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
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