Hello,
Amber9 attempted to manually set the mpi libraries rather than trusting the
MPI wrappers. Assuming you have properly installed openMPI, you can do the
following: replace all ifort with mpif90 in the config.h file. You can also
get rid of all of the MPI_LIB or MPI_LIBRARY definitions, since mpif90 takes
care of that implicitly. Also make sure MPI_HOME is set (although this MAY
not be necessary). MPI_HOME I think is only required if the preprocessor
needs to know about mpif.h, in which case mpif90 doesn't take care of that.
MPI_HOME should be set to the directory containing bin/mpif90. For example,
if "which mpif90" returns /usr/local/bin/mpif90, then MPI_HOME should be
/usr/local.
Good luck!
Jason
On Tue, Jun 29, 2010 at 2:41 PM, Yubo Fan <yubofan.mail.chem.tamu.edu>wrote:
> Jason,
>
> The serial compilation worked now. But the parallel one did not with
> error message:
>
> >./configure -openmpi -bintraj ifort_x86_64
> >make clean
> >make parallel
> ================
> make[3]: Leaving directory `/opt/amber9/src/netcdf/src'
> Not making `cxx/install' because no C++ compiler
> make[2]: Leaving directory `/opt/amber9/src/netcdf/src'
> cp ../netcdf/include/*.mod .
> cpp -traditional -Iopenmpi-1.4.2-intel64/include -P -DMPI -DMKL
> -DBINTRAJ evb_vars.f > _evb_vars.f
> ifort -c -w95 -mp1 -O0 -FR -o evb_vars.o _evb_vars.f
> cpp -traditional -Iopenmpi-1.4.2-intel64/include -P -DMPI -DMKL
> -DBINTRAJ evb_input.f > _evb_input.f
> ifort -c -w95 -mp1 -O0 -FR -o evb_input.o _evb_input.f
> cpp -traditional -Iopenmpi-1.4.2-intel64/include -P -DMPI -DMKL
> -DBINTRAJ evb_init.f > _evb_init.f
> evb_init.f:18: error: mpif.h: No such file or directory
> make[1]: *** [evb_init.o] Error 1
> make[1]: Leaving directory `/opt/amber9/src/sander'
> make: *** [parallel] Error 2
> ================
>
> BTW, the environment setting is good for the compilation of Amber11.
> Any advice?
>
> Best,
> Yubo
>
>
> On Tue, 29 Jun 2010 09:46:24 -0400
> Jason Swails <jason.swails.gmail.com> wrote:
> > Edit the config.h file and change -lvml to -lsvml wherever it occurs
> >in that
> > file. Then try again.
> >
> > Good luck!
> > Jason
> >
> > On Tue, Jun 29, 2010 at 9:39 AM, Yubo Fan
> ><yubofan.mail.chem.tamu.edu>wrote:
> >
> >> Hi, everyone,
> >>
> >> I tried to compile Amber 9 and it failed with the following message:
> >>
> >> >./configure -bintraj ifort_x86_64
> >> >make clean
> >> >make serial
> >>
> >> =====
> >> make[2]: `nxtsec.o' is up to date.
> >> make[2]: Leaving directory `/opt/amber9/src/lib'
> >> ifort -o addles lesmain.o addspace.o readprm.o writprm.o
> >>readcrd.o
> >> writcrd.o pick.o rline.o nxt.o intgr.o find.o of.o
> >> geti.o unit.o getc.o alert.o echo.o get4c.o getd.o
> >> wlesprm.o lesprm.o les2prm.o checksz.o ../lib/random.o
> >> ../lib/mexit.o ../lib/nxtsec.o
> >> -L/opt/intel/Compiler/11.1/072/mkl/lib/em64t -lvml -lmkl_lapack
> >>-lmkl
> >> -lguide -lpthread
> >> ld: cannot find -lvml
> >> make[1]: *** [addles] Error 1
> >> make[1]: Leaving directory `/opt/amber9/src/addles'
> >> make: *** [serial] Error 2
> >> =====
> >>
> >> The compiling of Amber 11 was succeeded. The intel compiler is
> >>version
> >> 11. Is it too new? Any advice?
> >>
> >> Sincerely,
> >>
> >> Yubo Fan
> >> Computational Chemistry and Drug Design Lab
> >> Bioengineering and Bioinformatics Program
> >> The Methodist Hospital Research Institute (TMHRI)
> >> 6565 Fannin St B5-022
> >> Houston, TX 77030
> >> Email: yfan.tmhs.org
> >> Phone: (713) 441-8681
> >>
> >> _______________________________________________
> >> AMBER mailing list
> >> AMBER.ambermd.org
> >> http://lists.ambermd.org/mailman/listinfo/amber
> >>
> >
> >
> >
> > --
> > Jason M. Swails
> > Quantum Theory Project,
> > University of Florida
> > Ph.D. Graduate Student
> > 352-392-4032
> > _______________________________________________
> > AMBER mailing list
> > AMBER.ambermd.org
> > http://lists.ambermd.org/mailman/listinfo/amber
>
> Yubo Fan
> Computational Chemistry and Drug Design Lab
> Bioengineering and Bioinformatics Program
> The Methodist Hospital Research Institute (TMHRI)
> 6565 Fannin St B5-022
> Houston, TX 77030
> Email: yfan.tmhs.org
> Phone: (713) 441-8681
>
> _______________________________________________
> AMBER mailing list
> AMBER.ambermd.org
> http://lists.ambermd.org/mailman/listinfo/amber
>
--
Jason M. Swails
Quantum Theory Project,
University of Florida
Ph.D. Graduate Student
352-392-4032
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AMBER mailing list
AMBER.ambermd.org
http://lists.ambermd.org/mailman/listinfo/amber
Received on Tue Jun 29 2010 - 12:30:03 PDT
