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HDF 4.2.12 pre-release

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HDF 4.2.12 pre-release

Binh-Minh Ribler

Dear HDF4 users,


We are preparing to release HDF 4.2.12 in less than two weeks.  In this release, Java HDF JNI library is integrated into the HDF repository and a few bug fixes and improvements are done in tools and library functions. Please try on your platforms and let us know if you see any problems.


The pre-released HDF 4.2.12 tar files are available at:


ftp://ftp.hdfgroup.uiuc.edu/pub/outgoing/hdf4/hdf-4.2.12-pre1/


Or, you may ftp as followed:

  ftp ftp.hdfgroup.uiuc.edu
  <log in as "anonymous">
  bin (put in binary mode)
  cd pub/outgoing/hdf4/hdf-4.2.12-pre1
  get <file>

Thank you very much,

Binh-Minh

=============

The HDF Group



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Re: HDF 4.2.12 pre-release

Thompson, Matt (GSFC-610.1)[SCIENCE SYSTEMS AND APPLICATIONS INC]
On 06/21/2016 01:04 PM, Binh-Minh Ribler wrote:
> Dear HDF4 users,
>
>
> We are preparing to release HDF 4.2.12 in less than two weeks.  In this
> release, Java HDF JNI library is integrated into the HDF repository
> and a few bug fixes and improvements are done in tools and library
> functions. Please try on your platforms and let us know if you see any
> problems.

This pre-release has an issue your older ones do as well. When I try to
build with gcc 5.3.0 at NAS at NASA Ames I get:

> configure: error: linking to Fortran libraries from C fails
> See `config.log' for more details

I've attached my config.log. I believe the issue is due to the oddity of
how gcc5 was built at NAS using pkgsrc or spack or something; the
'-Wl,-R' in 'gcc -v' is my prime culprit. It's like HDF4 is seeing -Wl
flags for ld and thinking that -R then goes right to gcc?

Now, I have in the past built GCC myself with a very simple configure
that doesn't have the pkgsrc or anything bits the system folks there
build with and it works (with 4.2.11), so that's why I suspect the -Wl bits.

Matt

--
Matt Thompson, SSAI, Sr Scientific Programmer/Analyst
NASA GSFC,    Global Modeling and Assimilation Office
Code 610.1,  8800 Greenbelt Rd,  Greenbelt,  MD 20771
Phone: 301-614-6712                 Fax: 301-614-6246
http://science.gsfc.nasa.gov/sed/bio/matthew.thompson

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config.log (69K) Download Attachment
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Re: HDF 4.2.12 pre-release

bljones
In reply to this post by Binh-Minh Ribler

Hello Matt,

 

We tried building HDF4 with gcc 5.3.0 and 6.0.1 on Linux CentOS 7 and could not reproduce the issue. However, our gcc is not built with pkgsrc.

On our machine gcc 5.3 is configured like this:

 

$ /opt/gcc/5.3.0/bin/gcc -v

Using built-in specs.

COLLECT_GCC=/opt/gcc/5.3.0/bin/gcc

COLLECT_LTO_WRAPPER=/opt/gcc/5.3.0/libexec/gcc/x86_64-unknown-linux-gnu/5.3.0/lto-wrapper

Target: x86_64-unknown-linux-gnu

Configured with: ../gcc-5.3.0/configure --prefix=/opt/gcc/5.3.0/ --enable-languages=c,c++,fortran

Thread model: posix

gcc version 5.3.0 (GCC)

 

 

Looking at your config.log file we see this for the gcc configure line:

 

Configured with: ../gcc-5.3.0/configure --disable-libstdcxx-pch --enable-nls --with-libiconv-prefix=/usr --disable-multilib --enable-__cxa_atexit --with-gxx-include-dir=/nasa/pkgsrc/2015Q4/gcc5/include/c++/ --enable-languages='c obj-c++ objc fortran c++' --enable-shared --enable-long-long --with-local-prefix=/nasa/pkgsrc/2015Q4/gcc5 --enable-libssp --enable-threads=posix --with-boot-ldflags='-static-libstdc++ -static-libgcc -Wl,-R/nasa/pkgsrc/2015Q4/lib ' --with-arch=nocona --with-tune=nocona --with-fpmath=sse --prefix=/nasa/pkgsrc/2015Q4/gcc5 --build=x86_64-unknown-linux --host=x86_64-unknown-linux --infodir=/nasa/pkgsrc/2015Q4/gcc5/info --mandir=/nasa/pkgsrc/2015Q4/gcc5/man

 

We are wondering if the issue could be due to single quotes being used for option values rather than double quotes. For example:

    --with-boot-ldflags='-static-libstdc++ -static-libgcc -Wl,-R/nasa/pkgsrc/2015Q4/lib '

 

The HDF4 configure puts double quotes around options.

 

You could try setting the correct options in LDFLAGS before configuring HDF4. That will override the choices made by configure.
However, it is not clear whether that will help or not, since these options are with gcc, not HDF4.

 

If that doesn’t help please send us your Makefiles and we will look at them to see what we can find.

 

Thanks!

-Barbara

[hidden email]

 


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Re: HDF 4.2.12 pre-release

Thompson, Matt (GSFC-610.1)[SCIENCE SYSTEMS AND APPLICATIONS INC]
On 06/22/2016 03:06 PM, Barbara Jones wrote:

> Hello Matt,
>
> We tried building HDF4 with gcc 5.3.0 and 6.0.1 on Linux CentOS 7 and
> could not reproduce the issue. However, our gcc is not built with pkgsrc.
>
> On our machine gcc 5.3 is configured like this:
>
> $ /opt/gcc/5.3.0/bin/gcc -v
>
> Using built-in specs.
>
> COLLECT_GCC=/opt/gcc/5.3.0/bin/gcc
>
> COLLECT_LTO_WRAPPER=/opt/gcc/5.3.0/libexec/gcc/x86_64-unknown-linux-gnu/5.3.0/lto-wrapper
>
> Target: x86_64-unknown-linux-gnu
>
> Configured with: ../gcc-5.3.0/configure --prefix=/opt/gcc/5.3.0/
> --enable-languages=c,c++,fortran
>
> Thread model: posix
>
> gcc version 5.3.0 (GCC)
>
> Looking at your config.log file we see this for the gcc configure line:
>
> Configured with: ../gcc-5.3.0/configure --disable-libstdcxx-pch
> --enable-nls --with-libiconv-prefix=/usr --disable-multilib
> --enable-__cxa_atexit
> --with-gxx-include-dir=/nasa/pkgsrc/2015Q4/gcc5/include/c++/
> --enable-languages='c obj-c++ objc fortran c++' --enable-shared
> --enable-long-long --with-local-prefix=/nasa/pkgsrc/2015Q4/gcc5
> --enable-libssp --enable-threads=posix
> --with-boot-ldflags='-static-libstdc++ -static-libgcc
> -Wl,-R/nasa/pkgsrc/2015Q4/lib ' --with-arch=nocona --with-tune=nocona
> --with-fpmath=sse --prefix=/nasa/pkgsrc/2015Q4/gcc5
> --build=x86_64-unknown-linux --host=x86_64-unknown-linux
> --infodir=/nasa/pkgsrc/2015Q4/gcc5/info
> --mandir=/nasa/pkgsrc/2015Q4/gcc5/man
>
> We are wondering if the issue could be due to single quotes being used
> for option values rather than double quotes. For example:
>
> --with-boot-ldflags='-static-libstdc++ -static-libgcc
> -Wl,-R/nasa/pkgsrc/2015Q4/lib '
>
> The HDF4 configure puts double quotes around options.
>
> You could try setting the correct options in LDFLAGS before configuring
> HDF4. That will override the choices made by configure.
> However, it is not clear whether that will help or not, since these
> options are with gcc, not HDF4.
>
> If that doesn’t help please send us your Makefiles and we will look at
> them to see what we can find.
>
> Thanks!
>
> -Barbara

Barbara,

Yes, I too don't see this issue on my builds of GCC. It's only this one
from NAS. I've contacted my contact (hmm...) at NAS to see if he can try
building GCC with double quotes and we can try that. As I'm not even
sure how they build with all their stuff, I can't try it myself.

Of course, being GCC, it might be a day or so before I can report
results. Even 'make -j2000' doesn't make building GCC a "quick" affair.

Matt


--
Matt Thompson, SSAI, Sr Scientific Programmer/Analyst
NASA GSFC,    Global Modeling and Assimilation Office
Code 610.1,  8800 Greenbelt Rd,  Greenbelt,  MD 20771
Phone: 301-614-6712                 Fax: 301-614-6246
http://science.gsfc.nasa.gov/sed/bio/matthew.thompson

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