On Thu, Apr 25, 2013 at 9:32 PM, Eugene Yedvabny <eyedvabny.berkeley.edu>wrote:
> Hello,
>
> I am trying to compile the new AmberTools release and am running into
> issues with FFTW3 compilation when configuring with the -openmp flag.
> Specifically, the installation dies because it can't include libfftw3.a
> when compiling pbsa. The machine is CentOS 6.4 with Intel Composer 13 and
> GCC 4.4.6 and I've tried compiling with both of the compilers, with and
> without MKL.
>
It works just fine for me. I don't have exactly the same ifort version you
have, but it's at least in the same release family:
swails.Batman ~/amber (master) $ ifort --version
ifort (IFORT) 13.0.1 20121010
Copyright (C) 1985-2012 Intel Corporation. All rights reserved.
>
> gfortran -DFFTW -DBINTRAJ -DLIBPBSA -c -O3 -mtune=native -ffree-form
> -I/home/eyedvabny/amber12/include -I/home/eyedvabny/amber12/include -o
> fftw3.LIBPBSA.o fftw3.F90
> fftw3.F90:5: Error: Can't open included file 'fftw3.f03'
>
> ifort -DFFTW -DBINTRAJ -DLIBPBSA -c -ip -O3 -xHost -FR
> -I/home/eyedvabny/amber12/include -I/home/eyedvabny/amber12/include -o
> fftw3.LIBPBSA.o fftw3.F90
> fftw3.F90(5): error #5102: Cannot open include file 'fftw3.f03'
>
> ifort -DFFTW -DMKL -DBINTRAJ -DLIBPBSA -c -ip -O3 -xHost -FR
> -I/home/eyedvabny/amber12/include -I/home/eyedvabny/amber12/include
> -I/share/apps/intel/composer_xe_2013.2.146/mkl/include -o fftw3.LIBPBSA.o
> fftw3.F90
> fftw3.F90(5): error #5102: Cannot open include file 'fftw3.f03'
>
These errors make it seem like fftw is not getting built correctly...
>
> I am not planning on using pbsa and so can live with -nofftw, but
> unfortunately some OpenMP problems persist:
>
> /home/eyedvabny/amber12/bin/nab -o matextract matextract.o
> icc: error #10236: File not found:
> '/share/apps/intel/composer_xe_2013.2.146/lib/intel64/ifort/libiomp5.a'
> cc failed!
>
> The correct path should be
> /share/apps/intel/composer_xe_2013.2.146/compiler/lib/intel64/libiomp5.a,
> so it looks like Amber uses the old Intel folder structure. My
> LD_LIBRARY_PATH includes the .../compiler/lib/intel64/ directory so the lib
> would have been found if not for the hard-coded path. Compilation seems to
> complete successfully for OpenMP with both Intel and GNU (there are some
> issues in the make log but they don't seem fatal) if I exclude MKL and
> fftw3. But now I am losing all performance gains of using an optimized
> library.
>
This is not an Amber issue, I don't think (Amber makes no assumptions about
where the intel libraries are--the intel compilers have them built-in).
This sounds more like an issue with how your compilers are set up and/or
accessed...
Also, what exact commands did you execute (in which directories) to get
these errors?
HTH,
Jason
>
> If anyone has encountered this error and has suggestions on how to bypass
> it, any help would be much appreciated. I tried going through the FFTW3's
> config.log but it's so full of extraneous info that it's hard to narrow
> down the root cause.
>
> Thank you,
> Eugene Yedvabny
>
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>
--
Jason M. Swails
Quantum Theory Project,
University of Florida
Ph.D. Candidate
352-392-4032
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Received on Sat Apr 27 2013 - 07:00:03 PDT
