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

[Rongliang Wu]

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 :)

Sincerely,

Liang