[gmx-users] Problems compiling GROMACS on IBM Blue Gene/L

Fiona Reid fiona at epcc.ed.ac.uk
Mon Nov 26 17:16:41 CET 2007

Dear Gromacs-Users,

I'm hoping you can help.

I've tried compiling both version 3.3.1 and 3.3.2 of GROMACS on an IBM 
Blue Gene/L system but get the same error message with each version. The 
error is similar to that obtained by Hiroshi Fujisaki in thread:
Unfortunately no solution to this problem was ever posted to the list.

To compile the GROMACS I've used the following settings/configure flags.

export MPICC="mpixlc"
export CC="blrts_xlc"
export CXX="blrts_xlC"
export F77="blrts_xlf"
export LDFLAGS="${LDFLAGS} -L/bgl/local/lib/fftw/lib"
export CPPFLAGS="${CPPFLAGS} -I/bgl/local/lib/fftw/include"
export FFLAGS="-O3 -qarch=440 -qtune=440 -qmaxmem=-1 -qhot"
export CFLAGS="-O3 -qarch=440 -qtune=440 -qmaxmem=-1 -qhot"
** Note: mpixlc is a wrapper script which bundles up all the library paths 
** to ensure they are linked in the correct order.

./configure --prefix=${PREFIX} --without-xml --without-x --with-fft=fftw2 --disable-float --enable-mpi --program-suffix="_mpi_d" --build=ppc-linux-gnu --host=powerpc  >& $LOGFILE
make mdrun

The error message I get is:

$ make mdrun
(cd ./src/gmxlib && make ; exit 0)
make[1]: Entering directory `/home/b00/fiona/gromacs-3.3.1/src/gmxlib'
Making all in nonbonded
make[2]: Entering directory 
Making all in nb_kernel
make[3]: Entering directory 
rm -f kernel-stamp
./mknb -double  -software_invsqrt
>>> Gromacs nonbonded kernel generator (-h for help)
>>> Generating double precision functions in C.
>>> Using Gromacs software version of 1/sqrt(x).
Error: Cannot open nb_kernel010_c.c for writing.
make[3]: *** [kernel-stamp] Error 1
make[3]: Leaving directory 
make[2]: *** [all-recursive] Error 1
make[2]: Leaving directory 
make[1]: *** [all-recursive] Error 1
make[1]: Leaving directory `/home/b00/fiona/gromacs-3.3.1/src/gmxlib'
(cd ./src/mdlib && make ; exit 0)
make[1]: Entering directory `/home/b00/fiona/gromacs-3.3.1/src/mdlib'
make[1]: Nothing to be done for `all'.
make[1]: Leaving directory `/home/b00/fiona/gromacs-3.3.1/src/mdlib'
(cd ./src/kernel && make mdrun ; exit 0)
make[1]: Entering directory `/home/b00/fiona/gromacs-3.3.1/src/kernel'
make[1]: *** No rule to make target `../gmxlib/libgmx_mpi_d.la', needed by `mdrun'.  Stop.
make[1]: Leaving directory `/home/b00/fiona/gromacs-3.3.1/src/kernel'

Any help or suggestions would be much appreciated.

Thanks in advance,


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