Re: [gmx-users] New maintenance release: gromacs-4.5.4
Hi, try to add the --disable-shared flag to your invocation of .configure. Carsten On Mar 22, 2011, at 3:26 PM, Ye MEI wrote: > Thank you for the new version of gromacs. > But the compilation of gromacs failed on my computer. The commands are as > follows: > make distclean > export CC=icc > export F77=ifort > export CXX=icc > export CFLAGS="-xS -I/apps/fftw3/include" > export FFLAGS="-xS -I/apps/fftw3/include" > export CXXFLAGS="-I/apps/fftw3/include" > export LDFLAGS="-L/apps/fftw3/lib -lfftw3f" > ./configure --prefix=/apps/gromacs4.5 --with-fft=fftw3 --with-x > --with-qmmm-gaussian > make > > and the error message is > icc -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/ymei/gromacs-4.5.4/src/gmxlib/.libs -Wl,--rpath > -Wl,/apps/gromacs4.5/lib -lxml2 -L/apps/fftw3/lib /apps/fftw3/lib/libfftw3f.a > ../gmxlib/.libs/libgmx.so -lnsl -pthread -Wl,-soname -Wl,libmd.so.6 -o > .libs/libmd.so.6.0.0 > ld: /apps/fftw3/lib/libfftw3f.a(problem.o): relocation R_X86_64_32 against `a > local symbol' can not be used when making a shared object; recompile with > -fPIC > /apps/fftw3/lib/libfftw3f.a: could not read symbols: Bad value > > However, it works fine for gromacs 4.5.3. Can anyone help? > > Ye MEI > > 2011-03-22 > > > > From： Rossen Apostolov > Date： 2011-03-22 03:24:55 > To： Discussion list for GROMACS development; Discussion list for GROMACS > users; gmx-announce > CC： > Subject： [gmx-users] New maintenance release: gromacs-4.5.4 > > Dear Gromacs community, > A new maintenance release of Gromacs is available for download at > ftp://ftp.gromacs.org/pub/gromacs/gromacs-4.5.4.tar.gz. > Some notable updates in this release: > * Fixed pdb2gmx picking up force field from local instead of library > directory > * Made pdb2gmx vsite generation work again for certain His namings. > * Fixed incorrect virial and pressure averages with certain nst... > values (instantaneous values correct) > * Fixed incorrect cosine viscosity output > * New -multidir alternative for mdrun -multi option > * Several minor fixes in analysis tools > * Several updates to the program documentation > Big thanks to all developers and users! > Happy simulating! > Rossen > -- > gmx-users mailing listgmx-users@gromacs.org > 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 gmx-users-requ...@gromacs.org. > Can't post? Read http://www.gromacs.org/Support/Mailing_Lists > -- > gmx-users mailing listgmx-users@gromacs.org > 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 gmx-users-requ...@gromacs.org. > Can't post? Read http://www.gromacs.org/Support/Mailing_Lists -- gmx-users mailing listgmx-users@gromacs.org 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 gmx-users-requ...@gromacs.org. Can't post? Read http://www.gromacs.org/Support/Mailing_Lists
Re: [gmx-users] New maintenance release: gromacs-4.5.4
On Tue, Mar 22, 2011 at 10:26 AM, Ye MEI wrote: > Thank you for the new version of gromacs. > But the compilation of gromacs failed on my computer. The commands are as > follows: > make distclean > export CC=icc > export F77=ifort > export CXX=icc > export CFLAGS="-xS -I/apps/fftw3/include" > export FFLAGS="-xS -I/apps/fftw3/include" > export CXXFLAGS="-I/apps/fftw3/include" > export LDFLAGS="-L/apps/fftw3/lib -lfftw3f" > ./configure --prefix=/apps/gromacs4.5 --with-fft=fftw3 --with-x > --with-qmmm-gaussian > make > > and the error message is > icc -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/ymei/gromacs-4.5.4/src/gmxlib/.libs -Wl,--rpath > -Wl,/apps/gromacs4.5/lib -lxml2 -L/apps/fftw3/lib /apps/fftw3/lib/libfftw3f.a > ../gmxlib/.libs/libgmx.so -lnsl -pthread -Wl,-soname -Wl,libmd.so.6 -o > .libs/libmd.so.6.0.0 > ld: /apps/fftw3/lib/libfftw3f.a(problem.o): relocation R_X86_64_32 against `a > local symbol' can not be used when making a shared object; recompile with > -fPIC > /apps/fftw3/lib/libfftw3f.a: could not read symbols: Bad value Either recompile fftw with additional flag --with-pic or recompile GROMACS with --disable-shared. Roland > > However, it works fine for gromacs 4.5.3. Can anyone help? > > Ye MEI > > 2011-03-22 > > > > From： Rossen Apostolov > Date： 2011-03-22 03:24:55 > To： Discussion list for GROMACS development; Discussion list for GROMACS > users; gmx-announce > CC： > Subject： [gmx-users] New maintenance release: gromacs-4.5.4 > > Dear Gromacs community, > A new maintenance release of Gromacs is available for download at > ftp://ftp.gromacs.org/pub/gromacs/gromacs-4.5.4.tar.gz. > Some notable updates in this release: > * Fixed pdb2gmx picking up force field from local instead of library > directory > * Made pdb2gmx vsite generation work again for certain His namings. > * Fixed incorrect virial and pressure averages with certain nst... > values (instantaneous values correct) > * Fixed incorrect cosine viscosity output > * New -multidir alternative for mdrun -multi option > * Several minor fixes in analysis tools > * Several updates to the program documentation > Big thanks to all developers and users! > Happy simulating! > Rossen > -- > gmx-users mailing list gmx-users@gromacs.org > 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 gmx-users-requ...@gromacs.org. > Can't post? Read http://www.gromacs.org/Support/Mailing_Lists > > -- > gmx-users mailing list gmx-users@gromacs.org > 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 gmx-users-requ...@gromacs.org. > Can't post? Read http://www.gromacs.org/Support/Mailing_Lists > -- ORNL/UT Center for Molecular Biophysics cmb.ornl.gov 865-241-1537, ORNL PO BOX 2008 MS6309 -- gmx-users mailing listgmx-users@gromacs.org 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 gmx-users-requ...@gromacs.org. Can't post? Read http://www.gromacs.org/Support/Mailing_Lists
Re: [gmx-users] New maintenance release: gromacs-4.5.4
Thank you for the new version of gromacs. But the compilation of gromacs failed on my computer. The commands are as follows: make distclean export CC=icc export F77=ifort export CXX=icc export CFLAGS="-xS -I/apps/fftw3/include" export FFLAGS="-xS -I/apps/fftw3/include" export CXXFLAGS="-I/apps/fftw3/include" export LDFLAGS="-L/apps/fftw3/lib -lfftw3f" ./configure --prefix=/apps/gromacs4.5 --with-fft=fftw3 --with-x --with-qmmm-gaussian make and the error message is icc -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/ymei/gromacs-4.5.4/src/gmxlib/.libs -Wl,--rpath -Wl,/apps/gromacs4.5/lib -lxml2 -L/apps/fftw3/lib /apps/fftw3/lib/libfftw3f.a ../gmxlib/.libs/libgmx.so -lnsl -pthread -Wl,-soname -Wl,libmd.so.6 -o .libs/libmd.so.6.0.0 ld: /apps/fftw3/lib/libfftw3f.a(problem.o): relocation R_X86_64_32 against `a local symbol' can not be used when making a shared object; recompile with -fPIC /apps/fftw3/lib/libfftw3f.a: could not read symbols: Bad value However, it works fine for gromacs 4.5.3. Can anyone help? Ye MEI 2011-03-22 From： Rossen Apostolov Date： 2011-03-22 03:24:55 To： Discussion list for GROMACS development; Discussion list for GROMACS users; gmx-announce CC： Subject： [gmx-users] New maintenance release: gromacs-4.5.4 Dear Gromacs community, A new maintenance release of Gromacs is available for download at ftp://ftp.gromacs.org/pub/gromacs/gromacs-4.5.4.tar.gz. Some notable updates in this release: * Fixed pdb2gmx picking up force field from local instead of library directory * Made pdb2gmx vsite generation work again for certain His namings. * Fixed incorrect virial and pressure averages with certain nst... values (instantaneous values correct) * Fixed incorrect cosine viscosity output * New -multidir alternative for mdrun -multi option * Several minor fixes in analysis tools * Several updates to the program documentation Big thanks to all developers and users! Happy simulating! Rossen -- gmx-users mailing listgmx-users@gromacs.org 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 gmx-users-requ...@gromacs.org. Can't post? Read http://www.gromacs.org/Support/Mailing_Lists -- gmx-users mailing listgmx-users@gromacs.org 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 gmx-users-requ...@gromacs.org. Can't post? Read http://www.gromacs.org/Support/Mailing_Lists
[gmx-users] New maintenance release: gromacs-4.5.4
Dear Gromacs community, A new maintenance release of Gromacs is available for download at ftp://ftp.gromacs.org/pub/gromacs/gromacs-4.5.4.tar.gz. Some notable updates in this release: * Fixed pdb2gmx picking up force field from local instead of library directory * Made pdb2gmx vsite generation work again for certain His namings. * Fixed incorrect virial and pressure averages with certain nst... values (instantaneous values correct) * Fixed incorrect cosine viscosity output * New -multidir alternative for mdrun -multi option * Several minor fixes in analysis tools * Several updates to the program documentation Big thanks to all developers and users! Happy simulating! Rossen -- gmx-users mailing listgmx-users@gromacs.org 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 gmx-users-requ...@gromacs.org. Can't post? Read http://www.gromacs.org/Support/Mailing_Lists
