On 3/27/13 6:57 AM, Qinghua Liao wrote:
Dear gmx users,
I tried to compile gromacs 4.5.4 with double precision, but it failed. The
reason was a little wired.
Firstly, I used the following commands to compile gromacs 4.5.4 together
with fftw 3.3 for serial and parallel version with single precision, and I
made it successfully.
1014 ./configure --prefix=/usr/users/iff_th2/liao/fftw-3.3 --enable-sse
--enable-threads --enable-float --enable-shared CC=gcc
1015 make
1016 make install
1017 make distclean
1018 export CPPFLAGS=-I/usr/users/iff_th2/liao/fftw-3.3/include
1019 export LDFLAGS=-L/usr/users/iff_th2/liao/fftw-3.3/lib
1022 mv gromacs-4.5.4 gromacs454
1023 cd gromacs454/
1026 ./configure --prefix=/usr/users/iff_th2/liao/gromacs454/
--enable-float --enable-threads CC=gcc --disable-gcc41-check
1027 make
1028 make install
1031 make distclean
1032 cd ../fftw-3.3
1034 ./configure --prefix=/usr/users/iff_th2/liao/fftw-3.3 --enable-sse
--enable-threads --enable-float --enable-shared --enable-mpi CC=gcc
1035 make
1036 make install
1037 make distclean
1038 cd ../gromacs454/
1039 ls
1040 make distclean
1041 ./configure --prefix=/usr/users/iff_th2/liao/gromacs454/
--enable-float --enable-threads CC=gcc --disable-gcc41-check --enable-mpi
--program-suffix=_mpi
1042 make
1043 make install
1044 make distclean
But when I used these similar commands to compile for the double precision,
it failed.
1049 ./configure --prefix=/usr/users/iff_th2/liao/fftw-3.3
--enable-long-double --enable-threads --enable-shared --enable-mpi CC=gcc
1050 make
1051 make install
1052 make distclean
1053 cd ../gromacs454/
1054 make distclean
1055 ./configure --prefix=/usr/users/iff_th2/liao/gromacs454/
--enable-double --enable-threads CC=gcc --disable-gcc41-check --enable-mpi
--program-suffix=_d
1056 make
The error showed to me was:
/usr/bin/ld: /usr/local/lib/libfftw3.a(plan-dft-c2r-2d.o): relocation
R_X86_64_32 against `a local symbol' can not be used when making a shared
object; recompile with -fPIC /usr/local/lib/libfftw3.a: could not read
symbols: Bad value
I added the option of --with-fPIC, but it was not recognized, and then I
changed it to --with-pic, but the error was still the same.
I don't know why gromacs can recognize the fftw library when doing the
single float compilation, but not for the double float compilation, I
already used the shared option. Could someone give me some suggestions to
help me this out? Any reply will be appreciated.
In your last step, you're not using --enable-shared like you did in every
preceding step. Adding that flag should fix it.
http://www.gromacs.org/Documentation/Installation_Instructions_4.5#Details_for_building_the_FFTW_prerequisite
Gromacs 4.5.4 is pretty old; is there any reason you're not using a new version?
You'll get much better performance from 4.6.1.
-Justin
--
========================================
Justin A. Lemkul, Ph.D.
Research Scientist
Department of Biochemistry
Virginia Tech
Blacksburg, VA
jalemkul[at]vt.edu | (540) 231-9080
http://www.bevanlab.biochem.vt.edu/Pages/Personal/justin
========================================
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