[gmx-users] Performance

[Myunggi Yi]

Dear users,

I have two questions.


1. I used to run typical simulations with the following command.

gmx mdrun -deffnm md

I had no problem.


Now I am running a simulation with "Dry_Martini" FF with the following
input.


integrator               = sd
tinit                    = 0.0
dt                       = 0.040
nsteps                   = 1000000

nstlog                   = 5000
nstenergy                = 5000
nstxout-compressed       = 5000
compressed-x-precision   = 100

cutoff-scheme            = Verlet
nstlist                  = 10
ns_type                  = grid
pbc                      = xyz
verlet-buffer-tolerance  = 0.005

epsilon_r                = 15
coulombtype              = reaction-field
rcoulomb                 = 1.1
vdw_type                 = cutoff
vdw-modifier             = Potential-shift-verlet
rvdw                     = 1.1

tc-grps                  = system
tau_t                    = 4.0
ref_t                    = 310

; Pressure coupling:
Pcoupl                   = no

; GENERATE VELOCITIES FOR STARTUP RUN:
gen_vel                  = yes
gen_temp                 = 310
gen_seed                 = 1521731368



If I use the same command to submit the job.
I got the following error. I don't know why.

-------------------------------------------------------
Program:     gmx mdrun, version 2018.1
Source file: src/gromacs/taskassignment/resourcedivision.cpp (line 224)

Fatal error:
When using GPUs, setting the number of OpenMP threads without specifying the
number of ranks can lead to conflicting demands. Please specify the number
of
thread-MPI ranks as well (option -ntmpi).

For more information and tips for troubleshooting, please check the GROMACS
website at http://www.gromacs.org/Documentation/Errors
-------------------------------------------------------


So I did run simulation with the following command.


gmx mdrun -deffnm md -ntmpi 1


Now the performance is extremely bad.
Since yesterday, the log file still reporting the first step's energy.

2. This is the second question. Why?

Can anyone help?


Myunggi Yi