[gmx-users] handling particle decomposition with distance restraints

[Chris Neale]

We are running SUSE Linux

It's best to keep all of this on the mailing list in case it becomes 
useful to somebody else.


jayant james wrote:
> Hi!
> thanks for your mail. I have never used pull code before and so I am a 
> bit apprehensive but I do accept your suggestion and I am working on 
> that. By the wat what is the OS that you are using? Is it Suse or Fedora?
> Thanks
> Jayant James
>
> On Thu, Jun 25, 2009 at 4:31 PM, Chris Neale <chris.neale at utoronto.ca 
> <mailto:chris.neale at utoronto.ca>> wrote:
>
>     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 here:
>
>     http://lists.gromacs.org/pipermail/gmx-users/2009-March/040844.html
>
>
>     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.
>     http://www.mail-archive.com/gmx-users@gromacs.org/msg08257.html
>
>     Chris
>
>     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>
>         <mailto: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>
>         <http://www.chick.com/reading/tracts/0096/0096_01.asp>)
>
>
>
>
>
> -- 
> Jayasundar Jayant James
>
> www.chick.com/reading/tracts/0096/0096_01.asp 
> <http://www.chick.com/reading/tracts/0096/0096_01.asp>)
>