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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