Dear all
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.
To compile the GROMACS I've used the following settings/configure flags:
./configure \
--enable-mpi
\
--enable-float
\
--program-suffix=_mpi
\
--prefix=/home/phd/04/mbuanjha/soft/gmx332
\
--enable-type-prefix
\
--enable-all-static
\
--disable-nice
\
--disable-shared
\
--disable-threads
\
--without-motif
\
--without-x
\
--without-malloc
\
--with-fft=fftw3
\
--enable-ppc-altivec
\
--build=i686-linux-gnu
\
--host=powerpc
\
CC=/bgl/BlueLight/ppcfloor/bglsys/bin/mpixlc
\
F77=/bgl/BlueLight/ppcfloor/bglsys/bin/mpixlf77
\
CXX=/bgl/BlueLight/ppcfloor/bglsys/bin/mpixlcxx
\
MPICC=/bgl/BlueLight/ppcfloor/bglsys/bin/mpixlc
\
CFLAGS="-O3 -qarch=440d -qtune=440 -qhot"
\
FFLAGS="-O3 -qarch=440d -qtune=440 -qhot"
\
CXXFLAGS="-O3 -qarch=440d -qtune=440 -qhot"
\
LDFLAGS="-L/home/phd/04/mbuanjha/soft/fftw312/lib/
-L/home/phd/04/mbuanjha/soft/MYINC" \
CPPFLAGS="-I/home/phd/04/mbuanjha/soft/fftw312/include/
-I/home/phd/04/mbuanjha/soft/MYINC" \
LIBS="-lmpich.rts -lmsglayer.rts -lrts.rts -ldevices.rts -lcxxmpich.rts
-lnsl"
at the time of running this, i got few warning, as:
configure:26419: WARNING: Couldn't find XDR headers and/or libraries - using our
own
configure:26428: checking for working memcmp
configure:26517: result: no
but when i make mdrun, it gives error:
(cd ./src/gmxlib && make ; exit 0)
make[1]: Entering directory
`/home/phd/04/mbuanjha/soft/gromacs-3.3.2/src/gmxlib'
Making all in nonbonded
make[2]: Entering directory
`/home/phd/04/mbuanjha/soft/gromacs-3.3.2/src/gmxlib/nonbonded'
Making all in nb_kernel
make[3]: Entering directory
`/home/phd/04/mbuanjha/soft/gromacs-3.3.2/src/gmxlib/nonbonded/nb_kernel'
rm -f kernel-stamp
./mknb -software_invsqrt
>>> Gromacs nonbonded kernel generator (-h for help)
>>> Generating single 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
`/home/phd/04/mbuanjha/soft/gromacs-3.3.2/src/gmxlib/nonbonded/nb_kernel'
make[2]: *** [all-recursive] Error 1
make[2]: Leaving directory
`/home/phd/04/mbuanjha/soft/gromacs-3.3.2/src/gmxlib/nonbonded'
make[1]: *** [all-recursive] Error 1
make[1]: Leaving directory `/home/phd/04/mbuanjha/soft/gromacs-3.3.2/src/gmxlib'
(cd ./src/mdlib && make ; exit 0)
make[1]: Entering directory `/home/phd/04/mbuanjha/soft/gromacs-3.3.2/src/mdlib'
make[1]: Nothing to be done for `all'.
make[1]: Leaving directory `/home/phd/04/mbuanjha/soft/gromacs-3.3.2/src/mdlib'
(cd ./src/kernel && make mdrun ; exit 0)
make[1]: Entering directory
`/home/phd/04/mbuanjha/soft/gromacs-3.3.2/src/kernel'
make[1]: *** No rule to make target `../gmxlib/libgmx_mpi.la', needed by
`mdrun'. Stop.
make[1]: Leaving directory `/home/phd/04/mbuanjha/soft/gromacs-3.3.2/src/kernel'
and stops.
thanks in advance
anupam
--
Science is facts; just as houses are made of stone, so is science is made of
facts; but a pile of stones is not a house, and a collection of facts is not
necessarily science.
Anupam Nath Jha
Ph. D. Student
Saraswathi Vishveshwara Lab
Molecular Biophysics Unit
IISc,Bangalore-560012
Karnataka
Ph. no.-22932611
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