Re: [AMBER] parallel compiling failure of Amber 11

From: Yubo Fan <yubofan.mail.chem.tamu.edu>
Date: Tue, 22 Jun 2010 09:56:54 -0500

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


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Received on Tue Jun 22 2010 - 08:00:04 PDT
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