[gmx-users] mpirun error

Tue Nov 20 22:33:49 CET 2012

On 11/20/12 3:55 PM, Parisa Rahmani wrote:
> Yes, I ran two test simulations , one with 5 cpu and another with 1;
>
> 5 cpu simulation :
> step 50380, will finish at Wed Nov 21 01:46:25 2012
> step 50020, will finish at Wed Nov 21 01:48:36 2012
> step 50320, will finish at Wed Nov 21 01:46:49 2012
> step 50270, will finish at Wed Nov 21 01:47:07 2012
> *Time command :*
> *real 153m1.968s*
> *user 0m0.472s*
> *sys 0m2.072s*
> *
> *
> 1 cpu simulation :(started almost 5 minutes later)
> step 56000, will finish at Wed Nov 21 02:02:07 2012
> *Time command :*
> *real 177m25.541s*
> *user 177m23.041s*
> *sys 0m0.352s*
> *
> *
>

It appears to me that mdrun is functioning correctly, but overall performance is 
based on how large the system is and how good the hardware is.  It just seems to 
me that you're not getting particularly great scaling.

-Justin

> On Tue, Nov 20, 2012 at 8:06 PM, Justin Lemkul <jalemkul at vt.edu> wrote:
>
>>
>>
>> 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://vt.edu/Pages/Personal/justin>
>>>> <h**ttp://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<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

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