Re: [gmx-users] parallel install gromacs-4.0.4
Hongyan Xiao wrote: Dear Mark, I do not understand your meaning. Can you explain it to me again? Thanks! Since the problem stems from shared objects, don't use --enable-shared. -Justin H.Y. Xiao ___ gmx-users mailing listgmx-users@gromacs.org http://www.gromacs.org/mailman/listinfo/gmx-users Please search the archive at http://www.gromacs.org/search before posting! Please don't post (un)subscribe requests to the list. Use the www interface or send it to gmx-users-requ...@gromacs.org. Can't post? Read http://www.gromacs.org/mailing_lists/users.php -- Justin A. Lemkul Graduate Research Assistant ICTAS Doctoral Scholar Department of Biochemistry Virginia Tech Blacksburg, VA jalemkul[at]vt.edu | (540) 231-9080 http://www.bevanlab.biochem.vt.edu/Pages/Personal/justin ___ gmx-users mailing listgmx-users@gromacs.org http://www.gromacs.org/mailman/listinfo/gmx-users Please search the archive at http://www.gromacs.org/search before posting! Please don't post (un)subscribe requests to the list. Use the www interface or send it to gmx-users-requ...@gromacs.org. Can't post? Read http://www.gromacs.org/mailing_lists/users.php
[gmx-users] parallel install gromacs-4.0.4
Dear Mark, I do not understand your meaning. Can you explain it to me again? Thanks! H.Y. Xiao ___ gmx-users mailing listgmx-users@gromacs.org http://www.gromacs.org/mailman/listinfo/gmx-users Please search the archive at http://www.gromacs.org/search before posting! Please don't post (un)subscribe requests to the list. Use the www interface or send it to gmx-users-requ...@gromacs.org. Can't post? Read http://www.gromacs.org/mailing_lists/users.php
Re: [gmx-users] parallel install gromacs-4.0.4
Hongyan Xiao wrote: 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 .libs/libmd_mpi.so.5.0.0 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 -fPIC How to solve these problem? Hope for your help. Thank you very much! Start by not trying to make shared objects? Mark ___ gmx-users mailing listgmx-users@gromacs.org http://www.gromacs.org/mailman/listinfo/gmx-users Please search the archive at http://www.gromacs.org/search before posting! Please don't post (un)subscribe requests to the list. Use the www interface or send it to gmx-users-requ...@gromacs.org. Can't post? Read http://www.gromacs.org/mailing_lists/users.php
[gmx-users] parallel install gromacs-4.0.4
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 .libs/libmd_mpi.so.5.0.0 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 -fPIC /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 ___ gmx-users mailing listgmx-users@gromacs.org http://www.gromacs.org/mailman/listinfo/gmx-users Please search the archive at http://www.gromacs.org/search before posting! Please don't post (un)subscribe requests to the list. Use the www interface or send it to gmx-users-requ...@gromacs.org. Can't post? Read http://www.gromacs.org/mailing_lists/users.php
