Thanks Gerrit! I remember that page from a while back, but forgot
about it while building a fresh GROMACS on my new machine - I thought
that a vanilla build of MOPAC7 would have worked. Thanks for
refreshing my memory. Is this information contained in any of the
documentation for GROMACS? I couldn't find it in my cursory search
(googling, site search), and I'm sure others who are as uninformed as
I am would run into the same issue.
Another problem I've run into (this is OT) is the '--enable-threads'
option. I know (from other mailing list posts) that this doesn't
work in any of the releases, but how about CVS? If it doesn't work,
why include the option in the configure script? It seems like with
the trend of cramming more cores into a single box, threads would
become more and more important. MPI just seems kind of ridiculous
for work on a single machine, when you could use threads.
Thanks again, Gerrit.
--Jake
On Oct 7, 2006, at 1:51 AM, Gerrit Groenhof wrote:
Hi Jake,
Did you add to the mopac library the gmxmop.o, and dcart.o (http://
rugmd4.chem.rug.nl/~groenhof/qmmm.html#code) before linking to
gromacs?
The functions domldt and domop are in gmxmop.
Gerrit
On Oct 6, 2006, at 8:41 PM, Jake Michaelson wrote:
Hi all,
I'm trying to build a qmmm-enabled version of gromacs 3.31 with
MOPAC7.
My specs:
Intel Core 2 Duo
Ubuntu 6.06 with kernel 2.6.18-ck1 (x86-64)
compiling with Intel MKL 8.1.1, icc v 9.1, ifort v 9.1
MOPAC7 v 1.10
MOPAC compiles nicely with the above, but when I try to build gromacs
with:
export LIBS="-lmkl -lguide -lpthread -lmkl_lapack -lmopac7 -lg2c"
./configure --prefix=/usr --with-fft=mkl --with-external-blas
--with-external-lapack --with-qmmm-mopac --with-x
Make eventually dies with (snippet):
../mdlib/.libs/libmd.a(qm_mopac.o): In function `/bin/sh ../../
libtool
--tag=CC --mode=link /opt/intel/cce/9.1.043/bin/icc -openmp -xT
-L/usr/atlas/lib -L/opt/intel/cce/9.1.043/lib
-L/opt/intel/fce/9.1.037/lib -L/usr/lib64 -o protonate hackblock.o
ter_db.o h_db.o genhydro.o pgutil.o resall.o add_par.o topexcl.o
toputil.o topdirs.o protonate.o ../mdlib/libmd.la ../gmxlib/libgmx.la
-L/usr/X11R6/lib -lnsl -lmkl -lmkl -lguide -lpthread -lmkl_lapack
-lmopac7 -lg2c -lSM -lICE -lX11
call_mopac':qm_mopac.c:(.text+0x135): undefined reference to `domop_'
../mdlib/.libs/libmd.a(qm_mopac.o): In function
`call_mopac_SH':qm_mopac.c:(.text+0x38f): undefined reference to
`domop_'
../mdlib/.libs/libmd.a(qm_mopac.o): In function
`init_mopac':qm_mopac.c:(.text+0x541): undefined reference to
`domldt_'
make[3]: *** [mdrun] Error 1
...basically undefined references to domop_ and domldt_ in
qm_mopac.c.
I'm not sure where these are supposed to be found. Can anyone
give me a
hand on this?
For what it's worth I've also tried building both MOPAC7 and
gromacs with gcc, but I got exactly the same error, which suggests
that this is not a compiler-specific problem.
Thanks,
Jake
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