[gmx-users] mdrun stuck with PME on BlueGene/P

[Mark Abraham]

On 5/12/2011 9:03 AM, Rongliang Wu wrote:
> Dear all,
>
> I have compiled the gromacs 4.5.5 version on BlueGene/P both on the 
> front end and bgp using the following script :
> with the front end as an example
> ------------------------------------------------------------------------------------------------------ 
>
> version=$1
>
> PREFIX=/home/users/wurl/software/gromacs$version
>
> export ac_cv_sizeof_int=4
> export ac_cv_sizeof_long_int=4
> export ac_cv_sizeof_long_long_int=8
>
> export CC="xlc_r"
> export CFLAGS="-O3 -I/.../fftw3.3/include -qarch=auto -qtune=auto"
> export CPPFLAGS="-I/.../fftw3.3/include"
> export CXX="xlc_r"
> export CXXFLAGS="-O3 -qarch=auto -qtune=auto"
>
> export F77="xlf_r"
> export FFLAGS="-O3 -qnoprefetch -qarch=auto -qtune=auto"
>
> export LDFLAGS=" -L/.../fftw3.3/lib"
> export LIBS="-lmass"
>
> echo make distclean
> make distclean
>
> ../configure --prefix=$PREFIX \
>              --with-fft=fftw3 \
>              --disable-ppc-altivec \
>              --without-x \
>              --disable-software-sqrt \
>              --enable-ppc-sqrt \
>              --disable-float \
>              --disable-shared
>
> ------------------------------------------------------------------------------------------------------ 
>
>
> in both ways, the program gets stuck and doing nothing when using PME:
>
> -------------------------------------------
> Back Off! I just backed up md.log to ./#md.log.10#
> Getting Loaded...
> Reading file topol.tpr, VERSION 4.5.5 (double precision)
> Loaded with Money
> -------------------------------------------
>
> I compiled the debug version of mdrun and it told me the problem of fftw
>
> -------------------------------------------
> Program received signal SIGINT, Interrupt.
> [Switching to Thread -134504448 (LWP 31644)]
> 0x1010dd1c in fftwf_cpy2d ()
> ------------------------------------------
>
> my compilation of fftw is :
> ------------------------------------------
> version=$1
>
> PREFIX=/home/users/wurl/software/fftw$version
>
> export ac_cv_sizeof_int=4
> export ac_cv_sizeof_long_int=4
> export ac_cv_sizeof_long_long_int=8
>
> export CC="xlc_r"
> export CFLAGS="-O5 -qarch=auto -qtune=auto"
> export CXX="xlc_r"
> export CXXFLAGS="-O5 -qarch=auto -qtune=auto"
>
> export F77="xlf_r"
> export FFLAGS="-O5 -qnoprefetch -qarch=auto -qtune=auto"
>
> export LIBS="-lmass"
>
> echo make distclean
> make distclean
>
> ../configure --prefix=$PREFIX \
>              --disable-fortran \
> #             --enable-float \
>
> ------------------------------------------
>
> When not using PME, the program went well. I also found the same 
> problems on the mailing list, but it did not seem to solve the problem 
> exactly. Does anyone know how to have this problem solved? I cannot do 
> without PME for accurate MD simulations :)

If you want mdrun available on both front and back ends, you will need 
to link each with the corresponding FFTW library. It's not clear to me 
that you are doing that. You will also need to enable MPI to get any 
value out of the back end version.

Mark