Compile error with HDF5-1.8.5-patch-1

I’m having this error when calling “make” to compile HDF5-1.8.5-patch-1 using PGI Fortran 11.1 on Ubuntu 9.04 x86-64.

./configure --prefix=/usr/local/hdf5 --enable-fortran --enable-cxx --with-szlib=/usr/local/szip/

make[3]: Entering directory `/home/minhtuan/install_download/hdf5/hdf5-1.8.5-patch1/fortran/src’
/bin/bash …/…/libtool --tag=FC --mode=link pgf95 -I…/…/src -I…/…/fortran/src -version-info 6:4:0 -L/usr/local/szip//lib -o -rpath /usr/local/hdf5/lib H5f90global.lo H5fortran_types.lo H5_ff.lo H5Aff.lo H5Dff.lo H5Eff.lo H5Fff.lo H5Gff.lo H5Iff.lo H5Lff.lo H5Off.lo H5Pff.lo H5Rff.lo H5Sff.lo H5Tff.lo H5Zff.lo H5_DBLE_InterfaceInclude.lo H5f90kit.lo H5_f.lo H5Af.lo H5Df.lo H5Ef.lo H5Ff.lo H5Gf.lo H5If.lo H5Lf.lo H5Of.lo H5Pf.lo H5Rf.lo H5Sf.lo H5Tf.lo H5Zf.lo HDF5.lo -lsz -lz -lm
libtool: link: pgf95 -shared -fpic -Mnomain .libs/H5f90global.o .libs/H5fortran_types.o .libs/H5_ff.o .libs/H5Aff.o .libs/H5Dff.o .libs/H5Eff.o .libs/H5Fff.o .libs/H5Gff.o .libs/H5Iff.o .libs/H5Lff.o .libs/H5Off.o .libs/H5Pff.o .libs/H5Rff.o .libs/H5Sff.o .libs/H5Tff.o .libs/H5Zff.o .libs/H5_DBLE_InterfaceInclude.o .libs/H5f90kit.o .libs/H5_f.o .libs/H5Af.o .libs/H5Df.o .libs/H5Ef.o .libs/H5Ff.o .libs/H5Gf.o .libs/H5If.o .libs/H5Lf.o .libs/H5Of.o .libs/H5Pf.o .libs/H5Rf.o .libs/H5Sf.o .libs/H5Tf.o .libs/H5Zf.o .libs/HDF5.o -Wl,-rpath -Wl,/usr/local/szip/lib -Wl,-rpath -Wl,/usr/local/szip/lib -L/usr/local/szip//lib /usr/local/szip/lib/ -lz -L/opt/pgi/linux86-64/11.1/libso -L/opt/pgi/linux86-64/11.1/lib -L/usr/lib64 -L/usr/lib/gcc/x86_64-linux-gnu/4.3.3 -lpgmp -lpgf90 -lpgf90_rpm1 -lpgf902 -lpgf90rtl -lpgftnrtl -lnspgc -lpgc -lrt -lpthread -lm -lc -lgcc -Wl,-soname -Wl, -o .libs/

**/usr/bin/ld: /opt/pgi/linux86-64/11.1/lib/libpgbind.a(bindsa.o): relocation R_X86_64_PC32 against undefined symbol syscall@@GLIBC_2.2.5' can not be used when making a shared object; recompile with -fPIC** /usr/bin/ld: final link failed: Bad value make[3]: *** [] Error 2 make[3]: Leaving directory /home/minhtuan/install_download/hdf5/hdf5-1.8.5-patch1/fortran/src’
make[2]: *** [all] Error 2
make[2]: Leaving directory /home/minhtuan/install_download/hdf5/hdf5-1.8.5-patch1/fortran/src' make[1]: *** [all-recursive] Error 1 make[1]: Leaving directory /home/minhtuan/install_download/hdf5/hdf5-1.8.5-patch1/fortran’


UPDATED: I have no problem with PGI Fortran 10.9. So, there should be some change in the compiler that mess it up.

Hi Tuan,

As part of the the 11.0 release, we started to link in our OpenMP libraries by default. libpgbind handles the core and memory binding on NUMA based systems. However, we failed to get the correct fpic version of libpgbind.a when creating shared libraries.

This problem will go away in this week’s 11.2 release since we’re able to move this functionality elsewhere and remove the libpgbind library altogether. In the mean time add the flag “-nomp” to your link to remove this library.

Hope this helps,

Many thanks Mat.