Unable to build HDF5 with pgi compilers

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Unable to build HDF5 with pgi compilers

ashwin .D
Hello,
         I already have an existing installation of HDF5 1.8.17 compiled with gfortran. Now for another project on the same machine I need to compile with PGI compilers i.e. pgcc , pgc++and pgf90. The installation directory will be separate as well i.e. /opt/local/lib and /opt/local/include.

This is how I try to build hdf5

CPPFLAGS=/opt/local/include CXXFLAGS=/opt//local/include LDFLAGS=/opt//local/lib CC=pgcc CXX=pgc++ FC=pgf90 F77=pgf77   ./configure --prefix=/opt/local --with-zlib=/opt/local --enable-fortran --enable-cxx.

and when I try doing this I get this error message -

checking for a BSD-compatible install... /usr/bin/install -c
checking whether build environment is sane... yes
checking for a thread-safe mkdir -p... /bin/mkdir -p
checking for gawk... no
checking for mawk... mawk
checking whether make sets $(MAKE)... yes
checking whether make supports nested variables... yes
checking whether make supports nested variables... (cached) yes
checking whether to enable maintainer-specific portions of Makefiles... no
checking build system type... x86_64-unknown-linux-gnu
checking host system type... x86_64-unknown-linux-gnu
checking shell variables initial values... done
checking if basename works... yes
checking if xargs works... yes
checking for cached host... none
checking for config x86_64-unknown-linux-gnu... no
checking for config x86_64-unknown-linux-gnu... no
checking for config unknown-linux-gnu... no
checking for config unknown-linux-gnu... no
checking for config x86_64-linux-gnu... no
checking for config x86_64-linux-gnu... no
checking for config x86_64-unknown... no
checking for config linux-gnu... found
compiler 'pgcc' is PGI pgcc-17.4-0
compiler 'pgf90' is PGI pgf90-17.4-0
No match to get cxx_version_info for pgc++
checking for config ./config/site-specific/host-Vostro-3800... no
checking for gcc... pgcc
checking whether the C compiler works... no
configure: error: in `/home//hdf5-1.8.17':
configure: error: C compiler cannot create executables
See `config.log' for more details

Any suggestions on how to build will be appreciated.

Best regards,
Ashwin.

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Re: Unable to build HDF5 with pgi compilers

George N. White III
On 26 June 2017 at 03:42, ashwin .D <[hidden email]> wrote:
Hello,
         I already have an existing installation of HDF5 1.8.17 compiled with gfortran. Now for another project on the same machine I need to compile with PGI compilers i.e. pgcc , pgc++and pgf90. The installation directory will be separate as well i.e. /opt/local/lib and /opt/local/include.

This is how I try to build hdf5

CPPFLAGS=/opt/local/include CXXFLAGS=/opt//local/include LDFLAGS=/opt//local/lib CC=pgcc CXX=pgc++ FC=pgf90 F77=pgf77   ./configure --prefix=/opt/local --with-zlib=/opt/local --enable-fortran --enable-cxx.

and when I try doing this I get this error message -

checking for a BSD-compatible install... /usr/bin/install -c
checking whether build environment is sane... yes
[...] 
checking for gcc... pgcc
checking whether the C compiler works... no
configure: error: in `/home//hdf5-1.8.17':
configure: error: C compiler cannot create executables
See `config.log' for more details                  <<<<<<<<<<<<<<<<<<<<

Any suggestions on how to build will be appreciated.


Your flags settings need "-I" or "-L" as appropriate.

If that does't solve your problem, it might help if you provide the OS and version as well as the compiler version.  
Someone on the list may have advice for your particular platform.  

It  would also be helpful if you could post relevant "more details" from the config.log file. 


--
George N. White III <[hidden email]>
Head of St. Margarets Bay, Nova Scotia

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Re: Unable to build HDF5 with pgi compilers

Carl Ponder
In reply to this post by ashwin .D
On 06/26/2017 01:42 AM, ashwin .D wrote:
I already have an existing installation of HDF5 1.8.17 compiled with gfortran. Now for another project on the same machine I need to compile with PGI compilers i.e. pgcc , pgc++and pgf90. The installation directory will be separate as well i.e. /opt/local/lib and /opt/local/include.

Ashwin -- here's a script that I use to build HDF5 1.10.1 using the PGI 17.5 compiler.
You might try testing with these components first to see if you can get it to build, and then go backlevel on the pieces that you want to use.

        -- Carl



This is how I try to build hdf5
CPPFLAGS=/opt/local/include CXXFLAGS=/opt//local/include LDFLAGS=/opt//local/lib CC=pgcc CXX=pgc++ FC=pgf90 F77=pgf77   ./configure --prefix=/opt/local --with-zlib=/opt/local --enable-fortran --enable-cxx.
and when I try doing this I get this error message -
checking for a BSD-compatible install... /usr/bin/install -c
checking whether build environment is sane... yes
checking for a thread-safe mkdir -p... /bin/mkdir -p
checking for gawk... no
checking for mawk... mawk
checking whether make sets $(MAKE)... yes
checking whether make supports nested variables... yes
checking whether make supports nested variables... (cached) yes
checking whether to enable maintainer-specific portions of Makefiles... no
checking build system type... x86_64-unknown-linux-gnu
checking host system type... x86_64-unknown-linux-gnu
checking shell variables initial values... done
checking if basename works... yes
checking if xargs works... yes
checking for cached host... none
checking for config x86_64-unknown-linux-gnu... no
checking for config x86_64-unknown-linux-gnu... no
checking for config unknown-linux-gnu... no
checking for config unknown-linux-gnu... no
checking for config x86_64-linux-gnu... no
checking for config x86_64-linux-gnu... no
checking for config x86_64-unknown... no
checking for config linux-gnu... found
compiler 'pgcc' is PGI pgcc-17.4-0
compiler 'pgf90' is PGI pgf90-17.4-0
No match to get cxx_version_info for pgc++
checking for config ./config/site-specific/host-Vostro-3800... no
checking for gcc... pgcc
checking whether the C compiler works... no
configure: error: in `/home//hdf5-1.8.17':
configure: error: C compiler cannot create executables
See `config.log' for more details
Any suggestions on how to build will be appreciated.



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Re: Unable to build HDF5 with pgi compilers

ashwin .D
George, Matt and Carl.
                                   Thanks much for all the suggestions. I was able to move past the configure errors by using a combination of all the tips you recommended. I in fact downloaded the hdf-1.10.1 version and while running make did not give any problems I have  a whole bunch of redundant macro warnings and which when I looked up is identical to this one - https://lists.hdfgroup.org/pipermail/hdf-forum_lists.hdfgroup.org/2010-July/003304.html.
I have enclosed a trimmed version of my logs. Is it good to proceed forward or is there something I need to edit with the header files as well ? Note these warnings  do not occur with gfortran.

Best regards,
Ashwin.

On Tue, Jun 27, 2017 at 3:09 AM, Carl Ponder <[hidden email]> wrote:
On 06/26/2017 01:42 AM, ashwin .D wrote:
I already have an existing installation of HDF5 1.8.17 compiled with gfortran. Now for another project on the same machine I need to compile with PGI compilers i.e. pgcc , pgc++and pgf90. The installation directory will be separate as well i.e. /opt/local/lib and /opt/local/include.

Ashwin -- here's a script that I use to build HDF5 1.10.1 using the PGI 17.5 compiler.
You might try testing with these components first to see if you can get it to build, and then go backlevel on the pieces that you want to use.

        -- Carl



This is how I try to build hdf5
CPPFLAGS=/opt/local/include CXXFLAGS=/opt//local/include LDFLAGS=/opt//local/lib CC=pgcc CXX=pgc++ FC=pgf90 F77=pgf77   ./configure --prefix=/opt/local --with-zlib=/opt/local --enable-fortran --enable-cxx.
and when I try doing this I get this error message -
checking for a BSD-compatible install... /usr/bin/install -c
checking whether build environment is sane... yes
checking for a thread-safe mkdir -p... /bin/mkdir -p
checking for gawk... no
checking for mawk... mawk
checking whether make sets $(MAKE)... yes
checking whether make supports nested variables... yes
checking whether make supports nested variables... (cached) yes
checking whether to enable maintainer-specific portions of Makefiles... no
checking build system type... x86_64-unknown-linux-gnu
checking host system type... x86_64-unknown-linux-gnu
checking shell variables initial values... done
checking if basename works... yes
checking if xargs works... yes
checking for cached host... none
checking for config x86_64-unknown-linux-gnu... no
checking for config x86_64-unknown-linux-gnu... no
checking for config unknown-linux-gnu... no
checking for config unknown-linux-gnu... no
checking for config x86_64-linux-gnu... no
checking for config x86_64-linux-gnu... no
checking for config x86_64-unknown... no
checking for config linux-gnu... found
compiler 'pgcc' is PGI pgcc-17.4-0
compiler 'pgf90' is PGI pgf90-17.4-0
No match to get cxx_version_info for pgc++
checking for config ./config/site-specific/host-Vostro-3800... no
checking for gcc... pgcc
checking whether the C compiler works... no
configure: error: in `/home//hdf5-1.8.17':
configure: error: C compiler cannot create executables
See `config.log' for more details
Any suggestions on how to build will be appreciated.



This email message is for the sole use of the intended recipient(s) and may contain confidential information.  Any unauthorized review, use, disclosure or distribution is prohibited.  If you are not the intended recipient, please contact the sender by reply email and destroy all copies of the original message.



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Re: Unable to build HDF5 with pgi compilers

George N. White III


On 27 June 2017 at 00:06, ashwin .D <[hidden email]> wrote:
George, Matt and Carl.
                                   Thanks much for all the suggestions. I was able to move past the configure errors by using a combination of all the tips you recommended. I in fact downloaded the hdf-1.10.1 version and while running make did not give any problems I have  a whole bunch of redundant macro warnings and which when I looked up is identical to this one - https://lists.hdfgroup.org/pipermail/hdf-forum_lists.hdfgroup.org/2010-July/003304.html.
I have enclosed a trimmed version of my logs. Is it good to proceed forward or is there something I need to edit with the header files as well ? Note these warnings  do not occur with gfortran.

Best regards,
Ashwin. 

Sounds promissing.

The post you cite above encounters "PGC-S-..." lines, where the "-S-" indicates a "Severe" error.  Your log has "PGC-I-..." ("Information) and "PGC-W-..." ("Warning") lines.  These generally don't affect the operation of the compiled code, but are things the developers may want to examine, especially if they appear when compiling end-user code.  You certainly want to run "make check" (perhaps with HDF5TestExpress=0) and look over the results carefully.  On macOS with PGI I see:

Testing soft denormalized float -> double conversions                 *WARNING*
[...]
maximum warnings reached, aborting test...

For hdf5-1.8.17, release_docs/INSTALL has a section "A.2.  Building and testing with PGI compilers" which says:
  

     set the environment variable CXX to "pgCC -tlocal"

--
George N. White III <[hidden email]>
Head of St. Margarets Bay, Nova Scotia

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[hidden email]
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Re: Unable to build HDF5 with pgi compilers

ashwin .D
In reply to this post by ashwin .D
> George, Matt and Carl.
>                                    Thanks much for all the suggestions. I
> was able to move past the configure errors by using a combination of all
> the tips you recommended. I in fact downloaded the hdf-1.10.1 version and
> while running make did not give any problems I have  a whole bunch of
> redundant macro warnings and which when I looked up is identical to this
> one - https://lists.hdfgroup.org/pipermail/hdf-forum_lists.
> hdfgroup.org/2010-July/003304.html.
> I have enclosed a trimmed version of my logs. Is it good to proceed
> forward or is there something I need to edit with the header files as well
> ? Note these warnings  do not occur with gfortran.
>
> Best regards,
> Ashwin.
>

>Sounds promissing.

>The post you cite above encounters "PGC-S-..." lines, where the "-S-"
>indicates a "Severe" error.  Your log has "PGC-I-..." ("Information) and
>"PGC-W-..." ("Warning") lines.  These generally don't affect the operation
>of the compiled code, but are things the developers may want to examine,
>especially if they appear when compiling end-user code.  You certainly want
>to run "make check" (perhaps with HDF5TestExpress=0) and look over the
>results carefully.  On macOS with PGI I see:

>Testing soft denormalized float -> double conversions
>*WARNING*
>[...]
>maximum warnings reached, aborting test...


>For hdf5-1.8.17, release_docs/INSTALL has a section "A.2.  Building and
>testing with PGI compilers" which says:


 >    set the environment variable CXX to "pgCC -tlocal"
Thanks I will definitely try that. But I have to let Carl and you know that I do not have a pgCC on my box. I only have  a pgc++. I checked for a pgCC under my installation and I could not find it.
What about modifying the header files as indicated in that post I linked ?
Are they not required ?

On Tue, Jun 27, 2017 at 8:36 AM, ashwin .D <[hidden email]> wrote:
George, Matt and Carl.
                                   Thanks much for all the suggestions. I was able to move past the configure errors by using a combination of all the tips you recommended. I in fact downloaded the hdf-1.10.1 version and while running make did not give any problems I have  a whole bunch of redundant macro warnings and which when I looked up is identical to this one - https://lists.hdfgroup.org/pipermail/hdf-forum_lists.hdfgroup.org/2010-July/003304.html.
I have enclosed a trimmed version of my logs. Is it good to proceed forward or is there something I need to edit with the header files as well ? Note these warnings  do not occur with gfortran.

Best regards,
Ashwin.

On Tue, Jun 27, 2017 at 3:09 AM, Carl Ponder <[hidden email]> wrote:
On 06/26/2017 01:42 AM, ashwin .D wrote:
I already have an existing installation of HDF5 1.8.17 compiled with gfortran. Now for another project on the same machine I need to compile with PGI compilers i.e. pgcc , pgc++and pgf90. The installation directory will be separate as well i.e. /opt/local/lib and /opt/local/include.

Ashwin -- here's a script that I use to build HDF5 1.10.1 using the PGI 17.5 compiler.
You might try testing with these components first to see if you can get it to build, and then go backlevel on the pieces that you want to use.

        -- Carl



This is how I try to build hdf5
CPPFLAGS=/opt/local/include CXXFLAGS=/opt//local/include LDFLAGS=/opt//local/lib CC=pgcc CXX=pgc++ FC=pgf90 F77=pgf77   ./configure --prefix=/opt/local --with-zlib=/opt/local --enable-fortran --enable-cxx.
and when I try doing this I get this error message -
checking for a BSD-compatible install... /usr/bin/install -c
checking whether build environment is sane... yes
checking for a thread-safe mkdir -p... /bin/mkdir -p
checking for gawk... no
checking for mawk... mawk
checking whether make sets $(MAKE)... yes
checking whether make supports nested variables... yes
checking whether make supports nested variables... (cached) yes
checking whether to enable maintainer-specific portions of Makefiles... no
checking build system type... x86_64-unknown-linux-gnu
checking host system type... x86_64-unknown-linux-gnu
checking shell variables initial values... done
checking if basename works... yes
checking if xargs works... yes
checking for cached host... none
checking for config x86_64-unknown-linux-gnu... no
checking for config x86_64-unknown-linux-gnu... no
checking for config unknown-linux-gnu... no
checking for config unknown-linux-gnu... no
checking for config x86_64-linux-gnu... no
checking for config x86_64-linux-gnu... no
checking for config x86_64-unknown... no
checking for config linux-gnu... found
compiler 'pgcc' is PGI pgcc-17.4-0
compiler 'pgf90' is PGI pgf90-17.4-0
No match to get cxx_version_info for pgc++
checking for config ./config/site-specific/host-Vostro-3800... no
checking for gcc... pgcc
checking whether the C compiler works... no
configure: error: in `/home//hdf5-1.8.17':
configure: error: C compiler cannot create executables
See `config.log' for more details
Any suggestions on how to build will be appreciated.



This email message is for the sole use of the intended recipient(s) and may contain confidential information.  Any unauthorized review, use, disclosure or distribution is prohibited.  If you are not the intended recipient, please contact the sender by reply email and destroy all copies of the original message.




_______________________________________________
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Re: Unable to build HDF5 with pgi compilers

ashwin .D
I encountered no problems with make check in HDF5. So I went ahead and installed it under /opt/local. Then I went downstream and compiled netcdf-4.4.1 while pointing to the HDF5 installation under /opt/local and could compile that as well. But when I did a make check on that one I got a lot of HDF 5 related errors. So obviously my HDF5 compilation is not a done deal yet.

On Tue, Jun 27, 2017 at 4:52 PM, ashwin .D <[hidden email]> wrote:
> George, Matt and Carl.
>                                    Thanks much for all the suggestions. I
> was able to move past the configure errors by using a combination of all
> the tips you recommended. I in fact downloaded the hdf-1.10.1 version and
> while running make did not give any problems I have  a whole bunch of
> redundant macro warnings and which when I looked up is identical to this
> one - https://lists.hdfgroup.org/pipermail/hdf-forum_lists.
> hdfgroup.org/2010-July/003304.html.
> I have enclosed a trimmed version of my logs. Is it good to proceed
> forward or is there something I need to edit with the header files as well
> ? Note these warnings  do not occur with gfortran.
>
> Best regards,
> Ashwin.
>

>Sounds promissing.

>The post you cite above encounters "PGC-S-..." lines, where the "-S-"
>indicates a "Severe" error.  Your log has "PGC-I-..." ("Information) and
>"PGC-W-..." ("Warning") lines.  These generally don't affect the operation
>of the compiled code, but are things the developers may want to examine,
>especially if they appear when compiling end-user code.  You certainly want
>to run "make check" (perhaps with HDF5TestExpress=0) and look over the
>results carefully.  On macOS with PGI I see:

>Testing soft denormalized float -> double conversions
>*WARNING*
>[...]
>maximum warnings reached, aborting test...


>For hdf5-1.8.17, release_docs/INSTALL has a section "A.2.  Building and
>testing with PGI compilers" which says:


 >    set the environment variable CXX to "pgCC -tlocal"
Thanks I will definitely try that. But I have to let Carl and you know that I do not have a pgCC on my box. I only have  a pgc++. I checked for a pgCC under my installation and I could not find it.
What about modifying the header files as indicated in that post I linked ?
Are they not required ?

On Tue, Jun 27, 2017 at 8:36 AM, ashwin .D <[hidden email]> wrote:
George, Matt and Carl.
                                   Thanks much for all the suggestions. I was able to move past the configure errors by using a combination of all the tips you recommended. I in fact downloaded the hdf-1.10.1 version and while running make did not give any problems I have  a whole bunch of redundant macro warnings and which when I looked up is identical to this one - https://lists.hdfgroup.org/pipermail/hdf-forum_lists.hdfgroup.org/2010-July/003304.html.
I have enclosed a trimmed version of my logs. Is it good to proceed forward or is there something I need to edit with the header files as well ? Note these warnings  do not occur with gfortran.

Best regards,
Ashwin.

On Tue, Jun 27, 2017 at 3:09 AM, Carl Ponder <[hidden email]> wrote:
On 06/26/2017 01:42 AM, ashwin .D wrote:
I already have an existing installation of HDF5 1.8.17 compiled with gfortran. Now for another project on the same machine I need to compile with PGI compilers i.e. pgcc , pgc++and pgf90. The installation directory will be separate as well i.e. /opt/local/lib and /opt/local/include.

Ashwin -- here's a script that I use to build HDF5 1.10.1 using the PGI 17.5 compiler.
You might try testing with these components first to see if you can get it to build, and then go backlevel on the pieces that you want to use.

        -- Carl



This is how I try to build hdf5
CPPFLAGS=/opt/local/include CXXFLAGS=/opt//local/include LDFLAGS=/opt//local/lib CC=pgcc CXX=pgc++ FC=pgf90 F77=pgf77   ./configure --prefix=/opt/local --with-zlib=/opt/local --enable-fortran --enable-cxx.
and when I try doing this I get this error message -
checking for a BSD-compatible install... /usr/bin/install -c
checking whether build environment is sane... yes
checking for a thread-safe mkdir -p... /bin/mkdir -p
checking for gawk... no
checking for mawk... mawk
checking whether make sets $(MAKE)... yes
checking whether make supports nested variables... yes
checking whether make supports nested variables... (cached) yes
checking whether to enable maintainer-specific portions of Makefiles... no
checking build system type... x86_64-unknown-linux-gnu
checking host system type... x86_64-unknown-linux-gnu
checking shell variables initial values... done
checking if basename works... yes
checking if xargs works... yes
checking for cached host... none
checking for config x86_64-unknown-linux-gnu... no
checking for config x86_64-unknown-linux-gnu... no
checking for config unknown-linux-gnu... no
checking for config unknown-linux-gnu... no
checking for config x86_64-linux-gnu... no
checking for config x86_64-linux-gnu... no
checking for config x86_64-unknown... no
checking for config linux-gnu... found
compiler 'pgcc' is PGI pgcc-17.4-0
compiler 'pgf90' is PGI pgf90-17.4-0
No match to get cxx_version_info for pgc++
checking for config ./config/site-specific/host-Vostro-3800... no
checking for gcc... pgcc
checking whether the C compiler works... no
configure: error: in `/home//hdf5-1.8.17':
configure: error: C compiler cannot create executables
See `config.log' for more details
Any suggestions on how to build will be appreciated.



This email message is for the sole use of the intended recipient(s) and may contain confidential information.  Any unauthorized review, use, disclosure or distribution is prohibited.  If you are not the intended recipient, please contact the sender by reply email and destroy all copies of the original message.





_______________________________________________
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http://lists.hdfgroup.org/mailman/listinfo/hdf-forum_lists.hdfgroup.org
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Re: Unable to build HDF5 with pgi compilers

George N. White III

On 27 June 2017 at 08:24, ashwin .D <[hidden email]> wrote:
I encountered no problems with make check in HDF5. So I went ahead and installed it under /opt/local. Then I went downstream and compiled netcdf-4.4.1 while pointing to the HDF5 installation under /opt/local and could compile that as well. But when I did a make check on that one I got a lot of HDF 5 related errors. So obviously my HDF5 compilation is not a done deal yet.

On Tue, Jun 27, 2017 at 4:52 PM, ashwin .D <[hidden email]> wrote:
> George, Matt and Carl.
>                                    Thanks much for all the suggestions. I
> was able to move past the configure errors by using a combination of all
> the tips you recommended. I in fact downloaded the hdf-1.10.1 version and
> while running make did not give any problems I have  a whole bunch of
> redundant macro warnings and which when I looked up is identical to this
> one - https://lists.hdfgroup.org/pipermail/hdf-forum_lists.
> hdfgroup.org/2010-July/003304.html.
> I have enclosed a trimmed version of my logs. Is it good to proceed
> forward or is there something I need to edit with the header files as well
> ? Note these warnings  do not occur with gfortran.
>
> Best regards,
> Ashwin.
>

>Sounds promissing.

>The post you cite above encounters "PGC-S-..." lines, where the "-S-"
>indicates a "Severe" error.  Your log has "PGC-I-..." ("Information) and
>"PGC-W-..." ("Warning") lines.  These generally don't affect the operation
>of the compiled code, but are things the developers may want to examine,
>especially if they appear when compiling end-user code.  You certainly want
>to run "make check" (perhaps with HDF5TestExpress=0) and look over the
>results carefully.  On macOS with PGI I see:

>Testing soft denormalized float -> double conversions
>*WARNING*
>[...]
>maximum warnings reached, aborting test...


>For hdf5-1.8.17, release_docs/INSTALL has a section "A.2.  Building and
>testing with PGI compilers" which says:


 >    set the environment variable CXX to "pgCC -tlocal"
Thanks I will definitely try that. But I have to let Carl and you know that I do not have a pgCC on my box. I only have  a pgc++. I checked for a pgCC under my installation and I could not find it.
What about modifying the header files as indicated in that post I linked ?

The changes to the header files should just hide the redundant defines, so shouldn't affect the compilation.  

It looks like the "pgCC -tlocal" usage is for an older version of the PGI compilers.  From an old PGI manual 
on the web, the -tlocal option is to make separate functions of each template instantiaion.  The current 
pgi17ug_x64.pdf (page 135) says:

"On Linux and macOS, the GNU-compatible pgc++ compiler uses the GNU g++ header files and Standard 

Template Library (STL) directly. The versions used are dependent on the version of the GNU compilers 

installed on your system, or specified when makelocalrc was run during installation of the PGI compilers. "  

 
Are they not required ?

Hard to answer without seeing the errors for the netcdf compile, but in general, once you have hdf5 libraries 
that pass the tests, problems using the libraries are not fixed by changes in the hdf5 build.  For those you may 
want to post on a netcdf forum. Although many people reading this list use netcdf, others who run into the 
same problems you are having when building netcdf will be looking for answers in netcdf forums, so for the 
sake of future users it is best to keep hdf5 separate from netcdf.

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Re: Unable to build HDF5 with pgi compilers

Carl Ponder
In reply to this post by ashwin .D
On 06/26/2017 10:06 PM, ashwin .D wrote:
Thanks much for all the suggestions. I was able to move past the configure errors by using a combination of all the tips you recommended. I in fact downloaded the hdf-1.10.1 version and while running make did not give any problems I have  a whole bunch of redundant macro warnings and which when I looked up is identical to this one - https://lists.hdfgroup.org/pipermail/hdf-forum_lists.hdfgroup.org/2010-July/003304.html.
I have enclosed a trimmed version of my logs. Is it good to proceed forward or is there something I need to edit with the header files as well ? Note these warnings  do not occur with gfortran.

Ashwin -- I have the same warnings in my logs.
I'm guessing that the same file is being include'd indirectly somehow, in which case the redundant definitions would be identical and not cause problems.
You'd have to ask the HDF5 developers about this, although I'd be interested in knowing the answer myself.
In the link you reference above, I see the warnings but they are in reference to an earlier posting and the reply was not included.

When you ran the regression-tests

make -i -k check

did they almost all pass?


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Re: Unable to build HDF5 with pgi compilers

ashwin .D
Carl,
           When I ran that command make -i -k check it passed every singe test. There wasn't a single error whatsoever. By the way I was able to fix that HDF5 error associated with netCDF as well. There is an environmental variable (that George hinted at) you have to set and and so I am all set now with the configuration of HDF5.

Ashwin.

On Tue, Jun 27, 2017 at 9:37 PM, Carl Ponder <[hidden email]> wrote:
On 06/26/2017 10:06 PM, ashwin .D wrote:
Thanks much for all the suggestions. I was able to move past the configure errors by using a combination of all the tips you recommended. I in fact downloaded the hdf-1.10.1 version and while running make did not give any problems I have  a whole bunch of redundant macro warnings and which when I looked up is identical to this one - https://lists.hdfgroup.org/pipermail/hdf-forum_lists.hdfgroup.org/2010-July/003304.html.
I have enclosed a trimmed version of my logs. Is it good to proceed forward or is there something I need to edit with the header files as well ? Note these warnings  do not occur with gfortran.

Ashwin -- I have the same warnings in my logs.
I'm guessing that the same file is being include'd indirectly somehow, in which case the redundant definitions would be identical and not cause problems.
You'd have to ask the HDF5 developers about this, although I'd be interested in knowing the answer myself.
In the link you reference above, I see the warnings but they are in reference to an earlier posting and the reply was not included.

When you ran the regression-tests

make -i -k check

did they almost all pass?


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Re: Unable to build HDF5 with pgi compilers

Carl Ponder
On 06/27/2017 11:32 AM, ashwin .D wrote:
When I ran that command make -i -k check it passed every singe test. There wasn't a single error whatsoever. By the way I was able to fix that HDF5 error associated with netCDF as well. There is an environmental variable (that George hinted at) you have to set and and so I am all set now with the configuration of HDF5.

What was the NetCDF setting? I'll have to check what I'm doing.

        -- Carl



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Re: Unable to build HDF5 with pgi compilers

ashwin .D
This maybe off topic so there is some background to that issue. After a successful configuration of HDF5 I went ahead and recompiled NetCDF with PGI compilers. Following that compilation I went ahead and ran make check and all of the HDF5 tests failed. So I was not sure whether the HDF5 compilation/configuration was successful or not because of the log messages that we just discussed. Then it turns out after some searching on the web you need to have this environment variable set on Linux (and only for Linux) CPPFLAGS = -DpgiFortran  -I/opt/local/include. This then ensures that all of the HDF5 tests associated with NetCDF successfully complete.

On Tue, Jun 27, 2017 at 10:07 PM, Carl Ponder <[hidden email]> wrote:
On 06/27/2017 11:32 AM, ashwin .D wrote:
When I ran that command make -i -k check it passed every singe test. There wasn't a single error whatsoever. By the way I was able to fix that HDF5 error associated with netCDF as well. There is an environmental variable (that George hinted at) you have to set and and so I am all set now with the configuration of HDF5.

What was the NetCDF setting? I'll have to check what I'm doing.

        -- Carl



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