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
help@hdfgroup.org<mailto:help@hdfgroup.org>
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
···
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
--
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
