subject:"\[gmx\-users\] Problem installin gmx"

Re: [gmx-users] Problem installin gmx

2010-02-13 Thread 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 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 > > wrote:
>>
>>
>>
>>On 02/13/10, *Chandan Choudhury * >> 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
>>
>>>
>>>
>>--
>>gmx-users mailing list gmx-users@gromacs.org
>>
>>
>>http://lists.gromacs.org/mailman/listinfo/gmx-users
>>Please search the archive at http://www.gromacs.org/search before
>>posting!
>>Please don't post (un)subscribe requests to the list. Use the
>>www interface or send it to gmx-users-requ...@gromacs.org
>>.
>>
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>>
>>
>>  --
> gmx-users mailing listgmx-users@gromacs.org
> http://lists.gromacs.org/mailman/listinfo/gmx-users
> Please search the archive at http://www.gromacs.org/search before posting!
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Re: [gmx-users] Problem installin gmx

2010-02-12 Thread Mark Abraham


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 mailto:mark.abra...@anu.edu.au>> wrote:



On 02/13/10, *Chandan Choudhury * mailto:iitd...@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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Re: [gmx-users] Problem installin gmx

2010-02-12 Thread Chandan Choudhury

What is a cross-compiler? My system is
x86_64 x86_64 x86_64 GNU/Linux
model name: Intel(R) Xeon(R) CPU   E5520  @ 2.27GHz
vendor id: GenuineIntel

Chandan

--
Chandan kumar Choudhury
NCL, Pune
INDIA


On Sat, Feb 13, 2010 at 6:30 AM, Mark Abraham wrote:

>
>
> On 02/13/10, *Chandan Choudhury *  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
>
>
>
> --
> gmx-users mailing listgmx-users@gromacs.org
> http://lists.gromacs.org/mailman/listinfo/gmx-users
> Please search the archive at http://www.gromacs.org/search before posting!
> Please don't post (un)subscribe requests to the list. Use the
> www interface or send it to gmx-users-requ...@gromacs.org.
> Can't post? Read http://www.gromacs.org/mailing_lists/users.php
>
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Re: [gmx-users] Problem installin gmx

2010-02-12 Thread Mark Abraham

On 02/13/10, Chandan Choudhury   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.


$makemake[5]: Entering directory `/home/vanka/NUM-GEN/gromacs-4.0.7/src/gmxlib/nonbonded/nb_kernel'rm -f kernel-stamp./mknb  -software_invsqrtmake[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 1make[4]: Leaving directory `/home/vanka/NUM-GEN/gromacs-4.0.7/src/gmxlib/nonbonded'make[3]: *** [all-recursive] Error 1make[3]: Leaving directory `/home/vanka/NUM-GEN/gromacs-4.0.7/src/gmxlib'


make[2]: *** [all-recursive] Error 1make[2]: Leaving directory `/home/vanka/NUM-GEN/gromacs-4.0.7/src'make[1]: *** [all] Error 2make[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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[gmx-users] Problem installin gmx

2010-02-12 Thread Chandan Choudhury

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

Cannot get the error

Chandan


--
Chandan kumar Choudhury
NCL, Pune
INDIA
-- 
gmx-users mailing listgmx-users@gromacs.org
http://lists.gromacs.org/mailman/listinfo/gmx-users
Please search the archive at http://www.gromacs.org/search before posting!
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Re: [gmx-users] Problem installin gmx

Re: [gmx-users] Problem installin gmx

Re: [gmx-users] Problem installin gmx

Re: [gmx-users] Problem installin gmx

[gmx-users] Problem installin gmx

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