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.
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'
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.
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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Received on Thu Apr 25 2013 - 19:00:02 PDT
