Hello,
Your problem is that you're installing openMPI with the gnu compilers, but
you're telling configure to use the intel compilers for some reason. Run
configure like this instead:
./configure -mpi gnu
Then make parallel. You have to use the compilers used to build the MPI
you're using to compile Amber in parallel. If you want an MPI to build with
the intel compilers, you will have to compile from source, setting
F90=ifort, F77=ifort, CC=icc, and CXX=icpc.
All the best,
Jason
On Tue, Jun 22, 2010 at 10:56 AM, Yubo Fan <yubofan.mail.chem.tamu.edu>wrote:
> Jason,
>
> I reinstalled openmpi and it is in /usr/lib/openmpi/1.4-gcc/. I ran
> ./configure -mpi intel in /opt/amber11/AmberTools/src and the error message
> came out as:
> Configuring Parallel NetCDF; (may be time-consuming)
>
> Error: parallel NetCDF configure returned 77
> Parallel NetCDF configure failed! Check the pnetcdf/config.log file.
> Continuing but parallel NetCDF will be skipped.
>
> Configuring NetCDF; (may be time-consuming)
>
> NetCDF configure succeeded.
>
> Configuring fftw-2.1.5; (may be time-consuming)
>
> Error: fftw configure returned 1
> fftw configure failed! Check the fftw2_config.log file.
>
> The two log files are attached.
>
> I used "yum install openmpi*" to install openmpi. Do I have install openmpi
> individually?
>
> Thanks,
> Yubo
>
>
> mpif90 -show
>>
> gfortran -I/usr/lib/openmpi/1.4-gcc/include -m32 -pthread
> -I/usr/lib/openmpi/1.4-gcc/lib -L/usr/lib/openmpi/1.4-gcc/lib -lmpi_f90
> -lmpi_f77 -lmpi -lopen-rte -lopen-pal -ldl -Wl,--export-dynamic -lnsl -lutil
> -lm -ldl
>
> mpicc -show
>>
> gcc -I/usr/lib/openmpi/1.4-gcc/include -m32 -pthread
> -L/usr/lib/openmpi/1.4-gcc/lib -lmpi -lopen-rte -lopen-pal -ldl
> -Wl,--export-dynamic -lnsl -lutil -lm -ldl
>
> On Mon, 21 Jun 2010 16:29:43 -0400
> Jason Swails <jason.swails.gmail.com> wrote:
>
>> Hello,
>>
>> See my comments below.
>>
>> On Mon, Jun 21, 2010 at 4:25 PM, Yubo Fan <yubofan.mail.chem.tamu.edu
>> >wrote:
>>
>> Dr. Case,
>>>
>>> I got a problem to compile parallel version of Amber on my local
>>> machine. The commands and error message are shown below:
>>>
>>>
>>>
>>> =================================================================================
>>> [root.localhost src]# ./configure -mpi intel
>>> Your AMBERHOME environment variable should be set to /opt/amber11
>>>
>>> Using Intel MKL libraries in
>>> /opt/intel/Compiler/11.1/072/mkl/lib/em64t
>>> MKL Version 10 or 11 assumed.
>>>
>>> Testing the icc compiler:
>>> icc -D_FILE_OFFSET_BITS=64 -D_LARGEFILE_SOURCE -o testp testp.c
>>> OK
>>>
>>> Testing the ifort compiler:
>>> ifort -O0 -o testp testp.f
>>> OK
>>>
>>> Testing mixed C/Fortran compilation:
>>> icc -D_FILE_OFFSET_BITS=64 -D_LARGEFILE_SOURCE -c -o testp.c.o
>>> testp.c
>>> ifort -O0 -c -o testp.f.o testp.f
>>> icc -o testp testp.c.o testp.f.o
>>> -L/opt/intel/Compiler/11.1/072/lib/intel64/ -lifport -lifcore -lsvml
>>> /opt/intel/Compiler/11.1/072/lib/intel64/libimf.so: warning: warning:
>>> feupdateenv is not implemented and will always fail
>>> OK
>>>
>>> Testing pointer size:
>>> icc -D_FILE_OFFSET_BITS=64 -D_LARGEFILE_SOURCE -o
>>> test_pointer_size test_pointer_size.c
>>> Detected 64 bit operating system.
>>>
>>> Testing flex:
>>> OK
>>>
>>> Configuring Parallel NetCDF; (may be time-consuming)
>>>
>>> Error: parallel NetCDF configure returned 77
>>> Parallel NetCDF configure failed! Check the pnetcdf/config.log
>>> file.
>>>
>>>
>> What does pnetcdf/config.log say?
>>
>>
>> Continuing but parallel NetCDF will be skipped.
>>>
>>> Configuring NetCDF; (may be time-consuming)
>>>
>>> NetCDF configure succeeded.
>>>
>>> Configuring fftw-2.1.5; (may be time-consuming)
>>>
>>> Error: fftw configure returned 1
>>> fftw configure failed! Check the fftw2_config.log file.
>>>
>>>
>> What does this file say?
>>
>> It may be that you don't have a working MPI, or you're using a mis-match
>> of
>> MPIs. This is especially true for personal systems, since users may not
>> have properly built their MPIs. What does "mpif90 -show" and "mpicc
>> -show"
>> return on your system?
>>
>> Good luck!
>> Jason
>>
>>
>>
>>>
>>> =================================================================================
>>>
>>> Any advice?
>>>
>>> Regards,
>>> Yubo
>>>
>>> On Mon, 14 Jun 2010 12:34:13 -0400
>>> case <case.biomaps.rutgers.edu> wrote:
>>> > On Mon, Jun 14, 2010, Yubo Fan wrote:
>>> >>
>>> >> When I ran 'make parallel' at $AMBERHOME/src, the error message
>>> >> appears as:
>>> >> Error: config.h is not of type parallel!
>>> >> Rerun ./configure and specify an MPI implementation.
>>> >> make: *** [configured_parallel] Error 2
>>> >>
>>> >> The making of AmberTools and 'make serial' passed already. I ran
>>> >> './configure -openmp intel' to create a config.h file at
>>> >
>>> > This is wrong, although perhaps an understandable error.
>>> >
>>> > 1. AmberTools can be made in parallel in two ways: using openmp or
>>> >MPI.
>>> >
>>> > 2. However, Amber itself can only be made in parallel using MPI.
>>> > So, from
>>> > the point of view of Amber, using the "-openmp" option is not enough
>>> >to give
>>> > a "parallel" config.h. You need to run the configure script using
>>> >the "-mpi"
>>> > option, not the "openmp" one.
>>> >
>>> > ....dac
>>>
>>> >
>>> >
>>> > _______________________________________________
>>> > AMBER mailing list
>>> > AMBER.ambermd.org
>>> > http://lists.ambermd.org/mailman/listinfo/amber
>>>
>>> Yubo Fan
>>> Chemistry Department
>>> Texas A & M University
>>> Tel: (979) 845-5237
>>> Email: yubofan.mail.chem.tamu.edu
>>>
>>>
>>> _______________________________________________
>>> 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
> Chemistry Department
> Texas A & M University
> Tel: (979) 845-5237
> Email: yubofan.mail.chem.tamu.edu
>
--
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
Received on Tue Jun 22 2010 - 08:30:06 PDT
