Message: 4 Date: Tue, 22 Mar 2011 22:26:04 +0800 From: " Ye MEI " <y...@itcs.ecnu.edu.cn> Subject: Re: [gmx-users] New maintenance release: gromacs-4.5.4 To: " Discussion list for GROMACS users " <gmx-users@gromacs.org> Message-ID: <201103222226031153...@itcs.ecnu.edu.cn> Content-Type: text/plain; charset="utf-8"
Check your error output, you need the -fPIC flag turned on when you are compiling FFTW which will generate a shared object so that it can be linked to other library. 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 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! End of gmx-users Digest, Vol 83, Issue 153 ****************************************** -- ================================================= Xiaohu Li Post-doctoral Research Associate Department of Chemistry Northwestern University 2145 Sheridan Road Evanston IL 60208 U.S.A =================================================
-- 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