[gmx-users] Problem installin gmx

Mark Abraham Mark.Abraham at anu.edu.au
Sat Feb 13 06:01:33 CET 2010

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.


> Chandan kumar Choudhury
> NCL, Pune
> On Sat, Feb 13, 2010 at 6:30 AM, Mark Abraham <mark.abraham at anu.edu.au
> <mailto:mark.abraham at anu.edu.au>> wrote:
>     On 02/13/10, *Chandan Choudhury * <iitdckc at gmail.com
>     <mailto:iitdckc at gmail.com>> 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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