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

[Yudong Sun]

Mark Abraham wrote, On 12/11/2010 17:02:
> On 13/11/2010 3:15 AM, Yudong Sun wrote:
>> 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
>
> So how does configure use this information? (hint: providing the
> configure command line is essential for us to understand any context!)
>
>>
>> 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.
>
> Sounds like configure isn't handling pgcc properly. However, GROMACS is
> using very vanilla autoconf stuff, so I'm strongly of the opinion that
> the problem isn't on the GROMACS side.
>
>>
>> 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.
>
> Don't know. Ask the autoconf list.
>
>>
>> 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?
>
> Don't bother with PGI compilers. GROMACS performance is 99%
> compiler-independent, thanks to hand-coded assembly for the inner loops.
> Use gcc.
>

I have tried GCC. It has the same static link problem:

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

Yudong

> Mark

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