You will need to edit the config.h file after each ./configure so that it has the appropriate link line if you have newer Intel compilers.
For an exact link line, please refer to:
http://software.intel.com/en-us/articles/intel-mkl-link-line-advisor/
Also, please make sure that you source the proper ifortvars.sh/iccvars.sh/mklvars*.sh before you attempt to "make" Amber.
It appears you have done what is necessary for the serial version, so I think the link line advisor is the place to visit first.
On Jul 22, 2010, at 10:43 AM, Yubo Fan wrote:
> 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
> AMBER.ambermd.org
> http://lists.ambermd.org/mailman/listinfo/amber
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Received on Thu Jul 22 2010 - 09:30:03 PDT
