 > > > _______________________________________________ > netcdfgroup mailing list > netcdfgroup@xxxxxxxxxxxxxxxx > For list information or to unsubscribe, visit: > http://www.unidata.ucar.edu/mailing_lists/ >
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