[gmx-users] handling particle decomposition with distance restraints

Chris Neale chris.neale at utoronto.ca
Thu Jun 25 22:31:10 CEST 2009

Let me re-emphasize that the pull code may be a good solution for you.

As per your request, I currently use the following without any problems:

fftw 3.1.2
gromacs 3.3.1 or 4.0.4
openmpi 1.2.6

Be especially aware that openmpi 1.3.0 and 1.3.1 are broken, as I posted 


To be clear, I have never experienced any openmpi-based problems with 
any version of gromacs 4 and openmpi 1.2.6.

I posted the original notice of our problems with openmpi (1.2.1) that 
were solved by using lam here.


jayant james wrote:
> Hi!
> thanks for your mail. Could you please share what OS and versions of 
> fftw, openmpi and gmx you are currently using.
> Thanks you
> JJ
> On Thu, Jun 25, 2009 at 12:28 PM, <chris.neale at utoronto.ca 
> <mailto:chris.neale at utoronto.ca>> wrote:
>     Why not use the pull code? If you haev to use distance restraints,
>     then try LAM mpi with your pd run. We had similar error messages
>     with vanilla .mdp files using openmpi with large and complex
>     systems that went away when we switched to LAM MPI. Our problems
>     disappeared in gmx 4 so we went back to openmpi for all systems as
>     that mdrun_mpi version is faster in our hands.
>     I admit, there is no good reason why LAM would work and openMPI
>     would not, but I have seen it happen before so it's worth a shot.
>     -- original message--
>     The energy minimization went on without any problem on 4
>     processors but the
>     problem occurs when I perform the MD run. Also, I did not get any
>     error
>     message with relevance to LINCS etc...
>     JJ
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> -- 
> Jayasundar Jayant James
> www.chick.com/reading/tracts/0096/0096_01.asp 
> <http://www.chick.com/reading/tracts/0096/0096_01.asp>)

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