[gmx-users] Re: gmx-users Digest, Vol 83, Issue 153

[Xiaohu Li]

Message: 4
Date: Tue, 22 Mar 2011 22:26:04 +0800
From: " Ye MEI " <ymei at itcs.ecnu.edu.cn>
Subject: Re: [gmx-users] New maintenance release: gromacs-4.5.4
To: " Discussion list for GROMACS users "       <gmx-users at gromacs.org>
Message-ID: <201103222226031153122 at 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
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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
=================================================
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