Nevena Todorova wrote:
Hi there,
i am trying to install (double precision, mpi )Gromacs 3.3 on an SGI Altix
system and during this process i encounter few problems.
I observe that you are trying to install 3.3 on the APAC ac machine. If
you want a double precision MPI version, I'm sure the admins will do
that for you in no time flat - they've always done so for me, as
evidenced by the plethora of pre-release 3.3 versions they still have
lying around! (see "module avail") Unless you need 3.3, you may as well
ask for 3.3.1 too!
I configure the system using the commmand:
./configure --enable-mpi --enable-shared --disable-nice --disable-float
--prefix=$HOME/g-3.3 --program-suffix=_d_mpi --with-fft=fftw2
and it seems to be running without problems untill the end where it stops
without an output line for a successful configuration. It is not giving me an
errors for missing programs, or environment set ups.
The end look like this:
"config.status: creating share/top/Makefile
config.status: creating share/html/Makefile
config.status: creating share/html/images/Makefile
config.status: creating share/html/online/Makefile
config.status: creating man/Makefile
config.status: creating man/man1/Makefile
config.status: creating src/config.h
config.status: executing depfiles commands
That is a normal finish.
If i try to run "make" after this, it is compiling for some time until it stops
with the following output:
": multiple definition of `fftwnd_f77_destroy_plan_'
nonbonded/.libs/libnonbonded.a(fftwf77.o)(.text+0x680): first defined here
/opt/fftw-2.1.5/intel-9.0/lib/libdfftw.a(fftwf77.o)(.text+0x700): In function
`fftwnd_f77_':
: multiple definition of `fftwnd_f77_'
My guess is that all of this gibberish is some kind of library/compiler
unavailablity or incompatibility. You want to be sure you have loaded a
compatible set of modules for the compiler and fftw library.
I use modules intel-cc/9.0.031 and fftw/2.1.5-intel-9.0 and scsl/1.6.0.0
(the latter means you are using linear algebra stuff optimized for this
machine instead of generic BLAS/LAPACK... not hugely important though)
and for non-MPI have used
./configure --prefix=/home/224/mxa224/progs --with-fft=fftw2
--without-motif --with-external-blas --with-external-lapack
CPPFLAGS=-I/opt/fftw-2.1.5/intel-9.0/include
LDFLAGS='-L/opt/fftw-2.1.5/intel-9.0/lib/ -lscs'
and for MPI have used
./configure --prefix=/home/224/mxa224/progs --with-fft=fftw2
--without-motif --with-external-blas --with-external-lapack
CPPFLAGS=-I/opt/fftw-2.1.5/intel-9.0/include
LDFLAGS='-L/opt/fftw-2.1.5/intel-9.0/lib/ -lscs -lmpi'
--program-suffix=_mpi --enable-mpi
all successfully.
Mark
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