Re: [gmx-users] New maintenance release: gromacs-4.5.4

Ye MEI ymei at
Tue Mar 22 15:26:04 CET 2011

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

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/ -lnsl  -pthread -Wl,-soname -Wl, -o .libs/
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?



From: Rossen Apostolov 
Date: 2011-03-22  03:24:55 
To: Discussion list for GROMACS development; Discussion list for GROMACS users; gmx-announce 
Subject: [gmx-users] New maintenance release: gromacs-4.5.4 
Dear Gromacs community,
A new maintenance release of Gromacs is available for download at
Some notable updates in this release:
* Fixed pdb2gmx picking up force field from local instead of library 
* 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!
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