[gmx-users] parallel install gromacs-4.0.4

Hongyan Xiao hyxiao at mail.ipc.ac.cn
Sun Mar 29 14:25:58 CEST 2009

Dear gmx-users,

When I parallel install gromacs-4.0.4. I encountered the problem. The 
following is my installation steps.

Step 1: install fftw-3.1.2
          # cd fftw-3.1.2
          # ./configure --enable-float --enable-mpi -enable-threads
          # make
          # make install
Step 2: install gromacs-4.0.4
           # cd gromacs-4.0.4
           #./configure  --enable-mpi --with-fftw3 --program-suffix=_mpi 
--enable-shared   --enable-sse
           # make
then I encountered the following errors:
mpicc -shared  .libs/calcmu.o .libs/calcvir.o .libs/constr.o 
.libs/coupling.o .libs/domdec.o .libs/domdec_con.o .libs/domdec_network.o 
.libs/domdec_setup.o .libs/domdec_top.o .libs/ebin.o .libs/edsam.o 
.libs/ewald.o .libs/fftgrid.o .libs/force.o .libs/ghat.o .libs/init.o 
.libs/mdatom.o .libs/mdebin.o .libs/minimize.o .libs/mvxvf.o .libs/ns.o 
.libs/nsgrid.o .libs/perf_est.o .libs/pme.o .libs/pme_pp.o .libs/pppm.o 
.libs/partdec.o .libs/pull.o .libs/pullutil.o .libs/rf_util.o .libs/shakef.o 
.libs/sim_util.o .libs/shellfc.o .libs/stat.o .libs/tables.o .libs/tgroup.o 
.libs/update.o .libs/vcm.o .libs/vsite.o .libs/wall.o .libs/wnblist.o 
.libs/csettle.o .libs/clincs.o .libs/qmmm.o .libs/gmx_fft.o 
.libs/gmx_parallel_3dfft.o .libs/gmx_wallcycle.o .libs/qm_gaussian.o 
.libs/gmx_fft_fftw3.o  -Wl,--rpath 
-Wl,/usr/local/gromacs-4.0.4/src/gmxlib/.libs -Wl,--rpath 
-Wl,/usr/local/gromacs/lib ../gmxlib/.libs/libgmx_mpi.so -L/usr/lib64 -lxml2 
-lnsl -lfftw3f -lSM -lICE -lX11  -Wl,-soname -Wl,libmd_mpi.so.5 -o 
ld: /usr/local/lib/libfftw3f.a(mapflags.o): relocation R_X86_64_32S against 
`a local symbol' can not be used when making a shared object; recompile with 
/usr/local/lib/libfftw3f.a: could not read symbols: Bad value
make[3]: *** [libmd_mpi.la] Error 1
make[3]: Leaving directory `/usr/local/gromacs-4.0.4/src/mdlib'
make[2]: *** [all-recursive] Error 1
make[2]: Leaving directory `/usr/local/gromacs-4.0.4/src'
make[1]: *** [all] Error 2
make[1]: Leaving directory `/usr/local/gromacs-4.0.4/src'
make: *** [all-recursive] Error 1

How to solve these problem?  Hope for your help. Thank you very much!

H.Y. Xiao
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