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
--
========================================
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
========================================
--
gmx-users mailing list [email protected]
http://lists.gromacs.org/mailman/listinfo/gmx-users
Please search the archive at
http://www.gromacs.org/Support/Mailing_Lists/Search before posting!
Please don't post (un)subscribe requests to the list. Use the
www interface or send it to [email protected].
Can't post? Read http://www.gromacs.org/Support/Mailing_Lists
