Error building PNetCDF 1.12.2 with NVHPC 22.1 under CentOS 8
Wei-Keng Liao
wkliao at northwestern.edu
Fri Jan 28 12:32:52 CST 2022
Thanks. I will add SEQ_CC to the help message.
I assume the value of "ac_cv_mpi_compiler_base_MPICC" is the
same as what you got from command `which pgcc`.
FYI. There are 3 utility programs that are designed to run
in serial: ncoffsets, ncvalidator, and pnetcdf_version.
In the cross-compile environment, I need to extract the C
compiler from the MPI compiler, which sets SEQ_CC.
Wei-keng
> On Jan 28, 2022, at 4:19 AM, Carl Ponder <cponder at nvidia.com> wrote:
>
>
> Ok this fixed the problem:
> export SEQ_CC=`which pgcc`
> The SEQ_CC setting isn't mentioned by the command
> ./confgure --help
> Could you get it to list somehow?
> I had to find it by looking at the messages in the script.
>
> Subject: Re: Error building PNetCDF 1.12.2 with NVHPC 22.1 under CentOS 8
> Date: Fri, 28 Jan 2022 03:16:00 -0600
> From: Carl Ponder <cponder at nvidia.com>
> Reply-To: Carl Ponder <cponder at nvidia.com>
> To: Wei-Keng Liao <wkliao at northwestern.edu>
>
>
>
> The value is this
> ac_cv_mpi_compiler_base_MPICC=/home/cponder/WRF/PGI/100.NVHPC/Linux_x86_64/21.11/compilers/bin/pgcc
> ac_cv_path_ac_cv_mpi_compiler_base_MPICC=/home/cponder/WRF/PGI/100.NVHPC/Linux_x86_64/21.11/compilers/bin/pgcc
> ac_cv_mpi_compiler_base_MPICC='/home/cponder/WRF/PGI/100.NVHPC/Linux_x86_64/21.11/compilers/bin/pgcc'
> which I *think* is what I want, since I built OpenMPI to use the PGI compiler.
> The problem, as I see it at least, is that for the Utility programs it's trying to use gcc instead:
> checking for mpiexec... /home/cponder/WRF/PGI/105.OpenMPI/bin/mpiexec
> checking for gcc... /bin/gcc
> checking C compiler for serial utility programs... /bin/gcc
>
> If I don't add the PGI inslude-paths, at least, then gcc doesn't use the wrong ones.
>
> Subject: Re: Error building PNetCDF 1.12.2 with NVHPC 22.1 under CentOS 8
> Date: Thu, 27 Jan 2022 22:34:41 +0000
> From: Wei-Keng Liao <wkliao at northwestern.edu>
> To: Carl Ponder <cponder at nvidia.com>
>
>
> External email: Use caution opening links or attachments
>
>
> Can you check the value of variable "ac_cv_mpi_compiler_base_MPICC"
> printed in your config.log?
>
> If it points to the PGI compiler, then configure.ac needs to be fixed.
> Otherwise, config.log can help me to identify the problem.
>
> Wei-keng
>
>> On Jan 27, 2022, at 4:29 PM, Carl Ponder <cponder at nvidia.com>
>> wrote:
>>
>>
>> I can get around the problem by *NOT* setting the include-paths to the NVHPC compiler:
>> # export CPATH+=:$PGI/include
>> # export C_INCLUDE_PATH+=:$PGI/include
>> # export INCLUDE_PATH+=:$PGI/include
>> I can work with this, but haven't had to do it with the other libs that use the CC/MPICC etc. compiler settings for everything.
>> Do you still need to see the config.log?
>>
>> Subject: Re: Error building PNetCDF 1.12.2 with NVHPC 22.1 under CentOS 8
>> Date: Thu, 27 Jan 2022 22:16:25 +0000
>> From: Wei-Keng Liao
>> <wkliao at northwestern.edu>
>>
>> To: Carl Ponder
>> <cponder at nvidia.com>
>>
>> CC:
>> parallel-netcdf at mcs.anl.gov <parallel-netcdf at mcs.anl.gov>
>>
>>
>>
>> External email: Use caution opening links or attachments
>>
>>
>> Hi, Carl
>>
>> Please send me file "config.log". I will take a look.
>>
>> Wei-keng
>>
>>
>>
>>> On Jan 27, 2022, at 3:42 PM, Carl Ponder <cponder at nvidia.com>
>>>
>>> wrote:
>>>
>>> I'm getting this error:
>>> /bin/gcc -I../../../src/utils/ncvalidator -o cdfdiff cdfdiff.c
>>> In file included from /usr/include/stdlib.h:55,
>>> from /home/cponder/WRF/PGI/100.NVHPC/Linux_x86_64/21.11/compilers/include/stdlib.h:13,
>>> from cdfdiff.c:19:
>>> /home/cponder/WRF/PGI/100.NVHPC/Linux_x86_64/21.11/compilers/include/bits/floatn.h:60:17: error: two or more data types in declaration specifiers
>>> typedef float _Float32;
>>> ^~~~~~~~
>>> /home/cponder/WRF/PGI/100.NVHPC/Linux_x86_64/21.11/compilers/include/bits/floatn.h:63:18: error: two or more data types in declaration specifiers
>>> typedef double _Float64;
>>> ^~~~~~~~
>>> /home/cponder/WRF/PGI/100.NVHPC/Linux_x86_64/21.11/compilers/include/bits/floatn.h:74:18: error: two or more data types in declaration specifiers
>>> typedef double _Float32x;
>>> ^~~~~~~~~
>>> /home/cponder/WRF/PGI/100.NVHPC/Linux_x86_64/21.11/compilers/include/bits/floatn.h:78:25: error: two or more data types in declaration specifiers
>>> typedef long double _Float64x;
>>> ^~~~~~~~~
>>> make[3]: *** [Makefile:847: cdfdiff] Error 1
>>> make[3]: Leaving directory '/home/cponder/WRF/PGI/A.106.PNetCDF/distro/src/utils/ncmpidiff'
>>> make[2]: *** [Makefile:545: all-recursive] Error 1
>>> make[2]: Leaving directory '/home/cponder/WRF/PGI/A.106.PNetCDF/distro/src/utils'
>>> make[1]: *** [Makefile:476: all-recursive] Error 1
>>> make[1]: Leaving directory '/home/cponder/WRF/PGI/A.106.PNetCDF/distro/src'
>>> make: *** [Makefile:533: all-recursive] Error 1
>>> I believe the problem is that it's trying to use the system-default gcc here
>>> checking for mpiexec... /home/cponder/WRF/PGI/105.OpenMPI/bin/mpiexec
>>> checking for gcc... /bin/gcc
>>> checking C compiler for serial utility programs... /bin/gcc
>>> which is incompatible with all the NVHPC_specific paths that I'm setting for the overall build:
>>> export CC=`which pgcc`
>>> export CXX=`which pgc++`
>>> export F77=`which pgf77`
>>> export F90=`which pgf90`
>>> export FC=`which pgfortran`
>>>
>>> export MPICC=`which mpicc`
>>> export MPICXX=`which mpicxx`
>>> export MPIF77=`which mpif77`
>>> export MPIF90=`which mpif90`
>>>
>>> export CFLAGS="-fPIC -m64 -tp=px"
>>> export CXXFLAGS="-fPIC -m64 -tp=px"
>>> export FCFLAGS="-fPIC -m64 -tp=px"
>>>
>>> export LDFLAGS+=" -L$PGI/cuda/lib64 -lnvidia-ml"
>>> I'm guessing that the old compilers & old OS levels didn't enable these types so there was no collision during the compilation.
>>> Is there a way to override the gcc default for the utilities? I don't see any such setting in the configure --help output.
>>>
>>>
>>>
>>>
>>
>
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