[gmx-users] Installation - can I skip auto-vectorization?

[Nathan Moore]

Sorry, I'm not sure I understand you.

Don't I need to specify the full set of CFLAGS? if I'm cross-compiling.

Nathan

> On Wed, 2005-06-01 at 14:30 -0500, Nathan Moore wrote:
>> Thanks for the clarification on the install problem.  I'm now dealing
>> with
>> another issue.  The code dies half-way through make on the
>> auto-vectorization step.  I'm cross-compiling (on one PowerPC machine,
>> for
>> a different PowerPC architecture).  The output is,
>>
> try compiling mkinl with -g
> cd src/gmxlib
> make CFLAGS=-g mkinl
> cd ../..
> make install
>
>> ...
>> >>> This is the GROMACS code generator for MD & MC inner loops
>> >>> It will generate single precision C code in file innerc.c
>> >>> Using gromacs invsqrt code
>> >>> Inlining gromacs invsqrt code
>> >>> Using normal solvent optimized loops
>> >>> Prefetching forces in loops: none
>> >>> Nonthreaded inner loops
>> >>> Vectorizing invsqrt in loops:none
>> Error creating file innerc.c
>> make[3]: *** [innerc.c] Error 255
>> make[3]: Leaving directory
>> `/bglhome/usr2/ntmoore/GROMACS/gromacs-3.2/src/gmxlib'
>> make[2]: *** [all-recursive] Error 1
>> make[2]: Leaving directory
>> `/bglhome/usr2/ntmoore/GROMACS/gromacs-3.2/src'
>> make[1]: *** [all] Error 2
>> make[1]: Leaving directory
>> `/bglhome/usr2/ntmoore/GROMACS/gromacs-3.2/src'
>> make: *** [all-recursive] Error 1
>>
>> Is there a special config flag that I need to turn on to disable this
>> auto-vectorization?  Can I skip this section by inputting specifics of
>> the
>> chip (ie CFLAGS="-qarch=440d -qtune=440 -O4",  strangely, including
>> those
>> flags in the following way causes configure to fail:
>>
>> ./configure \
>>         --enable-mpi \
>>         F77='xlf' \
>>         CC='cc' \
>>         MPICC='cc' \
>>         CFLAGS="-I/sys/include" \
>>         CPPFLAGS="-qarch=440d -qtune=440 -O4
>> -I/home/usr/ntmoore/lib/fftw-mpi-single/include" \
>>         LDFLAGS="-L/sys/lib -L/home/usr/ntmoore/lib/fftw-mpi-single/lib"
>> \
>>         LIBS=" -lmpich.rts -lmsglayer.rts -lrts.rts -ldevices.rts -lfftw
>> -lfftw_mpi -lrfftw -lrfftw_mpi" \
>>         --build=ppc-linux-gnu \
>>         --target=ppc-bgl-blrtsgnu \
>>         --host=powerpc
>>
>> )?
>>
>> Thanks again - I do appreciate the help!
>>
>> Nathan Moore
>> University of Minnesota Physics
>>
>>
>>
>> > On Tue, 2005-05-31 at 16:58 -0500, Nathan Moore wrote:
>> >> Greetings,
>> >>
>> >> I'm working to install GROMACS on a parallel machine.  I have MPIch
>> >> available, as well as the FFTW library.  Several questions have
>> arisen:
>> >>
>> >> (1) What is the difference between the value of "LIBS" and "LDFLAGS"
>> in
>> >> the configure script?  Is, for example, the following ./configure
>> >> argument
>> >> acceptable:
>> >> LDFLAGS="-I/home/usr/ntmoore/lib/fftw-mpi-single/include -L/sys/lib
>> >> -lmpich.rts -lfftw_mpi"
>> >
>> > CPPFLAGS="-I/home/usr/ntmoore/lib/fftw-mpi-single/include"
>> > LDFLAGS="-L/sys/lib -L/home/usr/ntmoore/lib/fftw-mpi-single/lib"
>> > LIBS="-lmpich.rts"
>> > CC=mpicc
>> >
>> >>
>> >> (2) I noticed after compiling fftw that several variations of the
>> >> library
>> >> were created.  Which of the available set, {libfftw libfftw_mpi
>> librfftw
>> >> librfftw_mpi}, should I include?
>> > configure will find the right one if you give it the right directory
>> > (see above)
>> >>
>> >> (3) Is it possible to replace fftw with a vendor-supplied Lapack fft
>> >> package?  (essl/cxml/sgimath/sunperf etc)?
>> > Not yet.
>> >>
>> >> (4) any example config scripts from an MPI machine would be greatly
>> >> appreciated!
>> >>
>> >> Best Regards,
>> >>
>> >> Nathan Moore
>> >> University of Minnesota Physics
>> >>
>> >>
>> >> _______________________________________________
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>> > --
>> > David.
>> > ________________________________________________________________________
>> > David van der Spoel, PhD, Assoc. Prof., Molecular Biophysics group,
>> > Dept. of Cell and Molecular Biology, Uppsala University.
>> > Husargatan 3, Box 596,          75124 Uppsala, Sweden
>> > phone:  46 18 471 4205          fax: 46 18 511 755
>> > spoel at xray.bmc.uu.se    spoel at gromacs.org
>> http://xray.bmc.uu.se/~spoel
>> > ++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++
>> >
>> >
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>>
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> --
> David.
> ________________________________________________________________________
> David van der Spoel, PhD, Assoc. Prof., Molecular Biophysics group,
> Dept. of Cell and Molecular Biology, Uppsala University.
> Husargatan 3, Box 596,          75124 Uppsala, Sweden
> phone:  46 18 471 4205          fax: 46 18 511 755
> spoel at xray.bmc.uu.se    spoel at gromacs.org   http://xray.bmc.uu.se/~spoel
> ++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++
>
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