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Message: 4<br>
Date: Tue, 22 Mar 2011 22:26:04 +0800<br>
From: " Ye MEI " <<a href="mailto:ymei@itcs.ecnu.edu.cn">ymei@itcs.ecnu.edu.cn</a>><br>
Subject: Re: [gmx-users] New maintenance release: gromacs-4.5.4<br>
To: " Discussion list for GROMACS users " <<a href="mailto:gmx-users@gromacs.org">gmx-users@gromacs.org</a>><br>
Message-ID: <<a href="mailto:201103222226031153122@itcs.ecnu.edu.cn">201103222226031153122@itcs.ecnu.edu.cn</a>><br><div>
Content-Type: text/plain; charset="utf-8"<br></div><div><br></div><div><br></div><div>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.</div>
<div><br></div>
<br>
Thank you for the new version of gromacs.<br>
But the compilation of gromacs failed on my computer. The commands are as follows:<br>
make distclean<br>
export CC=icc<br>
export F77=ifort<br>
export CXX=icc<br>
export CFLAGS="-xS -I/apps/fftw3/include"<br>
export FFLAGS="-xS -I/apps/fftw3/include"<br>
export CXXFLAGS="-I/apps/fftw3/include"<br>
export LDFLAGS="-L/apps/fftw3/lib -lfftw3f"<br>
./configure --prefix=/apps/gromacs4.5 --with-fft=fftw3 --with-x --with-qmmm-gaussian<br>
make<br>
<br>
and the error message is<br>
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<br>
.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<br>
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<br>
/apps/fftw3/lib/libfftw3f.a: could not read symbols: Bad value<br>
<br>
However, it works fine for gromacs 4.5.3. Can anyone help?<br>
<br>
Ye MEI<br>
<br>
2011-03-22<br>
<br>
<br>
<br>
From： Rossen Apostolov<br>
Date： 2011-03-22 03:24:55<br>
To： Discussion list for GROMACS development; Discussion list for GROMACS users; gmx-announce<br>
CC：<br>
Subject： [gmx-users] New maintenance release: gromacs-4.5.4<br>
<br>
Dear Gromacs community,<br>
A new maintenance release of Gromacs is available for download at<br>
<a href="ftp://ftp.gromacs.org/pub/gromacs/gromacs-4.5.4.tar.gz" target="_blank">ftp://ftp.gromacs.org/pub/gromacs/gromacs-4.5.4.tar.gz</a>.<br>
Some notable updates in this release:<br>
* Fixed pdb2gmx picking up force field from local instead of library<br>
directory<br>
* Made pdb2gmx vsite generation work again for certain His namings.<br>
* Fixed incorrect virial and pressure averages with certain nst...<br>
values (instantaneous values correct)<br>
* Fixed incorrect cosine viscosity output<br>
* New -multidir alternative for mdrun -multi option<br>
* Several minor fixes in analysis tools<br>
* Several updates to the program documentation<br>
Big thanks to all developers and users!<br>
Happy simulating!<br>
Rossen<br>
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End of gmx-users Digest, Vol 83, Issue 153<br>
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</font><br><br clear="all"><br>-- <br>=================================================<br>Xiaohu Li<br>Post-doctoral Research Associate<br>Department of Chemistry<br>Northwestern University<br>2145 Sheridan Road<br>Evanston IL 60208<br>
U.S.A<br>=================================================<br><br>