On 2/23/15 9:32 AM, soumadwip ghosh wrote:
Dear all,
I started an MDrun of Barstar protein in TIP3P water and 8M
urea, neutralized by the required number of counterions. Until the mdrun,
there was no issue with either energy minimization and equilibration steps.
But whenever I want to start MD run, a fatal error shows up saying...
Reading file mdrun_100ns.tpr, VERSION 4.5.6 (single precision)
Starting 80 threads
Will use 70 particle-particle and 10 PME only nodes
This is a guess, check the performance at the end of the log file
-------------------------------------------------------
Program mdrun, VERSION 4.5.6
Source code file: domdec.c, line: 6436
Fatal error:
There is no domain decomposition for 70 nodes that is compatible with the
given box and a minimum cell size of 0.952625 nm
Change the number of nodes or mdrun option -rcon or -dds or your LINCS
settings
I am sure I am not doing parallel runs on any other processor. It is
written in the GROMACS error analysis that' If you didn't think you were
running a parallel calculation, be aware that from 4.5, GROMACS uses
thread-based
parallelism <http://www.gromacs.org/Documentation/Terminology/Threading> by
default. To prevent this, you can either give mdrun
<http://www.gromacs.org/Documentation/Gromacs_Utilities/mdrun> the "-nt 1"
command line option, or build GROMACS so that it will not use threads.
Otherwise, you might be using an MPI-enabled GROMACS and not be aware of
the fact.'
Therefore, according to the suggestion I have used the option -nt 1 in the
md run command line. The problem is the simulation is getting slower than
most of the other calculations I 've performed with the same system. Can
anyone tell me why is it so? I 've never done parallel computation to
accelerate the simulations. Also, with the option -nt 1 do I ensure correct
sampling of the system? I hope I'm not asking for much..
You need to figure out what hardware you actually have (e.g. number of cores,
whether or not the processors support hyperthreading, etc), how GROMACS was
compiled (if you didn't do it yourself), what your OMP_NUM_THREADS environment
variable is set to, etc. Normally, GROMACS finds and uses all available
processors; you didn't show us your original command that tried to use 80
threads, so we don't know if you set something wrong or what's going on.
-Justin
--
==================================================
Justin A. Lemkul, Ph.D.
Ruth L. Kirschstein NRSA Postdoctoral Fellow
Department of Pharmaceutical Sciences
School of Pharmacy
Health Sciences Facility II, Room 629
University of Maryland, Baltimore
20 Penn St.
Baltimore, MD 21201
jalem...@outerbanks.umaryland.edu | (410) 706-7441
http://mackerell.umaryland.edu/~jalemkul
==================================================
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