[gmx-users] mpirun error

Tue Nov 20 21:55:35 CET 2012

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*
*
*

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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