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:
[EMAIL PROTECTED]:~/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:
[EMAIL PROTECTED]:~/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:
[EMAIL PROTECTED]:~/gromacs-3.3.3$ ./configure --prefix=$HOME/GROMACS333 >
result
I get the following:
configure: WARNING: unknown Fortran name-mangling scheme
./configure[24445]: ACX_FIXED_FUNC_FSEEKO: not found
And a grep for fftw in the file result yields:
[EMAIL PROTECTED]:~/gromacs-3.3.3$ grep fftw result
checking for fftw3.h... yes
checking for main in -lfftw3f... yes
And tail result gives:
[EMAIL PROTECTED]:~/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:
[EMAIL PROTECTED]:~/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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