Re: [AMBER-Developers] nofftw3 and MKL

From: Andreas Goetz <>
Date: Fri, 17 Oct 2014 21:27:13 -0700

>> -nofftw3 is there because fftw3 requires a minimum of GNU 4.3 and Intel
>> 9. It used to be that the minimum compiler version we supported was GNU
>> 4.1.2. Id be happy to get rid of this restriction.
> I think we should assume compilers able to handle fftw3. I also note that
> pmemd uses -DPUBFFT even though fftw3 has been configured and is available,
> say with gnu compilers chosen. Does anyone know why this is?

To add to this discussion, the current master fails to configure fftw3 if Intel MPI is used. I am not familiar with fftw3 so have not spent time trying to fix this. The -nofftw3 flag, though, came in handy.

$> ./configure -intelmpi intel
Checking for updates...
Checking for available patches online. This may take a few seconds...

Available AmberTools 15 patches:

No patches available

Available Amber 15 patches:

No patches available
Searching for python2... Found python2.7: /usr/local/bin/python2.7
   Detected icc version 14
   Detected ifort version 14
Using Intel MKL libraries in /server-home3/netbin/intel2013/composer_xe_2013_sp1.0.080/mkl/lib/intel64
MKL Version 10 or greater assumed.

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

Testing the icpc compiler:
     icpc -fpic -o testp testp.cpp

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

Testing mixed C/Fortran compilation:
     icc -fpic -D_FILE_OFFSET_BITS=64 -D_LARGEFILE_SOURCE -c -o testp.c.o testp.c
     ifort -fpic -O0 -c -o testp.f.o testp.f
     icc -fpic -D_FILE_OFFSET_BITS=64 -D_LARGEFILE_SOURCE -o testp testp.c.o testp.f.o -lifport -lifcore -lsvml

Testing pointer size:
     icc -fpic -D_FILE_OFFSET_BITS=64 -D_LARGEFILE_SOURCE -o test_pointer_size test_pointer_size.c
Detected 64 bit operating system.

Testing flex: OK

Checking NetCDF...
        Using bundled NetCDF library.
        Using existing NetCDF in '/server-home1/agoetz/sources/AMBER/'

Checking for zlib: OK

Checking for libbz2: OK

Configuring MKL FFTW for PMEMD...

     MKL_HOME set to /server-home3/netbin/intel2013/composer_xe_2013_sp1.0.080/mkl

Configuring fftw-3.3 (may be time-consuming)...

    Error: FFTW configure returned 1
    FFTW configure failed! Check the fftw3_config.log file
    in the /server-home1/agoetz/sources/AMBER/ directory.
Configure failed due to the errors above!

$> tail AmberTools/src/fftw3_config.log
checking whether stripping libraries is possible... yes
checking if libtool supports shared libraries... yes
checking whether to build shared libraries... yes
checking whether to build static libraries... yes
checking for ocamlbuild... no
checking for mpicc... mpicc
checking for MPI_Init... no
checking for MPI_Init in -lmpi... no
checking for MPI_Init in -lmpich... no
configure: error: could not find mpi library for --enable-mpi

All the best,

Dr. Andreas W. Goetz
Assistant Project Scientist
San Diego Supercomputer Center
Tel  : +1-858-822-4771
Web  :
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Received on Fri Oct 17 2014 - 21:30:03 PDT
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