Luca Bellucci wrote:
Hi all,
I have encountered the same problem.
With this command:
./configure --with-fft=mkl --prefix=/path/gmx-4.5.3 --enable-mpi
"make mdrun" works well
When i used the same option with gmx 4.5.4
./configure --with-fft=mkl --prefix=/path/gmx-4.5.4 --enable-mpi
"make mdrun" did not work.
The compilation reported this error:
ld: /usr/local/mpich2-1.3.2p2-install/lib/libmpich.a(allreduce.o): relocation
R_X86_64_32 against `_2__STRING.14' can not be used when making a shared
object; recompile with -fPIC
etc..
the problem here seems to be the use of shared or static libraries.
I done configure command several times using the " --with-pic" and other
combinations, however I did not resolve the problem. Perhaps there is an
option that I have not seen!!
Anyway I released that there is a different default behavior of the "configure"
command.
In fact using the options reported above the configure command gives in
configure.ac for 4.5.3 at line ~27:
AC_DISABLE_SHARED
whereas in configure.ac for 4.5.4 ther is
AC_ENABLE_SHARED
test "$enable_mpi" = "yes" && AC_DISABLE_SHARED
When i changed these two lines in AC_DISABLE_SHARED also gmx4.5.4 is compiled.
I think there may indeed be a problem with the build system, after all. When I
checked the configuration output, I saw:
...
checking whether to build shared libraries...yes
checking whether to build static libraries...yes
...
Please file a redmine issue so that this can be investigated, and fixed if
necessary.
redmine.gromacs.org
-Justin
Luca
Pablo Englebienne wrote:
Hi all,
I'm trying to compile release 4.5.4 on a system that has been running
every release since 4.0.4 without a problem. Even 4.5.3 compiled fine
with the following configure:
LDFLAGS="-L/cvos/shared/apps/fftw/gcc/64/3.2/lib"
CPPFLAGS="-I/cvos/shared/apps/fftw/gcc/64/3.2/include" ./configure
--prefix=$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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