[gmx-users] PGI link error: unknown switch --rpath & attempted static link of dynamic object fftw/lib/libfftw3.so

[Yudong Sun]

Hi,

I have some troubles when compiling GROMACS 4.5.3 using PGI compiler on 
the -rpath flag and also a static link to dynamic libfftw3.so.

I use the pre-installed FFTW 3.2.2.1 library on my Linux system. The 
FFTW library is managed by the Modules package. The fftw module 
automatically sets the environ variable as:

FFTW_POST_LINK_OPTS = -L/opt/fftw/3.2.2.1/lib 
-Wl,-rpath=/opt/fftw/3.2.2.1/lib -lfftw3 -lfftw3f

When compiling, an error occurs on the -rpath:

pgcc -fast -o grompp grompp.o  ./.libs/libgmxpreprocess_mpi_d.a 
/usr/local/packages/nag/GROMACS/gromacs-4.5.3/src/mdlib/.libs/libmd_mpi_d.a 
../mdlib/.libs/libmd_mpi_d.a /opt/fftw/3.2.2.1/lib/libfftw3.so 
/usr/local/packages/nag/GROMACS/gromacs-4.5.3/src/gmxlib/.libs/libgmx_mpi_d.a 
../gmxlib/.libs/libgmx_mpi_d.a -ldl -lnsl -lm   --rpath 
/opt/fftw/3.2.2.1/lib --rpath /opt/fftw/3.2.2.1/lib
pgcc-Error-Unknown switch: --rpath
pgcc-Error-Unknown switch: --rpath

Pgcc doesn't recognize --rpath. The correct format is a single dash only 
-rpath.

If I manually remove the extra '-' (-rpath /opt/fftw/3.2.2.1/lib) and 
rerun the command line, a link error appears:

/usr/bin/ld: attempted static link of dynamic object 
`/opt/fftw/3.2.2.1/lib/libfftw3.so'

The command line links the dynamic fftw library. As the 'configure 
--help' shows the default is a static build. Why doesn't the configure 
pick the libfftw3.a but the libfftw3.so? The fftw library on my system 
contains both static and dynamic libraries.

I have also tried to make the old GROMACS 4.0.7 which has shown the same 
problems as above.

Any workarounds to the problems or what options should I pass to the 
configure?

Thanks,

Yudong

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