[gmx-users] mpirun error

[Justin Lemkul]

On 11/20/12 8:43 AM, Parisa Rahmani wrote:
> Thanks for your reply.
> I have also tried installing with _mpi suffix
> Here is the output of ldd:
>
> gromacs3.3/bin$ ldd mdrun_mpi
> linux-vdso.so.1 =>  (0x00007fff4658c000)
> libnsl.so.1 => /lib/x86_64-linux-gnu/libnsl.so.1 (0x00007f7d7afe9000)
> libfftw3f.so.3 => /usr/lib/libfftw3f.so.3 (0x00007f7d7ac76000)
> libm.so.6 => /lib/x86_64-linux-gnu/libm.so.6 (0x00007f7d7a9f3000)
> libmpich.so.3 => /usr/lib/libmpich.so.3 (0x00007f7d7a603000)
> libopa.so.1 => /usr/lib/libopa.so.1 (0x00007f7d7a402000)
> libmpl.so.1 => /usr/lib/libmpl.so.1 (0x00007f7d7a1fd000)
> librt.so.1 => /lib/x86_64-linux-gnu/librt.so.1 (0x00007f7d79ff5000)
> libcr.so.0 => /usr/lib/libcr.so.0 (0x00007f7d79deb000)
> libpthread.so.0 => /lib/x86_64-linux-gnu/libpthread.so.0
> (0x00007f7d79bce000)
> libc.so.6 => /lib/x86_64-linux-gnu/libc.so.6 (0x00007f7d79847000)
> /lib64/ld-linux-x86-64.so.2 (0x00007f7d7b216000)
> libdl.so.2 => /lib/x86_64-linux-gnu/libdl.so.2 (0x00007f7d79642000)
>
> --------------------------------------------------------------------------------------------------------------------
> gromacs3.3/bin$ ldd mdrun_mpi | grep mpi
> libmpich.so.3 => /usr/lib/libmpich.so.3 (0x00007fc78fb5c000)
> It seems that gromacs has been compiled with mpich.
>

Does this executable still give the error listed below?  Performance is one 
thing, errors are another.  You may not necessarily obtain great scaling, 
depending on the contents of the system.

-Justin

>
>
> On Tue, Nov 20, 2012 at 4:15 AM, Justin Lemkul <jalemkul at vt.edu> wrote:
>
>>
>>
>> On 11/19/12 12:09 PM, Parisa Rahmani wrote:
>>
>>> Dear gmx users
>>>
>>> I have a problem with running parallel jobs on my Debian system(Openmpi
>>> installed on it),
>>> **Linux debian 3.2.0-1-amd64 #1 SMP , UTC 2012 x86_64 GNU/Linux**
>>> I am using gmx 3.3.3, because of the *lambda dynamics* method which is
>>>
>>> implemented in it.
>>>
>>> AS I know ,in gmx 3.x, the number of processors supplied for the
>>> subsequent
>>> mdrun needed to match the input file. but when i use **grompp -np 6 &
>>> mpirun -np 6 mdrun** the following error appears :
>>>
>>> ERROR : run input file md.tpr was made for 6 nodes,
>>> while mdrun expected it to be for 1 nodes.
>>>
>>> through search of mailing list i found similar problems, but non of
>>> the solutions worked for my case.
>>>
>>> wihtout -np option in grompp the error disappears, and then with each
>>> of these commands
>>>
>>> **
>>>
>>> 1)mpirun -np 6 mdrun -deffnm md
>>>
>>> 2)mpirun -np 6 mdrun -deffnm md -N 6
>>>
>>> 3)mpirun -np 6 mdrun -np 6 -deffnm md
>>>
>>> 4)mdrun -np 6 -s md -N 6
>>>
>>>
>>> **it uses 6 processors(each one at nearly 100%), but the simulation
>>> time is the same as for 1 processor.
>>>
>>> I have no problem with parallel jobs on our cluster(gmx 3.3.3 &
>>> openmpi), with following command:
>>>
>>> **
>>> grompp -np 6 -f ...
>>> mpiexec mdrun ...(number of processors is specified in the bash file)
>>> **
>>> ,
>>> but i can't run it on my 6 core system.
>>>
>>> Also, I have no problem with newer version of gmx (4.5.x), but i
>>> should use this version, and Hope someone can help me.
>>>
>>>
>> Have you properly compiled an MPI-enabled mdrun?  The default executable
>> name should be mdrun_mpi.  It should be linked against libmpi, so running
>> ldd on the mdrun executable should tell you.
>>
>> -Justin
>>
>> --
>> ==============================**==========
>>
>> Justin A. Lemkul, Ph.D.
>> Research Scientist
>> Department of Biochemistry
>> Virginia Tech
>> Blacksburg, VA
>> jalemkul[at]vt.edu | (540) 231-9080
>> http://www.bevanlab.biochem.**vt.edu/Pages/Personal/justin<http://www.bevanlab.biochem.vt.edu/Pages/Personal/justin>
>>
>> ==============================**==========
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-- 
========================================

Justin A. Lemkul, Ph.D.
Research Scientist
Department of Biochemistry
Virginia Tech
Blacksburg, VA
jalemkul[at]vt.edu | (540) 231-9080
http://www.bevanlab.biochem.vt.edu/Pages/Personal/justin

========================================