Re: [AMBER] parallel compiling failure of Amber 11

From: Yubo Fan <>
Date: Mon, 21 Jun 2010 15:25:10 -0500

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
MKL Version 10 or 11 assumed.

Testing the icc compiler:
      icc -D_FILE_OFFSET_BITS=64 -D_LARGEFILE_SOURCE -o testp testp.c

Testing the ifort compiler:
      ifort -O0 -o testp testp.f

Testing mixed C/Fortran compilation:
      icc -D_FILE_OFFSET_BITS=64 -D_LARGEFILE_SOURCE -c -o testp.c.o
      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/ warning: warning:
feupdateenv is not implemented and will always fail

Testing pointer size:
test_pointer_size test_pointer_size.c
Detected 64 bit operating system.

Testing flex:

Configuring Parallel NetCDF; (may be time-consuming)

     Error: parallel NetCDF configure returned 77
     Parallel NetCDF configure failed! Check the pnetcdf/config.log
     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?


On Mon, 14 Jun 2010 12:34:13 -0400
  case <> 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
> 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

Yubo Fan
Chemistry Department
Texas A & M University
Tel: (979) 845-5237

AMBER mailing list
Received on Mon Jun 21 2010 - 13:30:04 PDT
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