[gmx-users] domain decomposition
jampanis at gmail.com
Fri May 7 15:32:15 CEST 2010
Try with -dd 2 x 2 x 2 option with 8 nodes and check the performance. I too
got the same problems, i could overcome with symmetrical -dd option.
On Fri, May 7, 2010 at 8:57 AM, irene farabella <
i.farabella at mail.cryst.bbk.ac.uk> wrote:
> I am new to Gromacs and especially at parallel runs. I have some problem
> running my system using domain decomposition. I apologize but it will
> be a long mail...
> My system is made up by a membrane protein embedded is a mixed lipid
> bilayer (POPE/POPG).
> I tried to run it on 8 nodes but the simulation crashed due to "A charge
> group moved too far between two domain decomposition steps" and
> high % of load imbalance between nodes. I then tested the same run on a
> single node and it worked. I tried then different amount of nodes,
> changing DD (using mdrun -dd option) and it seems that more node I am
> using the less the performance in terms of ns/day although the load
> imbalance % is highly variable. During this test I found that the
> optimal nodes for my system is running it on 6 node with a DD 3:2:1 (vol
> 0.80 imb F 1% )
> ---- from the log file:
> Initializing Domain Decomposition on 6 nodes
> Dynamic load balancing: auto
> Will sort the charge groups at every domain (re)decomposition
> Initial maximum inter charge-group distances:
> two-body bonded interactions: 0.703 nm, LJ-14, atoms 21579 21587
> multi-body bonded interactions: 2.038 nm, Proper Dih., atoms 20434 20405
> Minimum cell size due to bonded interactions: 2.241 nm
> Maximum distance for 5 constraints, at 120 deg. angles, all-trans: 0.820 nm
> Estimated maximum distance required for P-LINCS: 0.820 nm
> Domain decomposition grid 3 x 2 x 1, separate PME nodes 0
> Domain decomposition nodeid 0, coordinates 0 0 0
> Table routines are used for coulomb: TRUE
> Table routines are used for vdw: FALSE
> Will do PME sum in reciprocal space.
> Making 2D domain decomposition grid 3 x 2 x 1, home cell index 0 0 0
> Center of mass motion removal mode is Linear
> We have the following groups for center of mass motion removal:
> 0: Protein_POPE_POPG
> 1: SOL_NA+_CL-
> There are: 82711 Atoms
> Charge group distribution at step 2000000: 5512 5533 5668 5694 5535 5626
> Grid: 7 x 10 x 14 cells
> Initial temperature: 309.243 K
> Using this setting I finally managed to equilibrate my system by going
> trough a
> series of restrained runs.
> Surprisingly after 6,5 ns of non-restrained run (Step 3289500) the
> crashes with :
> "Fatal error:
> A charge group moved too far between two domain decomposition steps
> This usually means that your system is not well equilibrated ".
> It seems strange that it crashes only at 3289500 steps of a non-restrained
> I am now running a short run starting from a short while before the
> crash step using a single processor and, as suspected, it is going
> smoothly. My guess is that something is going wrong with the domain
> decomposition of a such non-homogeneous system, considering that there
> are also charged lipids that complicate it but I have no idea how to
> solve/improve it.
> I am using gromacs-4.0.5.
> Any suggestion are welcome.
> Irene Farabella
> Wellcome Trust PhD student
> Institute of Structural and Molecular Biology
> Department of of Biological Sciences
> University of London
> Malet Street
> London WC1E 7HX
> Telephone +44 (0)20 7631 6815
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J. Srinivasa Rao
Post-doctoral Research Associate
C/o Prof. Luis R Cruz Cruz
Computational Biophysics Group
Department of Physics
3141 Chestnut St
Philadelphia, PA 19104, USA.
Ph: Off: 215-895-1989
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