Path oddity in PNetCDF build/configure
Wei-Keng Liao
wkliao at northwestern.edu
Sun Oct 24 18:53:02 CDT 2021
I also suggest to remove "--enable-large-single-req".
As far as I know none of existing MPI-IO implementation
supports reading or writing > 2GB data elements in a single call.
This option is to disable an internal checking in PnetCDF
for any single request size > 2GB and let the underneath MPI-IO
to check this condition.
Wei-keng
On Oct 24, 2021, at 6:35 PM, Carl Ponder <cponder at nvidia.com<mailto:cponder at nvidia.com>> wrote:
Ok -- yes -- I got a clean build by removing the --with-mpi flag.
What about this --enable-large-single-req flag, though?
Does it require that I build OpenMPI specially, or use a specific kind of switch or FileSystem?
I only use 64-but systems these days...
Thanks,
Carl
________________________________
Subject: Re: Path oddity in PNetCDF build/configure
Date: Sun, 24 Oct 2021 21:27:44 +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>
External email: Use caution opening links or attachments
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>
External email: Use caution opening links or attachments
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>
External email: Use caution opening links or attachments
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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