On Apr 27, 2013, at 8:53 AM, Jason Swails wrote:
> 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.
>
FFTW3 failed this way for me, as well. I did not follow up at the time, just
did without. But mine was an -openmp compile as well, but with gnu compilers:
gfortran -v
Using built-in specs.
COLLECT_GCC=gfortran
COLLECT_LTO_WRAPPER=/opt/local/libexec/gcc/x86_64-apple-darwin11/4.6.3/lto-wrapper
Target: x86_64-apple-darwin11
Configured with: ../gcc-4.6.3/configure --prefix=/opt/local --build=x86_64-apple-darwin11 --enable-languages=c,c++,objc,obj-c++,lto,fortran --libdir=/opt/local/lib/gcc46 --includedir=/opt/local/include/gcc46 --infodir=/opt/local/share/info --mandir=/opt/local/share/man --datarootdir=/opt/local/share/gcc-4.6 --with-local-prefix=/opt/local --with-libiconv-prefix=/opt/local --with-system-zlib --disable-nls --program-suffix=-mp-4.6 --with-gxx-include-dir=/opt/local/include/gcc46/c++/ --with-gmp=/opt/local --with-mpfr=/opt/local --with-mpc=/opt/local --with-ppl=/opt/local --with-cloog=/opt/local --enable-cloog-backend=isl --enable-stage1-checking --disable-multilib --enable-lto --with-as=/opt/local/bin/as --with-ld=/opt/local/bin/ld --with-ar=/opt/local/bin/ar --with-bugurl=https://trac.macports.org/newticket --with-pkgversion='MacPorts gcc46 4.6.3_2'
Thread model: posix
gcc version 4.6.3 (MacPorts gcc46 4.6.3_2)
I was going to mention this to you at the end of our conversation over the other
issue, but forgot.
>
>>
>> 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
>
I don't think the problem is limited to Intel compilers. See above.
Bud Dodson
>
>>
>> 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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>> http://lists.ambermd.org/mailman/listinfo/amber
>>
>
>
>
> --
> Jason M. Swails
> Quantum Theory Project,
> University of Florida
> Ph.D. Candidate
> 352-392-4032
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--
M. L. Dodson
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Gmail: mlesterdodson-at-gmail-dot-com
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Received on Sat Apr 27 2013 - 07:30:02 PDT
