[gmx-users] Problem installin gmx

[Chandan Choudhury]

Thanks Mark.
What I did I copied gmx from one of the servers, in which it was installed
paralley.

Will have a look at your suggestions, if I get into trouble.

Chandan

--
Chandan kumar Choudhury
NCL, Pune
INDIA


On Sat, Feb 13, 2010 at 10:31 AM, Mark Abraham <Mark.Abraham at anu.edu.au>wrote:

> 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 <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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