Jason,
The compiling still failed with error message "ld: cannot find -lmkl".
I've already changed lvml to lsvml as you instructed. I think MPI_HOME
were correctly set. Is it possible that the Intel Compiler I'm using
is too new? Any advice?
On Tue, 29 Jun 2010 15:27:29 -0400
Jason Swails <jason.swails.gmail.com> wrote:
> 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
> _______________________________________________
> AMBER mailing list
> AMBER.ambermd.org
> http://lists.ambermd.org/mailman/listinfo/amber
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
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http://lists.ambermd.org/mailman/listinfo/amber
Received on Thu Jul 22 2010 - 09:00:04 PDT
