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[netCDF #NDY-294972]: very slow nccopy with netcdf 4.6.3
- Subject: [netCDF #NDY-294972]: very slow nccopy with netcdf 4.6.3
- Date: Mon, 20 May 2019 11:02:24 -0600
Can you send us that file, or at least the output
of "ncdump -h" ?
> Dear support,
>
> I have build netcdf 4.6.3 on openSUSE and CentOS and see a very slow
> progress, very slow means 2h execution time instead of 20 s, for a
> command like this:
>
> nccopy -d2 wind_2008.nc4 wind_2008.nc4_4.6.3
>
> With nccopy from version 4.4.1.1 this task is ready in 20s.
>
> netcdf 4.6.3 is build and tested with szip 2.1.1 and hdf5 1.8.19, 1.8.20
> and 1.10.4 as well. The compiler is gcc-7, but with intel/19 and
> gcc-4.8.5 the same slow execution is observed.
>
> I am configuring with
>
> export CFLAGS="-fPIC -O2 -I$HDF_INC -I$SZIP_INC"
> export CPPFLAGS="-I$HDF_INC -I$SZIP_INC"
> export LDFLAGS="-fPIC -L$HDF_LIB -lhdf5 -lhdf5_hl -L$SZIP_LIB -lsz"
>
> ./configure --prefix=$NETCDF_ROOT \
> --enable-netcdf-4\
> --enable-cdf5 \
> --enable-dap-long-tests \
> --enable-large-file-tests \
> --with-temp-large=/fast/mschmidt \
> --enable-doxygen \
> --enable-mmap \
> --enable-jna
>
> config.status and config.log are attached.
>
> compilation fails in "include/ncconfigure.h", line 29, extern char*
> strdup(const char*); HAVE_STRDUP is defined in config.status. I do not
> understand this, but commenting this line, the compilation goes through
> and all tests are passed successfully.
>
> The library is used on a HPC linked into an ocean model and behaves well
> in this context. It is also linked into ferret and works well, except
> the "deflate" flag is simply ignored when a netcdf-file is written in
> compressed mode.
>
> I am not sure, if netcdf or hdf5 is the error source. hdf5 passes
> through all checks too. Linking with the old hdf5 that works well
> together with netcdf 4.4.1.1, does not resolve the problem. So I send
> the report to unidata first.
>
> Finally, I have also compiled the latest netcdf-c release and get the
> same behaviour.
>
>
=Dennis Heimbigner
Unidata
Ticket Details
===================
Ticket ID: NDY-294972
Department: Support netCDF
Priority: Normal
Status: Closed
===================
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