Re: [netcdfgroup] Predictable NetCDF: HDF error

To: Gustavo Correa <gus@xxxxxxxxxxxxxxxxx>
Subject: Re: [netcdfgroup] Predictable NetCDF: HDF error
From: "Ian Harris (ENV)" <I.Harris@xxxxxxxxx>
Date: Mon, 26 Jun 2017 10:44:01 +0000
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Hi Gustavo,

That hasn’t been my experience. If I create a file in classic format, then
using (eg) nf_put_vara_real() results in an error. Creating it as nf_netcdf4
works. That’s the only change I need to make.

I understand that it *ought* to work :)

I’m also finding it nearly impossible to install valgrind on OSX 10.12.5
('Sierra'); they have snapshot builds that get close, but I really don’t have
the time (or probably the expertise) to help them debug it.

Cheers

Harry

On 25 Jun 2017, at 23:37, Gustavo Correa
<gus@xxxxxxxxxxxxxxxxx<mailto:gus@xxxxxxxxxxxxxxxxx>> wrote:

Hi Ian

As far as I know the F77 netCDF interface of netCDF-3 and
netCDF-4 (the latter compiled *without* --enable-netcdf4 or with it)
support Fortran REAL variables (single precision floating point).
Functions specific to REAL variables,
such as nf_get_var1_real that appear in your program,
are supported and work fine.

Gus Correa

On Jun 24, 2017, at 8:58 AM, aitch wrote:

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<mailto: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<mailto: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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Ian "Harry” Harris
NCAS-Climate
Climatic Research Unit
School of Environmental Sciences
University of East Anglia
Norwich NR4 7TJ
United Kingdom

References:
- [netcdfgroup] NetCDF OPeNDAP , R and Windows
  - From: Capehart, William J
- Re: [netcdfgroup] NetCDF OPeNDAP , R and Windows
  - From: David W. Pierce
- Re: [netcdfgroup] NetCDF OPeNDAP , R and Windows
  - From: David W. Pierce
- [netcdfgroup] Predictable NetCDF: HDF error
  - From: Ian Harris (ENV)
- Re: [netcdfgroup] Predictable NetCDF: HDF error
  - From: dmh@xxxxxxxx
- Re: [netcdfgroup] Predictable NetCDF: HDF error
  - From: Gus Correa
- Re: [netcdfgroup] Predictable NetCDF: HDF error
  - From: dmh@xxxxxxxx
- Re: [netcdfgroup] Predictable NetCDF: HDF error
  - From: aitch
- Re: [netcdfgroup] Predictable NetCDF: HDF error
  - From: Gustavo Correa

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