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.
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.
=================================================================================
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
>
>
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Yubo Fan
Chemistry Department
Texas A & M University
Tel: (979) 845-5237
Email: yubofan.mail.chem.tamu.edu
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Received on Mon Jun 21 2010 - 13:30:04 PDT
