[gmx-users] QM / MM assistance

Eric Smoll ericsmoll at gmail.com
Sun Sep 14 18:59:12 CEST 2014 

Hello Johnny,

Thanks for the suggestion. I dumped the contents of CMakeError.log below. I
am not sure why the C compiler failed. The error occurs on directory
change? Later in the log, libmopac.a fails. Is this a static/shared problem?

This page (http://wwwuser.gwdg.de/~ggroenh/qmmm.html) contains the
following instructions. "Compile all mopac files (f77 -O2 -c *.f), except
mopac.f, moldat.f and deriv.f (thes ones are to be replaced by gmxmop.f),
and collect the objects (*.o) into a library (ar rcv libmopac.a *.o;ranlib
libmopac.a). Or if you are using linux, simply download libmopac.a
instead." libmopac.a is not working for me. mopac.f is not
in mopac7-1.11/fortran. Should I ignore its absence or
replace mopac7app.f and mopac7lib.f instead?

- Eric

******************** mopac7-1.11/fortran

[ fortran ] $ ls
aababc.f  chrge.f    deri1.f   dgetf2.f  dofs.f    exchng.f  getgeg.f
 ilaenv.f     matout.f     parsav.f  repp.f      thermo.f
addfck.f  cnvg.f     deri21.f  dgetrf.f  dot.f     fdate.c   getgeo.f
 initsv.f     matpak.f     partxy.f  rotate.f    timer.f
addhcr.f  compfg.f   deri22.f  dgetri.f  drc.f     ffhpol.f  getsym.f
 interp.f     mecid.f      pathk.f   rotat.f     timout.f
addnuc.f  consts.f   deri23.f  diag.f    drcout.f  flepo.f   gettxt.f
 iter.f       meci.f       paths.f   rsp.f       update.f
analyt.f  cqden.f    deri2.f   diat2.f   dtrmm.f   fmat.f    gmetry.f
 jcarin.f     mecih.f      perm.f    search.f    upsurf.f
anavib.f  c_src_bak  deritr.f  diat.f    dtrmv.f   fock1.f   gover.f
linmin.f     mecip.f      polar.f   second.f    vecprt.f
axis.f    datin.f    deriv.f   diegrd.f  dtrsm.f   fock2.f   greenf.f
 local.f      moldat.f     powsav.f  setupg.f    writmo.f
block.f   dcart.f    dernvo.f  dielen.f  dtrti2.f  force.f   grid.f
 locmin.f     molval.f     powsq.f   SIZES       wrtkey.f
bonds.f   delmol.f   ders.f    diis.f    dtrtri.f  formxy.f  h1elec.f
 lsame.f      mopac7app.f  prtdrc.f  SIZES.orig  wrttxt.f
brlzon.f  delri.f    dfock2.f  dijkl1.f  dvfill.f  forsav.f  haddon.f
 Makefile.am  mopac7lib.f  quadr.f   solrot.f    xerbla.f
btoc.f    denrot.f   dfpsav.f  dijkl2.f  ef.f      frame.f   hcore.f
Makefile.in  mullik.f     react1.f  swap.f      xyzint.f
calpar.f  densit.f   dgemm.f   dipind.f  enpart.f  freqcy.f  helect.f
 makpol.f     mult.f       reada.f   sympro.f
capcor.f  depvar.f   dgemv.f   dipole.f  esp.f     geout.f   hqrii.f
mamult.f     nllsq.f      readmo.f  symtry.f
cdiag.f   deri0.f    dger.f    dlaswp.f  etime.c   geoutg.f  ijkl.f
 matou1.f     nuchar.f     refer.f   symtrz.f

[ fortran ] $ ls | grep "mopac.f"


******************* CMakeFiles/CMakeError.log

Determining if the C compiler works failed with the following output:
Change Dir: /a/b/c/QMMM/gromacs-build/CMakeFiles/CMakeTmp

Run Build Command:/usr/bin/gmake "cmTryCompileExec3939207614/fast"
/usr/bin/gmake -f CMakeFiles/cmTryCompileExec3939207614.dir/build.make
CMakeFiles/cmTryCompileExec3939207614.dir/build
gmake[1]: Entering directory `/a/b/c/QMMM/gromacs-build/CMakeFiles/CMakeTmp'
/opt/apps/cmake/2.8.9/bin/cmake -E cmake_progress_report
/a/b/c/QMMM/gromacs-build/CMakeFiles/CMakeTmp/CMakeFiles 1
Building C object
CMakeFiles/cmTryCompileExec3939207614.dir/testCCompiler.c.o
/opt/apps/intel/13/composer_xe_2013_sp1.1.106/bin/intel64/icc    -o
CMakeFiles/cmTryCompileExec3939207614.dir/testCCompiler.c.o   -c
/a/b/c/QMMM/gromacs-build/CMakeFiles/CMakeTmp/testCCompiler.c
Linking C executable cmTryCompileExec3939207614
/opt/apps/cmake/2.8.9/bin/cmake -E cmake_link_script
CMakeFiles/cmTryCompileExec3939207614.dir/link.txt --verbose=1
/opt/apps/intel/13/composer_xe_2013_sp1.1.106/bin/intel64/icc
 /a/b/c/QMMM/mopac/lib/libmopac.a
CMakeFiles/cmTryCompileExec3939207614.dir/testCCompiler.c.o  -o
cmTryCompileExec3939207614 -rdynamic
/a/b/c/QMMM/mopac/lib/libmopac.a: could not read symbols: File in wrong
format
gmake[1]: *** [cmTryCompileExec3939207614] Error 1
gmake[1]: Leaving directory `/a/b/c/QMMM/gromacs-build/CMakeFiles/CMakeTmp'
gmake: *** [cmTryCompileExec3939207614/fast] Error 2


On Sun, Sep 14, 2014 at 7:13 AM, Johnny Lu <johnny.lu128 at gmail.com> wrote:

> ...
>
> I just have a similar problem at this moment. It seems that
> CMakeFiles/CMakeError.log has some clues.
>
> Usually I save the output of cmake too.
>
> On Sun, Sep 14, 2014 at 9:03 AM, Johnny Lu <johnny.lu128 at gmail.com> wrote:
>
> > The log file may tell a bit more.
> > Sometimes it says a library is missing or many other possible reasons.
> >
> > On Sun, Sep 14, 2014 at 6:27 AM, Eric Smoll <ericsmoll at gmail.com> wrote:
> >
> >> Hello Gromacs users,
> >>
> >> As far as I understand, the most up-to-date reference for compiling
> >> gromacs
> >> for QM/MM calculations is shown here:
> >>
> >> http://wwwuser.gwdg.de/~ggroenh/qmmm.html
> >>
> >> I am trying to follow the MOPAC instructions with Gromacs 4.6.7.
> >>
> >> When I try to use the provided precompiled library, I get the following
> >> error:
> >>
> >> QMMM/mopac/lib/libmopac.a: could not read symbols: File in wrong format
> >>
> >> When I go to build the library myself (as suggested in the link above) I
> >> am
> >> unable to find and remove the file mopac.f. It does not exist. Does
> anyone
> >> know how to proceed?
> >>
> >>
> >>
> >>
> >> Also, I am also getting this error from cmake:
> >>
> >> -- Check for working C compiler:
> >> /opt/apps/intel/13/composer_xe_2013_sp1.1.106/bin/intel64/icc -- broken
> >> CMake Error at
> >>
> /opt/apps/cmake/2.8.9/share/cmake-2.8/Modules/CMakeTestCCompiler.cmake:52
> >> (MESSAGE):
> >>   The C compiler
> >>   "/opt/apps/intel/13/composer_xe_2013_sp1.1.106/bin/intel64/icc" is not
> >> able
> >>   to compile a simple test program.
> >>
> >> However, I have the compiler available and it runs. I pass it to cmake
> as
> >> suggested.
> >>
> >> -DCMAKE_CXX_COMPILER=icpc
> >> -DCMAKE_C_COMPILER=icc
> >>
> >> What am I doing wrong? Could I ask for some assistance?
> >>
> >> -Eric
> >> --
> >> Gromacs Users mailing list
> >>
> >> * Please search the archive at
> >> http://www.gromacs.org/Support/Mailing_Lists/GMX-Users_List before
> >> posting!
> >>
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> >>
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> >>
> >
> >
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