Hi all
I am trying to compile gromacs with mopac but I'm experience some
problems using libmopac.a. I have a x86_64 processor and I'm trying with
gromacs-4.5.5. I've followed the instructions at the website (i.e. to
compile libmopac.a, I've used the alternte dcart.f and gmxmop.f) but I
didn't succeed. I've also seen that this topic have some times appeared
in the mailing list but the trick proposed didn't work for me.
Here you have the steps with different scenarios I've gone through:
**A: Compilation of libmopac.a with fortran compiler then gromacs
installation**
[ in mopac fortran folder]
javier@mopac/fortran/folder> $FC -O2 -c *.f (where FC=gfortran or
ifort)
javier@mopac/fortran/folder> ar rcv libmopac.a *.o;ranlib libmopac.a
javier@mopac/fortran/folder> cp libmopac.a ~/lib/
[in gromacs folder]
javier@gromacs/folder> ./configure --prefix
/home/cerezo/Programas/gromacs-4.5.5_with_mopac/ --with-qmmm-mopac
--without-qmmm-gaussian --disable-threads --disable-shared
LDFLAGS="-L/home/cerezo/lib" CPPFLAGS="-DUSE_MOPAC" LIBS="-lmopac"
javier@gromacs/folder> make -j 4
Then I get lots of "undefined reference" errors:
cc -O3 -fomit-frame-pointer -finline-functions -Wall -Wno-unused -msse2
-funroll-all-loops -std=gnu99 -fexcess-precision=fast -o tpbconv
tpbconv.o -L/home/cerezo/lib ./.libs/libgmxpreprocess.a
/home/cerezo/Programas/src/GROMACS_vX/gromacs-4.5.5/src/mdlib/.libs/libmd.a
../mdlib/.libs/libmd.a -lfftw3f
/home/cerezo/Programas/src/GROMACS_vX/gromacs-4.5.5/src/gmxlib/.libs/libgmx.a
../gmxlib/.libs/libgmx.a -ldl -lnsl -lm -lmopac
/bin/bash ../../libtool --tag=CC --mode=link cc -O3
-fomit-frame-pointer -finline-functions -Wall -Wno-unused -msse2
-funroll-all-loops -std=gnu99 -fexcess-precision=fast
-L/home/cerezo/lib -o g_protonate g_protonate.o libgmxpreprocess.la
../mdlib/libmd.la ../gmxlib/libgmx.la -lnsl -lm -lmopac
/bin/bash ../../libtool --tag=CC --mode=link cc -O3
-fomit-frame-pointer -finline-functions -Wall -Wno-unused -msse2
-funroll-all-loops -std=gnu99 -fexcess-precision=fast
-L/home/cerezo/lib -o g_luck g_luck.o libgmxpreprocess.la
../mdlib/libmd.la ../gmxlib/libgmx.la -lnsl -lm -lmopac
/home/cerezo/lib/libmopac.a(gmxmop.o): In function `donhco_':
gmxmop.f:(.text+0x23e): undefined reference to `for_f90_index'
gmxmop.f:(.text+0x26c): undefined reference to `for_f90_index'
gmxmop.f:(.text+0x298): undefined reference to `for_f90_index'
...
/home/cerezo/lib/libmopac.a(gmxmop.o): In function `deriv_':
gmxmop.f:(.text+0x792): undefined reference to `for_f90_index'
gmxmop.f:(.text+0x7c0): undefined reference to `for_f90_index'
gmxmop.f:(.text+0x7e1): undefined reference to `for_f90_index'
/home/javier/lib/libmopac.a(timer.o)(.text+0x11d): In function `timer_':
: undefined reference to `for_write_seq_fmt'
... (an so on for each mopac object)
Where I think these refer to internal intel fortran functions
(compilation with ifort, analogous errors come with gfortran internal
functions). So probably I'm missing something to include this function
at gromacs compilation time
---
**B: Compilation of libmopac.a with f2c+gcc then gromacs installation**
javier@mopac/fortran/folder> f2c *.f
javier@mopac/fortran/folder> gcc -O2 -c *.c
javier@mopac/fortran/folder> ar rcv libmopac.a *.o;ranlib libmopac.a
javier@mopac/fortran/folder> cp libmopac.a ~/lib
[in gromacs folder]
javier@gromacs/folder> ./configure --prefix
/home/cerezo/Programas/gromacs-4.5.5_with_mopac/ --with-qmmm-mopac
--without-qmmm-gaussian --disable-threads --disable-shared
LDFLAGS="-L/home/cerezo/lib" CPPFLAGS="-DUSE_MOPAC" LIBS="-lmopac"
javier@gromacs/folder> make -j 4
This time I also get "undefined reference errors", but related to f2c
funtions:
+timout.c0x105:)(:. textundefined+ 0x3c8reference) :to undefined`
do_fioreference'
totimer.c :`(do_fio.'text
In this case, do I need to include the f2c.h file somewhere in the
gromacs qmmm interface code?
Could someone point me out where I'm mistaking and what should I do to
complete the installation?
Thanks
Javier
--
Javier CEREZO BASTIDA
PhD Student
Physical Chemistry
Universidad de Murcia
Murcia (Spain)
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