[gmx-users] Error compiling Gromacs 4.5.4: "relocation R_X86_64_32 against `a local symbol' can not be used when making a shared object; recompile with -fPIC"

[Justin A. Lemkul]

Pablo Englebienne wrote:
> Hi all,
> 
> I'm trying to compile release 4.5.4 on a system that has been running 
> every release since 4.0.4 without a problem. Even 4.5.3 compiled fine 
> with the following configure:
> 
> LDFLAGS="-L/cvos/shared/apps/fftw/gcc/64/3.2/lib" 
> CPPFLAGS="-I/cvos/shared/apps/fftw/gcc/64/3.2/include" ./configure 
> --prefix=$HOME/software
> 
> The LDFLAGS and CPPFLAGS specify the (non-standard) location of the FFTW 
> libraries and headers. Configure succeeds in creating the Makefiles, but 
> when running make it aborts at this point:
> 
> cc  -shared  .libs/calcmu.o .libs/calcvir.o .libs/constr.o 
> .libs/coupling.o .libs/domdec.o .libs/domdec_box.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/force.o .libs/forcerec.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/genborn.o 
> .libs/genborn_sse2_single.o .libs/genborn_sse2_double.o 
> .libs/genborn_allvsall.o .libs/genborn_allvsall_sse2_single.o 
> .libs/genborn_allvsall_sse2_double.o .libs/gmx_qhop_parm.o 
> .libs/gmx_qhop_xml.o .libs/groupcoord.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/tpi.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/fft5d.o .libs/gmx_wallcycle.o .libs/qm_gaussian.o .libs/qm_mopac.o 
> .libs/qm_gamess.o .libs/gmx_fft_fftw2.o .libs/gmx_fft_fftw3.o 
> .libs/gmx_fft_fftpack.o .libs/gmx_fft_mkl.o .libs/qm_orca.o 
> .libs/mdebin_bar.o  -Wl,--rpath 
> -Wl,/home/penglebie/downloads/gromacs-4.5.4/src/gmxlib/.libs -Wl,--rpath 
> -Wl,/home/penglebie/software/lib 
> /cvos/shared/apps/fftw/gcc/64/3.2/lib/libfftw3f.a -lxml2 
> -L/cvos/shared/apps/fftw/gcc/64/3.2/lib ../gmxlib/.libs/libgmx.so -lnsl 
> -lm  -msse2 -pthread -Wl,-soname -Wl,libmd.so.6 -o .libs/libmd.so.6.0.0
> /usr/bin/ld: 
> /cvos/shared/apps/fftw/gcc/64/3.2/lib/libfftw3f.a(plan-many-dft-r2c.o): 
> relocation R_X86_64_32 against `a local symbol' can not be used when 
> making a shared object; recompile with -fPIC
> /cvos/shared/apps/fftw/gcc/64/3.2/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/penglebie/downloads/gromacs-4.5.4/src/mdlib'
> make[2]: *** [all-recursive] Error 1
> make[2]: Leaving directory `/home/penglebie/downloads/gromacs-4.5.4/src'
> make[1]: *** [all] Error 2
> make[1]: Leaving directory `/home/penglebie/downloads/gromacs-4.5.4/src'
> make: *** [all-recursive] Error 1
> 
> I see that recently 
> (http://lists.gromacs.org/pipermail/gmx-users/2011-April/059919.html) 
> another user encountered the same problem but this time with version 
> 4.5.3; in my case 4.5.3 compiles fine, the only issue is with 4.5.4.
> 

The solution is discussed in the installation instructions:

http://www.gromacs.org/Downloads/Installation_Instructions#Prerequisites

> The system is running Scientific Linux 5.5.
> 
> $ uname -a
> 
> Linux ST-HPC-Main 2.6.18-128.7.1.el5 #1 SMP Mon Aug 24 08:12:52 EDT 2009 
> x86_64 x86_64 x86_64 GNU/Linux
> 
> 
> I am puzzled as to why it doesn't work in 4.5.4 but did until the 
> previous release. Did something change in this respect?
> 

Maybe, but the fact that this issue has come up numerous times in several 
versions suggests not.  As for why 4.5.3 works and 4.5.4 doesn't, I can't say 
specifically.  Please follow the instructions linked above and see if it fixes 
your problem.

-Justin

> Regards,
> Pablo
> 

-- 
========================================

Justin A. Lemkul
Ph.D. Candidate
ICTAS Doctoral Scholar
MILES-IGERT Trainee
Department of Biochemistry
Virginia Tech
Blacksburg, VA
jalemkul[at]vt.edu | (540) 231-9080
http://www.bevanlab.biochem.vt.edu/Pages/Personal/justin

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