On Sat, Apr 27, 2013 at 10:21 AM, M. L. Dodson <mldodson.comcast.net> wrote:
>
> 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:
>
Ah. It appears that Dave found the problem. I was indeed able to
reproduce this issue after I tried an OpenMP build from a completely clean
tree.
The issue is that the OpenMP build should invoke the THIRDPARTY rule to
make sure that fftw gets built. If you do an OpenMP build after either a
standard serial or parallel installation, fftw will already be built, so
this error will not occur. I'm guessing we'll release an update to fix
this...
>
> >>
> >> 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.
>
Sorry, I was unclear. The 'intel' error I was referring to was this one:
icc: error #10236: File not found:
'/share/apps/intel/composer_xe_2013.2.146/lib/intel64/ifort/libiomp5.a'
cc failed!
All the best,
Jason
--
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 - 15:00:03 PDT
