Thank you both for your speedy suggestions!
Unfortunately I need NetCDF-4 for this, because the F77 NetCDF interface won’t
allow REAL otherwise. However, I will try what combinations I can manage on
Monday (screen sharing over a VPN is not ideal for *nix tinkering).
Cheers
Harry
> On 23 Jun 2017, at 21:38, dmh@xxxxxxxx wrote:
>
> All good suggestions.
> The goal is to try to isolate the problem
> to see if the error is associated with HDF5, or mpi, or
> the core netcdf-c library.
>
> On 6/23/2017 2:17 PM, Gus Correa wrote:
>> Hi Ian, Dennis
>> May I suggest a workaround?
>> If your files are netCDF "Classic" or "64 bit offset" ('ncdump -k' will
>> tell) they don't need
>> NetCDF-4 or HDF5 support to be processed.
>> Am I right?
>> If so, you could compile the netCDF 3.6.3 library and link your program to
>> it instead.
>> Alternatively, you could compile netCDF 4.4.1 disabling netCDF-4 (run
>> configure without --enable-netcdf4).
>> Either one doesn't require HDF5, and *may* not have these errors.
>> Other than this, perhaps lowering the compiler optimization level,
>> or turning off OpenMP, if it is on.
>> I hope this helps,
>> Gus Correa
>> On 06/23/2017 03:32 PM, dmh@xxxxxxxx wrote:
>>> Is there any chance that you can run this using valgrind?
>>> My speculation is that it is a memory leak of some kind.
>>> =Dennis Heimbigner
>>> Unidata
>>>
>>>
>>> On 6/23/2017 7:38 AM, Ian Harris (ENV) wrote:
>>>> Hi,
>>>>
>>>> I have NetCDF installed (netcdf library version 4.4.1 per ncdump) on a
>>>> fairly powerful iMac (4GHz i7, 16GB). I use Fortran 77 (yes, I know, but
>>>> it’s very fast).
>>>>
>>>> I’m processing a lot of data, inputs and outputs all NetCDF, in loops, and
>>>> it’s dying at predictable and reproducible points.
>>>>
>>>> One example is a simple prog I knocked up; it opens a nc file, then
>>>> continually reads the first time value in a loop until it dies.
>>>>
>>>> The last successful loop is 16777187, which may sound familiar, as it’s
>>>> been here before:
>>>>
>>>> http://www.unidata.ucar.edu/mailing_lists/archives/netcdfgroup/2014/msg00173.html
>>>>
>>>>
>>>> The error is usually 'NetCDF: HDF error', though occasionally 'NetCDF:
>>>> Error initializing for parallel access'.
>>>>
>>>> I should note that a much more complicated program, which reads in three
>>>> files and writes one, also dies like this after a fixed number of runs
>>>> through the loops (taking over an hour).
>>>>
>>>> The simple test program is below.
>>>>
>>>> Please can anyone hazard a guess as to what’s happening?
>>>>
>>>> Cheers
>>>>
>>>> Harry
>>>>
>>>>
>>>> Here’s the entire program:
>>>>
>>>> program netcdftestloop
>>>> c NETCDFTESTLOOP Testing iteration counts before it dies
>>>> implicit none
>>>> include 'netcdf.inc'
>>>> integer nits,st,ncid,tvarid
>>>> real rday
>>>>
>>>> nits = 0
>>>> st = nf_open('Prec_daily_WFD_CRU_grid_198605.nc',0,ncid)
>>>> if (st.ne.nf_noerr) call handle_err(st,'openff')
>>>> st = nf_inq_varid(ncid,'time',tvarid)
>>>> if (st.ne.nf_noerr) call handle_err(st,'inqtvi')
>>>> do
>>>> nits=nits+1
>>>> if (mod(nits,100000).eq.0) write(*,'(i10)')nits !
>>>> keep track
>>>> st = nf_get_var1_real(ncid,tvarid,1,rday) !
>>>> get day 1 time value
>>>> if (st.ne.nf_noerr) then
>>>> write(*,'("N. iterations = ",i10)')nits
>>>> call handle_err(st,'getday')
>>>> endif
>>>> enddo
>>>> st = nf_close(ncid) !
>>>> totally unnecessary close file
>>>> if (st.ne.nf_noerr) call handle_err(st,'closef')
>>>> stop
>>>> end
>>>>
>>>>
>>>> c
>>>> ***********************************************************************************************
>>>>
>>>> subroutine handle_err(errcode,code)
>>>> implicit none
>>>> include 'netcdf.inc'
>>>> integer errcode
>>>> character code*6
>>>>
>>>> print *, 'Error: ', code, ': ', nf_strerror(errcode)
>>>> stop
>>>> end
>>>>
>>>> c
>>>> ***********************************************************************************************
>>>>
>>>>
>>>> In a more complicated program, I get a different error, ('')
>>>>
>>>>
>>>> Ian "Harry” Harris
>>>> NCAS-Climate
>>>> Climatic Research Unit
>>>> School of Environmental Sciences
>>>> University of East Anglia
>>>> Norwich NR4 7TJ
>>>> United Kingdom
>>>>
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>>>>
>>>>
>>>>
>>>>
>>>>
>>>>
>>>>
>>>>
>>>>
>>>>
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