On 29/05/2012 6:37 PM, a a wrote:
Dear Sir/Madam,
Thanks for the insightful comments from the experts. Follows the
steps, I found the source of error:
This what I have done:
====================================================
In the following directory /home/softwares/fftw-3.0.1:
./configure --enable-shared --prefix=/home/softwares/fftw301
make
make install
In the .bash file:
export CPPFLAGS="-I/home/softwares/fftw301/include"
export LDFLAGS="-L/home/softwares/fftw301/lib"
go to the following directory /home/softwares/gromacs-4.5.5:
./configure --enable-shared --prefix=/home/softwares/g455
make
============================================= ==============
In the middle of the make, I found this error message:
==========================================================
/usr/bin/ld: /usr/local/lib/libfftw3f.a(alloc.o): relocation
R_X86_64_32 against `.rodata.str1.1' can not be used when making a
shared object; recompile with -fPIC
/usr/local/lib/libfftw3f.a: could not read symbols: Bad value
collect2: ld returned 1 exit status
make[3]: *** [libmd.la] Error 1
make[3]: Leaving directory `/home/softwares/gromacs-4.5.5/src/mdlib'
make[2]: *** [all-recursive] Error 1
make[2]: Leaving directory `/home/softwares/gromacs-4.5.5/src'
make[1]: *** [all] Error 2
make[1]: Leaving directory `/home/softwares/gromacs-4.5.5/src'
make: *** [all-recursive] Error 1
============================================================
It seems to be a problem of 64 and 32 bit, my workstation is a 64 bit
machine and the OS is also 64 bit, what should I do to make sure both
the fftw-3.0.1 library and GROMACS are compiled with 64 bit settings?
I would start by observing that those error messages pertain to an
installation of FFTW that configure found in /usr/local/lib, and not the
one in /home/softwares. You have to sort that out first, since this
error messages indicates the need to use FFTW configured with
--enable-shared, per the link I gave last time.
Mark
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