[netCDF #OEM-105874]: Flag -pthread in NetCDF/C linkage

I think this is occurring in the file 'configure' and was
added by the automake code. See if the string '-pthread' occurs
in your copy of configure.ac.
I suspect your only alternative is to use the cmake build.

> I'm building NetCDF.C 4.6.1 and NetCDF/F 4.4.4 using the PGI compiler.
> The final linkage steps are using the flag -pthread which is illegal
> with the PGI compiler
> 
> pgcc-Warning-Unknown switch: -pthread
> pgfortran-Warning-Unknown switch: -pthread
> 
> I'm able to get the linkage to work by adding the PGI -noswitcherror
> flag to my scripts, so it's not a huge deal.
> But I've only recently started seeing the problem, and had to hack a bit
> to get it inserted into the final link phase, evidently adding it to
> LDFLAGS wasn't enough for some reason.
> Note that this is separate from the -lpthread linkage flag, which works ok.
> 
> I'm using these configure flags
> 
> ./configure
> --prefix=/gpfs/fs1/SHARE/Utils/NetCDF-C/4.6.1/PGI-18.7_OpenMPI-3.1.2_PNetCDF-1.10.0_HDF5-1.10.4
> --disable-doxygen --enable-pnetcdf --enable-extra-example-tests
> --enable-parallel-tests --enable-large-file-tests --enable-extra-tests
> ./configure
> --prefix=/gpfs/fs1/SHARE/Utils/NetCDF-F/4.4.4/PGI-18.7_OpenMPI-3.1.2_NetCDF-C-4.6.1
> --disable-doxygen --enable-extra-example-tests
> --enable-parallel-tests --enable-large-file-tests --enable-extra-tests
> 
> and got these summaries:
> 
> # NetCDF C Configuration Summary
> ==============================
> 
> # General
> -------
> NetCDF Version:     4.6.1
> Configured On:      Tue Oct 16 05:14:07 PDT 2018
> Host System:        x86_64-pc-linux-gnu
> Build Directory:
> /gpfs/fs1/SHARE/Utils/NetCDF-C/4.6.1/PGI-18.7_OpenMPI-3.1.2_PNetCDF-1.10.0_HDF5-1.10.4/distro
> Install Prefix:
> /gpfs/fs1/SHARE/Utils/NetCDF-C/4.6.1/PGI-18.7_OpenMPI-3.1.2_PNetCDF-1.10.0_HDF5-1.10.4
> 
> # Compiling Options
> -----------------
> C Compiler:
> /gpfs/fs1/SHARE/Utils/OpenMPI/3.1.2/PGI-18.7_CUDA-9.2.148.1_396.37_HWLoc-1.11.11_ZLib-1.2.11/bin/mpicc
> -noswitcherror
> CFLAGS:         -fPIC -m64 -tp=px
> CPPFLAGS:       -DpgiFortran
> LDFLAGS:        -L/usr/lib/nvidia-410
> -L/gpfs/fs1/SHARE/Utils/CUDA/9.2.148.1_396.37/lib64
> -L/usr/lib/x86_64-linux-gnu
> -L/gpfs/fs1/SHARE/Utils/CUDA/9.2.148.1_396.37/extras/CUPTI/lib64
> -L/gpfs/fs1/SHARE/Utils/CUDA/9.2.148.1_396.37/extras/Debugger/lib64
> -L/gpfs/fs1/SHARE/Utils/CUDA/9.2.148.1_396.37/nvvm/lib64
> -L/gpfs/fs1/SHARE/Utils/ZLib/1.2.11/PGI-18.7/lib
> -L/gpfs/fs1/SHARE/Utils/HWLoc/1.11.11/PGI-18.7_CUDA-9.2.148.1_396.37/lib
> -L/gpfs/fs1/SHARE/Utils/OpenMPI/3.1.2/PGI-18.7_CUDA-9.2.148.1_396.37_HWLoc-1.11.11_ZLib-1.2.11/lib
> -L/gpfs/fs1/SHARE/Utils/SZip/2.1.1/PGI-18.7/lib
> -L/gpfs/fs1/SHARE/Utils/HDF5/1.10.4/PGI-18.7_OpenMPI-3.1.2_SZip-2.1.1_ZLib-1.2.11/lib
> -L/gpfs/fs1/SHARE/Utils/PNetCDF/1.10.0/PGI-18.7_OpenMPI-3.1.2/lib
> -L/gpfs/fs1/SHARE/Utils/PNetCDF/1.10.0/PGI-18.7_OpenMPI-3.1.2/lib
> -L/gpfs/fs1/SHARE/Utils/HDF5/1.10.4/PGI-18.7_OpenMPI-3.1.2_SZip-2.1.1_ZLib-1.2.11/lib
> -L/gpfs/fs1/SHARE/Utils/SZip/2.1.1/PGI-18.7/lib -L/usr/lib64
> -L/gpfs/fs1/SHARE/Utils/PGI/18.7/linux86-64/2018/lib
> AM_CFLAGS:
> AM_CPPFLAGS:
> AM_LDFLAGS:
> Shared Library:     yes
> Static Library:     yes
> Extra libraries:    -lpnetcdf -lsz -lhdf5_hl -lhdf5 -lm -lz -lcurl
> 
> # Features
> --------
> NetCDF-2 API:       yes
> HDF4 Support:       no
> NetCDF-4 API:       yes
> NC-4 Parallel Support:  yes
> PNetCDF Support:    yes
> DAP2 Support:       yes
> DAP4 Support:       yes
> Diskless Support:   yes
> MMap Support:       no
> JNA Support:        no
> CDF5 Support:       yes
> ERANGE fill Support:    yes
> 
> 
> _NetCDF/F_
> 
>   --cc        ->
> /gpfs/fs1/SHARE/Utils/OpenMPI/3.1.2/PGI-18.7_CUDA-9.2.148.1_396.37_UCX-2018-10-03_HWLoc-1.11.11_ZLib-1.2.11/bin/mpicc
>   --cflags    ->
> -I/gpfs/fs1/SHARE/Utils/NetCDF-F/4.4.4/PGI-18.7_OpenMPI-3.1.2_NetCDF-C-4.6.1/include
> 
> 
>   --fc        ->
> /gpfs/fs1/SHARE/Utils/OpenMPI/3.1.2/PGI-18.7_CUDA-9.2.148.1_396.37_UCX-2018-10-03_HWLoc-1.11.11_ZLib-1.2.11/bin/mpifort
> -noswitcherror
>   --fflags    ->
> -I/gpfs/fs1/SHARE/Utils/NetCDF-F/4.4.4/PGI-18.7_OpenMPI-3.1.2_NetCDF-C-4.6.1/include
>   --flibs     ->
> -L/gpfs/fs1/SHARE/Utils/NetCDF-F/4.4.4/PGI-18.7_OpenMPI-3.1.2_NetCDF-C-4.6.1/lib
> -lnetcdff
> -L/gpfs/fs1/SHARE/Utils/NetCDF-C/4.6.1/PGI-18.7_OpenMPI-3.1.2_PNetCDF-1.10.0_HDF5-1.10.3/lib
> -L/usr/lib64 -L/usr/lib/x86_64-linux-gnu -lnetcdf -lnetcdf
>   --has-f90   -> no
>   --has-f03   -> yes
> 
>   --has-nc2   -> yes
>   --has-nc4   -> yes
> 
>   --prefix    ->
> /gpfs/fs1/SHARE/Utils/NetCDF-F/4.4.4/PGI-18.7_OpenMPI-3.1.2_NetCDF-C-4.6.1
>   --includedir->
> /gpfs/fs1/SHARE/Utils/NetCDF-F/4.4.4/PGI-18.7_OpenMPI-3.1.2_NetCDF-C-4.6.1/include
>   --version   -> netCDF-Fortran 4.4.4
> 
> 
> 
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> 

=Dennis Heimbigner
  Unidata


Ticket Details
===================
Ticket ID: OEM-105874
Department: Support netCDF
Priority: Normal
Status: Open
===================
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