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<div class="moz-forward-container">I'm not set up to use the Git
branches, I only download the versioned tar-files.<br>
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<th valign="BASELINE" nowrap="nowrap" align="RIGHT">Subject:
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<td>Re: Error building PNetCDF 1.12.2 with NVHPC 22.1 under
CentOS 8</td>
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<th valign="BASELINE" nowrap="nowrap" align="RIGHT">Date: </th>
<td>Fri, 28 Jan 2022 18:51:17 +0000</td>
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<th valign="BASELINE" nowrap="nowrap" align="RIGHT">From: </th>
<td>Wei-Keng Liao <a class="moz-txt-link-rfc2396E" href="mailto:wkliao@northwestern.edu"><wkliao@northwestern.edu></a></td>
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<th valign="BASELINE" nowrap="nowrap" align="RIGHT">To: </th>
<td>Carl Ponder <a class="moz-txt-link-rfc2396E" href="mailto:cponder@nvidia.com"><cponder@nvidia.com></a></td>
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<th valign="BASELINE" nowrap="nowrap" align="RIGHT">CC: </th>
<td><a class="moz-txt-link-abbreviated" href="mailto:parallel-netcdf@mcs.anl.gov">parallel-netcdf@mcs.anl.gov</a>
<a class="moz-txt-link-rfc2396E" href="mailto:parallel-netcdf@mcs.anl.gov"><parallel-netcdf@mcs.anl.gov></a></td>
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<br>
External email: Use caution opening links or attachments<br>
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Hi, Carl<br>
<br>
I pushed a fix to the master branch.<br>
Could you please give it a try and let me know<br>
if it works (without setting SEQ_CC)?<br>
<br>
Wei-keng<br>
<br>
<blockquote type="cite">
<pre class="moz-quote-pre" wrap="">On Jan 28, 2022, at 12:32 PM, Wei-Keng Liao <a class="moz-txt-link-rfc2396E" href="mailto:wkliao@northwestern.edu"><wkliao@northwestern.edu></a> wrote:
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
<blockquote type="cite"><pre class="moz-quote-pre" wrap="">On Jan 28, 2022, at 4:19 AM, Carl Ponder <a class="moz-txt-link-rfc2396E" href="mailto:cponder@nvidia.com"><cponder@nvidia.com></a> 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 <a class="moz-txt-link-rfc2396E" href="mailto:cponder@nvidia.com"><cponder@nvidia.com></a>
Reply-To: Carl Ponder <a class="moz-txt-link-rfc2396E" href="mailto:cponder@nvidia.com"><cponder@nvidia.com></a>
To: Wei-Keng Liao <a class="moz-txt-link-rfc2396E" href="mailto:wkliao@northwestern.edu"><wkliao@northwestern.edu></a>
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 <a class="moz-txt-link-rfc2396E" href="mailto:wkliao@northwestern.edu"><wkliao@northwestern.edu></a>
To: Carl Ponder <a class="moz-txt-link-rfc2396E" href="mailto:cponder@nvidia.com"><cponder@nvidia.com></a>
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
<blockquote type="cite"><pre class="moz-quote-pre" wrap="">On Jan 27, 2022, at 4:29 PM, Carl Ponder <a class="moz-txt-link-rfc2396E" href="mailto:cponder@nvidia.com"><cponder@nvidia.com></a>
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
<a class="moz-txt-link-rfc2396E" href="mailto:wkliao@northwestern.edu"><wkliao@northwestern.edu></a>
To: Carl Ponder
<a class="moz-txt-link-rfc2396E" href="mailto:cponder@nvidia.com"><cponder@nvidia.com></a>
CC:
<a class="moz-txt-link-abbreviated" href="mailto:parallel-netcdf@mcs.anl.gov">parallel-netcdf@mcs.anl.gov</a> <a class="moz-txt-link-rfc2396E" href="mailto:parallel-netcdf@mcs.anl.gov"><parallel-netcdf@mcs.anl.gov></a>
External email: Use caution opening links or attachments
Hi, Carl
Please send me file "config.log". I will take a look.
Wei-keng
<blockquote type="cite"><pre class="moz-quote-pre" wrap="">On Jan 27, 2022, at 3:42 PM, Carl Ponder <a class="moz-txt-link-rfc2396E" href="mailto:cponder@nvidia.com"><cponder@nvidia.com></a>
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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