[gmx-users] GROMACS 4.5.3 simulation stop without mesages in Ubuntu 10.10

[Justin A. Lemkul]

Alcides Nicastro wrote:
> Users:
> I'm running a simulation of a lipid bilayer. At some point (sometimes 
> close to the steps 300000-500000) the terminal fails to inform the 
> development of simulation and the files stop writing, but the processors 
> are fully occupied. There is no message for this.
> 
> Details:
> 128 DPPC bilayer with 3655 water molecules
> Intel i3 processor.
> Ubuntu 10.10 64 bits
> GROMACS 4.5.3
> LAM 7.1.4 ( -np 2 for simulations)
> 

Many users report problems when using LAM.  It is old and deprecated.  What's 
more, for Gromacs 4.5.x on a system like this, one does not need external MPI 
libraries to run in parallel.  Make use of threading (./configure 
--enable-threads etc) to use an internal thread-MPI library.  Otherwise, if you 
really want to link against an MPI distribution, at least use an up-to-date one 
like OpenMPI.

-Justin

> I appreciate any help.
> Best regards,
> 
> 
> Lic. *Alcides Nicastro*
> Departamento de Física
> Fac. de Bioq. y Cs. Biológicas
> Universidad Nacional del Litoral
> 3000 - Santa Fe - Argentina
> Tel. trabajo: 0342-4575213
> Tel. particular: 0342-4539185
> ó 0342-155471071
> 

-- 
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Justin A. Lemkul
Ph.D. Candidate
ICTAS Doctoral Scholar
MILES-IGERT Trainee
Department of Biochemistry
Virginia Tech
Blacksburg, VA
jalemkul[at]vt.edu | (540) 231-9080
http://www.bevanlab.biochem.vt.edu/Pages/Personal/justin

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