On 13/02/10 15:29, Chandan Choudhury wrote:
What is a cross-compiler?
One that compiles an executable for architecture other than the one on
which compilation occurs.
My system is
x86_64 x86_64 x86_64 GNU/Linux
model name: Intel(R) Xeon(R) CPU E5520 @ 2.27GHz
vendor id: GenuineIntel
OK, well that shouldn't be problematic.
My next guess is that your mpicc will only compile executables that will
run with mpirun - this is a special case of cross-compilation. During
the build process, GROMACS builds the C program mknb on the compilation
machine, and then executes it normally on the compilation machine
generate source files, which are then compiled for the execution
machine. However if the MPI compiler can only generate code suitable for
execution in the parallel environment, this procedure will fail.
In my experience, that's abnormal behaviour for mpicc - perhaps this
suggests an update of the MPI library.
You can see if this is the problem by seeing whether you get the same
issue with ./configure --disable-mpi from a fresh copy of the GROMACS
source. If this works correctly, then you can work around the issue by
running ./configure --enable-mpi on a different fresh copy of the
source, then copying over the contents of src/gmxlib/nonbonded/nb_kernel
from the MPI-disabled version to the MPI-enabled version (perhaps then
running "touch src/gmxlib/nonbonded/nb_kernel/kernel-stamp") to make
sure the Makefiles are fooled). Now when you issue make, at the relevant
point the make process will avoid needing to run mknb.
Another solution is to run ./configure --enable-mpi, then edit
src/gmxlib/nonbonded/nb_kernel/Makefile to correctly run mknb as a
parallel program, boot a parallel environment, then run make.
Mark
Chandan kumar Choudhury
NCL, Pune
INDIA
On Sat, Feb 13, 2010 at 6:30 AM, Mark Abraham <[email protected]
<mailto:[email protected]>> wrote:
On 02/13/10, *Chandan Choudhury * <[email protected]
<mailto:[email protected]>> wrote:
Hello gmx users !!
I installed successfully installed fftw. Then tried compiling gmx
parallely
I executed the command
$ ./configure --enable-mpi --prefix=/home/vanka/NUM-GEN/GRO/
It didnot show any problem.
$make
make[5]: Entering directory
`/home/vanka/NUM-GEN/gromacs-4.0.7/src/gmxlib/nonbonded/nb_kernel'
rm -f kernel-stamp
./mknb -software_invsqrt
make[5]: *** [kernel-stamp] Segmentation fault
make[5]: Leaving directory
`/home/vanka/NUM-GEN/gromacs-4.0.7/src/gmxlib/nonbonded/nb_kernel'
make[4]: *** [all-recursive] Error 1
make[4]: Leaving directory
`/home/vanka/NUM-GEN/gromacs-4.0.7/src/gmxlib/nonbonded'
make[3]: *** [all-recursive] Error 1
make[3]: Leaving directory
`/home/vanka/NUM-GEN/gromacs-4.0.7/src/gmxlib'
make[2]: *** [all-recursive] Error 1
make[2]: Leaving directory `/home/vanka/NUM-GEN/gromacs-4.0.7/src'
make[1]: *** [all] Error 2
make[1]: Leaving directory `/home/vanka/NUM-GEN/gromacs-4.0.7/src'
make: *** [all-recursive] Error 1
This usually means you're using a system that needs a
cross-compiler, but since you haven't told us anything about your
computer system, you're making everybody's life hard :-)
Mark
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