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 "$enable_mpi" = "yes" && AC_DISABLE_SHARED When i changed these two lines in AC_DISABLE_SHARED also gmx4.5.4 is compiled. Luca > Pablo Englebienne wrote: > > Hi all, > > > > I'm trying to compile release 4.5.4 on a system that has been running > > every release since 4.0.4 without a problem. Even 4.5.3 compiled fine > > with the following configure: > > > > LDFLAGS="-L/cvos/shared/apps/fftw/gcc/64/3.2/lib" > > CPPFLAGS="-I/cvos/shared/apps/fftw/gcc/64/3.2/include" ./configure > > --prefix=$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 -- gmx-users mailing list [email protected] http://lists.gromacs.org/mailman/listinfo/gmx-users Please search the archive at http://www.gromacs.org/Support/Mailing_Lists/Search before posting! Please don't post (un)subscribe requests to the list. Use the www interface or send it to [email protected]. Can't post? Read http://www.gromacs.org/Support/Mailing_Lists
