[gmx-users] GROMACS Domain decomposition

[NguyenDuyVy]

Dear gmx-users,

Would you mind giving me some instruction on this.

I am learning Gromacs tutorial #1 of mdtutotials.com. However to the 5th
step: EM,  http://www.mdtutorials.com/gmx/lysozyme/05_EM.html
I got the error:
"Domain decomposition does not support simple neighbor searching, use grid
searching or run with one MPI rank"

Running on 1 thread of PC by changing from
gmx mdrun -v -deffnm em
to
gmx mdrun -nt 1 -s -v -deffnm em
gives no problem but it's too slow, (50k steps, 2seconds/1step)

Thank you very much for your kind helps,
Best regards,

The full log is as follows
-------------------------------------------------------------------------------------
GROMACS:      gmx mdrun, VERSION 5.1.1
Executable:   /usr/local/gromacs/bin/gmx
Data prefix:  /usr/local/gromacs
Command line:
  gmx mdrun -s -deffnm em

Back Off! I just backed up em.log to ./#em.log.33#

Running on 1 node with total 12 cores, 24 logical cores
Hardware detected:
  CPU info:
    Vendor: GenuineIntel
    Brand:  Intel(R) Xeon(R) CPU           X5650  @ 2.67GHz
    SIMD instructions most likely to fit this hardware: SSE4.1
    SIMD instructions selected at GROMACS compile time: SSE4.1

Reading file em.tpr, VERSION 5.1.1 (single precision)
-------------------------------------------------------
Program gmx mdrun, VERSION 5.1.1
Source code file:
/home/nguyenduyvy/Downloads/gromacs-5.1.1/src/gromacs/domdec/domdec.cpp,
line: 6542

Fatal error:
Domain decomposition does not support simple neighbor searching, use grid
searching or run with one MPI rank
For more information and tips for troubleshooting, please check the GROMACS
website at http://www.gromacs.org/Documentation/Errors

-------------------------------------------------------------------------------------

Yours sincerely,
Nguyen Duy Vy