I replied to Dr. Case yesterday but I guess my email disappeared into the
nether. Thank you for investigating the issues- I was able to resolve them
by modifying $AMBERHOME/AmberTools/src/Makefile and configure2
1) configure2 on lines 783/784 uses 'which ifort' piped into sed to get the
Intel lib folder. Unfortunately it seems Intel changed their paths and so
$fl and $flibs_arch were incorrectly set. I've hardcoded my paths but the
sed script can be easily modified. Since the paths are so drastically
different, the generic fix might involve an if-else, but I don't have
Composer 11 to verify.
2) As you mentioned in your reply, FFTW3 isn't built if 'make openmp' is
run without serial, hence my problems. I circumvented it by adding
THIRDPARTY to the nabonly target.
There's still a minor inconsistency though- FFTW3's configure gets called
only if FFTW3 is meant to be used in RISM or pbsa, but its make is called
every time $(FFTW3) or THIRDPARTY is called. So effectively Amber is
building FFTW3 regardless of whether it's going to use it or not. There are
checks in place to not use FFTW3 if it's not needed, but more appropriate
fix would be to not build it unnecessarily in the first place
Thank you,
Eugene Yedvabny
On Sat, Apr 27, 2013 at 2:43 PM, Jason Swails <jason.swails.gmail.com>wrote:
> 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 - 15:30:02 PDT
