[gmx-users] mpirun error

[Parisa Rahmani]

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.



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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