Path oddity in PNetCDF build/configure

[Wei-Keng Liao]

I checked the configure command line used.
While debugging this issue, I suggest you to remove
"--with-mpi --enable-large-single-req" from the configure command.

Option --with-mpi was designed to let users to provide the
path of MPI installation, e.g. --with-mpi=/usr/local

Use option --enable-large-single-req is when the underlying
MPI-IO supports reading and writing more than 2GiB in a
single call (i.e. MPI_File_read and MPI_File_write call.)

Wei-keng

On Oct 24, 2021, at 4:07 PM, Carl Ponder <cponder at nvidia.com<mailto:cponder at nvidia.com>> wrote:


I attached the config.log here, but it doesn't show the steps used in the mpiccchecking:
configure:4284: result: /usr/bin/sed -i''
configure:4682: checking mpicc under yes
configure:4689: result: no
configure:4772: error:
   -----------------------------------------------------------------------
     Specified MPI C compiler "mpicc" cannot be found under yes
     PnetCDF requires a working MPI C compiler. Please specify the location
     of an MPI C compiler, either in the MPICC environment variable
     (not CC variable) or through --with-mpi configure flag. Abort.
   -----------------------------------------------------------------------
The command-line I used was
./configure --prefix=/usr/local --enable-shared --with-mpi --enable-large-single-req

________________________________
Subject:        Re: Path oddity in PNetCDF build/configure
Date:   Sun, 24 Oct 2021 19:22:06 +0000
From:   Wei-Keng Liao <wkliao at northwestern.edu><mailto:wkliao at northwestern.edu>
To:     Carl Ponder <cponder at nvidia.com><mailto:cponder at nvidia.com>
CC:     Bruno Pagani <bruno.pagani at astrophysics.eu><mailto:bruno.pagani at astrophysics.eu>, parallel-netcdf at lists.mcs.anl.gov<mailto:parallel-netcdf at lists.mcs.anl.gov> <parallel-netcdf at lists.mcs.anl.gov><mailto:parallel-netcdf at lists.mcs.anl.gov>


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Please let me know the configure command used.

Wei-keng
________________________________

Subject:        Re: Path oddity in PNetCDF build/configure
Date:   Sun, 24 Oct 2021 17:06:01 +0000
From:   Wei-Keng Liao <wkliao at northwestern.edu><mailto:wkliao at northwestern.edu>
To:     Carl Ponder <cponder at nvidia.com><mailto:cponder at nvidia.com>
CC:     parallel-netcdf at lists.mcs.anl.gov<mailto:parallel-netcdf at lists.mcs.anl.gov> <parallel-netcdf at lists.mcs.anl.gov><mailto:parallel-netcdf at lists.mcs.anl.gov>


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Hi, Carl

Please send me the file config.log.

Wei-keng

________________________________
On Oct 24, 2021, at 1:29 PM, Carl Ponder <cponder at nvidia.com<mailto:cponder at nvidia.com>> wrote:


This is in a Dockerfile rather than my usual bash scripting.
Here's the PATH being printed during the build
Step 95/156 : RUN echo ${PATH}
 ---> Running in 8586a4aef68a
/usr/local/nvidia/bin:/usr/local/cuda/bin:/usr/local/sbin:/usr/local/bin:/usr/sbin:/usr/bin:/sbin:/bin:/usr/local/bin:/usr/local/cuda/bin:/usr/local/pgi/Linux_x86_64/21.9/compilers/bin
And the mpicc location tests correctly:
Step 95/155 : RUN which mpicc
 ---> Running in e2161d554278
/usr/local/bin/mpicc
________________________________
Subject:        Re: Path oddity in PNetCDF build/configure
Date:   Sun, 24 Oct 2021 16:32:42 +0400
From:   Bruno Pagani <bruno.pagani at astrophysics.eu><mailto:bruno.pagani at astrophysics.eu>
To:     Carl Ponder <cponder at nvidia.com><mailto:cponder at nvidia.com>, Wei-keng Liao <wkliao at eecs.northwestern.edu><mailto:wkliao at eecs.northwestern.edu>
CC:     parallel-netcdf at lists.mcs.anl.gov<mailto:parallel-netcdf at lists.mcs.anl.gov>


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How do you set PATH? Did you quote it? Seems somehow your path end up being yes, likely due to expansion of its previous value.


________________________________
Le 24 octobre 2021 16:30:03 GMT+04:00, Carl Ponder <cponder at nvidia.com><mailto:cponder at nvidia.com> a écrit :
When I build PNetCDF with MPICC=mpicc and mpicc on my $PATH, I see this during the configure phase:
ENV PATH=${PATH}:/usr/local/bin
ENV MPICC mpicc
...
checking for sed handling option -i ... /usr/bin/sed -i''
checking mpicc under yes... no
configure: error:
   -----------------------------------------------------------------------
     Specified MPI C compiler "mpicc" cannot be found under yes
     PnetCDF requires a working MPI C compiler. Please specify the location
     of an MPI C compiler, either in the MPICC environment variable
     (not CC variable) or through --with-mpi configure flag. Abort.
   -----------------------------------------------------------------------
I can work around it by making the path absolute
ENV MPICC /usr/local/bin/mpicc
...
checking for sed handling option -i ... /usr/bin/sed -i''
checking whether /usr/local/bin/mpicc exists and is executable... yes
But, based on the first message, I'm thinking there's an incorrect path-search during the configure phase.
This is with PNetCDF 1.12.2.

<config.log>

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