[gmx-users] FFTW & Gromacs installation on AIX 5.3
Justin A. Lemkul
jalemkul at vt.edu
Wed Aug 20 13:05:20 CEST 2008
We recently ran into this issue, and it was solved by re-compiling FFTW in
single precision. I would suggest talking to your sysadmin to see if you can
get the right precision compiled. Not a bad idea to have both single and double
precision available to you, anyway :)
-Justin
Senthil Kumar M wrote:
> Hi,
>
> Earlier i had faced problems installing FFTW on IBM p595. Thankfully
> now I had found out that they were already installed and I assumed
> they weren't:
>
> z193csd at gaia:~/gromacs-3.3.3$ ls -al /applic/local/lib/libfftw3.*
> -rw-r--r-- 1 applic in0007 2507094 Nov 12 2007
> /applic/local/lib/libfftw3.a
> -rwxr-xr-x 1 applic in0007 766 Nov 12 2007
> /applic/local/lib/libfftw3.la
>
> And here:
>
> z193csd at gaia:~/gromacs-3.3.3$ ls -al /applic/local/include/fftw3.*
> -rw-r--r-- 1 applic in0007 2373 Nov 12 2007
> /applic/local/include/fftw3.f
> -rw-r--r-- 1 applic in0007 14011 Nov 12 2007
> /applic/local/include/fftw3.h
>
> I have added the following lines to my .bashrc:
>
> # for Gromacs
> export CPPFLAGS=-I/applic/local/include
> export LDFLAGS=-L/applic/local/lib
>
> export AR='ar -X 32'
> export CC='xlc_r -q32'
> export F77='xlf_r -q32'
> export CXX='xlC_r -q32'
> export OBJECT_MODE=32
> export FFLAGS='-O2 -qarch=pwr5 -qtune=pwr5 -qmaxmem=-1 -qstrict'
> export CFLAGS='-O2 -qarch=pwr5 -qtune=pwr5 -qmaxmem=-1 -qstrict'
> export FFLAGS='-O4 -qmaxmem=-1 -qstrict'
> export CFLAGS='-O4 -qmaxmem=-1 -qstrict'
> export MPICC=mpicc
>
> After that, I do:
> z193csd at gaia:~/gromacs-3.3.3$ ./configure --prefix=$HOME/GROMACS333 > result
>
> I get the following:
>
> configure: WARNING: unknown Fortran name-mangling scheme
> ./configure[24445]: ACX_FIXED_FUNC_FSEEKO: not found
>
> And a grep for fftw in the file result yields:
>
> z193csd at gaia:~/gromacs-3.3.3$ grep fftw result
> checking for fftw3.h... yes
> checking for main in -lfftw3f... yes
>
>
> And tail result gives:
> z193csd at gaia:~/gromacs-3.3.3$ tail result
> config.status: creating share/template/Makefile
> config.status: creating share/top/Makefile
> config.status: creating share/html/Makefile
> config.status: creating share/html/images/Makefile
> config.status: creating share/html/online/Makefile
> config.status: creating man/Makefile
> config.status: creating man/man1/Makefile
> config.status: creating src/config.h
> config.status: executing depfiles commands
>
> And a grep for fftw in the config.log file yields:
> z193csd at gaia:~/gromacs-3.3.3$ grep fftw config.log
> configure:25588: checking for fftw3.h
> configure:25636: checking for main in -lfftw3f
> configure:25673: xlc_r -q32 -o conftest -O4 -qmaxmem=-1 -qstrict
> -I/applic/local/include -L/applic/local/lib conftest.c -lfftw3f -lm
>> &5
> 1586-403 (E) Library file "fftw3f" not found.
> configure:26248: xlc_r -q32 -o conftest -O4 -qmaxmem=-1 -qstrict
> -I/applic/local/include -L/applic/local/lib conftest.c -lnsl -lfftw3f
> -lm >&5
> 1586-403 (E) Library file "fftw3f" not found.
> configure:26323: xlc_r -q32 -o conftest -O4 -qmaxmem=-1 -qstrict
> -I/applic/local/include -L/applic/local/lib conftest.c -lnsl -lfftw3f
> -lm >&5
> 1586-403 (E) Library file "fftw3f" not found.
> configure:26423: xlc_r -q32 -o conftest -O4 -qmaxmem=-1 -qstrict
> -I/applic/local/include -L/applic/local/lib conftest.c -lnsl -lfftw3f
> -lm >&5
> 1586-403 (E) Library file "fftw3f" not found.
> configure:26593: xlc_r -q32 -o conftest -O4 -qmaxmem=-1 -qstrict
> -I/applic/local/include -L/applic/local/lib conftest.c -lnsl -lfftw3f
> -lm >&5
> 1586-403 (E) Library file "fftw3f" not found.
> configure:26688: xlc_r -q32 -o conftest -O4 -qmaxmem=-1 -qstrict
> -I/applic/local/include -L/applic/local/lib conftest.c -lnsl -lfftw3f
> -lm >&5
> 1586-403 (E) Library file "fftw3f" not found.
> configure:26818: xlc_r -q32 -o conftest -O4 -qmaxmem=-1 -qstrict
> -I/applic/local/include -L/applic/local/lib conftest.c -lnsl -lfftw3f
> -lm >&5
> 1586-403 (E) Library file "fftw3f" not found.
> configure:26920: xlc_r -q32 -o conftest -O4 -qmaxmem=-1 -qstrict
> -I/applic/local/include -L/applic/local/lib conftest.c -lnsl -lfftw3f
> -lm >&5
> 1586-403 (E) Library file "fftw3f" not found.
> configure:27206: xlc_r -q32 -o conftest -O4 -qmaxmem=-1 -qstrict
> -I/applic/local/include -L/applic/local/lib conftest.c -lX11 -lnsl
> -lfftw3f -lm >&5
> 1586-403 (E) Library file "fftw3f" not found.
> configure:27456: xlc_r -q32 -o conftest -O4 -qmaxmem=-1 -qstrict
> -I/applic/local/include -L/applic/local/lib conftest.c -lnsl -lfftw3f
> -lm -lX11 >&5
> 1586-403 (E) Library file "fftw3f" not found.
> configure:27699: xlc_r -q32 -o conftest -O4 -qmaxmem=-1 -qstrict
> -I/applic/local/include -L/applic/local/lib conftest.c -lnsl -lfftw3f
> -lm >&5
> 1586-403 (E) Library file "fftw3f" not found.
> configure:27947: xlc_r -q32 -o conftest -O4 -qmaxmem=-1 -qstrict
> -I/applic/local/include -L/applic/local/lib conftest.c -lnsl -lfftw3f
> -lm >&5
> 1586-403 (E) Library file "fftw3f" not found.
> configure:28114: xlc_r -q32 -o conftest -O4 -qmaxmem=-1 -qstrict
> -I/applic/local/include -L/applic/local/lib conftest.c -lnsl -lfftw3f
> -lm >&5
> 1586-403 (E) Library file "fftw3f" not found.
> configure:28281: xlc_r -q32 -o conftest -O4 -qmaxmem=-1 -qstrict
> -I/applic/local/include -L/applic/local/lib conftest.c -lnsl -lfftw3f
> -lm >&5
> 1586-403 (E) Library file "fftw3f" not found.
> configure:28436: xlc_r -q32 -o conftest -O4 -qmaxmem=-1 -qstrict
> -I/applic/local/include -L/applic/local/lib conftest.c -lICE -lnsl
> -lfftw3f -lm >&5
> 1586-403 (E) Library file "fftw3f" not found.
> configure:28654: xlc_r -q32 -o conftest -O4 -qmaxmem=-1 -qstrict
> -I/applic/local/include -L/applic/local/lib conftest.c -lSM -lICE
> -lXm -lXt -lX11 -lnsl -lfftw3f -lm >&5
> 1586-403 (E) Library file "fftw3f" not found.
> configure:28798: xlc_r -q32 -o conftest -O4 -qmaxmem=-1 -qstrict
> -I/applic/local/include -L/applic/local/lib conftest.c -lSM -lICE
> -lX11 -lnsl -lfftw3f -lm -lXm -lXt -lXext -lXp >&5
> 1586-403 (E) Library file "fftw3f" not found.
> ac_cv_lib_fftw3f_main=yes
> LIBS=' -lnsl -lfftw3f -lm -lXm -lXt -lSM -lICE -lXext -lXp -lX11
> -link -L/applic/local/lib -lxlf90 -L/usr/lpp/xlf/lib -lxlopt -lxlf
> -lxlomp_ser -lpthreads -lm -lc)'
> MDLIB_LIBOBJS=' qm_gaussian.lo gmx_fft_fftw3.lo'
>
> I am not sure how fftw was compiled in the system (ie whether with
> --enable-float option or not). Could someone point out what is wrong
> here ? I am sorry for my naive questions, I am new to GROMACS and a
> search in the archives and web did not help.
>
> Thank you for your help,
>
> Sincerely Yours,
>
> Senthil
>
> --/
> "You have heard me speak of Professor Moriarty?"
> "The famous scientific criminal, as famous among crooks as --"
> "My blushes, Watson," Holmes murmured, in a deprecating voice.
> "I was about to say 'as he is unknown to the public.'"
> -- A. Conan Doyle, "The Valley of Fear"
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--
========================================
Justin A. Lemkul
Graduate Research Assistant
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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