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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