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
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Received on Mon Jun 21 2010 - 14:00:04 PDT
